{"diffoscope-json-version": 1, "source1": "/srv/reproducible-results/rbuild-debian/r-b-build.vPWgae5w/b1/apbs_3.0.0+dfsg1-3_amd64.changes", "source2": "/srv/reproducible-results/rbuild-debian/r-b-build.vPWgae5w/b2/apbs_3.0.0+dfsg1-3_amd64.changes", "unified_diff": null, "details": [{"source1": "Files", "source2": "Files", "unified_diff": "@@ -1,9 +1,9 @@\n \n- 894f46bd33cc3c0cef85050a90ac82a8 226109292 science optional apbs-data_3.0.0+dfsg1-3_all.deb\n+ b458145b7db34824f4dfd3c287712f65 226028740 science optional apbs-data_3.0.0+dfsg1-3_all.deb\n  1011146d2d8ae0254178da5b12dbda2d 155676 debug optional apbs-dbgsym_3.0.0+dfsg1-3_amd64.deb\n  e4287361ef811c49836be7f6d456913f 86220 science optional apbs_3.0.0+dfsg1-3_amd64.deb\n  e19dc8c906029323e8d574f5314cded1 66316 libdevel optional libapbs-dev_3.0.0+dfsg1-3_amd64.deb\n  bfd49b75417c538a2a7d8921e37add84 549024 debug optional libapbs3-dbgsym_3.0.0+dfsg1-3_amd64.deb\n  4bcd9ce52876b5e01ad2312dc6038a1b 246052 libs optional libapbs3_3.0.0+dfsg1-3_amd64.deb\n  33d074bcb3d448c1ddfb7763842f72c3 162076 debug optional python3-apbslib-dbgsym_3.0.0+dfsg1-3_amd64.deb\n  02c1f42dd64ac5389ffbdec50e6f9f09 104516 python optional python3-apbslib_3.0.0+dfsg1-3_amd64.deb\n"}, {"source1": "apbs-data_3.0.0+dfsg1-3_all.deb", "source2": "apbs-data_3.0.0+dfsg1-3_all.deb", "unified_diff": null, "details": [{"source1": "file list", "source2": "file list", "unified_diff": "@@ -1,3 +1,3 @@\n -rw-r--r--   0        0        0        4 2020-07-23 09:35:23.000000 debian-binary\n--rw-r--r--   0        0        0    13236 2020-07-23 09:35:23.000000 control.tar.xz\n--rw-r--r--   0        0        0 226095864 2020-07-23 09:35:23.000000 data.tar.xz\n+-rw-r--r--   0        0        0    13260 2020-07-23 09:35:23.000000 control.tar.xz\n+-rw-r--r--   0        0        0 226015288 2020-07-23 09:35:23.000000 data.tar.xz\n"}, {"source1": "control.tar.xz", "source2": "control.tar.xz", "unified_diff": null, "details": [{"source1": "control.tar", "source2": "control.tar", "unified_diff": null, "details": [{"source1": "./md5sums", "source2": "./md5sums", "unified_diff": null, "details": [{"source1": "./md5sums", "source2": "./md5sums", "comments": ["Files differ"], "unified_diff": null}]}]}]}, {"source1": "data.tar.xz", "source2": "data.tar.xz", "unified_diff": null, "details": [{"source1": "data.tar", "source2": "data.tar", "unified_diff": null, "details": [{"source1": "./usr/share/apbs/examples/FKBP/io.mc", "source2": "./usr/share/apbs/examples/FKBP/io.mc", "unified_diff": "@@ -1,10 +1,10 @@\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 06:38:21 2025\n+# Creation Date and Time:  Tue Jan  9 04:38:55 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path 1d7h-dmso-complex.pqr\n@@ -637,32 +637,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.239660\n+Vacc_SASA: Time elapsed: 1.284976\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.550225e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.395125e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.492900e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 4.728200e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.393209e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.053918e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.344471e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.660890e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.211746e-02\n Vprtstp: contraction number = 6.211746e-02\n Vprtstp: iteration = 2\n@@ -736,30 +736,30 @@\n Vprtstp: contraction number = 6.956346e-01\n Vprtstp: iteration = 25\n Vprtstp: relative residual = 1.302234e-06\n Vprtstp: contraction number = 6.974500e-01\n Vprtstp: iteration = 26\n Vprtstp: relative residual = 9.101840e-07\n Vprtstp: contraction number = 6.989406e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.208282e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.235683e+02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 7.259198e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.479336e+01\n Vpmg_setPart:  lower corner = (-22.1255, -29.651, -28.888)\n Vpmg_setPart:  upper corner = (73.8745, 66.349, 67.112)\n Vpmg_setPart:  actual minima = (-22.1255, -29.651, -28.888)\n Vpmg_setPart:  actual maxima = (73.8745, 66.349, 67.112)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 8.506409949028E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.200000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.030000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 26.5287\n Vpbe_ctor2:  solute dimensions = 50.733 x 37.661 x 37.832\n Vpbe_ctor2:  solute charge = 0.991\n@@ -807,30 +807,30 @@\n VPMG::extEnergy: extQfEnergy = 7766.58 kT\n VPMG::extEnergy: extDiEnergy = 3755.14 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.245786\n+Vacc_SASA: Time elapsed: 1.307904\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.690680e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.837740e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.636000e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.567600e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.129497e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.063623e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.309004e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.196495e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.221522e-01\n Vprtstp: contraction number = 1.221522e-01\n Vprtstp: iteration = 2\n@@ -862,30 +862,30 @@\n Vprtstp: contraction number = 4.471936e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 1.248629e-06\n Vprtstp: contraction number = 4.746468e-01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 6.237535e-07\n Vprtstp: contraction number = 4.995506e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 4.822686e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 5.016557e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.484642e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.664846e+01\n Vpmg_setPart:  lower corner = (10.551, 10.5695, 13.2915)\n Vpmg_setPart:  upper corner = (24.951, 24.9695, 27.6915)\n Vpmg_setPart:  actual minima = (10.551, 10.5695, 13.2915)\n Vpmg_setPart:  actual maxima = (24.951, 24.9695, 27.6915)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 3.428963535142E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.430000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.130000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 26.5287\n Vpbe_ctor2:  solute dimensions = 50.733 x 37.661 x 37.832\n Vpbe_ctor2:  solute charge = 0.991\n@@ -908,32 +908,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.243802\n+Vacc_SASA: Time elapsed: 1.225212\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.866242e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.629314e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.341810e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.638360e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.331711e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.955950e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.856521e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.225319e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.215755e-02\n Vprtstp: contraction number = 2.215755e-02\n Vprtstp: iteration = 2\n@@ -947,32 +947,32 @@\n Vprtstp: contraction number = 9.587608e-02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 1.603412e-06\n Vprtstp: contraction number = 9.909475e-02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.626039e-07\n Vprtstp: contraction number = 1.014112e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.594046e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.847742e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.737935e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.939304e+01\n Vpmg_setPart:  lower corner = (-22.1255, -29.651, -28.888)\n Vpmg_setPart:  upper corner = (73.8745, 66.349, 67.112)\n Vpmg_setPart:  actual minima = (-22.1255, -29.651, -28.888)\n Vpmg_setPart:  actual maxima = (73.8745, 66.349, 67.112)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.121921918409E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.160000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.450000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 26.5287\n Vpbe_ctor2:  solute dimensions = 50.733 x 37.661 x 37.832\n Vpbe_ctor2:  solute charge = 0.991\n Vpbe_ctor2:  bulk ionic strength = 0.01\n Vpbe_ctor2:  xkappa = 0.205309\n@@ -1018,30 +1018,30 @@\n VPMG::extEnergy: extQfEnergy = 10309.9 kT\n VPMG::extEnergy: extDiEnergy = 4985.22 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.326307\n+Vacc_SASA: Time elapsed: 1.276877\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.899139e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.711957e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.976500e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.352500e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.362936e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.508240e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.157914e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.433465e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.329182e-01\n Vprtstp: contraction number = 1.329182e-01\n Vprtstp: iteration = 2\n@@ -1058,30 +1058,30 @@\n Vprtstp: contraction number = 1.009933e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.280625e-06\n Vprtstp: contraction number = 1.024328e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.326631e-07\n Vprtstp: contraction number = 1.035924e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.345748e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.570890e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.081467e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.246525e+01\n Vpmg_setPart:  lower corner = (10.551, 10.5695, 13.2915)\n Vpmg_setPart:  upper corner = (24.951, 24.9695, 27.6915)\n Vpmg_setPart:  actual minima = (10.551, 10.5695, 13.2915)\n Vpmg_setPart:  actual maxima = (24.951, 24.9695, 27.6915)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 3.696401888033E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.470000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.210000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3.80966\n Vpbe_ctor2:  solute dimensions = 5.374 x 6.581 x 6.611\n Vpbe_ctor2:  solute charge = 2.77556e-17\n@@ -1104,32 +1104,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.002693\n+Vacc_SASA: Time elapsed: 0.001673\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.480220e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.398950e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.416610e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.324980e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.276139e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.104898e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.421519e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.667311e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.503042e-01\n Vprtstp: contraction number = 1.503042e-01\n Vprtstp: iteration = 2\n@@ -1146,30 +1146,30 @@\n Vprtstp: contraction number = 1.186135e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 3.304907e-06\n Vprtstp: contraction number = 1.191339e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.951730e-07\n Vprtstp: contraction number = 1.195716e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.607646e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.841862e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.886296e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.083680e+01\n Vpmg_setPart:  lower corner = (-30.249, -30.2305, -27.5085)\n Vpmg_setPart:  upper corner = (65.751, 65.7695, 68.4915)\n Vpmg_setPart:  actual minima = (-30.249, -30.2305, -27.5085)\n Vpmg_setPart:  actual maxima = (65.751, 65.7695, 68.4915)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 3.176059394103E+01 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.400000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.000000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3.80966\n Vpbe_ctor2:  solute dimensions = 5.374 x 6.581 x 6.611\n Vpbe_ctor2:  solute charge = 2.77556e-17\n@@ -1217,30 +1217,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00535489 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.001705\n+Vacc_SASA: Time elapsed: 0.001706\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.866350e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.620660e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.674700e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.564800e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.308390e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.052775e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.709140e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.879045e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.268584e-01\n Vprtstp: contraction number = 2.268584e-01\n Vprtstp: iteration = 2\n@@ -1269,32 +1269,32 @@\n Vprtstp: contraction number = 3.027355e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 2.523815e-06\n Vprtstp: contraction number = 3.032958e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 7.666858e-07\n Vprtstp: contraction number = 3.037805e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 4.311558e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.538585e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.058981e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.241424e+01\n Vpmg_setPart:  lower corner = (10.551, 10.5695, 13.2915)\n Vpmg_setPart:  upper corner = (24.951, 24.9695, 27.6915)\n Vpmg_setPart:  actual minima = (10.551, 10.5695, 13.2915)\n Vpmg_setPart:  actual maxima = (24.951, 24.9695, 27.6915)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 5.709734790786E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.498000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.700000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3.80966\n Vpbe_ctor2:  solute dimensions = 5.374 x 6.581 x 6.611\n Vpbe_ctor2:  solute charge = 2.77556e-17\n Vpbe_ctor2:  bulk ionic strength = 0.01\n Vpbe_ctor2:  xkappa = 0.205309\n@@ -1315,32 +1315,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.002042\n+Vacc_SASA: Time elapsed: 0.001707\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.482120e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.533150e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 3.272100e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.288820e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.363021e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.268480e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.173244e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.212496e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.197218e-01\n Vprtstp: contraction number = 1.197218e-01\n Vprtstp: iteration = 2\n@@ -1357,32 +1357,32 @@\n Vprtstp: contraction number = 1.080232e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.668171e-06\n Vprtstp: contraction number = 1.086670e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.821545e-07\n Vprtstp: contraction number = 1.091941e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.133017e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.393507e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.953915e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.176948e+01\n Vpmg_setPart:  lower corner = (-30.249, -30.2305, -27.5085)\n Vpmg_setPart:  upper corner = (65.751, 65.7695, 68.4915)\n Vpmg_setPart:  actual minima = (-30.249, -30.2305, -27.5085)\n Vpmg_setPart:  actual maxima = (65.751, 65.7695, 68.4915)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 5.413483938867E+01 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.000000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.700000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3.80966\n Vpbe_ctor2:  solute dimensions = 5.374 x 6.581 x 6.611\n Vpbe_ctor2:  solute charge = 2.77556e-17\n Vpbe_ctor2:  bulk ionic strength = 0.01\n Vpbe_ctor2:  xkappa = 0.205309\n@@ -1428,30 +1428,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0422608 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.002220\n+Vacc_SASA: Time elapsed: 0.001710\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.657080e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.210150e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.243330e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.019800e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.432894e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.114410e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.518559e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.429559e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.511608e-01\n Vprtstp: contraction number = 1.511608e-01\n Vprtstp: iteration = 2\n@@ -1468,30 +1468,30 @@\n Vprtstp: contraction number = 1.062405e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.836009e-06\n Vprtstp: contraction number = 1.072929e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.984242e-07\n Vprtstp: contraction number = 1.080737e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.438697e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.717082e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.955972e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.132197e+01\n Vpmg_setPart:  lower corner = (10.551, 10.5695, 13.2915)\n Vpmg_setPart:  upper corner = (24.951, 24.9695, 27.6915)\n Vpmg_setPart:  actual minima = (10.551, 10.5695, 13.2915)\n Vpmg_setPart:  actual maxima = (24.951, 24.9695, 27.6915)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 5.884571864356E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.000000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.900000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 26.5287\n Vpbe_ctor2:  solute dimensions = 50.733 x 37.661 x 37.832\n Vpbe_ctor2:  solute charge = 0.991\n@@ -1514,32 +1514,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.382812\n+Vacc_SASA: Time elapsed: 1.203074\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.600997e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.295662e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.347900e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.443670e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.024701e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.658970e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.820368e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.677240e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.148454e-02\n Vprtstp: contraction number = 6.148454e-02\n Vprtstp: iteration = 2\n@@ -1613,32 +1613,32 @@\n Vprtstp: contraction number = 7.027151e-01\n Vprtstp: iteration = 25\n Vprtstp: relative residual = 1.401142e-06\n Vprtstp: contraction number = 7.044026e-01\n Vprtstp: iteration = 26\n Vprtstp: relative residual = 9.889238e-07\n Vprtstp: contraction number = 7.057985e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 8.457785e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.667832e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 8.234966e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.420201e+01\n Vpmg_setPart:  lower corner = (-22.1255, -29.651, -28.888)\n Vpmg_setPart:  upper corner = (73.8745, 66.349, 67.112)\n Vpmg_setPart:  actual minima = (-22.1255, -29.651, -28.888)\n Vpmg_setPart:  actual maxima = (73.8745, 66.349, 67.112)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 8.486452023042E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.460000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.100000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 26.5287\n Vpbe_ctor2:  solute dimensions = 50.733 x 37.661 x 37.832\n Vpbe_ctor2:  solute charge = 0.991\n Vpbe_ctor2:  bulk ionic strength = 0.01\n Vpbe_ctor2:  xkappa = 0.0328757\n@@ -1684,30 +1684,30 @@\n VPMG::extEnergy: extQfEnergy = 7766.05 kT\n VPMG::extEnergy: extDiEnergy = 3755.1 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.361590\n+Vacc_SASA: Time elapsed: 1.270440\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.867446e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.740486e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.123700e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.301200e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.127694e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.070439e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.704348e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.538665e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.211906e-01\n Vprtstp: contraction number = 1.211906e-01\n Vprtstp: iteration = 2\n@@ -1739,32 +1739,32 @@\n Vprtstp: contraction number = 4.581101e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 1.399352e-06\n Vprtstp: contraction number = 4.836226e-01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 7.075712e-07\n Vprtstp: contraction number = 5.056422e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 4.189897e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.381851e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.669276e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.872499e+01\n Vpmg_setPart:  lower corner = (10.551, 10.5695, 13.2915)\n Vpmg_setPart:  upper corner = (24.951, 24.9695, 27.6915)\n Vpmg_setPart:  actual minima = (10.551, 10.5695, 13.2915)\n Vpmg_setPart:  actual maxima = (24.951, 24.9695, 27.6915)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 3.371923967456E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.630000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.340000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 26.5287\n Vpbe_ctor2:  solute dimensions = 50.733 x 37.661 x 37.832\n Vpbe_ctor2:  solute charge = 0.991\n Vpbe_ctor2:  bulk ionic strength = 0.01\n Vpbe_ctor2:  xkappa = 0.205309\n@@ -1785,32 +1785,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.359712\n+Vacc_SASA: Time elapsed: 1.190975\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.698524e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.408092e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.029880e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.200660e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.141873e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.177646e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.182867e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.961892e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.219671e-02\n Vprtstp: contraction number = 2.219671e-02\n Vprtstp: iteration = 2\n@@ -1824,30 +1824,30 @@\n Vprtstp: contraction number = 9.588702e-02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 1.611478e-06\n Vprtstp: contraction number = 9.903019e-02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.632204e-07\n Vprtstp: contraction number = 1.012861e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.929552e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.148474e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.654703e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.870080e+01\n Vpmg_setPart:  lower corner = (-22.1255, -29.651, -28.888)\n Vpmg_setPart:  upper corner = (73.8745, 66.349, 67.112)\n Vpmg_setPart:  actual minima = (-22.1255, -29.651, -28.888)\n Vpmg_setPart:  actual maxima = (73.8745, 66.349, 67.112)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.119297547416E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.950000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.050000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 26.5287\n Vpbe_ctor2:  solute dimensions = 50.733 x 37.661 x 37.832\n Vpbe_ctor2:  solute charge = 0.991\n@@ -1895,30 +1895,30 @@\n VPMG::extEnergy: extQfEnergy = 10305.9 kT\n VPMG::extEnergy: extDiEnergy = 4984.29 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.366479\n+Vacc_SASA: Time elapsed: 1.261545\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.807883e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.749710e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.980800e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.338600e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.611535e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.006559e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.423214e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.162259e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.325279e-01\n Vprtstp: contraction number = 1.325279e-01\n Vprtstp: iteration = 2\n@@ -1935,44 +1935,44 @@\n Vprtstp: contraction number = 1.009444e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.272261e-06\n Vprtstp: contraction number = 1.024006e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.317723e-07\n Vprtstp: contraction number = 1.035733e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.321210e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.605056e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.093922e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.265479e+01\n Vpmg_setPart:  lower corner = (10.551, 10.5695, 13.2915)\n Vpmg_setPart:  upper corner = (24.951, 24.9695, 27.6915)\n Vpmg_setPart:  actual minima = (10.551, 10.5695, 13.2915)\n Vpmg_setPart:  actual maxima = (24.951, 24.9695, 27.6915)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 3.638817315582E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.650000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.170000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 5.657970e+02\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 4.374429e+02\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 06:39:34 2025\n+# Creation Date and Time:  Tue Jan  9 04:40:25 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path 1d7h-dmso-complex.pqr\n@@ -2605,32 +2605,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.393030\n+Vacc_SASA: Time elapsed: 1.291352\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.682009e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.473126e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 3.466100e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.307100e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.151763e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.079497e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.968456e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.790715e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.251961e-02\n Vprtstp: contraction number = 3.251961e-02\n Vprtstp: iteration = 2\n@@ -2647,30 +2647,30 @@\n Vprtstp: contraction number = 1.569967e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.728368e-06\n Vprtstp: contraction number = 1.692265e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.127259e-07\n Vprtstp: contraction number = 1.809371e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.240628e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.462524e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.045011e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.270632e+01\n Vpmg_setPart:  lower corner = (-22.1255, -29.651, -28.888)\n Vpmg_setPart:  upper corner = (73.8745, 66.349, 67.112)\n Vpmg_setPart:  actual minima = (-22.1255, -29.651, -28.888)\n Vpmg_setPart:  actual maxima = (73.8745, 66.349, 67.112)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 8.619056487019E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.580000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.270000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 26.5287\n Vpbe_ctor2:  solute dimensions = 50.733 x 37.661 x 37.832\n Vpbe_ctor2:  solute charge = 0.991\n@@ -2718,30 +2718,30 @@\n VPMG::extEnergy: extQfEnergy = 7853.47 kT\n VPMG::extEnergy: extDiEnergy = 3800.32 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.406413\n+Vacc_SASA: Time elapsed: 1.218662\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.042488e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.825349e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 3.097600e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.426400e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.080252e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.032802e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.239585e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.000890e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.054672e-01\n Vprtstp: contraction number = 1.054672e-01\n Vprtstp: iteration = 2\n@@ -2758,30 +2758,30 @@\n Vprtstp: contraction number = 1.551340e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 4.573968e-06\n Vprtstp: contraction number = 1.730130e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 8.440650e-07\n Vprtstp: contraction number = 1.845367e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.201796e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.390051e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.931838e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.118479e+01\n Vpmg_setPart:  lower corner = (10.551, 10.5695, 13.2915)\n Vpmg_setPart:  upper corner = (24.951, 24.9695, 27.6915)\n Vpmg_setPart:  actual minima = (10.551, 10.5695, 13.2915)\n Vpmg_setPart:  actual maxima = (24.951, 24.9695, 27.6915)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 3.439357878013E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.370000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.480000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 26.5287\n Vpbe_ctor2:  solute dimensions = 50.733 x 37.661 x 37.832\n Vpbe_ctor2:  solute charge = 0.991\n@@ -2804,32 +2804,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.371180\n+Vacc_SASA: Time elapsed: 1.250992\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.907947e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.806283e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.602600e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.803950e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.018317e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.038227e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.047600e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.509900e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.215755e-02\n Vprtstp: contraction number = 2.215755e-02\n Vprtstp: iteration = 2\n@@ -2843,30 +2843,30 @@\n Vprtstp: contraction number = 9.587608e-02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 1.603412e-06\n Vprtstp: contraction number = 9.909475e-02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.626039e-07\n Vprtstp: contraction number = 1.014112e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.891972e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.098959e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.783232e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.973390e+01\n Vpmg_setPart:  lower corner = (-22.1255, -29.651, -28.888)\n Vpmg_setPart:  upper corner = (73.8745, 66.349, 67.112)\n Vpmg_setPart:  actual minima = (-22.1255, -29.651, -28.888)\n Vpmg_setPart:  actual maxima = (73.8745, 66.349, 67.112)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.121921918409E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.140000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.400000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 26.5287\n Vpbe_ctor2:  solute dimensions = 50.733 x 37.661 x 37.832\n Vpbe_ctor2:  solute charge = 0.991\n@@ -2914,30 +2914,30 @@\n VPMG::extEnergy: extQfEnergy = 10309.9 kT\n VPMG::extEnergy: extDiEnergy = 4985.22 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.373971\n+Vacc_SASA: Time elapsed: 1.242435\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.806696e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.737998e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.535000e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.403900e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.205994e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.557390e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.345458e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.656172e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.329182e-01\n Vprtstp: contraction number = 1.329182e-01\n Vprtstp: iteration = 2\n@@ -2954,30 +2954,30 @@\n Vprtstp: contraction number = 1.009933e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.280625e-06\n Vprtstp: contraction number = 1.024328e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.326631e-07\n Vprtstp: contraction number = 1.035924e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.392626e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.609001e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.145378e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.331345e+01\n Vpmg_setPart:  lower corner = (10.551, 10.5695, 13.2915)\n Vpmg_setPart:  upper corner = (24.951, 24.9695, 27.6915)\n Vpmg_setPart:  actual minima = (10.551, 10.5695, 13.2915)\n Vpmg_setPart:  actual maxima = (24.951, 24.9695, 27.6915)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 3.696401888033E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.560000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.620000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3.80966\n Vpbe_ctor2:  solute dimensions = 5.374 x 6.581 x 6.611\n Vpbe_ctor2:  solute charge = 2.77556e-17\n@@ -3000,32 +3000,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.001828\n+Vacc_SASA: Time elapsed: 0.001795\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.139610e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.684080e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.269190e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.153970e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.160778e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.252328e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.103017e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.010079e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.464441e-01\n Vprtstp: contraction number = 1.464441e-01\n Vprtstp: iteration = 2\n@@ -3042,30 +3042,30 @@\n Vprtstp: contraction number = 1.083801e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.974607e-06\n Vprtstp: contraction number = 1.096829e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.183173e-07\n Vprtstp: contraction number = 1.105624e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.275285e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.488789e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.172526e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.398493e+01\n Vpmg_setPart:  lower corner = (-30.249, -30.2305, -27.5085)\n Vpmg_setPart:  upper corner = (65.751, 65.7695, 68.4915)\n Vpmg_setPart:  actual minima = (-30.249, -30.2305, -27.5085)\n Vpmg_setPart:  actual maxima = (65.751, 65.7695, 68.4915)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 2.982504155807E+01 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.800000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.500000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3.80966\n Vpbe_ctor2:  solute dimensions = 5.374 x 6.581 x 6.611\n Vpbe_ctor2:  solute charge = 2.77556e-17\n@@ -3113,30 +3113,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0085798 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.001926\n+Vacc_SASA: Time elapsed: 0.001801\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.584610e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.153960e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.032100e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 9.394000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.032162e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.199059e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.354969e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.254615e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.791557e-01\n Vprtstp: contraction number = 1.791557e-01\n Vprtstp: iteration = 2\n@@ -3156,30 +3156,30 @@\n Vprtstp: contraction number = 1.764760e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.223991e-06\n Vprtstp: contraction number = 1.794914e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 5.841505e-07\n Vprtstp: contraction number = 1.811887e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.650978e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.830506e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.468005e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.676901e+01\n Vpmg_setPart:  lower corner = (10.551, 10.5695, 13.2915)\n Vpmg_setPart:  upper corner = (24.951, 24.9695, 27.6915)\n Vpmg_setPart:  actual minima = (10.551, 10.5695, 13.2915)\n Vpmg_setPart:  actual maxima = (24.951, 24.9695, 27.6915)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 5.713502079454E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.800000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.600000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3.80966\n Vpbe_ctor2:  solute dimensions = 5.374 x 6.581 x 6.611\n Vpbe_ctor2:  solute charge = 2.77556e-17\n@@ -3202,32 +3202,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.002068\n+Vacc_SASA: Time elapsed: 0.001685\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.348410e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.312320e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.595910e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.540820e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.046595e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.264010e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.649852e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.526445e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.197218e-01\n Vprtstp: contraction number = 1.197218e-01\n Vprtstp: iteration = 2\n@@ -3244,32 +3244,32 @@\n Vprtstp: contraction number = 1.080232e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.668171e-06\n Vprtstp: contraction number = 1.086670e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.821545e-07\n Vprtstp: contraction number = 1.091941e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.500837e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.731933e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.949993e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.134753e+01\n Vpmg_setPart:  lower corner = (-30.249, -30.2305, -27.5085)\n Vpmg_setPart:  upper corner = (65.751, 65.7695, 68.4915)\n Vpmg_setPart:  actual minima = (-30.249, -30.2305, -27.5085)\n Vpmg_setPart:  actual maxima = (65.751, 65.7695, 68.4915)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 5.413483938867E+01 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.000000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.600000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3.80966\n Vpbe_ctor2:  solute dimensions = 5.374 x 6.581 x 6.611\n Vpbe_ctor2:  solute charge = 2.77556e-17\n Vpbe_ctor2:  bulk ionic strength = 0.01\n Vpbe_ctor2:  xkappa = 0.205309\n@@ -3315,30 +3315,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0422608 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.001891\n+Vacc_SASA: Time elapsed: 0.001695\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.332700e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.481440e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.049400e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.378000e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.080253e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.174607e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.924289e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.746596e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.511608e-01\n Vprtstp: contraction number = 1.511608e-01\n Vprtstp: iteration = 2\n@@ -3355,30 +3355,30 @@\n Vprtstp: contraction number = 1.062405e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.836009e-06\n Vprtstp: contraction number = 1.072929e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.984242e-07\n Vprtstp: contraction number = 1.080737e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.309713e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.493443e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.242226e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.434122e+01\n Vpmg_setPart:  lower corner = (10.551, 10.5695, 13.2915)\n Vpmg_setPart:  upper corner = (24.951, 24.9695, 27.6915)\n Vpmg_setPart:  actual minima = (10.551, 10.5695, 13.2915)\n Vpmg_setPart:  actual maxima = (24.951, 24.9695, 27.6915)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 5.884571864356E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.800000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.900000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 26.5287\n Vpbe_ctor2:  solute dimensions = 50.733 x 37.661 x 37.832\n Vpbe_ctor2:  solute charge = 0.991\n@@ -3401,32 +3401,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.347389\n+Vacc_SASA: Time elapsed: 1.271560\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.672016e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.489645e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.069110e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.518240e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.162295e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.172306e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.215698e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.029224e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.257199e-02\n Vprtstp: contraction number = 3.257199e-02\n Vprtstp: iteration = 2\n@@ -3443,30 +3443,30 @@\n Vprtstp: contraction number = 1.541269e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.608808e-06\n Vprtstp: contraction number = 1.652212e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.820839e-07\n Vprtstp: contraction number = 1.753372e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.251928e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.480593e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.951866e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.179761e+01\n Vpmg_setPart:  lower corner = (-22.1255, -29.651, -28.888)\n Vpmg_setPart:  upper corner = (73.8745, 66.349, 67.112)\n Vpmg_setPart:  actual minima = (-22.1255, -29.651, -28.888)\n Vpmg_setPart:  actual maxima = (73.8745, 66.349, 67.112)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 8.592645225811E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.910000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.870000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 26.5287\n Vpbe_ctor2:  solute dimensions = 50.733 x 37.661 x 37.832\n Vpbe_ctor2:  solute charge = 0.991\n@@ -3514,30 +3514,30 @@\n VPMG::extEnergy: extQfEnergy = 7853.32 kT\n VPMG::extEnergy: extDiEnergy = 3800.2 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.348983\n+Vacc_SASA: Time elapsed: 1.260281\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.979335e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.754342e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.886000e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.343400e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.166959e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.103381e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.480342e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.260787e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.051303e-01\n Vprtstp: contraction number = 1.051303e-01\n Vprtstp: iteration = 2\n@@ -3554,30 +3554,30 @@\n Vprtstp: contraction number = 1.566068e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 4.652962e-06\n Vprtstp: contraction number = 1.751224e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 8.683754e-07\n Vprtstp: contraction number = 1.866285e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.324043e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.514267e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.020450e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.204370e+01\n Vpmg_setPart:  lower corner = (10.551, 10.5695, 13.2915)\n Vpmg_setPart:  upper corner = (24.951, 24.9695, 27.6915)\n Vpmg_setPart:  actual minima = (10.551, 10.5695, 13.2915)\n Vpmg_setPart:  actual maxima = (24.951, 24.9695, 27.6915)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 3.382181498242E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.580000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.370000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 26.5287\n Vpbe_ctor2:  solute dimensions = 50.733 x 37.661 x 37.832\n Vpbe_ctor2:  solute charge = 0.991\n@@ -3600,32 +3600,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.364372\n+Vacc_SASA: Time elapsed: 1.177449\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.735940e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.572824e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.252100e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.493620e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.195693e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.085680e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.772165e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.518301e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.219671e-02\n Vprtstp: contraction number = 2.219671e-02\n Vprtstp: iteration = 2\n@@ -3639,30 +3639,30 @@\n Vprtstp: contraction number = 9.588702e-02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 1.611478e-06\n Vprtstp: contraction number = 9.903019e-02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.632204e-07\n Vprtstp: contraction number = 1.012861e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.980398e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.194170e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.667978e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.858153e+01\n Vpmg_setPart:  lower corner = (-22.1255, -29.651, -28.888)\n Vpmg_setPart:  upper corner = (73.8745, 66.349, 67.112)\n Vpmg_setPart:  actual minima = (-22.1255, -29.651, -28.888)\n Vpmg_setPart:  actual maxima = (73.8745, 66.349, 67.112)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.119297547416E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.510000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.470000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 26.5287\n Vpbe_ctor2:  solute dimensions = 50.733 x 37.661 x 37.832\n Vpbe_ctor2:  solute charge = 0.991\n@@ -3710,30 +3710,30 @@\n VPMG::extEnergy: extQfEnergy = 10305.9 kT\n VPMG::extEnergy: extDiEnergy = 4984.29 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.321757\n+Vacc_SASA: Time elapsed: 1.259905\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.947946e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.773951e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.122900e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.374600e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.144342e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.021198e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.009719e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.721331e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.325279e-01\n Vprtstp: contraction number = 1.325279e-01\n Vprtstp: iteration = 2\n@@ -3750,44 +3750,44 @@\n Vprtstp: contraction number = 1.009444e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.272261e-06\n Vprtstp: contraction number = 1.024006e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.317723e-07\n Vprtstp: contraction number = 1.035733e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.225244e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.419871e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.082120e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.261824e+01\n Vpmg_setPart:  lower corner = (10.551, 10.5695, 13.2915)\n Vpmg_setPart:  upper corner = (24.951, 24.9695, 27.6915)\n Vpmg_setPart:  actual minima = (10.551, 10.5695, 13.2915)\n Vpmg_setPart:  actual maxima = (24.951, 24.9695, 27.6915)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 3.638817315582E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.660000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.270000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 3.235128e+02\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 2.931865e+02\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 06:40:32 2025\n+# Creation Date and Time:  Tue Jan  9 04:41:30 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path 1d7i-dss-complex.pqr\n@@ -4420,32 +4420,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.386164\n+Vacc_SASA: Time elapsed: 1.273951\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.513778e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.410887e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.795800e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.453500e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.077841e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.071103e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.668406e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.521366e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.573903e-02\n Vprtstp: contraction number = 6.573903e-02\n Vprtstp: iteration = 2\n@@ -4516,30 +4516,30 @@\n Vprtstp: contraction number = 6.827181e-01\n Vprtstp: iteration = 24\n Vprtstp: relative residual = 1.259903e-06\n Vprtstp: contraction number = 6.840214e-01\n Vprtstp: iteration = 25\n Vprtstp: relative residual = 8.633870e-07\n Vprtstp: contraction number = 6.852808e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 8.439114e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.647565e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 6.944475e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.149215e+01\n Vpmg_setPart:  lower corner = (-22.7365, -29.0115, -28.878)\n Vpmg_setPart:  upper corner = (73.2635, 66.9885, 67.122)\n Vpmg_setPart:  actual minima = (-22.7365, -29.0115, -28.878)\n Vpmg_setPart:  actual maxima = (73.2635, 66.9885, 67.122)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 7.345051831139E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.310000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.320000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 26.3256\n Vpbe_ctor2:  solute dimensions = 49.571 x 38.32 x 37.678\n Vpbe_ctor2:  solute charge = 0.991\n@@ -4587,30 +4587,30 @@\n VPMG::extEnergy: extQfEnergy = 6529.57 kT\n VPMG::extEnergy: extDiEnergy = 2987.06 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.397506\n+Vacc_SASA: Time elapsed: 1.265416\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.921290e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.735807e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.716800e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.993600e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.166939e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.947120e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.396157e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.849985e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.216933e-01\n Vprtstp: contraction number = 1.216933e-01\n Vprtstp: iteration = 2\n@@ -4639,30 +4639,30 @@\n Vprtstp: contraction number = 3.953520e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.724728e-06\n Vprtstp: contraction number = 4.218661e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 7.702114e-07\n Vprtstp: contraction number = 4.465699e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.472666e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.666682e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.220545e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.393529e+01\n Vpmg_setPart:  lower corner = (10.1405, 12.011, 13.303)\n Vpmg_setPart:  upper corner = (24.5405, 26.411, 27.703)\n Vpmg_setPart:  actual minima = (10.1405, 12.011, 13.303)\n Vpmg_setPart:  actual maxima = (24.5405, 26.411, 27.703)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 3.171725099545E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.600000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.590000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 26.3256\n Vpbe_ctor2:  solute dimensions = 49.571 x 38.32 x 37.678\n Vpbe_ctor2:  solute charge = 0.991\n@@ -4685,32 +4685,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.341565\n+Vacc_SASA: Time elapsed: 1.280853\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.859575e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.737092e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.951300e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.608980e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.075663e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.142189e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.347165e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.167011e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.208737e-02\n Vprtstp: contraction number = 2.208737e-02\n Vprtstp: iteration = 2\n@@ -4724,30 +4724,30 @@\n Vprtstp: contraction number = 9.525881e-02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 1.554352e-06\n Vprtstp: contraction number = 9.854831e-02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.569345e-07\n Vprtstp: contraction number = 1.009646e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.954228e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.162301e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.745011e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.966854e+01\n Vpmg_setPart:  lower corner = (-22.7365, -29.0115, -28.878)\n Vpmg_setPart:  upper corner = (73.2635, 66.9885, 67.122)\n Vpmg_setPart:  actual minima = (-22.7365, -29.0115, -28.878)\n Vpmg_setPart:  actual maxima = (73.2635, 66.9885, 67.122)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.014263549371E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.040000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.190000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 26.3256\n Vpbe_ctor2:  solute dimensions = 49.571 x 38.32 x 37.678\n Vpbe_ctor2:  solute charge = 0.991\n@@ -4795,30 +4795,30 @@\n VPMG::extEnergy: extQfEnergy = 9211.28 kT\n VPMG::extEnergy: extDiEnergy = 4239.53 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.265743\n+Vacc_SASA: Time elapsed: 1.240661\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.782977e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.667450e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.795900e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.607700e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.166849e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.075671e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.582888e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.377220e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.291558e-01\n Vprtstp: contraction number = 1.291558e-01\n Vprtstp: iteration = 2\n@@ -4835,30 +4835,30 @@\n Vprtstp: contraction number = 1.003267e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.195888e-06\n Vprtstp: contraction number = 1.018284e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.232544e-07\n Vprtstp: contraction number = 1.030651e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.347975e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.564429e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.033008e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.215713e+01\n Vpmg_setPart:  lower corner = (10.1405, 12.011, 13.303)\n Vpmg_setPart:  upper corner = (24.5405, 26.411, 27.703)\n Vpmg_setPart:  actual minima = (10.1405, 12.011, 13.303)\n Vpmg_setPart:  actual maxima = (24.5405, 26.411, 27.703)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 3.449231705544E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.350000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 9.600000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 5.02661\n Vpbe_ctor2:  solute dimensions = 5.303 x 9.299 x 6.49\n Vpbe_ctor2:  solute charge = -8.32667e-17\n@@ -4881,32 +4881,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.003048\n+Vacc_SASA: Time elapsed: 0.002872\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.503720e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.301720e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.260130e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.544830e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.153811e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.249541e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.843380e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.609610e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.937868e-02\n Vprtstp: contraction number = 9.937868e-02\n Vprtstp: iteration = 2\n@@ -4923,30 +4923,30 @@\n Vprtstp: contraction number = 1.252714e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.602930e-06\n Vprtstp: contraction number = 1.287705e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.415857e-07\n Vprtstp: contraction number = 1.312312e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.349968e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.558260e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.040940e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.273209e+01\n Vpmg_setPart:  lower corner = (-30.6595, -28.789, -27.497)\n Vpmg_setPart:  upper corner = (65.3405, 67.211, 68.503)\n Vpmg_setPart:  actual minima = (-30.6595, -28.789, -27.497)\n Vpmg_setPart:  actual maxima = (65.3405, 67.211, 68.503)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 7.561986028141E+01 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.000000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.300000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 5.02661\n Vpbe_ctor2:  solute dimensions = 5.303 x 9.299 x 6.49\n Vpbe_ctor2:  solute charge = -8.32667e-17\n@@ -4994,30 +4994,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00497505 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.002940\n+Vacc_SASA: Time elapsed: 0.002845\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.464140e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.184700e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.299700e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.144610e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.095061e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.047357e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.103866e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.836526e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.636290e-01\n Vprtstp: contraction number = 2.636290e-01\n Vprtstp: iteration = 2\n@@ -5049,30 +5049,30 @@\n Vprtstp: contraction number = 3.506954e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 1.726432e-06\n Vprtstp: contraction number = 3.673674e-01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 6.664171e-07\n Vprtstp: contraction number = 3.860084e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.971824e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.185245e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.343971e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.532729e+01\n Vpmg_setPart:  lower corner = (10.1405, 12.011, 13.303)\n Vpmg_setPart:  upper corner = (24.5405, 26.411, 27.703)\n Vpmg_setPart:  actual minima = (10.1405, 12.011, 13.303)\n Vpmg_setPart:  actual maxima = (24.5405, 26.411, 27.703)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.344916094234E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.700000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.200000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 5.02661\n Vpbe_ctor2:  solute dimensions = 5.303 x 9.299 x 6.49\n Vpbe_ctor2:  solute charge = -8.32667e-17\n@@ -5095,32 +5095,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.015188\n+Vacc_SASA: Time elapsed: 0.002568\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.611620e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.685000e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.141330e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.779700e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.069180e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.294438e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.525446e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.196650e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.352196e-02\n Vprtstp: contraction number = 6.352196e-02\n Vprtstp: iteration = 2\n@@ -5134,32 +5134,32 @@\n Vprtstp: contraction number = 1.012293e-01\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 6.271886e-06\n Vprtstp: contraction number = 1.033361e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 6.595226e-07\n Vprtstp: contraction number = 1.051554e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.907896e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.106775e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.700605e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.913750e+01\n Vpmg_setPart:  lower corner = (-30.6595, -28.789, -27.497)\n Vpmg_setPart:  upper corner = (65.3405, 67.211, 68.503)\n Vpmg_setPart:  actual minima = (-30.6595, -28.789, -27.497)\n Vpmg_setPart:  actual maxima = (65.3405, 67.211, 68.503)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 9.389840581990E+01 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.500000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.900000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 5.02661\n Vpbe_ctor2:  solute dimensions = 5.303 x 9.299 x 6.49\n Vpbe_ctor2:  solute charge = -8.32667e-17\n Vpbe_ctor2:  bulk ionic strength = 0.01\n Vpbe_ctor2:  xkappa = 0.205309\n@@ -5205,30 +5205,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0518244 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.002786\n+Vacc_SASA: Time elapsed: 0.003053\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.887400e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.889780e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 9.957500e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.659500e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.107932e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.800750e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.739863e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.387321e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.573900e-01\n Vprtstp: contraction number = 1.573900e-01\n Vprtstp: iteration = 2\n@@ -5245,30 +5245,30 @@\n Vprtstp: contraction number = 1.046499e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.765958e-06\n Vprtstp: contraction number = 1.060018e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.889858e-07\n Vprtstp: contraction number = 1.070160e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.295091e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.493947e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.963131e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.129807e+01\n Vpmg_setPart:  lower corner = (10.1405, 12.011, 13.303)\n Vpmg_setPart:  upper corner = (24.5405, 26.411, 27.703)\n Vpmg_setPart:  actual minima = (10.1405, 12.011, 13.303)\n Vpmg_setPart:  actual maxima = (24.5405, 26.411, 27.703)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.361370594878E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.600000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.000000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 26.3256\n Vpbe_ctor2:  solute dimensions = 49.571 x 38.32 x 37.678\n Vpbe_ctor2:  solute charge = 0.991\n@@ -5291,32 +5291,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.356712\n+Vacc_SASA: Time elapsed: 1.220687\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.620896e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.348893e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 3.380400e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.156240e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.184691e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.431500e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.027992e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.636560e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.573435e-02\n Vprtstp: contraction number = 6.573435e-02\n Vprtstp: iteration = 2\n@@ -5387,32 +5387,32 @@\n Vprtstp: contraction number = 6.841463e-01\n Vprtstp: iteration = 24\n Vprtstp: relative residual = 1.230794e-06\n Vprtstp: contraction number = 6.854643e-01\n Vprtstp: iteration = 25\n Vprtstp: relative residual = 8.453252e-07\n Vprtstp: contraction number = 6.868128e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 8.198749e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.413230e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 6.941846e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.129383e+01\n Vpmg_setPart:  lower corner = (-22.7365, -29.0115, -28.878)\n Vpmg_setPart:  upper corner = (73.2635, 66.9885, 67.122)\n Vpmg_setPart:  actual minima = (-22.7365, -29.0115, -28.878)\n Vpmg_setPart:  actual maxima = (73.2635, 66.9885, 67.122)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 7.248457904492E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.650000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.150000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 26.3256\n Vpbe_ctor2:  solute dimensions = 49.571 x 38.32 x 37.678\n Vpbe_ctor2:  solute charge = 0.991\n Vpbe_ctor2:  bulk ionic strength = 0.01\n Vpbe_ctor2:  xkappa = 0.0328757\n@@ -5458,30 +5458,30 @@\n VPMG::extEnergy: extQfEnergy = 6529.31 kT\n VPMG::extEnergy: extDiEnergy = 2986.91 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.333453\n+Vacc_SASA: Time elapsed: 1.218681\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.884905e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.658049e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.820000e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.442300e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.143703e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.210838e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.886872e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.368502e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.206113e-01\n Vprtstp: contraction number = 1.206113e-01\n Vprtstp: iteration = 2\n@@ -5510,30 +5510,30 @@\n Vprtstp: contraction number = 3.809962e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.385263e-06\n Vprtstp: contraction number = 4.084139e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 6.028523e-07\n Vprtstp: contraction number = 4.351898e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.709891e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.904885e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.402719e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.606459e+01\n Vpmg_setPart:  lower corner = (10.1405, 12.011, 13.303)\n Vpmg_setPart:  upper corner = (24.5405, 26.411, 27.703)\n Vpmg_setPart:  actual minima = (10.1405, 12.011, 13.303)\n Vpmg_setPart:  actual maxima = (24.5405, 26.411, 27.703)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 3.037057682028E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.170000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.120000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 26.3256\n Vpbe_ctor2:  solute dimensions = 49.571 x 38.32 x 37.678\n Vpbe_ctor2:  solute charge = 0.991\n@@ -5556,32 +5556,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.336589\n+Vacc_SASA: Time elapsed: 1.167394\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.700320e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.502440e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.057000e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.618160e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.065149e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.646280e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.315346e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.763311e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.233304e-02\n Vprtstp: contraction number = 2.233304e-02\n Vprtstp: iteration = 2\n@@ -5595,30 +5595,30 @@\n Vprtstp: contraction number = 9.522390e-02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 1.574058e-06\n Vprtstp: contraction number = 9.845638e-02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.587415e-07\n Vprtstp: contraction number = 1.008486e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.931756e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.129877e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.671806e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.862111e+01\n Vpmg_setPart:  lower corner = (-22.7365, -29.0115, -28.878)\n Vpmg_setPart:  upper corner = (73.2635, 66.9885, 67.122)\n Vpmg_setPart:  actual minima = (-22.7365, -29.0115, -28.878)\n Vpmg_setPart:  actual maxima = (73.2635, 66.9885, 67.122)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.004264667397E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.330000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.550000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 26.3256\n Vpbe_ctor2:  solute dimensions = 49.571 x 38.32 x 37.678\n Vpbe_ctor2:  solute charge = 0.991\n@@ -5666,30 +5666,30 @@\n VPMG::extEnergy: extQfEnergy = 9208.92 kT\n VPMG::extEnergy: extDiEnergy = 4238.63 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.352093\n+Vacc_SASA: Time elapsed: 1.203261\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.748933e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.660015e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.697700e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.641000e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.219077e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.045575e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.547919e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.965262e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.281343e-01\n Vprtstp: contraction number = 1.281343e-01\n Vprtstp: iteration = 2\n@@ -5706,44 +5706,44 @@\n Vprtstp: contraction number = 1.003059e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.185212e-06\n Vprtstp: contraction number = 1.017952e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.220913e-07\n Vprtstp: contraction number = 1.030122e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.362010e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.572181e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.185015e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.358919e+01\n Vpmg_setPart:  lower corner = (10.1405, 12.011, 13.303)\n Vpmg_setPart:  upper corner = (24.5405, 26.411, 27.703)\n Vpmg_setPart:  actual minima = (10.1405, 12.011, 13.303)\n Vpmg_setPart:  actual maxima = (24.5405, 26.411, 27.703)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 3.314075450214E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.220000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.410000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 4.786482e+02\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 4.186329e+02\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 06:41:47 2025\n+# Creation Date and Time:  Tue Jan  9 04:42:53 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path 1d7i-dss-complex.pqr\n@@ -6376,32 +6376,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.399997\n+Vacc_SASA: Time elapsed: 1.223234\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.706640e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.585610e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 3.476500e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 3.068300e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.796020e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.996230e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.755885e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.698768e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.298567e-02\n Vprtstp: contraction number = 3.298567e-02\n Vprtstp: iteration = 2\n@@ -6418,30 +6418,30 @@\n Vprtstp: contraction number = 1.536726e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.666279e-06\n Vprtstp: contraction number = 1.683668e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.055929e-07\n Vprtstp: contraction number = 1.833984e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.247411e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.445306e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.930372e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.135865e+01\n Vpmg_setPart:  lower corner = (-22.7365, -29.0115, -28.878)\n Vpmg_setPart:  upper corner = (73.2635, 66.9885, 67.122)\n Vpmg_setPart:  actual minima = (-22.7365, -29.0115, -28.878)\n Vpmg_setPart:  actual maxima = (73.2635, 66.9885, 67.122)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 7.725356066403E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.408000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.190000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 26.3256\n Vpbe_ctor2:  solute dimensions = 49.571 x 38.32 x 37.678\n Vpbe_ctor2:  solute charge = 0.991\n@@ -6489,30 +6489,30 @@\n VPMG::extEnergy: extQfEnergy = 6899.51 kT\n VPMG::extEnergy: extDiEnergy = 3158.85 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.374485\n+Vacc_SASA: Time elapsed: 1.241227\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.020465e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.857025e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 3.230300e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.542200e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.270928e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.032867e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.270751e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.862990e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.032281e-01\n Vprtstp: contraction number = 1.032281e-01\n Vprtstp: iteration = 2\n@@ -6529,30 +6529,30 @@\n Vprtstp: contraction number = 1.485117e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 3.842446e-06\n Vprtstp: contraction number = 1.674805e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 6.939533e-07\n Vprtstp: contraction number = 1.806019e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.536062e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.774441e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.970666e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.145685e+01\n Vpmg_setPart:  lower corner = (10.1405, 12.011, 13.303)\n Vpmg_setPart:  upper corner = (24.5405, 26.411, 27.703)\n Vpmg_setPart:  actual minima = (10.1405, 12.011, 13.303)\n Vpmg_setPart:  actual maxima = (24.5405, 26.411, 27.703)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 3.209791610861E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.480000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.160000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 26.3256\n Vpbe_ctor2:  solute dimensions = 49.571 x 38.32 x 37.678\n Vpbe_ctor2:  solute charge = 0.991\n@@ -6575,32 +6575,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.370850\n+Vacc_SASA: Time elapsed: 1.247615\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.951960e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.787999e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.901100e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.048780e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.115656e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.021814e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.432584e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.426969e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.208737e-02\n Vprtstp: contraction number = 2.208737e-02\n Vprtstp: iteration = 2\n@@ -6614,30 +6614,30 @@\n Vprtstp: contraction number = 9.525881e-02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 1.554352e-06\n Vprtstp: contraction number = 9.854831e-02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.569345e-07\n Vprtstp: contraction number = 1.009646e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.890243e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.112567e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.650070e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.857767e+01\n Vpmg_setPart:  lower corner = (-22.7365, -29.0115, -28.878)\n Vpmg_setPart:  upper corner = (73.2635, 66.9885, 67.122)\n Vpmg_setPart:  actual minima = (-22.7365, -29.0115, -28.878)\n Vpmg_setPart:  actual maxima = (73.2635, 66.9885, 67.122)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.014263549371E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.350000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.466000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 26.3256\n Vpbe_ctor2:  solute dimensions = 49.571 x 38.32 x 37.678\n Vpbe_ctor2:  solute charge = 0.991\n@@ -6685,30 +6685,30 @@\n VPMG::extEnergy: extQfEnergy = 9211.28 kT\n VPMG::extEnergy: extDiEnergy = 4239.53 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.405800\n+Vacc_SASA: Time elapsed: 1.255362\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.009123e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.784151e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.105800e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.535600e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.322997e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.047269e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.738574e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.436691e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.291558e-01\n Vprtstp: contraction number = 1.291558e-01\n Vprtstp: iteration = 2\n@@ -6725,32 +6725,32 @@\n Vprtstp: contraction number = 1.003267e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.195888e-06\n Vprtstp: contraction number = 1.018284e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.232544e-07\n Vprtstp: contraction number = 1.030651e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.305502e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.517449e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.973346e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.149628e+01\n Vpmg_setPart:  lower corner = (10.1405, 12.011, 13.303)\n Vpmg_setPart:  upper corner = (24.5405, 26.411, 27.703)\n Vpmg_setPart:  actual minima = (10.1405, 12.011, 13.303)\n Vpmg_setPart:  actual maxima = (24.5405, 26.411, 27.703)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 3.449231705544E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.730000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.010000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 5.02661\n Vpbe_ctor2:  solute dimensions = 5.303 x 9.299 x 6.49\n Vpbe_ctor2:  solute charge = -8.32667e-17\n Vpbe_ctor2:  bulk ionic strength = 0.01\n Vpbe_ctor2:  xkappa = 0.0328757\n@@ -6771,32 +6771,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.003185\n+Vacc_SASA: Time elapsed: 0.002744\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.796360e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.774510e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.065760e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.187810e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.074357e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.402220e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.133099e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.652602e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.464737e-02\n Vprtstp: contraction number = 8.464737e-02\n Vprtstp: iteration = 2\n@@ -6813,32 +6813,32 @@\n Vprtstp: contraction number = 1.071698e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.052787e-06\n Vprtstp: contraction number = 1.084632e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.152581e-07\n Vprtstp: contraction number = 1.094790e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.278185e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.487769e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.924632e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.091812e+01\n Vpmg_setPart:  lower corner = (-30.6595, -28.789, -27.497)\n Vpmg_setPart:  upper corner = (65.3405, 67.211, 68.503)\n Vpmg_setPart:  actual minima = (-30.6595, -28.789, -27.497)\n Vpmg_setPart:  actual maxima = (65.3405, 67.211, 68.503)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 6.368169150406E+01 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.600000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.300000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 5.02661\n Vpbe_ctor2:  solute dimensions = 5.303 x 9.299 x 6.49\n Vpbe_ctor2:  solute charge = -8.32667e-17\n Vpbe_ctor2:  bulk ionic strength = 0.01\n Vpbe_ctor2:  xkappa = 0.0328757\n@@ -6884,30 +6884,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00594757 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.003222\n+Vacc_SASA: Time elapsed: 0.002541\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.934140e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.623620e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.220400e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.866000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.088191e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.212020e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.387822e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.180381e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.027171e-01\n Vprtstp: contraction number = 2.027171e-01\n Vprtstp: iteration = 2\n@@ -6927,30 +6927,30 @@\n Vprtstp: contraction number = 1.717621e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.164324e-06\n Vprtstp: contraction number = 1.754898e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 5.631488e-07\n Vprtstp: contraction number = 1.779681e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.665835e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.868725e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.249570e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.407112e+01\n Vpmg_setPart:  lower corner = (10.1405, 12.011, 13.303)\n Vpmg_setPart:  upper corner = (24.5405, 26.411, 27.703)\n Vpmg_setPart:  actual minima = (10.1405, 12.011, 13.303)\n Vpmg_setPart:  actual maxima = (24.5405, 26.411, 27.703)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.345277247759E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.600000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.800000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 5.02661\n Vpbe_ctor2:  solute dimensions = 5.303 x 9.299 x 6.49\n Vpbe_ctor2:  solute charge = -8.32667e-17\n@@ -6973,32 +6973,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.002861\n+Vacc_SASA: Time elapsed: 0.002797\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.298710e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.562480e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.216410e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.023050e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.040645e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.465080e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.680885e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.429499e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.352196e-02\n Vprtstp: contraction number = 6.352196e-02\n Vprtstp: iteration = 2\n@@ -7012,32 +7012,32 @@\n Vprtstp: contraction number = 1.012293e-01\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 6.271886e-06\n Vprtstp: contraction number = 1.033361e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 6.595226e-07\n Vprtstp: contraction number = 1.051554e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.919508e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.112878e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.693661e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.864849e+01\n Vpmg_setPart:  lower corner = (-30.6595, -28.789, -27.497)\n Vpmg_setPart:  upper corner = (65.3405, 67.211, 68.503)\n Vpmg_setPart:  actual minima = (-30.6595, -28.789, -27.497)\n Vpmg_setPart:  actual maxima = (65.3405, 67.211, 68.503)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 9.389840581990E+01 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.400000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.200000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 5.02661\n Vpbe_ctor2:  solute dimensions = 5.303 x 9.299 x 6.49\n Vpbe_ctor2:  solute charge = -8.32667e-17\n Vpbe_ctor2:  bulk ionic strength = 0.01\n Vpbe_ctor2:  xkappa = 0.205309\n@@ -7083,30 +7083,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0518244 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.002854\n+Vacc_SASA: Time elapsed: 0.002715\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.107990e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.132900e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.821600e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.472900e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.081229e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.555140e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.898058e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.619817e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.573900e-01\n Vprtstp: contraction number = 1.573900e-01\n Vprtstp: iteration = 2\n@@ -7123,32 +7123,32 @@\n Vprtstp: contraction number = 1.046499e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.765958e-06\n Vprtstp: contraction number = 1.060018e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.889858e-07\n Vprtstp: contraction number = 1.070160e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.257380e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.446124e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.004277e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.154844e+01\n Vpmg_setPart:  lower corner = (10.1405, 12.011, 13.303)\n Vpmg_setPart:  upper corner = (24.5405, 26.411, 27.703)\n Vpmg_setPart:  actual minima = (10.1405, 12.011, 13.303)\n Vpmg_setPart:  actual maxima = (24.5405, 26.411, 27.703)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.361370594878E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.000000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.700000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 26.3256\n Vpbe_ctor2:  solute dimensions = 49.571 x 38.32 x 37.678\n Vpbe_ctor2:  solute charge = 0.991\n Vpbe_ctor2:  bulk ionic strength = 0.01\n Vpbe_ctor2:  xkappa = 0.0328757\n@@ -7169,32 +7169,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.369548\n+Vacc_SASA: Time elapsed: 1.247979\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.671741e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.371317e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.557700e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.917880e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.008633e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.116468e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.181975e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.875754e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.328224e-02\n Vprtstp: contraction number = 3.328224e-02\n Vprtstp: iteration = 2\n@@ -7211,30 +7211,30 @@\n Vprtstp: contraction number = 1.553323e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.764269e-06\n Vprtstp: contraction number = 1.696908e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.244306e-07\n Vprtstp: contraction number = 1.838895e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.278536e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.484392e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.998006e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.211173e+01\n Vpmg_setPart:  lower corner = (-22.7365, -29.0115, -28.878)\n Vpmg_setPart:  upper corner = (73.2635, 66.9885, 67.122)\n Vpmg_setPart:  actual minima = (-22.7365, -29.0115, -28.878)\n Vpmg_setPart:  actual maxima = (73.2635, 66.9885, 67.122)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 7.622871644072E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.390000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.330000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 26.3256\n Vpbe_ctor2:  solute dimensions = 49.571 x 38.32 x 37.678\n Vpbe_ctor2:  solute charge = 0.991\n@@ -7282,30 +7282,30 @@\n VPMG::extEnergy: extQfEnergy = 6899.11 kT\n VPMG::extEnergy: extDiEnergy = 3158.68 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.382697\n+Vacc_SASA: Time elapsed: 1.263188\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.939750e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.742751e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.223700e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.378400e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.029622e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.025955e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.449186e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.111395e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.025309e-01\n Vprtstp: contraction number = 1.025309e-01\n Vprtstp: iteration = 2\n@@ -7322,30 +7322,30 @@\n Vprtstp: contraction number = 1.507031e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 3.981847e-06\n Vprtstp: contraction number = 1.699776e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 7.281025e-07\n Vprtstp: contraction number = 1.828555e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.383303e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.578818e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.947661e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.124140e+01\n Vpmg_setPart:  lower corner = (10.1405, 12.011, 13.303)\n Vpmg_setPart:  upper corner = (24.5405, 26.411, 27.703)\n Vpmg_setPart:  actual minima = (10.1405, 12.011, 13.303)\n Vpmg_setPart:  actual maxima = (24.5405, 26.411, 27.703)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 3.075005771448E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.610000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.130000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 26.3256\n Vpbe_ctor2:  solute dimensions = 49.571 x 38.32 x 37.678\n Vpbe_ctor2:  solute charge = 0.991\n@@ -7368,32 +7368,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.289100\n+Vacc_SASA: Time elapsed: 1.251188\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.662970e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.552131e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.027800e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.484430e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.100733e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.276480e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.745470e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.360994e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.233304e-02\n Vprtstp: contraction number = 2.233304e-02\n Vprtstp: iteration = 2\n@@ -7407,30 +7407,30 @@\n Vprtstp: contraction number = 9.522390e-02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 1.574058e-06\n Vprtstp: contraction number = 9.845638e-02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.587415e-07\n Vprtstp: contraction number = 1.008486e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.024555e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.230119e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.669589e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.855099e+01\n Vpmg_setPart:  lower corner = (-22.7365, -29.0115, -28.878)\n Vpmg_setPart:  upper corner = (73.2635, 66.9885, 67.122)\n Vpmg_setPart:  actual minima = (-22.7365, -29.0115, -28.878)\n Vpmg_setPart:  actual maxima = (73.2635, 66.9885, 67.122)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.004264667397E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.670000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.140000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 26.3256\n Vpbe_ctor2:  solute dimensions = 49.571 x 38.32 x 37.678\n Vpbe_ctor2:  solute charge = 0.991\n@@ -7478,30 +7478,30 @@\n VPMG::extEnergy: extQfEnergy = 9208.92 kT\n VPMG::extEnergy: extDiEnergy = 4238.63 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.359317\n+Vacc_SASA: Time elapsed: 1.253610\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.881872e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.715285e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.841800e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.360500e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.018181e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.115510e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.985626e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.566605e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.281343e-01\n Vprtstp: contraction number = 1.281343e-01\n Vprtstp: iteration = 2\n@@ -7518,34 +7518,34 @@\n Vprtstp: contraction number = 1.003059e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.185212e-06\n Vprtstp: contraction number = 1.017952e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.220913e-07\n Vprtstp: contraction number = 1.030122e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.411369e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.589923e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.960891e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.167871e+01\n Vpmg_setPart:  lower corner = (10.1405, 12.011, 13.303)\n Vpmg_setPart:  upper corner = (24.5405, 26.411, 27.703)\n Vpmg_setPart:  actual minima = (10.1405, 12.011, 13.303)\n Vpmg_setPart:  actual maxima = (24.5405, 26.411, 27.703)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 3.314075450214E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.490000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.290000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 3.229222e+02\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 2.765693e+02\n"}, {"source1": "./usr/share/apbs/examples/actin-dimer/io.mc", "source2": "./usr/share/apbs/examples/actin-dimer/io.mc", "unified_diff": "@@ -1,10 +1,10 @@\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 05:38:06 2025\n+# Creation Date and Time:  Tue Jan  9 03:22:14 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path mol1.pqr\n@@ -262,217 +262,217 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 2.892765\n+Vacc_SASA: Time elapsed: 2.973694\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.598363e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.354817e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (161, 161, 161)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.942520e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.086740e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (081, 081, 081)\n Vbuildops: Galer: (041, 041, 041)\n Vbuildops: Galer: (021, 021, 021)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.102662e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.996341e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.565387e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.306005e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 7775242.648804\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.089839e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.057456e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.252805e+05\n Vprtstp: contraction number = 5.252805e+05\n Vnewton: Attempting damping, relres = 0.062556\n Vnewton: Attempting damping, relres = 0.525334\n Vnewton: Damping accepted, relres = 0.062556\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.255619e-02\n Vprtstp: contraction number = 6.255619e-02\n Vnewton: Using errtol_s: 486389.547875\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.283042e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.226262e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.109788e+05\n Vprtstp: contraction number = 1.109788e+05\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.292368e-02\n Vprtstp: contraction number = 2.065932e-01\n Vnewton: Using errtol_s: 100484.762247\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.557953e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.212919e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.281526e+04\n Vprtstp: contraction number = 3.281526e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 3.798952e-03\n Vprtstp: contraction number = 2.939527e-01\n Vnewton: Using errtol_s: 29537.770540\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.092474e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.200085e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.139405e+04\n Vprtstp: contraction number = 1.139405e+04\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.318894e-03\n Vprtstp: contraction number = 3.471731e-01\n Vnewton: Using errtol_s: 10254.719067\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.434974e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.115268e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.292845e+03\n Vprtstp: contraction number = 4.292845e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.969084e-04\n Vprtstp: contraction number = 3.767615e-01\n Vnewton: Using errtol_s: 3863.583447\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.670563e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.113508e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.746643e+03\n Vprtstp: contraction number = 1.746643e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.021786e-04\n Vprtstp: contraction number = 4.068730e-01\n Vnewton: Using errtol_s: 1571.987642\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.010807e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.310056e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.833563e+02\n Vprtstp: contraction number = 7.833563e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 9.067555e-05\n Vprtstp: contraction number = 4.484923e-01\n Vnewton: Using errtol_s: 705.024393\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.340797e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.503058e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.880760e+02\n Vprtstp: contraction number = 3.880760e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 4.492075e-05\n Vprtstp: contraction number = 4.954009e-01\n Vnewton: Using errtol_s: 349.269694\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.688971e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.702131e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.071891e+02\n Vprtstp: contraction number = 2.071891e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.398262e-05\n Vprtstp: contraction number = 5.338875e-01\n Vnewton: Using errtol_s: 186.470725\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.018916e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.891446e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.168433e+02\n Vprtstp: contraction number = 1.168433e+02\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.352487e-05\n Vprtstp: contraction number = 5.639446e-01\n Vnewton: Using errtol_s: 105.159166\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.379928e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.086532e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.826136e+01\n Vprtstp: contraction number = 6.826136e+01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 7.901399e-06\n Vprtstp: contraction number = 5.842124e-01\n Vnewton: Using errtol_s: 61.435293\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.701243e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.280513e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.091749e+01\n Vprtstp: contraction number = 4.091749e+01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 4.736285e-06\n Vprtstp: contraction number = 5.994236e-01\n Vnewton: Using errtol_s: 36.825768\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.017053e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.472961e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.493482e+01\n Vprtstp: contraction number = 2.493482e+01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 2.886257e-06\n Vprtstp: contraction number = 6.093926e-01\n Vnewton: Using errtol_s: 22.441349\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.325606e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.667113e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.538748e+01\n Vprtstp: contraction number = 1.538748e+01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 1.781132e-06\n Vprtstp: contraction number = 6.171079e-01\n Vnewton: Using errtol_s: 13.848733\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.642059e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.857663e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.579209e+00\n Vprtstp: contraction number = 9.579209e+00\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 1.108813e-06\n Vprtstp: contraction number = 6.225327e-01\n Vnewton: Using errtol_s: 8.621289\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.949916e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.043579e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.005674e+00\n Vprtstp: contraction number = 6.005674e+00\n Vprtstp: iteration = 16\n Vprtstp: relative residual = 6.951690e-07\n Vprtstp: contraction number = 6.269489e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 5.155945e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 5.182685e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 3.152466e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.178913e+02\n Vpmg_setPart:  lower corner = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  upper corner = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -481,17 +481,17 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 4.412172567798E+00 kT\n Vpmg_energy:  qfEnergy = 1.232438411967E+05 kT\n Vpmg_energy:  dielEnergy = 6.161638379331E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.339740e-01\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.480560e-01\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 39.7309\n Vpbe_ctor2:  solute dimensions = 68.682 x 69.075 x 70.346\n Vpbe_ctor2:  solute charge = -12\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.0735516\n@@ -537,193 +537,193 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.294338 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 2.818112\n+Vacc_SASA: Time elapsed: 3.112433\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.145108e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.474388e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (161, 161, 161)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.180780e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.226970e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (081, 081, 081)\n Vbuildops: Galer: (041, 041, 041)\n Vbuildops: Galer: (021, 021, 021)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.535873e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.233701e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.317450e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.312338e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 9262588.477712\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.357525e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.343838e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.740096e+05\n Vprtstp: contraction number = 9.740096e+05\n Vnewton: Attempting damping, relres = 0.096135\n Vnewton: Attempting damping, relres = 0.545161\n Vnewton: Damping accepted, relres = 0.096135\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.613536e-02\n Vprtstp: contraction number = 9.613536e-02\n Vnewton: Using errtol_s: 890462.283513\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.694054e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.563842e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.907605e+05\n Vprtstp: contraction number = 1.907605e+05\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.859794e-02\n Vprtstp: contraction number = 1.934558e-01\n Vnewton: Using errtol_s: 172265.062018\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.954373e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.756053e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.138633e+04\n Vprtstp: contraction number = 5.138633e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 4.994948e-03\n Vprtstp: contraction number = 2.685753e-01\n Vnewton: Using errtol_s: 46266.149079\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.200859e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.946491e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.656736e+04\n Vprtstp: contraction number = 1.656736e+04\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.610090e-03\n Vprtstp: contraction number = 3.223437e-01\n Vnewton: Using errtol_s: 14913.601487\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.465019e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.145088e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.837272e+03\n Vprtstp: contraction number = 5.837272e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.672493e-04\n Vprtstp: contraction number = 3.523090e-01\n Vnewton: Using errtol_s: 5254.196377\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.711138e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.343452e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.147141e+03\n Vprtstp: contraction number = 2.147141e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.086390e-04\n Vprtstp: contraction number = 3.678083e-01\n Vnewton: Using errtol_s: 1932.536910\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.938506e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.536932e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.193498e+02\n Vprtstp: contraction number = 8.193498e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 7.961379e-05\n Vprtstp: contraction number = 3.815864e-01\n Vnewton: Using errtol_s: 737.429804\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.177591e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.729846e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.352547e+02\n Vprtstp: contraction number = 3.352547e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 3.257526e-05\n Vprtstp: contraction number = 4.091660e-01\n Vnewton: Using errtol_s: 301.731240\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.423613e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.921721e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.500666e+02\n Vprtstp: contraction number = 1.500666e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 1.458127e-05\n Vprtstp: contraction number = 4.476179e-01\n Vnewton: Using errtol_s: 135.060298\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.668846e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.114492e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.280398e+01\n Vprtstp: contraction number = 7.280398e+01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 7.074013e-06\n Vprtstp: contraction number = 4.851438e-01\n Vnewton: Using errtol_s: 65.523671\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.915342e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.308832e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.740960e+01\n Vprtstp: contraction number = 3.740960e+01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.634908e-06\n Vprtstp: contraction number = 5.138397e-01\n Vnewton: Using errtol_s: 33.668661\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.146790e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.512259e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.000118e+01\n Vprtstp: contraction number = 2.000118e+01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.943416e-06\n Vprtstp: contraction number = 5.346535e-01\n Vnewton: Using errtol_s: 18.001066\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.385863e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.708797e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.094514e+01\n Vprtstp: contraction number = 1.094514e+01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 1.063486e-06\n Vprtstp: contraction number = 5.472249e-01\n Vnewton: Using errtol_s: 9.850631\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.623615e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.902864e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.085292e+00\n Vprtstp: contraction number = 6.085292e+00\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 5.912779e-07\n Vprtstp: contraction number = 5.559810e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 3.528145e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.559702e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.776830e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.805890e+02\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  actual maxima = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -732,17 +732,17 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 4.418972427545E+00 kT\n Vpmg_energy:  qfEnergy = 2.355397093328E+05 kT\n Vpmg_energy:  dielEnergy = 1.177642501639E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.562930e-01\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.275980e-01\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.0735516\n@@ -763,217 +763,217 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.306036\n+Vacc_SASA: Time elapsed: 2.907081\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.724543e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.275398e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (161, 161, 161)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.588030e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.058430e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (081, 081, 081)\n Vbuildops: Galer: (041, 041, 041)\n Vbuildops: Galer: (021, 021, 021)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.462686e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.049199e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.928490e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.161057e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 7837779.438687\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.967108e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.196945e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.264175e+05\n Vprtstp: contraction number = 5.264175e+05\n Vnewton: Attempting damping, relres = 0.062206\n Vnewton: Attempting damping, relres = 0.525499\n Vnewton: Damping accepted, relres = 0.062206\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.220619e-02\n Vprtstp: contraction number = 6.220619e-02\n Vnewton: Using errtol_s: 487558.369599\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.242448e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.415781e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.104882e+05\n Vprtstp: contraction number = 1.104882e+05\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.277305e-02\n Vprtstp: contraction number = 2.053340e-01\n Vnewton: Using errtol_s: 100112.332342\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.471864e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.606983e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.234516e+04\n Vprtstp: contraction number = 3.234516e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 3.716136e-03\n Vprtstp: contraction number = 2.909357e-01\n Vnewton: Using errtol_s: 29126.250452\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.726556e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.809159e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.113222e+04\n Vprtstp: contraction number = 1.113222e+04\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.278517e-03\n Vprtstp: contraction number = 3.440448e-01\n Vnewton: Using errtol_s: 10020.735856\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.969650e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.998535e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.146765e+03\n Vprtstp: contraction number = 4.146765e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.761620e-04\n Vprtstp: contraction number = 3.724330e-01\n Vnewton: Using errtol_s: 3732.052866\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.021705e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.210834e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.647764e+03\n Vprtstp: contraction number = 1.647764e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.891857e-04\n Vprtstp: contraction number = 3.973138e-01\n Vnewton: Using errtol_s: 1482.795933\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.047493e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.417973e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.190477e+02\n Vprtstp: contraction number = 7.190477e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 8.256252e-05\n Vprtstp: contraction number = 4.364099e-01\n Vnewton: Using errtol_s: 647.106851\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.074641e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.627959e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.514586e+02\n Vprtstp: contraction number = 3.514586e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 4.035656e-05\n Vprtstp: contraction number = 4.888000e-01\n Vnewton: Using errtol_s: 316.305821\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.099201e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.831915e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.878144e+02\n Vprtstp: contraction number = 1.878144e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.156625e-05\n Vprtstp: contraction number = 5.343927e-01\n Vnewton: Using errtol_s: 169.031531\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.124304e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.036908e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.065907e+02\n Vprtstp: contraction number = 1.065907e+02\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.223961e-05\n Vprtstp: contraction number = 5.675353e-01\n Vnewton: Using errtol_s: 95.931363\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.148736e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.231642e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.270317e+01\n Vprtstp: contraction number = 6.270317e+01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 7.200099e-06\n Vprtstp: contraction number = 5.882621e-01\n Vnewton: Using errtol_s: 56.432788\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.174140e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.436335e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.774740e+01\n Vprtstp: contraction number = 3.774740e+01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 4.334473e-06\n Vprtstp: contraction number = 6.020019e-01\n Vnewton: Using errtol_s: 33.972645\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.199054e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.633316e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.304758e+01\n Vprtstp: contraction number = 2.304758e+01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 2.646517e-06\n Vprtstp: contraction number = 6.105742e-01\n Vnewton: Using errtol_s: 20.742819\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.221030e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.832582e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.421587e+01\n Vprtstp: contraction number = 1.421587e+01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 1.632386e-06\n Vprtstp: contraction number = 6.168053e-01\n Vnewton: Using errtol_s: 12.794282\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.244238e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.047242e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.829808e+00\n Vprtstp: contraction number = 8.829808e+00\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 1.013913e-06\n Vprtstp: contraction number = 6.211233e-01\n Vnewton: Using errtol_s: 7.946827\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.268089e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.248188e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.514712e+00\n Vprtstp: contraction number = 5.514712e+00\n Vprtstp: iteration = 16\n Vprtstp: relative residual = 6.332457e-07\n Vprtstp: contraction number = 6.245562e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 3.980243e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.012680e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 3.278934e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.305320e+02\n Vpmg_setPart:  lower corner = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  upper corner = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -982,15 +982,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 4.438982867308E+00 kT\n Vpmg_energy:  qfEnergy = 1.232481159173E+05 kT\n Vpmg_energy:  dielEnergy = 6.161845360142E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.597550e-01\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.313600e-01\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -1038,182 +1038,182 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.338388 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.232039\n+Vacc_SASA: Time elapsed: 2.908521\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.625350e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.125464e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (161, 161, 161)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.633930e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.072810e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (081, 081, 081)\n Vbuildops: Galer: (041, 041, 041)\n Vbuildops: Galer: (021, 021, 021)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.620594e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.097644e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.300186e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.520972e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 9316156.472817\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.303922e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.556122e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.759901e+05\n Vprtstp: contraction number = 9.759901e+05\n Vnewton: Attempting damping, relres = 0.095792\n Vnewton: Attempting damping, relres = 0.545068\n Vnewton: Damping accepted, relres = 0.095792\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.579182e-02\n Vprtstp: contraction number = 9.579182e-02\n Vnewton: Using errtol_s: 892411.563062\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.329981e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.774749e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.903231e+05\n Vprtstp: contraction number = 1.903231e+05\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.845161e-02\n Vprtstp: contraction number = 1.926220e-01\n Vnewton: Using errtol_s: 171898.088650\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.356822e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.974591e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.121980e+04\n Vprtstp: contraction number = 5.121980e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 4.949951e-03\n Vprtstp: contraction number = 2.682666e-01\n Vnewton: Using errtol_s: 46114.513884\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.380385e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.018199e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.657747e+04\n Vprtstp: contraction number = 1.657747e+04\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.601844e-03\n Vprtstp: contraction number = 3.236081e-01\n Vnewton: Using errtol_s: 14923.031227\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.406374e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.038186e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.880103e+03\n Vprtstp: contraction number = 5.880103e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.681354e-04\n Vprtstp: contraction number = 3.546758e-01\n Vnewton: Using errtol_s: 5292.838197\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.429183e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.058478e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.176489e+03\n Vprtstp: contraction number = 2.176489e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.102777e-04\n Vprtstp: contraction number = 3.701190e-01\n Vnewton: Using errtol_s: 1958.979878\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.453474e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.078168e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.247695e+02\n Vprtstp: contraction number = 8.247695e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 7.968018e-05\n Vprtstp: contraction number = 3.789284e-01\n Vnewton: Using errtol_s: 742.313034\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.476423e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.097518e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.261401e+02\n Vprtstp: contraction number = 3.261401e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 3.150750e-05\n Vprtstp: contraction number = 3.954245e-01\n Vnewton: Using errtol_s: 293.528762\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.499312e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.116594e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.384546e+02\n Vprtstp: contraction number = 1.384546e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 1.337564e-05\n Vprtstp: contraction number = 4.245224e-01\n Vnewton: Using errtol_s: 124.609538\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.521854e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.135956e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.300596e+01\n Vprtstp: contraction number = 6.300596e+01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 6.086783e-06\n Vprtstp: contraction number = 4.550649e-01\n Vnewton: Using errtol_s: 56.705427\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.546646e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.156062e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.026431e+01\n Vprtstp: contraction number = 3.026431e+01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.923726e-06\n Vprtstp: contraction number = 4.803401e-01\n Vnewton: Using errtol_s: 27.237888\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.570327e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.174939e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.506906e+01\n Vprtstp: contraction number = 1.506906e+01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.455768e-06\n Vprtstp: contraction number = 4.979152e-01\n Vnewton: Using errtol_s: 13.562159\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.594871e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.194534e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.684345e+00\n Vprtstp: contraction number = 7.684345e+00\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 7.423567e-07\n Vprtstp: contraction number = 5.099418e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 3.189387e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.223087e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.602078e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.628981e+02\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  actual maxima = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -1222,17 +1222,17 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 4.434662074417E+00 kT\n Vpmg_energy:  qfEnergy = 2.352136568668E+05 kT\n Vpmg_energy:  dielEnergy = 1.176012292477E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.594710e-01\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.275060e-01\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.0735516\n@@ -1253,217 +1253,217 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 6.926182\n+Vacc_SASA: Time elapsed: 6.477284\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.035951e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.355905e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (161, 161, 161)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.933950e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.013700e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (081, 081, 081)\n Vbuildops: Galer: (041, 041, 041)\n Vbuildops: Galer: (021, 021, 021)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.615438e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.156611e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.631944e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.223623e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 15819726.247791\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.635878e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.226802e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.061014e+06\n Vprtstp: contraction number = 1.061014e+06\n Vnewton: Attempting damping, relres = 0.062452\n Vnewton: Attempting damping, relres = 0.525397\n Vnewton: Damping accepted, relres = 0.062452\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.245176e-02\n Vprtstp: contraction number = 6.245176e-02\n Vnewton: Using errtol_s: 987969.694273\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.660860e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.250252e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.221439e+05\n Vprtstp: contraction number = 2.221439e+05\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.274712e-02\n Vprtstp: contraction number = 2.041114e-01\n Vnewton: Using errtol_s: 201655.898404\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.683451e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.271192e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.509302e+04\n Vprtstp: contraction number = 6.509302e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 3.704570e-03\n Vprtstp: contraction number = 2.906202e-01\n Vnewton: Using errtol_s: 58605.278995\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.708389e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.292410e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.250351e+04\n Vprtstp: contraction number = 2.250351e+04\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.280353e-03\n Vprtstp: contraction number = 3.456144e-01\n Vnewton: Using errtol_s: 20254.828172\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.732469e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.312564e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.447408e+03\n Vprtstp: contraction number = 8.447408e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.805791e-04\n Vprtstp: contraction number = 3.753490e-01\n Vnewton: Using errtol_s: 7602.629655\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.756252e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.332041e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.399185e+03\n Vprtstp: contraction number = 3.399185e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.933739e-04\n Vprtstp: contraction number = 4.023769e-01\n Vnewton: Using errtol_s: 3059.122762\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.779573e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.351498e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.505025e+03\n Vprtstp: contraction number = 1.505025e+03\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 8.562081e-05\n Vprtstp: contraction number = 4.427733e-01\n Vnewton: Using errtol_s: 1354.497766\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.803670e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.371029e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.407337e+02\n Vprtstp: contraction number = 7.407337e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 4.214082e-05\n Vprtstp: contraction number = 4.921797e-01\n Vnewton: Using errtol_s: 666.656280\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.827684e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.391422e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.955938e+02\n Vprtstp: contraction number = 3.955938e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.250569e-05\n Vprtstp: contraction number = 5.340591e-01\n Vnewton: Using errtol_s: 356.033867\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.851538e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.411652e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.238069e+02\n Vprtstp: contraction number = 2.238069e+02\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.273259e-05\n Vprtstp: contraction number = 5.657500e-01\n Vnewton: Using errtol_s: 201.426156\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.876016e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.431049e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.312226e+02\n Vprtstp: contraction number = 1.312226e+02\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 7.465385e-06\n Vprtstp: contraction number = 5.863208e-01\n Vnewton: Using errtol_s: 118.100345\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.899826e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.451875e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.886374e+01\n Vprtstp: contraction number = 7.886374e+01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 4.486638e-06\n Vprtstp: contraction number = 6.009922e-01\n Vnewton: Using errtol_s: 70.977384\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.924370e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.472317e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.812776e+01\n Vprtstp: contraction number = 4.812776e+01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 2.738037e-06\n Vprtstp: contraction number = 6.102647e-01\n Vnewton: Using errtol_s: 43.314994\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.947353e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.493312e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.971066e+01\n Vprtstp: contraction number = 2.971066e+01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 1.690269e-06\n Vprtstp: contraction number = 6.173289e-01\n Vnewton: Using errtol_s: 26.739596\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.971616e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.512832e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.848360e+01\n Vprtstp: contraction number = 1.848360e+01\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 1.051550e-06\n Vprtstp: contraction number = 6.221201e-01\n Vnewton: Using errtol_s: 16.635240\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.993631e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.532290e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.157246e+01\n Vprtstp: contraction number = 1.157246e+01\n Vprtstp: iteration = 16\n Vprtstp: relative residual = 6.583687e-07\n Vprtstp: contraction number = 6.260933e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 3.842781e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.877339e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 3.277813e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.304637e+02\n Vpmg_setPart:  lower corner = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  upper corner = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -1472,17 +1472,17 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 9.734614944651E+00 kT\n Vpmg_energy:  qfEnergy = 2.465748372430E+05 kT\n Vpmg_energy:  dielEnergy = 1.232753607231E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.850660e-01\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.203500e-01\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 4.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.0735516\n@@ -1528,182 +1528,182 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.649873 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 7.401554\n+Vacc_SASA: Time elapsed: 6.507143\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.140444e+01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.789210e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (161, 161, 161)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.716900e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.986160e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (081, 081, 081)\n Vbuildops: Galer: (041, 041, 041)\n Vbuildops: Galer: (021, 021, 021)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 3.323758e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.990013e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.032468e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.564025e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 18647566.992070\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.036600e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.567395e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.941752e+06\n Vprtstp: contraction number = 1.941752e+06\n Vnewton: Attempting damping, relres = 0.095497\n Vnewton: Attempting damping, relres = 0.544786\n Vnewton: Damping accepted, relres = 0.095497\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.549656e-02\n Vprtstp: contraction number = 9.549656e-02\n Vnewton: Using errtol_s: 1780778.449755\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.061911e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.589278e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.788571e+05\n Vprtstp: contraction number = 3.788571e+05\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.837082e-02\n Vprtstp: contraction number = 1.923715e-01\n Vnewton: Using errtol_s: 342571.038812\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.085913e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.609209e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.019639e+05\n Vprtstp: contraction number = 1.019639e+05\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 4.923062e-03\n Vprtstp: contraction number = 2.679828e-01\n Vnewton: Using errtol_s: 91803.137006\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.110196e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.628964e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.295911e+04\n Vprtstp: contraction number = 3.295911e+04\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.591047e-03\n Vprtstp: contraction number = 3.231823e-01\n Vnewton: Using errtol_s: 29669.150960\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.135239e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.649340e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.167703e+04\n Vprtstp: contraction number = 1.167703e+04\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.636468e-04\n Vprtstp: contraction number = 3.542616e-01\n Vnewton: Using errtol_s: 10510.641014\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.160482e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.669726e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.318326e+03\n Vprtstp: contraction number = 4.318326e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.084308e-04\n Vprtstp: contraction number = 3.697898e-01\n Vnewton: Using errtol_s: 3886.727604\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.184838e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.689729e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.645707e+03\n Vprtstp: contraction number = 1.645707e+03\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 7.942966e-05\n Vprtstp: contraction number = 3.810841e-01\n Vnewton: Using errtol_s: 1481.169947\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.209844e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.708793e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.631576e+02\n Vprtstp: contraction number = 6.631576e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 3.200666e-05\n Vprtstp: contraction number = 4.029560e-01\n Vnewton: Using errtol_s: 596.846318\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.232270e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.727670e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.897130e+02\n Vprtstp: contraction number = 2.897130e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 1.398265e-05\n Vprtstp: contraction number = 4.368670e-01\n Vnewton: Using errtol_s: 260.742452\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.256976e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.746475e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.365123e+02\n Vprtstp: contraction number = 1.365123e+02\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 6.588595e-06\n Vprtstp: contraction number = 4.711978e-01\n Vnewton: Using errtol_s: 122.861265\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.279866e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.765590e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.809649e+01\n Vprtstp: contraction number = 6.809649e+01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.286589e-06\n Vprtstp: contraction number = 4.988300e-01\n Vnewton: Using errtol_s: 61.286879\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.302484e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.786273e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.533208e+01\n Vprtstp: contraction number = 3.533208e+01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.705256e-06\n Vprtstp: contraction number = 5.188530e-01\n Vnewton: Using errtol_s: 31.798881\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.326655e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.808982e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.878604e+01\n Vprtstp: contraction number = 1.878604e+01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 9.066833e-07\n Vprtstp: contraction number = 5.316991e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 3.155282e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.199743e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.653675e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.679336e+02\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  actual maxima = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -1712,23 +1712,23 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 9.745937546040E+00 kT\n Vpmg_energy:  qfEnergy = 4.708379041028E+05 kT\n Vpmg_energy:  dielEnergy = 2.354068218640E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.225770e-01\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.162250e-01\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 2.348340e+03\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.829692e+03\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 05:44:44 2025\n+# Creation Date and Time:  Tue Jan  9 03:30:03 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path mol1.pqr\n@@ -1986,140 +1986,140 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.262692\n+Vacc_SASA: Time elapsed: 3.140210\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.321242e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.047550e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (161, 161, 161)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.626980e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.065520e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (081, 081, 081)\n Vbuildops: Galer: (041, 041, 041)\n Vbuildops: Galer: (021, 021, 021)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.589778e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.105981e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.001873e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.081124e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 7775242.648804\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.419799e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.218574e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.519208e+05\n Vprtstp: contraction number = 4.519208e+05\n Vnewton: Attempting damping, relres = 0.054343\n Vnewton: Attempting damping, relres = 0.522411\n Vnewton: Damping accepted, relres = 0.054343\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.434337e-02\n Vprtstp: contraction number = 5.434337e-02\n Vnewton: Using errtol_s: 422532.874830\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.169493e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.487133e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.825836e+04\n Vprtstp: contraction number = 6.825836e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 8.031654e-03\n Vprtstp: contraction number = 1.477946e-01\n Vnewton: Using errtol_s: 62448.057923\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.332540e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.358503e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.274799e+04\n Vprtstp: contraction number = 1.274799e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.476725e-03\n Vprtstp: contraction number = 1.838631e-01\n Vnewton: Using errtol_s: 11481.894443\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.803139e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.418079e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.642149e+03\n Vprtstp: contraction number = 2.642149e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 3.058466e-04\n Vprtstp: contraction number = 2.071114e-01\n Vnewton: Using errtol_s: 2378.031723\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.117711e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.337134e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.907005e+02\n Vprtstp: contraction number = 5.907005e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 6.837606e-05\n Vprtstp: contraction number = 2.235632e-01\n Vnewton: Using errtol_s: 531.640431\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.340764e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.133038e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.434663e+02\n Vprtstp: contraction number = 1.434663e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.660675e-05\n Vprtstp: contraction number = 2.428738e-01\n Vnewton: Using errtol_s: 129.121507\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.563987e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.325206e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.897369e+01\n Vprtstp: contraction number = 3.897369e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.511300e-06\n Vprtstp: contraction number = 2.716546e-01\n Vnewton: Using errtol_s: 35.076449\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.773868e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.513102e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.167165e+01\n Vprtstp: contraction number = 1.167165e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.351022e-06\n Vprtstp: contraction number = 2.994751e-01\n Vnewton: Using errtol_s: 10.504522\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.996174e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.703039e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.750775e+00\n Vprtstp: contraction number = 3.750775e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 4.341599e-07\n Vprtstp: contraction number = 3.213567e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.104386e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.137722e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.783534e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.810740e+02\n Vpmg_setPart:  lower corner = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  upper corner = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -2128,17 +2128,17 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 4.649154177944E+00 kT\n Vpmg_energy:  qfEnergy = 1.233253101346E+05 kT\n Vpmg_energy:  dielEnergy = 6.165668863925E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.548010e-01\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.403070e-01\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 39.7309\n Vpbe_ctor2:  solute dimensions = 68.682 x 69.075 x 70.346\n Vpbe_ctor2:  solute charge = -12\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.0735516\n@@ -2184,138 +2184,138 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.297837 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.354377\n+Vacc_SASA: Time elapsed: 2.977897\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.522165e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.717274e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (161, 161, 161)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.559490e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.963540e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (081, 081, 081)\n Vbuildops: Galer: (041, 041, 041)\n Vbuildops: Galer: (021, 021, 021)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.484110e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.058387e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.313610e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.970493e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 9261641.900268\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.348566e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.003089e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.279613e+05\n Vprtstp: contraction number = 8.279613e+05\n Vnewton: Attempting damping, relres = 0.082099\n Vnewton: Attempting damping, relres = 0.538543\n Vnewton: Damping accepted, relres = 0.082099\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.209891e-02\n Vprtstp: contraction number = 8.209891e-02\n Vnewton: Using errtol_s: 760370.715975\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.608187e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.222716e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.156529e+05\n Vprtstp: contraction number = 1.156529e+05\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.133997e-02\n Vprtstp: contraction number = 1.381257e-01\n Vnewton: Using errtol_s: 105026.724448\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.855183e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.435446e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.966463e+04\n Vprtstp: contraction number = 1.966463e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.911861e-03\n Vprtstp: contraction number = 1.685949e-01\n Vnewton: Using errtol_s: 17706.967510\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.080937e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.629117e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.721579e+03\n Vprtstp: contraction number = 3.721579e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 3.617487e-04\n Vprtstp: contraction number = 1.892129e-01\n Vnewton: Using errtol_s: 3350.387034\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.323858e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.834212e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.320600e+02\n Vprtstp: contraction number = 7.320600e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 7.114465e-05\n Vprtstp: contraction number = 1.966687e-01\n Vnewton: Using errtol_s: 658.916270\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.543446e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.032709e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.450384e+02\n Vprtstp: contraction number = 1.450384e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.409447e-05\n Vprtstp: contraction number = 1.981101e-01\n Vnewton: Using errtol_s: 130.537961\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.796361e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.240690e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.437556e+01\n Vprtstp: contraction number = 3.437556e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.340452e-06\n Vprtstp: contraction number = 2.370044e-01\n Vnewton: Using errtol_s: 30.938074\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.048583e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.442575e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.059415e+01\n Vprtstp: contraction number = 1.059415e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.029507e-06\n Vprtstp: contraction number = 3.081938e-01\n Vnewton: Using errtol_s: 9.534923\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.293076e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.639584e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.916133e+00\n Vprtstp: contraction number = 3.916133e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.805503e-07\n Vprtstp: contraction number = 3.696433e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.186261e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.217025e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.855141e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.881206e+02\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  actual maxima = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -2324,15 +2324,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 4.591945419500E+00 kT\n Vpmg_energy:  qfEnergy = 2.356288022123E+05 kT\n Vpmg_energy:  dielEnergy = 1.178084778246E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.490440e-01\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.385940e-01\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -2355,140 +2355,140 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.207383\n+Vacc_SASA: Time elapsed: 3.013342\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.287817e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.942955e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (161, 161, 161)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.539540e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.994850e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (081, 081, 081)\n Vbuildops: Galer: (041, 041, 041)\n Vbuildops: Galer: (021, 021, 021)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.638483e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.990402e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.598429e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.913245e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 7837779.438687\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.638551e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.943879e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.514612e+05\n Vprtstp: contraction number = 4.514612e+05\n Vnewton: Attempting damping, relres = 0.053797\n Vnewton: Attempting damping, relres = 0.522401\n Vnewton: Damping accepted, relres = 0.053797\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.379672e-02\n Vprtstp: contraction number = 5.379672e-02\n Vnewton: Using errtol_s: 421646.851825\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.901832e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.155001e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.805281e+04\n Vprtstp: contraction number = 6.805281e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 7.947357e-03\n Vprtstp: contraction number = 1.477294e-01\n Vnewton: Using errtol_s: 62289.628218\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.149807e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.345016e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.276985e+04\n Vprtstp: contraction number = 1.276985e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.467975e-03\n Vprtstp: contraction number = 1.847124e-01\n Vnewton: Using errtol_s: 11505.665992\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.369507e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.540033e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.685314e+03\n Vprtstp: contraction number = 2.685314e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 3.083318e-04\n Vprtstp: contraction number = 2.100388e-01\n Vnewton: Using errtol_s: 2416.636290\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.642316e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.755708e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.970818e+02\n Vprtstp: contraction number = 5.970818e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 6.855221e-05\n Vprtstp: contraction number = 2.223326e-01\n Vnewton: Using errtol_s: 537.297133\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.860821e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.963127e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.381270e+02\n Vprtstp: contraction number = 1.381270e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.586035e-05\n Vprtstp: contraction number = 2.313616e-01\n Vnewton: Using errtol_s: 124.309951\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.089597e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.168605e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.581259e+01\n Vprtstp: contraction number = 3.581259e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.112278e-06\n Vprtstp: contraction number = 2.592804e-01\n Vnewton: Using errtol_s: 32.231131\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.359903e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.380960e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.075720e+01\n Vprtstp: contraction number = 1.075720e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.235235e-06\n Vprtstp: contraction number = 3.003774e-01\n Vnewton: Using errtol_s: 9.681503\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.589275e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.578629e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.606387e+00\n Vprtstp: contraction number = 3.606387e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 4.141158e-07\n Vprtstp: contraction number = 3.352525e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.236350e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.268831e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.859586e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.884869e+02\n Vpmg_setPart:  lower corner = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  upper corner = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -2497,15 +2497,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 4.659237014157E+00 kT\n Vpmg_energy:  qfEnergy = 1.233789041891E+05 kT\n Vpmg_energy:  dielEnergy = 6.168342765954E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.551490e-01\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.393240e-01\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -2553,138 +2553,138 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.338577 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.274149\n+Vacc_SASA: Time elapsed: 3.045563\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.270374e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.884512e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (161, 161, 161)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.224260e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.148260e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (081, 081, 081)\n Vbuildops: Galer: (041, 041, 041)\n Vbuildops: Galer: (021, 021, 021)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.245990e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.887832e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.938727e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.868806e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 9315222.001185\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.972985e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.903788e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.310439e+05\n Vprtstp: contraction number = 8.310439e+05\n Vnewton: Attempting damping, relres = 0.081942\n Vnewton: Attempting damping, relres = 0.538517\n Vnewton: Damping accepted, relres = 0.081942\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.194219e-02\n Vprtstp: contraction number = 8.194219e-02\n Vnewton: Using errtol_s: 763309.735899\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.245256e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.120094e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.164941e+05\n Vprtstp: contraction number = 1.164941e+05\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.135719e-02\n Vprtstp: contraction number = 1.386000e-01\n Vnewton: Using errtol_s: 105794.756542\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.486163e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.319251e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.004035e+04\n Vprtstp: contraction number = 2.004035e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.937352e-03\n Vprtstp: contraction number = 1.705837e-01\n Vnewton: Using errtol_s: 18046.864412\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.731873e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.524003e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.874509e+03\n Vprtstp: contraction number = 3.874509e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 3.744478e-04\n Vprtstp: contraction number = 1.932781e-01\n Vnewton: Using errtol_s: 3488.064314\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.950057e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.718997e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.934449e+02\n Vprtstp: contraction number = 7.934449e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 7.666874e-05\n Vprtstp: contraction number = 2.047515e-01\n Vnewton: Using errtol_s: 714.186341\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.200165e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.915289e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.631165e+02\n Vprtstp: contraction number = 1.631165e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.576011e-05\n Vprtstp: contraction number = 2.055611e-01\n Vnewton: Using errtol_s: 146.808940\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.464566e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.113629e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.992341e+01\n Vprtstp: contraction number = 3.992341e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.857249e-06\n Vprtstp: contraction number = 2.447475e-01\n Vnewton: Using errtol_s: 35.931127\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.744638e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.302587e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.373524e+01\n Vprtstp: contraction number = 1.373524e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.327082e-06\n Vprtstp: contraction number = 3.440488e-01\n Vnewton: Using errtol_s: 12.362061\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.028069e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.518916e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.506580e+00\n Vprtstp: contraction number = 5.506580e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.320241e-07\n Vprtstp: contraction number = 4.008978e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.372962e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.401196e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.831293e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.855475e+02\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  actual maxima = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -2693,17 +2693,17 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 4.613981699518E+00 kT\n Vpmg_energy:  qfEnergy = 2.353039534047E+05 kT\n Vpmg_energy:  dielEnergy = 1.176460315654E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.488120e-01\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.266380e-01\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.0735516\n@@ -2724,140 +2724,140 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 6.782559\n+Vacc_SASA: Time elapsed: 6.402204\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.048082e+01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.791752e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (161, 161, 161)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.410060e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.903970e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (081, 081, 081)\n Vbuildops: Galer: (041, 041, 041)\n Vbuildops: Galer: (021, 021, 021)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.488306e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.066837e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.450564e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.826915e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 15819726.247791\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.496444e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.860049e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.105286e+05\n Vprtstp: contraction number = 9.105286e+05\n Vnewton: Attempting damping, relres = 0.054151\n Vnewton: Attempting damping, relres = 0.522361\n Vnewton: Damping accepted, relres = 0.054151\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.415081e-02\n Vprtstp: contraction number = 5.415081e-02\n Vnewton: Using errtol_s: 856650.988867\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.822034e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.080115e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.365159e+05\n Vprtstp: contraction number = 1.365159e+05\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 7.938600e-03\n Vprtstp: contraction number = 1.466017e-01\n Vnewton: Using errtol_s: 125586.474947\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.012369e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.276803e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.543138e+04\n Vprtstp: contraction number = 2.543138e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.449191e-03\n Vprtstp: contraction number = 1.825500e-01\n Vnewton: Using errtol_s: 22925.804865\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.041315e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.479827e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.291506e+03\n Vprtstp: contraction number = 5.291506e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 3.010412e-04\n Vprtstp: contraction number = 2.077305e-01\n Vnewton: Using errtol_s: 4762.388621\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.070903e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.672455e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.180651e+03\n Vprtstp: contraction number = 1.180651e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 6.716597e-05\n Vprtstp: contraction number = 2.231123e-01\n Vnewton: Using errtol_s: 1062.547289\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.099708e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.872788e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.813654e+02\n Vprtstp: contraction number = 2.813654e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.600723e-05\n Vprtstp: contraction number = 2.383235e-01\n Vnewton: Using errtol_s: 253.229951\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.128448e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.068518e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.533652e+01\n Vprtstp: contraction number = 7.533652e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.285970e-06\n Vprtstp: contraction number = 2.677522e-01\n Vnewton: Using errtol_s: 67.802871\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.158097e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.270023e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.308540e+01\n Vprtstp: contraction number = 2.308540e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.313362e-06\n Vprtstp: contraction number = 3.064328e-01\n Vnewton: Using errtol_s: 20.777024\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.187648e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.455248e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.670717e+00\n Vprtstp: contraction number = 7.670717e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 4.363948e-07\n Vprtstp: contraction number = 3.322731e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.672632e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.703613e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.813351e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.839475e+02\n Vpmg_setPart:  lower corner = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  upper corner = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -2866,17 +2866,17 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.013375850535E+01 kT\n Vpmg_energy:  qfEnergy = 2.468101698845E+05 kT\n Vpmg_energy:  dielEnergy = 1.233922430579E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.343320e-01\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.266900e-01\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.0735516\n@@ -2922,138 +2922,138 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.652629 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 6.097201\n+Vacc_SASA: Time elapsed: 6.378658\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.116532e+01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.119874e+01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (161, 161, 161)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.663240e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 2.103180e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (081, 081, 081)\n Vbuildops: Galer: (041, 041, 041)\n Vbuildops: Galer: (021, 021, 021)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 2.499400e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.946512e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.226921e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.779609e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 18644287.879827\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.230970e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.809685e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.651555e+06\n Vprtstp: contraction number = 1.651555e+06\n Vnewton: Attempting damping, relres = 0.081643\n Vnewton: Attempting damping, relres = 0.538237\n Vnewton: Damping accepted, relres = 0.081643\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.164291e-02\n Vprtstp: contraction number = 8.164291e-02\n Vnewton: Using errtol_s: 1522173.863324\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.263832e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.002988e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.305601e+05\n Vprtstp: contraction number = 2.305601e+05\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.125644e-02\n Vprtstp: contraction number = 1.378740e-01\n Vnewton: Using errtol_s: 209868.227405\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.293718e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.022681e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.940032e+04\n Vprtstp: contraction number = 3.940032e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.903339e-03\n Vprtstp: contraction number = 1.690890e-01\n Vnewton: Using errtol_s: 35486.402387\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.323089e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.042250e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.544305e+03\n Vprtstp: contraction number = 7.544305e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 3.642891e-04\n Vprtstp: contraction number = 1.913948e-01\n Vnewton: Using errtol_s: 6791.911566\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.350695e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.062000e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.522155e+03\n Vprtstp: contraction number = 1.522155e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 7.348563e-05\n Vprtstp: contraction number = 2.017234e-01\n Vnewton: Using errtol_s: 1370.087193\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.380934e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.082522e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.106660e+02\n Vprtstp: contraction number = 3.106660e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.499708e-05\n Vprtstp: contraction number = 2.040818e-01\n Vnewton: Using errtol_s: 279.609899\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.411505e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.102880e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.690225e+01\n Vprtstp: contraction number = 7.690225e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.712245e-06\n Vprtstp: contraction number = 2.475312e-01\n Vnewton: Using errtol_s: 69.212171\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.440920e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.125699e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.600764e+01\n Vprtstp: contraction number = 2.600764e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.255497e-06\n Vprtstp: contraction number = 3.382042e-01\n Vnewton: Using errtol_s: 23.407850\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.469669e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.145880e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.011646e+01\n Vprtstp: contraction number = 1.011646e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 4.883437e-07\n Vprtstp: contraction number = 3.889644e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.693557e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.725001e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.859573e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.884128e+02\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  actual maxima = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -3062,23 +3062,23 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.005009553015E+01 kT\n Vpmg_energy:  qfEnergy = 4.710211065569E+05 kT\n Vpmg_energy:  dielEnergy = 2.354978106920E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.095670e-01\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.087100e-01\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.496583e+03\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.164205e+03\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 05:48:49 2025\n+# Creation Date and Time:  Tue Jan  9 03:35:21 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path mol1.pqr\n@@ -3431,250 +3431,250 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.269865\n+Vacc_SASA: Time elapsed: 2.972639\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.222976e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.926962e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.996800e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.423200e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.226778e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.101410e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.973775e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.542233e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4300910.832168\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.591018e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.451080e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.136321e+05\n Vprtstp: contraction number = 2.136321e+05\n Vnewton: Attempting damping, relres = 0.047663\n Vnewton: Attempting damping, relres = 0.515490\n Vnewton: Damping accepted, relres = 0.047663\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.766304e-02\n Vprtstp: contraction number = 4.766304e-02\n Vnewton: Using errtol_s: 204994.485638\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.848033e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.114942e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.587025e+04\n Vprtstp: contraction number = 4.587025e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 9.727679e-03\n Vprtstp: contraction number = 2.040927e-01\n Vnewton: Using errtol_s: 41837.880528\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.536016e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.320365e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.391016e+04\n Vprtstp: contraction number = 1.391016e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.912173e-03\n Vprtstp: contraction number = 2.993697e-01\n Vnewton: Using errtol_s: 12524.995351\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.334168e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.554097e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.237707e+03\n Vprtstp: contraction number = 5.237707e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.096054e-03\n Vprtstp: contraction number = 3.763697e-01\n Vnewton: Using errtol_s: 4714.028550\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.118835e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.854152e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.331453e+03\n Vprtstp: contraction number = 2.331453e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.878779e-04\n Vprtstp: contraction number = 4.451223e-01\n Vnewton: Using errtol_s: 2098.319320\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.858982e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.214177e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.189035e+03\n Vprtstp: contraction number = 1.189035e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.488161e-04\n Vprtstp: contraction number = 5.099966e-01\n Vnewton: Using errtol_s: 1070.135650\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.162116e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.291804e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.678182e+02\n Vprtstp: contraction number = 6.678182e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.397467e-04\n Vprtstp: contraction number = 5.616468e-01\n Vnewton: Using errtol_s: 601.038216\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.336651e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.410729e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.994733e+02\n Vprtstp: contraction number = 3.994733e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.359319e-05\n Vprtstp: contraction number = 5.981764e-01\n Vnewton: Using errtol_s: 359.526862\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.505996e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.083427e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.488647e+02\n Vprtstp: contraction number = 2.488647e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.207703e-05\n Vprtstp: contraction number = 6.229817e-01\n Vnewton: Using errtol_s: 223.978670\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.651975e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.198531e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.588671e+02\n Vprtstp: contraction number = 1.588671e+02\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.324425e-05\n Vprtstp: contraction number = 6.383669e-01\n Vnewton: Using errtol_s: 142.980568\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.811810e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.321755e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.030284e+02\n Vprtstp: contraction number = 1.030284e+02\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.155954e-05\n Vprtstp: contraction number = 6.485194e-01\n Vnewton: Using errtol_s: 92.725673\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.975437e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.440515e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.760657e+01\n Vprtstp: contraction number = 6.760657e+01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.414722e-05\n Vprtstp: contraction number = 6.561932e-01\n Vnewton: Using errtol_s: 60.845953\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.157568e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.560827e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.480217e+01\n Vprtstp: contraction number = 4.480217e+01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 9.375216e-06\n Vprtstp: contraction number = 6.626894e-01\n Vnewton: Using errtol_s: 40.321969\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.341967e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.692133e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.990735e+01\n Vprtstp: contraction number = 2.990735e+01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 6.258355e-06\n Vprtstp: contraction number = 6.675424e-01\n Vnewton: Using errtol_s: 26.916626\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.515964e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.821655e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.008505e+01\n Vprtstp: contraction number = 2.008505e+01\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 4.202958e-06\n Vprtstp: contraction number = 6.715755e-01\n Vnewton: Using errtol_s: 18.076547\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.705425e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.964383e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.356100e+01\n Vprtstp: contraction number = 1.356100e+01\n Vprtstp: iteration = 16\n Vprtstp: relative residual = 2.837748e-06\n Vprtstp: contraction number = 6.751787e-01\n Vnewton: Using errtol_s: 12.204901\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.876765e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.087198e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.198733e+00\n Vprtstp: contraction number = 9.198733e+00\n Vprtstp: iteration = 17\n Vprtstp: relative residual = 1.924909e-06\n Vprtstp: contraction number = 6.783227e-01\n Vnewton: Using errtol_s: 8.278861\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.056393e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.214003e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.265697e+00\n Vprtstp: contraction number = 6.265697e+00\n Vprtstp: iteration = 18\n Vprtstp: relative residual = 1.311147e-06\n Vprtstp: contraction number = 6.811478e-01\n Vnewton: Using errtol_s: 5.639128\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.231823e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.344878e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.284635e+00\n Vprtstp: contraction number = 4.284635e+00\n Vprtstp: iteration = 19\n Vprtstp: relative residual = 8.965941e-07\n Vprtstp: contraction number = 6.838241e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 3.322793e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.337143e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.400402e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.413616e+02\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (2.518, -2.4645, 16.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -3683,17 +3683,17 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 7.479770161201E-01 kT\n Vpmg_energy:  qfEnergy = 1.169401599673E+03 kT\n Vpmg_energy:  dielEnergy = 6.300507194512E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.449200e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 9.462000e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 39.7309\n Vpbe_ctor2:  solute dimensions = 68.682 x 69.075 x 70.346\n Vpbe_ctor2:  solute charge = -12\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -3739,171 +3739,171 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00578902 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 2.885858\n+Vacc_SASA: Time elapsed: 3.050067\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.103478e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.345777e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.252300e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.146600e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.163806e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.064942e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.439460e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.512944e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 3431662.159805\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.467676e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.533681e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.373293e+05\n Vprtstp: contraction number = 3.373293e+05\n Vnewton: Attempting damping, relres = 0.089626\n Vnewton: Attempting damping, relres = 0.541581\n Vnewton: Damping accepted, relres = 0.089626\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.962597e-02\n Vprtstp: contraction number = 8.962597e-02\n Vnewton: Using errtol_s: 307566.035257\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.732449e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.713994e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.223173e+04\n Vprtstp: contraction number = 6.223173e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.639798e-02\n Vprtstp: contraction number = 1.829601e-01\n Vnewton: Using errtol_s: 56272.319668\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.991407e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.892793e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.604081e+04\n Vprtstp: contraction number = 1.604081e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 4.208259e-03\n Vprtstp: contraction number = 2.566328e-01\n Vnewton: Using errtol_s: 14441.323490\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.226807e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.075611e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.994316e+03\n Vprtstp: contraction number = 4.994316e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.309837e-03\n Vprtstp: contraction number = 3.112539e-01\n Vnewton: Using errtol_s: 4494.917566\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.479963e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.239713e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.695194e+03\n Vprtstp: contraction number = 1.695194e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.445882e-04\n Vprtstp: contraction number = 3.394226e-01\n Vnewton: Using errtol_s: 1525.676669\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.702899e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.402986e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.988429e+02\n Vprtstp: contraction number = 5.988429e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.570548e-04\n Vprtstp: contraction number = 3.532589e-01\n Vnewton: Using errtol_s: 538.958849\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.946943e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.565951e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.157694e+02\n Vprtstp: contraction number = 2.157694e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 5.658847e-05\n Vprtstp: contraction number = 3.603104e-01\n Vnewton: Using errtol_s: 194.192499\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.185298e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.717097e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.859364e+01\n Vprtstp: contraction number = 7.859364e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.061225e-05\n Vprtstp: contraction number = 3.642483e-01\n Vnewton: Using errtol_s: 70.734280\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.416019e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.880081e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.887021e+01\n Vprtstp: contraction number = 2.887021e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 7.571604e-06\n Vprtstp: contraction number = 3.673351e-01\n Vnewton: Using errtol_s: 25.983185\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.646928e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.025524e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.070116e+01\n Vprtstp: contraction number = 1.070116e+01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 2.806524e-06\n Vprtstp: contraction number = 3.706644e-01\n Vnewton: Using errtol_s: 9.631041\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.899607e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.170582e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.050515e+00\n Vprtstp: contraction number = 4.050515e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 1.062302e-06\n Vprtstp: contraction number = 3.785119e-01\n Vnewton: Using errtol_s: 3.645463\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.165077e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.332150e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.586893e+00\n Vprtstp: contraction number = 1.586893e+00\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 4.161843e-07\n Vprtstp: contraction number = 3.917757e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.944336e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.958250e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.984993e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.996997e+02\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (2.518, -2.4645, 16.7425)\n Vpmg_setPart:  actual minima = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  actual maxima = (13.3006, 6.29637, 27.9102)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -3912,15 +3912,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 7.504529533890E-01 kT\n Vpmg_energy:  qfEnergy = 1.061382616797E+04 kT\n Vpmg_energy:  dielEnergy = 5.339258817013E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.254800e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.434200e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -3943,272 +3943,272 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 2.836661\n+Vacc_SASA: Time elapsed: 2.907000\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.811049e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.753170e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.875800e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.185100e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.397405e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.041755e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.437493e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.547652e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4276578.139223\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.466510e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.565869e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.113974e+05\n Vprtstp: contraction number = 2.113974e+05\n Vnewton: Attempting damping, relres = 0.047573\n Vnewton: Attempting damping, relres = 0.515375\n Vnewton: Damping accepted, relres = 0.047573\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.757263e-02\n Vprtstp: contraction number = 4.757263e-02\n Vnewton: Using errtol_s: 203448.048803\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.639868e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.695716e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.589098e+04\n Vprtstp: contraction number = 4.589098e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 9.811582e-03\n Vprtstp: contraction number = 2.062443e-01\n Vnewton: Using errtol_s: 41959.996661\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.831488e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.821505e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.404662e+04\n Vprtstp: contraction number = 1.404662e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.960291e-03\n Vprtstp: contraction number = 3.017139e-01\n Vnewton: Using errtol_s: 12659.913691\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.021128e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.936777e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.279840e+03\n Vprtstp: contraction number = 5.279840e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.111524e-03\n Vprtstp: contraction number = 3.754781e-01\n Vnewton: Using errtol_s: 4753.520446\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.197186e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.051149e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.336921e+03\n Vprtstp: contraction number = 2.336921e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.918609e-04\n Vprtstp: contraction number = 4.425102e-01\n Vnewton: Using errtol_s: 2103.481419\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.390099e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.172204e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.194576e+03\n Vprtstp: contraction number = 1.194576e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.514070e-04\n Vprtstp: contraction number = 5.111344e-01\n Vnewton: Using errtol_s: 1075.161658\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.577366e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.293273e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.792983e+02\n Vprtstp: contraction number = 6.792983e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.429594e-04\n Vprtstp: contraction number = 5.686374e-01\n Vnewton: Using errtol_s: 611.377148\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.758751e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.409036e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.154648e+02\n Vprtstp: contraction number = 4.154648e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.743449e-05\n Vprtstp: contraction number = 6.116036e-01\n Vnewton: Using errtol_s: 373.920435\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.929428e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.513096e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.660684e+02\n Vprtstp: contraction number = 2.660684e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.599388e-05\n Vprtstp: contraction number = 6.404095e-01\n Vnewton: Using errtol_s: 239.462182\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.110332e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.638258e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.755593e+02\n Vprtstp: contraction number = 1.755593e+02\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.694626e-05\n Vprtstp: contraction number = 6.598268e-01\n Vnewton: Using errtol_s: 158.003576\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.300790e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.766592e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.183176e+02\n Vprtstp: contraction number = 1.183176e+02\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.489979e-05\n Vprtstp: contraction number = 6.739462e-01\n Vnewton: Using errtol_s: 106.485913\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.490002e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.920417e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.102710e+01\n Vprtstp: contraction number = 8.102710e+01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.705205e-05\n Vprtstp: contraction number = 6.848271e-01\n Vnewton: Using errtol_s: 72.924443\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.665318e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.032578e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.628393e+01\n Vprtstp: contraction number = 5.628393e+01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 1.184488e-05\n Vprtstp: contraction number = 6.946308e-01\n Vnewton: Using errtol_s: 50.655566\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.847752e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.159205e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.955755e+01\n Vprtstp: contraction number = 3.955755e+01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 8.324836e-06\n Vprtstp: contraction number = 7.028213e-01\n Vnewton: Using errtol_s: 35.601810\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.037930e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.285828e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.808103e+01\n Vprtstp: contraction number = 2.808103e+01\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 5.909617e-06\n Vprtstp: contraction number = 7.098779e-01\n Vnewton: Using errtol_s: 25.272937\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.213770e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.417076e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.010039e+01\n Vprtstp: contraction number = 2.010039e+01\n Vprtstp: iteration = 16\n Vprtstp: relative residual = 4.230100e-06\n Vprtstp: contraction number = 7.157995e-01\n Vnewton: Using errtol_s: 18.090355\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.394898e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.540130e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.449222e+01\n Vprtstp: contraction number = 1.449222e+01\n Vprtstp: iteration = 17\n Vprtstp: relative residual = 3.049867e-06\n Vprtstp: contraction number = 7.209918e-01\n Vnewton: Using errtol_s: 13.042997\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.578826e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.675501e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.051084e+01\n Vprtstp: contraction number = 1.051084e+01\n Vprtstp: iteration = 18\n Vprtstp: relative residual = 2.211992e-06\n Vprtstp: contraction number = 7.252749e-01\n Vnewton: Using errtol_s: 9.459758\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.742711e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.788152e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.663626e+00\n Vprtstp: contraction number = 7.663626e+00\n Vprtstp: iteration = 19\n Vprtstp: relative residual = 1.612800e-06\n Vprtstp: contraction number = 7.291164e-01\n Vnewton: Using errtol_s: 6.897264\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.898173e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.908281e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.612195e+00\n Vprtstp: contraction number = 5.612195e+00\n Vprtstp: iteration = 20\n Vprtstp: relative residual = 1.181079e-06\n Vprtstp: contraction number = 7.323158e-01\n Vnewton: Using errtol_s: 5.050976\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.008051e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.034128e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.124624e+00\n Vprtstp: contraction number = 4.124624e+00\n Vprtstp: iteration = 21\n Vprtstp: relative residual = 8.680215e-07\n Vprtstp: contraction number = 7.349396e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 3.813118e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.827995e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.609277e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.620491e+02\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (2.518, -2.4645, 16.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -4217,15 +4217,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 8.521116242377E-01 kT\n Vpmg_energy:  qfEnergy = 2.321247419853E+03 kT\n Vpmg_energy:  dielEnergy = 1.153524159473E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.361600e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.831200e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -4273,193 +4273,193 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0721278 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.177106\n+Vacc_SASA: Time elapsed: 2.883383\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.595692e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.247583e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.096100e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.230200e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.352658e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.061751e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.031253e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.212749e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 3863048.260999\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.034248e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.234804e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.079329e+05\n Vprtstp: contraction number = 4.079329e+05\n Vnewton: Attempting damping, relres = 0.096763\n Vnewton: Attempting damping, relres = 0.545251\n Vnewton: Damping accepted, relres = 0.096763\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.676296e-02\n Vprtstp: contraction number = 9.676296e-02\n Vnewton: Using errtol_s: 373799.984181\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.060759e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.416700e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.732785e+04\n Vprtstp: contraction number = 7.732785e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.807372e-02\n Vprtstp: contraction number = 1.867834e-01\n Vnewton: Using errtol_s: 69819.644697\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.086861e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.602093e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.985652e+04\n Vprtstp: contraction number = 1.985652e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 4.627077e-03\n Vprtstp: contraction number = 2.560113e-01\n Vnewton: Using errtol_s: 17874.621452\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.111429e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.809042e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.114622e+03\n Vprtstp: contraction number = 6.114622e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.424617e-03\n Vprtstp: contraction number = 3.078870e-01\n Vnewton: Using errtol_s: 5503.364448\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.133217e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.012320e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.092890e+03\n Vprtstp: contraction number = 2.092890e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.875987e-04\n Vprtstp: contraction number = 3.422665e-01\n Vnewton: Using errtol_s: 1883.617345\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.157420e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.203869e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.574998e+02\n Vprtstp: contraction number = 7.574998e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.764801e-04\n Vprtstp: contraction number = 3.619372e-01\n Vnewton: Using errtol_s: 681.751152\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.182329e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.371933e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.922283e+02\n Vprtstp: contraction number = 2.922283e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 6.808241e-05\n Vprtstp: contraction number = 3.857795e-01\n Vnewton: Using errtol_s: 263.005621\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.207281e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.536463e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.230857e+02\n Vprtstp: contraction number = 1.230857e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.867611e-05\n Vprtstp: contraction number = 4.211970e-01\n Vnewton: Using errtol_s: 110.777182\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.232718e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.684696e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.644162e+01\n Vprtstp: contraction number = 5.644162e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 1.314958e-05\n Vprtstp: contraction number = 4.585554e-01\n Vnewton: Using errtol_s: 50.797474\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.257468e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.843676e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.814912e+01\n Vprtstp: contraction number = 2.814912e+01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 6.558089e-06\n Vprtstp: contraction number = 4.987298e-01\n Vnewton: Using errtol_s: 25.334216\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.283261e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.007757e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.477957e+01\n Vprtstp: contraction number = 1.477957e+01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.443295e-06\n Vprtstp: contraction number = 5.250454e-01\n Vnewton: Using errtol_s: 13.301614\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.311132e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.155445e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.444333e+00\n Vprtstp: contraction number = 8.444333e+00\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.967333e-06\n Vprtstp: contraction number = 5.713519e-01\n Vnewton: Using errtol_s: 7.599902\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.338435e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.312252e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.056221e+00\n Vprtstp: contraction number = 5.056221e+00\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 1.177982e-06\n Vprtstp: contraction number = 5.987712e-01\n Vnewton: Using errtol_s: 4.550602\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.364783e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.468281e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.242153e+00\n Vprtstp: contraction number = 3.242153e+00\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 7.553462e-07\n Vprtstp: contraction number = 6.412203e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 3.544183e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.558612e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.407014e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.418806e+02\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (2.518, -2.4645, 16.7425)\n Vpmg_setPart:  actual minima = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  actual maxima = (13.3006, 6.29637, 27.9102)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -4468,15 +4468,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 9.360671447276E-01 kT\n Vpmg_energy:  qfEnergy = 1.843358669820E+04 kT\n Vpmg_energy:  dielEnergy = 9.205607078702E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.300800e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.263600e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n@@ -4499,261 +4499,261 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 5.926909\n+Vacc_SASA: Time elapsed: 6.335142\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.151098e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.530256e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.704000e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.353000e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.286031e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.832810e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.394348e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.707039e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 8699406.430616\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.397568e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.728636e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.298565e+05\n Vprtstp: contraction number = 4.298565e+05\n Vnewton: Attempting damping, relres = 0.048079\n Vnewton: Attempting damping, relres = 0.515481\n Vnewton: Damping accepted, relres = 0.048079\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.807904e-02\n Vprtstp: contraction number = 4.807904e-02\n Vnewton: Using errtol_s: 418259.137179\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.422965e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.887918e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.275297e+04\n Vprtstp: contraction number = 9.275297e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 9.791706e-03\n Vprtstp: contraction number = 2.036585e-01\n Vnewton: Using errtol_s: 85182.030508\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.446423e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.003353e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.830324e+04\n Vprtstp: contraction number = 2.830324e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.931540e-03\n Vprtstp: contraction number = 2.993901e-01\n Vnewton: Using errtol_s: 25502.653903\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.468384e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.017533e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.066383e+04\n Vprtstp: contraction number = 1.066383e+04\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.103407e-03\n Vprtstp: contraction number = 3.763916e-01\n Vnewton: Using errtol_s: 9598.985602\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.487903e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.032035e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.725476e+03\n Vprtstp: contraction number = 4.725476e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.889004e-04\n Vprtstp: contraction number = 4.430826e-01\n Vnewton: Using errtol_s: 4253.143226\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.505402e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.045459e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.402868e+03\n Vprtstp: contraction number = 2.402868e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.485940e-04\n Vprtstp: contraction number = 5.084757e-01\n Vnewton: Using errtol_s: 2162.620089\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.521972e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.058577e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.352802e+03\n Vprtstp: contraction number = 1.352802e+03\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.399556e-04\n Vprtstp: contraction number = 5.629888e-01\n Vnewton: Using errtol_s: 1217.530795\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.537963e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.071657e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.164880e+02\n Vprtstp: contraction number = 8.164880e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.447037e-05\n Vprtstp: contraction number = 6.035512e-01\n Vnewton: Using errtol_s: 734.842122\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.552818e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.085054e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.157033e+02\n Vprtstp: contraction number = 5.157033e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.335238e-05\n Vprtstp: contraction number = 6.316106e-01\n Vnewton: Using errtol_s: 464.134076\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.571323e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.099488e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.352095e+02\n Vprtstp: contraction number = 3.352095e+02\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.467926e-05\n Vprtstp: contraction number = 6.500040e-01\n Vnewton: Using errtol_s: 301.688999\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.586527e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.114032e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.222234e+02\n Vprtstp: contraction number = 2.222234e+02\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.299022e-05\n Vprtstp: contraction number = 6.629387e-01\n Vnewton: Using errtol_s: 200.001301\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.601513e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.127439e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.495221e+02\n Vprtstp: contraction number = 1.495221e+02\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.546887e-05\n Vprtstp: contraction number = 6.728456e-01\n Vnewton: Using errtol_s: 134.569993\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.620313e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.141084e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.018836e+02\n Vprtstp: contraction number = 1.018836e+02\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 1.054041e-05\n Vprtstp: contraction number = 6.813949e-01\n Vnewton: Using errtol_s: 91.695311\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.636253e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.154629e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.012825e+01\n Vprtstp: contraction number = 7.012825e+01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 7.255144e-06\n Vprtstp: contraction number = 6.883171e-01\n Vnewton: Using errtol_s: 63.115450\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.652192e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.167759e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.869976e+01\n Vprtstp: contraction number = 4.869976e+01\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 5.038252e-06\n Vprtstp: contraction number = 6.944386e-01\n Vnewton: Using errtol_s: 43.829803\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.667537e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.181467e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.408035e+01\n Vprtstp: contraction number = 3.408035e+01\n Vprtstp: iteration = 16\n Vprtstp: relative residual = 3.525795e-06\n Vprtstp: contraction number = 6.998052e-01\n Vnewton: Using errtol_s: 30.672326\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.682609e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.196104e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.401453e+01\n Vprtstp: contraction number = 2.401453e+01\n Vprtstp: iteration = 17\n Vprtstp: relative residual = 2.484432e-06\n Vprtstp: contraction number = 7.046444e-01\n Vnewton: Using errtol_s: 21.613084\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.697714e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.211289e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.702723e+01\n Vprtstp: contraction number = 1.702723e+01\n Vprtstp: iteration = 18\n Vprtstp: relative residual = 1.761558e-06\n Vprtstp: contraction number = 7.090385e-01\n Vnewton: Using errtol_s: 15.324508\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.713260e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.225343e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.214065e+01\n Vprtstp: contraction number = 1.214065e+01\n Vprtstp: iteration = 19\n Vprtstp: relative residual = 1.256015e-06\n Vprtstp: contraction number = 7.130137e-01\n Vnewton: Using errtol_s: 10.926584\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.729304e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.239058e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.699962e+00\n Vprtstp: contraction number = 8.699962e+00\n Vprtstp: iteration = 20\n Vprtstp: relative residual = 9.000575e-07\n Vprtstp: contraction number = 7.165978e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 3.495143e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.508919e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.810831e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.821380e+02\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (2.518, -2.4645, 16.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -4762,17 +4762,17 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.970329890600E+00 kT\n Vpmg_energy:  qfEnergy = 3.499206035649E+03 kT\n Vpmg_energy:  dielEnergy = 1.787861710155E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.820000e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.312700e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -4818,182 +4818,182 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.081031 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 6.810462\n+Vacc_SASA: Time elapsed: 6.359925\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.759341e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.116707e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.764300e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.230200e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.290260e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.053722e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.754089e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.261150e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 7257742.969900\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.756318e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.263603e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.332655e+05\n Vprtstp: contraction number = 7.332655e+05\n Vnewton: Attempting damping, relres = 0.092954\n Vnewton: Attempting damping, relres = 0.543087\n Vnewton: Damping accepted, relres = 0.092954\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.295377e-02\n Vprtstp: contraction number = 9.295377e-02\n Vnewton: Using errtol_s: 674634.557796\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.778603e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.281784e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.375383e+05\n Vprtstp: contraction number = 1.375383e+05\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.716852e-02\n Vprtstp: contraction number = 1.846995e-01\n Vnewton: Using errtol_s: 124604.673279\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.797117e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.299542e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.550512e+04\n Vprtstp: contraction number = 3.550512e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 4.404594e-03\n Vprtstp: contraction number = 2.565507e-01\n Vnewton: Using errtol_s: 31967.413641\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.816409e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.316143e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.099641e+04\n Vprtstp: contraction number = 1.099641e+04\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.363650e-03\n Vprtstp: contraction number = 3.095972e-01\n Vnewton: Using errtol_s: 9897.022727\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.834921e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.332968e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.730401e+03\n Vprtstp: contraction number = 3.730401e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.625937e-04\n Vprtstp: contraction number = 3.392320e-01\n Vnewton: Using errtol_s: 3357.386399\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.854349e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.349544e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.301607e+03\n Vprtstp: contraction number = 1.301607e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.614068e-04\n Vprtstp: contraction number = 3.489169e-01\n Vnewton: Using errtol_s: 1171.448936\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.873351e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.365660e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.645153e+02\n Vprtstp: contraction number = 4.645153e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 5.760250e-05\n Vprtstp: contraction number = 3.568778e-01\n Vnewton: Using errtol_s: 418.064161\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.892556e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.381619e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.772219e+02\n Vprtstp: contraction number = 1.772219e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.197650e-05\n Vprtstp: contraction number = 3.815199e-01\n Vnewton: Using errtol_s: 159.499808\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.910348e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.398026e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.471028e+01\n Vprtstp: contraction number = 7.471028e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 9.264488e-06\n Vprtstp: contraction number = 4.215634e-01\n Vnewton: Using errtol_s: 67.239276\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.929147e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.414736e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.443502e+01\n Vprtstp: contraction number = 3.443502e+01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 4.270137e-06\n Vprtstp: contraction number = 4.609145e-01\n Vnewton: Using errtol_s: 30.991559\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.949018e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.431514e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.720700e+01\n Vprtstp: contraction number = 1.720700e+01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.133763e-06\n Vprtstp: contraction number = 4.996942e-01\n Vnewton: Using errtol_s: 15.486302\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.967416e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.448696e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.259710e+00\n Vprtstp: contraction number = 9.259710e+00\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.148258e-06\n Vprtstp: contraction number = 5.381377e-01\n Vnewton: Using errtol_s: 8.333763\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.987588e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.464663e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.358358e+00\n Vprtstp: contraction number = 5.358358e+00\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 6.644658e-07\n Vprtstp: contraction number = 5.786728e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.511820e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.525583e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.188870e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.200693e+02\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (2.518, -2.4645, 16.7425)\n Vpmg_setPart:  actual minima = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  actual maxima = (13.3006, 6.29637, 27.9102)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -5002,27 +5002,27 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.140717793128E+00 kT\n Vpmg_energy:  qfEnergy = 2.905500135129E+04 kT\n Vpmg_energy:  dielEnergy = 1.454863407382E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.788600e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.297500e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  printing only subset of domain\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 2.005950e+03\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.480661e+03\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 05:52:39 2025\n+# Creation Date and Time:  Tue Jan  9 03:40:33 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path mol1.pqr\n@@ -5375,250 +5375,250 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.169283\n+Vacc_SASA: Time elapsed: 3.048833\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.277428e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.920904e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.872400e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.322500e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.213537e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 8.694140e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.004490e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.295078e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4300910.832168\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.196883e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.394920e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.136321e+05\n Vprtstp: contraction number = 2.136321e+05\n Vnewton: Attempting damping, relres = 0.047663\n Vnewton: Attempting damping, relres = 0.515490\n Vnewton: Damping accepted, relres = 0.047663\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.766304e-02\n Vprtstp: contraction number = 4.766304e-02\n Vnewton: Using errtol_s: 204994.485638\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.445230e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.170622e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.587025e+04\n Vprtstp: contraction number = 4.587025e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 9.727679e-03\n Vprtstp: contraction number = 2.040927e-01\n Vnewton: Using errtol_s: 41837.880528\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.797624e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.438435e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.391016e+04\n Vprtstp: contraction number = 1.391016e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.912173e-03\n Vprtstp: contraction number = 2.993697e-01\n Vnewton: Using errtol_s: 12524.995351\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.169436e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.604267e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.237707e+03\n Vprtstp: contraction number = 5.237707e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.096054e-03\n Vprtstp: contraction number = 3.763697e-01\n Vnewton: Using errtol_s: 4714.028550\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.471336e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.010586e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.331453e+03\n Vprtstp: contraction number = 2.331453e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.878779e-04\n Vprtstp: contraction number = 4.451223e-01\n Vnewton: Using errtol_s: 2098.319320\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.831097e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.371545e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.189035e+03\n Vprtstp: contraction number = 1.189035e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.488161e-04\n Vprtstp: contraction number = 5.099966e-01\n Vnewton: Using errtol_s: 1070.135650\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.209544e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.521103e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.678182e+02\n Vprtstp: contraction number = 6.678182e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.397467e-04\n Vprtstp: contraction number = 5.616468e-01\n Vnewton: Using errtol_s: 601.038216\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.044904e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.621274e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.994733e+02\n Vprtstp: contraction number = 3.994733e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.359319e-05\n Vprtstp: contraction number = 5.981764e-01\n Vnewton: Using errtol_s: 359.526862\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.176419e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.068045e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.488647e+02\n Vprtstp: contraction number = 2.488647e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.207703e-05\n Vprtstp: contraction number = 6.229817e-01\n Vnewton: Using errtol_s: 223.978670\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.323933e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.189122e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.588671e+02\n Vprtstp: contraction number = 1.588671e+02\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.324425e-05\n Vprtstp: contraction number = 6.383669e-01\n Vnewton: Using errtol_s: 142.980568\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.455368e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.302333e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.030284e+02\n Vprtstp: contraction number = 1.030284e+02\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.155954e-05\n Vprtstp: contraction number = 6.485194e-01\n Vnewton: Using errtol_s: 92.725673\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.595426e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.411369e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.760657e+01\n Vprtstp: contraction number = 6.760657e+01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.414722e-05\n Vprtstp: contraction number = 6.561932e-01\n Vnewton: Using errtol_s: 60.845953\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.741480e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.518345e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.480217e+01\n Vprtstp: contraction number = 4.480217e+01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 9.375216e-06\n Vprtstp: contraction number = 6.626894e-01\n Vnewton: Using errtol_s: 40.321969\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.873510e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.636479e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.990735e+01\n Vprtstp: contraction number = 2.990735e+01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 6.258355e-06\n Vprtstp: contraction number = 6.675424e-01\n Vnewton: Using errtol_s: 26.916626\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.008464e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.749228e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.008505e+01\n Vprtstp: contraction number = 2.008505e+01\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 4.202958e-06\n Vprtstp: contraction number = 6.715755e-01\n Vnewton: Using errtol_s: 18.076547\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.160681e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.868046e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.356100e+01\n Vprtstp: contraction number = 1.356100e+01\n Vprtstp: iteration = 16\n Vprtstp: relative residual = 2.837748e-06\n Vprtstp: contraction number = 6.751787e-01\n Vnewton: Using errtol_s: 12.204901\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.326015e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.989090e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.198733e+00\n Vprtstp: contraction number = 9.198733e+00\n Vprtstp: iteration = 17\n Vprtstp: relative residual = 1.924909e-06\n Vprtstp: contraction number = 6.783227e-01\n Vnewton: Using errtol_s: 8.278861\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.457019e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.116080e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.265697e+00\n Vprtstp: contraction number = 6.265697e+00\n Vprtstp: iteration = 18\n Vprtstp: relative residual = 1.311147e-06\n Vprtstp: contraction number = 6.811478e-01\n Vnewton: Using errtol_s: 5.639128\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.629576e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.237638e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.284635e+00\n Vprtstp: contraction number = 4.284635e+00\n Vprtstp: iteration = 19\n Vprtstp: relative residual = 8.965941e-07\n Vprtstp: contraction number = 6.838241e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.728721e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.742540e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.298821e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.309391e+02\n Vpmg_setPart:  lower corner = (2.518, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, -2.4645, 16.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -5627,15 +5627,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 4.939690296929E-01 kT\n Vpmg_energy:  qfEnergy = 9.376673747482E+03 kT\n Vpmg_energy:  dielEnergy = 4.692177592704E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.572900e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.238600e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 39.7309\n Vpbe_ctor2:  solute dimensions = 68.682 x 69.075 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -5683,171 +5683,171 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0309075 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.262622\n+Vacc_SASA: Time elapsed: 2.994248\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.921680e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.530572e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 7.401100e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.502500e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.213290e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.147535e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.852831e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.411694e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 6495765.822087\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.881330e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.433550e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.362765e+05\n Vprtstp: contraction number = 6.362765e+05\n Vnewton: Attempting damping, relres = 0.088746\n Vnewton: Attempting damping, relres = 0.541895\n Vnewton: Damping accepted, relres = 0.088746\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.874646e-02\n Vprtstp: contraction number = 8.874646e-02\n Vnewton: Using errtol_s: 576476.204773\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.124796e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.612625e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.170231e+05\n Vprtstp: contraction number = 1.170231e+05\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.623146e-02\n Vprtstp: contraction number = 1.828970e-01\n Vnewton: Using errtol_s: 105435.741217\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.386143e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.782392e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.955662e+04\n Vprtstp: contraction number = 2.955662e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 4.095304e-03\n Vprtstp: contraction number = 2.523066e-01\n Vnewton: Using errtol_s: 26602.134295\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.657559e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.949587e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.995691e+03\n Vprtstp: contraction number = 8.995691e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.246378e-03\n Vprtstp: contraction number = 3.043434e-01\n Vnewton: Using errtol_s: 8096.182717\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.926316e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.118415e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.013650e+03\n Vprtstp: contraction number = 3.013650e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.175484e-04\n Vprtstp: contraction number = 3.350093e-01\n Vnewton: Using errtol_s: 2712.296685\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.179465e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.266187e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.048604e+03\n Vprtstp: contraction number = 1.048604e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.452864e-04\n Vprtstp: contraction number = 3.479510e-01\n Vnewton: Using errtol_s: 943.746446\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.441135e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.414438e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.603662e+02\n Vprtstp: contraction number = 3.603662e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.992953e-05\n Vprtstp: contraction number = 3.436628e-01\n Vnewton: Using errtol_s: 324.330531\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.684876e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.562092e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.297355e+02\n Vprtstp: contraction number = 1.297355e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.797512e-05\n Vprtstp: contraction number = 3.600099e-01\n Vnewton: Using errtol_s: 116.762190\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.911863e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.715773e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.314764e+01\n Vprtstp: contraction number = 5.314764e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 7.363712e-06\n Vprtstp: contraction number = 4.096613e-01\n Vnewton: Using errtol_s: 47.832946\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.109895e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.871831e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.432172e+01\n Vprtstp: contraction number = 2.432172e+01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.369821e-06\n Vprtstp: contraction number = 4.576253e-01\n Vnewton: Using errtol_s: 21.889567\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.313786e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.025341e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.198142e+01\n Vprtstp: contraction number = 1.198142e+01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 1.660048e-06\n Vprtstp: contraction number = 4.926220e-01\n Vnewton: Using errtol_s: 10.783282\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.529987e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.186092e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.178209e+00\n Vprtstp: contraction number = 6.178209e+00\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 8.560021e-07\n Vprtstp: contraction number = 5.156491e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.868480e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.882327e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.921926e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.934824e+02\n Vpmg_setPart:  lower corner = (2.518, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, -2.4645, 16.7425)\n Vpmg_setPart:  actual minima = (-8.26461, -47.9645, -41.2575)\n Vpmg_setPart:  actual maxima = (58.518, 6.29637, 27.9102)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -5856,17 +5856,17 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 5.088785414018E-01 kT\n Vpmg_energy:  qfEnergy = 7.513083652575E+04 kT\n Vpmg_energy:  dielEnergy = 3.773034744692E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.534800e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.111900e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -5887,272 +5887,272 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.283275\n+Vacc_SASA: Time elapsed: 3.018673\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.293980e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.815632e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.070000e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.341200e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.224437e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.015728e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.778316e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.385042e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4276578.139223\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.807038e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.403305e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.113974e+05\n Vprtstp: contraction number = 2.113974e+05\n Vnewton: Attempting damping, relres = 0.047573\n Vnewton: Attempting damping, relres = 0.515375\n Vnewton: Damping accepted, relres = 0.047573\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.757263e-02\n Vprtstp: contraction number = 4.757263e-02\n Vnewton: Using errtol_s: 203448.048803\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.997094e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.543875e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.589098e+04\n Vprtstp: contraction number = 4.589098e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 9.811582e-03\n Vprtstp: contraction number = 2.062443e-01\n Vnewton: Using errtol_s: 41959.996661\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.132294e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.678751e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.404662e+04\n Vprtstp: contraction number = 1.404662e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.960291e-03\n Vprtstp: contraction number = 3.017139e-01\n Vnewton: Using errtol_s: 12659.913691\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.266744e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.802525e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.279840e+03\n Vprtstp: contraction number = 5.279840e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.111524e-03\n Vprtstp: contraction number = 3.754781e-01\n Vnewton: Using errtol_s: 4753.520446\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.411495e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.915788e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.336921e+03\n Vprtstp: contraction number = 2.336921e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.918609e-04\n Vprtstp: contraction number = 4.425102e-01\n Vnewton: Using errtol_s: 2103.481419\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.544980e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.041112e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.194576e+03\n Vprtstp: contraction number = 1.194576e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.514070e-04\n Vprtstp: contraction number = 5.111344e-01\n Vnewton: Using errtol_s: 1075.161658\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.679896e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.181143e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.792983e+02\n Vprtstp: contraction number = 6.792983e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.429594e-04\n Vprtstp: contraction number = 5.686374e-01\n Vnewton: Using errtol_s: 611.377148\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.824046e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.308136e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.154648e+02\n Vprtstp: contraction number = 4.154648e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.743449e-05\n Vprtstp: contraction number = 6.116036e-01\n Vnewton: Using errtol_s: 373.920435\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.963639e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.434221e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.660684e+02\n Vprtstp: contraction number = 2.660684e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.599388e-05\n Vprtstp: contraction number = 6.404095e-01\n Vnewton: Using errtol_s: 239.462182\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.121108e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.550444e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.755593e+02\n Vprtstp: contraction number = 1.755593e+02\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.694626e-05\n Vprtstp: contraction number = 6.598268e-01\n Vnewton: Using errtol_s: 158.003576\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.266765e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.679224e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.183176e+02\n Vprtstp: contraction number = 1.183176e+02\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.489979e-05\n Vprtstp: contraction number = 6.739462e-01\n Vnewton: Using errtol_s: 106.485913\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.414174e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.817017e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.102710e+01\n Vprtstp: contraction number = 8.102710e+01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.705205e-05\n Vprtstp: contraction number = 6.848271e-01\n Vnewton: Using errtol_s: 72.924443\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.549737e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.941643e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.628393e+01\n Vprtstp: contraction number = 5.628393e+01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 1.184488e-05\n Vprtstp: contraction number = 6.946308e-01\n Vnewton: Using errtol_s: 50.655566\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.693346e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.072332e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.955755e+01\n Vprtstp: contraction number = 3.955755e+01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 8.324836e-06\n Vprtstp: contraction number = 7.028213e-01\n Vnewton: Using errtol_s: 35.601810\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.828177e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.180303e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.808103e+01\n Vprtstp: contraction number = 2.808103e+01\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 5.909617e-06\n Vprtstp: contraction number = 7.098779e-01\n Vnewton: Using errtol_s: 25.272937\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.964422e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.295188e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.010039e+01\n Vprtstp: contraction number = 2.010039e+01\n Vprtstp: iteration = 16\n Vprtstp: relative residual = 4.230100e-06\n Vprtstp: contraction number = 7.157995e-01\n Vnewton: Using errtol_s: 18.090355\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.099286e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.408009e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.449222e+01\n Vprtstp: contraction number = 1.449222e+01\n Vprtstp: iteration = 17\n Vprtstp: relative residual = 3.049867e-06\n Vprtstp: contraction number = 7.209918e-01\n Vnewton: Using errtol_s: 13.042997\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.232678e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.526604e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.051084e+01\n Vprtstp: contraction number = 1.051084e+01\n Vprtstp: iteration = 18\n Vprtstp: relative residual = 2.211992e-06\n Vprtstp: contraction number = 7.252749e-01\n Vnewton: Using errtol_s: 9.459758\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.373449e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.657517e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.663626e+00\n Vprtstp: contraction number = 7.663626e+00\n Vprtstp: iteration = 19\n Vprtstp: relative residual = 1.612800e-06\n Vprtstp: contraction number = 7.291164e-01\n Vnewton: Using errtol_s: 6.897264\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.520824e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.793089e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.612195e+00\n Vprtstp: contraction number = 5.612195e+00\n Vprtstp: iteration = 20\n Vprtstp: relative residual = 1.181079e-06\n Vprtstp: contraction number = 7.323158e-01\n Vnewton: Using errtol_s: 5.050976\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.678535e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.907675e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.124624e+00\n Vprtstp: contraction number = 4.124624e+00\n Vprtstp: iteration = 21\n Vprtstp: relative residual = 8.680215e-07\n Vprtstp: contraction number = 7.349396e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 3.025342e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.038586e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.639612e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.651198e+02\n Vpmg_setPart:  lower corner = (2.518, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, -2.4645, 16.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -6161,15 +6161,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 4.529259077785E-03 kT\n Vpmg_energy:  qfEnergy = 0.000000000000E+00 kT\n Vpmg_energy:  dielEnergy = 3.922111986755E-02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.737500e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.838400e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -6217,149 +6217,149 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00111335 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.164993\n+Vacc_SASA: Time elapsed: 3.023970\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.988486e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.879956e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.701000e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.197400e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.205335e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.066056e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.859334e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.077995e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 659220.576503\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.883142e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.098837e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.405229e+04\n Vprtstp: contraction number = 7.405229e+04\n Vnewton: Attempting damping, relres = 0.101194\n Vnewton: Attempting damping, relres = 0.547249\n Vnewton: Damping accepted, relres = 0.101194\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.011936e-01\n Vprtstp: contraction number = 1.011936e-01\n Vnewton: Using errtol_s: 66708.882844\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.018615e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.218730e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.227539e+04\n Vprtstp: contraction number = 1.227539e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.676045e-02\n Vprtstp: contraction number = 1.656277e-01\n Vnewton: Using errtol_s: 11048.836228\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.145974e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.324154e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.508807e+03\n Vprtstp: contraction number = 2.508807e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 3.425225e-03\n Vprtstp: contraction number = 2.043635e-01\n Vnewton: Using errtol_s: 2257.978588\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.278952e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.436063e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.967621e+02\n Vprtstp: contraction number = 5.967621e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 8.147347e-04\n Vprtstp: contraction number = 2.378632e-01\n Vnewton: Using errtol_s: 537.089910\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.415193e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.542092e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.589401e+02\n Vprtstp: contraction number = 1.589401e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 2.169933e-04\n Vprtstp: contraction number = 2.663361e-01\n Vnewton: Using errtol_s: 143.046443\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.569463e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.646582e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.567685e+01\n Vprtstp: contraction number = 4.567685e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 6.236027e-05\n Vprtstp: contraction number = 2.873834e-01\n Vnewton: Using errtol_s: 41.109175\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.709453e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.758696e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.380678e+01\n Vprtstp: contraction number = 1.380678e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.884969e-05\n Vprtstp: contraction number = 3.022708e-01\n Vnewton: Using errtol_s: 12.426102\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.865514e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.874252e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.334509e+00\n Vprtstp: contraction number = 4.334509e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 5.917683e-06\n Vprtstp: contraction number = 3.139406e-01\n Vnewton: Using errtol_s: 3.901058\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.003468e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.989883e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.401869e+00\n Vprtstp: contraction number = 1.401869e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 1.913900e-06\n Vprtstp: contraction number = 3.234205e-01\n Vnewton: Using errtol_s: 1.261682\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.020214e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.093682e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.640279e-01\n Vprtstp: contraction number = 4.640279e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 6.335135e-07\n Vprtstp: contraction number = 3.310066e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.502260e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.516850e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.111843e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.124835e+02\n Vpmg_setPart:  lower corner = (2.518, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, -2.4645, 16.7425)\n Vpmg_setPart:  actual minima = (-8.26461, -47.9645, -41.2575)\n Vpmg_setPart:  actual maxima = (58.518, 6.29637, 27.9102)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -6368,15 +6368,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 4.628092645566E-03 kT\n Vpmg_energy:  qfEnergy = 0.000000000000E+00 kT\n Vpmg_energy:  dielEnergy = 3.231942662448E-02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.907200e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.337200e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n@@ -6399,261 +6399,261 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 5.916552\n+Vacc_SASA: Time elapsed: 6.375112\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.206472e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.464499e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.109500e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.563000e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.245701e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.148760e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.044875e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.276452e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 8699406.430616\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.047807e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.297148e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.298565e+05\n Vprtstp: contraction number = 4.298565e+05\n Vnewton: Attempting damping, relres = 0.048079\n Vnewton: Attempting damping, relres = 0.515481\n Vnewton: Damping accepted, relres = 0.048079\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.807904e-02\n Vprtstp: contraction number = 4.807904e-02\n Vnewton: Using errtol_s: 418259.137179\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.070708e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.459093e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.275297e+04\n Vprtstp: contraction number = 9.275297e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 9.791706e-03\n Vprtstp: contraction number = 2.036585e-01\n Vnewton: Using errtol_s: 85182.030508\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.092264e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.598335e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.830324e+04\n Vprtstp: contraction number = 2.830324e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.931540e-03\n Vprtstp: contraction number = 2.993901e-01\n Vnewton: Using errtol_s: 25502.653903\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.114306e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.732330e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.066383e+04\n Vprtstp: contraction number = 1.066383e+04\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.103407e-03\n Vprtstp: contraction number = 3.763916e-01\n Vnewton: Using errtol_s: 9598.985602\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.132580e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.874595e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.725476e+03\n Vprtstp: contraction number = 4.725476e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.889004e-04\n Vprtstp: contraction number = 4.430826e-01\n Vnewton: Using errtol_s: 4253.143226\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.152526e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.023394e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.402868e+03\n Vprtstp: contraction number = 2.402868e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.485940e-04\n Vprtstp: contraction number = 5.084757e-01\n Vnewton: Using errtol_s: 2162.620089\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.172920e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.164151e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.352802e+03\n Vprtstp: contraction number = 1.352802e+03\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.399556e-04\n Vprtstp: contraction number = 5.629888e-01\n Vnewton: Using errtol_s: 1217.530795\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.191358e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.292067e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.164880e+02\n Vprtstp: contraction number = 8.164880e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.447037e-05\n Vprtstp: contraction number = 6.035512e-01\n Vnewton: Using errtol_s: 734.842122\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.207567e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.419543e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.157033e+02\n Vprtstp: contraction number = 5.157033e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.335238e-05\n Vprtstp: contraction number = 6.316106e-01\n Vnewton: Using errtol_s: 464.134076\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.226205e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.550699e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.352095e+02\n Vprtstp: contraction number = 3.352095e+02\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.467926e-05\n Vprtstp: contraction number = 6.500040e-01\n Vnewton: Using errtol_s: 301.688999\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.245836e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.702716e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.222234e+02\n Vprtstp: contraction number = 2.222234e+02\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.299022e-05\n Vprtstp: contraction number = 6.629387e-01\n Vnewton: Using errtol_s: 200.001301\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.264523e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.851422e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.495221e+02\n Vprtstp: contraction number = 1.495221e+02\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.546887e-05\n Vprtstp: contraction number = 6.728456e-01\n Vnewton: Using errtol_s: 134.569993\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.282009e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.989442e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.018836e+02\n Vprtstp: contraction number = 1.018836e+02\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 1.054041e-05\n Vprtstp: contraction number = 6.813949e-01\n Vnewton: Using errtol_s: 91.695311\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.300211e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.012546e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.012825e+01\n Vprtstp: contraction number = 7.012825e+01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 7.255144e-06\n Vprtstp: contraction number = 6.883171e-01\n Vnewton: Using errtol_s: 63.115450\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.319173e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.026191e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.869976e+01\n Vprtstp: contraction number = 4.869976e+01\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 5.038252e-06\n Vprtstp: contraction number = 6.944386e-01\n Vnewton: Using errtol_s: 43.829803\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.338390e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.038931e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.408035e+01\n Vprtstp: contraction number = 3.408035e+01\n Vprtstp: iteration = 16\n Vprtstp: relative residual = 3.525795e-06\n Vprtstp: contraction number = 6.998052e-01\n Vnewton: Using errtol_s: 30.672326\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.355111e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.051501e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.401453e+01\n Vprtstp: contraction number = 2.401453e+01\n Vprtstp: iteration = 17\n Vprtstp: relative residual = 2.484432e-06\n Vprtstp: contraction number = 7.046444e-01\n Vnewton: Using errtol_s: 21.613084\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.371817e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.066052e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.702723e+01\n Vprtstp: contraction number = 1.702723e+01\n Vprtstp: iteration = 18\n Vprtstp: relative residual = 1.761558e-06\n Vprtstp: contraction number = 7.090385e-01\n Vnewton: Using errtol_s: 15.324508\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.391962e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.081293e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.214065e+01\n Vprtstp: contraction number = 1.214065e+01\n Vprtstp: iteration = 19\n Vprtstp: relative residual = 1.256015e-06\n Vprtstp: contraction number = 7.130137e-01\n Vnewton: Using errtol_s: 10.926584\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.409945e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.096881e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.699962e+00\n Vprtstp: contraction number = 8.699962e+00\n Vprtstp: iteration = 20\n Vprtstp: relative residual = 9.000575e-07\n Vprtstp: contraction number = 7.165978e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 3.807480e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.820513e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.820955e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.831386e+02\n Vpmg_setPart:  lower corner = (2.518, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, -2.4645, 16.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -6662,17 +6662,17 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 5.345658970657E-01 kT\n Vpmg_energy:  qfEnergy = 9.376279132276E+03 kT\n Vpmg_energy:  dielEnergy = 4.692311982408E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.790700e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.089100e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 5.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -6718,171 +6718,171 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0354778 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 6.229078\n+Vacc_SASA: Time elapsed: 6.513737\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.177122e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.284057e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.642200e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.453700e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.293011e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.002416e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.435321e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.119220e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 7084866.598925\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.438266e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.121278e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.984768e+05\n Vprtstp: contraction number = 6.984768e+05\n Vnewton: Attempting damping, relres = 0.089369\n Vnewton: Attempting damping, relres = 0.542089\n Vnewton: Damping accepted, relres = 0.089369\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.936880e-02\n Vprtstp: contraction number = 8.936880e-02\n Vnewton: Using errtol_s: 633166.041219\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.462651e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.141612e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.273163e+05\n Vprtstp: contraction number = 1.273163e+05\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.619364e-02\n Vprtstp: contraction number = 1.812001e-01\n Vnewton: Using errtol_s: 114729.758442\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.487015e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.161901e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.151737e+04\n Vprtstp: contraction number = 3.151737e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 4.003932e-03\n Vprtstp: contraction number = 2.472534e-01\n Vnewton: Using errtol_s: 28367.322157\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.509993e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.180047e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.393741e+03\n Vprtstp: contraction number = 9.393741e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.193311e-03\n Vprtstp: contraction number = 2.980349e-01\n Vnewton: Using errtol_s: 8454.451884\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.533286e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.197411e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.092776e+03\n Vprtstp: contraction number = 3.092776e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.928814e-04\n Vprtstp: contraction number = 3.292363e-01\n Vnewton: Using errtol_s: 2783.512220\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.556340e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.215798e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.061371e+03\n Vprtstp: contraction number = 1.061371e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.348278e-04\n Vprtstp: contraction number = 3.431770e-01\n Vnewton: Using errtol_s: 955.237298\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.578361e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.233355e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.607964e+02\n Vprtstp: contraction number = 3.607964e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.583260e-05\n Vprtstp: contraction number = 3.399342e-01\n Vnewton: Using errtol_s: 324.717847\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.601114e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.248144e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.293597e+02\n Vprtstp: contraction number = 1.293597e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.643277e-05\n Vprtstp: contraction number = 3.585389e-01\n Vnewton: Using errtol_s: 116.423976\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.626194e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.263793e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.299042e+01\n Vprtstp: contraction number = 5.299042e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 6.731454e-06\n Vprtstp: contraction number = 4.096360e-01\n Vnewton: Using errtol_s: 47.691450\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.646867e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.279683e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.428459e+01\n Vprtstp: contraction number = 2.428459e+01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.084907e-06\n Vprtstp: contraction number = 4.582824e-01\n Vnewton: Using errtol_s: 21.856153\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.669155e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.296750e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.197548e+01\n Vprtstp: contraction number = 1.197548e+01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 1.521262e-06\n Vprtstp: contraction number = 4.931307e-01\n Vnewton: Using errtol_s: 10.777941\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.689208e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.312585e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.181341e+00\n Vprtstp: contraction number = 6.181341e+00\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 7.852242e-07\n Vprtstp: contraction number = 5.161662e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.732225e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.746512e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.082549e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.094036e+02\n Vpmg_setPart:  lower corner = (2.518, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, -2.4645, 16.7425)\n Vpmg_setPart:  actual minima = (-8.26461, -47.9645, -41.2575)\n Vpmg_setPart:  actual maxima = (58.518, 6.29637, 27.9102)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -6891,27 +6891,27 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 5.684722914233E-01 kT\n Vpmg_energy:  qfEnergy = 7.513063949705E+04 kT\n Vpmg_energy:  dielEnergy = 3.773049125938E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.743800e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.986000e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  printing only subset of domain\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.709208e+03\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.328047e+03\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 05:56:15 2025\n+# Creation Date and Time:  Tue Jan  9 03:45:24 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path mol1.pqr\n@@ -7264,250 +7264,250 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.207737\n+Vacc_SASA: Time elapsed: 2.911818\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.242726e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.740992e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 6.126000e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.245000e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.132321e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.035880e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.885769e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.258553e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4300910.832168\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.252476e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.451467e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.136321e+05\n Vprtstp: contraction number = 2.136321e+05\n Vnewton: Attempting damping, relres = 0.047663\n Vnewton: Attempting damping, relres = 0.515490\n Vnewton: Damping accepted, relres = 0.047663\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.766304e-02\n Vprtstp: contraction number = 4.766304e-02\n Vnewton: Using errtol_s: 204994.485638\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.395999e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.247591e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.587025e+04\n Vprtstp: contraction number = 4.587025e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 9.727679e-03\n Vprtstp: contraction number = 2.040927e-01\n Vnewton: Using errtol_s: 41837.880528\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.827683e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.553392e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.391016e+04\n Vprtstp: contraction number = 1.391016e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.912173e-03\n Vprtstp: contraction number = 2.993697e-01\n Vnewton: Using errtol_s: 12524.995351\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.404552e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.810876e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.237707e+03\n Vprtstp: contraction number = 5.237707e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.096054e-03\n Vprtstp: contraction number = 3.763697e-01\n Vnewton: Using errtol_s: 4714.028550\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.850027e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.041381e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.331453e+03\n Vprtstp: contraction number = 2.331453e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.878779e-04\n Vprtstp: contraction number = 4.451223e-01\n Vnewton: Using errtol_s: 2098.319320\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.248942e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.339595e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.189035e+03\n Vprtstp: contraction number = 1.189035e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.488161e-04\n Vprtstp: contraction number = 5.099966e-01\n Vnewton: Using errtol_s: 1070.135650\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.562331e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.688578e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.678182e+02\n Vprtstp: contraction number = 6.678182e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.397467e-04\n Vprtstp: contraction number = 5.616468e-01\n Vnewton: Using errtol_s: 601.038216\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.093982e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.932101e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.994733e+02\n Vprtstp: contraction number = 3.994733e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.359319e-05\n Vprtstp: contraction number = 5.981764e-01\n Vnewton: Using errtol_s: 359.526862\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.231432e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.115808e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.488647e+02\n Vprtstp: contraction number = 2.488647e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.207703e-05\n Vprtstp: contraction number = 6.229817e-01\n Vnewton: Using errtol_s: 223.978670\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.378952e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.243394e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.588671e+02\n Vprtstp: contraction number = 1.588671e+02\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.324425e-05\n Vprtstp: contraction number = 6.383669e-01\n Vnewton: Using errtol_s: 142.980568\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.525126e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.362719e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.030284e+02\n Vprtstp: contraction number = 1.030284e+02\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.155954e-05\n Vprtstp: contraction number = 6.485194e-01\n Vnewton: Using errtol_s: 92.725673\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.668065e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.470323e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.760657e+01\n Vprtstp: contraction number = 6.760657e+01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.414722e-05\n Vprtstp: contraction number = 6.561932e-01\n Vnewton: Using errtol_s: 60.845953\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.820398e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.581451e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.480217e+01\n Vprtstp: contraction number = 4.480217e+01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 9.375216e-06\n Vprtstp: contraction number = 6.626894e-01\n Vnewton: Using errtol_s: 40.321969\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.975192e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.708456e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.990735e+01\n Vprtstp: contraction number = 2.990735e+01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 6.258355e-06\n Vprtstp: contraction number = 6.675424e-01\n Vnewton: Using errtol_s: 26.916626\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.157573e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.834030e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.008505e+01\n Vprtstp: contraction number = 2.008505e+01\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 4.202958e-06\n Vprtstp: contraction number = 6.715755e-01\n Vnewton: Using errtol_s: 18.076547\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.332337e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.950730e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.356100e+01\n Vprtstp: contraction number = 1.356100e+01\n Vprtstp: iteration = 16\n Vprtstp: relative residual = 2.837748e-06\n Vprtstp: contraction number = 6.751787e-01\n Vnewton: Using errtol_s: 12.204901\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.516425e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.057220e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.198733e+00\n Vprtstp: contraction number = 9.198733e+00\n Vprtstp: iteration = 17\n Vprtstp: relative residual = 1.924909e-06\n Vprtstp: contraction number = 6.783227e-01\n Vnewton: Using errtol_s: 8.278861\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.704030e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.178040e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.265697e+00\n Vprtstp: contraction number = 6.265697e+00\n Vprtstp: iteration = 18\n Vprtstp: relative residual = 1.311147e-06\n Vprtstp: contraction number = 6.811478e-01\n Vnewton: Using errtol_s: 5.639128\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.883689e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.287122e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.284635e+00\n Vprtstp: contraction number = 4.284635e+00\n Vprtstp: iteration = 19\n Vprtstp: relative residual = 8.965941e-07\n Vprtstp: contraction number = 6.838241e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.971695e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.984635e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.343461e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.355630e+02\n Vpmg_setPart:  lower corner = (-53.482, -2.4645, -41.2575)\n Vpmg_setPart:  upper corner = (2.518, 43.0355, 16.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -7516,17 +7516,17 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 4.966602122039E-02 kT\n Vpmg_energy:  qfEnergy = 3.975619983960E+01 kT\n Vpmg_energy:  dielEnergy = 4.589187237063E+01 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.299900e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.707000e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 39.7309\n Vpbe_ctor2:  solute dimensions = 68.682 x 69.075 x 70.346\n Vpbe_ctor2:  solute charge = -12\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -7572,160 +7572,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00234933 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.048278\n+Vacc_SASA: Time elapsed: 3.064701\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.211448e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.126743e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 7.396900e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.769200e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.269233e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.018244e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.087825e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.450274e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2418328.609890\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.115016e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.470160e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.297991e+05\n Vprtstp: contraction number = 2.297991e+05\n Vnewton: Attempting damping, relres = 0.085636\n Vnewton: Attempting damping, relres = 0.540011\n Vnewton: Damping accepted, relres = 0.085636\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.563556e-02\n Vprtstp: contraction number = 8.563556e-02\n Vnewton: Using errtol_s: 207094.936691\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.347712e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.643088e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.943259e+04\n Vprtstp: contraction number = 3.943259e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.467770e-02\n Vprtstp: contraction number = 1.713972e-01\n Vnewton: Using errtol_s: 35495.493076\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.410784e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.800313e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.192651e+03\n Vprtstp: contraction number = 9.192651e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 3.421180e-03\n Vprtstp: contraction number = 2.330870e-01\n Vnewton: Using errtol_s: 8273.537556\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.502512e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.960450e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.625902e+03\n Vprtstp: contraction number = 2.625902e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 9.772537e-04\n Vprtstp: contraction number = 2.856481e-01\n Vnewton: Using errtol_s: 2363.320499\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.711719e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.118843e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.336695e+02\n Vprtstp: contraction number = 8.336695e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.102569e-04\n Vprtstp: contraction number = 3.174784e-01\n Vnewton: Using errtol_s: 750.303246\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.947209e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.276519e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.790113e+02\n Vprtstp: contraction number = 2.790113e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.038363e-04\n Vprtstp: contraction number = 3.346783e-01\n Vnewton: Using errtol_s: 251.110249\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.171477e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.437550e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.595120e+01\n Vprtstp: contraction number = 9.595120e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.570900e-05\n Vprtstp: contraction number = 3.438971e-01\n Vnewton: Using errtol_s: 86.356086\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.400077e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.599718e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.363636e+01\n Vprtstp: contraction number = 3.363636e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.251804e-05\n Vprtstp: contraction number = 3.505570e-01\n Vnewton: Using errtol_s: 30.272729\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.672877e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.760136e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.212621e+01\n Vprtstp: contraction number = 1.212621e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 4.512865e-06\n Vprtstp: contraction number = 3.605089e-01\n Vnewton: Using errtol_s: 10.913589\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.903134e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.917550e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.547757e+00\n Vprtstp: contraction number = 4.547757e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.692484e-06\n Vprtstp: contraction number = 3.750353e-01\n Vnewton: Using errtol_s: 4.092981\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.103528e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.071702e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.787566e+00\n Vprtstp: contraction number = 1.787566e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 6.652567e-07\n Vprtstp: contraction number = 3.930654e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.204055e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.218688e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.769636e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.781830e+02\n Vpmg_setPart:  lower corner = (-53.482, -2.4645, -41.2575)\n Vpmg_setPart:  upper corner = (2.518, 43.0355, 16.7425)\n Vpmg_setPart:  actual minima = (-53.482, -11.2254, -41.2575)\n Vpmg_setPart:  actual maxima = (13.3006, 43.0355, 27.9102)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -7734,17 +7734,17 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 6.201138998655E-02 kT\n Vpmg_energy:  qfEnergy = 4.154611536454E+02 kT\n Vpmg_energy:  dielEnergy = 2.802895931375E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.990300e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.013100e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -7765,272 +7765,272 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.164501\n+Vacc_SASA: Time elapsed: 3.066815\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.151979e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.891181e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.401200e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.746400e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.198944e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.012851e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.347185e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.271126e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4276578.139223\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.372135e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.292903e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.113974e+05\n Vprtstp: contraction number = 2.113974e+05\n Vnewton: Attempting damping, relres = 0.047573\n Vnewton: Attempting damping, relres = 0.515375\n Vnewton: Damping accepted, relres = 0.047573\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.757263e-02\n Vprtstp: contraction number = 4.757263e-02\n Vnewton: Using errtol_s: 203448.048803\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.533336e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.423852e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.589098e+04\n Vprtstp: contraction number = 4.589098e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 9.811582e-03\n Vprtstp: contraction number = 2.062443e-01\n Vnewton: Using errtol_s: 41959.996661\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.694376e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.539745e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.404662e+04\n Vprtstp: contraction number = 1.404662e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.960291e-03\n Vprtstp: contraction number = 3.017139e-01\n Vnewton: Using errtol_s: 12659.913691\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.846257e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.650242e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.279840e+03\n Vprtstp: contraction number = 5.279840e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.111524e-03\n Vprtstp: contraction number = 3.754781e-01\n Vnewton: Using errtol_s: 4753.520446\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.997889e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.763524e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.336921e+03\n Vprtstp: contraction number = 2.336921e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.918609e-04\n Vprtstp: contraction number = 4.425102e-01\n Vnewton: Using errtol_s: 2103.481419\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.138419e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.879510e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.194576e+03\n Vprtstp: contraction number = 1.194576e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.514070e-04\n Vprtstp: contraction number = 5.111344e-01\n Vnewton: Using errtol_s: 1075.161658\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.284949e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.991378e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.792983e+02\n Vprtstp: contraction number = 6.792983e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.429594e-04\n Vprtstp: contraction number = 5.686374e-01\n Vnewton: Using errtol_s: 611.377148\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.459828e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.101582e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.154648e+02\n Vprtstp: contraction number = 4.154648e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.743449e-05\n Vprtstp: contraction number = 6.116036e-01\n Vnewton: Using errtol_s: 373.920435\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.606297e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.218406e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.660684e+02\n Vprtstp: contraction number = 2.660684e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.599388e-05\n Vprtstp: contraction number = 6.404095e-01\n Vnewton: Using errtol_s: 239.462182\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.747717e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.332725e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.755593e+02\n Vprtstp: contraction number = 1.755593e+02\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.694626e-05\n Vprtstp: contraction number = 6.598268e-01\n Vnewton: Using errtol_s: 158.003576\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.890830e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.446203e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.183176e+02\n Vprtstp: contraction number = 1.183176e+02\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.489979e-05\n Vprtstp: contraction number = 6.739462e-01\n Vnewton: Using errtol_s: 106.485913\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.039357e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.572708e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.102710e+01\n Vprtstp: contraction number = 8.102710e+01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.705205e-05\n Vprtstp: contraction number = 6.848271e-01\n Vnewton: Using errtol_s: 72.924443\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.185513e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.713861e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.628393e+01\n Vprtstp: contraction number = 5.628393e+01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 1.184488e-05\n Vprtstp: contraction number = 6.946308e-01\n Vnewton: Using errtol_s: 50.655566\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.331862e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.831347e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.955755e+01\n Vprtstp: contraction number = 3.955755e+01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 8.324836e-06\n Vprtstp: contraction number = 7.028213e-01\n Vnewton: Using errtol_s: 35.601810\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.488507e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.933039e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.808103e+01\n Vprtstp: contraction number = 2.808103e+01\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 5.909617e-06\n Vprtstp: contraction number = 7.098779e-01\n Vnewton: Using errtol_s: 25.272937\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.629464e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.044821e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.010039e+01\n Vprtstp: contraction number = 2.010039e+01\n Vprtstp: iteration = 16\n Vprtstp: relative residual = 4.230100e-06\n Vprtstp: contraction number = 7.157995e-01\n Vnewton: Using errtol_s: 18.090355\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.771524e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.155066e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.449222e+01\n Vprtstp: contraction number = 1.449222e+01\n Vprtstp: iteration = 17\n Vprtstp: relative residual = 3.049867e-06\n Vprtstp: contraction number = 7.209918e-01\n Vnewton: Using errtol_s: 13.042997\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.910525e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.273858e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.051084e+01\n Vprtstp: contraction number = 1.051084e+01\n Vprtstp: iteration = 18\n Vprtstp: relative residual = 2.211992e-06\n Vprtstp: contraction number = 7.252749e-01\n Vnewton: Using errtol_s: 9.459758\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.081354e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.425113e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.663626e+00\n Vprtstp: contraction number = 7.663626e+00\n Vprtstp: iteration = 19\n Vprtstp: relative residual = 1.612800e-06\n Vprtstp: contraction number = 7.291164e-01\n Vnewton: Using errtol_s: 6.897264\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.212681e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.536571e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.612195e+00\n Vprtstp: contraction number = 5.612195e+00\n Vprtstp: iteration = 20\n Vprtstp: relative residual = 1.181079e-06\n Vprtstp: contraction number = 7.323158e-01\n Vnewton: Using errtol_s: 5.050976\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.349585e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.648777e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.124624e+00\n Vprtstp: contraction number = 4.124624e+00\n Vprtstp: iteration = 21\n Vprtstp: relative residual = 8.680215e-07\n Vprtstp: contraction number = 7.349396e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 3.161980e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.175003e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.503305e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.514452e+02\n Vpmg_setPart:  lower corner = (-53.482, -2.4645, -41.2575)\n Vpmg_setPart:  upper corner = (2.518, 43.0355, 16.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -8039,17 +8039,17 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.651047489982E-01 kT\n Vpmg_energy:  qfEnergy = 3.716292902858E+03 kT\n Vpmg_energy:  dielEnergy = 1.798539842617E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.055800e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.306000e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -8095,160 +8095,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00429089 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.169713\n+Vacc_SASA: Time elapsed: 2.931294\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.500015e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.161687e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.685500e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.459600e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.121680e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.872100e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.568066e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.828565e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 3456404.072365\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.590380e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.847257e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.424168e+05\n Vprtstp: contraction number = 3.424168e+05\n Vnewton: Attempting damping, relres = 0.089811\n Vnewton: Attempting damping, relres = 0.542258\n Vnewton: Damping accepted, relres = 0.089811\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.981102e-02\n Vprtstp: contraction number = 8.981102e-02\n Vnewton: Using errtol_s: 310423.190924\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.801539e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.029665e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.148381e+04\n Vprtstp: contraction number = 6.148381e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.602901e-02\n Vprtstp: contraction number = 1.784748e-01\n Vnewton: Using errtol_s: 55402.729239\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.977969e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.194380e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.483491e+04\n Vprtstp: contraction number = 1.483491e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 3.863008e-03\n Vprtstp: contraction number = 2.410011e-01\n Vnewton: Using errtol_s: 13352.116026\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.154086e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.360312e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.268024e+03\n Vprtstp: contraction number = 4.268024e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.111340e-03\n Vprtstp: contraction number = 2.876878e-01\n Vnewton: Using errtol_s: 3841.240882\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.345232e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.524596e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.355750e+03\n Vprtstp: contraction number = 1.355750e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.530190e-04\n Vprtstp: contraction number = 3.176516e-01\n Vnewton: Using errtol_s: 1220.176206\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.530031e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.685253e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.554936e+02\n Vprtstp: contraction number = 4.554936e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.186043e-04\n Vprtstp: contraction number = 3.359715e-01\n Vnewton: Using errtol_s: 409.944430\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.724277e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.841139e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.577730e+02\n Vprtstp: contraction number = 1.577730e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.108191e-05\n Vprtstp: contraction number = 3.463779e-01\n Vnewton: Using errtol_s: 141.995679\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.921889e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.992919e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.547816e+01\n Vprtstp: contraction number = 5.547816e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.444575e-05\n Vprtstp: contraction number = 3.516328e-01\n Vnewton: Using errtol_s: 49.930345\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.014411e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.140219e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.964653e+01\n Vprtstp: contraction number = 1.964653e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.115686e-06\n Vprtstp: contraction number = 3.541309e-01\n Vnewton: Using errtol_s: 17.681880\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.038701e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.318420e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.015901e+00\n Vprtstp: contraction number = 7.015901e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.826844e-06\n Vprtstp: contraction number = 3.571063e-01\n Vnewton: Using errtol_s: 6.314311\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.059900e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.490814e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.553268e+00\n Vprtstp: contraction number = 2.553268e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 6.648357e-07\n Vprtstp: contraction number = 3.639258e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.234816e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.246867e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.812991e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.824072e+02\n Vpmg_setPart:  lower corner = (-53.482, -2.4645, -41.2575)\n Vpmg_setPart:  upper corner = (2.518, 43.0355, 16.7425)\n Vpmg_setPart:  actual minima = (-53.482, -11.2254, -41.2575)\n Vpmg_setPart:  actual maxima = (13.3006, 43.0355, 27.9102)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -8257,15 +8257,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.579314308709E-01 kT\n Vpmg_energy:  qfEnergy = 2.986093532858E+04 kT\n Vpmg_energy:  dielEnergy = 1.486705407480E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.760500e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.822800e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n@@ -8288,261 +8288,261 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 6.664610\n+Vacc_SASA: Time elapsed: 6.337709\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.973637e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.536708e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.899400e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.282900e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.360275e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.933100e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.089772e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.729089e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 8699406.430616\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.092393e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.749454e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.298565e+05\n Vprtstp: contraction number = 4.298565e+05\n Vnewton: Attempting damping, relres = 0.048079\n Vnewton: Attempting damping, relres = 0.515481\n Vnewton: Damping accepted, relres = 0.048079\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.807904e-02\n Vprtstp: contraction number = 4.807904e-02\n Vnewton: Using errtol_s: 418259.137179\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.112213e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.911185e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.275297e+04\n Vprtstp: contraction number = 9.275297e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 9.791706e-03\n Vprtstp: contraction number = 2.036585e-01\n Vnewton: Using errtol_s: 85182.030508\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.129670e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.051301e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.830324e+04\n Vprtstp: contraction number = 2.830324e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.931540e-03\n Vprtstp: contraction number = 2.993901e-01\n Vnewton: Using errtol_s: 25502.653903\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.146673e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.190724e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.066383e+04\n Vprtstp: contraction number = 1.066383e+04\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.103407e-03\n Vprtstp: contraction number = 3.763916e-01\n Vnewton: Using errtol_s: 9598.985602\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.163696e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.325968e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.725476e+03\n Vprtstp: contraction number = 4.725476e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.889004e-04\n Vprtstp: contraction number = 4.430826e-01\n Vnewton: Using errtol_s: 4253.143226\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.183221e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.461082e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.402868e+03\n Vprtstp: contraction number = 2.402868e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.485940e-04\n Vprtstp: contraction number = 5.084757e-01\n Vnewton: Using errtol_s: 2162.620089\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.199784e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.596929e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.352802e+03\n Vprtstp: contraction number = 1.352802e+03\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.399556e-04\n Vprtstp: contraction number = 5.629888e-01\n Vnewton: Using errtol_s: 1217.530795\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.218192e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.730691e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.164880e+02\n Vprtstp: contraction number = 8.164880e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.447037e-05\n Vprtstp: contraction number = 6.035512e-01\n Vnewton: Using errtol_s: 734.842122\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.238754e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.866040e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.157033e+02\n Vprtstp: contraction number = 5.157033e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.335238e-05\n Vprtstp: contraction number = 6.316106e-01\n Vnewton: Using errtol_s: 464.134076\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.253280e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.000046e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.352095e+02\n Vprtstp: contraction number = 3.352095e+02\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.467926e-05\n Vprtstp: contraction number = 6.500040e-01\n Vnewton: Using errtol_s: 301.688999\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.267886e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.014348e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.222234e+02\n Vprtstp: contraction number = 2.222234e+02\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.299022e-05\n Vprtstp: contraction number = 6.629387e-01\n Vnewton: Using errtol_s: 200.001301\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.283863e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.029540e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.495221e+02\n Vprtstp: contraction number = 1.495221e+02\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.546887e-05\n Vprtstp: contraction number = 6.728456e-01\n Vnewton: Using errtol_s: 134.569993\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.301096e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.043524e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.018836e+02\n Vprtstp: contraction number = 1.018836e+02\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 1.054041e-05\n Vprtstp: contraction number = 6.813949e-01\n Vnewton: Using errtol_s: 91.695311\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.319565e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.058052e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.012825e+01\n Vprtstp: contraction number = 7.012825e+01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 7.255144e-06\n Vprtstp: contraction number = 6.883171e-01\n Vnewton: Using errtol_s: 63.115450\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.333913e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.071443e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.869976e+01\n Vprtstp: contraction number = 4.869976e+01\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 5.038252e-06\n Vprtstp: contraction number = 6.944386e-01\n Vnewton: Using errtol_s: 43.829803\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.352365e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.084758e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.408035e+01\n Vprtstp: contraction number = 3.408035e+01\n Vprtstp: iteration = 16\n Vprtstp: relative residual = 3.525795e-06\n Vprtstp: contraction number = 6.998052e-01\n Vnewton: Using errtol_s: 30.672326\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.368092e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.098302e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.401453e+01\n Vprtstp: contraction number = 2.401453e+01\n Vprtstp: iteration = 17\n Vprtstp: relative residual = 2.484432e-06\n Vprtstp: contraction number = 7.046444e-01\n Vnewton: Using errtol_s: 21.613084\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.385094e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.111207e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.702723e+01\n Vprtstp: contraction number = 1.702723e+01\n Vprtstp: iteration = 18\n Vprtstp: relative residual = 1.761558e-06\n Vprtstp: contraction number = 7.090385e-01\n Vnewton: Using errtol_s: 15.324508\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.399651e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.124267e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.214065e+01\n Vprtstp: contraction number = 1.214065e+01\n Vprtstp: iteration = 19\n Vprtstp: relative residual = 1.256015e-06\n Vprtstp: contraction number = 7.130137e-01\n Vnewton: Using errtol_s: 10.926584\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.414814e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.136973e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.699962e+00\n Vprtstp: contraction number = 8.699962e+00\n Vprtstp: iteration = 20\n Vprtstp: relative residual = 9.000575e-07\n Vprtstp: contraction number = 7.165978e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 3.383989e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.398485e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.767694e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.778381e+02\n Vpmg_setPart:  lower corner = (-53.482, -2.4645, -41.2575)\n Vpmg_setPart:  upper corner = (2.518, 43.0355, 16.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -8551,17 +8551,17 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.659936219773E-01 kT\n Vpmg_energy:  qfEnergy = 3.771591154168E+03 kT\n Vpmg_energy:  dielEnergy = 1.850889250612E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.002200e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.026900e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -8607,160 +8607,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0122306 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 6.881220\n+Vacc_SASA: Time elapsed: 6.232352\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.599205e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.868258e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.271500e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.229900e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.007915e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.103486e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.438058e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.158821e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 5774426.010351\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.440062e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.160962e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.536200e+05\n Vprtstp: contraction number = 5.536200e+05\n Vnewton: Attempting damping, relres = 0.086816\n Vnewton: Attempting damping, relres = 0.540697\n Vnewton: Damping accepted, relres = 0.086816\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.681646e-02\n Vprtstp: contraction number = 8.681646e-02\n Vnewton: Using errtol_s: 501315.229123\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.461813e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.180517e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.813919e+04\n Vprtstp: contraction number = 9.813919e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.530865e-02\n Vprtstp: contraction number = 1.763335e-01\n Vnewton: Using errtol_s: 88398.668796\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.480194e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.198281e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.359807e+04\n Vprtstp: contraction number = 2.359807e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 3.678183e-03\n Vprtstp: contraction number = 2.402683e-01\n Vnewton: Using errtol_s: 21239.395305\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.498426e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.219657e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.835940e+03\n Vprtstp: contraction number = 6.835940e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.065460e-03\n Vprtstp: contraction number = 2.896703e-01\n Vnewton: Using errtol_s: 6152.421286\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.515849e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.239776e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.186690e+03\n Vprtstp: contraction number = 2.186690e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.408183e-04\n Vprtstp: contraction number = 3.198790e-01\n Vnewton: Using errtol_s: 1968.030266\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.534736e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.258608e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.369221e+02\n Vprtstp: contraction number = 7.369221e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.148566e-04\n Vprtstp: contraction number = 3.370025e-01\n Vnewton: Using errtol_s: 663.231119\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.554658e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.278321e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.557331e+02\n Vprtstp: contraction number = 2.557331e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.985850e-05\n Vprtstp: contraction number = 3.470283e-01\n Vnewton: Using errtol_s: 230.159953\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.573524e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.295968e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.020719e+01\n Vprtstp: contraction number = 9.020719e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.405966e-05\n Vprtstp: contraction number = 3.527394e-01\n Vnewton: Using errtol_s: 81.186485\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.595130e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.312267e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.225420e+01\n Vprtstp: contraction number = 3.225420e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.027128e-06\n Vprtstp: contraction number = 3.575568e-01\n Vnewton: Using errtol_s: 29.028780\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.614687e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.327760e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.171930e+01\n Vprtstp: contraction number = 1.171930e+01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.826566e-06\n Vprtstp: contraction number = 3.633419e-01\n Vnewton: Using errtol_s: 10.547373\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.633694e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.343239e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.353564e+00\n Vprtstp: contraction number = 4.353564e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 6.785449e-07\n Vprtstp: contraction number = 3.714865e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.140875e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.152622e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.986661e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.998383e+02\n Vpmg_setPart:  lower corner = (-53.482, -2.4645, -41.2575)\n Vpmg_setPart:  upper corner = (2.518, 43.0355, 16.7425)\n Vpmg_setPart:  actual minima = (-53.482, -11.2254, -41.2575)\n Vpmg_setPart:  actual maxima = (13.3006, 43.0355, 27.9102)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -8769,27 +8769,27 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 3.126180200466E-01 kT\n Vpmg_energy:  qfEnergy = 3.029835397910E+04 kT\n Vpmg_energy:  dielEnergy = 1.515709858498E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.248500e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.355400e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  printing only subset of domain\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.652822e+03\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.358043e+03\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 06:00:15 2025\n+# Creation Date and Time:  Tue Jan  9 03:50:25 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path mol1.pqr\n@@ -9142,250 +9142,250 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.168591\n+Vacc_SASA: Time elapsed: 2.938683\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.191183e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.905051e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 6.869600e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.194700e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.252627e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.282150e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.968801e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.286143e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4300910.832168\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.578330e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.433557e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.136321e+05\n Vprtstp: contraction number = 2.136321e+05\n Vnewton: Attempting damping, relres = 0.047663\n Vnewton: Attempting damping, relres = 0.515490\n Vnewton: Damping accepted, relres = 0.047663\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.766304e-02\n Vprtstp: contraction number = 4.766304e-02\n Vnewton: Using errtol_s: 204994.485638\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.353235e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.117736e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.587025e+04\n Vprtstp: contraction number = 4.587025e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 9.727679e-03\n Vprtstp: contraction number = 2.040927e-01\n Vnewton: Using errtol_s: 41837.880528\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.059703e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.364590e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.391016e+04\n Vprtstp: contraction number = 1.391016e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.912173e-03\n Vprtstp: contraction number = 2.993697e-01\n Vnewton: Using errtol_s: 12524.995351\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.594811e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.532585e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.237707e+03\n Vprtstp: contraction number = 5.237707e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.096054e-03\n Vprtstp: contraction number = 3.763697e-01\n Vnewton: Using errtol_s: 4714.028550\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.955556e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.769296e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.331453e+03\n Vprtstp: contraction number = 2.331453e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.878779e-04\n Vprtstp: contraction number = 4.451223e-01\n Vnewton: Using errtol_s: 2098.319320\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.191298e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.960305e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.189035e+03\n Vprtstp: contraction number = 1.189035e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.488161e-04\n Vprtstp: contraction number = 5.099966e-01\n Vnewton: Using errtol_s: 1070.135650\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.657400e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.227220e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.678182e+02\n Vprtstp: contraction number = 6.678182e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.397467e-04\n Vprtstp: contraction number = 5.616468e-01\n Vnewton: Using errtol_s: 601.038216\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.122403e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.696507e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.994733e+02\n Vprtstp: contraction number = 3.994733e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.359319e-05\n Vprtstp: contraction number = 5.981764e-01\n Vnewton: Using errtol_s: 359.526862\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.253748e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.118423e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.488647e+02\n Vprtstp: contraction number = 2.488647e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.207703e-05\n Vprtstp: contraction number = 6.229817e-01\n Vnewton: Using errtol_s: 223.978670\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.398547e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.245200e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.588671e+02\n Vprtstp: contraction number = 1.588671e+02\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.324425e-05\n Vprtstp: contraction number = 6.383669e-01\n Vnewton: Using errtol_s: 142.980568\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.552403e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.358126e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.030284e+02\n Vprtstp: contraction number = 1.030284e+02\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.155954e-05\n Vprtstp: contraction number = 6.485194e-01\n Vnewton: Using errtol_s: 92.725673\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.694820e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.476267e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.760657e+01\n Vprtstp: contraction number = 6.760657e+01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.414722e-05\n Vprtstp: contraction number = 6.561932e-01\n Vnewton: Using errtol_s: 60.845953\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.832803e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.586589e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.480217e+01\n Vprtstp: contraction number = 4.480217e+01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 9.375216e-06\n Vprtstp: contraction number = 6.626894e-01\n Vnewton: Using errtol_s: 40.321969\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.981721e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.701150e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.990735e+01\n Vprtstp: contraction number = 2.990735e+01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 6.258355e-06\n Vprtstp: contraction number = 6.675424e-01\n Vnewton: Using errtol_s: 26.916626\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.145919e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.814187e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.008505e+01\n Vprtstp: contraction number = 2.008505e+01\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 4.202958e-06\n Vprtstp: contraction number = 6.715755e-01\n Vnewton: Using errtol_s: 18.076547\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.285686e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.928589e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.356100e+01\n Vprtstp: contraction number = 1.356100e+01\n Vprtstp: iteration = 16\n Vprtstp: relative residual = 2.837748e-06\n Vprtstp: contraction number = 6.751787e-01\n Vnewton: Using errtol_s: 12.204901\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.434329e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.042258e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.198733e+00\n Vprtstp: contraction number = 9.198733e+00\n Vprtstp: iteration = 17\n Vprtstp: relative residual = 1.924909e-06\n Vprtstp: contraction number = 6.783227e-01\n Vnewton: Using errtol_s: 8.278861\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.597301e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.154350e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.265697e+00\n Vprtstp: contraction number = 6.265697e+00\n Vprtstp: iteration = 18\n Vprtstp: relative residual = 1.311147e-06\n Vprtstp: contraction number = 6.811478e-01\n Vnewton: Using errtol_s: 5.639128\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.747212e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.263803e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.284635e+00\n Vprtstp: contraction number = 4.284635e+00\n Vprtstp: iteration = 19\n Vprtstp: relative residual = 8.965941e-07\n Vprtstp: contraction number = 6.838241e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.827200e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.841361e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.329128e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.339853e+02\n Vpmg_setPart:  lower corner = (2.518, -2.4645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 16.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -9394,15 +9394,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.475399192616E+00 kT\n Vpmg_energy:  qfEnergy = 1.444578731292E+04 kT\n Vpmg_energy:  dielEnergy = 7.168962891577E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.426700e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.426900e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 39.7309\n Vpbe_ctor2:  solute dimensions = 68.682 x 69.075 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -9450,171 +9450,171 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.244357 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.147254\n+Vacc_SASA: Time elapsed: 2.968849\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.777573e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.538360e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 6.476300e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.280800e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.202674e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.976580e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.949627e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.440546e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 7151537.194828\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.976374e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.459722e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.220296e+05\n Vprtstp: contraction number = 7.220296e+05\n Vnewton: Attempting damping, relres = 0.092215\n Vnewton: Attempting damping, relres = 0.543248\n Vnewton: Damping accepted, relres = 0.092215\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.221458e-02\n Vprtstp: contraction number = 9.221458e-02\n Vnewton: Using errtol_s: 659475.973035\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.241923e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.647523e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.360213e+05\n Vprtstp: contraction number = 1.360213e+05\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.716437e-02\n Vprtstp: contraction number = 1.861351e-01\n Vnewton: Using errtol_s: 122751.620274\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.486649e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.816318e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.560242e+04\n Vprtstp: contraction number = 3.560242e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 4.482910e-03\n Vprtstp: contraction number = 2.611753e-01\n Vnewton: Using errtol_s: 32059.695083\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.740043e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.996916e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.131656e+04\n Vprtstp: contraction number = 1.131656e+04\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.424570e-03\n Vprtstp: contraction number = 3.177779e-01\n Vnewton: Using errtol_s: 10187.862459\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.951569e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.182365e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.913208e+03\n Vprtstp: contraction number = 3.913208e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.925362e-04\n Vprtstp: contraction number = 3.457439e-01\n Vnewton: Using errtol_s: 3522.390814\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.201553e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.369172e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.383064e+03\n Vprtstp: contraction number = 1.383064e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.740621e-04\n Vprtstp: contraction number = 3.533996e-01\n Vnewton: Using errtol_s: 1244.811552\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.445043e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.528692e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.895564e+02\n Vprtstp: contraction number = 4.895564e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 6.160970e-05\n Vprtstp: contraction number = 3.539524e-01\n Vnewton: Using errtol_s: 440.604077\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.717136e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.696975e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.817812e+02\n Vprtstp: contraction number = 1.817812e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.287666e-05\n Vprtstp: contraction number = 3.713159e-01\n Vnewton: Using errtol_s: 163.603290\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.968154e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.893297e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.297744e+01\n Vprtstp: contraction number = 7.297744e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 9.184003e-06\n Vprtstp: contraction number = 4.014573e-01\n Vnewton: Using errtol_s: 65.679739\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.221284e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.081697e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.147662e+01\n Vprtstp: contraction number = 3.147662e+01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.961242e-06\n Vprtstp: contraction number = 4.313197e-01\n Vnewton: Using errtol_s: 28.328967\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.465302e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.244101e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.429069e+01\n Vprtstp: contraction number = 1.429069e+01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 1.798442e-06\n Vprtstp: contraction number = 4.540096e-01\n Vnewton: Using errtol_s: 12.861624\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.724177e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.395236e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.773546e+00\n Vprtstp: contraction number = 6.773546e+00\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 8.524311e-07\n Vprtstp: contraction number = 4.739831e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 3.016509e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.030835e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.098364e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.109706e+02\n Vpmg_setPart:  lower corner = (2.518, -2.4645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 16.7425)\n Vpmg_setPart:  actual minima = (-8.26461, -11.2254, -41.2575)\n Vpmg_setPart:  actual maxima = (58.518, 43.0355, 27.9102)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -9623,15 +9623,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.623170000406E+00 kT\n Vpmg_energy:  qfEnergy = 1.125246141954E+05 kT\n Vpmg_energy:  dielEnergy = 5.603584772163E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.258300e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.029100e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -9654,272 +9654,272 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 2.750742\n+Vacc_SASA: Time elapsed: 2.877803\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.743959e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.706521e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.383100e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.114000e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.154359e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.074703e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.016782e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.589338e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4276578.139223\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.044606e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.610851e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.113974e+05\n Vprtstp: contraction number = 2.113974e+05\n Vnewton: Attempting damping, relres = 0.047573\n Vnewton: Attempting damping, relres = 0.515375\n Vnewton: Damping accepted, relres = 0.047573\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.757263e-02\n Vprtstp: contraction number = 4.757263e-02\n Vnewton: Using errtol_s: 203448.048803\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.247432e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.742080e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.589098e+04\n Vprtstp: contraction number = 4.589098e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 9.811582e-03\n Vprtstp: contraction number = 2.062443e-01\n Vnewton: Using errtol_s: 41959.996661\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.429602e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.880799e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.404662e+04\n Vprtstp: contraction number = 1.404662e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.960291e-03\n Vprtstp: contraction number = 3.017139e-01\n Vnewton: Using errtol_s: 12659.913691\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.604915e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.002590e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.279840e+03\n Vprtstp: contraction number = 5.279840e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.111524e-03\n Vprtstp: contraction number = 3.754781e-01\n Vnewton: Using errtol_s: 4753.520446\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.774421e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.122680e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.336921e+03\n Vprtstp: contraction number = 2.336921e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.918609e-04\n Vprtstp: contraction number = 4.425102e-01\n Vnewton: Using errtol_s: 2103.481419\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.946014e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.254421e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.194576e+03\n Vprtstp: contraction number = 1.194576e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.514070e-04\n Vprtstp: contraction number = 5.111344e-01\n Vnewton: Using errtol_s: 1075.161658\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.113034e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.370560e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.792983e+02\n Vprtstp: contraction number = 6.792983e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.429594e-04\n Vprtstp: contraction number = 5.686374e-01\n Vnewton: Using errtol_s: 611.377148\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.296735e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.488763e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.154648e+02\n Vprtstp: contraction number = 4.154648e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.743449e-05\n Vprtstp: contraction number = 6.116036e-01\n Vnewton: Using errtol_s: 373.920435\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.464419e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.607142e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.660684e+02\n Vprtstp: contraction number = 2.660684e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.599388e-05\n Vprtstp: contraction number = 6.404095e-01\n Vnewton: Using errtol_s: 239.462182\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.609489e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.721977e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.755593e+02\n Vprtstp: contraction number = 1.755593e+02\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.694626e-05\n Vprtstp: contraction number = 6.598268e-01\n Vnewton: Using errtol_s: 158.003576\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.770572e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.842978e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.183176e+02\n Vprtstp: contraction number = 1.183176e+02\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.489979e-05\n Vprtstp: contraction number = 6.739462e-01\n Vnewton: Using errtol_s: 106.485913\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.960715e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.975639e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.102710e+01\n Vprtstp: contraction number = 8.102710e+01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.705205e-05\n Vprtstp: contraction number = 6.848271e-01\n Vnewton: Using errtol_s: 72.924443\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.153767e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.077869e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.628393e+01\n Vprtstp: contraction number = 5.628393e+01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 1.184488e-05\n Vprtstp: contraction number = 6.946308e-01\n Vnewton: Using errtol_s: 50.655566\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.334943e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.191763e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.955755e+01\n Vprtstp: contraction number = 3.955755e+01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 8.324836e-06\n Vprtstp: contraction number = 7.028213e-01\n Vnewton: Using errtol_s: 35.601810\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.516682e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.311085e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.808103e+01\n Vprtstp: contraction number = 2.808103e+01\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 5.909617e-06\n Vprtstp: contraction number = 7.098779e-01\n Vnewton: Using errtol_s: 25.272937\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.693585e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.429479e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.010039e+01\n Vprtstp: contraction number = 2.010039e+01\n Vprtstp: iteration = 16\n Vprtstp: relative residual = 4.230100e-06\n Vprtstp: contraction number = 7.157995e-01\n Vnewton: Using errtol_s: 18.090355\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.882755e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.551035e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.449222e+01\n Vprtstp: contraction number = 1.449222e+01\n Vprtstp: iteration = 17\n Vprtstp: relative residual = 3.049867e-06\n Vprtstp: contraction number = 7.209918e-01\n Vnewton: Using errtol_s: 13.042997\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.072290e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.682625e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.051084e+01\n Vprtstp: contraction number = 1.051084e+01\n Vprtstp: iteration = 18\n Vprtstp: relative residual = 2.211992e-06\n Vprtstp: contraction number = 7.252749e-01\n Vnewton: Using errtol_s: 9.459758\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.216502e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.806440e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.663626e+00\n Vprtstp: contraction number = 7.663626e+00\n Vprtstp: iteration = 19\n Vprtstp: relative residual = 1.612800e-06\n Vprtstp: contraction number = 7.291164e-01\n Vnewton: Using errtol_s: 6.897264\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.369988e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.936344e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.612195e+00\n Vprtstp: contraction number = 5.612195e+00\n Vprtstp: iteration = 20\n Vprtstp: relative residual = 1.181079e-06\n Vprtstp: contraction number = 7.323158e-01\n Vnewton: Using errtol_s: 5.050976\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.527741e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.089115e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.124624e+00\n Vprtstp: contraction number = 4.124624e+00\n Vprtstp: iteration = 21\n Vprtstp: relative residual = 8.680215e-07\n Vprtstp: contraction number = 7.349396e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 3.634135e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.646426e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.609775e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.621520e+02\n Vpmg_setPart:  lower corner = (2.518, -2.4645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 16.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -9928,15 +9928,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 4.730884767842E-02 kT\n Vpmg_energy:  qfEnergy = 0.000000000000E+00 kT\n Vpmg_energy:  dielEnergy = 2.814808503921E-01 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.450600e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.176900e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -9984,160 +9984,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.000691975 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.128837\n+Vacc_SASA: Time elapsed: 2.656890\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.106435e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.523896e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.751700e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.104700e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.135674e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.002595e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.705692e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.249212e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 951047.684475\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.726361e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.269496e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.162547e+05\n Vprtstp: contraction number = 1.162547e+05\n Vnewton: Attempting damping, relres = 0.112161\n Vnewton: Attempting damping, relres = 0.552182\n Vnewton: Damping accepted, relres = 0.112161\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.121606e-01\n Vprtstp: contraction number = 1.121606e-01\n Vnewton: Using errtol_s: 106670.078940\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.892581e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.403057e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.126153e+04\n Vprtstp: contraction number = 2.126153e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.016407e-02\n Vprtstp: contraction number = 1.797785e-01\n Vnewton: Using errtol_s: 19176.991465\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.005453e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.524193e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.910429e+03\n Vprtstp: contraction number = 4.910429e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 4.647657e-03\n Vprtstp: contraction number = 2.304920e-01\n Vnewton: Using errtol_s: 4420.143642\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.022961e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.632702e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.327403e+03\n Vprtstp: contraction number = 1.327403e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.256188e-03\n Vprtstp: contraction number = 2.702841e-01\n Vnewton: Using errtol_s: 1194.694354\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.039941e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.760262e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.951603e+02\n Vprtstp: contraction number = 3.951603e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.739525e-04\n Vprtstp: contraction number = 2.976884e-01\n Vnewton: Using errtol_s: 355.646671\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.056894e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.877179e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.251397e+02\n Vprtstp: contraction number = 1.251397e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.184231e-04\n Vprtstp: contraction number = 3.166794e-01\n Vnewton: Using errtol_s: 112.625980\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.074838e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.989419e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.114263e+01\n Vprtstp: contraction number = 4.114263e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.893431e-05\n Vprtstp: contraction number = 3.287731e-01\n Vnewton: Using errtol_s: 37.028389\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.092078e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.101238e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.383573e+01\n Vprtstp: contraction number = 1.383573e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.309310e-05\n Vprtstp: contraction number = 3.362869e-01\n Vnewton: Using errtol_s: 12.452161\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.110103e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.218966e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.725230e+00\n Vprtstp: contraction number = 4.725230e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 4.471602e-06\n Vprtstp: contraction number = 3.415236e-01\n Vnewton: Using errtol_s: 4.252707\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.126309e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.331749e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.633794e+00\n Vprtstp: contraction number = 1.633794e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.546100e-06\n Vprtstp: contraction number = 3.457598e-01\n Vnewton: Using errtol_s: 1.470415\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.142297e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.447950e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.703633e-01\n Vprtstp: contraction number = 5.703633e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 5.397489e-07\n Vprtstp: contraction number = 3.491035e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.833263e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.846501e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.306034e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.318906e+02\n Vpmg_setPart:  lower corner = (2.518, -2.4645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 16.7425)\n Vpmg_setPart:  actual minima = (-8.26461, -11.2254, -41.2575)\n Vpmg_setPart:  actual maxima = (58.518, 43.0355, 27.9102)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -10146,15 +10146,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 5.677193160789E-02 kT\n Vpmg_energy:  qfEnergy = 0.000000000000E+00 kT\n Vpmg_energy:  dielEnergy = 2.890717240309E-01 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.491400e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.980500e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n@@ -10177,261 +10177,261 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 6.820348\n+Vacc_SASA: Time elapsed: 6.278918\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.071951e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.458886e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.671400e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.085000e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.169718e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.109154e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.163272e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.642520e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 8699406.430616\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.166008e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.663605e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.298565e+05\n Vprtstp: contraction number = 4.298565e+05\n Vnewton: Attempting damping, relres = 0.048079\n Vnewton: Attempting damping, relres = 0.515481\n Vnewton: Damping accepted, relres = 0.048079\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.807904e-02\n Vprtstp: contraction number = 4.807904e-02\n Vnewton: Using errtol_s: 418259.137179\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.185478e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.835584e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.275297e+04\n Vprtstp: contraction number = 9.275297e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 9.791706e-03\n Vprtstp: contraction number = 2.036585e-01\n Vnewton: Using errtol_s: 85182.030508\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.200035e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.976602e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.830324e+04\n Vprtstp: contraction number = 2.830324e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.931540e-03\n Vprtstp: contraction number = 2.993901e-01\n Vnewton: Using errtol_s: 25502.653903\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.216173e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.106674e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.066383e+04\n Vprtstp: contraction number = 1.066383e+04\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.103407e-03\n Vprtstp: contraction number = 3.763916e-01\n Vnewton: Using errtol_s: 9598.985602\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.235038e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.241407e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.725476e+03\n Vprtstp: contraction number = 4.725476e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.889004e-04\n Vprtstp: contraction number = 4.430826e-01\n Vnewton: Using errtol_s: 4253.143226\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.252659e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.374131e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.402868e+03\n Vprtstp: contraction number = 2.402868e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.485940e-04\n Vprtstp: contraction number = 5.084757e-01\n Vnewton: Using errtol_s: 2162.620089\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.269222e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.506338e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.352802e+03\n Vprtstp: contraction number = 1.352802e+03\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.399556e-04\n Vprtstp: contraction number = 5.629888e-01\n Vnewton: Using errtol_s: 1217.530795\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.285030e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.645829e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.164880e+02\n Vprtstp: contraction number = 8.164880e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.447037e-05\n Vprtstp: contraction number = 6.035512e-01\n Vnewton: Using errtol_s: 734.842122\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.299953e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.780939e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.157033e+02\n Vprtstp: contraction number = 5.157033e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.335238e-05\n Vprtstp: contraction number = 6.316106e-01\n Vnewton: Using errtol_s: 464.134076\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.315906e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.928074e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.352095e+02\n Vprtstp: contraction number = 3.352095e+02\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.467926e-05\n Vprtstp: contraction number = 6.500040e-01\n Vnewton: Using errtol_s: 301.688999\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.332294e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.005737e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.222234e+02\n Vprtstp: contraction number = 2.222234e+02\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.299022e-05\n Vprtstp: contraction number = 6.629387e-01\n Vnewton: Using errtol_s: 200.001301\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.350406e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.019051e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.495221e+02\n Vprtstp: contraction number = 1.495221e+02\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.546887e-05\n Vprtstp: contraction number = 6.728456e-01\n Vnewton: Using errtol_s: 134.569993\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.364099e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.032411e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.018836e+02\n Vprtstp: contraction number = 1.018836e+02\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 1.054041e-05\n Vprtstp: contraction number = 6.813949e-01\n Vnewton: Using errtol_s: 91.695311\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.377358e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.045492e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.012825e+01\n Vprtstp: contraction number = 7.012825e+01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 7.255144e-06\n Vprtstp: contraction number = 6.883171e-01\n Vnewton: Using errtol_s: 63.115450\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.393527e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.059689e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.869976e+01\n Vprtstp: contraction number = 4.869976e+01\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 5.038252e-06\n Vprtstp: contraction number = 6.944386e-01\n Vnewton: Using errtol_s: 43.829803\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.407478e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.073390e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.408035e+01\n Vprtstp: contraction number = 3.408035e+01\n Vprtstp: iteration = 16\n Vprtstp: relative residual = 3.525795e-06\n Vprtstp: contraction number = 6.998052e-01\n Vnewton: Using errtol_s: 30.672326\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.421350e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.086087e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.401453e+01\n Vprtstp: contraction number = 2.401453e+01\n Vprtstp: iteration = 17\n Vprtstp: relative residual = 2.484432e-06\n Vprtstp: contraction number = 7.046444e-01\n Vnewton: Using errtol_s: 21.613084\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.437684e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.099390e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.702723e+01\n Vprtstp: contraction number = 1.702723e+01\n Vprtstp: iteration = 18\n Vprtstp: relative residual = 1.761558e-06\n Vprtstp: contraction number = 7.090385e-01\n Vnewton: Using errtol_s: 15.324508\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.453945e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.112366e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.214065e+01\n Vprtstp: contraction number = 1.214065e+01\n Vprtstp: iteration = 19\n Vprtstp: relative residual = 1.256015e-06\n Vprtstp: contraction number = 7.130137e-01\n Vnewton: Using errtol_s: 10.926584\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.468728e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.125100e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.699962e+00\n Vprtstp: contraction number = 8.699962e+00\n Vprtstp: iteration = 20\n Vprtstp: relative residual = 9.000575e-07\n Vprtstp: contraction number = 7.165978e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 3.199805e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.212213e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.725605e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.737411e+02\n Vpmg_setPart:  lower corner = (2.518, -2.4645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 16.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -10440,15 +10440,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.633470349209E+00 kT\n Vpmg_energy:  qfEnergy = 1.444874244202E+04 kT\n Vpmg_energy:  dielEnergy = 7.168739971796E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.668200e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.359600e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n@@ -10496,171 +10496,171 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.23862 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 6.827271\n+Vacc_SASA: Time elapsed: 6.302504\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.714003e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.050043e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.608900e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.167200e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.143376e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.530550e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.493292e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.146019e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 8022421.271471\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.496047e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.148087e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.182694e+05\n Vprtstp: contraction number = 8.182694e+05\n Vnewton: Attempting damping, relres = 0.093297\n Vnewton: Attempting damping, relres = 0.543649\n Vnewton: Damping accepted, relres = 0.093297\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.329693e-02\n Vprtstp: contraction number = 9.329693e-02\n Vnewton: Using errtol_s: 748467.258105\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.518365e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.165914e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.535104e+05\n Vprtstp: contraction number = 1.535104e+05\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.727080e-02\n Vprtstp: contraction number = 1.851165e-01\n Vnewton: Using errtol_s: 138553.663149\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.535809e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.181982e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.960039e+04\n Vprtstp: contraction number = 3.960039e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 4.444863e-03\n Vprtstp: contraction number = 2.573628e-01\n Vnewton: Using errtol_s: 35658.564568\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.555795e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.197648e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.238461e+04\n Vprtstp: contraction number = 1.238461e+04\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.389740e-03\n Vprtstp: contraction number = 3.126620e-01\n Vnewton: Using errtol_s: 11149.079578\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.576560e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.214025e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.220923e+03\n Vprtstp: contraction number = 4.220923e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.735885e-04\n Vprtstp: contraction number = 3.407749e-01\n Vnewton: Using errtol_s: 3799.326730\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.597617e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.230946e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.473378e+03\n Vprtstp: contraction number = 1.473378e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.652984e-04\n Vprtstp: contraction number = 3.490339e-01\n Vnewton: Using errtol_s: 1326.093695\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.619459e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.246997e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.152403e+02\n Vprtstp: contraction number = 5.152403e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 5.780294e-05\n Vprtstp: contraction number = 3.496884e-01\n Vnewton: Using errtol_s: 463.719535\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.640079e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.262700e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.890344e+02\n Vprtstp: contraction number = 1.890344e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.120696e-05\n Vprtstp: contraction number = 3.668838e-01\n Vnewton: Using errtol_s: 170.131203\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.660222e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.278563e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.514797e+01\n Vprtstp: contraction number = 7.514797e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 8.430525e-06\n Vprtstp: contraction number = 3.975357e-01\n Vnewton: Using errtol_s: 67.633227\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.681589e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.294711e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.220080e+01\n Vprtstp: contraction number = 3.220080e+01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.612467e-06\n Vprtstp: contraction number = 4.284985e-01\n Vnewton: Using errtol_s: 28.980733\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.705164e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.311801e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.453992e+01\n Vprtstp: contraction number = 1.453992e+01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 1.631169e-06\n Vprtstp: contraction number = 4.515389e-01\n Vnewton: Using errtol_s: 13.085928\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.728709e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.328862e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.875948e+00\n Vprtstp: contraction number = 6.875948e+00\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 7.713824e-07\n Vprtstp: contraction number = 4.729015e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.567647e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.579889e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.007019e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.017231e+02\n Vpmg_setPart:  lower corner = (2.518, -2.4645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 16.7425)\n Vpmg_setPart:  actual minima = (-8.26461, -11.2254, -41.2575)\n Vpmg_setPart:  actual maxima = (58.518, 43.0355, 27.9102)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -10669,27 +10669,27 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.853787896122E+00 kT\n Vpmg_energy:  qfEnergy = 1.125276033199E+05 kT\n Vpmg_energy:  dielEnergy = 5.603543842121E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.196200e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.688200e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  printing only subset of domain\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.750662e+03\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.347273e+03\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 06:04:00 2025\n+# Creation Date and Time:  Tue Jan  9 03:54:48 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path mol1.pqr\n@@ -11042,250 +11042,250 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 2.933221\n+Vacc_SASA: Time elapsed: 2.887576\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.025533e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.929680e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.556500e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.094600e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.104604e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.072406e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.630070e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.448462e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4300910.832168\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.150187e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.310247e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.136321e+05\n Vprtstp: contraction number = 2.136321e+05\n Vnewton: Attempting damping, relres = 0.047663\n Vnewton: Attempting damping, relres = 0.515490\n Vnewton: Damping accepted, relres = 0.047663\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.766304e-02\n Vprtstp: contraction number = 4.766304e-02\n Vnewton: Using errtol_s: 204994.485638\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.769552e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.069279e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.587025e+04\n Vprtstp: contraction number = 4.587025e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 9.727679e-03\n Vprtstp: contraction number = 2.040927e-01\n Vnewton: Using errtol_s: 41837.880528\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.577929e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.291078e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.391016e+04\n Vprtstp: contraction number = 1.391016e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.912173e-03\n Vprtstp: contraction number = 2.993697e-01\n Vnewton: Using errtol_s: 12524.995351\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.405897e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.494317e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.237707e+03\n Vprtstp: contraction number = 5.237707e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.096054e-03\n Vprtstp: contraction number = 3.763697e-01\n Vnewton: Using errtol_s: 4714.028550\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.260642e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.797103e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.331453e+03\n Vprtstp: contraction number = 2.331453e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.878779e-04\n Vprtstp: contraction number = 4.451223e-01\n Vnewton: Using errtol_s: 2098.319320\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.954048e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.183624e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.189035e+03\n Vprtstp: contraction number = 1.189035e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.488161e-04\n Vprtstp: contraction number = 5.099966e-01\n Vnewton: Using errtol_s: 1070.135650\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.159727e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.406116e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.678182e+02\n Vprtstp: contraction number = 6.678182e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.397467e-04\n Vprtstp: contraction number = 5.616468e-01\n Vnewton: Using errtol_s: 601.038216\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.329350e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.589695e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.994733e+02\n Vprtstp: contraction number = 3.994733e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.359319e-05\n Vprtstp: contraction number = 5.981764e-01\n Vnewton: Using errtol_s: 359.526862\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.503738e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.075827e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.488647e+02\n Vprtstp: contraction number = 2.488647e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.207703e-05\n Vprtstp: contraction number = 6.229817e-01\n Vnewton: Using errtol_s: 223.978670\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.687769e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.189188e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.588671e+02\n Vprtstp: contraction number = 1.588671e+02\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.324425e-05\n Vprtstp: contraction number = 6.383669e-01\n Vnewton: Using errtol_s: 142.980568\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.869234e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.308387e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.030284e+02\n Vprtstp: contraction number = 1.030284e+02\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.155954e-05\n Vprtstp: contraction number = 6.485194e-01\n Vnewton: Using errtol_s: 92.725673\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.048450e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.427630e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.760657e+01\n Vprtstp: contraction number = 6.760657e+01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.414722e-05\n Vprtstp: contraction number = 6.561932e-01\n Vnewton: Using errtol_s: 60.845953\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.212742e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.553376e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.480217e+01\n Vprtstp: contraction number = 4.480217e+01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 9.375216e-06\n Vprtstp: contraction number = 6.626894e-01\n Vnewton: Using errtol_s: 40.321969\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.379167e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.689995e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.990735e+01\n Vprtstp: contraction number = 2.990735e+01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 6.258355e-06\n Vprtstp: contraction number = 6.675424e-01\n Vnewton: Using errtol_s: 26.916626\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.539708e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.802168e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.008505e+01\n Vprtstp: contraction number = 2.008505e+01\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 4.202958e-06\n Vprtstp: contraction number = 6.715755e-01\n Vnewton: Using errtol_s: 18.076547\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.704106e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.930011e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.356100e+01\n Vprtstp: contraction number = 1.356100e+01\n Vprtstp: iteration = 16\n Vprtstp: relative residual = 2.837748e-06\n Vprtstp: contraction number = 6.751787e-01\n Vnewton: Using errtol_s: 12.204901\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.878595e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.049705e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.198733e+00\n Vprtstp: contraction number = 9.198733e+00\n Vprtstp: iteration = 17\n Vprtstp: relative residual = 1.924909e-06\n Vprtstp: contraction number = 6.783227e-01\n Vnewton: Using errtol_s: 8.278861\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.065986e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.162465e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.265697e+00\n Vprtstp: contraction number = 6.265697e+00\n Vprtstp: iteration = 18\n Vprtstp: relative residual = 1.311147e-06\n Vprtstp: contraction number = 6.811478e-01\n Vnewton: Using errtol_s: 5.639128\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.243461e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.289109e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.284635e+00\n Vprtstp: contraction number = 4.284635e+00\n Vprtstp: iteration = 19\n Vprtstp: relative residual = 8.965941e-07\n Vprtstp: contraction number = 6.838241e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 3.342261e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.354818e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.341759e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.353914e+02\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, 16.7425)\n Vpmg_setPart:  upper corner = (2.518, -2.4645, 74.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -11294,15 +11294,15 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 8.108926489514E-02 kT\n Vpmg_energy:  qfEnergy = 2.835800313442E+02 kT\n Vpmg_energy:  dielEnergy = 1.215330905259E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.450000e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.489300e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 39.7309\n Vpbe_ctor2:  solute dimensions = 68.682 x 69.075 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -11350,160 +11350,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.001948 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.011559\n+Vacc_SASA: Time elapsed: 2.896420\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.052235e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.011873e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 6.056400e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.363500e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.161271e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.042420e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.454991e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.450069e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1613641.621006\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.482117e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.470236e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.672701e+05\n Vprtstp: contraction number = 1.672701e+05\n Vnewton: Attempting damping, relres = 0.093643\n Vnewton: Attempting damping, relres = 0.544180\n Vnewton: Damping accepted, relres = 0.093643\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.364296e-02\n Vprtstp: contraction number = 9.364296e-02\n Vnewton: Using errtol_s: 151106.180064\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.738488e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.645640e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.923422e+04\n Vprtstp: contraction number = 2.923422e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.630658e-02\n Vprtstp: contraction number = 1.741357e-01\n Vnewton: Using errtol_s: 26312.974291\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.982353e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.800624e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.609437e+03\n Vprtstp: contraction number = 6.609437e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 3.686501e-03\n Vprtstp: contraction number = 2.260744e-01\n Vnewton: Using errtol_s: 5948.690797\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.221661e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.960277e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.798444e+03\n Vprtstp: contraction number = 1.798444e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.003087e-03\n Vprtstp: contraction number = 2.720974e-01\n Vnewton: Using errtol_s: 1618.623129\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.415420e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.138989e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.516770e+02\n Vprtstp: contraction number = 5.516770e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.076965e-04\n Vprtstp: contraction number = 3.067495e-01\n Vnewton: Using errtol_s: 496.511822\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.617254e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.302429e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.808462e+02\n Vprtstp: contraction number = 1.808462e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.008662e-04\n Vprtstp: contraction number = 3.278106e-01\n Vnewton: Using errtol_s: 162.761828\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.796895e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.473668e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.118139e+01\n Vprtstp: contraction number = 6.118139e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.412361e-05\n Vprtstp: contraction number = 3.383059e-01\n Vnewton: Using errtol_s: 55.063279\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.992092e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.630194e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.100954e+01\n Vprtstp: contraction number = 2.100954e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.171796e-05\n Vprtstp: contraction number = 3.433974e-01\n Vnewton: Using errtol_s: 18.908586\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.186137e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.800069e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.287024e+00\n Vprtstp: contraction number = 7.287024e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 4.064299e-06\n Vprtstp: contraction number = 3.468436e-01\n Vnewton: Using errtol_s: 6.558322\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.372521e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.965948e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.550680e+00\n Vprtstp: contraction number = 2.550680e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.422628e-06\n Vprtstp: contraction number = 3.500304e-01\n Vnewton: Using errtol_s: 2.295612\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.564167e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.129068e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.008406e-01\n Vprtstp: contraction number = 9.008406e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 5.024390e-07\n Vprtstp: contraction number = 3.531767e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.272329e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.287098e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.827926e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.840392e+02\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, 16.7425)\n Vpmg_setPart:  upper corner = (2.518, -2.4645, 74.7425)\n Vpmg_setPart:  actual minima = (-53.482, -47.9645, 5.5748)\n Vpmg_setPart:  actual maxima = (13.3006, 6.29637, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -11512,17 +11512,17 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 8.604850020008E-02 kT\n Vpmg_energy:  qfEnergy = 2.451766100693E+03 kT\n Vpmg_energy:  dielEnergy = 1.154345982163E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.767300e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.427900e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -11543,272 +11543,272 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.201931\n+Vacc_SASA: Time elapsed: 2.904477\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.140372e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.817846e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.795200e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.461700e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.128344e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.909870e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.781731e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.328812e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4276578.139223\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.809232e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.349198e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.113974e+05\n Vprtstp: contraction number = 2.113974e+05\n Vnewton: Attempting damping, relres = 0.047573\n Vnewton: Attempting damping, relres = 0.515375\n Vnewton: Damping accepted, relres = 0.047573\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.757263e-02\n Vprtstp: contraction number = 4.757263e-02\n Vnewton: Using errtol_s: 203448.048803\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.956525e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.484782e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.589098e+04\n Vprtstp: contraction number = 4.589098e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 9.811582e-03\n Vprtstp: contraction number = 2.062443e-01\n Vnewton: Using errtol_s: 41959.996661\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.083272e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.604449e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.404662e+04\n Vprtstp: contraction number = 1.404662e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.960291e-03\n Vprtstp: contraction number = 3.017139e-01\n Vnewton: Using errtol_s: 12659.913691\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.210587e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.724955e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.279840e+03\n Vprtstp: contraction number = 5.279840e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.111524e-03\n Vprtstp: contraction number = 3.754781e-01\n Vnewton: Using errtol_s: 4753.520446\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.369394e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.842398e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.336921e+03\n Vprtstp: contraction number = 2.336921e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.918609e-04\n Vprtstp: contraction number = 4.425102e-01\n Vnewton: Using errtol_s: 2103.481419\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.501070e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.958411e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.194576e+03\n Vprtstp: contraction number = 1.194576e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.514070e-04\n Vprtstp: contraction number = 5.111344e-01\n Vnewton: Using errtol_s: 1075.161658\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.640969e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.073202e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.792983e+02\n Vprtstp: contraction number = 6.792983e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.429594e-04\n Vprtstp: contraction number = 5.686374e-01\n Vnewton: Using errtol_s: 611.377148\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.788300e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.190860e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.154648e+02\n Vprtstp: contraction number = 4.154648e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.743449e-05\n Vprtstp: contraction number = 6.116036e-01\n Vnewton: Using errtol_s: 373.920435\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.929525e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.325319e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.660684e+02\n Vprtstp: contraction number = 2.660684e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.599388e-05\n Vprtstp: contraction number = 6.404095e-01\n Vnewton: Using errtol_s: 239.462182\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.069427e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.443364e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.755593e+02\n Vprtstp: contraction number = 1.755593e+02\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.694626e-05\n Vprtstp: contraction number = 6.598268e-01\n Vnewton: Using errtol_s: 158.003576\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.212657e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.562712e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.183176e+02\n Vprtstp: contraction number = 1.183176e+02\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.489979e-05\n Vprtstp: contraction number = 6.739462e-01\n Vnewton: Using errtol_s: 106.485913\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.356811e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.680581e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.102710e+01\n Vprtstp: contraction number = 8.102710e+01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.705205e-05\n Vprtstp: contraction number = 6.848271e-01\n Vnewton: Using errtol_s: 72.924443\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.501234e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.791092e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.628393e+01\n Vprtstp: contraction number = 5.628393e+01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 1.184488e-05\n Vprtstp: contraction number = 6.946308e-01\n Vnewton: Using errtol_s: 50.655566\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.644392e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.908365e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.955755e+01\n Vprtstp: contraction number = 3.955755e+01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 8.324836e-06\n Vprtstp: contraction number = 7.028213e-01\n Vnewton: Using errtol_s: 35.601810\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.781992e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.020814e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.808103e+01\n Vprtstp: contraction number = 2.808103e+01\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 5.909617e-06\n Vprtstp: contraction number = 7.098779e-01\n Vnewton: Using errtol_s: 25.272937\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.925635e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.138328e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.010039e+01\n Vprtstp: contraction number = 2.010039e+01\n Vprtstp: iteration = 16\n Vprtstp: relative residual = 4.230100e-06\n Vprtstp: contraction number = 7.157995e-01\n Vnewton: Using errtol_s: 18.090355\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.066506e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.254558e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.449222e+01\n Vprtstp: contraction number = 1.449222e+01\n Vprtstp: iteration = 17\n Vprtstp: relative residual = 3.049867e-06\n Vprtstp: contraction number = 7.209918e-01\n Vnewton: Using errtol_s: 13.042997\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.205050e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.367815e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.051084e+01\n Vprtstp: contraction number = 1.051084e+01\n Vprtstp: iteration = 18\n Vprtstp: relative residual = 2.211992e-06\n Vprtstp: contraction number = 7.252749e-01\n Vnewton: Using errtol_s: 9.459758\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.344175e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.489021e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.663626e+00\n Vprtstp: contraction number = 7.663626e+00\n Vprtstp: iteration = 19\n Vprtstp: relative residual = 1.612800e-06\n Vprtstp: contraction number = 7.291164e-01\n Vnewton: Using errtol_s: 6.897264\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.485239e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.606594e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.612195e+00\n Vprtstp: contraction number = 5.612195e+00\n Vprtstp: iteration = 20\n Vprtstp: relative residual = 1.181079e-06\n Vprtstp: contraction number = 7.323158e-01\n Vnewton: Using errtol_s: 5.050976\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.626965e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.730786e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.124624e+00\n Vprtstp: contraction number = 4.124624e+00\n Vprtstp: iteration = 21\n Vprtstp: relative residual = 8.680215e-07\n Vprtstp: contraction number = 7.349396e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.986895e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.999045e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.514306e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.525160e+02\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, 16.7425)\n Vpmg_setPart:  upper corner = (2.518, -2.4645, 74.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -11817,15 +11817,15 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.931678298316E+00 kT\n Vpmg_energy:  qfEnergy = 1.306896751937E+04 kT\n Vpmg_energy:  dielEnergy = 6.531231404824E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.024700e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.301200e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -11873,193 +11873,193 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.211097 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.126777\n+Vacc_SASA: Time elapsed: 2.909249\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.715177e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.478161e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.579700e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.190300e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.249519e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.012233e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.830300e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.900568e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 6738070.309592\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.853844e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.922249e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.878637e+05\n Vprtstp: contraction number = 6.878637e+05\n Vnewton: Attempting damping, relres = 0.093216\n Vnewton: Attempting damping, relres = 0.543864\n Vnewton: Damping accepted, relres = 0.093216\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.321581e-02\n Vprtstp: contraction number = 9.321581e-02\n Vnewton: Using errtol_s: 628094.651911\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.065225e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.108317e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.296036e+05\n Vprtstp: contraction number = 1.296036e+05\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.735879e-02\n Vprtstp: contraction number = 1.862215e-01\n Vnewton: Using errtol_s: 116964.740632\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.266415e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.268682e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.402622e+04\n Vprtstp: contraction number = 3.402622e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 4.547490e-03\n Vprtstp: contraction number = 2.619705e-01\n Vnewton: Using errtol_s: 30641.306038\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.445820e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.434537e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.090470e+04\n Vprtstp: contraction number = 1.090470e+04\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.456938e-03\n Vprtstp: contraction number = 3.203829e-01\n Vnewton: Using errtol_s: 9816.950613\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.620628e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.604381e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.894978e+03\n Vprtstp: contraction number = 3.894978e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.203198e-04\n Vprtstp: contraction number = 3.571324e-01\n Vnewton: Using errtol_s: 3505.951173\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.806680e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.763245e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.485775e+03\n Vprtstp: contraction number = 1.485775e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.984627e-04\n Vprtstp: contraction number = 3.814246e-01\n Vnewton: Using errtol_s: 1337.255961\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.989711e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.922660e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.014858e+02\n Vprtstp: contraction number = 6.014858e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 8.034105e-05\n Vprtstp: contraction number = 4.048168e-01\n Vnewton: Using errtol_s: 541.343626\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.018886e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.078468e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.638957e+02\n Vprtstp: contraction number = 2.638957e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 3.524853e-05\n Vprtstp: contraction number = 4.387363e-01\n Vnewton: Using errtol_s: 237.507104\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.036571e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.235156e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.262556e+02\n Vprtstp: contraction number = 1.262556e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 1.686391e-05\n Vprtstp: contraction number = 4.784287e-01\n Vnewton: Using errtol_s: 113.630225\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.054553e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.399789e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.580661e+01\n Vprtstp: contraction number = 6.580661e+01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 8.789758e-06\n Vprtstp: contraction number = 5.212170e-01\n Vnewton: Using errtol_s: 59.226009\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.075975e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.573600e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.615710e+01\n Vprtstp: contraction number = 3.615710e+01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 4.829486e-06\n Vprtstp: contraction number = 5.494446e-01\n Vnewton: Using errtol_s: 32.541413\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.095819e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.733397e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.063008e+01\n Vprtstp: contraction number = 2.063008e+01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 2.755549e-06\n Vprtstp: contraction number = 5.705677e-01\n Vnewton: Using errtol_s: 18.567080\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.113182e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.896309e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.211023e+01\n Vprtstp: contraction number = 1.211023e+01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 1.617557e-06\n Vprtstp: contraction number = 5.870182e-01\n Vnewton: Using errtol_s: 10.899214\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.131371e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.083323e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.261707e+00\n Vprtstp: contraction number = 7.261707e+00\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 9.699420e-07\n Vprtstp: contraction number = 5.996338e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.667184e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.680931e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.329540e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.340373e+02\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, 16.7425)\n Vpmg_setPart:  upper corner = (2.518, -2.4645, 74.7425)\n Vpmg_setPart:  actual minima = (-53.482, -47.9645, 5.5748)\n Vpmg_setPart:  actual maxima = (13.3006, 6.29637, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -12068,15 +12068,15 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.021244083579E+00 kT\n Vpmg_energy:  qfEnergy = 1.026826573171E+05 kT\n Vpmg_energy:  dielEnergy = 5.129339951363E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.156500e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.374200e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n@@ -12099,261 +12099,261 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 7.144800\n+Vacc_SASA: Time elapsed: 6.379459\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.375222e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.533162e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 6.067600e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.318800e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.069817e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.030180e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.159422e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.317969e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 8699406.430616\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.161589e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.336694e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.298565e+05\n Vprtstp: contraction number = 4.298565e+05\n Vnewton: Attempting damping, relres = 0.048079\n Vnewton: Attempting damping, relres = 0.515481\n Vnewton: Damping accepted, relres = 0.048079\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.807904e-02\n Vprtstp: contraction number = 4.807904e-02\n Vnewton: Using errtol_s: 418259.137179\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.180524e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.482730e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.275297e+04\n Vprtstp: contraction number = 9.275297e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 9.791706e-03\n Vprtstp: contraction number = 2.036585e-01\n Vnewton: Using errtol_s: 85182.030508\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.196796e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.613554e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.830324e+04\n Vprtstp: contraction number = 2.830324e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.931540e-03\n Vprtstp: contraction number = 2.993901e-01\n Vnewton: Using errtol_s: 25502.653903\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.214485e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.746274e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.066383e+04\n Vprtstp: contraction number = 1.066383e+04\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.103407e-03\n Vprtstp: contraction number = 3.763916e-01\n Vnewton: Using errtol_s: 9598.985602\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.230741e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.875304e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.725476e+03\n Vprtstp: contraction number = 4.725476e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.889004e-04\n Vprtstp: contraction number = 4.430826e-01\n Vnewton: Using errtol_s: 4253.143226\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.249082e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.000966e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.402868e+03\n Vprtstp: contraction number = 2.402868e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.485940e-04\n Vprtstp: contraction number = 5.084757e-01\n Vnewton: Using errtol_s: 2162.620089\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.266968e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.014749e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.352802e+03\n Vprtstp: contraction number = 1.352802e+03\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.399556e-04\n Vprtstp: contraction number = 5.629888e-01\n Vnewton: Using errtol_s: 1217.530795\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.282622e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.027833e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.164880e+02\n Vprtstp: contraction number = 8.164880e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.447037e-05\n Vprtstp: contraction number = 6.035512e-01\n Vnewton: Using errtol_s: 734.842122\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.298802e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.041218e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.157033e+02\n Vprtstp: contraction number = 5.157033e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.335238e-05\n Vprtstp: contraction number = 6.316106e-01\n Vnewton: Using errtol_s: 464.134076\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.315048e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.054922e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.352095e+02\n Vprtstp: contraction number = 3.352095e+02\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.467926e-05\n Vprtstp: contraction number = 6.500040e-01\n Vnewton: Using errtol_s: 301.688999\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.333202e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.067712e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.222234e+02\n Vprtstp: contraction number = 2.222234e+02\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.299022e-05\n Vprtstp: contraction number = 6.629387e-01\n Vnewton: Using errtol_s: 200.001301\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.348460e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.080940e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.495221e+02\n Vprtstp: contraction number = 1.495221e+02\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.546887e-05\n Vprtstp: contraction number = 6.728456e-01\n Vnewton: Using errtol_s: 134.569993\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.363058e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.094381e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.018836e+02\n Vprtstp: contraction number = 1.018836e+02\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 1.054041e-05\n Vprtstp: contraction number = 6.813949e-01\n Vnewton: Using errtol_s: 91.695311\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.381042e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.106991e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.012825e+01\n Vprtstp: contraction number = 7.012825e+01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 7.255144e-06\n Vprtstp: contraction number = 6.883171e-01\n Vnewton: Using errtol_s: 63.115450\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.398727e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.119926e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.869976e+01\n Vprtstp: contraction number = 4.869976e+01\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 5.038252e-06\n Vprtstp: contraction number = 6.944386e-01\n Vnewton: Using errtol_s: 43.829803\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.416539e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.133477e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.408035e+01\n Vprtstp: contraction number = 3.408035e+01\n Vprtstp: iteration = 16\n Vprtstp: relative residual = 3.525795e-06\n Vprtstp: contraction number = 6.998052e-01\n Vnewton: Using errtol_s: 30.672326\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.430326e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.146912e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.401453e+01\n Vprtstp: contraction number = 2.401453e+01\n Vprtstp: iteration = 17\n Vprtstp: relative residual = 2.484432e-06\n Vprtstp: contraction number = 7.046444e-01\n Vnewton: Using errtol_s: 21.613084\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.447653e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.159690e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.702723e+01\n Vprtstp: contraction number = 1.702723e+01\n Vprtstp: iteration = 18\n Vprtstp: relative residual = 1.761558e-06\n Vprtstp: contraction number = 7.090385e-01\n Vnewton: Using errtol_s: 15.324508\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.465505e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.173521e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.214065e+01\n Vprtstp: contraction number = 1.214065e+01\n Vprtstp: iteration = 19\n Vprtstp: relative residual = 1.256015e-06\n Vprtstp: contraction number = 7.130137e-01\n Vnewton: Using errtol_s: 10.926584\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.481937e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.186983e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.699962e+00\n Vprtstp: contraction number = 8.699962e+00\n Vprtstp: iteration = 20\n Vprtstp: relative residual = 9.000575e-07\n Vprtstp: contraction number = 7.165978e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 3.389028e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.400795e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.677144e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.688079e+02\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, 16.7425)\n Vpmg_setPart:  upper corner = (2.518, -2.4645, 74.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -12362,15 +12362,15 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.165566732606E+00 kT\n Vpmg_energy:  qfEnergy = 1.340422491969E+04 kT\n Vpmg_energy:  dielEnergy = 6.679021613149E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.676400e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.090900e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n@@ -12418,193 +12418,193 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.211587 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 6.868675\n+Vacc_SASA: Time elapsed: 6.220255\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.819004e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.101759e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.012000e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.216600e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.128847e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.058143e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.508394e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.208838e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 8285587.408912\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.510808e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.210873e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.439767e+05\n Vprtstp: contraction number = 8.439767e+05\n Vnewton: Attempting damping, relres = 0.093056\n Vnewton: Attempting damping, relres = 0.543707\n Vnewton: Damping accepted, relres = 0.093056\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.305605e-02\n Vprtstp: contraction number = 9.305605e-02\n Vnewton: Using errtol_s: 771024.060477\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.529580e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.228927e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.575262e+05\n Vprtstp: contraction number = 1.575262e+05\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.715846e-02\n Vprtstp: contraction number = 1.843885e-01\n Vnewton: Using errtol_s: 142167.953902\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.549719e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.244951e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.047316e+04\n Vprtstp: contraction number = 4.047316e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 4.398299e-03\n Vprtstp: contraction number = 2.563341e-01\n Vnewton: Using errtol_s: 36442.493025\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.571011e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.260857e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.265955e+04\n Vprtstp: contraction number = 1.265955e+04\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.375423e-03\n Vprtstp: contraction number = 3.127169e-01\n Vnewton: Using errtol_s: 11396.183497\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.591220e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.276285e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.418878e+03\n Vprtstp: contraction number = 4.418878e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.800426e-04\n Vprtstp: contraction number = 3.490147e-01\n Vnewton: Using errtol_s: 3977.435333\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.611321e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.292381e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.644482e+03\n Vprtstp: contraction number = 1.644482e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.786343e-04\n Vprtstp: contraction number = 3.721217e-01\n Vnewton: Using errtol_s: 1480.089823\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.632837e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.309153e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.478261e+02\n Vprtstp: contraction number = 6.478261e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 7.036914e-05\n Vprtstp: contraction number = 3.939286e-01\n Vnewton: Using errtol_s: 583.049663\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.651146e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.325252e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.772344e+02\n Vprtstp: contraction number = 2.772344e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 3.011396e-05\n Vprtstp: contraction number = 4.279428e-01\n Vnewton: Using errtol_s: 249.511882\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.667708e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.341317e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.301479e+02\n Vprtstp: contraction number = 1.301479e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 1.413700e-05\n Vprtstp: contraction number = 4.694500e-01\n Vnewton: Using errtol_s: 117.133345\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.688180e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.357765e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.695205e+01\n Vprtstp: contraction number = 6.695205e+01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 7.272497e-06\n Vprtstp: contraction number = 5.144300e-01\n Vnewton: Using errtol_s: 60.256908\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.707680e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.373758e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.650946e+01\n Vprtstp: contraction number = 3.650946e+01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.965746e-06\n Vprtstp: contraction number = 5.453073e-01\n Vnewton: Using errtol_s: 32.858531\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.725254e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.390301e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.073747e+01\n Vprtstp: contraction number = 2.073747e+01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 2.252553e-06\n Vprtstp: contraction number = 5.680025e-01\n Vnewton: Using errtol_s: 18.663727\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.745411e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.405755e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.213300e+01\n Vprtstp: contraction number = 1.213300e+01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 1.317915e-06\n Vprtstp: contraction number = 5.850760e-01\n Vnewton: Using errtol_s: 10.919699\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.763736e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.421688e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.261261e+00\n Vprtstp: contraction number = 7.261261e+00\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 7.887354e-07\n Vprtstp: contraction number = 5.984722e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.726949e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.739129e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.277253e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.288944e+02\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, 16.7425)\n Vpmg_setPart:  upper corner = (2.518, -2.4645, 74.7425)\n Vpmg_setPart:  actual minima = (-53.482, -47.9645, 5.5748)\n Vpmg_setPart:  actual maxima = (13.3006, 6.29637, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -12613,27 +12613,27 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.328637769519E+00 kT\n Vpmg_energy:  qfEnergy = 1.051514241768E+05 kT\n Vpmg_energy:  dielEnergy = 5.245601958271E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.510300e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 9.348400e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  printing only subset of domain\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.781756e+03\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.437273e+03\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 06:08:18 2025\n+# Creation Date and Time:  Tue Jan  9 03:59:19 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path mol1.pqr\n@@ -12986,250 +12986,250 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.240567\n+Vacc_SASA: Time elapsed: 2.914526\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.181405e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.785260e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 7.025400e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.113800e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.119987e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.918050e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.826030e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.214103e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4300910.832168\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.587772e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.998254e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.136321e+05\n Vprtstp: contraction number = 2.136321e+05\n Vnewton: Attempting damping, relres = 0.047663\n Vnewton: Attempting damping, relres = 0.515490\n Vnewton: Damping accepted, relres = 0.047663\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.766304e-02\n Vprtstp: contraction number = 4.766304e-02\n Vnewton: Using errtol_s: 204994.485638\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.626491e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.104752e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.587025e+04\n Vprtstp: contraction number = 4.587025e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 9.727679e-03\n Vprtstp: contraction number = 2.040927e-01\n Vnewton: Using errtol_s: 41837.880528\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.314712e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.429157e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.391016e+04\n Vprtstp: contraction number = 1.391016e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.912173e-03\n Vprtstp: contraction number = 2.993697e-01\n Vnewton: Using errtol_s: 12524.995351\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.777542e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.686427e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.237707e+03\n Vprtstp: contraction number = 5.237707e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.096054e-03\n Vprtstp: contraction number = 3.763697e-01\n Vnewton: Using errtol_s: 4714.028550\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.239079e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.908129e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.331453e+03\n Vprtstp: contraction number = 2.331453e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.878779e-04\n Vprtstp: contraction number = 4.451223e-01\n Vnewton: Using errtol_s: 2098.319320\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.715384e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.096487e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.189035e+03\n Vprtstp: contraction number = 1.189035e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.488161e-04\n Vprtstp: contraction number = 5.099966e-01\n Vnewton: Using errtol_s: 1070.135650\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.033647e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.297748e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.678182e+02\n Vprtstp: contraction number = 6.678182e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.397467e-04\n Vprtstp: contraction number = 5.616468e-01\n Vnewton: Using errtol_s: 601.038216\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.185526e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.477464e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.994733e+02\n Vprtstp: contraction number = 3.994733e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.359319e-05\n Vprtstp: contraction number = 5.981764e-01\n Vnewton: Using errtol_s: 359.526862\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.331622e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.063898e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.488647e+02\n Vprtstp: contraction number = 2.488647e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.207703e-05\n Vprtstp: contraction number = 6.229817e-01\n Vnewton: Using errtol_s: 223.978670\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.463079e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.191945e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.588671e+02\n Vprtstp: contraction number = 1.588671e+02\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.324425e-05\n Vprtstp: contraction number = 6.383669e-01\n Vnewton: Using errtol_s: 142.980568\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.621762e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.317186e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.030284e+02\n Vprtstp: contraction number = 1.030284e+02\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.155954e-05\n Vprtstp: contraction number = 6.485194e-01\n Vnewton: Using errtol_s: 92.725673\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.772664e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.437770e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.760657e+01\n Vprtstp: contraction number = 6.760657e+01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.414722e-05\n Vprtstp: contraction number = 6.561932e-01\n Vnewton: Using errtol_s: 60.845953\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.935125e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.558554e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.480217e+01\n Vprtstp: contraction number = 4.480217e+01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 9.375216e-06\n Vprtstp: contraction number = 6.626894e-01\n Vnewton: Using errtol_s: 40.321969\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.103072e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.683044e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.990735e+01\n Vprtstp: contraction number = 2.990735e+01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 6.258355e-06\n Vprtstp: contraction number = 6.675424e-01\n Vnewton: Using errtol_s: 26.916626\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.280030e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.801745e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.008505e+01\n Vprtstp: contraction number = 2.008505e+01\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 4.202958e-06\n Vprtstp: contraction number = 6.715755e-01\n Vnewton: Using errtol_s: 18.076547\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.438467e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.918007e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.356100e+01\n Vprtstp: contraction number = 1.356100e+01\n Vprtstp: iteration = 16\n Vprtstp: relative residual = 2.837748e-06\n Vprtstp: contraction number = 6.751787e-01\n Vnewton: Using errtol_s: 12.204901\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.580686e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.036373e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.198733e+00\n Vprtstp: contraction number = 9.198733e+00\n Vprtstp: iteration = 17\n Vprtstp: relative residual = 1.924909e-06\n Vprtstp: contraction number = 6.783227e-01\n Vnewton: Using errtol_s: 8.278861\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.715597e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.150372e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.265697e+00\n Vprtstp: contraction number = 6.265697e+00\n Vprtstp: iteration = 18\n Vprtstp: relative residual = 1.311147e-06\n Vprtstp: contraction number = 6.811478e-01\n Vnewton: Using errtol_s: 5.639128\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.847568e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.266290e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.284635e+00\n Vprtstp: contraction number = 4.284635e+00\n Vprtstp: iteration = 19\n Vprtstp: relative residual = 8.965941e-07\n Vprtstp: contraction number = 6.838241e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.906172e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.919033e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.325386e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.336632e+02\n Vpmg_setPart:  lower corner = (2.518, -47.9645, 16.7425)\n Vpmg_setPart:  upper corner = (58.518, -2.4645, 74.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -13238,17 +13238,17 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.135373636445E-01 kT\n Vpmg_energy:  qfEnergy = 1.691003222948E+03 kT\n Vpmg_energy:  dielEnergy = 8.436188542984E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.253500e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.676400e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 39.7309\n Vpbe_ctor2:  solute dimensions = 68.682 x 69.075 x 70.346\n Vpbe_ctor2:  solute charge = -12\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -13294,160 +13294,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00329728 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.237207\n+Vacc_SASA: Time elapsed: 2.807774\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.514717e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.094159e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.952500e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.128200e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.103434e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.068068e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.023116e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.431726e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2672785.067134\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.045433e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.449762e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.848718e+05\n Vprtstp: contraction number = 2.848718e+05\n Vnewton: Attempting damping, relres = 0.096187\n Vnewton: Attempting damping, relres = 0.545650\n Vnewton: Damping accepted, relres = 0.096187\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.618699e-02\n Vprtstp: contraction number = 9.618699e-02\n Vnewton: Using errtol_s: 257087.160547\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.263118e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.617608e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.201088e+04\n Vprtstp: contraction number = 5.201088e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.751490e-02\n Vprtstp: contraction number = 1.820922e-01\n Vnewton: Using errtol_s: 46813.558642\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.461296e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.782844e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.230808e+04\n Vprtstp: contraction number = 1.230808e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 4.144590e-03\n Vprtstp: contraction number = 2.366322e-01\n Vnewton: Using errtol_s: 11077.597147\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.658731e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.949308e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.460119e+03\n Vprtstp: contraction number = 3.460119e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.165151e-03\n Vprtstp: contraction number = 2.811258e-01\n Vnewton: Using errtol_s: 3114.198540\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.866939e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.110630e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.085640e+03\n Vprtstp: contraction number = 1.085640e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.655733e-04\n Vprtstp: contraction number = 3.137561e-01\n Vnewton: Using errtol_s: 977.098856\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.099172e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.276275e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.609545e+02\n Vprtstp: contraction number = 3.609545e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.215452e-04\n Vprtstp: contraction number = 3.324784e-01\n Vnewton: Using errtol_s: 324.864231\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.267935e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.426137e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.235133e+02\n Vprtstp: contraction number = 1.235133e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.159074e-05\n Vprtstp: contraction number = 3.421833e-01\n Vnewton: Using errtol_s: 111.163117\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.445767e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.586832e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.301270e+01\n Vprtstp: contraction number = 4.301270e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.448364e-05\n Vprtstp: contraction number = 3.482419e-01\n Vnewton: Using errtol_s: 38.711660\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.639722e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.755840e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.517421e+01\n Vprtstp: contraction number = 1.517421e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.109589e-06\n Vprtstp: contraction number = 3.527835e-01\n Vnewton: Using errtol_s: 13.656834\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.823263e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.917773e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.423218e+00\n Vprtstp: contraction number = 5.423218e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.826149e-06\n Vprtstp: contraction number = 3.573964e-01\n Vnewton: Using errtol_s: 4.880904\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.012240e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.090254e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.968727e+00\n Vprtstp: contraction number = 1.968727e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 6.629250e-07\n Vprtstp: contraction number = 3.630180e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.152349e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.165396e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.811475e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.824122e+02\n Vpmg_setPart:  lower corner = (2.518, -47.9645, 16.7425)\n Vpmg_setPart:  upper corner = (58.518, -2.4645, 74.7425)\n Vpmg_setPart:  actual minima = (-8.26461, -47.9645, 5.5748)\n Vpmg_setPart:  actual maxima = (58.518, 6.29637, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -13456,15 +13456,15 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.950394306049E-01 kT\n Vpmg_energy:  qfEnergy = 1.339241623976E+04 kT\n Vpmg_energy:  dielEnergy = 6.685521460249E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.057800e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.217600e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -13487,272 +13487,272 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.082353\n+Vacc_SASA: Time elapsed: 2.918334\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.081073e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.725966e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.212200e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.390400e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.125417e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.028096e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.229422e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.293536e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4276578.139223\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.250844e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.313804e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.113974e+05\n Vprtstp: contraction number = 2.113974e+05\n Vnewton: Attempting damping, relres = 0.047573\n Vnewton: Attempting damping, relres = 0.515375\n Vnewton: Damping accepted, relres = 0.047573\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.757263e-02\n Vprtstp: contraction number = 4.757263e-02\n Vnewton: Using errtol_s: 203448.048803\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.408548e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.450155e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.589098e+04\n Vprtstp: contraction number = 4.589098e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 9.811582e-03\n Vprtstp: contraction number = 2.062443e-01\n Vnewton: Using errtol_s: 41959.996661\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.550201e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.568521e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.404662e+04\n Vprtstp: contraction number = 1.404662e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.960291e-03\n Vprtstp: contraction number = 3.017139e-01\n Vnewton: Using errtol_s: 12659.913691\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.700062e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.682963e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.279840e+03\n Vprtstp: contraction number = 5.279840e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.111524e-03\n Vprtstp: contraction number = 3.754781e-01\n Vnewton: Using errtol_s: 4753.520446\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.840007e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.791683e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.336921e+03\n Vprtstp: contraction number = 2.336921e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.918609e-04\n Vprtstp: contraction number = 4.425102e-01\n Vnewton: Using errtol_s: 2103.481419\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.991636e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.903775e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.194576e+03\n Vprtstp: contraction number = 1.194576e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.514070e-04\n Vprtstp: contraction number = 5.111344e-01\n Vnewton: Using errtol_s: 1075.161658\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.142787e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.025252e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.792983e+02\n Vprtstp: contraction number = 6.792983e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.429594e-04\n Vprtstp: contraction number = 5.686374e-01\n Vnewton: Using errtol_s: 611.377148\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.281256e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.141455e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.154648e+02\n Vprtstp: contraction number = 4.154648e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.743449e-05\n Vprtstp: contraction number = 6.116036e-01\n Vnewton: Using errtol_s: 373.920435\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.426752e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.264578e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.660684e+02\n Vprtstp: contraction number = 2.660684e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.599388e-05\n Vprtstp: contraction number = 6.404095e-01\n Vnewton: Using errtol_s: 239.462182\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.578783e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.380210e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.755593e+02\n Vprtstp: contraction number = 1.755593e+02\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.694626e-05\n Vprtstp: contraction number = 6.598268e-01\n Vnewton: Using errtol_s: 158.003576\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.715672e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.501300e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.183176e+02\n Vprtstp: contraction number = 1.183176e+02\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.489979e-05\n Vprtstp: contraction number = 6.739462e-01\n Vnewton: Using errtol_s: 106.485913\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.854864e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.620271e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.102710e+01\n Vprtstp: contraction number = 8.102710e+01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.705205e-05\n Vprtstp: contraction number = 6.848271e-01\n Vnewton: Using errtol_s: 72.924443\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.991422e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.737596e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.628393e+01\n Vprtstp: contraction number = 5.628393e+01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 1.184488e-05\n Vprtstp: contraction number = 6.946308e-01\n Vnewton: Using errtol_s: 50.655566\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.140904e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.854288e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.955755e+01\n Vprtstp: contraction number = 3.955755e+01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 8.324836e-06\n Vprtstp: contraction number = 7.028213e-01\n Vnewton: Using errtol_s: 35.601810\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.291256e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.990428e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.808103e+01\n Vprtstp: contraction number = 2.808103e+01\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 5.909617e-06\n Vprtstp: contraction number = 7.098779e-01\n Vnewton: Using errtol_s: 25.272937\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.446700e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.107868e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.010039e+01\n Vprtstp: contraction number = 2.010039e+01\n Vprtstp: iteration = 16\n Vprtstp: relative residual = 4.230100e-06\n Vprtstp: contraction number = 7.157995e-01\n Vnewton: Using errtol_s: 18.090355\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.577356e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.228394e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.449222e+01\n Vprtstp: contraction number = 1.449222e+01\n Vprtstp: iteration = 17\n Vprtstp: relative residual = 3.049867e-06\n Vprtstp: contraction number = 7.209918e-01\n Vnewton: Using errtol_s: 13.042997\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.731822e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.342526e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.051084e+01\n Vprtstp: contraction number = 1.051084e+01\n Vprtstp: iteration = 18\n Vprtstp: relative residual = 2.211992e-06\n Vprtstp: contraction number = 7.252749e-01\n Vnewton: Using errtol_s: 9.459758\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.911748e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.457880e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.663626e+00\n Vprtstp: contraction number = 7.663626e+00\n Vprtstp: iteration = 19\n Vprtstp: relative residual = 1.612800e-06\n Vprtstp: contraction number = 7.291164e-01\n Vnewton: Using errtol_s: 6.897264\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.086112e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.588266e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.612195e+00\n Vprtstp: contraction number = 5.612195e+00\n Vprtstp: iteration = 20\n Vprtstp: relative residual = 1.181079e-06\n Vprtstp: contraction number = 7.323158e-01\n Vnewton: Using errtol_s: 5.050976\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.228119e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.704646e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.124624e+00\n Vprtstp: contraction number = 4.124624e+00\n Vprtstp: iteration = 21\n Vprtstp: relative residual = 8.680215e-07\n Vprtstp: contraction number = 7.349396e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 3.131155e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.143599e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.519317e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.531030e+02\n Vpmg_setPart:  lower corner = (2.518, -47.9645, 16.7425)\n Vpmg_setPart:  upper corner = (58.518, -2.4645, 74.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -13761,17 +13761,17 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.295996694910E-02 kT\n Vpmg_energy:  qfEnergy = 0.000000000000E+00 kT\n Vpmg_energy:  dielEnergy = 1.633599871123E-01 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.858400e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.206600e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -13817,149 +13817,149 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00296493 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.282361\n+Vacc_SASA: Time elapsed: 2.891096\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.177142e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.773690e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.419000e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.240600e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.151156e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.997150e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.416920e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.864945e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1184087.054280\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.444075e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.884787e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.354114e+05\n Vprtstp: contraction number = 1.354114e+05\n Vnewton: Attempting damping, relres = 0.103158\n Vnewton: Attempting damping, relres = 0.548288\n Vnewton: Damping accepted, relres = 0.103158\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.031582e-01\n Vprtstp: contraction number = 1.031582e-01\n Vnewton: Using errtol_s: 122148.348169\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.626101e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.005839e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.326538e+04\n Vprtstp: contraction number = 2.326538e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.769124e-02\n Vprtstp: contraction number = 1.714961e-01\n Vnewton: Using errtol_s: 20947.970777\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.789618e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.136893e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.939304e+03\n Vprtstp: contraction number = 4.939304e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 3.754561e-03\n Vprtstp: contraction number = 2.122271e-01\n Vnewton: Using errtol_s: 4445.727289\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.959714e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.245980e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.225369e+03\n Vprtstp: contraction number = 1.225369e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 9.313919e-04\n Vprtstp: contraction number = 2.480695e-01\n Vnewton: Using errtol_s: 1102.849143\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.128392e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.353192e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.425596e+02\n Vprtstp: contraction number = 3.425596e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 2.603732e-04\n Vprtstp: contraction number = 2.795528e-01\n Vnewton: Using errtol_s: 308.304585\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.309066e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.461311e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.033702e+02\n Vprtstp: contraction number = 1.033702e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 7.856958e-05\n Vprtstp: contraction number = 3.017575e-01\n Vnewton: Using errtol_s: 93.033224\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.490640e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.569050e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.261191e+01\n Vprtstp: contraction number = 3.261191e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.478764e-05\n Vprtstp: contraction number = 3.154865e-01\n Vnewton: Using errtol_s: 29.350728\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.659759e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.673827e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.060426e+01\n Vprtstp: contraction number = 1.060426e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.060077e-06\n Vprtstp: contraction number = 3.251651e-01\n Vnewton: Using errtol_s: 9.543833\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.824972e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.784887e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.527652e+00\n Vprtstp: contraction number = 3.527652e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.681295e-06\n Vprtstp: contraction number = 3.326637e-01\n Vnewton: Using errtol_s: 3.174887\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.954642e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.896935e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.192253e+00\n Vprtstp: contraction number = 1.192253e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 9.062069e-07\n Vprtstp: contraction number = 3.379736e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.672148e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.685595e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.148021e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.160469e+02\n Vpmg_setPart:  lower corner = (2.518, -47.9645, 16.7425)\n Vpmg_setPart:  upper corner = (58.518, -2.4645, 74.7425)\n Vpmg_setPart:  actual minima = (-8.26461, -47.9645, 5.5748)\n Vpmg_setPart:  actual maxima = (58.518, 6.29637, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -13968,17 +13968,17 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.599961867885E-02 kT\n Vpmg_energy:  qfEnergy = 0.000000000000E+00 kT\n Vpmg_energy:  dielEnergy = 1.358968211460E-01 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 9.281100e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.426000e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -13999,261 +13999,261 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 6.743055\n+Vacc_SASA: Time elapsed: 6.241198\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.955127e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.408961e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.385400e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.398000e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.501948e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.007505e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.018679e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.099304e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 8699406.430616\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.021824e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.120930e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.298565e+05\n Vprtstp: contraction number = 4.298565e+05\n Vnewton: Attempting damping, relres = 0.048079\n Vnewton: Attempting damping, relres = 0.515481\n Vnewton: Damping accepted, relres = 0.048079\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.807904e-02\n Vprtstp: contraction number = 4.807904e-02\n Vnewton: Using errtol_s: 418259.137179\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.045596e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.278190e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.275297e+04\n Vprtstp: contraction number = 9.275297e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 9.791706e-03\n Vprtstp: contraction number = 2.036585e-01\n Vnewton: Using errtol_s: 85182.030508\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.067175e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.432982e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.830324e+04\n Vprtstp: contraction number = 2.830324e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.931540e-03\n Vprtstp: contraction number = 2.993901e-01\n Vnewton: Using errtol_s: 25502.653903\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.089549e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.571632e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.066383e+04\n Vprtstp: contraction number = 1.066383e+04\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.103407e-03\n Vprtstp: contraction number = 3.763916e-01\n Vnewton: Using errtol_s: 9598.985602\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.111028e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.697214e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.725476e+03\n Vprtstp: contraction number = 4.725476e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.889004e-04\n Vprtstp: contraction number = 4.430826e-01\n Vnewton: Using errtol_s: 4253.143226\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.132426e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.824501e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.402868e+03\n Vprtstp: contraction number = 2.402868e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.485940e-04\n Vprtstp: contraction number = 5.084757e-01\n Vnewton: Using errtol_s: 2162.620089\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.151602e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.955727e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.352802e+03\n Vprtstp: contraction number = 1.352802e+03\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.399556e-04\n Vprtstp: contraction number = 5.629888e-01\n Vnewton: Using errtol_s: 1217.530795\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.170499e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.082059e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.164880e+02\n Vprtstp: contraction number = 8.164880e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.447037e-05\n Vprtstp: contraction number = 6.035512e-01\n Vnewton: Using errtol_s: 734.842122\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.192464e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.209633e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.157033e+02\n Vprtstp: contraction number = 5.157033e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.335238e-05\n Vprtstp: contraction number = 6.316106e-01\n Vnewton: Using errtol_s: 464.134076\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.213958e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.344733e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.352095e+02\n Vprtstp: contraction number = 3.352095e+02\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.467926e-05\n Vprtstp: contraction number = 6.500040e-01\n Vnewton: Using errtol_s: 301.688999\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.229775e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.468809e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.222234e+02\n Vprtstp: contraction number = 2.222234e+02\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.299022e-05\n Vprtstp: contraction number = 6.629387e-01\n Vnewton: Using errtol_s: 200.001301\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.245887e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.601060e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.495221e+02\n Vprtstp: contraction number = 1.495221e+02\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.546887e-05\n Vprtstp: contraction number = 6.728456e-01\n Vnewton: Using errtol_s: 134.569993\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.266416e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.733049e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.018836e+02\n Vprtstp: contraction number = 1.018836e+02\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 1.054041e-05\n Vprtstp: contraction number = 6.813949e-01\n Vnewton: Using errtol_s: 91.695311\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.282371e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.864247e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.012825e+01\n Vprtstp: contraction number = 7.012825e+01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 7.255144e-06\n Vprtstp: contraction number = 6.883171e-01\n Vnewton: Using errtol_s: 63.115450\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.296929e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.996735e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.869976e+01\n Vprtstp: contraction number = 4.869976e+01\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 5.038252e-06\n Vprtstp: contraction number = 6.944386e-01\n Vnewton: Using errtol_s: 43.829803\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.311781e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.012747e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.408035e+01\n Vprtstp: contraction number = 3.408035e+01\n Vprtstp: iteration = 16\n Vprtstp: relative residual = 3.525795e-06\n Vprtstp: contraction number = 6.998052e-01\n Vnewton: Using errtol_s: 30.672326\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.331385e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.027758e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.401453e+01\n Vprtstp: contraction number = 2.401453e+01\n Vprtstp: iteration = 17\n Vprtstp: relative residual = 2.484432e-06\n Vprtstp: contraction number = 7.046444e-01\n Vnewton: Using errtol_s: 21.613084\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.349365e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.043694e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.702723e+01\n Vprtstp: contraction number = 1.702723e+01\n Vprtstp: iteration = 18\n Vprtstp: relative residual = 1.761558e-06\n Vprtstp: contraction number = 7.090385e-01\n Vnewton: Using errtol_s: 15.324508\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.365952e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.059823e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.214065e+01\n Vprtstp: contraction number = 1.214065e+01\n Vprtstp: iteration = 19\n Vprtstp: relative residual = 1.256015e-06\n Vprtstp: contraction number = 7.130137e-01\n Vnewton: Using errtol_s: 10.926584\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.384594e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.074592e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.699962e+00\n Vprtstp: contraction number = 8.699962e+00\n Vprtstp: iteration = 20\n Vprtstp: relative residual = 9.000575e-07\n Vprtstp: contraction number = 7.165978e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 3.827996e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.843973e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.776345e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.787164e+02\n Vpmg_setPart:  lower corner = (2.518, -47.9645, 16.7425)\n Vpmg_setPart:  upper corner = (58.518, -2.4645, 74.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -14262,15 +14262,15 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.987808702613E-01 kT\n Vpmg_energy:  qfEnergy = 1.699917781088E+03 kT\n Vpmg_energy:  dielEnergy = 8.464002723965E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.817200e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.179000e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n@@ -14318,160 +14318,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0125918 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 6.435985\n+Vacc_SASA: Time elapsed: 6.371584\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.000062e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.803677e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.397300e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.334100e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.129035e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.975970e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.410857e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.096584e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 3745818.555400\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.413372e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.098592e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.036148e+05\n Vprtstp: contraction number = 4.036148e+05\n Vnewton: Attempting damping, relres = 0.097470\n Vnewton: Attempting damping, relres = 0.545903\n Vnewton: Damping accepted, relres = 0.097470\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.746961e-02\n Vprtstp: contraction number = 9.746961e-02\n Vnewton: Using errtol_s: 365103.476411\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.438008e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.117375e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.291408e+04\n Vprtstp: contraction number = 7.291408e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.752435e-02\n Vprtstp: contraction number = 1.797929e-01\n Vnewton: Using errtol_s: 65643.018240\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.461591e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.133451e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.675888e+04\n Vprtstp: contraction number = 1.675888e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 4.026892e-03\n Vprtstp: contraction number = 2.297884e-01\n Vnewton: Using errtol_s: 15084.007144\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.485872e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.149568e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.533188e+03\n Vprtstp: contraction number = 4.533188e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.089215e-03\n Vprtstp: contraction number = 2.704853e-01\n Vnewton: Using errtol_s: 4080.002297\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.509219e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.165048e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.369611e+03\n Vprtstp: contraction number = 1.369611e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.290808e-04\n Vprtstp: contraction number = 3.021265e-01\n Vnewton: Using errtol_s: 1232.676861\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.528892e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.182449e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.398009e+02\n Vprtstp: contraction number = 4.398009e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.056716e-04\n Vprtstp: contraction number = 3.211115e-01\n Vnewton: Using errtol_s: 395.826722\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.549298e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.198106e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.460593e+02\n Vprtstp: contraction number = 1.460593e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.509370e-05\n Vprtstp: contraction number = 3.321014e-01\n Vnewton: Using errtol_s: 131.454614\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.574262e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.214620e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.960244e+01\n Vprtstp: contraction number = 4.960244e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.191794e-05\n Vprtstp: contraction number = 3.396035e-01\n Vnewton: Using errtol_s: 44.642449\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.599546e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.231307e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.713194e+01\n Vprtstp: contraction number = 1.713194e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 4.116267e-06\n Vprtstp: contraction number = 3.453841e-01\n Vnewton: Using errtol_s: 15.418791\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.625107e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.247254e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.017264e+00\n Vprtstp: contraction number = 6.017264e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.445758e-06\n Vprtstp: contraction number = 3.512303e-01\n Vnewton: Using errtol_s: 5.415546\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.648254e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.262713e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.154066e+00\n Vprtstp: contraction number = 2.154066e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 5.175534e-07\n Vprtstp: contraction number = 3.579807e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.555922e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.567947e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.823244e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.834231e+02\n Vpmg_setPart:  lower corner = (2.518, -47.9645, 16.7425)\n Vpmg_setPart:  upper corner = (58.518, -2.4645, 74.7425)\n Vpmg_setPart:  actual minima = (-8.26461, -47.9645, 5.5748)\n Vpmg_setPart:  actual maxima = (58.518, 6.29637, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -14480,27 +14480,27 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 3.620792182088E-01 kT\n Vpmg_energy:  qfEnergy = 1.339466431031E+04 kT\n Vpmg_energy:  dielEnergy = 6.686807644409E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.296900e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.318300e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  printing only subset of domain\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.667109e+03\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.279461e+03\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 06:11:59 2025\n+# Creation Date and Time:  Tue Jan  9 04:03:30 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path mol1.pqr\n@@ -14853,250 +14853,250 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.169920\n+Vacc_SASA: Time elapsed: 2.899746\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.222114e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.915152e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 6.173700e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.250000e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.004271e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.175058e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.681147e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.526231e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4300910.832168\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.580842e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.893403e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.136321e+05\n Vprtstp: contraction number = 2.136321e+05\n Vnewton: Attempting damping, relres = 0.047663\n Vnewton: Attempting damping, relres = 0.515490\n Vnewton: Damping accepted, relres = 0.047663\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.766304e-02\n Vprtstp: contraction number = 4.766304e-02\n Vnewton: Using errtol_s: 204994.485638\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.559124e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.233538e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.587025e+04\n Vprtstp: contraction number = 4.587025e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 9.727679e-03\n Vprtstp: contraction number = 2.040927e-01\n Vnewton: Using errtol_s: 41837.880528\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.598157e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.386271e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.391016e+04\n Vprtstp: contraction number = 1.391016e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.912173e-03\n Vprtstp: contraction number = 2.993697e-01\n Vnewton: Using errtol_s: 12524.995351\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.259934e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.486427e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.237707e+03\n Vprtstp: contraction number = 5.237707e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.096054e-03\n Vprtstp: contraction number = 3.763697e-01\n Vnewton: Using errtol_s: 4714.028550\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.817873e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.604780e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.331453e+03\n Vprtstp: contraction number = 2.331453e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.878779e-04\n Vprtstp: contraction number = 4.451223e-01\n Vnewton: Using errtol_s: 2098.319320\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.474496e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.863225e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.189035e+03\n Vprtstp: contraction number = 1.189035e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.488161e-04\n Vprtstp: contraction number = 5.099966e-01\n Vnewton: Using errtol_s: 1070.135650\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.131470e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.017267e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.678182e+02\n Vprtstp: contraction number = 6.678182e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.397467e-04\n Vprtstp: contraction number = 5.616468e-01\n Vnewton: Using errtol_s: 601.038216\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.301617e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.195469e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.994733e+02\n Vprtstp: contraction number = 3.994733e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.359319e-05\n Vprtstp: contraction number = 5.981764e-01\n Vnewton: Using errtol_s: 359.526862\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.470353e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.051479e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.488647e+02\n Vprtstp: contraction number = 2.488647e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.207703e-05\n Vprtstp: contraction number = 6.229817e-01\n Vnewton: Using errtol_s: 223.978670\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.644953e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.169834e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.588671e+02\n Vprtstp: contraction number = 1.588671e+02\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.324425e-05\n Vprtstp: contraction number = 6.383669e-01\n Vnewton: Using errtol_s: 142.980568\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.822498e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.296452e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.030284e+02\n Vprtstp: contraction number = 1.030284e+02\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.155954e-05\n Vprtstp: contraction number = 6.485194e-01\n Vnewton: Using errtol_s: 92.725673\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.996510e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.413420e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.760657e+01\n Vprtstp: contraction number = 6.760657e+01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.414722e-05\n Vprtstp: contraction number = 6.561932e-01\n Vnewton: Using errtol_s: 60.845953\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.190191e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.526435e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.480217e+01\n Vprtstp: contraction number = 4.480217e+01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 9.375216e-06\n Vprtstp: contraction number = 6.626894e-01\n Vnewton: Using errtol_s: 40.321969\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.388838e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.642273e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.990735e+01\n Vprtstp: contraction number = 2.990735e+01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 6.258355e-06\n Vprtstp: contraction number = 6.675424e-01\n Vnewton: Using errtol_s: 26.916626\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.578783e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.763376e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.008505e+01\n Vprtstp: contraction number = 2.008505e+01\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 4.202958e-06\n Vprtstp: contraction number = 6.715755e-01\n Vnewton: Using errtol_s: 18.076547\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.781616e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.885762e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.356100e+01\n Vprtstp: contraction number = 1.356100e+01\n Vprtstp: iteration = 16\n Vprtstp: relative residual = 2.837748e-06\n Vprtstp: contraction number = 6.751787e-01\n Vnewton: Using errtol_s: 12.204901\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.988018e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.009071e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.198733e+00\n Vprtstp: contraction number = 9.198733e+00\n Vprtstp: iteration = 17\n Vprtstp: relative residual = 1.924909e-06\n Vprtstp: contraction number = 6.783227e-01\n Vnewton: Using errtol_s: 8.278861\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.185395e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.129432e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.265697e+00\n Vprtstp: contraction number = 6.265697e+00\n Vprtstp: iteration = 18\n Vprtstp: relative residual = 1.311147e-06\n Vprtstp: contraction number = 6.811478e-01\n Vnewton: Using errtol_s: 5.639128\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.382167e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.248634e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.284635e+00\n Vprtstp: contraction number = 4.284635e+00\n Vprtstp: iteration = 19\n Vprtstp: relative residual = 8.965941e-07\n Vprtstp: contraction number = 6.838241e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 3.500494e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.512296e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.298915e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.312048e+02\n Vpmg_setPart:  lower corner = (-53.482, -2.4645, 16.7425)\n Vpmg_setPart:  upper corner = (2.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -15105,17 +15105,17 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 7.410514495807E-03 kT\n Vpmg_energy:  qfEnergy = 0.000000000000E+00 kT\n Vpmg_energy:  dielEnergy = 1.129100557647E+00 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.416600e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.841900e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 4.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 39.7309\n Vpbe_ctor2:  solute dimensions = 68.682 x 69.075 x 70.346\n Vpbe_ctor2:  solute charge = -12\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -15161,160 +15161,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.000190853 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 2.920557\n+Vacc_SASA: Time elapsed: 3.005916\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.775708e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.916325e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.536100e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.206400e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.244667e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.051628e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.611441e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.408154e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1032634.725607\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.636601e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.428638e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.090058e+05\n Vprtstp: contraction number = 1.090058e+05\n Vnewton: Attempting damping, relres = 0.095383\n Vnewton: Attempting damping, relres = 0.544753\n Vnewton: Damping accepted, relres = 0.095383\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.538325e-02\n Vprtstp: contraction number = 9.538325e-02\n Vnewton: Using errtol_s: 98496.056858\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.879550e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.577637e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.829312e+04\n Vprtstp: contraction number = 1.829312e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.595089e-02\n Vprtstp: contraction number = 1.672295e-01\n Vnewton: Using errtol_s: 16471.442714\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.072341e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.715317e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.867524e+03\n Vprtstp: contraction number = 3.867524e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 3.370960e-03\n Vprtstp: contraction number = 2.113337e-01\n Vnewton: Using errtol_s: 3480.970171\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.271720e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.845191e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.812010e+02\n Vprtstp: contraction number = 9.812010e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 8.551815e-04\n Vprtstp: contraction number = 2.536908e-01\n Vnewton: Using errtol_s: 883.090100\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.463928e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.975440e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.836594e+02\n Vprtstp: contraction number = 2.836594e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 2.472259e-04\n Vprtstp: contraction number = 2.890917e-01\n Vnewton: Using errtol_s: 255.294034\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.662920e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.106509e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.927772e+01\n Vprtstp: contraction number = 8.927772e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 7.781068e-05\n Vprtstp: contraction number = 3.147352e-01\n Vnewton: Using errtol_s: 80.350015\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.866079e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.229742e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.937189e+01\n Vprtstp: contraction number = 2.937189e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.559929e-05\n Vprtstp: contraction number = 3.289945e-01\n Vnewton: Using errtol_s: 26.434712\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.071396e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.358346e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.890447e+00\n Vprtstp: contraction number = 9.890447e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.620089e-06\n Vprtstp: contraction number = 3.367316e-01\n Vnewton: Using errtol_s: 8.901403\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.267499e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.488059e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.377400e+00\n Vprtstp: contraction number = 3.377400e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.943597e-06\n Vprtstp: contraction number = 3.414810e-01\n Vnewton: Using errtol_s: 3.039660\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.467320e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.612662e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.164729e+00\n Vprtstp: contraction number = 1.164729e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.015127e-06\n Vprtstp: contraction number = 3.448595e-01\n Vnewton: Using errtol_s: 1.048256\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.625475e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.738971e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.047354e-01\n Vprtstp: contraction number = 4.047354e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.527500e-07\n Vprtstp: contraction number = 3.474933e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.180482e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.196252e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.456506e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.470327e+02\n Vpmg_setPart:  lower corner = (-53.482, -2.4645, 16.7425)\n Vpmg_setPart:  upper corner = (2.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-53.482, -11.2254, 5.5748)\n Vpmg_setPart:  actual maxima = (13.3006, 43.0355, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -15323,15 +15323,15 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 6.262250874476E-03 kT\n Vpmg_energy:  qfEnergy = 0.000000000000E+00 kT\n Vpmg_energy:  dielEnergy = 7.842003689004E-01 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.782100e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.268700e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -15354,272 +15354,272 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.064804\n+Vacc_SASA: Time elapsed: 2.970586\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.069769e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.792726e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.593500e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.433800e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.162192e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.999470e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.846270e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.914631e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4276578.139223\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.870537e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.937115e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.113974e+05\n Vprtstp: contraction number = 2.113974e+05\n Vnewton: Attempting damping, relres = 0.047573\n Vnewton: Attempting damping, relres = 0.515375\n Vnewton: Damping accepted, relres = 0.047573\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.757263e-02\n Vprtstp: contraction number = 4.757263e-02\n Vnewton: Using errtol_s: 203448.048803\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.058551e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.077213e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.589098e+04\n Vprtstp: contraction number = 4.589098e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 9.811582e-03\n Vprtstp: contraction number = 2.062443e-01\n Vnewton: Using errtol_s: 41959.996661\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.216868e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.227686e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.404662e+04\n Vprtstp: contraction number = 1.404662e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.960291e-03\n Vprtstp: contraction number = 3.017139e-01\n Vnewton: Using errtol_s: 12659.913691\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.374479e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.345348e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.279840e+03\n Vprtstp: contraction number = 5.279840e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.111524e-03\n Vprtstp: contraction number = 3.754781e-01\n Vnewton: Using errtol_s: 4753.520446\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.522118e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.454546e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.336921e+03\n Vprtstp: contraction number = 2.336921e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.918609e-04\n Vprtstp: contraction number = 4.425102e-01\n Vnewton: Using errtol_s: 2103.481419\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.663681e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.569452e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.194576e+03\n Vprtstp: contraction number = 1.194576e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.514070e-04\n Vprtstp: contraction number = 5.111344e-01\n Vnewton: Using errtol_s: 1075.161658\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.814135e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.710423e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.792983e+02\n Vprtstp: contraction number = 6.792983e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.429594e-04\n Vprtstp: contraction number = 5.686374e-01\n Vnewton: Using errtol_s: 611.377148\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.970201e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.829370e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.154648e+02\n Vprtstp: contraction number = 4.154648e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.743449e-05\n Vprtstp: contraction number = 6.116036e-01\n Vnewton: Using errtol_s: 373.920435\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.131750e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.947330e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.660684e+02\n Vprtstp: contraction number = 2.660684e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.599388e-05\n Vprtstp: contraction number = 6.404095e-01\n Vnewton: Using errtol_s: 239.462182\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.290781e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.064287e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.755593e+02\n Vprtstp: contraction number = 1.755593e+02\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.694626e-05\n Vprtstp: contraction number = 6.598268e-01\n Vnewton: Using errtol_s: 158.003576\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.465212e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.205516e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.183176e+02\n Vprtstp: contraction number = 1.183176e+02\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.489979e-05\n Vprtstp: contraction number = 6.739462e-01\n Vnewton: Using errtol_s: 106.485913\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.641580e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.353653e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.102710e+01\n Vprtstp: contraction number = 8.102710e+01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.705205e-05\n Vprtstp: contraction number = 6.848271e-01\n Vnewton: Using errtol_s: 72.924443\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.824532e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.466768e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.628393e+01\n Vprtstp: contraction number = 5.628393e+01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 1.184488e-05\n Vprtstp: contraction number = 6.946308e-01\n Vnewton: Using errtol_s: 50.655566\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.001886e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.580380e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.955755e+01\n Vprtstp: contraction number = 3.955755e+01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 8.324836e-06\n Vprtstp: contraction number = 7.028213e-01\n Vnewton: Using errtol_s: 35.601810\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.192563e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.699097e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.808103e+01\n Vprtstp: contraction number = 2.808103e+01\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 5.909617e-06\n Vprtstp: contraction number = 7.098779e-01\n Vnewton: Using errtol_s: 25.272937\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.369057e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.805582e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.010039e+01\n Vprtstp: contraction number = 2.010039e+01\n Vprtstp: iteration = 16\n Vprtstp: relative residual = 4.230100e-06\n Vprtstp: contraction number = 7.157995e-01\n Vnewton: Using errtol_s: 18.090355\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.517358e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.941628e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.449222e+01\n Vprtstp: contraction number = 1.449222e+01\n Vprtstp: iteration = 17\n Vprtstp: relative residual = 3.049867e-06\n Vprtstp: contraction number = 7.209918e-01\n Vnewton: Using errtol_s: 13.042997\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.662447e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.058962e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.051084e+01\n Vprtstp: contraction number = 1.051084e+01\n Vprtstp: iteration = 18\n Vprtstp: relative residual = 2.211992e-06\n Vprtstp: contraction number = 7.252749e-01\n Vnewton: Using errtol_s: 9.459758\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.824901e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.176917e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.663626e+00\n Vprtstp: contraction number = 7.663626e+00\n Vprtstp: iteration = 19\n Vprtstp: relative residual = 1.612800e-06\n Vprtstp: contraction number = 7.291164e-01\n Vnewton: Using errtol_s: 6.897264\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.978015e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.306429e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.612195e+00\n Vprtstp: contraction number = 5.612195e+00\n Vprtstp: iteration = 20\n Vprtstp: relative residual = 1.181079e-06\n Vprtstp: contraction number = 7.323158e-01\n Vnewton: Using errtol_s: 5.050976\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.141367e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.426361e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.124624e+00\n Vprtstp: contraction number = 4.124624e+00\n Vprtstp: iteration = 21\n Vprtstp: relative residual = 8.680215e-07\n Vprtstp: contraction number = 7.349396e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 3.447175e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.460166e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.625724e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.636951e+02\n Vpmg_setPart:  lower corner = (-53.482, -2.4645, 16.7425)\n Vpmg_setPart:  upper corner = (2.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -15628,15 +15628,15 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.028844380467E+00 kT\n Vpmg_energy:  qfEnergy = 9.611210700866E+03 kT\n Vpmg_energy:  dielEnergy = 4.863079386675E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.690800e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.325400e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -15684,171 +15684,171 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0377574 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 2.941526\n+Vacc_SASA: Time elapsed: 2.846617\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.474940e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.404050e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.571600e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.099500e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.045920e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.829220e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.350689e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.596342e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 6079198.405761\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.371684e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.616403e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.898758e+05\n Vprtstp: contraction number = 5.898758e+05\n Vnewton: Attempting damping, relres = 0.088148\n Vnewton: Attempting damping, relres = 0.541560\n Vnewton: Damping accepted, relres = 0.088148\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.814828e-02\n Vprtstp: contraction number = 8.814828e-02\n Vnewton: Using errtol_s: 535870.896065\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.593187e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.811950e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.077049e+05\n Vprtstp: contraction number = 1.077049e+05\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.598309e-02\n Vprtstp: contraction number = 1.813205e-01\n Vnewton: Using errtol_s: 97164.364787\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.828269e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.999012e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.746148e+04\n Vprtstp: contraction number = 2.746148e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 4.065921e-03\n Vprtstp: contraction number = 2.543889e-01\n Vnewton: Using errtol_s: 24717.539236\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.008141e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.153811e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.490060e+03\n Vprtstp: contraction number = 8.490060e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.256932e-03\n Vprtstp: contraction number = 3.091382e-01\n Vnewton: Using errtol_s: 7641.136045\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.029426e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.321238e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.906153e+03\n Vprtstp: contraction number = 2.906153e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.302464e-04\n Vprtstp: contraction number = 3.422990e-01\n Vnewton: Using errtol_s: 2615.553137\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.047986e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.473885e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.038756e+03\n Vprtstp: contraction number = 1.038756e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.537840e-04\n Vprtstp: contraction number = 3.574324e-01\n Vnewton: Using errtol_s: 934.883311\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.070200e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.659474e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.756989e+02\n Vprtstp: contraction number = 3.756989e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 5.562081e-05\n Vprtstp: contraction number = 3.616814e-01\n Vnewton: Using errtol_s: 338.129920\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.090268e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.825626e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.372077e+02\n Vprtstp: contraction number = 1.372077e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.031307e-05\n Vprtstp: contraction number = 3.652064e-01\n Vnewton: Using errtol_s: 123.487196\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.109762e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.987234e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.308624e+01\n Vprtstp: contraction number = 5.308624e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 7.859206e-06\n Vprtstp: contraction number = 3.869039e-01\n Vnewton: Using errtol_s: 47.777672\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.128034e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.166064e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.247149e+01\n Vprtstp: contraction number = 2.247149e+01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.326814e-06\n Vprtstp: contraction number = 4.233015e-01\n Vnewton: Using errtol_s: 20.224360\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.152140e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.323199e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.031380e+01\n Vprtstp: contraction number = 1.031380e+01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 1.526916e-06\n Vprtstp: contraction number = 4.589724e-01\n Vnewton: Using errtol_s: 9.282423\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.176854e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.474859e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.018395e+00\n Vprtstp: contraction number = 5.018395e+00\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 7.429527e-07\n Vprtstp: contraction number = 4.865709e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.613590e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.624824e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.034291e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.044750e+02\n Vpmg_setPart:  lower corner = (-53.482, -2.4645, 16.7425)\n Vpmg_setPart:  upper corner = (2.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-53.482, -11.2254, 5.5748)\n Vpmg_setPart:  actual maxima = (13.3006, 43.0355, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -15857,15 +15857,15 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.101910647011E+00 kT\n Vpmg_energy:  qfEnergy = 7.806992325165E+04 kT\n Vpmg_energy:  dielEnergy = 3.916747531828E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.330100e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.012700e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n@@ -15888,261 +15888,261 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 6.485605\n+Vacc_SASA: Time elapsed: 6.225830\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.791198e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.285081e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.987200e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.322500e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.110509e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.497100e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.205446e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.715243e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 8699406.430616\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.207754e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.735607e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.298565e+05\n Vprtstp: contraction number = 4.298565e+05\n Vnewton: Attempting damping, relres = 0.048079\n Vnewton: Attempting damping, relres = 0.515481\n Vnewton: Damping accepted, relres = 0.048079\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.807904e-02\n Vprtstp: contraction number = 4.807904e-02\n Vnewton: Using errtol_s: 418259.137179\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.229067e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.898373e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.275297e+04\n Vprtstp: contraction number = 9.275297e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 9.791706e-03\n Vprtstp: contraction number = 2.036585e-01\n Vnewton: Using errtol_s: 85182.030508\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.248436e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.023496e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.830324e+04\n Vprtstp: contraction number = 2.830324e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.931540e-03\n Vprtstp: contraction number = 2.993901e-01\n Vnewton: Using errtol_s: 25502.653903\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.269218e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.158543e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.066383e+04\n Vprtstp: contraction number = 1.066383e+04\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.103407e-03\n Vprtstp: contraction number = 3.763916e-01\n Vnewton: Using errtol_s: 9598.985602\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.289481e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.306704e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.725476e+03\n Vprtstp: contraction number = 4.725476e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.889004e-04\n Vprtstp: contraction number = 4.430826e-01\n Vnewton: Using errtol_s: 4253.143226\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.310334e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.470149e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.402868e+03\n Vprtstp: contraction number = 2.402868e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.485940e-04\n Vprtstp: contraction number = 5.084757e-01\n Vnewton: Using errtol_s: 2162.620089\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.327898e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.602188e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.352802e+03\n Vprtstp: contraction number = 1.352802e+03\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.399556e-04\n Vprtstp: contraction number = 5.629888e-01\n Vnewton: Using errtol_s: 1217.530795\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.348287e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.733791e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.164880e+02\n Vprtstp: contraction number = 8.164880e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.447037e-05\n Vprtstp: contraction number = 6.035512e-01\n Vnewton: Using errtol_s: 734.842122\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.368693e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.864409e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.157033e+02\n Vprtstp: contraction number = 5.157033e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.335238e-05\n Vprtstp: contraction number = 6.316106e-01\n Vnewton: Using errtol_s: 464.134076\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.388989e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.989184e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.352095e+02\n Vprtstp: contraction number = 3.352095e+02\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.467926e-05\n Vprtstp: contraction number = 6.500040e-01\n Vnewton: Using errtol_s: 301.688999\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.406100e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.011903e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.222234e+02\n Vprtstp: contraction number = 2.222234e+02\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.299022e-05\n Vprtstp: contraction number = 6.629387e-01\n Vnewton: Using errtol_s: 200.001301\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.422183e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.024454e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.495221e+02\n Vprtstp: contraction number = 1.495221e+02\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.546887e-05\n Vprtstp: contraction number = 6.728456e-01\n Vnewton: Using errtol_s: 134.569993\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.438275e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.036334e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.018836e+02\n Vprtstp: contraction number = 1.018836e+02\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 1.054041e-05\n Vprtstp: contraction number = 6.813949e-01\n Vnewton: Using errtol_s: 91.695311\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.454337e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.048745e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.012825e+01\n Vprtstp: contraction number = 7.012825e+01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 7.255144e-06\n Vprtstp: contraction number = 6.883171e-01\n Vnewton: Using errtol_s: 63.115450\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.472035e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.061732e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.869976e+01\n Vprtstp: contraction number = 4.869976e+01\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 5.038252e-06\n Vprtstp: contraction number = 6.944386e-01\n Vnewton: Using errtol_s: 43.829803\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.491060e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.075266e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.408035e+01\n Vprtstp: contraction number = 3.408035e+01\n Vprtstp: iteration = 16\n Vprtstp: relative residual = 3.525795e-06\n Vprtstp: contraction number = 6.998052e-01\n Vnewton: Using errtol_s: 30.672326\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.510541e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.090590e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.401453e+01\n Vprtstp: contraction number = 2.401453e+01\n Vprtstp: iteration = 17\n Vprtstp: relative residual = 2.484432e-06\n Vprtstp: contraction number = 7.046444e-01\n Vnewton: Using errtol_s: 21.613084\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.530113e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.103514e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.702723e+01\n Vprtstp: contraction number = 1.702723e+01\n Vprtstp: iteration = 18\n Vprtstp: relative residual = 1.761558e-06\n Vprtstp: contraction number = 7.090385e-01\n Vnewton: Using errtol_s: 15.324508\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.549032e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.117100e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.214065e+01\n Vprtstp: contraction number = 1.214065e+01\n Vprtstp: iteration = 19\n Vprtstp: relative residual = 1.256015e-06\n Vprtstp: contraction number = 7.130137e-01\n Vnewton: Using errtol_s: 10.926584\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.567853e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.129870e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.699962e+00\n Vprtstp: contraction number = 8.699962e+00\n Vprtstp: iteration = 20\n Vprtstp: relative residual = 9.000575e-07\n Vprtstp: contraction number = 7.165978e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 3.790487e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.802289e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.702077e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.712149e+02\n Vpmg_setPart:  lower corner = (-53.482, -2.4645, 16.7425)\n Vpmg_setPart:  upper corner = (2.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -16151,15 +16151,15 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.017893422646E+00 kT\n Vpmg_energy:  qfEnergy = 9.611562953522E+03 kT\n Vpmg_energy:  dielEnergy = 4.865716990042E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.907000e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.127200e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n@@ -16207,171 +16207,171 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0371069 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 6.779965\n+Vacc_SASA: Time elapsed: 6.273276\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.613468e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.031797e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.804200e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.270900e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.301040e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.037572e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.594653e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.151002e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 6935084.404705\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.598064e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.153057e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.727592e+05\n Vprtstp: contraction number = 6.727592e+05\n Vnewton: Attempting damping, relres = 0.088102\n Vnewton: Attempting damping, relres = 0.541455\n Vnewton: Damping accepted, relres = 0.088102\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.810224e-02\n Vprtstp: contraction number = 8.810224e-02\n Vnewton: Using errtol_s: 610996.445538\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.623219e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.170117e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.225330e+05\n Vprtstp: contraction number = 1.225330e+05\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.593368e-02\n Vprtstp: contraction number = 1.808544e-01\n Vnewton: Using errtol_s: 110501.406789\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.647261e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.185580e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.085731e+04\n Vprtstp: contraction number = 3.085731e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 4.004954e-03\n Vprtstp: contraction number = 2.513515e-01\n Vnewton: Using errtol_s: 27774.696268\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.671170e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.202031e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.402021e+03\n Vprtstp: contraction number = 9.402021e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.220185e-03\n Vprtstp: contraction number = 3.046688e-01\n Vnewton: Using errtol_s: 8462.082872\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.696811e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.218619e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.175895e+03\n Vprtstp: contraction number = 3.175895e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.121575e-04\n Vprtstp: contraction number = 3.377829e-01\n Vnewton: Using errtol_s: 2858.347084\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.723493e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.233331e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.121720e+03\n Vprtstp: contraction number = 1.121720e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.455722e-04\n Vprtstp: contraction number = 3.531955e-01\n Vnewton: Using errtol_s: 1009.555317\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.749547e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.248838e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.008316e+02\n Vprtstp: contraction number = 4.008316e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 5.201806e-05\n Vprtstp: contraction number = 3.573352e-01\n Vnewton: Using errtol_s: 360.749636\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.775025e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.264242e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.444166e+02\n Vprtstp: contraction number = 1.444166e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.874168e-05\n Vprtstp: contraction number = 3.602918e-01\n Vnewton: Using errtol_s: 129.975153\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.799597e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.279319e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.512662e+01\n Vprtstp: contraction number = 5.512662e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 7.154062e-06\n Vprtstp: contraction number = 3.817193e-01\n Vnewton: Using errtol_s: 49.614025\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.823960e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.295320e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.308362e+01\n Vprtstp: contraction number = 2.308362e+01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 2.995677e-06\n Vprtstp: contraction number = 4.187379e-01\n Vnewton: Using errtol_s: 20.775274\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.849094e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.310836e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.051871e+01\n Vprtstp: contraction number = 1.051871e+01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 1.365066e-06\n Vprtstp: contraction number = 4.556784e-01\n Vnewton: Using errtol_s: 9.466845\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.874873e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.325872e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.098076e+00\n Vprtstp: contraction number = 5.098076e+00\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 6.616025e-07\n Vprtstp: contraction number = 4.846672e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 3.034086e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.047943e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.892548e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.903569e+02\n Vpmg_setPart:  lower corner = (-53.482, -2.4645, 16.7425)\n Vpmg_setPart:  upper corner = (2.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-53.482, -11.2254, 5.5748)\n Vpmg_setPart:  actual maxima = (13.3006, 43.0355, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -16380,27 +16380,27 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.129100275217E+00 kT\n Vpmg_energy:  qfEnergy = 7.806947604587E+04 kT\n Vpmg_energy:  dielEnergy = 3.916855498576E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 8.541200e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.559100e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  printing only subset of domain\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.898707e+03\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.340825e+03\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 06:15:33 2025\n+# Creation Date and Time:  Tue Jan  9 04:07:46 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path mol1.pqr\n@@ -16753,250 +16753,250 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 2.880593\n+Vacc_SASA: Time elapsed: 2.986895\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.963186e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.937282e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.952700e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.476300e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.238731e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.581710e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.649660e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.383361e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4300910.832168\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.481506e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.256491e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.136321e+05\n Vprtstp: contraction number = 2.136321e+05\n Vnewton: Attempting damping, relres = 0.047663\n Vnewton: Attempting damping, relres = 0.515490\n Vnewton: Damping accepted, relres = 0.047663\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.766304e-02\n Vprtstp: contraction number = 4.766304e-02\n Vnewton: Using errtol_s: 204994.485638\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.935128e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.968609e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.587025e+04\n Vprtstp: contraction number = 4.587025e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 9.727679e-03\n Vprtstp: contraction number = 2.040927e-01\n Vnewton: Using errtol_s: 41837.880528\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.711088e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.099267e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.391016e+04\n Vprtstp: contraction number = 1.391016e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.912173e-03\n Vprtstp: contraction number = 2.993697e-01\n Vnewton: Using errtol_s: 12524.995351\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.489317e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.259911e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.237707e+03\n Vprtstp: contraction number = 5.237707e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.096054e-03\n Vprtstp: contraction number = 3.763697e-01\n Vnewton: Using errtol_s: 4714.028550\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.316344e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.429163e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.331453e+03\n Vprtstp: contraction number = 2.331453e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.878779e-04\n Vprtstp: contraction number = 4.451223e-01\n Vnewton: Using errtol_s: 2098.319320\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.012985e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.551173e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.189035e+03\n Vprtstp: contraction number = 1.189035e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.488161e-04\n Vprtstp: contraction number = 5.099966e-01\n Vnewton: Using errtol_s: 1070.135650\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.195146e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.685906e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.678182e+02\n Vprtstp: contraction number = 6.678182e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.397467e-04\n Vprtstp: contraction number = 5.616468e-01\n Vnewton: Using errtol_s: 601.038216\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.391173e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.853764e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.994733e+02\n Vprtstp: contraction number = 3.994733e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.359319e-05\n Vprtstp: contraction number = 5.981764e-01\n Vnewton: Using errtol_s: 359.526862\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.583544e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.000298e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.488647e+02\n Vprtstp: contraction number = 2.488647e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.207703e-05\n Vprtstp: contraction number = 6.229817e-01\n Vnewton: Using errtol_s: 223.978670\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.771726e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.117313e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.588671e+02\n Vprtstp: contraction number = 1.588671e+02\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.324425e-05\n Vprtstp: contraction number = 6.383669e-01\n Vnewton: Using errtol_s: 142.980568\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.962145e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.231484e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.030284e+02\n Vprtstp: contraction number = 1.030284e+02\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.155954e-05\n Vprtstp: contraction number = 6.485194e-01\n Vnewton: Using errtol_s: 92.725673\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.162493e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.341263e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.760657e+01\n Vprtstp: contraction number = 6.760657e+01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.414722e-05\n Vprtstp: contraction number = 6.561932e-01\n Vnewton: Using errtol_s: 60.845953\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.355731e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.456921e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.480217e+01\n Vprtstp: contraction number = 4.480217e+01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 9.375216e-06\n Vprtstp: contraction number = 6.626894e-01\n Vnewton: Using errtol_s: 40.321969\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.552395e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.575074e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.990735e+01\n Vprtstp: contraction number = 2.990735e+01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 6.258355e-06\n Vprtstp: contraction number = 6.675424e-01\n Vnewton: Using errtol_s: 26.916626\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.750579e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.688056e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.008505e+01\n Vprtstp: contraction number = 2.008505e+01\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 4.202958e-06\n Vprtstp: contraction number = 6.715755e-01\n Vnewton: Using errtol_s: 18.076547\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.941745e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.805067e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.356100e+01\n Vprtstp: contraction number = 1.356100e+01\n Vprtstp: iteration = 16\n Vprtstp: relative residual = 2.837748e-06\n Vprtstp: contraction number = 6.751787e-01\n Vnewton: Using errtol_s: 12.204901\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.135405e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.921969e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.198733e+00\n Vprtstp: contraction number = 9.198733e+00\n Vprtstp: iteration = 17\n Vprtstp: relative residual = 1.924909e-06\n Vprtstp: contraction number = 6.783227e-01\n Vnewton: Using errtol_s: 8.278861\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.331434e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.038328e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.265697e+00\n Vprtstp: contraction number = 6.265697e+00\n Vprtstp: iteration = 18\n Vprtstp: relative residual = 1.311147e-06\n Vprtstp: contraction number = 6.811478e-01\n Vnewton: Using errtol_s: 5.639128\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.527799e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.151819e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.284635e+00\n Vprtstp: contraction number = 4.284635e+00\n Vprtstp: iteration = 19\n Vprtstp: relative residual = 8.965941e-07\n Vprtstp: contraction number = 6.838241e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 3.638259e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.653051e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.199267e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.210332e+02\n Vpmg_setPart:  lower corner = (2.518, -2.4645, 16.7425)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -17005,17 +17005,17 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.751162440734E-01 kT\n Vpmg_energy:  qfEnergy = 1.947112425311E+03 kT\n Vpmg_energy:  dielEnergy = 9.674060402300E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.754400e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.410900e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 39.7309\n Vpbe_ctor2:  solute dimensions = 68.682 x 69.075 x 70.346\n Vpbe_ctor2:  solute charge = -12\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -17061,160 +17061,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0113169 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 2.924330\n+Vacc_SASA: Time elapsed: 3.004726\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.229942e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.318039e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.735500e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.725000e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.230571e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.037707e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.752229e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.309280e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2854416.159669\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.778925e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.329348e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.073946e+05\n Vprtstp: contraction number = 3.073946e+05\n Vnewton: Attempting damping, relres = 0.097301\n Vnewton: Attempting damping, relres = 0.546102\n Vnewton: Damping accepted, relres = 0.097301\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.730086e-02\n Vprtstp: contraction number = 9.730086e-02\n Vnewton: Using errtol_s: 277737.152012\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.047346e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.497121e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.422127e+04\n Vprtstp: contraction number = 5.422127e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.709795e-02\n Vprtstp: contraction number = 1.757225e-01\n Vnewton: Using errtol_s: 48804.661136\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.320562e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.647913e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.206353e+04\n Vprtstp: contraction number = 1.206353e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 3.803701e-03\n Vprtstp: contraction number = 2.224653e-01\n Vnewton: Using errtol_s: 10857.344468\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.563150e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.797127e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.177380e+03\n Vprtstp: contraction number = 3.177380e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.001847e-03\n Vprtstp: contraction number = 2.633874e-01\n Vnewton: Using errtol_s: 2859.687867\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.794736e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.953676e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.523572e+02\n Vprtstp: contraction number = 9.523572e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.002837e-04\n Vprtstp: contraction number = 2.997301e-01\n Vnewton: Using errtol_s: 857.134538\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.989806e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.104873e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.079890e+02\n Vprtstp: contraction number = 3.079890e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 9.711021e-05\n Vprtstp: contraction number = 3.233949e-01\n Vnewton: Using errtol_s: 277.192960\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.236556e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.258986e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.041211e+02\n Vprtstp: contraction number = 1.041211e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.282966e-05\n Vprtstp: contraction number = 3.380660e-01\n Vnewton: Using errtol_s: 93.709510\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.485575e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.409440e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.682551e+01\n Vprtstp: contraction number = 3.682551e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.161114e-05\n Vprtstp: contraction number = 3.536784e-01\n Vnewton: Using errtol_s: 33.143025\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.752251e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.563677e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.414772e+01\n Vprtstp: contraction number = 1.414772e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 4.460791e-06\n Vprtstp: contraction number = 3.841820e-01\n Vnewton: Using errtol_s: 12.732955\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.007909e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.718404e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.014294e+00\n Vprtstp: contraction number = 6.014294e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.896313e-06\n Vprtstp: contraction number = 4.251068e-01\n Vnewton: Using errtol_s: 5.412865\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.268253e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.871092e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.770154e+00\n Vprtstp: contraction number = 2.770154e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 8.734323e-07\n Vprtstp: contraction number = 4.605951e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.746361e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.760106e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.707217e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.719069e+02\n Vpmg_setPart:  lower corner = (2.518, -2.4645, 16.7425)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-8.26461, -11.2254, 5.5748)\n Vpmg_setPart:  actual maxima = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -17223,15 +17223,15 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.831261294961E-01 kT\n Vpmg_energy:  qfEnergy = 1.781344550664E+04 kT\n Vpmg_energy:  dielEnergy = 8.939288545980E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.033820e-01\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.067100e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -17254,272 +17254,272 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 2.909651\n+Vacc_SASA: Time elapsed: 3.041901\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.884762e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.911304e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.277500e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.537100e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.240392e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.796340e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.552892e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.067628e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4276578.139223\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.580724e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.086336e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.113974e+05\n Vprtstp: contraction number = 2.113974e+05\n Vnewton: Attempting damping, relres = 0.047573\n Vnewton: Attempting damping, relres = 0.515375\n Vnewton: Damping accepted, relres = 0.047573\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.757263e-02\n Vprtstp: contraction number = 4.757263e-02\n Vnewton: Using errtol_s: 203448.048803\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.788670e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.214689e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.589098e+04\n Vprtstp: contraction number = 4.589098e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 9.811582e-03\n Vprtstp: contraction number = 2.062443e-01\n Vnewton: Using errtol_s: 41959.996661\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.951832e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.333382e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.404662e+04\n Vprtstp: contraction number = 1.404662e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.960291e-03\n Vprtstp: contraction number = 3.017139e-01\n Vnewton: Using errtol_s: 12659.913691\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.126920e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.448935e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.279840e+03\n Vprtstp: contraction number = 5.279840e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.111524e-03\n Vprtstp: contraction number = 3.754781e-01\n Vnewton: Using errtol_s: 4753.520446\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.306904e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.559967e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.336921e+03\n Vprtstp: contraction number = 2.336921e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.918609e-04\n Vprtstp: contraction number = 4.425102e-01\n Vnewton: Using errtol_s: 2103.481419\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.493065e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.671582e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.194576e+03\n Vprtstp: contraction number = 1.194576e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.514070e-04\n Vprtstp: contraction number = 5.111344e-01\n Vnewton: Using errtol_s: 1075.161658\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.676905e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.784038e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.792983e+02\n Vprtstp: contraction number = 6.792983e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.429594e-04\n Vprtstp: contraction number = 5.686374e-01\n Vnewton: Using errtol_s: 611.377148\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.864980e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.891782e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.154648e+02\n Vprtstp: contraction number = 4.154648e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.743449e-05\n Vprtstp: contraction number = 6.116036e-01\n Vnewton: Using errtol_s: 373.920435\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.054362e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.003251e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.660684e+02\n Vprtstp: contraction number = 2.660684e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.599388e-05\n Vprtstp: contraction number = 6.404095e-01\n Vnewton: Using errtol_s: 239.462182\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.248192e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.111146e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.755593e+02\n Vprtstp: contraction number = 1.755593e+02\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.694626e-05\n Vprtstp: contraction number = 6.598268e-01\n Vnewton: Using errtol_s: 158.003576\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.429746e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.236772e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.183176e+02\n Vprtstp: contraction number = 1.183176e+02\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.489979e-05\n Vprtstp: contraction number = 6.739462e-01\n Vnewton: Using errtol_s: 106.485913\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.613265e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.355125e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.102710e+01\n Vprtstp: contraction number = 8.102710e+01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.705205e-05\n Vprtstp: contraction number = 6.848271e-01\n Vnewton: Using errtol_s: 72.924443\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.800892e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.472065e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.628393e+01\n Vprtstp: contraction number = 5.628393e+01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 1.184488e-05\n Vprtstp: contraction number = 6.946308e-01\n Vnewton: Using errtol_s: 50.655566\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.988174e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.587257e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.955755e+01\n Vprtstp: contraction number = 3.955755e+01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 8.324836e-06\n Vprtstp: contraction number = 7.028213e-01\n Vnewton: Using errtol_s: 35.601810\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.164765e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.700001e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.808103e+01\n Vprtstp: contraction number = 2.808103e+01\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 5.909617e-06\n Vprtstp: contraction number = 7.098779e-01\n Vnewton: Using errtol_s: 25.272937\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.348474e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.815259e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.010039e+01\n Vprtstp: contraction number = 2.010039e+01\n Vprtstp: iteration = 16\n Vprtstp: relative residual = 4.230100e-06\n Vprtstp: contraction number = 7.157995e-01\n Vnewton: Using errtol_s: 18.090355\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.529515e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.927718e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.449222e+01\n Vprtstp: contraction number = 1.449222e+01\n Vprtstp: iteration = 17\n Vprtstp: relative residual = 3.049867e-06\n Vprtstp: contraction number = 7.209918e-01\n Vnewton: Using errtol_s: 13.042997\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.714112e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.039094e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.051084e+01\n Vprtstp: contraction number = 1.051084e+01\n Vprtstp: iteration = 18\n Vprtstp: relative residual = 2.211992e-06\n Vprtstp: contraction number = 7.252749e-01\n Vnewton: Using errtol_s: 9.459758\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.874036e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.149031e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.663626e+00\n Vprtstp: contraction number = 7.663626e+00\n Vprtstp: iteration = 19\n Vprtstp: relative residual = 1.612800e-06\n Vprtstp: contraction number = 7.291164e-01\n Vnewton: Using errtol_s: 6.897264\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.003805e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.256163e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.612195e+00\n Vprtstp: contraction number = 5.612195e+00\n Vprtstp: iteration = 20\n Vprtstp: relative residual = 1.181079e-06\n Vprtstp: contraction number = 7.323158e-01\n Vnewton: Using errtol_s: 5.050976\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.023201e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.367601e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.124624e+00\n Vprtstp: contraction number = 4.124624e+00\n Vprtstp: iteration = 21\n Vprtstp: relative residual = 8.680215e-07\n Vprtstp: contraction number = 7.349396e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 3.843504e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.856828e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.405599e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.416728e+02\n Vpmg_setPart:  lower corner = (2.518, -2.4645, 16.7425)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -17528,17 +17528,17 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.114658040660E-01 kT\n Vpmg_energy:  qfEnergy = 3.255454137160E+02 kT\n Vpmg_energy:  dielEnergy = 1.687649926413E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.034200e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.332700e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -17584,160 +17584,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00476673 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 2.870917\n+Vacc_SASA: Time elapsed: 3.016904\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.926587e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.014064e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.167200e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.325800e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.073014e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.487920e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.044997e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.526224e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1723088.414735\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.047494e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.544901e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.042446e+05\n Vprtstp: contraction number = 2.042446e+05\n Vnewton: Attempting damping, relres = 0.108739\n Vnewton: Attempting damping, relres = 0.550663\n Vnewton: Damping accepted, relres = 0.108739\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.087385e-01\n Vprtstp: contraction number = 1.087385e-01\n Vnewton: Using errtol_s: 187366.060856\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.067644e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.661302e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.786866e+04\n Vprtstp: contraction number = 3.786866e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.981324e-02\n Vprtstp: contraction number = 1.822100e-01\n Vnewton: Using errtol_s: 34139.969757\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.087420e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.769910e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.828513e+03\n Vprtstp: contraction number = 8.828513e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 4.612234e-03\n Vprtstp: contraction number = 2.327854e-01\n Vnewton: Using errtol_s: 7947.287090\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.106478e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.889091e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.384276e+03\n Vprtstp: contraction number = 2.384276e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.245382e-03\n Vprtstp: contraction number = 2.700171e-01\n Vnewton: Using errtol_s: 2145.903122\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.124610e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.997731e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.047320e+02\n Vprtstp: contraction number = 7.047320e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.680970e-04\n Vprtstp: contraction number = 2.955696e-01\n Vnewton: Using errtol_s: 634.263634\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.142851e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.105305e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.207559e+02\n Vprtstp: contraction number = 2.207559e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.153050e-04\n Vprtstp: contraction number = 3.132463e-01\n Vnewton: Using errtol_s: 198.680750\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.161171e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.213536e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.166503e+01\n Vprtstp: contraction number = 7.166503e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.743196e-05\n Vprtstp: contraction number = 3.246343e-01\n Vnewton: Using errtol_s: 64.498581\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.180249e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.316330e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.385676e+01\n Vprtstp: contraction number = 2.385676e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.246082e-05\n Vprtstp: contraction number = 3.328924e-01\n Vnewton: Using errtol_s: 21.471088\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.197968e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.427481e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.086151e+00\n Vprtstp: contraction number = 8.086151e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 4.223542e-06\n Vprtstp: contraction number = 3.389459e-01\n Vnewton: Using errtol_s: 7.277537\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.214958e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.535558e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.777094e+00\n Vprtstp: contraction number = 2.777094e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.450526e-06\n Vprtstp: contraction number = 3.434383e-01\n Vnewton: Using errtol_s: 2.499385\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.232929e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.646314e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.633001e-01\n Vprtstp: contraction number = 9.633001e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 5.031489e-07\n Vprtstp: contraction number = 3.468734e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.040930e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.053335e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.216597e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.227809e+02\n Vpmg_setPart:  lower corner = (2.518, -2.4645, 16.7425)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-8.26461, -11.2254, 5.5748)\n Vpmg_setPart:  actual maxima = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -17746,15 +17746,15 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.878540629655E-01 kT\n Vpmg_energy:  qfEnergy = 3.319538441543E+03 kT\n Vpmg_energy:  dielEnergy = 1.644040185021E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.236300e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.386000e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n@@ -17777,261 +17777,261 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 6.281376\n+Vacc_SASA: Time elapsed: 6.445349\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.517970e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.530409e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.649400e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.456700e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.193638e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.065525e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.258007e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.831086e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 8699406.430616\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.260630e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.849783e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.298565e+05\n Vprtstp: contraction number = 4.298565e+05\n Vnewton: Attempting damping, relres = 0.048079\n Vnewton: Attempting damping, relres = 0.515481\n Vnewton: Damping accepted, relres = 0.048079\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.807904e-02\n Vprtstp: contraction number = 4.807904e-02\n Vnewton: Using errtol_s: 418259.137179\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.278262e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.010522e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.275297e+04\n Vprtstp: contraction number = 9.275297e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 9.791706e-03\n Vprtstp: contraction number = 2.036585e-01\n Vnewton: Using errtol_s: 85182.030508\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.295492e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.145103e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.830324e+04\n Vprtstp: contraction number = 2.830324e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.931540e-03\n Vprtstp: contraction number = 2.993901e-01\n Vnewton: Using errtol_s: 25502.653903\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.314689e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.280866e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.066383e+04\n Vprtstp: contraction number = 1.066383e+04\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.103407e-03\n Vprtstp: contraction number = 3.763916e-01\n Vnewton: Using errtol_s: 9598.985602\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.336522e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.407182e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.725476e+03\n Vprtstp: contraction number = 4.725476e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.889004e-04\n Vprtstp: contraction number = 4.430826e-01\n Vnewton: Using errtol_s: 4253.143226\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.355528e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.538624e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.402868e+03\n Vprtstp: contraction number = 2.402868e+03\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.485940e-04\n Vprtstp: contraction number = 5.084757e-01\n Vnewton: Using errtol_s: 2162.620089\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.375349e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.661900e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.352802e+03\n Vprtstp: contraction number = 1.352802e+03\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.399556e-04\n Vprtstp: contraction number = 5.629888e-01\n Vnewton: Using errtol_s: 1217.530795\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.394574e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.795579e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.164880e+02\n Vprtstp: contraction number = 8.164880e+02\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.447037e-05\n Vprtstp: contraction number = 6.035512e-01\n Vnewton: Using errtol_s: 734.842122\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.415876e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.922124e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.157033e+02\n Vprtstp: contraction number = 5.157033e+02\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.335238e-05\n Vprtstp: contraction number = 6.316106e-01\n Vnewton: Using errtol_s: 464.134076\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.434907e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.050532e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.352095e+02\n Vprtstp: contraction number = 3.352095e+02\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 3.467926e-05\n Vprtstp: contraction number = 6.500040e-01\n Vnewton: Using errtol_s: 301.688999\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.453822e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.180295e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.222234e+02\n Vprtstp: contraction number = 2.222234e+02\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.299022e-05\n Vprtstp: contraction number = 6.629387e-01\n Vnewton: Using errtol_s: 200.001301\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.474833e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.308202e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.495221e+02\n Vprtstp: contraction number = 1.495221e+02\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.546887e-05\n Vprtstp: contraction number = 6.728456e-01\n Vnewton: Using errtol_s: 134.569993\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.491765e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.430659e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.018836e+02\n Vprtstp: contraction number = 1.018836e+02\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 1.054041e-05\n Vprtstp: contraction number = 6.813949e-01\n Vnewton: Using errtol_s: 91.695311\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.511319e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.566622e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.012825e+01\n Vprtstp: contraction number = 7.012825e+01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 7.255144e-06\n Vprtstp: contraction number = 6.883171e-01\n Vnewton: Using errtol_s: 63.115450\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.531791e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.689178e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.869976e+01\n Vprtstp: contraction number = 4.869976e+01\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 5.038252e-06\n Vprtstp: contraction number = 6.944386e-01\n Vnewton: Using errtol_s: 43.829803\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.551561e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.810272e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.408035e+01\n Vprtstp: contraction number = 3.408035e+01\n Vprtstp: iteration = 16\n Vprtstp: relative residual = 3.525795e-06\n Vprtstp: contraction number = 6.998052e-01\n Vnewton: Using errtol_s: 30.672326\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.571371e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.937028e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.401453e+01\n Vprtstp: contraction number = 2.401453e+01\n Vprtstp: iteration = 17\n Vprtstp: relative residual = 2.484432e-06\n Vprtstp: contraction number = 7.046444e-01\n Vnewton: Using errtol_s: 21.613084\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.592093e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.005914e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.702723e+01\n Vprtstp: contraction number = 1.702723e+01\n Vprtstp: iteration = 18\n Vprtstp: relative residual = 1.761558e-06\n Vprtstp: contraction number = 7.090385e-01\n Vnewton: Using errtol_s: 15.324508\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.612500e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.018043e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.214065e+01\n Vprtstp: contraction number = 1.214065e+01\n Vprtstp: iteration = 19\n Vprtstp: relative residual = 1.256015e-06\n Vprtstp: contraction number = 7.130137e-01\n Vnewton: Using errtol_s: 10.926584\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.632768e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.030482e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.699962e+00\n Vprtstp: contraction number = 8.699962e+00\n Vprtstp: iteration = 20\n Vprtstp: relative residual = 9.000575e-07\n Vprtstp: contraction number = 7.165978e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 3.920475e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.933088e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.590803e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.602355e+02\n Vpmg_setPart:  lower corner = (2.518, -2.4645, 16.7425)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -18040,15 +18040,15 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.211144338750E-01 kT\n Vpmg_energy:  qfEnergy = 2.301973448783E+03 kT\n Vpmg_energy:  dielEnergy = 1.153004707320E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.174700e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.089200e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n@@ -18096,160 +18096,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0260263 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 6.309574\n+Vacc_SASA: Time elapsed: 6.389996\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.861820e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.985205e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.700700e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.624600e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.119877e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.108180e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.659221e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.051244e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4514465.797290\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.661663e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.053011e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.961912e+05\n Vprtstp: contraction number = 4.961912e+05\n Vnewton: Attempting damping, relres = 0.099852\n Vnewton: Attempting damping, relres = 0.546981\n Vnewton: Damping accepted, relres = 0.099852\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.985216e-02\n Vprtstp: contraction number = 9.985216e-02\n Vnewton: Using errtol_s: 450779.157003\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.683252e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.068773e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.942393e+04\n Vprtstp: contraction number = 8.942393e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.783565e-02\n Vprtstp: contraction number = 1.786206e-01\n Vnewton: Using errtol_s: 80518.432475\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.703127e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.084497e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.031115e+04\n Vprtstp: contraction number = 2.031115e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 4.049611e-03\n Vprtstp: contraction number = 2.270515e-01\n Vnewton: Using errtol_s: 18281.831872\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.725590e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.100259e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.419185e+03\n Vprtstp: contraction number = 5.419185e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.080391e-03\n Vprtstp: contraction number = 2.667887e-01\n Vnewton: Using errtol_s: 4877.386053\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.748359e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.115583e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.625333e+03\n Vprtstp: contraction number = 1.625333e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.240293e-04\n Vprtstp: contraction number = 2.999187e-01\n Vnewton: Using errtol_s: 1462.819304\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.772275e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.130471e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.216368e+02\n Vprtstp: contraction number = 5.216368e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.039939e-04\n Vprtstp: contraction number = 3.209397e-01\n Vnewton: Using errtol_s: 469.476847\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.797400e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.145788e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.735595e+02\n Vprtstp: contraction number = 1.735595e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.460082e-05\n Vprtstp: contraction number = 3.327198e-01\n Vnewton: Using errtol_s: 156.204227\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.822429e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.161551e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.923935e+01\n Vprtstp: contraction number = 5.923935e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.180993e-05\n Vprtstp: contraction number = 3.413193e-01\n Vnewton: Using errtol_s: 53.315519\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.847757e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.177197e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.118946e+01\n Vprtstp: contraction number = 2.118946e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 4.224316e-06\n Vprtstp: contraction number = 3.576919e-01\n Vnewton: Using errtol_s: 19.070529\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.872526e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.192304e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.237698e+00\n Vprtstp: contraction number = 8.237698e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.642261e-06\n Vprtstp: contraction number = 3.887637e-01\n Vnewton: Using errtol_s: 7.413930\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.897678e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.207707e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.509994e+00\n Vprtstp: contraction number = 3.509994e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 6.997494e-07\n Vprtstp: contraction number = 4.260891e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.621683e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.634278e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.703178e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.713064e+02\n Vpmg_setPart:  lower corner = (2.518, -2.4645, 16.7425)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-8.26461, -11.2254, 5.5748)\n Vpmg_setPart:  actual maxima = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -18258,27 +18258,27 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 3.259341430721E-01 kT\n Vpmg_energy:  qfEnergy = 2.116108930828E+04 kT\n Vpmg_energy:  dielEnergy = 1.059930084642E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.166500e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.317900e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  printing only subset of domain\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.921929e+03\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.222207e+03\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 06:18:53 2025\n+# Creation Date and Time:  Tue Jan  9 04:13:20 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path mol1.pqr\n@@ -18631,129 +18631,129 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.098471\n+Vacc_SASA: Time elapsed: 3.068115\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.581079e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.444235e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 6.205000e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.472900e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.153100e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.528280e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.195460e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.846848e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4300910.832168\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.897445e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.733934e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.776390e+05\n Vprtstp: contraction number = 1.776390e+05\n Vnewton: Attempting damping, relres = 0.041319\n Vnewton: Attempting damping, relres = 0.513474\n Vnewton: Damping accepted, relres = 0.041319\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.131938e-02\n Vprtstp: contraction number = 4.131938e-02\n Vnewton: Using errtol_s: 177710.973970\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.785722e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.171859e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.677180e+04\n Vprtstp: contraction number = 2.677180e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 5.962101e-03\n Vprtstp: contraction number = 1.442931e-01\n Vnewton: Using errtol_s: 25642.465478\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.551051e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.436315e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.966549e+03\n Vprtstp: contraction number = 4.966549e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.056655e-03\n Vprtstp: contraction number = 1.772286e-01\n Vnewton: Using errtol_s: 4544.578762\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.629032e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.638276e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.011325e+03\n Vprtstp: contraction number = 1.011325e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.118038e-04\n Vprtstp: contraction number = 2.004475e-01\n Vnewton: Using errtol_s: 910.949292\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.504902e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.845448e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.253595e+02\n Vprtstp: contraction number = 2.253595e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.715911e-05\n Vprtstp: contraction number = 2.226547e-01\n Vnewton: Using errtol_s: 202.827138\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.032650e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.140467e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.445207e+01\n Vprtstp: contraction number = 5.445207e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.139456e-05\n Vprtstp: contraction number = 2.416194e-01\n Vnewton: Using errtol_s: 49.006980\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.237961e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.457286e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.420316e+01\n Vprtstp: contraction number = 1.420316e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.972126e-06\n Vprtstp: contraction number = 2.608373e-01\n Vnewton: Using errtol_s: 12.782849\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.418382e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.716056e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.022184e+00\n Vprtstp: contraction number = 4.022184e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.416744e-07\n Vprtstp: contraction number = 2.831893e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.557729e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.570993e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.029037e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.039947e+02\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (2.518, -2.4645, 16.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -18762,17 +18762,17 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 8.432004946158E-01 kT\n Vpmg_energy:  qfEnergy = 1.213065901878E+03 kT\n Vpmg_energy:  dielEnergy = 6.590634025531E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.620500e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.490700e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 39.7309\n Vpbe_ctor2:  solute dimensions = 68.682 x 69.075 x 70.346\n Vpbe_ctor2:  solute charge = -12\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -18818,127 +18818,127 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00609308 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 2.975870\n+Vacc_SASA: Time elapsed: 3.045141\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.791594e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.775552e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.578400e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.504500e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.241125e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.008936e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.682001e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.147623e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 3435589.940646\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.711931e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.167055e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.946642e+05\n Vprtstp: contraction number = 2.946642e+05\n Vnewton: Attempting damping, relres = 0.078398\n Vnewton: Attempting damping, relres = 0.536416\n Vnewton: Damping accepted, relres = 0.078398\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.839769e-02\n Vprtstp: contraction number = 7.839769e-02\n Vnewton: Using errtol_s: 269342.316546\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.006296e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.329372e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.926470e+04\n Vprtstp: contraction number = 3.926470e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.037644e-02\n Vprtstp: contraction number = 1.323565e-01\n Vnewton: Using errtol_s: 35649.206105\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.266079e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.483399e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.330351e+03\n Vprtstp: contraction number = 6.330351e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.659520e-03\n Vprtstp: contraction number = 1.599315e-01\n Vnewton: Using errtol_s: 5701.430665\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.530561e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.642174e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.149005e+03\n Vprtstp: contraction number = 1.149005e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 3.009992e-04\n Vprtstp: contraction number = 1.813772e-01\n Vnewton: Using errtol_s: 1034.109707\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.786311e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.794563e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.271091e+02\n Vprtstp: contraction number = 2.271091e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.949440e-05\n Vprtstp: contraction number = 1.976564e-01\n Vnewton: Using errtol_s: 204.398353\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.019115e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.945680e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.795044e+01\n Vprtstp: contraction number = 4.795044e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.256128e-05\n Vprtstp: contraction number = 2.111338e-01\n Vnewton: Using errtol_s: 43.155404\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.228078e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.107544e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.083630e+01\n Vprtstp: contraction number = 1.083630e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.838717e-06\n Vprtstp: contraction number = 2.259895e-01\n Vnewton: Using errtol_s: 9.752668\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.450885e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.263269e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.677103e+00\n Vprtstp: contraction number = 2.677103e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 7.013038e-07\n Vprtstp: contraction number = 2.470496e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.995599e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.009320e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.254612e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.266025e+02\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (2.518, -2.4645, 16.7425)\n Vpmg_setPart:  actual minima = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  actual maxima = (13.3006, 6.29637, 27.9102)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -18947,17 +18947,17 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 7.647117283033E-01 kT\n Vpmg_energy:  qfEnergy = 1.061546373318E+04 kT\n Vpmg_energy:  dielEnergy = 5.342705487083E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.180900e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.879400e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -18978,129 +18978,129 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.208530\n+Vacc_SASA: Time elapsed: 2.946505\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.509620e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.878046e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.604700e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.322700e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.563847e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.027141e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.740934e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.453571e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4276578.139223\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.771977e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.473487e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.716926e+05\n Vprtstp: contraction number = 1.716926e+05\n Vnewton: Attempting damping, relres = 0.040940\n Vnewton: Attempting damping, relres = 0.513162\n Vnewton: Damping accepted, relres = 0.040940\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.093968e-02\n Vprtstp: contraction number = 4.093968e-02\n Vnewton: Using errtol_s: 175081.721880\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.989476e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.613692e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.487025e+04\n Vprtstp: contraction number = 2.487025e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 5.724811e-03\n Vprtstp: contraction number = 1.398353e-01\n Vnewton: Using errtol_s: 24482.603484\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.170467e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.734539e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.528470e+03\n Vprtstp: contraction number = 4.528470e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 9.801406e-04\n Vprtstp: contraction number = 1.712092e-01\n Vnewton: Using errtol_s: 4191.647712\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.362555e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.852846e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.122748e+02\n Vprtstp: contraction number = 9.122748e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.923658e-04\n Vprtstp: contraction number = 1.962635e-01\n Vnewton: Using errtol_s: 822.667398\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.544570e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.975734e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.052635e+02\n Vprtstp: contraction number = 2.052635e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.319998e-05\n Vprtstp: contraction number = 2.245720e-01\n Vnewton: Using errtol_s: 184.748098\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.729601e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.100864e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.154123e+01\n Vprtstp: contraction number = 5.154123e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.084685e-05\n Vprtstp: contraction number = 2.510845e-01\n Vnewton: Using errtol_s: 46.387392\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.916948e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.227668e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.435770e+01\n Vprtstp: contraction number = 1.435770e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.021563e-06\n Vprtstp: contraction number = 2.785660e-01\n Vnewton: Using errtol_s: 12.921949\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.108148e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.353827e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.361187e+00\n Vprtstp: contraction number = 4.361187e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 9.178062e-07\n Vprtstp: contraction number = 3.037522e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.554598e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.572206e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.016036e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.026947e+02\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (2.518, -2.4645, 16.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -19109,15 +19109,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 9.317231145309E-01 kT\n Vpmg_energy:  qfEnergy = 2.397951074417E+03 kT\n Vpmg_energy:  dielEnergy = 1.196103394551E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.453100e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.371000e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -19165,149 +19165,149 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0717616 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.186405\n+Vacc_SASA: Time elapsed: 3.052957\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.724293e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.542202e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.812900e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.449400e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.617092e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.470240e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.361199e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.526798e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 3849668.809256\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.392443e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.545694e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.552766e+05\n Vprtstp: contraction number = 3.552766e+05\n Vnewton: Attempting damping, relres = 0.084988\n Vnewton: Attempting damping, relres = 0.539692\n Vnewton: Damping accepted, relres = 0.084988\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.498801e-02\n Vprtstp: contraction number = 8.498801e-02\n Vnewton: Using errtol_s: 327175.687931\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.644049e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.704469e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.008831e+04\n Vprtstp: contraction number = 5.008831e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.180515e-02\n Vprtstp: contraction number = 1.389037e-01\n Vnewton: Using errtol_s: 45445.906193\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.884545e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.853022e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.515214e+03\n Vprtstp: contraction number = 8.515214e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.991773e-03\n Vprtstp: contraction number = 1.687207e-01\n Vnewton: Using errtol_s: 7667.665331\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.087933e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.008530e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.650417e+03\n Vprtstp: contraction number = 1.650417e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 3.858749e-04\n Vprtstp: contraction number = 1.937344e-01\n Vnewton: Using errtol_s: 1485.490751\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.306348e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.159242e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.445276e+02\n Vprtstp: contraction number = 3.445276e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 8.054589e-05\n Vprtstp: contraction number = 2.087357e-01\n Vnewton: Using errtol_s: 310.075011\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.515534e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.313518e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.228113e+01\n Vprtstp: contraction number = 9.228113e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.157878e-05\n Vprtstp: contraction number = 2.679067e-01\n Vnewton: Using errtol_s: 83.071163\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.726288e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.470042e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.340270e+01\n Vprtstp: contraction number = 3.340270e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 7.809088e-06\n Vprtstp: contraction number = 3.618873e-01\n Vnewton: Using errtol_s: 30.062402\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.932952e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.617687e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.311951e+01\n Vprtstp: contraction number = 1.311951e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 3.067793e-06\n Vprtstp: contraction number = 3.928491e-01\n Vnewton: Using errtol_s: 11.809988\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.142933e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.765580e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.550050e+00\n Vprtstp: contraction number = 5.550050e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 1.297525e-06\n Vprtstp: contraction number = 4.229508e-01\n Vnewton: Using errtol_s: 4.995043\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.346840e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.925287e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.408064e+00\n Vprtstp: contraction number = 2.408064e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 5.629926e-07\n Vprtstp: contraction number = 4.338972e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.170762e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.187688e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.536003e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.546358e+02\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (2.518, -2.4645, 16.7425)\n Vpmg_setPart:  actual minima = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  actual maxima = (13.3006, 6.29637, 27.9102)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -19316,15 +19316,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 9.480336832725E-01 kT\n Vpmg_energy:  qfEnergy = 1.844029166481E+04 kT\n Vpmg_energy:  dielEnergy = 9.209478882547E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.473600e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.149400e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n@@ -19347,129 +19347,129 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 6.310035\n+Vacc_SASA: Time elapsed: 6.459561\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.671638e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.737244e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.356000e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.315100e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.150956e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.961900e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.622474e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.152316e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 8699406.430616\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.645902e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.170959e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.528464e+05\n Vprtstp: contraction number = 3.528464e+05\n Vnewton: Attempting damping, relres = 0.041605\n Vnewton: Attempting damping, relres = 0.513349\n Vnewton: Damping accepted, relres = 0.041605\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.160535e-02\n Vprtstp: contraction number = 4.160535e-02\n Vnewton: Using errtol_s: 361941.817774\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.886980e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.335509e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.210930e+04\n Vprtstp: contraction number = 5.210930e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 5.921711e-03\n Vprtstp: contraction number = 1.423305e-01\n Vnewton: Using errtol_s: 51515.371182\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.082468e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.479855e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.570568e+03\n Vprtstp: contraction number = 9.570568e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.018950e-03\n Vprtstp: contraction number = 1.720701e-01\n Vnewton: Using errtol_s: 8864.257334\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.288986e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.618568e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.944504e+03\n Vprtstp: contraction number = 1.944504e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.015521e-04\n Vprtstp: contraction number = 1.978037e-01\n Vnewton: Using errtol_s: 1753.383252\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.495357e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.763104e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.357668e+02\n Vprtstp: contraction number = 4.357668e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.508379e-05\n Vprtstp: contraction number = 2.236831e-01\n Vnewton: Using errtol_s: 392.202227\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.706634e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.905256e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.074784e+02\n Vprtstp: contraction number = 1.074784e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.111924e-05\n Vprtstp: contraction number = 2.466350e-01\n Vnewton: Using errtol_s: 96.730784\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.918677e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.051449e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.903808e+01\n Vprtstp: contraction number = 2.903808e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.004146e-06\n Vprtstp: contraction number = 2.701755e-01\n Vnewton: Using errtol_s: 26.134288\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.123354e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.196413e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.552738e+00\n Vprtstp: contraction number = 8.552738e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.848266e-07\n Vprtstp: contraction number = 2.945351e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.693128e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.705239e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.179296e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.189850e+02\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (2.518, -2.4645, 16.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -19478,15 +19478,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.111204276616E+00 kT\n Vpmg_energy:  qfEnergy = 3.618165500075E+03 kT\n Vpmg_energy:  dielEnergy = 1.858858240156E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.288200e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.193900e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n@@ -19534,138 +19534,138 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0804427 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 7.189843\n+Vacc_SASA: Time elapsed: 6.665222\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.160547e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.540113e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.640700e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.728600e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.062812e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.061838e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.419255e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.429369e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 7226173.981930\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.442514e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.448135e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.363534e+05\n Vprtstp: contraction number = 6.363534e+05\n Vnewton: Attempting damping, relres = 0.081351\n Vnewton: Attempting damping, relres = 0.537664\n Vnewton: Damping accepted, relres = 0.081351\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.135112e-02\n Vprtstp: contraction number = 8.135112e-02\n Vnewton: Using errtol_s: 587857.310633\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.685890e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.611797e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.753275e+04\n Vprtstp: contraction number = 8.753275e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.104343e-02\n Vprtstp: contraction number = 1.357502e-01\n Vnewton: Using errtol_s: 79801.757672\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.908050e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.764545e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.461031e+04\n Vprtstp: contraction number = 1.461031e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.821090e-03\n Vprtstp: contraction number = 1.649025e-01\n Vnewton: Using errtol_s: 13159.512971\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.011838e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.920379e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.736183e+03\n Vprtstp: contraction number = 2.736183e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 3.408124e-04\n Vprtstp: contraction number = 1.871475e-01\n Vnewton: Using errtol_s: 2462.769628\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.033697e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.073426e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.483227e+02\n Vprtstp: contraction number = 5.483227e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 6.829255e-05\n Vprtstp: contraction number = 2.003817e-01\n Vnewton: Using errtol_s: 493.493873\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.056122e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.222844e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.327802e+02\n Vprtstp: contraction number = 1.327802e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.654140e-05\n Vprtstp: contraction number = 2.422139e-01\n Vnewton: Using errtol_s: 119.531057\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.077884e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.377116e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.724135e+01\n Vprtstp: contraction number = 4.724135e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 5.883780e-06\n Vprtstp: contraction number = 3.557002e-01\n Vnewton: Using errtol_s: 42.517221\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.099795e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.527284e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.799945e+01\n Vprtstp: contraction number = 1.799945e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.242401e-06\n Vprtstp: contraction number = 3.811157e-01\n Vnewton: Using errtol_s: 16.203980\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.121752e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.677693e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.792899e+00\n Vprtstp: contraction number = 7.792899e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 9.705840e-07\n Vprtstp: contraction number = 4.328325e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.973258e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.984589e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.391463e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.402779e+02\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (2.518, -2.4645, 16.7425)\n Vpmg_setPart:  actual minima = (-53.482, -47.9645, -41.2575)\n Vpmg_setPart:  actual maxima = (13.3006, 6.29637, 27.9102)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -19674,27 +19674,27 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.121256399906E+00 kT\n Vpmg_energy:  qfEnergy = 2.906327571511E+04 kT\n Vpmg_energy:  dielEnergy = 1.455577366311E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.034700e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.407800e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  printing only subset of domain\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.139843e+03\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 7.827636e+02\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 06:21:20 2025\n+# Creation Date and Time:  Tue Jan  9 04:17:17 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path mol1.pqr\n@@ -20047,129 +20047,129 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.231347\n+Vacc_SASA: Time elapsed: 3.016151\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.827633e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.445466e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 6.602900e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.986700e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.234326e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.356970e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.645401e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.873603e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4300910.832168\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.948042e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.654106e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.776390e+05\n Vprtstp: contraction number = 1.776390e+05\n Vnewton: Attempting damping, relres = 0.041319\n Vnewton: Attempting damping, relres = 0.513474\n Vnewton: Damping accepted, relres = 0.041319\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.131938e-02\n Vprtstp: contraction number = 4.131938e-02\n Vnewton: Using errtol_s: 177710.973970\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.649824e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.186856e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.677180e+04\n Vprtstp: contraction number = 2.677180e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 5.962101e-03\n Vprtstp: contraction number = 1.442931e-01\n Vnewton: Using errtol_s: 25642.465478\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.182599e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.454548e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.966549e+03\n Vprtstp: contraction number = 4.966549e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.056655e-03\n Vprtstp: contraction number = 1.772286e-01\n Vnewton: Using errtol_s: 4544.578762\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.876022e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.724813e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.011325e+03\n Vprtstp: contraction number = 1.011325e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.118038e-04\n Vprtstp: contraction number = 2.004475e-01\n Vnewton: Using errtol_s: 910.949292\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.601379e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.024716e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.253595e+02\n Vprtstp: contraction number = 2.253595e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.715911e-05\n Vprtstp: contraction number = 2.226547e-01\n Vnewton: Using errtol_s: 202.827138\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.266766e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.400754e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.445207e+01\n Vprtstp: contraction number = 5.445207e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.139456e-05\n Vprtstp: contraction number = 2.416194e-01\n Vnewton: Using errtol_s: 49.006980\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.084165e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.630842e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.420316e+01\n Vprtstp: contraction number = 1.420316e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.972126e-06\n Vprtstp: contraction number = 2.608373e-01\n Vnewton: Using errtol_s: 12.782849\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.264405e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.887781e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.022184e+00\n Vprtstp: contraction number = 4.022184e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.416744e-07\n Vprtstp: contraction number = 2.831893e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.347732e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.362435e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.049809e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.060539e+02\n Vpmg_setPart:  lower corner = (2.518, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, -2.4645, 16.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -20178,15 +20178,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 5.829504544268E-01 kT\n Vpmg_energy:  qfEnergy = 9.542693128993E+03 kT\n Vpmg_energy:  dielEnergy = 4.766198316119E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.947900e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.393900e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 39.7309\n Vpbe_ctor2:  solute dimensions = 68.682 x 69.075 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -20234,127 +20234,127 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0324776 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.199270\n+Vacc_SASA: Time elapsed: 2.915309\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.259248e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.924558e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 6.370000e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.860500e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.150565e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.278050e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.480310e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.169136e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 6495890.956801\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.502827e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.189005e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.477908e+05\n Vprtstp: contraction number = 5.477908e+05\n Vnewton: Attempting damping, relres = 0.076573\n Vnewton: Attempting damping, relres = 0.536204\n Vnewton: Damping accepted, relres = 0.076573\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.657334e-02\n Vprtstp: contraction number = 7.657334e-02\n Vnewton: Using errtol_s: 497412.042043\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.701006e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.352956e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.388713e+04\n Vprtstp: contraction number = 7.388713e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.027070e-02\n Vprtstp: contraction number = 1.341289e-01\n Vnewton: Using errtol_s: 66717.354364\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.899253e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.505365e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.213780e+04\n Vprtstp: contraction number = 1.213780e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.681990e-03\n Vprtstp: contraction number = 1.637659e-01\n Vnewton: Using errtol_s: 10926.025346\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.112404e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.660511e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.238925e+03\n Vprtstp: contraction number = 2.238925e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 3.102037e-04\n Vprtstp: contraction number = 1.844265e-01\n Vnewton: Using errtol_s: 2015.049122\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.305273e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.814351e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.343882e+02\n Vprtstp: contraction number = 4.343882e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 6.018448e-05\n Vprtstp: contraction number = 1.940160e-01\n Vnewton: Using errtol_s: 390.951807\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.492524e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.973369e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.935633e+01\n Vprtstp: contraction number = 7.935633e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.099479e-05\n Vprtstp: contraction number = 1.826848e-01\n Vnewton: Using errtol_s: 71.420957\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.687787e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.129550e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.530287e+01\n Vprtstp: contraction number = 1.530287e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.120201e-06\n Vprtstp: contraction number = 1.928369e-01\n Vnewton: Using errtol_s: 13.772596\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.887954e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.283024e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.453153e+00\n Vprtstp: contraction number = 3.453153e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 4.784317e-07\n Vprtstp: contraction number = 2.256539e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.597109e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.610095e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.256246e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.266913e+02\n Vpmg_setPart:  lower corner = (2.518, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, -2.4645, 16.7425)\n Vpmg_setPart:  actual minima = (-8.26461, -47.9645, -41.2575)\n Vpmg_setPart:  actual maxima = (58.518, 6.29637, 27.9102)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -20363,15 +20363,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 5.483471509223E-01 kT\n Vpmg_energy:  qfEnergy = 7.516233054559E+04 kT\n Vpmg_energy:  dielEnergy = 3.774236140842E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.601000e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.831900e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -20394,129 +20394,129 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 2.987836\n+Vacc_SASA: Time elapsed: 2.955406\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.070760e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.912052e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.419000e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.253700e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.212862e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.935230e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.132769e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.476570e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4276578.139223\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.158558e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.496132e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.716926e+05\n Vprtstp: contraction number = 1.716926e+05\n Vnewton: Attempting damping, relres = 0.040940\n Vnewton: Attempting damping, relres = 0.513162\n Vnewton: Damping accepted, relres = 0.040940\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.093968e-02\n Vprtstp: contraction number = 4.093968e-02\n Vnewton: Using errtol_s: 175081.721880\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.358196e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.647135e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.487025e+04\n Vprtstp: contraction number = 2.487025e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 5.724811e-03\n Vprtstp: contraction number = 1.398353e-01\n Vnewton: Using errtol_s: 24482.603484\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.523513e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.763392e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.528470e+03\n Vprtstp: contraction number = 4.528470e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 9.801406e-04\n Vprtstp: contraction number = 1.712092e-01\n Vnewton: Using errtol_s: 4191.647712\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.703359e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.883650e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.122748e+02\n Vprtstp: contraction number = 9.122748e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.923658e-04\n Vprtstp: contraction number = 1.962635e-01\n Vnewton: Using errtol_s: 822.667398\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.873286e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.004847e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.052635e+02\n Vprtstp: contraction number = 2.052635e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.319998e-05\n Vprtstp: contraction number = 2.245720e-01\n Vnewton: Using errtol_s: 184.748098\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.053851e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.125471e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.154123e+01\n Vprtstp: contraction number = 5.154123e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.084685e-05\n Vprtstp: contraction number = 2.510845e-01\n Vnewton: Using errtol_s: 46.387392\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.230359e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.248308e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.435770e+01\n Vprtstp: contraction number = 1.435770e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.021563e-06\n Vprtstp: contraction number = 2.785660e-01\n Vnewton: Using errtol_s: 12.921949\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.413816e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.371841e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.361187e+00\n Vprtstp: contraction number = 4.361187e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 9.178062e-07\n Vprtstp: contraction number = 3.037522e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.443119e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.455917e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.008293e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.018855e+02\n Vpmg_setPart:  lower corner = (2.518, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, -2.4645, 16.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -20525,15 +20525,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 5.849546283812E-03 kT\n Vpmg_energy:  qfEnergy = 0.000000000000E+00 kT\n Vpmg_energy:  dielEnergy = 5.146958313419E-02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.365500e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.391300e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -20581,127 +20581,127 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00106787 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.179446\n+Vacc_SASA: Time elapsed: 3.059971\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.443478e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.179732e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.681200e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.694700e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.177468e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.971500e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.634147e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.538643e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 652367.043511\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.656762e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.557201e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.625442e+04\n Vprtstp: contraction number = 6.625442e+04\n Vnewton: Attempting damping, relres = 0.091545\n Vnewton: Attempting damping, relres = 0.542935\n Vnewton: Damping accepted, relres = 0.091545\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.154497e-02\n Vprtstp: contraction number = 9.154497e-02\n Vnewton: Using errtol_s: 59720.919943\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.807292e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.670377e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.669735e+03\n Vprtstp: contraction number = 8.669735e+03\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.196277e-02\n Vprtstp: contraction number = 1.306764e-01\n Vnewton: Using errtol_s: 7804.116477\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.929155e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.770328e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.277730e+03\n Vprtstp: contraction number = 1.277730e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.762772e-03\n Vprtstp: contraction number = 1.473548e-01\n Vnewton: Using errtol_s: 1149.974141\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.049586e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.871863e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.050893e+02\n Vprtstp: contraction number = 2.050893e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.829401e-04\n Vprtstp: contraction number = 1.605086e-01\n Vnewton: Using errtol_s: 184.580789\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.172143e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.982048e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.556662e+01\n Vprtstp: contraction number = 3.556662e+01\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.906742e-05\n Vprtstp: contraction number = 1.734198e-01\n Vnewton: Using errtol_s: 32.009971\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.305898e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.086006e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.633566e+00\n Vprtstp: contraction number = 6.633566e+00\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 9.151612e-06\n Vprtstp: contraction number = 1.865109e-01\n Vnewton: Using errtol_s: 5.970210\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.425779e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.185553e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.319897e+00\n Vprtstp: contraction number = 1.319897e+00\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.820919e-06\n Vprtstp: contraction number = 1.989725e-01\n Vnewton: Using errtol_s: 1.187907\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.554811e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.293202e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.771301e-01\n Vprtstp: contraction number = 2.771301e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 3.823263e-07\n Vprtstp: contraction number = 2.099634e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.029705e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.042490e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 8.516799e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.623478e+01\n Vpmg_setPart:  lower corner = (2.518, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, -2.4645, 16.7425)\n Vpmg_setPart:  actual minima = (-8.26461, -47.9645, -41.2575)\n Vpmg_setPart:  actual maxima = (58.518, 6.29637, 27.9102)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -20710,15 +20710,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 5.030362261326E-03 kT\n Vpmg_energy:  qfEnergy = 0.000000000000E+00 kT\n Vpmg_energy:  dielEnergy = 4.051459785687E-02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.220100e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.999600e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n@@ -20741,129 +20741,129 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 6.965340\n+Vacc_SASA: Time elapsed: 6.315162\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.309012e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.592293e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.056700e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.408500e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.194808e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.738740e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.760520e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.478303e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 8699406.430616\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.782725e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.500379e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.528464e+05\n Vprtstp: contraction number = 3.528464e+05\n Vnewton: Attempting damping, relres = 0.041605\n Vnewton: Attempting damping, relres = 0.513349\n Vnewton: Damping accepted, relres = 0.041605\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.160535e-02\n Vprtstp: contraction number = 4.160535e-02\n Vnewton: Using errtol_s: 361941.817774\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.979940e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.674392e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.210930e+04\n Vprtstp: contraction number = 5.210930e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 5.921711e-03\n Vprtstp: contraction number = 1.423305e-01\n Vnewton: Using errtol_s: 51515.371182\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.137649e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.842545e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.570568e+03\n Vprtstp: contraction number = 9.570568e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.018950e-03\n Vprtstp: contraction number = 1.720701e-01\n Vnewton: Using errtol_s: 8864.257334\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.287993e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.982447e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.944504e+03\n Vprtstp: contraction number = 1.944504e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.015521e-04\n Vprtstp: contraction number = 1.978037e-01\n Vnewton: Using errtol_s: 1753.383252\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.492447e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.127541e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.357668e+02\n Vprtstp: contraction number = 4.357668e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.508379e-05\n Vprtstp: contraction number = 2.236831e-01\n Vnewton: Using errtol_s: 392.202227\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.691514e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.262885e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.074784e+02\n Vprtstp: contraction number = 1.074784e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.111924e-05\n Vprtstp: contraction number = 2.466350e-01\n Vnewton: Using errtol_s: 96.730784\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.883056e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.411288e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.903808e+01\n Vprtstp: contraction number = 2.903808e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.004146e-06\n Vprtstp: contraction number = 2.701755e-01\n Vnewton: Using errtol_s: 26.134288\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.092078e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.553423e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.552738e+00\n Vprtstp: contraction number = 8.552738e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.848266e-07\n Vprtstp: contraction number = 2.945351e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.490572e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.503245e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.222002e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.232335e+02\n Vpmg_setPart:  lower corner = (2.518, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, -2.4645, 16.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -20872,17 +20872,17 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 6.211035436477E-01 kT\n Vpmg_energy:  qfEnergy = 9.542244232526E+03 kT\n Vpmg_energy:  dielEnergy = 4.766290532541E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.745800e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.570800e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -20928,127 +20928,127 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0370217 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 6.985607\n+Vacc_SASA: Time elapsed: 6.235609\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.933476e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.013225e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.180800e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.227800e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.043189e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.025081e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.353004e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.793108e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 7064626.020092\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.374707e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.813065e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.009458e+05\n Vprtstp: contraction number = 6.009458e+05\n Vnewton: Attempting damping, relres = 0.077277\n Vnewton: Attempting damping, relres = 0.536445\n Vnewton: Damping accepted, relres = 0.077277\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.727667e-02\n Vprtstp: contraction number = 7.727667e-02\n Vnewton: Using errtol_s: 545930.796082\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.585265e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.981592e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.090350e+04\n Vprtstp: contraction number = 8.090350e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.034337e-02\n Vprtstp: contraction number = 1.338486e-01\n Vnewton: Using errtol_s: 73072.056615\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.779785e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.139689e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.317148e+04\n Vprtstp: contraction number = 1.317148e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.678394e-03\n Vprtstp: contraction number = 1.622676e-01\n Vnewton: Using errtol_s: 11857.226595\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.960573e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.305347e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.401584e+03\n Vprtstp: contraction number = 2.401584e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 3.059541e-04\n Vprtstp: contraction number = 1.822898e-01\n Vnewton: Using errtol_s: 2161.451428\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.143175e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.460169e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.616256e+02\n Vprtstp: contraction number = 4.616256e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.880932e-05\n Vprtstp: contraction number = 1.922161e-01\n Vnewton: Using errtol_s: 415.465831\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.327619e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.609620e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.389879e+01\n Vprtstp: contraction number = 8.389879e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.068835e-05\n Vprtstp: contraction number = 1.817458e-01\n Vnewton: Using errtol_s: 75.509189\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.529386e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.759336e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.600785e+01\n Vprtstp: contraction number = 1.600785e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.039328e-06\n Vprtstp: contraction number = 1.907991e-01\n Vnewton: Using errtol_s: 14.407086\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.725172e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.914782e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.576512e+00\n Vprtstp: contraction number = 3.576512e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 4.556310e-07\n Vprtstp: contraction number = 2.234222e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.540068e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.551476e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.253583e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.264933e+02\n Vpmg_setPart:  lower corner = (2.518, -47.9645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, -2.4645, 16.7425)\n Vpmg_setPart:  actual minima = (-8.26461, -47.9645, -41.2575)\n Vpmg_setPart:  actual maxima = (58.518, 6.29637, 27.9102)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -21057,27 +21057,27 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 6.057106214068E-01 kT\n Vpmg_energy:  qfEnergy = 7.516201956521E+04 kT\n Vpmg_energy:  dielEnergy = 3.774250460752E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.642800e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.091200e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  printing only subset of domain\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 8.899309e+02\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 7.052912e+02\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 06:23:46 2025\n+# Creation Date and Time:  Tue Jan  9 04:20:40 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path mol1.pqr\n@@ -21430,129 +21430,129 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.257354\n+Vacc_SASA: Time elapsed: 3.071561\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.819888e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.486178e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.854500e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.239400e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.837060e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.998950e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.294986e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.937974e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4300910.832168\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.112333e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.962600e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.776390e+05\n Vprtstp: contraction number = 1.776390e+05\n Vnewton: Attempting damping, relres = 0.041319\n Vnewton: Attempting damping, relres = 0.513474\n Vnewton: Damping accepted, relres = 0.041319\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.131938e-02\n Vprtstp: contraction number = 4.131938e-02\n Vnewton: Using errtol_s: 177710.973970\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.462130e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.374465e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.677180e+04\n Vprtstp: contraction number = 2.677180e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 5.962101e-03\n Vprtstp: contraction number = 1.442931e-01\n Vnewton: Using errtol_s: 25642.465478\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.957120e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.816750e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.966549e+03\n Vprtstp: contraction number = 4.966549e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.056655e-03\n Vprtstp: contraction number = 1.772286e-01\n Vnewton: Using errtol_s: 4544.578762\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.458638e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.084653e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.011325e+03\n Vprtstp: contraction number = 1.011325e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.118038e-04\n Vprtstp: contraction number = 2.004475e-01\n Vnewton: Using errtol_s: 910.949292\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.209573e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.446744e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.253595e+02\n Vprtstp: contraction number = 2.253595e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.715911e-05\n Vprtstp: contraction number = 2.226547e-01\n Vnewton: Using errtol_s: 202.827138\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.630399e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.677407e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.445207e+01\n Vprtstp: contraction number = 5.445207e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.139456e-05\n Vprtstp: contraction number = 2.416194e-01\n Vnewton: Using errtol_s: 49.006980\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.022956e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.969556e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.420316e+01\n Vprtstp: contraction number = 1.420316e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.972126e-06\n Vprtstp: contraction number = 2.608373e-01\n Vnewton: Using errtol_s: 12.782849\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.177203e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.017494e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.022184e+00\n Vprtstp: contraction number = 4.022184e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.416744e-07\n Vprtstp: contraction number = 2.831893e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.239158e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.250393e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.080135e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.091439e+02\n Vpmg_setPart:  lower corner = (-53.482, -2.4645, -41.2575)\n Vpmg_setPart:  upper corner = (2.518, 43.0355, 16.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -21561,17 +21561,17 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 6.136518672902E-02 kT\n Vpmg_energy:  qfEnergy = 4.355357372613E+01 kT\n Vpmg_energy:  dielEnergy = 4.752320511857E+01 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.035500e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.601300e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 4.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 39.7309\n Vpbe_ctor2:  solute dimensions = 68.682 x 69.075 x 70.346\n Vpbe_ctor2:  solute charge = -12\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -21617,127 +21617,127 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00231815 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.088743\n+Vacc_SASA: Time elapsed: 2.942979\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.829140e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.514091e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 6.899100e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.323200e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.215991e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.004609e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.364632e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.196677e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2402140.419777\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.389646e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.216673e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.993407e+05\n Vprtstp: contraction number = 1.993407e+05\n Vnewton: Attempting damping, relres = 0.074788\n Vnewton: Attempting damping, relres = 0.535005\n Vnewton: Damping accepted, relres = 0.074788\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.478844e-02\n Vprtstp: contraction number = 7.478844e-02\n Vnewton: Using errtol_s: 179652.345700\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.594036e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.396298e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.540846e+04\n Vprtstp: contraction number = 2.540846e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 9.520223e-03\n Vprtstp: contraction number = 1.272954e-01\n Vnewton: Using errtol_s: 22868.913120\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.779269e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.552434e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.863220e+03\n Vprtstp: contraction number = 3.863220e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.447432e-03\n Vprtstp: contraction number = 1.520376e-01\n Vnewton: Using errtol_s: 3476.934666\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.955135e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.702045e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.609951e+02\n Vprtstp: contraction number = 6.609951e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.476530e-04\n Vprtstp: contraction number = 1.710982e-01\n Vnewton: Using errtol_s: 594.897360\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.160801e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.853015e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.229316e+02\n Vprtstp: contraction number = 1.229316e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.605831e-05\n Vprtstp: contraction number = 1.859792e-01\n Vnewton: Using errtol_s: 110.638524\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.347130e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.011683e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.422381e+01\n Vprtstp: contraction number = 2.422381e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 9.075836e-06\n Vprtstp: contraction number = 1.970510e-01\n Vnewton: Using errtol_s: 21.801431\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.528855e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.162998e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.026312e+00\n Vprtstp: contraction number = 5.026312e+00\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.883187e-06\n Vprtstp: contraction number = 2.074947e-01\n Vnewton: Using errtol_s: 4.523681\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.746446e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.329229e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.096485e+00\n Vprtstp: contraction number = 1.096485e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 4.108154e-07\n Vprtstp: contraction number = 2.181490e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.562623e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.576325e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.290725e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.302063e+02\n Vpmg_setPart:  lower corner = (-53.482, -2.4645, -41.2575)\n Vpmg_setPart:  upper corner = (2.518, 43.0355, 16.7425)\n Vpmg_setPart:  actual minima = (-53.482, -11.2254, -41.2575)\n Vpmg_setPart:  actual maxima = (13.3006, 43.0355, 27.9102)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -21746,15 +21746,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 5.937401577775E-02 kT\n Vpmg_energy:  qfEnergy = 4.174168231022E+02 kT\n Vpmg_energy:  dielEnergy = 2.811735250011E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.869900e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.823600e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -21777,129 +21777,129 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.172633\n+Vacc_SASA: Time elapsed: 2.936544\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.335975e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.889540e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.586300e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.383600e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.127808e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.082389e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.983319e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.538687e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4276578.139223\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.001953e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.557633e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.716926e+05\n Vprtstp: contraction number = 1.716926e+05\n Vnewton: Attempting damping, relres = 0.040940\n Vnewton: Attempting damping, relres = 0.513162\n Vnewton: Damping accepted, relres = 0.040940\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.093968e-02\n Vprtstp: contraction number = 4.093968e-02\n Vnewton: Using errtol_s: 175081.721880\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.151162e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.702172e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.487025e+04\n Vprtstp: contraction number = 2.487025e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 5.724811e-03\n Vprtstp: contraction number = 1.398353e-01\n Vnewton: Using errtol_s: 24482.603484\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.283514e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.819397e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.528470e+03\n Vprtstp: contraction number = 4.528470e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 9.801406e-04\n Vprtstp: contraction number = 1.712092e-01\n Vnewton: Using errtol_s: 4191.647712\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.433004e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.947059e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.122748e+02\n Vprtstp: contraction number = 9.122748e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.923658e-04\n Vprtstp: contraction number = 1.962635e-01\n Vnewton: Using errtol_s: 822.667398\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.604391e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.076688e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.052635e+02\n Vprtstp: contraction number = 2.052635e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.319998e-05\n Vprtstp: contraction number = 2.245720e-01\n Vnewton: Using errtol_s: 184.748098\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.778375e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.217581e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.154123e+01\n Vprtstp: contraction number = 5.154123e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.084685e-05\n Vprtstp: contraction number = 2.510845e-01\n Vnewton: Using errtol_s: 46.387392\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.947724e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.370150e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.435770e+01\n Vprtstp: contraction number = 1.435770e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.021563e-06\n Vprtstp: contraction number = 2.785660e-01\n Vnewton: Using errtol_s: 12.921949\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.108115e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.507575e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.361187e+00\n Vprtstp: contraction number = 4.361187e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 9.178062e-07\n Vprtstp: contraction number = 3.037522e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.256544e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.268518e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.106781e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.118255e+02\n Vpmg_setPart:  lower corner = (-53.482, -2.4645, -41.2575)\n Vpmg_setPart:  upper corner = (2.518, 43.0355, 16.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -21908,15 +21908,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.911964187079E-01 kT\n Vpmg_energy:  qfEnergy = 3.802931672989E+03 kT\n Vpmg_energy:  dielEnergy = 1.840794517786E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.601600e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.271400e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -21964,127 +21964,127 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00427913 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.218706\n+Vacc_SASA: Time elapsed: 3.058760\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.708051e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.425711e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.842300e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.084600e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 8.832230e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.628080e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.298165e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.701123e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 3438753.706105\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.317189e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.725722e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.983675e+05\n Vprtstp: contraction number = 2.983675e+05\n Vnewton: Attempting damping, relres = 0.078821\n Vnewton: Attempting damping, relres = 0.537150\n Vnewton: Damping accepted, relres = 0.078821\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.882110e-02\n Vprtstp: contraction number = 7.882110e-02\n Vnewton: Using errtol_s: 271046.361497\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.528372e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.898434e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.000218e+04\n Vprtstp: contraction number = 4.000218e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.049665e-02\n Vprtstp: contraction number = 1.331706e-01\n Vnewton: Using errtol_s: 36095.399051\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.729604e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.065162e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.428391e+03\n Vprtstp: contraction number = 6.428391e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.682686e-03\n Vprtstp: contraction number = 1.603069e-01\n Vnewton: Using errtol_s: 5786.342471\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.939783e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.219652e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.149080e+03\n Vprtstp: contraction number = 1.149080e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 3.007422e-04\n Vprtstp: contraction number = 1.787275e-01\n Vnewton: Using errtol_s: 1034.178484\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.156172e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.364112e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.202083e+02\n Vprtstp: contraction number = 2.202083e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.763359e-05\n Vprtstp: contraction number = 1.916378e-01\n Vnewton: Using errtol_s: 198.187725\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.369539e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.507060e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.389925e+01\n Vprtstp: contraction number = 4.389925e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.148943e-05\n Vprtstp: contraction number = 1.993531e-01\n Vnewton: Using errtol_s: 39.509333\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.565053e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.666291e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.964795e+00\n Vprtstp: contraction number = 8.964795e+00\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.346291e-06\n Vprtstp: contraction number = 2.042129e-01\n Vnewton: Using errtol_s: 8.068316\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.738928e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.824200e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.877921e+00\n Vprtstp: contraction number = 1.877921e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 4.914947e-07\n Vprtstp: contraction number = 2.094773e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.631325e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.640959e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.273155e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.283422e+02\n Vpmg_setPart:  lower corner = (-53.482, -2.4645, -41.2575)\n Vpmg_setPart:  upper corner = (2.518, 43.0355, 16.7425)\n Vpmg_setPart:  actual minima = (-53.482, -11.2254, -41.2575)\n Vpmg_setPart:  actual maxima = (13.3006, 43.0355, 27.9102)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -22093,15 +22093,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.727005736130E-01 kT\n Vpmg_energy:  qfEnergy = 2.988671053842E+04 kT\n Vpmg_energy:  dielEnergy = 1.487788509003E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.528100e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.272100e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n@@ -22124,129 +22124,129 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 6.914039\n+Vacc_SASA: Time elapsed: 6.379015\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.262127e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.629652e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.504600e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.314600e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.134740e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.098840e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.024757e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.063295e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 8699406.430616\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.049090e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.083753e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.528464e+05\n Vprtstp: contraction number = 3.528464e+05\n Vnewton: Attempting damping, relres = 0.041605\n Vnewton: Attempting damping, relres = 0.513349\n Vnewton: Damping accepted, relres = 0.041605\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.160535e-02\n Vprtstp: contraction number = 4.160535e-02\n Vnewton: Using errtol_s: 361941.817774\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.270223e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.265817e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.210930e+04\n Vprtstp: contraction number = 5.210930e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 5.921711e-03\n Vprtstp: contraction number = 1.423305e-01\n Vnewton: Using errtol_s: 51515.371182\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.475246e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.410884e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.570568e+03\n Vprtstp: contraction number = 9.570568e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.018950e-03\n Vprtstp: contraction number = 1.720701e-01\n Vnewton: Using errtol_s: 8864.257334\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.677668e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.564995e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.944504e+03\n Vprtstp: contraction number = 1.944504e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.015521e-04\n Vprtstp: contraction number = 1.978037e-01\n Vnewton: Using errtol_s: 1753.383252\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.878260e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.715465e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.357668e+02\n Vprtstp: contraction number = 4.357668e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.508379e-05\n Vprtstp: contraction number = 2.236831e-01\n Vnewton: Using errtol_s: 392.202227\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.083601e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.854913e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.074784e+02\n Vprtstp: contraction number = 1.074784e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.111924e-05\n Vprtstp: contraction number = 2.466350e-01\n Vnewton: Using errtol_s: 96.730784\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.297956e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.047628e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.903808e+01\n Vprtstp: contraction number = 2.903808e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.004146e-06\n Vprtstp: contraction number = 2.701755e-01\n Vnewton: Using errtol_s: 26.134288\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.499248e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.195247e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.552738e+00\n Vprtstp: contraction number = 8.552738e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.848266e-07\n Vprtstp: contraction number = 2.945351e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.650673e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.662625e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.266667e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.278226e+02\n Vpmg_setPart:  lower corner = (-53.482, -2.4645, -41.2575)\n Vpmg_setPart:  upper corner = (2.518, 43.0355, 16.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -22255,15 +22255,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 3.095882318015E-01 kT\n Vpmg_energy:  qfEnergy = 3.878073055635E+03 kT\n Vpmg_energy:  dielEnergy = 1.902406349449E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.161600e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.297800e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n@@ -22311,127 +22311,127 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0124605 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 6.698321\n+Vacc_SASA: Time elapsed: 6.226451\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.364212e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.956439e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.555100e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.275600e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.166825e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.060953e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.771712e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.422450e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 5736524.194850\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.793549e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.443547e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.767730e+05\n Vprtstp: contraction number = 4.767730e+05\n Vnewton: Attempting damping, relres = 0.075286\n Vnewton: Attempting damping, relres = 0.535307\n Vnewton: Damping accepted, relres = 0.075286\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.528638e-02\n Vprtstp: contraction number = 7.528638e-02\n Vnewton: Using errtol_s: 431882.117004\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.013081e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.625459e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.255964e+04\n Vprtstp: contraction number = 6.255964e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 9.827684e-03\n Vprtstp: contraction number = 1.305373e-01\n Vnewton: Using errtol_s: 56376.745785\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.212226e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.781995e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.936134e+03\n Vprtstp: contraction number = 9.936134e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.558974e-03\n Vprtstp: contraction number = 1.586309e-01\n Vnewton: Using errtol_s: 8943.094496\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.405958e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.932629e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.786775e+03\n Vprtstp: contraction number = 1.786775e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.803288e-04\n Vprtstp: contraction number = 1.798162e-01\n Vnewton: Using errtol_s: 1608.113190\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.614041e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.091554e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.548476e+02\n Vprtstp: contraction number = 3.548476e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.567220e-05\n Vprtstp: contraction number = 1.985960e-01\n Vnewton: Using errtol_s: 319.364924\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.830724e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.246423e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.691838e+01\n Vprtstp: contraction number = 7.691838e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.206774e-05\n Vprtstp: contraction number = 2.167643e-01\n Vnewton: Using errtol_s: 69.226906\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.049954e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.388106e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.836013e+01\n Vprtstp: contraction number = 1.836013e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.880520e-06\n Vprtstp: contraction number = 2.386958e-01\n Vnewton: Using errtol_s: 16.524170\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.280639e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.538449e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.825966e+00\n Vprtstp: contraction number = 4.825966e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 7.571442e-07\n Vprtstp: contraction number = 2.628499e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.737968e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.750367e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.256107e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.267366e+02\n Vpmg_setPart:  lower corner = (-53.482, -2.4645, -41.2575)\n Vpmg_setPart:  upper corner = (2.518, 43.0355, 16.7425)\n Vpmg_setPart:  actual minima = (-53.482, -11.2254, -41.2575)\n Vpmg_setPart:  actual maxima = (13.3006, 43.0355, 27.9102)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -22440,27 +22440,27 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 3.027416628019E-01 kT\n Vpmg_energy:  qfEnergy = 3.032769300439E+04 kT\n Vpmg_energy:  dielEnergy = 1.516953015159E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 8.833900e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.168700e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  printing only subset of domain\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 9.516696e+02\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 7.684430e+02\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 06:26:20 2025\n+# Creation Date and Time:  Tue Jan  9 04:23:39 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path mol1.pqr\n@@ -22813,129 +22813,129 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 2.999484\n+Vacc_SASA: Time elapsed: 2.945509\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.527071e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.298004e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.421900e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.112600e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.071568e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.014400e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.015826e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.741805e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4300910.832168\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.365069e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.728223e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.776390e+05\n Vprtstp: contraction number = 1.776390e+05\n Vnewton: Attempting damping, relres = 0.041319\n Vnewton: Attempting damping, relres = 0.513474\n Vnewton: Damping accepted, relres = 0.041319\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.131938e-02\n Vprtstp: contraction number = 4.131938e-02\n Vnewton: Using errtol_s: 177710.973970\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.904697e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.217619e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.677180e+04\n Vprtstp: contraction number = 2.677180e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 5.962101e-03\n Vprtstp: contraction number = 1.442931e-01\n Vnewton: Using errtol_s: 25642.465478\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.930984e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.474668e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.966549e+03\n Vprtstp: contraction number = 4.966549e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.056655e-03\n Vprtstp: contraction number = 1.772286e-01\n Vnewton: Using errtol_s: 4544.578762\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.986407e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.005953e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.011325e+03\n Vprtstp: contraction number = 1.011325e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.118038e-04\n Vprtstp: contraction number = 2.004475e-01\n Vnewton: Using errtol_s: 910.949292\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.022799e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.569665e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.253595e+02\n Vprtstp: contraction number = 2.253595e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.715911e-05\n Vprtstp: contraction number = 2.226547e-01\n Vnewton: Using errtol_s: 202.827138\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.116389e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.858639e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.445207e+01\n Vprtstp: contraction number = 5.445207e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.139456e-05\n Vprtstp: contraction number = 2.416194e-01\n Vnewton: Using errtol_s: 49.006980\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.317272e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.212655e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.420316e+01\n Vprtstp: contraction number = 1.420316e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.972126e-06\n Vprtstp: contraction number = 2.608373e-01\n Vnewton: Using errtol_s: 12.782849\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.502022e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.051098e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.022184e+00\n Vprtstp: contraction number = 4.022184e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.416744e-07\n Vprtstp: contraction number = 2.831893e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.617975e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.629996e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.101354e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.112751e+02\n Vpmg_setPart:  lower corner = (2.518, -2.4645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 16.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -22944,15 +22944,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.578940273076E+00 kT\n Vpmg_energy:  qfEnergy = 1.464055888829E+04 kT\n Vpmg_energy:  dielEnergy = 7.268608527503E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.999000e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.876500e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 39.7309\n Vpbe_ctor2:  solute dimensions = 68.682 x 69.075 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -23000,138 +23000,138 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.246197 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 2.913639\n+Vacc_SASA: Time elapsed: 3.000320\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.140314e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.103700e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 6.145800e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.335700e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.175109e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.533760e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.743994e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.222607e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 7187187.181934\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.770142e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.244470e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.181171e+05\n Vprtstp: contraction number = 6.181171e+05\n Vnewton: Attempting damping, relres = 0.078820\n Vnewton: Attempting damping, relres = 0.536981\n Vnewton: Damping accepted, relres = 0.078820\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.881989e-02\n Vprtstp: contraction number = 7.881989e-02\n Vnewton: Using errtol_s: 566493.329521\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.018994e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.429481e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.371738e+04\n Vprtstp: contraction number = 8.371738e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.055690e-02\n Vprtstp: contraction number = 1.339370e-01\n Vnewton: Using errtol_s: 75874.442084\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.264819e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.582247e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.390337e+04\n Vprtstp: contraction number = 1.390337e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.741620e-03\n Vprtstp: contraction number = 1.649745e-01\n Vnewton: Using errtol_s: 12517.346695\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.495295e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.744251e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.648048e+03\n Vprtstp: contraction number = 2.648048e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 3.316551e-04\n Vprtstp: contraction number = 1.904291e-01\n Vnewton: Using errtol_s: 2383.666964\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.735448e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.901842e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.422627e+02\n Vprtstp: contraction number = 5.422627e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 6.790546e-05\n Vprtstp: contraction number = 2.047472e-01\n Vnewton: Using errtol_s: 488.049223\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.974421e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.061332e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.184576e+02\n Vprtstp: contraction number = 1.184576e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.483378e-05\n Vprtstp: contraction number = 2.184475e-01\n Vnewton: Using errtol_s: 106.613126\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.215287e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.253447e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.976808e+01\n Vprtstp: contraction number = 2.976808e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.727649e-06\n Vprtstp: contraction number = 2.512947e-01\n Vnewton: Using errtol_s: 26.791312\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.451526e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.419101e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.888808e+00\n Vprtstp: contraction number = 8.888808e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.113097e-06\n Vprtstp: contraction number = 2.986056e-01\n Vnewton: Using errtol_s: 8.000035\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.702516e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.571622e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.963970e+00\n Vprtstp: contraction number = 2.963970e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.711568e-07\n Vprtstp: contraction number = 3.334452e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.189955e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.203155e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.495999e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.507062e+02\n Vpmg_setPart:  lower corner = (2.518, -2.4645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 16.7425)\n Vpmg_setPart:  actual minima = (-8.26461, -11.2254, -41.2575)\n Vpmg_setPart:  actual maxima = (58.518, 43.0355, 27.9102)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -23140,17 +23140,17 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.679263931619E+00 kT\n Vpmg_energy:  qfEnergy = 1.125861211589E+05 kT\n Vpmg_energy:  dielEnergy = 5.606777456856E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.452800e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.742800e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -23171,129 +23171,129 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.178469\n+Vacc_SASA: Time elapsed: 2.670137\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.312364e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.676545e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.136100e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.190700e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.313778e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.041831e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.991872e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.767324e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4276578.139223\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.019571e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.788936e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.716926e+05\n Vprtstp: contraction number = 1.716926e+05\n Vnewton: Attempting damping, relres = 0.040940\n Vnewton: Attempting damping, relres = 0.513162\n Vnewton: Damping accepted, relres = 0.040940\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.093968e-02\n Vprtstp: contraction number = 4.093968e-02\n Vnewton: Using errtol_s: 175081.721880\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.245113e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.954880e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.487025e+04\n Vprtstp: contraction number = 2.487025e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 5.724811e-03\n Vprtstp: contraction number = 1.398353e-01\n Vnewton: Using errtol_s: 24482.603484\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.430065e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.111224e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.528470e+03\n Vprtstp: contraction number = 4.528470e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 9.801406e-04\n Vprtstp: contraction number = 1.712092e-01\n Vnewton: Using errtol_s: 4191.647712\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.633325e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.232492e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.122748e+02\n Vprtstp: contraction number = 9.122748e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.923658e-04\n Vprtstp: contraction number = 1.962635e-01\n Vnewton: Using errtol_s: 822.667398\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.829051e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.343167e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.052635e+02\n Vprtstp: contraction number = 2.052635e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.319998e-05\n Vprtstp: contraction number = 2.245720e-01\n Vnewton: Using errtol_s: 184.748098\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.026185e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.472116e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.154123e+01\n Vprtstp: contraction number = 5.154123e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.084685e-05\n Vprtstp: contraction number = 2.510845e-01\n Vnewton: Using errtol_s: 46.387392\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.209784e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.600741e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.435770e+01\n Vprtstp: contraction number = 1.435770e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.021563e-06\n Vprtstp: contraction number = 2.785660e-01\n Vnewton: Using errtol_s: 12.921949\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.400251e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.732370e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.361187e+00\n Vprtstp: contraction number = 4.361187e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 9.178062e-07\n Vprtstp: contraction number = 3.037522e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.559564e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.573992e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.079806e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.090855e+02\n Vpmg_setPart:  lower corner = (2.518, -2.4645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 16.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -23302,17 +23302,17 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 4.880126377174E-02 kT\n Vpmg_energy:  qfEnergy = 0.000000000000E+00 kT\n Vpmg_energy:  dielEnergy = 3.532414743910E-01 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.229700e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.419900e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -23358,127 +23358,127 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.000694544 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.213690\n+Vacc_SASA: Time elapsed: 2.996353\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.507782e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.217497e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.590900e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.061900e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.190841e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.983020e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.610761e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.901769e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 947577.428093\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.634231e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.921698e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.028571e+05\n Vprtstp: contraction number = 1.028571e+05\n Vnewton: Attempting damping, relres = 0.100178\n Vnewton: Attempting damping, relres = 0.546680\n Vnewton: Damping accepted, relres = 0.100178\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.001782e-01\n Vprtstp: contraction number = 1.001782e-01\n Vnewton: Using errtol_s: 94926.584698\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.793947e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.046931e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.470559e+04\n Vprtstp: contraction number = 1.470559e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.405726e-02\n Vprtstp: contraction number = 1.403226e-01\n Vnewton: Using errtol_s: 13320.343474\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.956062e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.155056e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.349875e+03\n Vprtstp: contraction number = 2.349875e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.232971e-03\n Vprtstp: contraction number = 1.588482e-01\n Vnewton: Using errtol_s: 2115.913123\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.120867e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.289403e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.041926e+02\n Vprtstp: contraction number = 4.041926e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 3.839085e-04\n Vprtstp: contraction number = 1.719272e-01\n Vnewton: Using errtol_s: 363.783073\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.281467e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.430457e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.386262e+01\n Vprtstp: contraction number = 7.386262e+01\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 7.015424e-05\n Vprtstp: contraction number = 1.827368e-01\n Vnewton: Using errtol_s: 66.476570\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.449474e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.535917e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.423266e+01\n Vprtstp: contraction number = 1.423266e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.351805e-05\n Vprtstp: contraction number = 1.926905e-01\n Vnewton: Using errtol_s: 12.809401\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.631054e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.640742e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.877145e+00\n Vprtstp: contraction number = 2.877145e+00\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.732685e-06\n Vprtstp: contraction number = 2.021508e-01\n Vnewton: Using errtol_s: 2.589431\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.796832e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.750859e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.073349e-01\n Vprtstp: contraction number = 6.073349e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 5.768409e-07\n Vprtstp: contraction number = 2.110894e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.342918e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.356163e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 9.405483e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 9.511429e+01\n Vpmg_setPart:  lower corner = (2.518, -2.4645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 16.7425)\n Vpmg_setPart:  actual minima = (-8.26461, -11.2254, -41.2575)\n Vpmg_setPart:  actual maxima = (58.518, 43.0355, 27.9102)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -23487,15 +23487,15 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 5.348045314741E-02 kT\n Vpmg_energy:  qfEnergy = 0.000000000000E+00 kT\n Vpmg_energy:  dielEnergy = 3.080172074466E-01 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.040600e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.582100e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n@@ -23518,129 +23518,129 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 6.826278\n+Vacc_SASA: Time elapsed: 6.218119\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.315835e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.511326e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.314700e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.288500e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.182351e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.034704e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.051490e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.929918e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 8699406.430616\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.076109e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.951080e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.528464e+05\n Vprtstp: contraction number = 3.528464e+05\n Vnewton: Attempting damping, relres = 0.041605\n Vnewton: Attempting damping, relres = 0.513349\n Vnewton: Damping accepted, relres = 0.041605\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.160535e-02\n Vprtstp: contraction number = 4.160535e-02\n Vnewton: Using errtol_s: 361941.817774\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.301317e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.117553e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.210930e+04\n Vprtstp: contraction number = 5.210930e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 5.921711e-03\n Vprtstp: contraction number = 1.423305e-01\n Vnewton: Using errtol_s: 51515.371182\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.510521e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.258327e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.570568e+03\n Vprtstp: contraction number = 9.570568e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.018950e-03\n Vprtstp: contraction number = 1.720701e-01\n Vnewton: Using errtol_s: 8864.257334\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.710298e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.396931e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.944504e+03\n Vprtstp: contraction number = 1.944504e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.015521e-04\n Vprtstp: contraction number = 1.978037e-01\n Vnewton: Using errtol_s: 1753.383252\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.918446e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.551127e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.357668e+02\n Vprtstp: contraction number = 4.357668e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.508379e-05\n Vprtstp: contraction number = 2.236831e-01\n Vnewton: Using errtol_s: 392.202227\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.115995e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.709779e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.074784e+02\n Vprtstp: contraction number = 1.074784e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.111924e-05\n Vprtstp: contraction number = 2.466350e-01\n Vnewton: Using errtol_s: 96.730784\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.330964e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.852278e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.903808e+01\n Vprtstp: contraction number = 2.903808e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.004146e-06\n Vprtstp: contraction number = 2.701755e-01\n Vnewton: Using errtol_s: 26.134288\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.540510e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.999319e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.552738e+00\n Vprtstp: contraction number = 8.552738e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.848266e-07\n Vprtstp: contraction number = 2.945351e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.682469e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.695062e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.216445e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.227359e+02\n Vpmg_setPart:  lower corner = (2.518, -2.4645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 16.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -23649,17 +23649,17 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.727728107537E+00 kT\n Vpmg_energy:  qfEnergy = 1.464487511349E+04 kT\n Vpmg_energy:  dielEnergy = 7.268391520583E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.991000e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.250800e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -23705,138 +23705,138 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.239586 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 6.120618\n+Vacc_SASA: Time elapsed: 6.301471\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.110541e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.273519e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.445400e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.355500e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.324746e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.872810e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.830834e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.241328e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 8056801.731105\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.859181e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.262517e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.019948e+05\n Vprtstp: contraction number = 7.019948e+05\n Vnewton: Attempting damping, relres = 0.080001\n Vnewton: Attempting damping, relres = 0.537427\n Vnewton: Damping accepted, relres = 0.080001\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.000142e-02\n Vprtstp: contraction number = 8.000142e-02\n Vnewton: Using errtol_s: 644555.552257\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.127070e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.430113e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.545628e+04\n Vprtstp: contraction number = 9.545628e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.074028e-02\n Vprtstp: contraction number = 1.342512e-01\n Vnewton: Using errtol_s: 86532.331514\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.376223e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.588380e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.576216e+04\n Vprtstp: contraction number = 1.576216e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.761379e-03\n Vprtstp: contraction number = 1.639975e-01\n Vnewton: Using errtol_s: 14191.084898\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.627632e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.752927e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.960538e+03\n Vprtstp: contraction number = 2.960538e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 3.307659e-04\n Vprtstp: contraction number = 1.877880e-01\n Vnewton: Using errtol_s: 2664.915408\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.880889e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.915733e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.967294e+02\n Vprtstp: contraction number = 5.967294e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 6.666049e-05\n Vprtstp: contraction number = 2.015337e-01\n Vnewton: Using errtol_s: 537.070343\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.010131e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.077247e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.275865e+02\n Vprtstp: contraction number = 1.275865e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.425245e-05\n Vprtstp: contraction number = 2.138065e-01\n Vnewton: Using errtol_s: 114.829153\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.034510e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.229548e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.141071e+01\n Vprtstp: contraction number = 3.141071e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.508796e-06\n Vprtstp: contraction number = 2.461890e-01\n Vnewton: Using errtol_s: 28.269675\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.056539e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.386811e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.244202e+00\n Vprtstp: contraction number = 9.244202e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.032654e-06\n Vprtstp: contraction number = 2.943044e-01\n Vnewton: Using errtol_s: 8.319891\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.080081e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.538913e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.069585e+00\n Vprtstp: contraction number = 3.069585e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.428937e-07\n Vprtstp: contraction number = 3.320508e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.181098e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.195046e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.424793e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.435307e+02\n Vpmg_setPart:  lower corner = (2.518, -2.4645, -41.2575)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 16.7425)\n Vpmg_setPart:  actual minima = (-8.26461, -11.2254, -41.2575)\n Vpmg_setPart:  actual maxima = (58.518, 43.0355, 27.9102)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -23845,27 +23845,27 @@\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.898743294947E+00 kT\n Vpmg_energy:  qfEnergy = 1.125893253171E+05 kT\n Vpmg_energy:  dielEnergy = 5.606732677067E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.083900e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.705800e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  printing only subset of domain\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.101940e+03\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 7.671919e+02\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 06:28:35 2025\n+# Creation Date and Time:  Tue Jan  9 04:26:38 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path mol1.pqr\n@@ -24218,129 +24218,129 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.036643\n+Vacc_SASA: Time elapsed: 2.984457\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.726694e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.247911e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 7.117000e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.266200e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.340552e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.260060e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.617973e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.618308e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4300910.832168\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.265428e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.586020e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.776390e+05\n Vprtstp: contraction number = 1.776390e+05\n Vnewton: Attempting damping, relres = 0.041319\n Vnewton: Attempting damping, relres = 0.513474\n Vnewton: Damping accepted, relres = 0.041319\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.131938e-02\n Vprtstp: contraction number = 4.131938e-02\n Vnewton: Using errtol_s: 177710.973970\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.056500e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.207566e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.677180e+04\n Vprtstp: contraction number = 2.677180e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 5.962101e-03\n Vprtstp: contraction number = 1.442931e-01\n Vnewton: Using errtol_s: 25642.465478\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.118120e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.383821e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.966549e+03\n Vprtstp: contraction number = 4.966549e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.056655e-03\n Vprtstp: contraction number = 1.772286e-01\n Vnewton: Using errtol_s: 4544.578762\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.199133e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.546296e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.011325e+03\n Vprtstp: contraction number = 1.011325e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.118038e-04\n Vprtstp: contraction number = 2.004475e-01\n Vnewton: Using errtol_s: 910.949292\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.276836e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.890407e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.253595e+02\n Vprtstp: contraction number = 2.253595e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.715911e-05\n Vprtstp: contraction number = 2.226547e-01\n Vnewton: Using errtol_s: 202.827138\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.159603e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.270133e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.445207e+01\n Vprtstp: contraction number = 5.445207e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.139456e-05\n Vprtstp: contraction number = 2.416194e-01\n Vnewton: Using errtol_s: 49.006980\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.362080e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.531380e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.420316e+01\n Vprtstp: contraction number = 1.420316e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.972126e-06\n Vprtstp: contraction number = 2.608373e-01\n Vnewton: Using errtol_s: 12.782849\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.561997e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.855709e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.022184e+00\n Vprtstp: contraction number = 4.022184e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.416744e-07\n Vprtstp: contraction number = 2.831893e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.682032e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.697409e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.052863e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.063422e+02\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, 16.7425)\n Vpmg_setPart:  upper corner = (2.518, -2.4645, 74.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -24349,15 +24349,15 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 8.439783180216E-02 kT\n Vpmg_energy:  qfEnergy = 2.890574221449E+02 kT\n Vpmg_energy:  dielEnergy = 1.267284045292E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.339800e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.892400e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 39.7309\n Vpbe_ctor2:  solute dimensions = 68.682 x 69.075 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -24405,127 +24405,127 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00201979 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 2.991440\n+Vacc_SASA: Time elapsed: 2.930157\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.769046e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.565062e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 8.180300e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.378800e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.403178e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.847320e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.812242e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.166506e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1602777.342155\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.836026e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.186749e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.455767e+05\n Vprtstp: contraction number = 1.455767e+05\n Vnewton: Attempting damping, relres = 0.082108\n Vnewton: Attempting damping, relres = 0.538752\n Vnewton: Damping accepted, relres = 0.082108\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.210786e-02\n Vprtstp: contraction number = 8.210786e-02\n Vnewton: Using errtol_s: 131600.616465\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.052953e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.387695e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.947215e+04\n Vprtstp: contraction number = 1.947215e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.093564e-02\n Vprtstp: contraction number = 1.331863e-01\n Vnewton: Using errtol_s: 17527.393818\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.271826e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.539288e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.986234e+03\n Vprtstp: contraction number = 2.986234e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.676878e-03\n Vprtstp: contraction number = 1.533407e-01\n Vnewton: Using errtol_s: 2687.662365\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.479832e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.692407e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.993905e+02\n Vprtstp: contraction number = 4.993905e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.804220e-04\n Vprtstp: contraction number = 1.672286e-01\n Vnewton: Using errtol_s: 449.454038\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.694459e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.842679e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.039598e+01\n Vprtstp: contraction number = 9.039598e+01\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.075969e-05\n Vprtstp: contraction number = 1.810118e-01\n Vnewton: Using errtol_s: 81.356480\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.918580e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.989859e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.755931e+01\n Vprtstp: contraction number = 1.755931e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 9.860000e-06\n Vprtstp: contraction number = 1.942486e-01\n Vnewton: Using errtol_s: 15.803384\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.124309e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.167714e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.630601e+00\n Vprtstp: contraction number = 3.630601e+00\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.038674e-06\n Vprtstp: contraction number = 2.067621e-01\n Vnewton: Using errtol_s: 3.267541\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.358033e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.315388e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.904977e-01\n Vprtstp: contraction number = 7.904977e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 4.438845e-07\n Vprtstp: contraction number = 2.177319e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.753749e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.769526e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.292065e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.303242e+02\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, 16.7425)\n Vpmg_setPart:  upper corner = (2.518, -2.4645, 74.7425)\n Vpmg_setPart:  actual minima = (-53.482, -47.9645, 5.5748)\n Vpmg_setPart:  actual maxima = (13.3006, 6.29637, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -24534,15 +24534,15 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 8.337843047091E-02 kT\n Vpmg_energy:  qfEnergy = 2.452499065480E+03 kT\n Vpmg_energy:  dielEnergy = 1.155272443356E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.358500e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.104100e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -24565,129 +24565,129 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.053203\n+Vacc_SASA: Time elapsed: 2.855685\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.110290e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.865049e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.522300e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.258800e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.138440e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.061533e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.620104e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.510359e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4276578.139223\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.643861e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.528323e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.716926e+05\n Vprtstp: contraction number = 1.716926e+05\n Vnewton: Attempting damping, relres = 0.040940\n Vnewton: Attempting damping, relres = 0.513162\n Vnewton: Damping accepted, relres = 0.040940\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.093968e-02\n Vprtstp: contraction number = 4.093968e-02\n Vnewton: Using errtol_s: 175081.721880\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.844859e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.670304e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.487025e+04\n Vprtstp: contraction number = 2.487025e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 5.724811e-03\n Vprtstp: contraction number = 1.398353e-01\n Vnewton: Using errtol_s: 24482.603484\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.032149e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.791233e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.528470e+03\n Vprtstp: contraction number = 4.528470e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 9.801406e-04\n Vprtstp: contraction number = 1.712092e-01\n Vnewton: Using errtol_s: 4191.647712\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.229973e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.915402e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.122748e+02\n Vprtstp: contraction number = 9.122748e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.923658e-04\n Vprtstp: contraction number = 1.962635e-01\n Vnewton: Using errtol_s: 822.667398\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.417307e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.049690e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.052635e+02\n Vprtstp: contraction number = 2.052635e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.319998e-05\n Vprtstp: contraction number = 2.245720e-01\n Vnewton: Using errtol_s: 184.748098\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.620549e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.179273e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.154123e+01\n Vprtstp: contraction number = 5.154123e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.084685e-05\n Vprtstp: contraction number = 2.510845e-01\n Vnewton: Using errtol_s: 46.387392\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.812717e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.304236e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.435770e+01\n Vprtstp: contraction number = 1.435770e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.021563e-06\n Vprtstp: contraction number = 2.785660e-01\n Vnewton: Using errtol_s: 12.921949\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.992104e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.437536e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.361187e+00\n Vprtstp: contraction number = 4.361187e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 9.178062e-07\n Vprtstp: contraction number = 3.037522e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.540187e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.552253e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.041056e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.052344e+02\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, 16.7425)\n Vpmg_setPart:  upper corner = (2.518, -2.4645, 74.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -24696,15 +24696,15 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.047547930931E+00 kT\n Vpmg_energy:  qfEnergy = 1.326714299389E+04 kT\n Vpmg_energy:  dielEnergy = 6.630706107593E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.062100e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.866400e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -24752,138 +24752,138 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.208695 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.154675\n+Vacc_SASA: Time elapsed: 2.854091\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.982683e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.538505e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.406400e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.186400e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.671282e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.055009e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.229370e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.609430e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 6744887.867090\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.256799e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.630589e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.873341e+05\n Vprtstp: contraction number = 5.873341e+05\n Vnewton: Attempting damping, relres = 0.079798\n Vnewton: Attempting damping, relres = 0.537526\n Vnewton: Damping accepted, relres = 0.079798\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.979817e-02\n Vprtstp: contraction number = 7.979817e-02\n Vnewton: Using errtol_s: 538229.715979\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.496211e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.797117e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.003940e+04\n Vprtstp: contraction number = 8.003940e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.075173e-02\n Vprtstp: contraction number = 1.347366e-01\n Vnewton: Using errtol_s: 72519.230886\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.717146e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.955828e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.324771e+04\n Vprtstp: contraction number = 1.324771e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.768162e-03\n Vprtstp: contraction number = 1.644537e-01\n Vnewton: Using errtol_s: 11926.055102\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.953341e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.113750e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.493439e+03\n Vprtstp: contraction number = 2.493439e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 3.328041e-04\n Vprtstp: contraction number = 1.882203e-01\n Vnewton: Using errtol_s: 2244.726103\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.198973e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.266644e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.093161e+02\n Vprtstp: contraction number = 5.093161e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 6.796477e-05\n Vprtstp: contraction number = 2.042186e-01\n Vnewton: Using errtol_s: 458.414752\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.439325e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.417637e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.115992e+02\n Vprtstp: contraction number = 1.115992e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.489139e-05\n Vprtstp: contraction number = 2.191046e-01\n Vnewton: Using errtol_s: 100.440778\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.667915e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.572095e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.141695e+01\n Vprtstp: contraction number = 3.141695e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.192112e-06\n Vprtstp: contraction number = 2.815124e-01\n Vnewton: Using errtol_s: 28.275326\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.919636e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.728671e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.143181e+01\n Vprtstp: contraction number = 1.143181e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.525422e-06\n Vprtstp: contraction number = 3.638791e-01\n Vnewton: Using errtol_s: 10.288800\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.140094e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.886364e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.900145e+00\n Vprtstp: contraction number = 4.900145e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 6.538480e-07\n Vprtstp: contraction number = 4.286342e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.115987e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.133378e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.445428e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.456582e+02\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, 16.7425)\n Vpmg_setPart:  upper corner = (2.518, -2.4645, 74.7425)\n Vpmg_setPart:  actual minima = (-53.482, -47.9645, 5.5748)\n Vpmg_setPart:  actual maxima = (13.3006, 6.29637, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -24892,15 +24892,15 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.068941239771E+00 kT\n Vpmg_energy:  qfEnergy = 1.027128342703E+05 kT\n Vpmg_energy:  dielEnergy = 5.130929384938E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 8.688500e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.818800e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n@@ -24923,129 +24923,129 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 6.620238\n+Vacc_SASA: Time elapsed: 6.186807\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.002316e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.418108e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.358200e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.213600e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.389289e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.003632e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.441949e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.141388e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 8699406.430616\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.468619e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.162534e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.528464e+05\n Vprtstp: contraction number = 3.528464e+05\n Vnewton: Attempting damping, relres = 0.041605\n Vnewton: Attempting damping, relres = 0.513349\n Vnewton: Damping accepted, relres = 0.041605\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.160535e-02\n Vprtstp: contraction number = 4.160535e-02\n Vnewton: Using errtol_s: 361941.817774\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.717178e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.331697e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.210930e+04\n Vprtstp: contraction number = 5.210930e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 5.921711e-03\n Vprtstp: contraction number = 1.423305e-01\n Vnewton: Using errtol_s: 51515.371182\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.932996e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.496779e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.570568e+03\n Vprtstp: contraction number = 9.570568e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.018950e-03\n Vprtstp: contraction number = 1.720701e-01\n Vnewton: Using errtol_s: 8864.257334\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.157588e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.682833e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.944504e+03\n Vprtstp: contraction number = 1.944504e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.015521e-04\n Vprtstp: contraction number = 1.978037e-01\n Vnewton: Using errtol_s: 1753.383252\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.383091e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.823499e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.357668e+02\n Vprtstp: contraction number = 4.357668e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.508379e-05\n Vprtstp: contraction number = 2.236831e-01\n Vnewton: Using errtol_s: 392.202227\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.600892e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.977730e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.074784e+02\n Vprtstp: contraction number = 1.074784e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.111924e-05\n Vprtstp: contraction number = 2.466350e-01\n Vnewton: Using errtol_s: 96.730784\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.815216e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.145365e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.903808e+01\n Vprtstp: contraction number = 2.903808e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.004146e-06\n Vprtstp: contraction number = 2.701755e-01\n Vnewton: Using errtol_s: 26.134288\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.027550e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.292356e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.552738e+00\n Vprtstp: contraction number = 8.552738e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.848266e-07\n Vprtstp: contraction number = 2.945351e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.798062e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.812710e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.311711e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.322313e+02\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, 16.7425)\n Vpmg_setPart:  upper corner = (2.518, -2.4645, 74.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -25054,15 +25054,15 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.318490670487E+00 kT\n Vpmg_energy:  qfEnergy = 1.359627523071E+04 kT\n Vpmg_energy:  dielEnergy = 6.777157121148E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.581500e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.486200e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n@@ -25110,138 +25110,138 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.208525 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 6.565731\n+Vacc_SASA: Time elapsed: 6.291818\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.695165e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.309246e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.614900e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.159300e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.014595e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.002091e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.339555e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.548379e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 8257970.099902\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.364970e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.567581e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.174738e+05\n Vprtstp: contraction number = 7.174738e+05\n Vnewton: Attempting damping, relres = 0.079654\n Vnewton: Attempting damping, relres = 0.537366\n Vnewton: Damping accepted, relres = 0.079654\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.965353e-02\n Vprtstp: contraction number = 7.965353e-02\n Vnewton: Using errtol_s: 657776.459467\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.601510e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.743751e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.738355e+04\n Vprtstp: contraction number = 9.738355e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.068030e-02\n Vprtstp: contraction number = 1.340844e-01\n Vnewton: Using errtol_s: 88197.583593\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.797806e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.903003e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.590859e+04\n Vprtstp: contraction number = 1.590859e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.734478e-03\n Vprtstp: contraction number = 1.623998e-01\n Vnewton: Using errtol_s: 14323.269837\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.990165e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.055466e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.927974e+03\n Vprtstp: contraction number = 2.927974e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 3.191803e-04\n Vprtstp: contraction number = 1.840209e-01\n Vnewton: Using errtol_s: 2635.781086\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.020631e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.213991e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.843569e+02\n Vprtstp: contraction number = 5.843569e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 6.369066e-05\n Vprtstp: contraction number = 1.995445e-01\n Vnewton: Using errtol_s: 525.955563\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.042480e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.369487e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.235877e+02\n Vprtstp: contraction number = 1.235877e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.346947e-05\n Vprtstp: contraction number = 2.114827e-01\n Vnewton: Using errtol_s: 111.230501\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.064704e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.518461e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.351690e+01\n Vprtstp: contraction number = 3.351690e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.652870e-06\n Vprtstp: contraction number = 2.711962e-01\n Vnewton: Using errtol_s: 30.165292\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.087223e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.676485e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.181991e+01\n Vprtstp: contraction number = 1.181991e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.288222e-06\n Vprtstp: contraction number = 3.526602e-01\n Vnewton: Using errtol_s: 10.638098\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.109757e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.832884e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.017523e+00\n Vprtstp: contraction number = 5.017523e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.468381e-07\n Vprtstp: contraction number = 4.244906e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.968684e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.979806e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.429952e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.440597e+02\n Vpmg_setPart:  lower corner = (-53.482, -47.9645, 16.7425)\n Vpmg_setPart:  upper corner = (2.518, -2.4645, 74.7425)\n Vpmg_setPart:  actual minima = (-53.482, -47.9645, 5.5748)\n Vpmg_setPart:  actual maxima = (13.3006, 6.29637, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -25250,27 +25250,27 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.367295559146E+00 kT\n Vpmg_energy:  qfEnergy = 1.051945297594E+05 kT\n Vpmg_energy:  dielEnergy = 5.247887391423E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.364200e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.026800e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  printing only subset of domain\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.131502e+03\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 7.983283e+02\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 06:31:07 2025\n+# Creation Date and Time:  Tue Jan  9 04:29:29 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path mol1.pqr\n@@ -25623,129 +25623,129 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.201811\n+Vacc_SASA: Time elapsed: 2.996652\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.786958e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.396213e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 6.223200e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.269200e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.139285e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.001561e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.415036e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.843447e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4300910.832168\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.856948e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.792707e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.776390e+05\n Vprtstp: contraction number = 1.776390e+05\n Vnewton: Attempting damping, relres = 0.041319\n Vnewton: Attempting damping, relres = 0.513474\n Vnewton: Damping accepted, relres = 0.041319\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.131938e-02\n Vprtstp: contraction number = 4.131938e-02\n Vnewton: Using errtol_s: 177710.973970\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.916334e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.307566e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.677180e+04\n Vprtstp: contraction number = 2.677180e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 5.962101e-03\n Vprtstp: contraction number = 1.442931e-01\n Vnewton: Using errtol_s: 25642.465478\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.772145e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.746361e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.966549e+03\n Vprtstp: contraction number = 4.966549e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.056655e-03\n Vprtstp: contraction number = 1.772286e-01\n Vnewton: Using errtol_s: 4544.578762\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.701976e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.074548e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.011325e+03\n Vprtstp: contraction number = 1.011325e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.118038e-04\n Vprtstp: contraction number = 2.004475e-01\n Vnewton: Using errtol_s: 910.949292\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.510622e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.295101e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.253595e+02\n Vprtstp: contraction number = 2.253595e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.715911e-05\n Vprtstp: contraction number = 2.226547e-01\n Vnewton: Using errtol_s: 202.827138\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.030766e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.560997e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.445207e+01\n Vprtstp: contraction number = 5.445207e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.139456e-05\n Vprtstp: contraction number = 2.416194e-01\n Vnewton: Using errtol_s: 49.006980\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.217497e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.941848e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.420316e+01\n Vprtstp: contraction number = 1.420316e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.972126e-06\n Vprtstp: contraction number = 2.608373e-01\n Vnewton: Using errtol_s: 12.782849\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.424647e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.033946e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.022184e+00\n Vprtstp: contraction number = 4.022184e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.416744e-07\n Vprtstp: contraction number = 2.831893e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.538250e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.551132e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.092016e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.103323e+02\n Vpmg_setPart:  lower corner = (2.518, -47.9645, 16.7425)\n Vpmg_setPart:  upper corner = (58.518, -2.4645, 74.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -25754,15 +25754,15 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.504309500280E-01 kT\n Vpmg_energy:  qfEnergy = 1.755208046486E+03 kT\n Vpmg_energy:  dielEnergy = 8.724652508101E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.046500e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.521700e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 39.7309\n Vpbe_ctor2:  solute dimensions = 68.682 x 69.075 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -25810,127 +25810,127 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00330279 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.158415\n+Vacc_SASA: Time elapsed: 2.887264\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.077857e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.628256e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 7.187700e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.210800e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.370004e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.083451e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.669391e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.210286e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2662068.021804\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.694170e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.231733e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.456208e+05\n Vprtstp: contraction number = 2.456208e+05\n Vnewton: Attempting damping, relres = 0.083386\n Vnewton: Attempting damping, relres = 0.539586\n Vnewton: Damping accepted, relres = 0.083386\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.338571e-02\n Vprtstp: contraction number = 8.338571e-02\n Vnewton: Using errtol_s: 221978.424581\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.949529e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.404378e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.405567e+04\n Vprtstp: contraction number = 3.405567e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.151500e-02\n Vprtstp: contraction number = 1.380932e-01\n Vnewton: Using errtol_s: 30653.716000\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.179359e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.560258e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.435916e+03\n Vprtstp: contraction number = 5.435916e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.837816e-03\n Vprtstp: contraction number = 1.596019e-01\n Vnewton: Using errtol_s: 4892.390079\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.402801e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.742667e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.557902e+02\n Vprtstp: contraction number = 9.557902e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 3.231381e-04\n Vprtstp: contraction number = 1.758273e-01\n Vnewton: Using errtol_s: 860.215698\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.614957e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.895121e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.830694e+02\n Vprtstp: contraction number = 1.830694e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 6.189280e-05\n Vprtstp: contraction number = 1.915367e-01\n Vnewton: Using errtol_s: 164.762841\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.837985e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.048295e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.747370e+01\n Vprtstp: contraction number = 3.747370e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.266923e-05\n Vprtstp: contraction number = 2.046964e-01\n Vnewton: Using errtol_s: 33.726360\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.054073e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.200673e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.392089e+00\n Vprtstp: contraction number = 8.392089e+00\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.837224e-06\n Vprtstp: contraction number = 2.239460e-01\n Vnewton: Using errtol_s: 7.552883\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.286288e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.359689e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.064121e+00\n Vprtstp: contraction number = 2.064121e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 6.978444e-07\n Vprtstp: contraction number = 2.459603e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.830994e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.846571e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.320139e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.332282e+02\n Vpmg_setPart:  lower corner = (2.518, -47.9645, 16.7425)\n Vpmg_setPart:  upper corner = (58.518, -2.4645, 74.7425)\n Vpmg_setPart:  actual minima = (-8.26461, -47.9645, 5.5748)\n Vpmg_setPart:  actual maxima = (58.518, 6.29637, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -25939,17 +25939,17 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.015842175556E-01 kT\n Vpmg_energy:  qfEnergy = 1.339968414661E+04 kT\n Vpmg_energy:  dielEnergy = 6.688675679646E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.748900e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.796400e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -25970,129 +25970,129 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 2.926263\n+Vacc_SASA: Time elapsed: 2.949667\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.138863e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.912186e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.154700e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.420600e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.287723e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.041834e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.556342e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.581741e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4276578.139223\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.582120e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.603996e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.716926e+05\n Vprtstp: contraction number = 1.716926e+05\n Vnewton: Attempting damping, relres = 0.040940\n Vnewton: Attempting damping, relres = 0.513162\n Vnewton: Damping accepted, relres = 0.040940\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.093968e-02\n Vprtstp: contraction number = 4.093968e-02\n Vnewton: Using errtol_s: 175081.721880\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.789564e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.766861e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.487025e+04\n Vprtstp: contraction number = 2.487025e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 5.724811e-03\n Vprtstp: contraction number = 1.398353e-01\n Vnewton: Using errtol_s: 24482.603484\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.968674e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.883960e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.528470e+03\n Vprtstp: contraction number = 4.528470e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 9.801406e-04\n Vprtstp: contraction number = 1.712092e-01\n Vnewton: Using errtol_s: 4191.647712\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.168664e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.005212e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.122748e+02\n Vprtstp: contraction number = 9.122748e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.923658e-04\n Vprtstp: contraction number = 1.962635e-01\n Vnewton: Using errtol_s: 822.667398\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.356404e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.128084e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.052635e+02\n Vprtstp: contraction number = 2.052635e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.319998e-05\n Vprtstp: contraction number = 2.245720e-01\n Vnewton: Using errtol_s: 184.748098\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.557067e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.256699e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.154123e+01\n Vprtstp: contraction number = 5.154123e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.084685e-05\n Vprtstp: contraction number = 2.510845e-01\n Vnewton: Using errtol_s: 46.387392\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.754933e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.409132e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.435770e+01\n Vprtstp: contraction number = 1.435770e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.021563e-06\n Vprtstp: contraction number = 2.785660e-01\n Vnewton: Using errtol_s: 12.921949\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.961192e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.551047e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.361187e+00\n Vprtstp: contraction number = 4.361187e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 9.178062e-07\n Vprtstp: contraction number = 3.037522e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.543489e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.557236e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.087744e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.098815e+02\n Vpmg_setPart:  lower corner = (2.518, -47.9645, 16.7425)\n Vpmg_setPart:  upper corner = (58.518, -2.4645, 74.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -26101,15 +26101,15 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.301986990892E-02 kT\n Vpmg_energy:  qfEnergy = 0.000000000000E+00 kT\n Vpmg_energy:  dielEnergy = 1.769795919653E-01 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.894300e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.750100e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -26157,127 +26157,127 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0030506 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.161539\n+Vacc_SASA: Time elapsed: 2.673624\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.496172e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.863363e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.406600e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.101600e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.133352e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.872010e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.157288e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.720345e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1183078.697095\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.178685e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.741243e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.216317e+05\n Vprtstp: contraction number = 1.216317e+05\n Vnewton: Attempting damping, relres = 0.092815\n Vnewton: Attempting damping, relres = 0.543699\n Vnewton: Damping accepted, relres = 0.092815\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.281548e-02\n Vprtstp: contraction number = 9.281548e-02\n Vnewton: Using errtol_s: 109808.011526\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.332278e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.878848e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.637169e+04\n Vprtstp: contraction number = 1.637169e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.245819e-02\n Vprtstp: contraction number = 1.342253e-01\n Vnewton: Using errtol_s: 14739.016153\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.481115e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.985524e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.481814e+03\n Vprtstp: contraction number = 2.481814e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.888035e-03\n Vprtstp: contraction number = 1.515497e-01\n Vnewton: Using errtol_s: 2233.693882\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.628080e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.101923e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.090266e+02\n Vprtstp: contraction number = 4.090266e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 3.111589e-04\n Vprtstp: contraction number = 1.648057e-01\n Vnewton: Using errtol_s: 368.125449\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.781423e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.222037e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.284721e+01\n Vprtstp: contraction number = 7.284721e+01\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.541690e-05\n Vprtstp: contraction number = 1.780984e-01\n Vnewton: Using errtol_s: 65.562559\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.923846e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.323644e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.403461e+01\n Vprtstp: contraction number = 1.403461e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.067651e-05\n Vprtstp: contraction number = 1.926581e-01\n Vnewton: Using errtol_s: 12.631156\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.042846e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.423187e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.928656e+00\n Vprtstp: contraction number = 2.928656e+00\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.227908e-06\n Vprtstp: contraction number = 2.086737e-01\n Vnewton: Using errtol_s: 2.635791\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.160084e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.552210e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.633899e-01\n Vprtstp: contraction number = 6.633899e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 5.046587e-07\n Vprtstp: contraction number = 2.265168e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.115123e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.127288e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 9.290707e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 9.395649e+01\n Vpmg_setPart:  lower corner = (2.518, -47.9645, 16.7425)\n Vpmg_setPart:  upper corner = (58.518, -2.4645, 74.7425)\n Vpmg_setPart:  actual minima = (-8.26461, -47.9645, 5.5748)\n Vpmg_setPart:  actual maxima = (58.518, 6.29637, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -26286,17 +26286,17 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.998704747523E-02 kT\n Vpmg_energy:  qfEnergy = 0.000000000000E+00 kT\n Vpmg_energy:  dielEnergy = 1.756383859488E-01 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.329000e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.162800e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -26317,129 +26317,129 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 6.962346\n+Vacc_SASA: Time elapsed: 5.770375\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.347251e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.063939e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.896800e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.261200e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.044954e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.049638e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.367632e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.732182e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 8699406.430616\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.389075e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.755738e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.528464e+05\n Vprtstp: contraction number = 3.528464e+05\n Vnewton: Attempting damping, relres = 0.041605\n Vnewton: Attempting damping, relres = 0.513349\n Vnewton: Damping accepted, relres = 0.041605\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.160535e-02\n Vprtstp: contraction number = 4.160535e-02\n Vnewton: Using errtol_s: 361941.817774\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.600553e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.938907e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.210930e+04\n Vprtstp: contraction number = 5.210930e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 5.921711e-03\n Vprtstp: contraction number = 1.423305e-01\n Vnewton: Using errtol_s: 51515.371182\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.777945e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.077690e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.570568e+03\n Vprtstp: contraction number = 9.570568e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.018950e-03\n Vprtstp: contraction number = 1.720701e-01\n Vnewton: Using errtol_s: 8864.257334\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.950769e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.225811e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.944504e+03\n Vprtstp: contraction number = 1.944504e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.015521e-04\n Vprtstp: contraction number = 1.978037e-01\n Vnewton: Using errtol_s: 1753.383252\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.136803e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.381614e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.357668e+02\n Vprtstp: contraction number = 4.357668e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.508379e-05\n Vprtstp: contraction number = 2.236831e-01\n Vnewton: Using errtol_s: 392.202227\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.306921e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.540861e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.074784e+02\n Vprtstp: contraction number = 1.074784e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.111924e-05\n Vprtstp: contraction number = 2.466350e-01\n Vnewton: Using errtol_s: 96.730784\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.476226e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.682495e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.903808e+01\n Vprtstp: contraction number = 2.903808e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.004146e-06\n Vprtstp: contraction number = 2.701755e-01\n Vnewton: Using errtol_s: 26.134288\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.664481e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.834518e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.552738e+00\n Vprtstp: contraction number = 8.552738e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.848266e-07\n Vprtstp: contraction number = 2.945351e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.478683e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.489808e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.239027e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.250099e+02\n Vpmg_setPart:  lower corner = (2.518, -47.9645, 16.7425)\n Vpmg_setPart:  upper corner = (58.518, -2.4645, 74.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -26448,15 +26448,15 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 3.337014891966E-01 kT\n Vpmg_energy:  qfEnergy = 1.757508966493E+03 kT\n Vpmg_energy:  dielEnergy = 8.741342460079E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.415000e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.881000e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n@@ -26504,127 +26504,127 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0127136 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 6.897545\n+Vacc_SASA: Time elapsed: 6.164931\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.726427e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.771199e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.387500e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.153400e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.077457e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.010348e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.946694e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.061176e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 3725039.964738\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.970144e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.080766e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.491722e+05\n Vprtstp: contraction number = 3.491722e+05\n Vnewton: Attempting damping, relres = 0.084831\n Vnewton: Attempting damping, relres = 0.540016\n Vnewton: Damping accepted, relres = 0.084831\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.483081e-02\n Vprtstp: contraction number = 8.483081e-02\n Vnewton: Using errtol_s: 315998.155182\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.173359e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.260963e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.811279e+04\n Vprtstp: contraction number = 4.811279e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.162816e-02\n Vprtstp: contraction number = 1.370747e-01\n Vnewton: Using errtol_s: 43315.357930\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.386371e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.428587e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.589005e+03\n Vprtstp: contraction number = 7.589005e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.833655e-03\n Vprtstp: contraction number = 1.576909e-01\n Vnewton: Using errtol_s: 6830.439897\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.612463e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.612997e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.299757e+03\n Vprtstp: contraction number = 1.299757e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 3.140354e-04\n Vprtstp: contraction number = 1.712619e-01\n Vnewton: Using errtol_s: 1169.794412\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.809927e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.765745e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.408127e+02\n Vprtstp: contraction number = 2.408127e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.818247e-05\n Vprtstp: contraction number = 1.852736e-01\n Vnewton: Using errtol_s: 216.732029\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.011235e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.918288e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.749053e+01\n Vprtstp: contraction number = 4.749053e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.147411e-05\n Vprtstp: contraction number = 1.972090e-01\n Vnewton: Using errtol_s: 42.741516\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.211848e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.075752e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.028045e+01\n Vprtstp: contraction number = 1.028045e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.483842e-06\n Vprtstp: contraction number = 2.164736e-01\n Vnewton: Using errtol_s: 9.252409\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.420948e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.232563e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.462555e+00\n Vprtstp: contraction number = 2.462555e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 5.949733e-07\n Vprtstp: contraction number = 2.395375e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.696009e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.707613e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.310309e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.321529e+02\n Vpmg_setPart:  lower corner = (2.518, -47.9645, 16.7425)\n Vpmg_setPart:  upper corner = (58.518, -2.4645, 74.7425)\n Vpmg_setPart:  actual minima = (-8.26461, -47.9645, 5.5748)\n Vpmg_setPart:  actual maxima = (58.518, 6.29637, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -26633,27 +26633,27 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 3.090781383417E-01 kT\n Vpmg_energy:  qfEnergy = 1.340160252589E+04 kT\n Vpmg_energy:  dielEnergy = 6.690276945765E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.759400e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.907400e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  printing only subset of domain\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 9.648834e+02\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 7.377811e+02\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 06:33:36 2025\n+# Creation Date and Time:  Tue Jan  9 04:32:15 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path mol1.pqr\n@@ -27006,129 +27006,129 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.222669\n+Vacc_SASA: Time elapsed: 3.027281\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.757505e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.393852e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 6.393800e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.322800e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.628250e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.036353e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.213347e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.828209e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4300910.832168\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.221761e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.236734e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.776390e+05\n Vprtstp: contraction number = 1.776390e+05\n Vnewton: Attempting damping, relres = 0.041319\n Vnewton: Attempting damping, relres = 0.513474\n Vnewton: Damping accepted, relres = 0.041319\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.131938e-02\n Vprtstp: contraction number = 4.131938e-02\n Vnewton: Using errtol_s: 177710.973970\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.639200e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.448335e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.677180e+04\n Vprtstp: contraction number = 2.677180e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 5.962101e-03\n Vprtstp: contraction number = 1.442931e-01\n Vnewton: Using errtol_s: 25642.465478\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.293193e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.792610e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.966549e+03\n Vprtstp: contraction number = 4.966549e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.056655e-03\n Vprtstp: contraction number = 1.772286e-01\n Vnewton: Using errtol_s: 4544.578762\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.969201e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.086188e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.011325e+03\n Vprtstp: contraction number = 1.011325e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.118038e-04\n Vprtstp: contraction number = 2.004475e-01\n Vnewton: Using errtol_s: 910.949292\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.729597e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.408935e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.253595e+02\n Vprtstp: contraction number = 2.253595e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.715911e-05\n Vprtstp: contraction number = 2.226547e-01\n Vnewton: Using errtol_s: 202.827138\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.463997e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.919309e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.445207e+01\n Vprtstp: contraction number = 5.445207e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.139456e-05\n Vprtstp: contraction number = 2.416194e-01\n Vnewton: Using errtol_s: 49.006980\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.136721e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.123504e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.420316e+01\n Vprtstp: contraction number = 1.420316e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.972126e-06\n Vprtstp: contraction number = 2.608373e-01\n Vnewton: Using errtol_s: 12.782849\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.323046e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.043198e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.022184e+00\n Vprtstp: contraction number = 4.022184e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.416744e-07\n Vprtstp: contraction number = 2.831893e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.434331e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.445393e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.098054e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.109717e+02\n Vpmg_setPart:  lower corner = (-53.482, -2.4645, 16.7425)\n Vpmg_setPart:  upper corner = (2.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -27137,17 +27137,17 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 8.018818357311E-03 kT\n Vpmg_energy:  qfEnergy = 0.000000000000E+00 kT\n Vpmg_energy:  dielEnergy = 1.967662971668E+00 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.869600e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.521000e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 5.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 39.7309\n Vpbe_ctor2:  solute dimensions = 68.682 x 69.075 x 70.346\n Vpbe_ctor2:  solute charge = -12\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -27193,127 +27193,127 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.000195471 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.027414\n+Vacc_SASA: Time elapsed: 2.988932\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.692314e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.486097e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 6.406800e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.758700e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.251975e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.031747e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.558583e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.213710e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1020818.402503\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.586535e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.234202e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.825199e+04\n Vprtstp: contraction number = 9.825199e+04\n Vnewton: Attempting damping, relres = 0.087060\n Vnewton: Attempting damping, relres = 0.541082\n Vnewton: Damping accepted, relres = 0.087060\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.706019e-02\n Vprtstp: contraction number = 8.706019e-02\n Vnewton: Using errtol_s: 88872.645048\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.805598e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.375660e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.300904e+04\n Vprtstp: contraction number = 1.300904e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.147153e-02\n Vprtstp: contraction number = 1.317655e-01\n Vnewton: Using errtol_s: 11710.349561\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.997880e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.504832e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.956340e+03\n Vprtstp: contraction number = 1.956340e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.724829e-03\n Vprtstp: contraction number = 1.503573e-01\n Vnewton: Using errtol_s: 1760.737119\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.181765e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.635229e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.204124e+02\n Vprtstp: contraction number = 3.204124e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.824911e-04\n Vprtstp: contraction number = 1.637792e-01\n Vnewton: Using errtol_s: 288.372159\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.363890e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.768130e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.671470e+01\n Vprtstp: contraction number = 5.671470e+01\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.000230e-05\n Vprtstp: contraction number = 1.770048e-01\n Vnewton: Using errtol_s: 51.043267\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.543400e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.905154e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.076760e+01\n Vprtstp: contraction number = 1.076760e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 9.493208e-06\n Vprtstp: contraction number = 1.898554e-01\n Vnewton: Using errtol_s: 9.690841\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.732676e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.042546e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.170593e+00\n Vprtstp: contraction number = 2.170593e+00\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.913693e-06\n Vprtstp: contraction number = 2.015855e-01\n Vnewton: Using errtol_s: 1.953533\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.927274e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.181500e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.603679e-01\n Vprtstp: contraction number = 4.603679e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 4.058813e-07\n Vprtstp: contraction number = 2.120932e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.551270e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.565710e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.091737e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.103394e+02\n Vpmg_setPart:  lower corner = (-53.482, -2.4645, 16.7425)\n Vpmg_setPart:  upper corner = (2.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-53.482, -11.2254, 5.5748)\n Vpmg_setPart:  actual maxima = (13.3006, 43.0355, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -27322,15 +27322,15 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 7.464558654899E-03 kT\n Vpmg_energy:  qfEnergy = 0.000000000000E+00 kT\n Vpmg_energy:  dielEnergy = 1.022303323465E+00 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 9.410400e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.805100e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -27353,129 +27353,129 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.164293\n+Vacc_SASA: Time elapsed: 2.891837\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.253925e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.901850e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.842500e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.387600e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.025929e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.750830e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.165254e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.355793e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4276578.139223\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.187811e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.376133e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.716926e+05\n Vprtstp: contraction number = 1.716926e+05\n Vnewton: Attempting damping, relres = 0.040940\n Vnewton: Attempting damping, relres = 0.513162\n Vnewton: Damping accepted, relres = 0.040940\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.093968e-02\n Vprtstp: contraction number = 4.093968e-02\n Vnewton: Using errtol_s: 175081.721880\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.361705e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.529473e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.487025e+04\n Vprtstp: contraction number = 2.487025e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 5.724811e-03\n Vprtstp: contraction number = 1.398353e-01\n Vnewton: Using errtol_s: 24482.603484\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.506358e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.665317e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.528470e+03\n Vprtstp: contraction number = 4.528470e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 9.801406e-04\n Vprtstp: contraction number = 1.712092e-01\n Vnewton: Using errtol_s: 4191.647712\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.673842e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.820890e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.122748e+02\n Vprtstp: contraction number = 9.122748e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.923658e-04\n Vprtstp: contraction number = 1.962635e-01\n Vnewton: Using errtol_s: 822.667398\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.853845e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.943507e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.052635e+02\n Vprtstp: contraction number = 2.052635e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.319998e-05\n Vprtstp: contraction number = 2.245720e-01\n Vnewton: Using errtol_s: 184.748098\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.026097e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.080366e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.154123e+01\n Vprtstp: contraction number = 5.154123e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.084685e-05\n Vprtstp: contraction number = 2.510845e-01\n Vnewton: Using errtol_s: 46.387392\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.209570e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.206352e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.435770e+01\n Vprtstp: contraction number = 1.435770e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.021563e-06\n Vprtstp: contraction number = 2.785660e-01\n Vnewton: Using errtol_s: 12.921949\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.399049e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.333500e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.361187e+00\n Vprtstp: contraction number = 4.361187e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 9.178062e-07\n Vprtstp: contraction number = 3.037522e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.405864e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.416848e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.088190e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.098586e+02\n Vpmg_setPart:  lower corner = (-53.482, -2.4645, 16.7425)\n Vpmg_setPart:  upper corner = (2.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -27484,15 +27484,15 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.242044176092E+00 kT\n Vpmg_energy:  qfEnergy = 9.791375610764E+03 kT\n Vpmg_energy:  dielEnergy = 4.948343269624E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.351300e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.332500e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n@@ -27540,127 +27540,127 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0380116 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 3.245633\n+Vacc_SASA: Time elapsed: 2.859673\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.820861e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.503164e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.354600e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.220100e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.137306e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.049648e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.633201e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.502184e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 6064250.335946\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.658391e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.525674e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.053112e+05\n Vprtstp: contraction number = 5.053112e+05\n Vnewton: Attempting damping, relres = 0.075900\n Vnewton: Attempting damping, relres = 0.535745\n Vnewton: Damping accepted, relres = 0.075900\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.590004e-02\n Vprtstp: contraction number = 7.590004e-02\n Vnewton: Using errtol_s: 460276.842537\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.922063e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.703480e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.689298e+04\n Vprtstp: contraction number = 6.689298e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 9.982301e-03\n Vprtstp: contraction number = 1.315191e-01\n Vnewton: Using errtol_s: 60535.174769\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.173627e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.867070e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.083906e+04\n Vprtstp: contraction number = 1.083906e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.608994e-03\n Vprtstp: contraction number = 1.611846e-01\n Vnewton: Using errtol_s: 9757.339468\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.432395e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.047390e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.965105e+03\n Vprtstp: contraction number = 1.965105e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.916449e-04\n Vprtstp: contraction number = 1.812592e-01\n Vnewton: Using errtol_s: 1768.607683\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.689263e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.217844e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.700829e+02\n Vprtstp: contraction number = 3.700829e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.492457e-05\n Vprtstp: contraction number = 1.883269e-01\n Vnewton: Using errtol_s: 333.076316\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.938695e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.370083e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.574998e+01\n Vprtstp: contraction number = 6.574998e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 9.758048e-06\n Vprtstp: contraction number = 1.776627e-01\n Vnewton: Using errtol_s: 59.175244\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.197538e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.517758e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.293454e+01\n Vprtstp: contraction number = 1.293454e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.919626e-06\n Vprtstp: contraction number = 1.967224e-01\n Vnewton: Using errtol_s: 11.641095\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.460532e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.672042e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.078562e+00\n Vprtstp: contraction number = 3.078562e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 4.568945e-07\n Vprtstp: contraction number = 2.380122e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.048182e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.060209e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.319756e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.330882e+02\n Vpmg_setPart:  lower corner = (-53.482, -2.4645, 16.7425)\n Vpmg_setPart:  upper corner = (2.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-53.482, -11.2254, 5.5748)\n Vpmg_setPart:  actual maxima = (13.3006, 43.0355, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -27669,15 +27669,15 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.156457994238E+00 kT\n Vpmg_energy:  qfEnergy = 7.809362574174E+04 kT\n Vpmg_energy:  dielEnergy = 3.917972751481E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.676600e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.982000e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n@@ -27700,129 +27700,129 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 6.765736\n+Vacc_SASA: Time elapsed: 6.406832\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.221679e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.743698e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.040400e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.868100e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.259279e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.001775e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.777627e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.911172e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 8699406.430616\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.808066e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.933188e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.528464e+05\n Vprtstp: contraction number = 3.528464e+05\n Vnewton: Attempting damping, relres = 0.041605\n Vnewton: Attempting damping, relres = 0.513349\n Vnewton: Damping accepted, relres = 0.041605\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.160535e-02\n Vprtstp: contraction number = 4.160535e-02\n Vnewton: Using errtol_s: 361941.817774\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.080154e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.108828e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.210930e+04\n Vprtstp: contraction number = 5.210930e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 5.921711e-03\n Vprtstp: contraction number = 1.423305e-01\n Vnewton: Using errtol_s: 51515.371182\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.308581e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.246851e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.570568e+03\n Vprtstp: contraction number = 9.570568e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.018950e-03\n Vprtstp: contraction number = 1.720701e-01\n Vnewton: Using errtol_s: 8864.257334\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.543285e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.385095e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.944504e+03\n Vprtstp: contraction number = 1.944504e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.015521e-04\n Vprtstp: contraction number = 1.978037e-01\n Vnewton: Using errtol_s: 1753.383252\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.773220e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.536831e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.357668e+02\n Vprtstp: contraction number = 4.357668e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.508379e-05\n Vprtstp: contraction number = 2.236831e-01\n Vnewton: Using errtol_s: 392.202227\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.002769e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.701471e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.074784e+02\n Vprtstp: contraction number = 1.074784e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.111924e-05\n Vprtstp: contraction number = 2.466350e-01\n Vnewton: Using errtol_s: 96.730784\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.242745e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.856622e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.903808e+01\n Vprtstp: contraction number = 2.903808e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.004146e-06\n Vprtstp: contraction number = 2.701755e-01\n Vnewton: Using errtol_s: 26.134288\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.481460e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.036947e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.552738e+00\n Vprtstp: contraction number = 8.552738e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.848266e-07\n Vprtstp: contraction number = 2.945351e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.923267e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.936576e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.290677e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.301343e+02\n Vpmg_setPart:  lower corner = (-53.482, -2.4645, 16.7425)\n Vpmg_setPart:  upper corner = (2.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -27831,15 +27831,15 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.221311774650E+00 kT\n Vpmg_energy:  qfEnergy = 9.790964149822E+03 kT\n Vpmg_energy:  dielEnergy = 4.950799444075E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.166300e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.445400e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n@@ -27887,127 +27887,127 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0371815 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 6.016808\n+Vacc_SASA: Time elapsed: 6.314734\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.910703e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.082864e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.345400e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.143700e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.245498e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.024085e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.793808e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.294855e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 6913573.322497\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.821415e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.313378e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.778762e+05\n Vprtstp: contraction number = 5.778762e+05\n Vnewton: Attempting damping, relres = 0.075994\n Vnewton: Attempting damping, relres = 0.535763\n Vnewton: Damping accepted, relres = 0.075994\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.599436e-02\n Vprtstp: contraction number = 7.599436e-02\n Vnewton: Using errtol_s: 525392.598640\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.077689e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.483418e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.670486e+04\n Vprtstp: contraction number = 7.670486e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.002063e-02\n Vprtstp: contraction number = 1.318602e-01\n Vnewton: Using errtol_s: 69278.365005\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.324732e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.649217e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.241801e+04\n Vprtstp: contraction number = 1.241801e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.616751e-03\n Vprtstp: contraction number = 1.613422e-01\n Vnewton: Using errtol_s: 11177.524829\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.586253e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.814117e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.271971e+03\n Vprtstp: contraction number = 2.271971e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.957685e-04\n Vprtstp: contraction number = 1.829401e-01\n Vnewton: Using errtol_s: 2044.817292\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.832497e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.987641e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.414335e+02\n Vprtstp: contraction number = 4.414335e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.746599e-05\n Vprtstp: contraction number = 1.942938e-01\n Vnewton: Using errtol_s: 397.295336\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.009561e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.150107e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.690501e+01\n Vprtstp: contraction number = 8.690501e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.131327e-05\n Vprtstp: contraction number = 1.968689e-01\n Vnewton: Using errtol_s: 78.215105\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.034651e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.305601e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.879618e+01\n Vprtstp: contraction number = 1.879618e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.446866e-06\n Vprtstp: contraction number = 2.162828e-01\n Vnewton: Using errtol_s: 16.916585\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.059919e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.465709e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.583329e+00\n Vprtstp: contraction number = 4.583329e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 5.966529e-07\n Vprtstp: contraction number = 2.438437e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.035064e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.048164e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.315507e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.327084e+02\n Vpmg_setPart:  lower corner = (-53.482, -2.4645, 16.7425)\n Vpmg_setPart:  upper corner = (2.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-53.482, -11.2254, 5.5748)\n Vpmg_setPart:  actual maxima = (13.3006, 43.0355, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -28016,27 +28016,27 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.139698158758E+00 kT\n Vpmg_energy:  qfEnergy = 7.809316280828E+04 kT\n Vpmg_energy:  dielEnergy = 3.918099666156E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 8.137000e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.236600e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  printing only subset of domain\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.083520e+03\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 7.616459e+02\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 06:35:47 2025\n+# Creation Date and Time:  Tue Jan  9 04:35:06 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path mol1.pqr\n@@ -28389,129 +28389,129 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 2.847896\n+Vacc_SASA: Time elapsed: 2.936075\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.337575e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.327645e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.443600e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.272000e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.104352e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.006473e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.851424e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.769610e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4300910.832168\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.270494e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.867037e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.776390e+05\n Vprtstp: contraction number = 1.776390e+05\n Vnewton: Attempting damping, relres = 0.041319\n Vnewton: Attempting damping, relres = 0.513474\n Vnewton: Damping accepted, relres = 0.041319\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.131938e-02\n Vprtstp: contraction number = 4.131938e-02\n Vnewton: Using errtol_s: 177710.973970\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.127551e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.288801e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.677180e+04\n Vprtstp: contraction number = 2.677180e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 5.962101e-03\n Vprtstp: contraction number = 1.442931e-01\n Vnewton: Using errtol_s: 25642.465478\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.095971e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.764158e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.966549e+03\n Vprtstp: contraction number = 4.966549e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.056655e-03\n Vprtstp: contraction number = 1.772286e-01\n Vnewton: Using errtol_s: 4544.578762\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.057078e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.292590e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.011325e+03\n Vprtstp: contraction number = 1.011325e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.118038e-04\n Vprtstp: contraction number = 2.004475e-01\n Vnewton: Using errtol_s: 910.949292\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.154916e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.593951e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.253595e+02\n Vprtstp: contraction number = 2.253595e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.715911e-05\n Vprtstp: contraction number = 2.226547e-01\n Vnewton: Using errtol_s: 202.827138\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.113559e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.949427e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.445207e+01\n Vprtstp: contraction number = 5.445207e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.139456e-05\n Vprtstp: contraction number = 2.416194e-01\n Vnewton: Using errtol_s: 49.006980\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.307042e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.257618e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.420316e+01\n Vprtstp: contraction number = 1.420316e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.972126e-06\n Vprtstp: contraction number = 2.608373e-01\n Vnewton: Using errtol_s: 12.782849\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.462530e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.051649e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.022184e+00\n Vprtstp: contraction number = 4.022184e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.416744e-07\n Vprtstp: contraction number = 2.831893e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.548702e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.561088e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.140142e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.151494e+02\n Vpmg_setPart:  lower corner = (2.518, -2.4645, 16.7425)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -28520,17 +28520,17 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.085287424313E-01 kT\n Vpmg_energy:  qfEnergy = 2.020959449622E+03 kT\n Vpmg_energy:  dielEnergy = 1.003436009271E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.668300e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.391200e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 39.7309\n Vpbe_ctor2:  solute dimensions = 68.682 x 69.075 x 70.346\n Vpbe_ctor2:  solute charge = -12\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -28576,127 +28576,127 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0111702 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 2.970145\n+Vacc_SASA: Time elapsed: 2.825353\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.802385e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.590554e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.724300e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.253800e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.148856e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.058446e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.669030e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.256597e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2843800.208997\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.694460e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.276448e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.648041e+05\n Vprtstp: contraction number = 2.648041e+05\n Vnewton: Attempting damping, relres = 0.084229\n Vnewton: Attempting damping, relres = 0.539926\n Vnewton: Damping accepted, relres = 0.084229\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.422893e-02\n Vprtstp: contraction number = 8.422893e-02\n Vnewton: Using errtol_s: 239530.237257\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.940480e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.442555e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.601789e+04\n Vprtstp: contraction number = 3.601789e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.140061e-02\n Vprtstp: contraction number = 1.353527e-01\n Vnewton: Using errtol_s: 32421.054732\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.190906e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.598989e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.547762e+03\n Vprtstp: contraction number = 5.547762e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.755765e-03\n Vprtstp: contraction number = 1.540062e-01\n Vnewton: Using errtol_s: 4993.043762\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.435591e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.753582e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.234937e+02\n Vprtstp: contraction number = 9.234937e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.922661e-04\n Vprtstp: contraction number = 1.664609e-01\n Vnewton: Using errtol_s: 831.146494\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.686869e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.905333e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.647026e+02\n Vprtstp: contraction number = 1.647026e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.212477e-05\n Vprtstp: contraction number = 1.783469e-01\n Vnewton: Using errtol_s: 148.232430\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.941845e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.065720e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.095227e+01\n Vprtstp: contraction number = 3.095227e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 9.795714e-06\n Vprtstp: contraction number = 1.879282e-01\n Vnewton: Using errtol_s: 27.857053\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.196573e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.239867e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.500935e+00\n Vprtstp: contraction number = 6.500935e+00\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.057403e-06\n Vprtstp: contraction number = 2.100309e-01\n Vnewton: Using errtol_s: 5.850843\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.446154e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.394967e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.529139e+00\n Vprtstp: contraction number = 1.529139e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 4.839389e-07\n Vprtstp: contraction number = 2.352183e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.014487e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.027355e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.290791e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.302648e+02\n Vpmg_setPart:  lower corner = (2.518, -2.4645, 16.7425)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-8.26461, -11.2254, 5.5748)\n Vpmg_setPart:  actual maxima = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -28705,17 +28705,17 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.004865379330E-01 kT\n Vpmg_energy:  qfEnergy = 1.781523307319E+04 kT\n Vpmg_energy:  dielEnergy = 8.939732950056E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.528600e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.950600e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -28736,129 +28736,129 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 2.832708\n+Vacc_SASA: Time elapsed: 2.801753\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.940383e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.889560e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.719900e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.111000e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.162063e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.728880e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.737355e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.597464e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4276578.139223\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.759548e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.618745e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.716926e+05\n Vprtstp: contraction number = 1.716926e+05\n Vnewton: Attempting damping, relres = 0.040940\n Vnewton: Attempting damping, relres = 0.513162\n Vnewton: Damping accepted, relres = 0.040940\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.093968e-02\n Vprtstp: contraction number = 4.093968e-02\n Vnewton: Using errtol_s: 175081.721880\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.962669e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.768425e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.487025e+04\n Vprtstp: contraction number = 2.487025e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 5.724811e-03\n Vprtstp: contraction number = 1.398353e-01\n Vnewton: Using errtol_s: 24482.603484\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.138630e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.905286e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.528470e+03\n Vprtstp: contraction number = 4.528470e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 9.801406e-04\n Vprtstp: contraction number = 1.712092e-01\n Vnewton: Using errtol_s: 4191.647712\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.294991e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.044899e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.122748e+02\n Vprtstp: contraction number = 9.122748e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.923658e-04\n Vprtstp: contraction number = 1.962635e-01\n Vnewton: Using errtol_s: 822.667398\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.453573e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.200552e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.052635e+02\n Vprtstp: contraction number = 2.052635e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.319998e-05\n Vprtstp: contraction number = 2.245720e-01\n Vnewton: Using errtol_s: 184.748098\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.628696e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.324579e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.154123e+01\n Vprtstp: contraction number = 5.154123e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.084685e-05\n Vprtstp: contraction number = 2.510845e-01\n Vnewton: Using errtol_s: 46.387392\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.821478e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.480404e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.435770e+01\n Vprtstp: contraction number = 1.435770e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.021563e-06\n Vprtstp: contraction number = 2.785660e-01\n Vnewton: Using errtol_s: 12.921949\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.019697e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.602504e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.361187e+00\n Vprtstp: contraction number = 4.361187e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 9.178062e-07\n Vprtstp: contraction number = 3.037522e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.461494e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.474757e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.114108e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.124647e+02\n Vpmg_setPart:  lower corner = (2.518, -2.4645, 16.7425)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -28867,17 +28867,17 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.162784451104E-01 kT\n Vpmg_energy:  qfEnergy = 3.383505562700E+02 kT\n Vpmg_energy:  dielEnergy = 1.754184182339E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.202200e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.639000e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 40.4102\n Vpbe_ctor2:  solute dimensions = 61.161 x 72.117 x 70.346\n Vpbe_ctor2:  solute charge = -12\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -28923,138 +28923,138 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00475113 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 2.746012\n+Vacc_SASA: Time elapsed: 2.892860\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.014341e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.097271e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.210100e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.228000e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.173983e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.035272e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.252464e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.765479e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1712482.416854\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.279123e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.785933e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.778057e+05\n Vprtstp: contraction number = 1.778057e+05\n Vnewton: Attempting damping, relres = 0.095206\n Vnewton: Attempting damping, relres = 0.544528\n Vnewton: Damping accepted, relres = 0.095206\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.520604e-02\n Vprtstp: contraction number = 9.520604e-02\n Vnewton: Using errtol_s: 163038.671160\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.491961e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.919661e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.588526e+04\n Vprtstp: contraction number = 2.588526e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.365073e-02\n Vprtstp: contraction number = 1.433809e-01\n Vnewton: Using errtol_s: 23376.634124\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.686281e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.062831e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.392675e+03\n Vprtstp: contraction number = 4.392675e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.309227e-03\n Vprtstp: contraction number = 1.691651e-01\n Vnewton: Using errtol_s: 3954.509988\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.861366e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.197070e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.232796e+02\n Vprtstp: contraction number = 8.232796e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 4.326939e-04\n Vprtstp: contraction number = 1.873761e-01\n Vnewton: Using errtol_s: 740.980697\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.049132e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.328676e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.669237e+02\n Vprtstp: contraction number = 1.669237e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 8.772776e-05\n Vprtstp: contraction number = 2.027479e-01\n Vnewton: Using errtol_s: 150.232247\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.230464e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.441072e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.642088e+01\n Vprtstp: contraction number = 3.642088e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.914112e-05\n Vprtstp: contraction number = 2.181877e-01\n Vnewton: Using errtol_s: 32.778836\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.401968e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.583998e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.545476e+00\n Vprtstp: contraction number = 8.545476e+00\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.491102e-06\n Vprtstp: contraction number = 2.346311e-01\n Vnewton: Using errtol_s: 7.690933\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.599449e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.707112e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.153814e+00\n Vprtstp: contraction number = 2.153814e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.131943e-06\n Vprtstp: contraction number = 2.520414e-01\n Vnewton: Using errtol_s: 1.938433\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.789992e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.822660e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.814982e-01\n Vprtstp: contraction number = 5.814982e-01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.056081e-07\n Vprtstp: contraction number = 2.699853e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.705877e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.718580e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.150974e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.161949e+02\n Vpmg_setPart:  lower corner = (2.518, -2.4645, 16.7425)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-8.26461, -11.2254, 5.5748)\n Vpmg_setPart:  actual maxima = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -29063,17 +29063,17 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.651168945816E-01 kT\n Vpmg_energy:  qfEnergy = 3.320671858523E+03 kT\n Vpmg_energy:  dielEnergy = 1.644537494834E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.321800e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.870100e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -29094,129 +29094,129 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 6.191971\n+Vacc_SASA: Time elapsed: 6.374376\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.549470e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.663751e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.243500e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.305200e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.309885e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.070969e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.048890e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.006195e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 8699406.430616\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.078735e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.026591e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.528464e+05\n Vprtstp: contraction number = 3.528464e+05\n Vnewton: Attempting damping, relres = 0.041605\n Vnewton: Attempting damping, relres = 0.513349\n Vnewton: Damping accepted, relres = 0.041605\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.160535e-02\n Vprtstp: contraction number = 4.160535e-02\n Vnewton: Using errtol_s: 361941.817774\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.248884e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.217513e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.210930e+04\n Vprtstp: contraction number = 5.210930e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 5.921711e-03\n Vprtstp: contraction number = 1.423305e-01\n Vnewton: Using errtol_s: 51515.371182\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.501309e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.359794e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.570568e+03\n Vprtstp: contraction number = 9.570568e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.018950e-03\n Vprtstp: contraction number = 1.720701e-01\n Vnewton: Using errtol_s: 8864.257334\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.707829e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.548569e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.944504e+03\n Vprtstp: contraction number = 1.944504e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.015521e-04\n Vprtstp: contraction number = 1.978037e-01\n Vnewton: Using errtol_s: 1753.383252\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.946211e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.720159e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.357668e+02\n Vprtstp: contraction number = 4.357668e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.508379e-05\n Vprtstp: contraction number = 2.236831e-01\n Vnewton: Using errtol_s: 392.202227\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.182830e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.873859e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.074784e+02\n Vprtstp: contraction number = 1.074784e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.111924e-05\n Vprtstp: contraction number = 2.466350e-01\n Vnewton: Using errtol_s: 96.730784\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.416872e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.017379e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.903808e+01\n Vprtstp: contraction number = 2.903808e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.004146e-06\n Vprtstp: contraction number = 2.701755e-01\n Vnewton: Using errtol_s: 26.134288\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.642974e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.157925e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.552738e+00\n Vprtstp: contraction number = 8.552738e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.848266e-07\n Vprtstp: contraction number = 2.945351e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.796730e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.810415e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.296569e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.307876e+02\n Vpmg_setPart:  lower corner = (2.518, -2.4645, 16.7425)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-75.482, -62.9645, -64.2575)\n Vpmg_setPart:  actual maxima = (80.518, 58.0355, 97.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -29225,17 +29225,17 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 2.317973104173E-01 kT\n Vpmg_energy:  qfEnergy = 2.391935061774E+03 kT\n Vpmg_energy:  dielEnergy = 1.197593144317E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.216000e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.351500e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 56.367\n Vpbe_ctor2:  solute dimensions = 94.322 x 73.942 x 97.846\n Vpbe_ctor2:  solute charge = -24\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.073486\n@@ -29281,127 +29281,127 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0257349 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 6.845823\n+Vacc_SASA: Time elapsed: 6.223435\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.682454e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.908880e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.679000e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.218500e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.122934e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.036704e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.945952e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.394315e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 4500132.646352\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.974611e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.415255e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.278020e+05\n Vprtstp: contraction number = 4.278020e+05\n Vnewton: Attempting damping, relres = 0.086415\n Vnewton: Attempting damping, relres = 0.540695\n Vnewton: Damping accepted, relres = 0.086415\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.641451e-02\n Vprtstp: contraction number = 8.641451e-02\n Vnewton: Using errtol_s: 388876.774521\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.216982e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.580821e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.967321e+04\n Vprtstp: contraction number = 5.967321e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 1.194851e-02\n Vprtstp: contraction number = 1.382697e-01\n Vnewton: Using errtol_s: 53769.886692\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.448774e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.760086e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.609884e+03\n Vprtstp: contraction number = 9.609884e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.922151e-03\n Vprtstp: contraction number = 1.608695e-01\n Vnewton: Using errtol_s: 8649.935921\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.695979e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.954579e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.688280e+03\n Vprtstp: contraction number = 1.688280e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 3.376534e-04\n Vprtstp: contraction number = 1.756643e-01\n Vnewton: Using errtol_s: 1519.485051\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.945480e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.114520e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.185424e+02\n Vprtstp: contraction number = 3.185424e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 6.370679e-05\n Vprtstp: contraction number = 1.886751e-01\n Vnewton: Using errtol_s: 286.689023\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.019869e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.269573e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.336866e+01\n Vprtstp: contraction number = 6.336866e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.267337e-05\n Vprtstp: contraction number = 1.989328e-01\n Vnewton: Using errtol_s: 57.031849\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.042571e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.431352e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.358194e+01\n Vprtstp: contraction number = 1.358194e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.716310e-06\n Vprtstp: contraction number = 2.143321e-01\n Vnewton: Using errtol_s: 12.223755\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.069398e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.590461e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.189745e+00\n Vprtstp: contraction number = 3.189745e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 6.379304e-07\n Vprtstp: contraction number = 2.348518e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.981395e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.993407e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.348859e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.359844e+02\n Vpmg_setPart:  lower corner = (2.518, -2.4645, 16.7425)\n Vpmg_setPart:  upper corner = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  actual minima = (-8.26461, -11.2254, 5.5748)\n Vpmg_setPart:  actual maxima = (58.518, 43.0355, 74.7425)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n@@ -29410,17 +29410,17 @@\n Vpmg_setPart:  bflag[DOWN] = 1\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 3.132873625516E-01 kT\n Vpmg_energy:  qfEnergy = 2.116420853422E+04 kT\n Vpmg_energy:  dielEnergy = 1.060038494093E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.948400e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.760700e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  printing only subset of domain\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.093401e+03\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 7.748275e+02\n"}, {"source1": "./usr/share/apbs/examples/alkanes/io.mc", "source2": "./usr/share/apbs/examples/alkanes/io.mc", "unified_diff": "@@ -1,10 +1,10 @@\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 06:37:54 2025\n+# Creation Date and Time:  Tue Jan  9 04:37:59 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path 2-methylbutane.pdb\n@@ -302,130 +302,130 @@\n Vclist_ctor2:  Using 1.05 max radius\n Vclist_setupGrid:  Grid lengths = (13.5347, 12.2207, 11.3787)\n Vclist_setupGrid:  Grid lower corner = (-6.76736, -6.11036, -5.68936)\n Vclist_assignAtoms:  Have 6745 atom entries\n Vacc_storeParms:  Surf. density = 100\n Vacc_storeParms:  Max area = 109.953\n Vacc_storeParms:  Using 11012-point reference sphere\n-Vacc_SASA: Time elapsed: 0.012782\n-initAPOL: Time elapsed: 2.784644\n+Vacc_SASA: Time elapsed: 0.012115\n+initAPOL: Time elapsed: 2.713510\n APOL: Setting up hash table and accessibility object...\n Vclist_ctor2:  Using 15 x 12 x 11 hash table\n Vclist_ctor2:  automatic domain setup.\n Vclist_ctor2:  Using 1.05 max radius\n Vclist_setupGrid:  Grid lengths = (13.0267, 11.7717, 11.1107)\n Vclist_setupGrid:  Grid lower corner = (-2.59636, -5.18336, -14.1304)\n Vclist_assignAtoms:  Have 4888 atom entries\n Vacc_storeParms:  Surf. density = 100\n Vacc_storeParms:  Max area = 109.953\n Vacc_storeParms:  Using 11012-point reference sphere\n-Vacc_SASA: Time elapsed: 0.010148\n-initAPOL: Time elapsed: 2.329102\n+Vacc_SASA: Time elapsed: 0.009158\n+initAPOL: Time elapsed: 2.236242\n APOL: Setting up hash table and accessibility object...\n Vclist_ctor2:  Using 14 x 12 x 15 hash table\n Vclist_ctor2:  automatic domain setup.\n Vclist_ctor2:  Using 1.05 max radius\n Vclist_setupGrid:  Grid lengths = (12.7417, 11.4947, 13.2787)\n Vclist_setupGrid:  Grid lower corner = (-5.24736, -5.15936, -5.87136)\n Vclist_assignAtoms:  Have 6902 atom entries\n Vacc_storeParms:  Surf. density = 100\n Vacc_storeParms:  Max area = 109.953\n Vacc_storeParms:  Using 11012-point reference sphere\n-Vacc_SASA: Time elapsed: 0.013442\n-initAPOL: Time elapsed: 3.041151\n+Vacc_SASA: Time elapsed: 0.012221\n+initAPOL: Time elapsed: 2.869847\n APOL: Setting up hash table and accessibility object...\n Vclist_ctor2:  Using 14 x 12 x 13 hash table\n Vclist_ctor2:  automatic domain setup.\n Vclist_ctor2:  Using 1.05 max radius\n Vclist_setupGrid:  Grid lengths = (12.4767, 11.4917, 12.3367)\n Vclist_setupGrid:  Grid lower corner = (-4.91836, -5.22036, -4.87936)\n Vclist_assignAtoms:  Have 4977 atom entries\n Vacc_storeParms:  Surf. density = 100\n Vacc_storeParms:  Max area = 109.953\n Vacc_storeParms:  Using 11012-point reference sphere\n-Vacc_SASA: Time elapsed: 0.009268\n-initAPOL: Time elapsed: 2.160104\n+Vacc_SASA: Time elapsed: 0.008476\n+initAPOL: Time elapsed: 2.061073\n APOL: Setting up hash table and accessibility object...\n Vclist_ctor2:  Using 9 x 9 x 10 hash table\n Vclist_ctor2:  automatic domain setup.\n Vclist_ctor2:  Using 1.05 max radius\n Vclist_setupGrid:  Grid lengths = (10.0327, 10.2387, 10.6647)\n Vclist_setupGrid:  Grid lower corner = (-4.79536, -5.14036, -4.56736)\n Vclist_assignAtoms:  Have 1946 atom entries\n Vacc_storeParms:  Surf. density = 100\n Vacc_storeParms:  Max area = 109.953\n Vacc_storeParms:  Using 11012-point reference sphere\n-Vacc_SASA: Time elapsed: 0.005370\n-initAPOL: Time elapsed: 1.349887\n+Vacc_SASA: Time elapsed: 0.004753\n+initAPOL: Time elapsed: 1.279999\n APOL: Setting up hash table and accessibility object...\n Vclist_ctor2:  Using 19 x 15 x 12 hash table\n Vclist_ctor2:  automatic domain setup.\n Vclist_ctor2:  Using 1.05 max radius\n Vclist_setupGrid:  Grid lengths = (15.0957, 13.1957, 11.4487)\n Vclist_setupGrid:  Grid lower corner = (-2.59636, -6.60736, -14.1304)\n Vclist_assignAtoms:  Have 9434 atom entries\n Vacc_storeParms:  Surf. density = 100\n Vacc_storeParms:  Max area = 109.953\n Vacc_storeParms:  Using 11012-point reference sphere\n-Vacc_SASA: Time elapsed: 0.015632\n-initAPOL: Time elapsed: 3.261023\n+Vacc_SASA: Time elapsed: 0.014546\n+initAPOL: Time elapsed: 3.184726\n APOL: Setting up hash table and accessibility object...\n Vclist_ctor2:  Using 13 x 12 x 14 hash table\n Vclist_ctor2:  automatic domain setup.\n Vclist_ctor2:  Using 1.05 max radius\n Vclist_setupGrid:  Grid lengths = (12.0577, 11.5517, 12.5037)\n Vclist_setupGrid:  Grid lower corner = (12.5656, 12.8626, 12.9606)\n Vclist_assignAtoms:  Have 5377 atom entries\n Vacc_storeParms:  Surf. density = 100\n Vacc_storeParms:  Max area = 109.953\n Vacc_storeParms:  Using 11012-point reference sphere\n-Vacc_SASA: Time elapsed: 0.009104\n-initAPOL: Time elapsed: 2.364457\n+Vacc_SASA: Time elapsed: 0.009475\n+initAPOL: Time elapsed: 2.334144\n APOL: Setting up hash table and accessibility object...\n Vclist_ctor2:  Using 9 x 9 x 8 hash table\n Vclist_ctor2:  automatic domain setup.\n Vclist_ctor2:  Using 1.05 max radius\n Vclist_setupGrid:  Grid lengths = (10.1767, 10.1117, 9.66772)\n Vclist_setupGrid:  Grid lower corner = (12.9396, 12.7376, 12.9816)\n Vclist_assignAtoms:  Have 1014 atom entries\n Vacc_storeParms:  Surf. density = 100\n Vacc_storeParms:  Max area = 109.953\n Vacc_storeParms:  Using 11012-point reference sphere\n-Vacc_SASA: Time elapsed: 0.002687\n-initAPOL: Time elapsed: 0.873033\n+Vacc_SASA: Time elapsed: 0.002836\n+initAPOL: Time elapsed: 0.852533\n APOL: Setting up hash table and accessibility object...\n Vclist_ctor2:  Using 13 x 13 x 14 hash table\n Vclist_ctor2:  automatic domain setup.\n Vclist_ctor2:  Using 1.05 max radius\n Vclist_setupGrid:  Grid lengths = (12.2347, 12.1667, 12.6837)\n Vclist_setupGrid:  Grid lower corner = (12.5496, 12.8526, 12.8586)\n Vclist_assignAtoms:  Have 6725 atom entries\n Vacc_storeParms:  Surf. density = 100\n Vacc_storeParms:  Max area = 109.953\n Vacc_storeParms:  Using 11012-point reference sphere\n-Vacc_SASA: Time elapsed: 0.013203\n-initAPOL: Time elapsed: 2.919042\n+Vacc_SASA: Time elapsed: 0.012472\n+initAPOL: Time elapsed: 2.885669\n APOL: Setting up hash table and accessibility object...\n Vclist_ctor2:  Using 17 x 14 x 11 hash table\n Vclist_ctor2:  automatic domain setup.\n Vclist_ctor2:  Using 1.05 max radius\n Vclist_setupGrid:  Grid lengths = (14.1127, 12.8537, 11.1297)\n Vclist_setupGrid:  Grid lower corner = (-2.59636, -6.26536, -14.1304)\n Vclist_assignAtoms:  Have 6650 atom entries\n Vacc_storeParms:  Surf. density = 100\n Vacc_storeParms:  Max area = 109.953\n Vacc_storeParms:  Using 11012-point reference sphere\n-Vacc_SASA: Time elapsed: 0.011781\n-initAPOL: Time elapsed: 2.734508\n+Vacc_SASA: Time elapsed: 0.012176\n+initAPOL: Time elapsed: 2.743769\n APOL: Setting up hash table and accessibility object...\n Vclist_ctor2:  Using 10 x 14 x 12 hash table\n Vclist_ctor2:  automatic domain setup.\n Vclist_ctor2:  Using 1.05 max radius\n Vclist_setupGrid:  Grid lengths = (10.9097, 12.4407, 11.4747)\n Vclist_setupGrid:  Grid lower corner = (12.9086, 12.7426, 12.8736)\n Vclist_assignAtoms:  Have 3766 atom entries\n Vacc_storeParms:  Surf. density = 100\n Vacc_storeParms:  Max area = 109.953\n Vacc_storeParms:  Using 11012-point reference sphere\n-Vacc_SASA: Time elapsed: 0.007267\n-initAPOL: Time elapsed: 1.863722\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 2.569055e+01\n+Vacc_SASA: Time elapsed: 0.007128\n+initAPOL: Time elapsed: 1.859174\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 2.503000e+01\n"}, {"source1": "./usr/share/apbs/examples/born/io.mc", "source2": "./usr/share/apbs/examples/born/io.mc", "unified_diff": "@@ -1,10 +1,10 @@\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 05:34:01 2025\n+# Creation Date and Time:  Tue Jan  9 03:15:56 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path ion.xml\n@@ -194,32 +194,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000284\n+Vacc_SASA: Time elapsed: 0.000406\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.362150e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.014260e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.688300e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 3.029300e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.131006e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.947950e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.927286e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.403535e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.252488e-01\n Vprtstp: contraction number = 1.252488e-01\n Vprtstp: iteration = 2\n@@ -242,31 +242,31 @@\n Vprtstp: contraction number = 2.345457e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.154547e-06\n Vprtstp: contraction number = 2.398447e-01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.798201e-07\n Vprtstp: contraction number = 2.423636e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 4.180504e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.408606e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.660295e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.849403e+01\n Vpmg_setPart:  lower corner = (-25, -25, -25)\n Vpmg_setPart:  upper corner = (25, 25, 25)\n Vpmg_setPart:  actual minima = (-25, -25, -25)\n Vpmg_setPart:  actual maxima = (25, 25, 25)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 7.750853990251E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.681000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.225000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n@@ -315,30 +315,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.111569 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000217\n+Vacc_SASA: Time elapsed: 0.000177\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.930390e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.710970e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.399200e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.576300e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.462112e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.053602e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.818881e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.179965e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.284366e-01\n Vprtstp: contraction number = 1.284366e-01\n Vprtstp: iteration = 2\n@@ -370,31 +370,31 @@\n Vprtstp: contraction number = 3.689006e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 1.340984e-06\n Vprtstp: contraction number = 3.689051e-01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 4.946966e-07\n Vprtstp: contraction number = 3.689058e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 4.796327e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 5.069624e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.614130e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.816368e+01\n Vpmg_setPart:  lower corner = (-12.2474, -12.2474, -12.2474)\n Vpmg_setPart:  upper corner = (12.2474, 12.2474, 12.2474)\n Vpmg_setPart:  actual minima = (-12.2474, -12.2474, -12.2474)\n Vpmg_setPart:  actual maxima = (12.2474, 12.2474, 12.2474)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.775144565213E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.426000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.155000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n@@ -443,30 +443,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.339539 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000232\n+Vacc_SASA: Time elapsed: 0.000202\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.358890e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.595780e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.098620e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 7.956900e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.351082e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.152415e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.973977e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.091259e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.377836e-01\n Vprtstp: contraction number = 1.377836e-01\n Vprtstp: iteration = 2\n@@ -501,31 +501,31 @@\n Vprtstp: contraction number = 3.896678e-01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.022958e-06\n Vprtstp: contraction number = 3.896627e-01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 3.986147e-07\n Vprtstp: contraction number = 3.896686e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 5.042333e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 5.311464e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 4.238423e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.452440e+01\n Vpmg_setPart:  lower corner = (-6, -6, -6)\n Vpmg_setPart:  upper corner = (6, 6, 6)\n Vpmg_setPart:  actual minima = (-6, -6, -6)\n Vpmg_setPart:  actual maxima = (6, 6, 6)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 3.817909770059E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.019000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.307000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n WARNING\n Vgrid_readGZ:  gzip read/write support is disabled in this build\n Vgrid_readGZ:  configure and compile without the --disable-zlib flag.\n WARNING\n Vnm_tstart: starting timer 27 (Setup timer)..\n@@ -552,28 +552,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.152510e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.298830e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.550080e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.356700e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.582463e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.020692e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.532527e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.155932e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.114962e-01\n Vprtstp: contraction number = 1.114962e-01\n Vprtstp: iteration = 2\n@@ -590,31 +590,31 @@\n Vprtstp: contraction number = 1.068021e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.473387e-06\n Vprtstp: contraction number = 1.075288e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.592943e-07\n Vprtstp: contraction number = 1.081144e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.487453e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.759489e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.970220e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.169421e+01\n Vpmg_setPart:  lower corner = (-25, -25, -25)\n Vpmg_setPart:  upper corner = (25, 25, 25)\n Vpmg_setPart:  actual minima = (-25, -25, -25)\n Vpmg_setPart:  actual maxima = (25, 25, 25)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 9.607786035504E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.042000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.108000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n@@ -661,28 +661,28 @@\n VPMG::extEnergy: extQmEnergy = 0 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 8.7631 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.838420e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.160060e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.332000e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.537900e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.071677e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.261570e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.921734e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.371617e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.114981e-01\n Vprtstp: contraction number = 1.114981e-01\n Vprtstp: iteration = 2\n@@ -699,31 +699,31 @@\n Vprtstp: contraction number = 1.068029e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.473476e-06\n Vprtstp: contraction number = 1.075295e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.593050e-07\n Vprtstp: contraction number = 1.081151e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.351251e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.732184e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.171956e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.331281e+01\n Vpmg_setPart:  lower corner = (-12.2474, -12.2474, -12.2474)\n Vpmg_setPart:  upper corner = (12.2474, 12.2474, 12.2474)\n Vpmg_setPart:  actual minima = (-12.2474, -12.2474, -12.2474)\n Vpmg_setPart:  actual maxima = (12.2474, 12.2474, 12.2474)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.961195484638E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 9.400000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.106000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n@@ -770,28 +770,28 @@\n VPMG::extEnergy: extQmEnergy = 0 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 26.656 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.993170e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.902190e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.274000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 9.035000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.411900e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.020209e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.285331e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.609603e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.114975e-01\n Vprtstp: contraction number = 1.114975e-01\n Vprtstp: iteration = 2\n@@ -808,39 +808,39 @@\n Vprtstp: contraction number = 1.068029e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.473471e-06\n Vprtstp: contraction number = 1.075296e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.593045e-07\n Vprtstp: contraction number = 1.081151e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.377171e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.637060e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.092322e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.272374e+01\n Vpmg_setPart:  lower corner = (-6, -6, -6)\n Vpmg_setPart:  upper corner = (6, 6, 6)\n Vpmg_setPart:  actual minima = (-6, -6, -6)\n Vpmg_setPart:  actual maxima = (6, 6, 6)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 4.003287887017E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.123000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.132000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 2.623871e+02\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.820401e+02\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 05:34:25 2025\n+# Creation Date and Time:  Tue Jan  9 03:16:32 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path ion.xml\n@@ -1028,32 +1028,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.004281\n+Vacc_SASA: Time elapsed: 0.000235\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.735560e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.316340e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.207200e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.570200e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.190624e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.113520e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.280752e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.696073e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.315574e-01\n Vprtstp: contraction number = 1.315574e-01\n Vprtstp: iteration = 2\n@@ -1073,31 +1073,31 @@\n Vprtstp: contraction number = 2.039480e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.384411e-06\n Vprtstp: contraction number = 2.095783e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 9.318373e-07\n Vprtstp: contraction number = 2.125342e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.521452e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.771144e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.781610e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.976955e+01\n Vpmg_setPart:  lower corner = (-25, -25, -25)\n Vpmg_setPart:  upper corner = (25, 25, 25)\n Vpmg_setPart:  actual minima = (-25, -25, -25)\n Vpmg_setPart:  actual maxima = (25, 25, 25)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 7.691034776619E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.207000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.053000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n@@ -1146,30 +1146,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.111618 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000442\n+Vacc_SASA: Time elapsed: 0.000205\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.044954e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.291400e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.667400e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.598200e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.369954e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.126741e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.212521e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.354118e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.204709e-01\n Vprtstp: contraction number = 1.204709e-01\n Vprtstp: iteration = 2\n@@ -1186,31 +1186,31 @@\n Vprtstp: contraction number = 1.476379e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 5.011380e-06\n Vprtstp: contraction number = 1.603001e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 8.492596e-07\n Vprtstp: contraction number = 1.694662e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.165629e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.419925e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.097410e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.298564e+01\n Vpmg_setPart:  lower corner = (-12.2474, -12.2474, -12.2474)\n Vpmg_setPart:  upper corner = (12.2474, 12.2474, 12.2474)\n Vpmg_setPart:  actual minima = (-12.2474, -12.2474, -12.2474)\n Vpmg_setPart:  actual maxima = (12.2474, 12.2474, 12.2474)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.775933047078E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.296000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.159000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n@@ -1259,30 +1259,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.339781 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000231\n+Vacc_SASA: Time elapsed: 0.000179\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.195238e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.963520e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.541900e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.611700e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.581910e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.636510e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.677252e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.738728e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.298995e-01\n Vprtstp: contraction number = 1.298995e-01\n Vprtstp: iteration = 2\n@@ -1302,33 +1302,33 @@\n Vprtstp: contraction number = 1.916174e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.164097e-06\n Vprtstp: contraction number = 1.993376e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 4.370219e-07\n Vprtstp: contraction number = 2.019420e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.346043e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.521611e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.451748e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.630843e+01\n Vpmg_setPart:  lower corner = (-6, -6, -6)\n Vpmg_setPart:  upper corner = (6, 6, 6)\n Vpmg_setPart:  actual minima = (-6, -6, -6)\n Vpmg_setPart:  actual maxima = (6, 6, 6)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 3.818523837085E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.000000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.339000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 4.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -1349,28 +1349,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.644440e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.232410e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 4.104300e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.345040e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.621912e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.849540e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.137028e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.402391e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.114962e-01\n Vprtstp: contraction number = 1.114962e-01\n Vprtstp: iteration = 2\n@@ -1387,31 +1387,31 @@\n Vprtstp: contraction number = 1.068021e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.473387e-06\n Vprtstp: contraction number = 1.075288e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.592943e-07\n Vprtstp: contraction number = 1.081144e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.461591e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.756438e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.046627e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.229600e+01\n Vpmg_setPart:  lower corner = (-25, -25, -25)\n Vpmg_setPart:  upper corner = (25, 25, 25)\n Vpmg_setPart:  actual minima = (-25, -25, -25)\n Vpmg_setPart:  actual maxima = (25, 25, 25)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 9.607786035504E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.179000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.088000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n@@ -1458,28 +1458,28 @@\n VPMG::extEnergy: extQmEnergy = 0 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 8.7631 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.432630e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.097450e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.549800e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.447000e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.502265e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.002953e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.513129e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.065046e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.114981e-01\n Vprtstp: contraction number = 1.114981e-01\n Vprtstp: iteration = 2\n@@ -1496,31 +1496,31 @@\n Vprtstp: contraction number = 1.068029e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.473476e-06\n Vprtstp: contraction number = 1.075295e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.593050e-07\n Vprtstp: contraction number = 1.081151e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.328500e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.598306e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.195801e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.370155e+01\n Vpmg_setPart:  lower corner = (-12.2474, -12.2474, -12.2474)\n Vpmg_setPart:  upper corner = (12.2474, 12.2474, 12.2474)\n Vpmg_setPart:  actual minima = (-12.2474, -12.2474, -12.2474)\n Vpmg_setPart:  actual maxima = (12.2474, 12.2474, 12.2474)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.961195484638E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.508000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.171000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n@@ -1567,28 +1567,28 @@\n VPMG::extEnergy: extQmEnergy = 0 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 26.656 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.023590e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.784830e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.462000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.864000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.099484e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.429935e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.885778e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.311906e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.114975e-01\n Vprtstp: contraction number = 1.114975e-01\n Vprtstp: iteration = 2\n@@ -1605,39 +1605,39 @@\n Vprtstp: contraction number = 1.068029e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.473471e-06\n Vprtstp: contraction number = 1.075296e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.593045e-07\n Vprtstp: contraction number = 1.081151e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.519221e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.891882e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.061446e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.308511e+01\n Vpmg_setPart:  lower corner = (-6, -6, -6)\n Vpmg_setPart:  upper corner = (6, 6, 6)\n Vpmg_setPart:  actual minima = (-6, -6, -6)\n Vpmg_setPart:  actual maxima = (6, 6, 6)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 4.003287887017E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.038000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.810500e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 2.239523e+02\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.519184e+02\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 05:34:45 2025\n+# Creation Date and Time:  Tue Jan  9 03:17:02 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path ion.xml\n@@ -1885,32 +1885,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000409\n+Vacc_SASA: Time elapsed: 0.000243\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.813990e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.433680e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.451400e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 3.233300e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.307294e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.078705e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.195460e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.673368e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.252488e-01\n Vprtstp: contraction number = 1.252488e-01\n Vprtstp: iteration = 2\n@@ -1933,31 +1933,31 @@\n Vprtstp: contraction number = 2.345457e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.154547e-06\n Vprtstp: contraction number = 2.398447e-01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.798201e-07\n Vprtstp: contraction number = 2.423636e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.988441e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.238816e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.019280e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.230914e+01\n Vpmg_setPart:  lower corner = (-6, -6, -6)\n Vpmg_setPart:  upper corner = (0, 0, 6)\n Vpmg_setPart:  actual minima = (-25, -25, -25)\n Vpmg_setPart:  actual maxima = (25, 25, 25)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 1\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.937713497535E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.115000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.069000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n@@ -2006,30 +2006,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0318856 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000293\n+Vacc_SASA: Time elapsed: 0.000213\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.854090e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.890440e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.608400e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 3.971300e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.527706e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.008108e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.677802e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.559348e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.311479e-01\n Vprtstp: contraction number = 1.311479e-01\n Vprtstp: iteration = 2\n@@ -2061,31 +2061,31 @@\n Vprtstp: contraction number = 3.924056e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.308381e-06\n Vprtstp: contraction number = 3.934819e-01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 9.098344e-07\n Vprtstp: contraction number = 3.941440e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 5.007086e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 5.293153e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.534086e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.727867e+01\n Vpmg_setPart:  lower corner = (-6, -6, -6)\n Vpmg_setPart:  upper corner = (0, 0, 6)\n Vpmg_setPart:  actual minima = (-11.8833, -11.8833, -12.2474)\n Vpmg_setPart:  actual maxima = (7.06083, 7.06083, 12.2474)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 1\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 6.569607552225E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.016000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.135000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n@@ -2134,30 +2134,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0917244 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000196\n+Vacc_SASA: Time elapsed: 0.000190\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.095880e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.913720e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.663500e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 9.975000e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.579904e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.000014e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.006538e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.367310e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.316256e-01\n Vprtstp: contraction number = 1.316256e-01\n Vprtstp: iteration = 2\n@@ -2195,33 +2195,33 @@\n Vprtstp: contraction number = 4.543160e-01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 1.790206e-06\n Vprtstp: contraction number = 4.616591e-01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 8.377288e-07\n Vprtstp: contraction number = 4.679511e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 6.775823e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.069741e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 4.198199e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.387374e+01\n Vpmg_setPart:  lower corner = (-6, -6, -6)\n Vpmg_setPart:  upper corner = (0, 0, 6)\n Vpmg_setPart:  actual minima = (-6, -6, -6)\n Vpmg_setPart:  actual maxima = (1.17757, 1.17757, 6)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 1\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.198283392867E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.044000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.949000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -2242,28 +2242,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.869980e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.656930e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.569850e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.314290e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.365214e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.420780e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.714992e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.179714e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.114962e-01\n Vprtstp: contraction number = 1.114962e-01\n Vprtstp: iteration = 2\n@@ -2280,31 +2280,31 @@\n Vprtstp: contraction number = 1.068021e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.473387e-06\n Vprtstp: contraction number = 1.075288e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.592943e-07\n Vprtstp: contraction number = 1.081144e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.156928e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.431655e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.124158e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.317121e+01\n Vpmg_setPart:  lower corner = (-6, -6, -6)\n Vpmg_setPart:  upper corner = (0, 0, 6)\n Vpmg_setPart:  actual minima = (-25, -25, -25)\n Vpmg_setPart:  actual maxima = (25, 25, 25)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 1\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.401946508821E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.105000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.231000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n@@ -2351,28 +2351,28 @@\n VPMG::extEnergy: extQmEnergy = 0 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 2.50448 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.511220e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.056640e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.378700e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.457100e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.734999e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.979850e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.064089e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.411636e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.114250e-01\n Vprtstp: contraction number = 1.114250e-01\n Vprtstp: iteration = 2\n@@ -2392,31 +2392,31 @@\n Vprtstp: contraction number = 1.974463e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.739617e-06\n Vprtstp: contraction number = 2.010776e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 5.579966e-07\n Vprtstp: contraction number = 2.036768e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.788478e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.092945e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.329006e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.498284e+01\n Vpmg_setPart:  lower corner = (-6, -6, -6)\n Vpmg_setPart:  upper corner = (0, 0, 6)\n Vpmg_setPart:  actual minima = (-11.8833, -11.8833, -12.2474)\n Vpmg_setPart:  actual maxima = (7.06083, 7.06083, 12.2474)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 1\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 7.099156934179E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.051000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.117000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n@@ -2463,28 +2463,28 @@\n VPMG::extEnergy: extQmEnergy = 0 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 7.21011 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.106870e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.948860e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.377000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.537000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.495436e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.012135e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.473336e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.664961e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.114069e-01\n Vprtstp: contraction number = 1.114069e-01\n Vprtstp: iteration = 2\n@@ -2516,39 +2516,39 @@\n Vprtstp: contraction number = 3.639461e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 1.623548e-06\n Vprtstp: contraction number = 3.646489e-01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 5.928874e-07\n Vprtstp: contraction number = 3.651801e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 5.951219e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 6.224453e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.533029e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.711015e+01\n Vpmg_setPart:  lower corner = (-6, -6, -6)\n Vpmg_setPart:  upper corner = (0, 0, 6)\n Vpmg_setPart:  actual minima = (-6, -6, -6)\n Vpmg_setPart:  actual maxima = (1.17757, 1.17757, 6)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 1\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.244769313627E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.043000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.268000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 3.069395e+02\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 2.019443e+02\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 05:35:11 2025\n+# Creation Date and Time:  Tue Jan  9 03:17:41 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path ion.xml\n@@ -2796,32 +2796,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000314\n+Vacc_SASA: Time elapsed: 0.000445\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.212700e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.098590e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 3.452000e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.465700e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.208465e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.044638e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.180581e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.623338e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.252488e-01\n Vprtstp: contraction number = 1.252488e-01\n Vprtstp: iteration = 2\n@@ -2844,31 +2844,31 @@\n Vprtstp: contraction number = 2.345457e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.154547e-06\n Vprtstp: contraction number = 2.398447e-01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.798201e-07\n Vprtstp: contraction number = 2.423636e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.738338e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.003179e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.685593e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.895832e+01\n Vpmg_setPart:  lower corner = (0, -6, -6)\n Vpmg_setPart:  upper corner = (6, 0, 6)\n Vpmg_setPart:  actual minima = (-25, -25, -25)\n Vpmg_setPart:  actual maxima = (25, 25, 25)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.937713497535E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.024000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.163000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n@@ -2917,30 +2917,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.031798 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000225\n+Vacc_SASA: Time elapsed: 0.000171\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.532610e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.252850e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.130000e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 3.442800e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.268869e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.890060e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.384447e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.214387e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.311630e-01\n Vprtstp: contraction number = 1.311630e-01\n Vprtstp: iteration = 2\n@@ -2972,31 +2972,31 @@\n Vprtstp: contraction number = 3.943689e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.411496e-06\n Vprtstp: contraction number = 3.954554e-01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 9.552609e-07\n Vprtstp: contraction number = 3.961279e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 5.256178e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 5.504293e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.514341e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.712116e+01\n Vpmg_setPart:  lower corner = (0, -6, -6)\n Vpmg_setPart:  upper corner = (6, 0, 6)\n Vpmg_setPart:  actual minima = (-7.06083, -11.8833, -12.2474)\n Vpmg_setPart:  actual maxima = (11.8833, 7.06083, 12.2474)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 6.569480660622E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.239000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.121000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n@@ -3045,30 +3045,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0914959 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000195\n+Vacc_SASA: Time elapsed: 0.000192\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.481990e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.284600e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.151600e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.609500e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.167423e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.917680e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.967463e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.009458e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.316347e-01\n Vprtstp: contraction number = 1.316347e-01\n Vprtstp: iteration = 2\n@@ -3106,31 +3106,31 @@\n Vprtstp: contraction number = 4.560576e-01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 1.840082e-06\n Vprtstp: contraction number = 4.634922e-01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 8.644979e-07\n Vprtstp: contraction number = 4.698149e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 5.398499e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 5.634818e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 4.212652e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.403775e+01\n Vpmg_setPart:  lower corner = (0, -6, -6)\n Vpmg_setPart:  upper corner = (6, 0, 6)\n Vpmg_setPart:  actual minima = (-1.17757, -6, -6)\n Vpmg_setPart:  actual maxima = (6, 1.17757, 6)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.198276421620E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.037000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.090000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n@@ -3153,28 +3153,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.238490e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.458780e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.462270e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.324480e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.551587e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.105962e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.569502e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.145989e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.114962e-01\n Vprtstp: contraction number = 1.114962e-01\n Vprtstp: iteration = 2\n@@ -3191,33 +3191,33 @@\n Vprtstp: contraction number = 1.068021e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.473387e-06\n Vprtstp: contraction number = 1.075288e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.592943e-07\n Vprtstp: contraction number = 1.081144e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.060988e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.352343e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.087864e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.292051e+01\n Vpmg_setPart:  lower corner = (0, -6, -6)\n Vpmg_setPart:  upper corner = (6, 0, 6)\n Vpmg_setPart:  actual minima = (-25, -25, -25)\n Vpmg_setPart:  actual maxima = (25, 25, 25)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.401946508821E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.590000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.092000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -3262,28 +3262,28 @@\n VPMG::extEnergy: extQmEnergy = 0 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 2.4976 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.771790e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.653940e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.625400e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.460200e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.848822e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.119352e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.908680e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.375786e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.114250e-01\n Vprtstp: contraction number = 1.114250e-01\n Vprtstp: iteration = 2\n@@ -3303,31 +3303,31 @@\n Vprtstp: contraction number = 1.974463e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.739617e-06\n Vprtstp: contraction number = 2.010776e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 5.579966e-07\n Vprtstp: contraction number = 2.036768e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.700214e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.001129e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.386895e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.568747e+01\n Vpmg_setPart:  lower corner = (0, -6, -6)\n Vpmg_setPart:  upper corner = (6, 0, 6)\n Vpmg_setPart:  actual minima = (-7.06083, -11.8833, -12.2474)\n Vpmg_setPart:  actual maxima = (11.8833, 7.06083, 12.2474)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 7.099156934179E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.042000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.220000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n@@ -3374,28 +3374,28 @@\n VPMG::extEnergy: extQmEnergy = 0 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 7.19142 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.453960e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.986460e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.724000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.727000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.456802e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.660410e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.308555e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.632672e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.114069e-01\n Vprtstp: contraction number = 1.114069e-01\n Vprtstp: iteration = 2\n@@ -3427,39 +3427,39 @@\n Vprtstp: contraction number = 3.639461e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 1.623548e-06\n Vprtstp: contraction number = 3.646489e-01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 5.928874e-07\n Vprtstp: contraction number = 3.651801e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 5.739776e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 6.008482e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.711864e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.867294e+01\n Vpmg_setPart:  lower corner = (0, -6, -6)\n Vpmg_setPart:  upper corner = (6, 0, 6)\n Vpmg_setPart:  actual minima = (-1.17757, -6, -6)\n Vpmg_setPart:  actual maxima = (6, 1.17757, 6)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.244769313627E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.045000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.109000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 2.884416e+02\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 2.005299e+02\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 05:35:36 2025\n+# Creation Date and Time:  Tue Jan  9 03:18:20 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path ion.xml\n@@ -3707,32 +3707,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000292\n+Vacc_SASA: Time elapsed: 0.000225\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.437170e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.986110e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 7.925500e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.400500e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.543492e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.102807e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.667588e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.620333e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.252488e-01\n Vprtstp: contraction number = 1.252488e-01\n Vprtstp: iteration = 2\n@@ -3755,31 +3755,31 @@\n Vprtstp: contraction number = 2.345457e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.154547e-06\n Vprtstp: contraction number = 2.398447e-01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.798201e-07\n Vprtstp: contraction number = 2.423636e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 4.520788e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.832164e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.750615e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.961662e+01\n Vpmg_setPart:  lower corner = (-6, 0, -6)\n Vpmg_setPart:  upper corner = (0, 6, 6)\n Vpmg_setPart:  actual minima = (-25, -25, -25)\n Vpmg_setPart:  actual maxima = (25, 25, 25)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 1\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.937713497591E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.084000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.068000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n@@ -3828,30 +3828,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.031798 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000221\n+Vacc_SASA: Time elapsed: 0.000191\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.668180e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.572620e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 9.935600e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 9.411900e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.016281e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.211480e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.182458e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.306148e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.311246e-01\n Vprtstp: contraction number = 1.311246e-01\n Vprtstp: iteration = 2\n@@ -3883,33 +3883,33 @@\n Vprtstp: contraction number = 3.922726e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.295236e-06\n Vprtstp: contraction number = 3.933610e-01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 9.043960e-07\n Vprtstp: contraction number = 3.940319e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 5.320851e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 5.534189e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.830124e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.055798e+01\n Vpmg_setPart:  lower corner = (-6, 0, -6)\n Vpmg_setPart:  upper corner = (0, 6, 6)\n Vpmg_setPart:  actual minima = (-11.8833, -7.06083, -12.2474)\n Vpmg_setPart:  actual maxima = (7.06083, 11.8833, 12.2474)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 1\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 6.569607562894E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.176000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 9.630000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -3956,30 +3956,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0914865 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000178\n+Vacc_SASA: Time elapsed: 0.000192\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.893420e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.349840e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.038700e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 9.448700e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.252660e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.159214e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.082654e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.435716e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.312535e-01\n Vprtstp: contraction number = 1.312535e-01\n Vprtstp: iteration = 2\n@@ -4017,31 +4017,31 @@\n Vprtstp: contraction number = 4.543257e-01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 1.762407e-06\n Vprtstp: contraction number = 4.617179e-01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 8.248702e-07\n Vprtstp: contraction number = 4.680361e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 6.735672e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 6.964983e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 4.266029e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.479482e+01\n Vpmg_setPart:  lower corner = (-6, 0, -6)\n Vpmg_setPart:  upper corner = (0, 6, 6)\n Vpmg_setPart:  actual minima = (-6, -1.17757, -6)\n Vpmg_setPart:  actual maxima = (1.17757, 6, 6)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 1\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.198283391562E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.011000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.614300e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n@@ -4064,28 +4064,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.869560e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.828170e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.806600e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.384510e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.614901e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.043627e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.789030e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.192757e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.114962e-01\n Vprtstp: contraction number = 1.114962e-01\n Vprtstp: iteration = 2\n@@ -4102,33 +4102,33 @@\n Vprtstp: contraction number = 1.068021e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.473387e-06\n Vprtstp: contraction number = 1.075288e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.592943e-07\n Vprtstp: contraction number = 1.081144e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.131542e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.425801e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.070599e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.260251e+01\n Vpmg_setPart:  lower corner = (-6, 0, -6)\n Vpmg_setPart:  upper corner = (0, 6, 6)\n Vpmg_setPart:  actual minima = (-25, -25, -25)\n Vpmg_setPart:  actual maxima = (25, 25, 25)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 1\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.401946508931E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 9.550000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.306000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -4173,28 +4173,28 @@\n VPMG::extEnergy: extQmEnergy = 0 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 2.4976 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.368130e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.997240e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.497200e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.513300e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.410147e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.068767e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.131225e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.421224e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.115250e-01\n Vprtstp: contraction number = 1.115250e-01\n Vprtstp: iteration = 2\n@@ -4214,31 +4214,31 @@\n Vprtstp: contraction number = 1.974179e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.739799e-06\n Vprtstp: contraction number = 2.010662e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 5.580347e-07\n Vprtstp: contraction number = 2.036772e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 4.031211e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.293254e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.135703e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.322951e+01\n Vpmg_setPart:  lower corner = (-6, 0, -6)\n Vpmg_setPart:  upper corner = (0, 6, 6)\n Vpmg_setPart:  actual minima = (-11.8833, -7.06083, -12.2474)\n Vpmg_setPart:  actual maxima = (7.06083, 11.8833, 12.2474)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 1\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 7.099156934185E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.032000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.140000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n@@ -4285,28 +4285,28 @@\n VPMG::extEnergy: extQmEnergy = 0 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 7.19142 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.522230e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.334280e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.160000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.528000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.578397e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.062878e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.565449e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.656324e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.116239e-01\n Vprtstp: contraction number = 1.116239e-01\n Vprtstp: iteration = 2\n@@ -4338,39 +4338,39 @@\n Vprtstp: contraction number = 3.639660e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 1.623522e-06\n Vprtstp: contraction number = 3.646624e-01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 5.928877e-07\n Vprtstp: contraction number = 3.651861e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 5.849780e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 6.130691e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.601024e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.786470e+01\n Vpmg_setPart:  lower corner = (-6, 0, -6)\n Vpmg_setPart:  upper corner = (0, 6, 6)\n Vpmg_setPart:  actual minima = (-6, -1.17757, -6)\n Vpmg_setPart:  actual maxima = (1.17757, 6, 6)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 1\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.244769313634E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.058000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.400000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 3.152354e+02\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 2.018281e+02\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 05:36:02 2025\n+# Creation Date and Time:  Tue Jan  9 03:18:59 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path ion.xml\n@@ -4618,32 +4618,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000373\n+Vacc_SASA: Time elapsed: 0.000222\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.427950e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.524900e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 9.027500e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.645700e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.427975e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.219091e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.584992e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.996578e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.252488e-01\n Vprtstp: contraction number = 1.252488e-01\n Vprtstp: iteration = 2\n@@ -4666,31 +4666,31 @@\n Vprtstp: contraction number = 2.345457e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.154547e-06\n Vprtstp: contraction number = 2.398447e-01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.798201e-07\n Vprtstp: contraction number = 2.423636e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 4.436493e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.729684e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.340190e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.573482e+01\n Vpmg_setPart:  lower corner = (0, 0, -6)\n Vpmg_setPart:  upper corner = (6, 6, 6)\n Vpmg_setPart:  actual minima = (-25, -25, -25)\n Vpmg_setPart:  actual maxima = (25, 25, 25)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.937713497591E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.407500e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.235000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n@@ -4739,30 +4739,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0317109 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000251\n+Vacc_SASA: Time elapsed: 0.002080\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.909660e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.763510e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 7.965300e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.031100e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.125842e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.044131e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.100180e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.915407e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.311373e-01\n Vprtstp: contraction number = 1.311373e-01\n Vprtstp: iteration = 2\n@@ -4794,33 +4794,33 @@\n Vprtstp: contraction number = 3.942499e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.398436e-06\n Vprtstp: contraction number = 3.953474e-01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 9.498453e-07\n Vprtstp: contraction number = 3.960269e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 4.712457e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.938645e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.870729e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.078787e+01\n Vpmg_setPart:  lower corner = (0, 0, -6)\n Vpmg_setPart:  upper corner = (6, 6, 6)\n Vpmg_setPart:  actual minima = (-7.06083, -7.06083, -12.2474)\n Vpmg_setPart:  actual maxima = (11.8833, 11.8833, 12.2474)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 6.569480671365E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.066000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.186000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -4867,30 +4867,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0912591 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000406\n+Vacc_SASA: Time elapsed: 0.000173\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.899360e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.701330e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.643590e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 9.988600e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.464134e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.114793e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.018419e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.074309e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.312625e-01\n Vprtstp: contraction number = 1.312625e-01\n Vprtstp: iteration = 2\n@@ -4928,31 +4928,31 @@\n Vprtstp: contraction number = 4.561186e-01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 1.813861e-06\n Vprtstp: contraction number = 4.635791e-01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 8.523872e-07\n Vprtstp: contraction number = 4.699296e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 6.170029e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 6.456681e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 4.206259e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.411248e+01\n Vpmg_setPart:  lower corner = (0, 0, -6)\n Vpmg_setPart:  upper corner = (6, 6, 6)\n Vpmg_setPart:  actual minima = (-1.17757, -1.17757, -6)\n Vpmg_setPart:  actual maxima = (6, 6, 6)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.198276420222E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.160000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.368000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n@@ -4975,28 +4975,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.611440e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.492540e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.264620e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 9.669100e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.106463e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.004982e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.678760e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.251976e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.114962e-01\n Vprtstp: contraction number = 1.114962e-01\n Vprtstp: iteration = 2\n@@ -5013,33 +5013,33 @@\n Vprtstp: contraction number = 1.068021e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.473387e-06\n Vprtstp: contraction number = 1.075288e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.592943e-07\n Vprtstp: contraction number = 1.081144e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.093690e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.485905e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.058233e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.263476e+01\n Vpmg_setPart:  lower corner = (0, 0, -6)\n Vpmg_setPart:  upper corner = (6, 6, 6)\n Vpmg_setPart:  actual minima = (-25, -25, -25)\n Vpmg_setPart:  actual maxima = (25, 25, 25)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.401946508931E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.414000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.376000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -5084,28 +5084,28 @@\n VPMG::extEnergy: extQmEnergy = 0 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 2.49076 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.001080e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.270400e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.542400e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.504000e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.595936e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.033696e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.018821e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.478317e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.115250e-01\n Vprtstp: contraction number = 1.115250e-01\n Vprtstp: iteration = 2\n@@ -5125,31 +5125,31 @@\n Vprtstp: contraction number = 1.974179e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.739799e-06\n Vprtstp: contraction number = 2.010662e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 5.580347e-07\n Vprtstp: contraction number = 2.036772e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.894228e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.172176e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.373284e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.549737e+01\n Vpmg_setPart:  lower corner = (0, 0, -6)\n Vpmg_setPart:  upper corner = (6, 6, 6)\n Vpmg_setPart:  actual minima = (-7.06083, -7.06083, -12.2474)\n Vpmg_setPart:  actual maxima = (11.8833, 11.8833, 12.2474)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 7.099156934185E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.106000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.353000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n@@ -5196,28 +5196,28 @@\n VPMG::extEnergy: extQmEnergy = 0 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 7.17281 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.067010e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.342510e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.053000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.640000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.351925e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.399910e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.437100e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.734828e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.116239e-01\n Vprtstp: contraction number = 1.116239e-01\n Vprtstp: iteration = 2\n@@ -5249,39 +5249,39 @@\n Vprtstp: contraction number = 3.639660e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 1.623522e-06\n Vprtstp: contraction number = 3.646624e-01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 5.928877e-07\n Vprtstp: contraction number = 3.651861e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 5.953245e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 6.215783e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.747673e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.911108e+01\n Vpmg_setPart:  lower corner = (0, 0, -6)\n Vpmg_setPart:  upper corner = (6, 6, 6)\n Vpmg_setPart:  actual minima = (-1.17757, -1.17757, -6)\n Vpmg_setPart:  actual maxima = (6, 6, 6)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.244769313634E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.160000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.187000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 3.033269e+02\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 2.110743e+02\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 05:36:27 2025\n+# Creation Date and Time:  Tue Jan  9 03:19:43 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path ion.xml\n@@ -5529,32 +5529,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000484\n+Vacc_SASA: Time elapsed: 0.000213\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.031744e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.791120e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.574600e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.408700e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.462332e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.440870e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.863964e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.627851e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.315574e-01\n Vprtstp: contraction number = 1.315574e-01\n Vprtstp: iteration = 2\n@@ -5574,33 +5574,33 @@\n Vprtstp: contraction number = 2.039480e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.384411e-06\n Vprtstp: contraction number = 2.095783e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 9.318373e-07\n Vprtstp: contraction number = 2.125342e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.939858e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.221763e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.459848e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.643602e+01\n Vpmg_setPart:  lower corner = (-6, -6, -6)\n Vpmg_setPart:  upper corner = (0, 0, 6)\n Vpmg_setPart:  actual minima = (-25, -25, -25)\n Vpmg_setPart:  actual maxima = (25, 25, 25)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 1\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.922758694117E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.085000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.118000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -5647,30 +5647,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0319041 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000194\n+Vacc_SASA: Time elapsed: 0.000182\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.100298e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.024353e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.614800e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.638700e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.538010e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.744790e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.723955e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.011956e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.251607e-01\n Vprtstp: contraction number = 1.251607e-01\n Vprtstp: iteration = 2\n@@ -5693,31 +5693,31 @@\n Vprtstp: contraction number = 2.197650e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.342799e-06\n Vprtstp: contraction number = 2.223851e-01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.012580e-07\n Vprtstp: contraction number = 2.243508e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 4.667264e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.949925e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.861095e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.042242e+01\n Vpmg_setPart:  lower corner = (-6, -6, -6)\n Vpmg_setPart:  upper corner = (0, 0, 6)\n Vpmg_setPart:  actual minima = (-11.8833, -11.8833, -12.2474)\n Vpmg_setPart:  actual maxima = (7.06083, 7.06083, 12.2474)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 1\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 6.571571268982E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.108000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.613000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n@@ -5766,30 +5766,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0918985 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000249\n+Vacc_SASA: Time elapsed: 0.000195\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.264544e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.056679e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.133600e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.673800e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.645950e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.135266e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.696041e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.178285e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.287586e-01\n Vprtstp: contraction number = 1.287586e-01\n Vprtstp: iteration = 2\n@@ -5821,31 +5821,31 @@\n Vprtstp: contraction number = 3.624968e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.194036e-06\n Vprtstp: contraction number = 3.635428e-01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 7.993852e-07\n Vprtstp: contraction number = 3.643446e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.833979e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.007061e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.642950e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.832796e+01\n Vpmg_setPart:  lower corner = (-6, -6, -6)\n Vpmg_setPart:  upper corner = (0, 0, 6)\n Vpmg_setPart:  actual minima = (-6, -6, -6)\n Vpmg_setPart:  actual maxima = (1.17757, 1.17757, 6)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 1\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.198500974871E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.116000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.118000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n@@ -5868,28 +5868,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.071950e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.355320e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.766360e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.265480e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.824379e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.856940e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.390934e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.004425e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.114962e-01\n Vprtstp: contraction number = 1.114962e-01\n Vprtstp: iteration = 2\n@@ -5906,31 +5906,31 @@\n Vprtstp: contraction number = 1.068021e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.473387e-06\n Vprtstp: contraction number = 1.075288e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.592943e-07\n Vprtstp: contraction number = 1.081144e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.378904e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.732440e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.106896e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.301446e+01\n Vpmg_setPart:  lower corner = (-6, -6, -6)\n Vpmg_setPart:  upper corner = (0, 0, 6)\n Vpmg_setPart:  actual minima = (-25, -25, -25)\n Vpmg_setPart:  actual maxima = (25, 25, 25)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 1\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.401946508821E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.118000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.066000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n@@ -5977,28 +5977,28 @@\n VPMG::extEnergy: extQmEnergy = 0 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 2.50448 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.532140e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.219680e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.578000e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.544000e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.391358e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.867380e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.756521e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.235040e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.114250e-01\n Vprtstp: contraction number = 1.114250e-01\n Vprtstp: iteration = 2\n@@ -6018,31 +6018,31 @@\n Vprtstp: contraction number = 1.974463e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.739617e-06\n Vprtstp: contraction number = 2.010776e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 5.579966e-07\n Vprtstp: contraction number = 2.036768e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.037404e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.284150e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.521728e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.691652e+01\n Vpmg_setPart:  lower corner = (-6, -6, -6)\n Vpmg_setPart:  upper corner = (0, 0, 6)\n Vpmg_setPart:  actual minima = (-11.8833, -11.8833, -12.2474)\n Vpmg_setPart:  actual maxima = (7.06083, 7.06083, 12.2474)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 1\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 7.099156934179E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.264000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.067000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n@@ -6089,28 +6089,28 @@\n VPMG::extEnergy: extQmEnergy = 0 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 7.21011 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.684490e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.846630e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 9.260000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.844000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.123032e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.062050e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.083765e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.507491e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.114069e-01\n Vprtstp: contraction number = 1.114069e-01\n Vprtstp: iteration = 2\n@@ -6142,39 +6142,39 @@\n Vprtstp: contraction number = 3.639461e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 1.623548e-06\n Vprtstp: contraction number = 3.646489e-01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 5.928874e-07\n Vprtstp: contraction number = 3.651801e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 4.492468e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.696350e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 4.008481e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.186707e+01\n Vpmg_setPart:  lower corner = (-6, -6, -6)\n Vpmg_setPart:  upper corner = (0, 0, 6)\n Vpmg_setPart:  actual minima = (-6, -6, -6)\n Vpmg_setPart:  actual maxima = (1.17757, 1.17757, 6)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 1\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.244769313627E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.989000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.078000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 2.534208e+02\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.909546e+02\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 05:36:50 2025\n+# Creation Date and Time:  Tue Jan  9 03:20:23 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path ion.xml\n@@ -6422,32 +6422,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000411\n+Vacc_SASA: Time elapsed: 0.000223\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.214470e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.618180e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.978500e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 3.653500e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.343497e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.035210e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.319202e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.877623e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.315574e-01\n Vprtstp: contraction number = 1.315574e-01\n Vprtstp: iteration = 2\n@@ -6467,31 +6467,31 @@\n Vprtstp: contraction number = 2.039480e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.384411e-06\n Vprtstp: contraction number = 2.095783e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 9.318373e-07\n Vprtstp: contraction number = 2.125342e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.202081e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.450560e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.446124e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.656585e+01\n Vpmg_setPart:  lower corner = (0, -6, -6)\n Vpmg_setPart:  upper corner = (6, 0, 6)\n Vpmg_setPart:  actual minima = (-25, -25, -25)\n Vpmg_setPart:  actual maxima = (25, 25, 25)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.922758694117E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.423000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.089000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n@@ -6540,30 +6540,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0318166 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000188\n+Vacc_SASA: Time elapsed: 0.000213\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.035170e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.907320e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.872400e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.538100e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.434047e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.567880e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.891962e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.029735e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.251837e-01\n Vprtstp: contraction number = 1.251837e-01\n Vprtstp: iteration = 2\n@@ -6586,33 +6586,33 @@\n Vprtstp: contraction number = 2.194352e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.332747e-06\n Vprtstp: contraction number = 2.220306e-01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.985011e-07\n Vprtstp: contraction number = 2.239743e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.745865e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.995586e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.654265e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.844163e+01\n Vpmg_setPart:  lower corner = (0, -6, -6)\n Vpmg_setPart:  upper corner = (6, 0, 6)\n Vpmg_setPart:  actual minima = (-7.06083, -11.8833, -12.2474)\n Vpmg_setPart:  actual maxima = (11.8833, 7.06083, 12.2474)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 6.571611855754E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.315000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.033000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -6659,30 +6659,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0916405 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000194\n+Vacc_SASA: Time elapsed: 0.000171\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.131895e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.050463e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.901800e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.584600e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.205701e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.037043e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.969856e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.972984e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.287503e-01\n Vprtstp: contraction number = 1.287503e-01\n Vprtstp: iteration = 2\n@@ -6714,31 +6714,31 @@\n Vprtstp: contraction number = 3.625355e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.195364e-06\n Vprtstp: contraction number = 3.635887e-01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 7.999739e-07\n Vprtstp: contraction number = 3.643923e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 4.711355e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.921411e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.564846e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.741906e+01\n Vpmg_setPart:  lower corner = (0, -6, -6)\n Vpmg_setPart:  upper corner = (6, 0, 6)\n Vpmg_setPart:  actual minima = (-1.17757, -6, -6)\n Vpmg_setPart:  actual maxima = (6, 1.17757, 6)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.198504468748E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.008000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.134000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n@@ -6761,28 +6761,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.830240e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.172480e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.433970e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.440630e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.350469e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.379526e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.296129e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.828944e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.114962e-01\n Vprtstp: contraction number = 1.114962e-01\n Vprtstp: iteration = 2\n@@ -6799,31 +6799,31 @@\n Vprtstp: contraction number = 1.068021e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.473387e-06\n Vprtstp: contraction number = 1.075288e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.592943e-07\n Vprtstp: contraction number = 1.081144e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.421032e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.668641e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.022034e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.285263e+01\n Vpmg_setPart:  lower corner = (0, -6, -6)\n Vpmg_setPart:  upper corner = (6, 0, 6)\n Vpmg_setPart:  actual minima = (-25, -25, -25)\n Vpmg_setPart:  actual maxima = (25, 25, 25)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.401946508821E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.688700e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.225000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n@@ -6870,28 +6870,28 @@\n VPMG::extEnergy: extQmEnergy = 0 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 2.4976 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.412740e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.599220e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.620700e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.402100e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.252655e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.907150e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.664353e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.204922e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.114250e-01\n Vprtstp: contraction number = 1.114250e-01\n Vprtstp: iteration = 2\n@@ -6911,33 +6911,33 @@\n Vprtstp: contraction number = 1.974463e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.739617e-06\n Vprtstp: contraction number = 2.010776e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 5.579966e-07\n Vprtstp: contraction number = 2.036768e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.071001e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.302066e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.461342e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.637400e+01\n Vpmg_setPart:  lower corner = (0, -6, -6)\n Vpmg_setPart:  upper corner = (6, 0, 6)\n Vpmg_setPart:  actual minima = (-7.06083, -11.8833, -12.2474)\n Vpmg_setPart:  actual maxima = (11.8833, 7.06083, 12.2474)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 7.099156934179E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.138000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.106000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -6982,28 +6982,28 @@\n VPMG::extEnergy: extQmEnergy = 0 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 7.19142 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.705230e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.885830e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.878000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.833000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.418758e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.013640e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.998434e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.472330e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.114069e-01\n Vprtstp: contraction number = 1.114069e-01\n Vprtstp: iteration = 2\n@@ -7035,39 +7035,39 @@\n Vprtstp: contraction number = 3.639461e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 1.623548e-06\n Vprtstp: contraction number = 3.646489e-01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 5.928874e-07\n Vprtstp: contraction number = 3.651801e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 5.392238e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 5.630471e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.650196e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.837956e+01\n Vpmg_setPart:  lower corner = (0, -6, -6)\n Vpmg_setPart:  upper corner = (6, 0, 6)\n Vpmg_setPart:  actual minima = (-1.17757, -6, -6)\n Vpmg_setPart:  actual maxima = (6, 1.17757, 6)\n Vpmg_setPart:  bflag[FRONT] = 1\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 1\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.244769313627E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.344000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.085000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 2.539572e+02\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.838566e+02\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 05:37:15 2025\n+# Creation Date and Time:  Tue Jan  9 03:20:59 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path ion.xml\n@@ -7315,32 +7315,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000393\n+Vacc_SASA: Time elapsed: 0.000383\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.230200e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.477080e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 4.439800e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.387750e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.219181e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.021244e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.282529e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.815852e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.315574e-01\n Vprtstp: contraction number = 1.315574e-01\n Vprtstp: iteration = 2\n@@ -7360,31 +7360,31 @@\n Vprtstp: contraction number = 2.039480e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.384411e-06\n Vprtstp: contraction number = 2.095783e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 9.318373e-07\n Vprtstp: contraction number = 2.125342e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.571999e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.816632e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.361562e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.557224e+01\n Vpmg_setPart:  lower corner = (-6, 0, -6)\n Vpmg_setPart:  upper corner = (0, 6, 6)\n Vpmg_setPart:  actual minima = (-25, -25, -25)\n Vpmg_setPart:  actual maxima = (25, 25, 25)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 1\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.922758694192E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.150000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.178000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n@@ -7433,30 +7433,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0318166 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000287\n+Vacc_SASA: Time elapsed: 0.000173\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.183805e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.189910e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.685800e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.625000e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.387993e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.135469e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.279548e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.948089e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.252629e-01\n Vprtstp: contraction number = 1.252629e-01\n Vprtstp: iteration = 2\n@@ -7479,31 +7479,31 @@\n Vprtstp: contraction number = 2.198448e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.343869e-06\n Vprtstp: contraction number = 2.224198e-01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.015100e-07\n Vprtstp: contraction number = 2.243596e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 4.418010e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.673775e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.575073e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.781011e+01\n Vpmg_setPart:  lower corner = (-6, 0, -6)\n Vpmg_setPart:  upper corner = (0, 6, 6)\n Vpmg_setPart:  actual minima = (-11.8833, -7.06083, -12.2474)\n Vpmg_setPart:  actual maxima = (7.06083, 11.8833, 12.2474)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 1\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 6.571571270505E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.107000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.163000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n@@ -7552,30 +7552,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0916602 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000183\n+Vacc_SASA: Time elapsed: 0.000172\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.185513e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.062239e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.569600e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.479500e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.445058e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.026667e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.072024e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.803843e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.283061e-01\n Vprtstp: contraction number = 1.283061e-01\n Vprtstp: iteration = 2\n@@ -7607,33 +7607,33 @@\n Vprtstp: contraction number = 3.626484e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.188308e-06\n Vprtstp: contraction number = 3.636628e-01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 7.975574e-07\n Vprtstp: contraction number = 3.644631e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 5.704118e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 5.954385e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.497814e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.663913e+01\n Vpmg_setPart:  lower corner = (-6, 0, -6)\n Vpmg_setPart:  upper corner = (0, 6, 6)\n Vpmg_setPart:  actual minima = (-6, -1.17757, -6)\n Vpmg_setPart:  actual maxima = (1.17757, 6, 6)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 1\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.198500974608E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.032000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.670000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -7654,28 +7654,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.792330e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.590040e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.464470e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.480520e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.286997e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.055862e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.518202e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.525642e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.114962e-01\n Vprtstp: contraction number = 1.114962e-01\n Vprtstp: iteration = 2\n@@ -7692,33 +7692,33 @@\n Vprtstp: contraction number = 1.068021e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.473387e-06\n Vprtstp: contraction number = 1.075288e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.592943e-07\n Vprtstp: contraction number = 1.081144e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.324479e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.697323e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.152267e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.347737e+01\n Vpmg_setPart:  lower corner = (-6, 0, -6)\n Vpmg_setPart:  upper corner = (0, 6, 6)\n Vpmg_setPart:  actual minima = (-25, -25, -25)\n Vpmg_setPart:  actual maxima = (25, 25, 25)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 1\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.401946508931E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.076000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.227000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -7763,28 +7763,28 @@\n VPMG::extEnergy: extQmEnergy = 0 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 2.4976 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.311010e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.049250e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.323000e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.594400e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.389274e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.062967e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.879232e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.188365e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.115250e-01\n Vprtstp: contraction number = 1.115250e-01\n Vprtstp: iteration = 2\n@@ -7804,31 +7804,31 @@\n Vprtstp: contraction number = 1.974179e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.739799e-06\n Vprtstp: contraction number = 2.010662e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 5.580347e-07\n Vprtstp: contraction number = 2.036772e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.679691e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.937783e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.365153e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.541909e+01\n Vpmg_setPart:  lower corner = (-6, 0, -6)\n Vpmg_setPart:  upper corner = (0, 6, 6)\n Vpmg_setPart:  actual minima = (-11.8833, -7.06083, -12.2474)\n Vpmg_setPart:  actual maxima = (7.06083, 11.8833, 12.2474)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 1\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 7.099156934185E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 9.460000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.253000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n@@ -7875,28 +7875,28 @@\n VPMG::extEnergy: extQmEnergy = 0 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 7.19142 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.401670e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.756830e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.679000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.641000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.450136e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.826690e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.275630e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.445018e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.116239e-01\n Vprtstp: contraction number = 1.116239e-01\n Vprtstp: iteration = 2\n@@ -7928,39 +7928,39 @@\n Vprtstp: contraction number = 3.639660e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 1.623522e-06\n Vprtstp: contraction number = 3.646624e-01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 5.928877e-07\n Vprtstp: contraction number = 3.651861e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 5.653921e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 5.909693e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.632305e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.808902e+01\n Vpmg_setPart:  lower corner = (-6, 0, -6)\n Vpmg_setPart:  upper corner = (0, 6, 6)\n Vpmg_setPart:  actual minima = (-6, -1.17757, -6)\n Vpmg_setPart:  actual maxima = (1.17757, 6, 6)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 1\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.244769313634E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.076000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.241000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 2.842444e+02\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.809109e+02\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 05:37:39 2025\n+# Creation Date and Time:  Tue Jan  9 03:21:35 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path ion.xml\n@@ -8208,32 +8208,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000303\n+Vacc_SASA: Time elapsed: 0.000238\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.153240e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.018170e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 4.453400e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 4.801600e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.255958e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.937730e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.468742e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.630407e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.315574e-01\n Vprtstp: contraction number = 1.315574e-01\n Vprtstp: iteration = 2\n@@ -8253,33 +8253,33 @@\n Vprtstp: contraction number = 2.039480e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.384411e-06\n Vprtstp: contraction number = 2.095783e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 9.318373e-07\n Vprtstp: contraction number = 2.125342e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.346616e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.600800e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.326858e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.518682e+01\n Vpmg_setPart:  lower corner = (0, 0, -6)\n Vpmg_setPart:  upper corner = (6, 6, 6)\n Vpmg_setPart:  actual minima = (-25, -25, -25)\n Vpmg_setPart:  actual maxima = (25, 25, 25)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.922758694192E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.543000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.094000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -8326,30 +8326,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0317294 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000248\n+Vacc_SASA: Time elapsed: 0.000175\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.948500e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.464240e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.749200e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.606300e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.237668e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.929840e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.015681e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.876231e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.252944e-01\n Vprtstp: contraction number = 1.252944e-01\n Vprtstp: iteration = 2\n@@ -8372,31 +8372,31 @@\n Vprtstp: contraction number = 2.195054e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.334000e-06\n Vprtstp: contraction number = 2.220609e-01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.987906e-07\n Vprtstp: contraction number = 2.239810e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.139198e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.357804e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.803525e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.987748e+01\n Vpmg_setPart:  lower corner = (0, 0, -6)\n Vpmg_setPart:  upper corner = (6, 6, 6)\n Vpmg_setPart:  actual minima = (-7.06083, -7.06083, -12.2474)\n Vpmg_setPart:  actual maxima = (11.8833, 11.8833, 12.2474)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 6.571611857350E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.239000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.175000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n@@ -8445,30 +8445,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0914032 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000175\n+Vacc_SASA: Time elapsed: 0.000196\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.081620e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.045552e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.452800e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.619300e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.270416e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.175699e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.491259e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.992119e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.282975e-01\n Vprtstp: contraction number = 1.282975e-01\n Vprtstp: iteration = 2\n@@ -8500,33 +8500,33 @@\n Vprtstp: contraction number = 3.626822e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.189511e-06\n Vprtstp: contraction number = 3.637026e-01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 7.980984e-07\n Vprtstp: contraction number = 3.645099e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 4.552175e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.771963e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.816893e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.018404e+01\n Vpmg_setPart:  lower corner = (0, 0, -6)\n Vpmg_setPart:  upper corner = (6, 6, 6)\n Vpmg_setPart:  actual minima = (-1.17757, -1.17757, -6)\n Vpmg_setPart:  actual maxima = (6, 6, 6)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.198504468496E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.400000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.552000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -8547,28 +8547,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.802510e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.914500e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.319590e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.622250e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.178405e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.247682e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.232506e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.007683e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.114962e-01\n Vprtstp: contraction number = 1.114962e-01\n Vprtstp: iteration = 2\n@@ -8585,33 +8585,33 @@\n Vprtstp: contraction number = 1.068021e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.473387e-06\n Vprtstp: contraction number = 1.075288e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.592943e-07\n Vprtstp: contraction number = 1.081144e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.850309e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.097944e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.156368e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.388817e+01\n Vpmg_setPart:  lower corner = (0, 0, -6)\n Vpmg_setPart:  upper corner = (6, 6, 6)\n Vpmg_setPart:  actual minima = (-25, -25, -25)\n Vpmg_setPart:  actual maxima = (25, 25, 25)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.401946508931E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.035700e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.184000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -8656,28 +8656,28 @@\n VPMG::extEnergy: extQmEnergy = 0 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 2.49076 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.154590e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.258110e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.510400e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.403900e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.122245e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.108695e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.553063e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.245299e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.115250e-01\n Vprtstp: contraction number = 1.115250e-01\n Vprtstp: iteration = 2\n@@ -8697,31 +8697,31 @@\n Vprtstp: contraction number = 1.974179e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.739799e-06\n Vprtstp: contraction number = 2.010662e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 5.580347e-07\n Vprtstp: contraction number = 2.036772e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.707280e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.032688e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.485402e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.675157e+01\n Vpmg_setPart:  lower corner = (0, 0, -6)\n Vpmg_setPart:  upper corner = (6, 6, 6)\n Vpmg_setPart:  actual minima = (-7.06083, -7.06083, -12.2474)\n Vpmg_setPart:  actual maxima = (11.8833, 11.8833, 12.2474)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 7.099156934185E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 9.190000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.257000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3\n Vpbe_ctor2:  solute dimensions = 6 x 6 x 6\n Vpbe_ctor2:  solute charge = 1\n@@ -8768,28 +8768,28 @@\n VPMG::extEnergy: extQmEnergy = 0 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 7.17281 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.709050e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.232320e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.565000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.622000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.647699e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.105127e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.968805e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.516367e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.116239e-01\n Vprtstp: contraction number = 1.116239e-01\n Vprtstp: iteration = 2\n@@ -8821,29 +8821,29 @@\n Vprtstp: contraction number = 3.639660e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 1.623522e-06\n Vprtstp: contraction number = 3.646624e-01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 5.928877e-07\n Vprtstp: contraction number = 3.651861e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 5.152726e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 5.576146e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.910199e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.105000e+01\n Vpmg_setPart:  lower corner = (0, 0, -6)\n Vpmg_setPart:  upper corner = (6, 6, 6)\n Vpmg_setPart:  actual minima = (-1.17757, -1.17757, -6)\n Vpmg_setPart:  actual maxima = (6, 6, 6)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 1\n Vpmg_setPart:  bflag[LEFT] = 1\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.244769313634E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.139000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.107000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 2.485811e+02\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.908614e+02\n"}, {"source1": "./usr/share/apbs/examples/hca-bind/io.mc", "source2": "./usr/share/apbs/examples/hca-bind/io.mc", "unified_diff": "@@ -1,10 +1,10 @@\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 06:42:43 2025\n+# Creation Date and Time:  Tue Jan  9 04:43:56 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path acet.pqr\n@@ -289,32 +289,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.048920\n+Vacc_SASA: Time elapsed: 0.036599\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.296510e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.694650e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 3.782700e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.528600e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.304899e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.299810e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.805009e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.711403e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.087255e-01\n Vprtstp: contraction number = 1.087255e-01\n Vprtstp: iteration = 2\n@@ -331,32 +331,32 @@\n Vprtstp: contraction number = 1.074047e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.481057e-06\n Vprtstp: contraction number = 1.080656e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.608051e-07\n Vprtstp: contraction number = 1.085746e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.316639e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.565060e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.115829e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.362010e+01\n Vpmg_setPart:  lower corner = (-54.0285, -44.1015, -32.821)\n Vpmg_setPart:  upper corner = (41.9715, 51.8985, 63.179)\n Vpmg_setPart:  actual minima = (-54.0285, -44.1015, -32.821)\n Vpmg_setPart:  actual maxima = (41.9715, 51.8985, 63.179)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.785902379684E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.400000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.400000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 6.35359\n Vpbe_ctor2:  solute dimensions = 7.389 x 11.027 x 9.931\n Vpbe_ctor2:  solute charge = -1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -402,30 +402,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.104294 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.024615\n+Vacc_SASA: Time elapsed: 0.068264\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.297470e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.783150e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.900400e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 4.131300e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.061405e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.628940e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.853746e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.596295e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.287269e-01\n Vprtstp: contraction number = 1.287269e-01\n Vprtstp: iteration = 2\n@@ -451,30 +451,30 @@\n Vprtstp: contraction number = 3.073619e-01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 1.517211e-06\n Vprtstp: contraction number = 3.092055e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 4.703221e-07\n Vprtstp: contraction number = 3.099912e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.385105e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.605473e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.726015e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.892298e+01\n Vpmg_setPart:  lower corner = (-24.6188, -14.6918, -3.41132)\n Vpmg_setPart:  upper corner = (12.5618, 22.4888, 33.7693)\n Vpmg_setPart:  actual minima = (-24.6188, -14.6918, -3.41132)\n Vpmg_setPart:  actual maxima = (12.5618, 22.4888, 33.7693)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.473001739532E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.700000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.200000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 6.35359\n Vpbe_ctor2:  solute dimensions = 7.389 x 11.027 x 9.931\n Vpbe_ctor2:  solute charge = -1\n@@ -522,30 +522,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.504504 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.052255\n+Vacc_SASA: Time elapsed: 0.024089\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.263340e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.480860e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.255900e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.416030e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.076334e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.203340e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.479506e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.546895e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.402627e-01\n Vprtstp: contraction number = 1.402627e-01\n Vprtstp: iteration = 2\n@@ -574,30 +574,30 @@\n Vprtstp: contraction number = 3.281873e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.285796e-06\n Vprtstp: contraction number = 3.294777e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 4.250794e-07\n Vprtstp: contraction number = 3.305964e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.530967e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.730475e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.109492e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.291652e+01\n Vpmg_setPart:  lower corner = (-13.2285, -3.3015, 7.979)\n Vpmg_setPart:  upper corner = (1.1715, 11.0985, 22.379)\n Vpmg_setPart:  actual minima = (-13.2285, -3.3015, 7.979)\n Vpmg_setPart:  actual maxima = (1.1715, 11.0985, 22.379)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 5.210605041355E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.300000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.300000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 31.0304\n Vpbe_ctor2:  solute dimensions = 49.637 x 47.533 x 56.913\n Vpbe_ctor2:  solute charge = 1\n@@ -620,32 +620,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.956442\n+Vacc_SASA: Time elapsed: 1.833617\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.342814e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.219735e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 9.375000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.724000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.247894e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.226112e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.047533e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.094763e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.838248e-02\n Vprtstp: contraction number = 7.838248e-02\n Vprtstp: iteration = 2\n@@ -707,32 +707,32 @@\n Vprtstp: contraction number = 6.567898e-01\n Vprtstp: iteration = 21\n Vprtstp: relative residual = 1.365716e-06\n Vprtstp: contraction number = 6.589433e-01\n Vprtstp: iteration = 22\n Vprtstp: relative residual = 9.028429e-07\n Vprtstp: contraction number = 6.610767e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 7.317589e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.538143e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 6.815202e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.023565e+01\n Vpmg_setPart:  lower corner = (-54.0285, -44.1015, -32.821)\n Vpmg_setPart:  upper corner = (41.9715, 51.8985, 63.179)\n Vpmg_setPart:  actual minima = (-54.0285, -44.1015, -32.821)\n Vpmg_setPart:  actual maxima = (41.9715, 51.8985, 63.179)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.689092374656E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.230000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.360000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 31.0304\n Vpbe_ctor2:  solute dimensions = 49.637 x 47.533 x 56.913\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -778,30 +778,30 @@\n VPMG::extEnergy: extQfEnergy = 4518.73 kT\n VPMG::extEnergy: extDiEnergy = 2191.64 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.879767\n+Vacc_SASA: Time elapsed: 1.697778\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.333705e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.182772e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.646600e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.369400e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.273093e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.151386e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.824405e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.633920e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.397950e-01\n Vprtstp: contraction number = 1.397950e-01\n Vprtstp: iteration = 2\n@@ -842,30 +842,30 @@\n Vprtstp: contraction number = 5.527064e-01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 1.277233e-06\n Vprtstp: contraction number = 5.598610e-01\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 7.227170e-07\n Vprtstp: contraction number = 5.658458e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 5.194121e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 5.402480e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 4.865096e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 5.071216e+01\n Vpmg_setPart:  lower corner = (-24.6188, -14.6918, -3.41132)\n Vpmg_setPart:  upper corner = (12.5618, 22.4888, 33.7693)\n Vpmg_setPart:  actual minima = (-24.6188, -14.6918, -3.41132)\n Vpmg_setPart:  actual maxima = (12.5618, 22.4888, 33.7693)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.222630775541E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.420000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.460000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 31.0304\n Vpbe_ctor2:  solute dimensions = 49.637 x 47.533 x 56.913\n Vpbe_ctor2:  solute charge = 1\n@@ -913,30 +913,30 @@\n VPMG::extEnergy: extQfEnergy = 110988 kT\n VPMG::extEnergy: extDiEnergy = 56275.9 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.886978\n+Vacc_SASA: Time elapsed: 1.738447\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.337017e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.137822e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 9.693000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.490000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.160637e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.217808e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.389132e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.163629e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.115653e-01\n Vprtstp: contraction number = 1.115653e-01\n Vprtstp: iteration = 2\n@@ -962,32 +962,32 @@\n Vprtstp: contraction number = 3.498142e-01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.355176e-06\n Vprtstp: contraction number = 3.685616e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 9.245419e-07\n Vprtstp: contraction number = 3.925575e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.452425e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.665931e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.974674e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.184462e+01\n Vpmg_setPart:  lower corner = (-13.2285, -3.3015, 7.979)\n Vpmg_setPart:  upper corner = (1.1715, 11.0985, 22.379)\n Vpmg_setPart:  actual minima = (-13.2285, -3.3015, 7.979)\n Vpmg_setPart:  actual maxima = (1.1715, 11.0985, 22.379)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.441218006192E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.590000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.230000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 31.0304\n Vpbe_ctor2:  solute dimensions = 49.637 x 47.533 x 56.913\n Vpbe_ctor2:  solute charge = -1.01863e-14\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -1008,32 +1008,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.911043\n+Vacc_SASA: Time elapsed: 1.730683\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.382846e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.143228e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.300900e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.290000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.377618e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.754680e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.783054e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.501112e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.658858e-02\n Vprtstp: contraction number = 7.658858e-02\n Vprtstp: iteration = 2\n@@ -1095,30 +1095,30 @@\n Vprtstp: contraction number = 6.561084e-01\n Vprtstp: iteration = 21\n Vprtstp: relative residual = 1.508067e-06\n Vprtstp: contraction number = 6.580134e-01\n Vprtstp: iteration = 22\n Vprtstp: relative residual = 9.954065e-07\n Vprtstp: contraction number = 6.600544e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 7.262939e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.501866e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 6.419324e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 6.597548e+01\n Vpmg_setPart:  lower corner = (-54.0285, -44.1015, -32.821)\n Vpmg_setPart:  upper corner = (41.9715, 51.8985, 63.179)\n Vpmg_setPart:  actual minima = (-54.0285, -44.1015, -32.821)\n Vpmg_setPart:  actual maxima = (41.9715, 51.8985, 63.179)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.698545237167E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.220000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.770000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 31.0304\n Vpbe_ctor2:  solute dimensions = 49.637 x 47.533 x 56.913\n Vpbe_ctor2:  solute charge = -1.01863e-14\n@@ -1166,30 +1166,30 @@\n VPMG::extEnergy: extQfEnergy = 4519.43 kT\n VPMG::extEnergy: extDiEnergy = 2191.49 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.895948\n+Vacc_SASA: Time elapsed: 1.692157\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.320328e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.087098e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.080700e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.503600e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.194998e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.083111e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.553091e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.183129e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.396668e-01\n Vprtstp: contraction number = 1.396668e-01\n Vprtstp: iteration = 2\n@@ -1230,32 +1230,32 @@\n Vprtstp: contraction number = 5.525486e-01\n Vprtstp: iteration = 14\n Vprtstp: relative residual = 1.290655e-06\n Vprtstp: contraction number = 5.600207e-01\n Vprtstp: iteration = 15\n Vprtstp: relative residual = 7.308313e-07\n Vprtstp: contraction number = 5.662486e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 5.016025e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 5.218269e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 4.254394e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.438080e+01\n Vpmg_setPart:  lower corner = (-24.6188, -14.6918, -3.41132)\n Vpmg_setPart:  upper corner = (12.5618, 22.4888, 33.7693)\n Vpmg_setPart:  actual minima = (-24.6188, -14.6918, -3.41132)\n Vpmg_setPart:  actual maxima = (12.5618, 22.4888, 33.7693)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.237049215096E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.470000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.670000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 31.0304\n Vpbe_ctor2:  solute dimensions = 49.637 x 47.533 x 56.913\n Vpbe_ctor2:  solute charge = -1.01863e-14\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -1301,30 +1301,30 @@\n VPMG::extEnergy: extQfEnergy = 110994 kT\n VPMG::extEnergy: extDiEnergy = 56275.1 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.874245\n+Vacc_SASA: Time elapsed: 1.698282\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.388272e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.164202e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 9.815000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.016000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.360907e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.095255e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.099705e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.648528e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.163858e-01\n Vprtstp: contraction number = 1.163858e-01\n Vprtstp: iteration = 2\n@@ -1353,38 +1353,38 @@\n Vprtstp: contraction number = 3.950088e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.396547e-06\n Vprtstp: contraction number = 4.328810e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 6.612158e-07\n Vprtstp: contraction number = 4.734646e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.593400e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.801852e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.273799e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.452110e+01\n Vpmg_setPart:  lower corner = (-13.2285, -3.3015, 7.979)\n Vpmg_setPart:  upper corner = (1.1715, 11.0985, 22.379)\n Vpmg_setPart:  actual minima = (-13.2285, -3.3015, 7.979)\n Vpmg_setPart:  actual maxima = (1.1715, 11.0985, 22.379)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.492900778210E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.550000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.110000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 4.461300e+02\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 3.978307e+02\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 06:43:56 2025\n+# Creation Date and Time:  Tue Jan  9 04:45:16 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path acet.pqr\n@@ -1669,32 +1669,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.103316\n+Vacc_SASA: Time elapsed: 0.024478\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.675560e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.830870e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.789300e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.376100e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.168343e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.043844e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.666460e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.345638e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.084928e-01\n Vprtstp: contraction number = 1.084928e-01\n Vprtstp: iteration = 2\n@@ -1711,32 +1711,32 @@\n Vprtstp: contraction number = 1.067805e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.430429e-06\n Vprtstp: contraction number = 1.075005e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.545898e-07\n Vprtstp: contraction number = 1.080723e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.270363e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.471391e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.081240e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.260278e+01\n Vpmg_setPart:  lower corner = (-54.0285, -44.1015, -32.821)\n Vpmg_setPart:  upper corner = (41.9715, 51.8985, 63.179)\n Vpmg_setPart:  actual minima = (-54.0285, -44.1015, -32.821)\n Vpmg_setPart:  actual maxima = (41.9715, 51.8985, 63.179)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.520701614302E+02 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.800000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.800000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 6.35359\n Vpbe_ctor2:  solute dimensions = 7.389 x 11.027 x 9.931\n Vpbe_ctor2:  solute charge = -1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -1782,30 +1782,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.105108 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.020519\n+Vacc_SASA: Time elapsed: 0.040217\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.757860e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.265710e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.845600e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.490300e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.369578e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.132378e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.834714e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.565221e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.225646e-01\n Vprtstp: contraction number = 1.225646e-01\n Vprtstp: iteration = 2\n@@ -1822,30 +1822,30 @@\n Vprtstp: contraction number = 1.454441e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 5.669194e-06\n Vprtstp: contraction number = 1.566066e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 9.449546e-07\n Vprtstp: contraction number = 1.666823e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.317988e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.545824e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.986653e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.165821e+01\n Vpmg_setPart:  lower corner = (-24.6188, -14.6918, -3.41132)\n Vpmg_setPart:  upper corner = (12.5618, 22.4888, 33.7693)\n Vpmg_setPart:  actual minima = (-24.6188, -14.6918, -3.41132)\n Vpmg_setPart:  actual maxima = (12.5618, 22.4888, 33.7693)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.468387819400E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.700000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.300000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 6.35359\n Vpbe_ctor2:  solute dimensions = 7.389 x 11.027 x 9.931\n Vpbe_ctor2:  solute charge = -1\n@@ -1893,30 +1893,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.520445 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.024251\n+Vacc_SASA: Time elapsed: 0.030817\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.340270e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.387760e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.742000e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.472600e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.205384e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.126444e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.418984e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.811266e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.305252e-01\n Vprtstp: contraction number = 1.305252e-01\n Vprtstp: iteration = 2\n@@ -1936,16 +1936,16 @@\n Vprtstp: contraction number = 1.733670e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.357163e-06\n Vprtstp: contraction number = 1.824572e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.550194e-07\n Vprtstp: contraction number = 1.879063e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.718866e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.923051e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.274080e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.477157e+01\n Vpmg_setPart:  lower corner = (-13.2285, -3.3015, 7.979)\n Vpmg_setPart:  upper corner = (1.1715, 11.0985, 22.379)\n Vpmg_setPart:  actual minima = (-13.2285, -3.3015, 7.979)\n Vpmg_setPart:  actual maxima = (1.1715, 11.0985, 22.379)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -1982,32 +1982,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.936671\n+Vacc_SASA: Time elapsed: 1.736844\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.375501e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.162950e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 9.670000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.503000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.108144e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.133590e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.570574e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.509491e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.136636e-02\n Vprtstp: contraction number = 5.136636e-02\n Vprtstp: iteration = 2\n@@ -2027,30 +2027,30 @@\n Vprtstp: contraction number = 2.406804e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.980432e-06\n Vprtstp: contraction number = 2.704556e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 5.800745e-07\n Vprtstp: contraction number = 2.929030e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.857609e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.045445e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.599088e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.800541e+01\n Vpmg_setPart:  lower corner = (-54.0285, -44.1015, -32.821)\n Vpmg_setPart:  upper corner = (41.9715, 51.8985, 63.179)\n Vpmg_setPart:  actual minima = (-54.0285, -44.1015, -32.821)\n Vpmg_setPart:  actual maxima = (41.9715, 51.8985, 63.179)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.766185147917E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.950000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.220000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 31.0304\n Vpbe_ctor2:  solute dimensions = 49.637 x 47.533 x 56.913\n Vpbe_ctor2:  solute charge = 1\n@@ -2098,30 +2098,30 @@\n VPMG::extEnergy: extQfEnergy = 4619.67 kT\n VPMG::extEnergy: extDiEnergy = 2259.75 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.867754\n+Vacc_SASA: Time elapsed: 1.726501\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.456027e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.272658e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.769800e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.327400e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.092854e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.006020e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.185236e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.051551e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.613067e-02\n Vprtstp: contraction number = 9.613067e-02\n Vprtstp: iteration = 2\n@@ -2141,32 +2141,32 @@\n Vprtstp: contraction number = 1.833548e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.811522e-06\n Vprtstp: contraction number = 1.939744e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 3.707504e-07\n Vprtstp: contraction number = 2.046624e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.070199e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.245500e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.195406e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.372648e+01\n Vpmg_setPart:  lower corner = (-24.6188, -14.6918, -3.41132)\n Vpmg_setPart:  upper corner = (12.5618, 22.4888, 33.7693)\n Vpmg_setPart:  actual minima = (-24.6188, -14.6918, -3.41132)\n Vpmg_setPart:  actual maxima = (12.5618, 22.4888, 33.7693)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.226315327863E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.120000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.520000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 31.0304\n Vpbe_ctor2:  solute dimensions = 49.637 x 47.533 x 56.913\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -2212,30 +2212,30 @@\n VPMG::extEnergy: extQfEnergy = 111278 kT\n VPMG::extEnergy: extDiEnergy = 55995.6 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.633465\n+Vacc_SASA: Time elapsed: 1.719829\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.277987e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.223880e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.321200e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.948000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.355316e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.139844e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.539881e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.313986e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.009208e-01\n Vprtstp: contraction number = 1.009208e-01\n Vprtstp: iteration = 2\n@@ -2252,30 +2252,30 @@\n Vprtstp: contraction number = 1.451140e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 3.266673e-06\n Vprtstp: contraction number = 1.668260e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 5.985159e-07\n Vprtstp: contraction number = 1.832188e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.115244e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.355615e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.108711e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.313155e+01\n Vpmg_setPart:  lower corner = (-13.2285, -3.3015, 7.979)\n Vpmg_setPart:  upper corner = (1.1715, 11.0985, 22.379)\n Vpmg_setPart:  actual minima = (-13.2285, -3.3015, 7.979)\n Vpmg_setPart:  actual maxima = (1.1715, 11.0985, 22.379)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.444499098932E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.490000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.040000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 31.0304\n Vpbe_ctor2:  solute dimensions = 49.637 x 47.533 x 56.913\n Vpbe_ctor2:  solute charge = -1.01863e-14\n@@ -2298,32 +2298,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.705975\n+Vacc_SASA: Time elapsed: 1.706983\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.248937e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.153404e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.946000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.653000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.413336e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.409800e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.899882e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.564579e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.894768e-02\n Vprtstp: contraction number = 4.894768e-02\n Vprtstp: iteration = 2\n@@ -2343,30 +2343,30 @@\n Vprtstp: contraction number = 2.414708e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.098574e-06\n Vprtstp: contraction number = 2.683582e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 6.050680e-07\n Vprtstp: contraction number = 2.883234e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.691291e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.946419e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.354108e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.528767e+01\n Vpmg_setPart:  lower corner = (-54.0285, -44.1015, -32.821)\n Vpmg_setPart:  upper corner = (41.9715, 51.8985, 63.179)\n Vpmg_setPart:  actual minima = (-54.0285, -44.1015, -32.821)\n Vpmg_setPart:  actual maxima = (41.9715, 51.8985, 63.179)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.771575298437E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.500000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.000000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 31.0304\n Vpbe_ctor2:  solute dimensions = 49.637 x 47.533 x 56.913\n Vpbe_ctor2:  solute charge = -1.01863e-14\n@@ -2414,30 +2414,30 @@\n VPMG::extEnergy: extQfEnergy = 4620.09 kT\n VPMG::extEnergy: extDiEnergy = 2259.49 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.931882\n+Vacc_SASA: Time elapsed: 1.756854\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.550464e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.200577e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.700900e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.471800e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.400500e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.029414e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.319353e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.840388e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.547807e-02\n Vprtstp: contraction number = 9.547807e-02\n Vprtstp: iteration = 2\n@@ -2457,30 +2457,30 @@\n Vprtstp: contraction number = 1.878215e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.896640e-06\n Vprtstp: contraction number = 1.994763e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 3.991489e-07\n Vprtstp: contraction number = 2.104505e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.581672e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.825261e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.197392e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.378497e+01\n Vpmg_setPart:  lower corner = (-24.6188, -14.6918, -3.41132)\n Vpmg_setPart:  upper corner = (12.5618, 22.4888, 33.7693)\n Vpmg_setPart:  actual minima = (-24.6188, -14.6918, -3.41132)\n Vpmg_setPart:  actual maxima = (12.5618, 22.4888, 33.7693)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.240652812594E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.410000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.630000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 31.0304\n Vpbe_ctor2:  solute dimensions = 49.637 x 47.533 x 56.913\n Vpbe_ctor2:  solute charge = -1.01863e-14\n@@ -2528,30 +2528,30 @@\n VPMG::extEnergy: extQfEnergy = 111288 kT\n VPMG::extEnergy: extDiEnergy = 55994.2 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.648445\n+Vacc_SASA: Time elapsed: 1.746752\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.036029e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.244950e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.863000e-03\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.157000e-03\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.378582e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.117410e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.723361e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.101237e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.031999e-01\n Vprtstp: contraction number = 1.031999e-01\n Vprtstp: iteration = 2\n@@ -2568,28 +2568,28 @@\n Vprtstp: contraction number = 1.434980e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 3.331639e-06\n Vprtstp: contraction number = 1.622112e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 5.872183e-07\n Vprtstp: contraction number = 1.762551e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.264141e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.513691e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.997259e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.178602e+01\n Vpmg_setPart:  lower corner = (-13.2285, -3.3015, 7.979)\n Vpmg_setPart:  upper corner = (1.1715, 11.0985, 22.379)\n Vpmg_setPart:  actual minima = (-13.2285, -3.3015, 7.979)\n Vpmg_setPart:  actual maxima = (1.1715, 11.0985, 22.379)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.496181357535E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.252000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 9.600000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 3.051664e+02\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 2.303478e+02\n"}, {"source1": "./usr/share/apbs/examples/ion-pmf/io.mc", "source2": "./usr/share/apbs/examples/ion-pmf/io.mc", "unified_diff": "@@ -1,10 +1,10 @@\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 06:46:07 2025\n+# Creation Date and Time:  Tue Jan  9 04:47:53 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path ion-pmf.pdb\n@@ -161,28 +161,28 @@\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefSpline...\n Vpmg_fillco:  filling coefficient arrays\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.292500e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.823380e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.564600e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.580800e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.152758e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.089719e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.714002e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.329214e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.194542e-01\n Vprtstp: contraction number = 1.194542e-01\n Vprtstp: iteration = 2\n@@ -202,33 +202,33 @@\n Vprtstp: contraction number = 1.749569e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.117484e-06\n Vprtstp: contraction number = 1.874072e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.180018e-07\n Vprtstp: contraction number = 1.950826e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.591414e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.838879e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.295412e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.509062e+01\n Vpmg_setPart:  lower corner = (-6.72, -6.72, -6.72)\n Vpmg_setPart:  upper corner = (6.72, 6.72, 6.72)\n Vpmg_setPart:  actual minima = (-6.72, -6.72, -6.72)\n Vpmg_setPart:  actual maxima = (6.72, 6.72, 6.72)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 6.324828953427E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.972100e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.097000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.204530e-01\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.984960e-01\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 4\n Vpbe_ctor2:  solute dimensions = 8 x 4 x 4\n Vpbe_ctor2:  solute charge = 2\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -249,28 +249,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.030970e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.897410e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.346900e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.878500e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.360148e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.234960e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.165936e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.781653e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.110640e-01\n Vprtstp: contraction number = 1.110640e-01\n Vprtstp: iteration = 2\n@@ -287,50 +287,50 @@\n Vprtstp: contraction number = 1.067494e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.466502e-06\n Vprtstp: contraction number = 1.074548e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.584103e-07\n Vprtstp: contraction number = 1.080191e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.234945e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.496803e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.126323e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.338709e+01\n Vpmg_setPart:  lower corner = (-6.72, -6.72, -6.72)\n Vpmg_setPart:  upper corner = (6.72, 6.72, 6.72)\n Vpmg_setPart:  actual minima = (-6.72, -6.72, -6.72)\n Vpmg_setPart:  actual maxima = (6.72, 6.72, 6.72)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 7.232617942545E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.135000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.091000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vpmg_dbForce: No force for uniform dielectric!\n Vpmg_dbForce: No force for uniform dielectric!\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.901000e-03\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 8.000000e-05\n APOL: Setting up hash table and accessibility object...\n Vclist_ctor2:  Using 16 x 8 x 8 hash table\n Vclist_ctor2:  automatic domain setup.\n Vclist_ctor2:  Using 1.8 max radius\n Vclist_setupGrid:  Grid lengths = (14.792, 10.792, 10.792)\n Vclist_setupGrid:  Grid lower corner = (-8.396, -5.396, -5.396)\n Vclist_assignAtoms:  Have 720 atom entries\n Vacc_storeParms:  Surf. density = 100\n Vacc_storeParms:  Max area = 181.458\n Vacc_storeParms:  Using 18030-point reference sphere\n forceAPOL: Trying atom surf...\n-forceAPOL: atom surf: Time elapsed: 0.003929\n-forceAPOL: Time elapsed: 5.131617\n-Vacc_SASA: Time elapsed: 0.000002\n-initAPOL: Time elapsed: 14.563825\n+forceAPOL: atom surf: Time elapsed: 0.078215\n+forceAPOL: Time elapsed: 5.011561\n+Vacc_SASA: Time elapsed: 0.000003\n+initAPOL: Time elapsed: 13.883924\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n@@ -339,8 +339,8 @@\n printForce:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 8.861772e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 6.298526e+01\n"}, {"source1": "./usr/share/apbs/examples/ionize/io.mc", "source2": "./usr/share/apbs/examples/ionize/io.mc", "unified_diff": "@@ -1,10 +1,10 @@\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 06:44:39 2025\n+# Creation Date and Time:  Tue Jan  9 04:46:10 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path acetic-acid.xml\n@@ -481,32 +481,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.001566\n+Vacc_SASA: Time elapsed: 0.001278\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.482090e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.465280e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.135400e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 4.786500e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.813590e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.219250e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.658666e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.199064e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.188999e-01\n Vprtstp: contraction number = 3.188999e-01\n Vprtstp: iteration = 2\n@@ -535,30 +535,30 @@\n Vprtstp: contraction number = 2.912126e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 2.816386e-06\n Vprtstp: contraction number = 2.924708e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 8.271441e-07\n Vprtstp: contraction number = 2.936899e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 5.096702e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 5.416193e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.412218e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.606073e+01\n Vpmg_setPart:  lower corner = (-6, -6.1535, -4.713)\n Vpmg_setPart:  upper corner = (6, 5.8465, 7.287)\n Vpmg_setPart:  actual minima = (-6, -6.1535, -4.713)\n Vpmg_setPart:  actual maxima = (6, 5.8465, 7.287)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 4.781227236323E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.100000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.400000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3.17612\n Vpbe_ctor2:  solute dimensions = 4.116 x 5.186 x 5.967\n Vpbe_ctor2:  solute charge = -1.66533e-16\n@@ -606,30 +606,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0505207 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.002156\n+Vacc_SASA: Time elapsed: 0.001175\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.342680e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.806760e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.593500e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 3.639800e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.634650e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.096190e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.836221e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.849203e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.598074e-01\n Vprtstp: contraction number = 2.598074e-01\n Vprtstp: iteration = 2\n@@ -661,30 +661,30 @@\n Vprtstp: contraction number = 3.326351e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 2.087103e-06\n Vprtstp: contraction number = 3.343120e-01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 7.014192e-07\n Vprtstp: contraction number = 3.360731e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 5.714525e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 6.020429e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.550851e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.712247e+01\n Vpmg_setPart:  lower corner = (-3, -3.1535, -1.713)\n Vpmg_setPart:  upper corner = (3, 2.8465, 4.287)\n Vpmg_setPart:  actual minima = (-3, -3.1535, -1.713)\n Vpmg_setPart:  actual maxima = (3, 2.8465, 4.287)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 8.039953678525E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.700000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.800000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3.17612\n Vpbe_ctor2:  solute dimensions = 4.116 x 5.186 x 5.967\n Vpbe_ctor2:  solute charge = -1.66533e-16\n@@ -707,28 +707,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.233850e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.000560e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 4.156200e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.196700e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.121701e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.897750e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.197613e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.618475e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.679930e-01\n Vprtstp: contraction number = 1.679930e-01\n Vprtstp: iteration = 2\n@@ -745,30 +745,30 @@\n Vprtstp: contraction number = 1.043091e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.862252e-06\n Vprtstp: contraction number = 1.059323e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.994142e-07\n Vprtstp: contraction number = 1.070823e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.395809e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.775565e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.247547e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.428000e+01\n Vpmg_setPart:  lower corner = (-6, -6.1535, -4.713)\n Vpmg_setPart:  upper corner = (6, 5.8465, 7.287)\n Vpmg_setPart:  actual minima = (-6, -6.1535, -4.713)\n Vpmg_setPart:  actual maxima = (6, 5.8465, 7.287)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 4.800125490193E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.000000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.200000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3.17612\n Vpbe_ctor2:  solute dimensions = 4.116 x 5.186 x 5.967\n Vpbe_ctor2:  solute charge = -1.66533e-16\n@@ -814,28 +814,28 @@\n Vpmg_qmEnergy:  Zero energy for zero ionic strength!\n VPMG::extEnergy: extQmEnergy = 0 kT\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 1.14339 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.367690e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.144640e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.524800e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.363500e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.742518e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.207175e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.568631e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.008158e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.651787e-01\n Vprtstp: contraction number = 1.651787e-01\n Vprtstp: iteration = 2\n@@ -852,30 +852,30 @@\n Vprtstp: contraction number = 1.055047e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.934803e-06\n Vprtstp: contraction number = 1.064764e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.073576e-07\n Vprtstp: contraction number = 1.071724e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.414875e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.701169e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.101378e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.293869e+01\n Vpmg_setPart:  lower corner = (-3, -3.1535, -1.713)\n Vpmg_setPart:  upper corner = (3, 2.8465, 4.287)\n Vpmg_setPart:  actual minima = (-3, -3.1535, -1.713)\n Vpmg_setPart:  actual maxima = (3, 2.8465, 4.287)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 8.058572238076E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.900000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.000000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3.17612\n Vpbe_ctor2:  solute dimensions = 4.116 x 5.186 x 5.967\n Vpbe_ctor2:  solute charge = -1\n@@ -898,32 +898,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.001209\n+Vacc_SASA: Time elapsed: 0.001201\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.127690e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.693800e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 9.470300e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.246030e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.494620e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.178704e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.946804e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.244032e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.669750e-01\n Vprtstp: contraction number = 1.669750e-01\n Vprtstp: iteration = 2\n@@ -952,30 +952,30 @@\n Vprtstp: contraction number = 3.348642e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 2.783762e-06\n Vprtstp: contraction number = 3.348981e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 9.322590e-07\n Vprtstp: contraction number = 3.348918e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 5.164478e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 5.455215e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.122877e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.340480e+01\n Vpmg_setPart:  lower corner = (-6, -6.1535, -4.713)\n Vpmg_setPart:  upper corner = (6, 5.8465, 7.287)\n Vpmg_setPart:  actual minima = (-6, -6.1535, -4.713)\n Vpmg_setPart:  actual maxima = (6, 5.8465, 7.287)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 6.748221698410E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.200000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.100000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3.17612\n Vpbe_ctor2:  solute dimensions = 4.116 x 5.186 x 5.967\n Vpbe_ctor2:  solute charge = -1\n@@ -1023,30 +1023,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.600233 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.001471\n+Vacc_SASA: Time elapsed: 0.001136\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.676040e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.511030e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.475300e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 3.318100e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.201923e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.065142e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.506187e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.580398e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.532338e-01\n Vprtstp: contraction number = 1.532338e-01\n Vprtstp: iteration = 2\n@@ -1078,30 +1078,30 @@\n Vprtstp: contraction number = 3.529902e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 1.276975e-06\n Vprtstp: contraction number = 3.528897e-01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 4.504551e-07\n Vprtstp: contraction number = 3.527516e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 5.729803e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 6.097985e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.717933e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.906791e+01\n Vpmg_setPart:  lower corner = (-3, -3.1535, -1.713)\n Vpmg_setPart:  upper corner = (3, 2.8465, 4.287)\n Vpmg_setPart:  actual minima = (-3, -3.1535, -1.713)\n Vpmg_setPart:  actual maxima = (3, 2.8465, 4.287)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.143395002184E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.300000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.600000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3.17612\n Vpbe_ctor2:  solute dimensions = 4.116 x 5.186 x 5.967\n Vpbe_ctor2:  solute charge = -1\n@@ -1124,28 +1124,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.947590e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.863270e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.152110e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.534900e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.554942e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.229160e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.113129e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.975922e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.140338e-01\n Vprtstp: contraction number = 1.140338e-01\n Vprtstp: iteration = 2\n@@ -1162,32 +1162,32 @@\n Vprtstp: contraction number = 1.066400e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.493481e-06\n Vprtstp: contraction number = 1.074330e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.613267e-07\n Vprtstp: contraction number = 1.080206e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.336388e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.630984e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.977619e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.183480e+01\n Vpmg_setPart:  lower corner = (-6, -6.1535, -4.713)\n Vpmg_setPart:  upper corner = (6, 5.8465, 7.287)\n Vpmg_setPart:  actual minima = (-6, -6.1535, -4.713)\n Vpmg_setPart:  actual maxima = (6, 5.8465, 7.287)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 6.912847895210E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.000000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.500000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3.17612\n Vpbe_ctor2:  solute dimensions = 4.116 x 5.186 x 5.967\n Vpbe_ctor2:  solute charge = -1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -1231,28 +1231,28 @@\n Vpmg_qmEnergy:  Zero energy for zero ionic strength!\n VPMG::extEnergy: extQmEnergy = 0 kT\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 22.4432 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.198340e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.073950e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.390700e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.538200e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.411788e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.159431e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.475001e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.195022e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.151233e-01\n Vprtstp: contraction number = 1.151233e-01\n Vprtstp: iteration = 2\n@@ -1269,32 +1269,32 @@\n Vprtstp: contraction number = 1.065071e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.498104e-06\n Vprtstp: contraction number = 1.072349e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.614370e-07\n Vprtstp: contraction number = 1.077609e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.228092e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.483264e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.963331e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.148833e+01\n Vpmg_setPart:  lower corner = (-3, -3.1535, -1.713)\n Vpmg_setPart:  upper corner = (3, 2.8465, 4.287)\n Vpmg_setPart:  actual minima = (-3, -3.1535, -1.713)\n Vpmg_setPart:  actual maxima = (3, 2.8465, 4.287)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.159793508256E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.000000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.300000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 1.15\n Vpbe_ctor2:  solute dimensions = 2.3 x 2.3 x 2.3\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0.15\n Vpbe_ctor2:  xkappa = 0.128839\n@@ -1315,32 +1315,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000129\n+Vacc_SASA: Time elapsed: 0.000095\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.466470e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.559630e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.510460e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.244040e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.544192e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.281748e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.833263e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.419179e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.470644e-01\n Vprtstp: contraction number = 1.470644e-01\n Vprtstp: iteration = 2\n@@ -1366,32 +1366,32 @@\n Vprtstp: contraction number = 2.846821e-01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 1.962532e-06\n Vprtstp: contraction number = 2.852652e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 5.602483e-07\n Vprtstp: contraction number = 2.854722e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 4.832639e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 5.128382e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.789563e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.024595e+01\n Vpmg_setPart:  lower corner = (-6, -6.1535, -4.713)\n Vpmg_setPart:  upper corner = (6, 5.8465, 7.287)\n Vpmg_setPart:  actual minima = (-6, -6.1535, -4.713)\n Vpmg_setPart:  actual maxima = (6, 5.8465, 7.287)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 3.170869129315E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.300000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.900000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 1.15\n Vpbe_ctor2:  solute dimensions = 2.3 x 2.3 x 2.3\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0.15\n Vpbe_ctor2:  xkappa = 0.128839\n@@ -1437,30 +1437,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.650584 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000143\n+Vacc_SASA: Time elapsed: 0.000091\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.733080e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.579950e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.149800e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.804900e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.434435e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.435260e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.347616e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.719978e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.382011e-01\n Vprtstp: contraction number = 1.382011e-01\n Vprtstp: iteration = 2\n@@ -1489,30 +1489,30 @@\n Vprtstp: contraction number = 3.143969e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.077403e-06\n Vprtstp: contraction number = 3.146378e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.391862e-07\n Vprtstp: contraction number = 3.148184e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 5.185495e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 5.464266e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.072374e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.261409e+01\n Vpmg_setPart:  lower corner = (-3, -3.1535, -1.713)\n Vpmg_setPart:  upper corner = (3, 2.8465, 4.287)\n Vpmg_setPart:  actual minima = (-3, -3.1535, -1.713)\n Vpmg_setPart:  actual maxima = (3, 2.8465, 4.287)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 5.162367825044E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.900000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.400000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 1.15\n Vpbe_ctor2:  solute dimensions = 2.3 x 2.3 x 2.3\n Vpbe_ctor2:  solute charge = 1\n@@ -1535,28 +1535,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.068640e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.298900e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.541400e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.793060e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.623658e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.978040e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.900364e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.048421e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.118955e-01\n Vprtstp: contraction number = 1.118955e-01\n Vprtstp: iteration = 2\n@@ -1573,30 +1573,30 @@\n Vprtstp: contraction number = 1.069169e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.490424e-06\n Vprtstp: contraction number = 1.076150e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.611536e-07\n Vprtstp: contraction number = 1.081260e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.336558e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.633043e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.303216e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.477021e+01\n Vpmg_setPart:  lower corner = (-6, -6.1535, -4.713)\n Vpmg_setPart:  upper corner = (6, 5.8465, 7.287)\n Vpmg_setPart:  actual minima = (-6, -6.1535, -4.713)\n Vpmg_setPart:  actual maxima = (6, 5.8465, 7.287)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 3.417301695136E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.300000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.600000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 1.15\n Vpbe_ctor2:  solute dimensions = 2.3 x 2.3 x 2.3\n Vpbe_ctor2:  solute charge = 1\n@@ -1642,28 +1642,28 @@\n Vpmg_qmEnergy:  Zero energy for zero ionic strength!\n VPMG::extEnergy: extQmEnergy = 0 kT\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 27.9953 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.519800e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.905460e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.720800e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.415300e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.314985e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.037130e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.277779e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.299607e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.111894e-01\n Vprtstp: contraction number = 1.111894e-01\n Vprtstp: iteration = 2\n@@ -1680,44 +1680,44 @@\n Vprtstp: contraction number = 1.067651e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.469870e-06\n Vprtstp: contraction number = 1.074950e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.588283e-07\n Vprtstp: contraction number = 1.080560e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.369116e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.776696e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.015729e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.200124e+01\n Vpmg_setPart:  lower corner = (-3, -3.1535, -1.713)\n Vpmg_setPart:  upper corner = (3, 2.8465, 4.287)\n Vpmg_setPart:  actual minima = (-3, -3.1535, -1.713)\n Vpmg_setPart:  actual maxima = (3, 2.8465, 4.287)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 5.406572492944E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.600000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.800000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 5.616695e+02\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 3.502640e+02\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 06:45:27 2025\n+# Creation Date and Time:  Tue Jan  9 04:47:06 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path acetic-acid.xml\n@@ -2194,32 +2194,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.001440\n+Vacc_SASA: Time elapsed: 0.001279\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.376490e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.836410e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.293200e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.192410e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.187116e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.148745e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.141909e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.759458e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.596091e-01\n Vprtstp: contraction number = 2.596091e-01\n Vprtstp: iteration = 2\n@@ -2239,30 +2239,30 @@\n Vprtstp: contraction number = 1.697798e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.455171e-06\n Vprtstp: contraction number = 1.730577e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 7.805682e-07\n Vprtstp: contraction number = 1.752050e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.616549e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.865355e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.238711e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.454870e+01\n Vpmg_setPart:  lower corner = (-6, -6.1535, -4.713)\n Vpmg_setPart:  upper corner = (6, 5.8465, 7.287)\n Vpmg_setPart:  actual minima = (-6, -6.1535, -4.713)\n Vpmg_setPart:  actual maxima = (6, 5.8465, 7.287)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 4.781452735910E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.100000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.600000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3.17612\n Vpbe_ctor2:  solute dimensions = 4.116 x 5.186 x 5.967\n Vpbe_ctor2:  solute charge = -1.66533e-16\n@@ -2310,30 +2310,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0553032 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.001127\n+Vacc_SASA: Time elapsed: 0.001241\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.413610e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.676730e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.323800e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.492000e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.413272e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.008750e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.250631e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.759998e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.192618e-01\n Vprtstp: contraction number = 2.192618e-01\n Vprtstp: iteration = 2\n@@ -2353,16 +2353,16 @@\n Vprtstp: contraction number = 1.807641e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 5.267839e-06\n Vprtstp: contraction number = 1.838237e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 9.807397e-07\n Vprtstp: contraction number = 1.861749e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.661336e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.912543e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.405194e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.581375e+01\n Vpmg_setPart:  lower corner = (-3, -3.1535, -1.713)\n Vpmg_setPart:  upper corner = (3, 2.8465, 4.287)\n Vpmg_setPart:  actual minima = (-3, -3.1535, -1.713)\n Vpmg_setPart:  actual maxima = (3, 2.8465, 4.287)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -2399,28 +2399,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.664220e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.635060e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.996300e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 9.825700e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.358136e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.148351e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.221429e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.400211e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.679930e-01\n Vprtstp: contraction number = 1.679930e-01\n Vprtstp: iteration = 2\n@@ -2437,30 +2437,30 @@\n Vprtstp: contraction number = 1.043091e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.862252e-06\n Vprtstp: contraction number = 1.059323e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.994142e-07\n Vprtstp: contraction number = 1.070823e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.152294e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.420282e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.959173e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.164616e+01\n Vpmg_setPart:  lower corner = (-6, -6.1535, -4.713)\n Vpmg_setPart:  upper corner = (6, 5.8465, 7.287)\n Vpmg_setPart:  actual minima = (-6, -6.1535, -4.713)\n Vpmg_setPart:  actual maxima = (6, 5.8465, 7.287)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 4.800125490193E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.300000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.700000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3.17612\n Vpbe_ctor2:  solute dimensions = 4.116 x 5.186 x 5.967\n Vpbe_ctor2:  solute charge = -1.66533e-16\n@@ -2506,28 +2506,28 @@\n Vpmg_qmEnergy:  Zero energy for zero ionic strength!\n VPMG::extEnergy: extQmEnergy = 0 kT\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 1.14339 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.206590e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.272510e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.685800e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.539400e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.549545e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.244727e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.166581e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.591115e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.651787e-01\n Vprtstp: contraction number = 1.651787e-01\n Vprtstp: iteration = 2\n@@ -2544,16 +2544,16 @@\n Vprtstp: contraction number = 1.055047e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.934803e-06\n Vprtstp: contraction number = 1.064764e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.073576e-07\n Vprtstp: contraction number = 1.071724e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.991750e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.256911e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.914409e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.118596e+01\n Vpmg_setPart:  lower corner = (-3, -3.1535, -1.713)\n Vpmg_setPart:  upper corner = (3, 2.8465, 4.287)\n Vpmg_setPart:  actual minima = (-3, -3.1535, -1.713)\n Vpmg_setPart:  actual maxima = (3, 2.8465, 4.287)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -2590,32 +2590,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.001385\n+Vacc_SASA: Time elapsed: 0.001146\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.657170e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.467580e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.560700e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.279520e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.729685e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.163167e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.504020e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.807248e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.505354e-01\n Vprtstp: contraction number = 1.505354e-01\n Vprtstp: iteration = 2\n@@ -2635,32 +2635,32 @@\n Vprtstp: contraction number = 1.898671e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.115563e-06\n Vprtstp: contraction number = 1.948490e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 6.143002e-07\n Vprtstp: contraction number = 1.971715e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.891586e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.193390e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.346793e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.579048e+01\n Vpmg_setPart:  lower corner = (-6, -6.1535, -4.713)\n Vpmg_setPart:  upper corner = (6, 5.8465, 7.287)\n Vpmg_setPart:  actual minima = (-6, -6.1535, -4.713)\n Vpmg_setPart:  actual maxima = (6, 5.8465, 7.287)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 6.749438220873E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.900000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.700000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3.17612\n Vpbe_ctor2:  solute dimensions = 4.116 x 5.186 x 5.967\n Vpbe_ctor2:  solute charge = -1\n Vpbe_ctor2:  bulk ionic strength = 0.15\n Vpbe_ctor2:  xkappa = 0.128839\n@@ -2706,30 +2706,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.607375 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.001175\n+Vacc_SASA: Time elapsed: 0.001298\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.067680e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.740130e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.486100e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.469000e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.060491e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 8.901860e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.935503e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.237925e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.420228e-01\n Vprtstp: contraction number = 1.420228e-01\n Vprtstp: iteration = 2\n@@ -2749,30 +2749,30 @@\n Vprtstp: contraction number = 1.900725e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.720330e-06\n Vprtstp: contraction number = 1.966740e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 5.430374e-07\n Vprtstp: contraction number = 1.996219e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.731056e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.088760e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.210776e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.370548e+01\n Vpmg_setPart:  lower corner = (-3, -3.1535, -1.713)\n Vpmg_setPart:  upper corner = (3, 2.8465, 4.287)\n Vpmg_setPart:  actual minima = (-3, -3.1535, -1.713)\n Vpmg_setPart:  actual maxima = (3, 2.8465, 4.287)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.143498275233E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.700000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.600000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3.17612\n Vpbe_ctor2:  solute dimensions = 4.116 x 5.186 x 5.967\n Vpbe_ctor2:  solute charge = -1\n@@ -2795,28 +2795,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.020590e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.120170e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 9.643200e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.530340e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.549786e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.345930e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.339946e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.479802e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.140338e-01\n Vprtstp: contraction number = 1.140338e-01\n Vprtstp: iteration = 2\n@@ -2833,30 +2833,30 @@\n Vprtstp: contraction number = 1.066400e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.493481e-06\n Vprtstp: contraction number = 1.074330e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.613267e-07\n Vprtstp: contraction number = 1.080206e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.079162e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.357989e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.855301e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.030101e+01\n Vpmg_setPart:  lower corner = (-6, -6.1535, -4.713)\n Vpmg_setPart:  upper corner = (6, 5.8465, 7.287)\n Vpmg_setPart:  actual minima = (-6, -6.1535, -4.713)\n Vpmg_setPart:  actual maxima = (6, 5.8465, 7.287)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 6.912847895210E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.500000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.800000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 3.17612\n Vpbe_ctor2:  solute dimensions = 4.116 x 5.186 x 5.967\n Vpbe_ctor2:  solute charge = -1\n@@ -2902,28 +2902,28 @@\n Vpmg_qmEnergy:  Zero energy for zero ionic strength!\n VPMG::extEnergy: extQmEnergy = 0 kT\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 22.4432 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.310110e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.386450e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.393500e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.473000e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.132539e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.063285e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.689153e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.687671e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.151233e-01\n Vprtstp: contraction number = 1.151233e-01\n Vprtstp: iteration = 2\n@@ -2940,16 +2940,16 @@\n Vprtstp: contraction number = 1.065071e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.498104e-06\n Vprtstp: contraction number = 1.072349e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.614370e-07\n Vprtstp: contraction number = 1.077609e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.880869e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.265408e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.959887e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.160543e+01\n Vpmg_setPart:  lower corner = (-3, -3.1535, -1.713)\n Vpmg_setPart:  upper corner = (3, 2.8465, 4.287)\n Vpmg_setPart:  actual minima = (-3, -3.1535, -1.713)\n Vpmg_setPart:  actual maxima = (3, 2.8465, 4.287)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -2986,32 +2986,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000091\n+Vacc_SASA: Time elapsed: 0.000101\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.119090e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.730260e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 9.162500e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.003470e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.455712e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.465070e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.011479e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.907026e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.382442e-01\n Vprtstp: contraction number = 1.382442e-01\n Vprtstp: iteration = 2\n@@ -3031,30 +3031,30 @@\n Vprtstp: contraction number = 1.741425e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.778515e-06\n Vprtstp: contraction number = 1.810766e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 3.297938e-07\n Vprtstp: contraction number = 1.854322e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.512262e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.777897e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.274734e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.445490e+01\n Vpmg_setPart:  lower corner = (-6, -6.1535, -4.713)\n Vpmg_setPart:  upper corner = (6, 5.8465, 7.287)\n Vpmg_setPart:  actual minima = (-6, -6.1535, -4.713)\n Vpmg_setPart:  actual maxima = (6, 5.8465, 7.287)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 3.171449807940E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.400000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.700000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 1.15\n Vpbe_ctor2:  solute dimensions = 2.3 x 2.3 x 2.3\n Vpbe_ctor2:  solute charge = 1\n@@ -3102,30 +3102,30 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.654498 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000099\n+Vacc_SASA: Time elapsed: 0.000102\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.662600e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.802820e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.505900e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.441200e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.422267e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.056440e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.393110e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.155989e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.297624e-01\n Vprtstp: contraction number = 1.297624e-01\n Vprtstp: iteration = 2\n@@ -3145,30 +3145,30 @@\n Vprtstp: contraction number = 1.701143e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.306208e-06\n Vprtstp: contraction number = 1.773242e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.371381e-07\n Vprtstp: contraction number = 1.815470e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.485180e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.728136e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.454453e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.603332e+01\n Vpmg_setPart:  lower corner = (-3, -3.1535, -1.713)\n Vpmg_setPart:  upper corner = (3, 2.8465, 4.287)\n Vpmg_setPart:  actual minima = (-3, -3.1535, -1.713)\n Vpmg_setPart:  actual maxima = (3, 2.8465, 4.287)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 5.163593499843E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.100000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.800000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 1.15\n Vpbe_ctor2:  solute dimensions = 2.3 x 2.3 x 2.3\n Vpbe_ctor2:  solute charge = 1\n@@ -3191,28 +3191,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.524700e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.991610e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.450700e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.535310e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.441425e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.206471e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.772310e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.427350e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.118955e-01\n Vprtstp: contraction number = 1.118955e-01\n Vprtstp: iteration = 2\n@@ -3229,30 +3229,30 @@\n Vprtstp: contraction number = 1.069169e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.490424e-06\n Vprtstp: contraction number = 1.076150e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.611536e-07\n Vprtstp: contraction number = 1.081260e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.263629e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.540665e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.051327e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.275763e+01\n Vpmg_setPart:  lower corner = (-6, -6.1535, -4.713)\n Vpmg_setPart:  upper corner = (6, 5.8465, 7.287)\n Vpmg_setPart:  actual minima = (-6, -6.1535, -4.713)\n Vpmg_setPart:  actual maxima = (6, 5.8465, 7.287)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 3.417301695136E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.900000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.200000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 1.15\n Vpbe_ctor2:  solute dimensions = 2.3 x 2.3 x 2.3\n Vpbe_ctor2:  solute charge = 1\n@@ -3298,28 +3298,28 @@\n Vpmg_qmEnergy:  Zero energy for zero ionic strength!\n VPMG::extEnergy: extQmEnergy = 0 kT\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 27.9953 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.009510e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.030160e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.441400e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.354700e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.607586e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.569600e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.127872e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.652907e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.111894e-01\n Vprtstp: contraction number = 1.111894e-01\n Vprtstp: iteration = 2\n@@ -3336,34 +3336,34 @@\n Vprtstp: contraction number = 1.067651e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.469870e-06\n Vprtstp: contraction number = 1.074950e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.588283e-07\n Vprtstp: contraction number = 1.080560e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.176253e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.443217e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.000061e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.176344e+01\n Vpmg_setPart:  lower corner = (-3, -3.1535, -1.713)\n Vpmg_setPart:  upper corner = (3, 2.8465, 4.287)\n Vpmg_setPart:  actual minima = (-3, -3.1535, -1.713)\n Vpmg_setPart:  actual maxima = (3, 2.8465, 4.287)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 5.406572492944E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.200000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.500000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 4.447572e+02\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 2.854185e+02\n"}, {"source1": "./usr/share/apbs/examples/pka-lig/io.mc", "source2": "./usr/share/apbs/examples/pka-lig/io.mc", "unified_diff": "@@ -1,10 +1,10 @@\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 06:46:29 2025\n+# Creation Date and Time:  Tue Jan  9 04:48:31 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path bx6_7_lig_apbs.pqr\n@@ -340,31 +340,31 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.269617\n+Vacc_SASA: Time elapsed: 0.141702\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.129250e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.118430e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 7.426600e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.367800e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.412044e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.203341e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.897805e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.414988e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.561608e-01\n Vprtstp: contraction number = 1.561608e-01\n Vprtstp: iteration = 2\n@@ -390,32 +390,32 @@\n Vprtstp: contraction number = 2.750705e-01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 1.932473e-06\n Vprtstp: contraction number = 2.767817e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 5.373027e-07\n Vprtstp: contraction number = 2.780389e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.133963e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.360454e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.918961e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.109401e+01\n Vpmg_setPart:  lower corner = (-6.031, -67.507, -7.978)\n Vpmg_setPart:  upper corner = (63.969, 2.493, 62.022)\n Vpmg_setPart:  actual minima = (-6.031, -67.507, -7.978)\n Vpmg_setPart:  actual maxima = (63.969, 2.493, 62.022)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.795090079491E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.300000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.100000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 10.66\n Vpbe_ctor2:  solute dimensions = 17.188 x 12.75 x 15.33\n Vpbe_ctor2:  solute charge = 1.11022e-16\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -461,29 +461,29 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.123733 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.160412\n+Vacc_SASA: Time elapsed: 0.223019\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.523240e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.820010e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.278300e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.204900e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.231450e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.335915e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.705850e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.434212e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.152775e-01\n Vprtstp: contraction number = 2.152775e-01\n Vprtstp: iteration = 2\n@@ -515,30 +515,30 @@\n Vprtstp: contraction number = 3.353090e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 1.328976e-06\n Vprtstp: contraction number = 3.371305e-01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 4.496116e-07\n Vprtstp: contraction number = 3.383143e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 4.460494e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.679984e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.266130e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.469300e+01\n Vpmg_setPart:  lower corner = (12.822, -45.153, 9.545)\n Vpmg_setPart:  upper corner = (36.822, -21.153, 33.545)\n Vpmg_setPart:  actual minima = (12.822, -45.153, 9.545)\n Vpmg_setPart:  actual maxima = (36.822, -21.153, 33.545)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 8.468794426258E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.100000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.300000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 37.837\n Vpbe_ctor2:  solute dimensions = 60.969 x 56.587 x 62.12\n Vpbe_ctor2:  solute charge = 1\n@@ -561,31 +561,31 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 2.166628\n+Vacc_SASA: Time elapsed: 2.267171\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.416596e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.504373e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.354300e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 4.253300e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.466722e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.324668e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.675516e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.170269e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.188493e-01\n Vprtstp: contraction number = 1.188493e-01\n Vprtstp: iteration = 2\n@@ -638,30 +638,30 @@\n Vprtstp: contraction number = 6.152114e-01\n Vprtstp: iteration = 18\n Vprtstp: relative residual = 1.141886e-06\n Vprtstp: contraction number = 6.186689e-01\n Vprtstp: iteration = 19\n Vprtstp: relative residual = 7.101689e-07\n Vprtstp: contraction number = 6.219261e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 7.918457e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 8.166664e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 4.933691e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 5.134235e+01\n Vpmg_setPart:  lower corner = (-6.031, -67.507, -7.978)\n Vpmg_setPart:  upper corner = (63.969, 2.493, 62.022)\n Vpmg_setPart:  actual minima = (-6.031, -67.507, -7.978)\n Vpmg_setPart:  actual maxima = (63.969, 2.493, 62.022)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.467100888191E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.875800e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.030000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 37.837\n Vpbe_ctor2:  solute dimensions = 60.969 x 56.587 x 62.12\n Vpbe_ctor2:  solute charge = 1\n@@ -709,29 +709,29 @@\n VPMG::extEnergy: extQfEnergy = 119417 kT\n VPMG::extEnergy: extDiEnergy = 58605.1 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 2.058625\n+Vacc_SASA: Time elapsed: 2.254185\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.480537e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.707052e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 4.238400e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 4.161500e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.399261e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.234119e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.708753e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.256887e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.393577e-01\n Vprtstp: contraction number = 1.393577e-01\n Vprtstp: iteration = 2\n@@ -766,30 +766,30 @@\n Vprtstp: contraction number = 4.796270e-01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.074713e-06\n Vprtstp: contraction number = 4.999984e-01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 5.553244e-07\n Vprtstp: contraction number = 5.167187e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 5.575301e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 5.800388e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.591331e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.775861e+01\n Vpmg_setPart:  lower corner = (12.822, -45.153, 9.545)\n Vpmg_setPart:  upper corner = (36.822, -21.153, 33.545)\n Vpmg_setPart:  actual minima = (12.822, -45.153, 9.545)\n Vpmg_setPart:  actual maxima = (36.822, -21.153, 33.545)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 2.427017897319E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.830000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.650000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 37.837\n Vpbe_ctor2:  solute dimensions = 60.969 x 56.587 x 62.12\n Vpbe_ctor2:  solute charge = 1\n@@ -812,31 +812,31 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 2.377675\n+Vacc_SASA: Time elapsed: 2.219868\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.881923e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.489690e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.988300e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.839500e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.328080e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.222243e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.319117e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.662583e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.189544e-01\n Vprtstp: contraction number = 1.189544e-01\n Vprtstp: iteration = 2\n@@ -889,32 +889,32 @@\n Vprtstp: contraction number = 6.138674e-01\n Vprtstp: iteration = 18\n Vprtstp: relative residual = 1.173454e-06\n Vprtstp: contraction number = 6.173088e-01\n Vprtstp: iteration = 19\n Vprtstp: relative residual = 7.281097e-07\n Vprtstp: contraction number = 6.204841e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 6.820578e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 7.058687e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 5.498416e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 5.693400e+01\n Vpmg_setPart:  lower corner = (-6.031, -67.507, -7.978)\n Vpmg_setPart:  upper corner = (63.969, 2.493, 62.022)\n Vpmg_setPart:  actual minima = (-6.031, -67.507, -7.978)\n Vpmg_setPart:  actual maxima = (63.969, 2.493, 62.022)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.485227452845E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 8.640000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.870000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 37.837\n Vpbe_ctor2:  solute dimensions = 60.969 x 56.587 x 62.12\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -960,29 +960,29 @@\n VPMG::extEnergy: extQfEnergy = 119415 kT\n VPMG::extEnergy: extDiEnergy = 58604.6 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 2.420705\n+Vacc_SASA: Time elapsed: 2.170779\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.778402e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.594388e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.508300e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 3.896900e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.412546e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.272750e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.053000e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.258521e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.423446e-01\n Vprtstp: contraction number = 1.423446e-01\n Vprtstp: iteration = 2\n@@ -1017,38 +1017,38 @@\n Vprtstp: contraction number = 4.820331e-01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 1.206020e-06\n Vprtstp: contraction number = 5.012326e-01\n Vprtstp: iteration = 13\n Vprtstp: relative residual = 6.232432e-07\n Vprtstp: contraction number = 5.167767e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 4.426553e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.641186e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.591167e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.771437e+01\n Vpmg_setPart:  lower corner = (12.822, -45.153, 9.545)\n Vpmg_setPart:  upper corner = (36.822, -21.153, 33.545)\n Vpmg_setPart:  actual minima = (12.822, -45.153, 9.545)\n Vpmg_setPart:  actual maxima = (36.822, -21.153, 33.545)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 2.511771058265E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.290000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.090000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 3.498192e+02\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 2.620811e+02\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 06:47:17 2025\n+# Creation Date and Time:  Tue Jan  9 04:49:28 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path bx6_7_lig_apbs.pqr\n@@ -1384,31 +1384,31 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.160186\n+Vacc_SASA: Time elapsed: 0.158029\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.482900e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.698830e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.240200e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.296100e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.292399e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.190311e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.108512e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.841325e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.452428e-01\n Vprtstp: contraction number = 1.452428e-01\n Vprtstp: iteration = 2\n@@ -1428,32 +1428,32 @@\n Vprtstp: contraction number = 1.683190e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.126022e-06\n Vprtstp: contraction number = 1.729184e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 3.755158e-07\n Vprtstp: contraction number = 1.766283e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.782866e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.988696e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.248963e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.436055e+01\n Vpmg_setPart:  lower corner = (-6.031, -67.507, -7.978)\n Vpmg_setPart:  upper corner = (63.969, 2.493, 62.022)\n Vpmg_setPart:  actual minima = (-6.031, -67.507, -7.978)\n Vpmg_setPart:  actual maxima = (63.969, 2.493, 62.022)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.796545857614E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.900000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.900000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 4.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 10.66\n Vpbe_ctor2:  solute dimensions = 17.188 x 12.75 x 15.33\n Vpbe_ctor2:  solute charge = 1.11022e-16\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -1499,29 +1499,29 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.131443 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.163577\n+Vacc_SASA: Time elapsed: 0.131382\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.081792e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.669320e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.903600e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.346400e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.508867e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.318772e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.460545e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.843147e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.793309e-01\n Vprtstp: contraction number = 1.793309e-01\n Vprtstp: iteration = 2\n@@ -1541,30 +1541,30 @@\n Vprtstp: contraction number = 1.800338e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.360443e-06\n Vprtstp: contraction number = 1.860813e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 6.400789e-07\n Vprtstp: contraction number = 1.904746e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.407133e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.649072e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.226571e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.429495e+01\n Vpmg_setPart:  lower corner = (12.822, -45.153, 9.545)\n Vpmg_setPart:  upper corner = (36.822, -21.153, 33.545)\n Vpmg_setPart:  actual minima = (12.822, -45.153, 9.545)\n Vpmg_setPart:  actual maxima = (36.822, -21.153, 33.545)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 8.475324562943E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.500000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.300000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 37.837\n Vpbe_ctor2:  solute dimensions = 60.969 x 56.587 x 62.12\n Vpbe_ctor2:  solute charge = 1\n@@ -1587,31 +1587,31 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 2.058896\n+Vacc_SASA: Time elapsed: 2.240073\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.542292e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.773821e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.340800e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 4.498400e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.507820e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.275823e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.386816e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.544436e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.027357e-02\n Vprtstp: contraction number = 9.027357e-02\n Vprtstp: iteration = 2\n@@ -1631,32 +1631,32 @@\n Vprtstp: contraction number = 1.817922e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.545186e-06\n Vprtstp: contraction number = 1.999061e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 3.371519e-07\n Vprtstp: contraction number = 2.181950e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.204584e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.443588e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.212737e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.395671e+01\n Vpmg_setPart:  lower corner = (-6.031, -67.507, -7.978)\n Vpmg_setPart:  upper corner = (63.969, 2.493, 62.022)\n Vpmg_setPart:  actual minima = (-6.031, -67.507, -7.978)\n Vpmg_setPart:  actual maxima = (63.969, 2.493, 62.022)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.474786197493E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.359000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.484000e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 37.837\n Vpbe_ctor2:  solute dimensions = 60.969 x 56.587 x 62.12\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -1702,29 +1702,29 @@\n VPMG::extEnergy: extQfEnergy = 120029 kT\n VPMG::extEnergy: extDiEnergy = 58911.7 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 2.209876\n+Vacc_SASA: Time elapsed: 2.166223\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.811261e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.787158e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 4.811000e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 4.018900e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.461452e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.221172e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.110931e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.228101e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.164650e-01\n Vprtstp: contraction number = 1.164650e-01\n Vprtstp: iteration = 2\n@@ -1744,32 +1744,32 @@\n Vprtstp: contraction number = 1.751675e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.167167e-06\n Vprtstp: contraction number = 1.847486e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.216013e-07\n Vprtstp: contraction number = 1.898626e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.149909e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.370583e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.189505e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.369520e+01\n Vpmg_setPart:  lower corner = (12.822, -45.153, 9.545)\n Vpmg_setPart:  upper corner = (36.822, -21.153, 33.545)\n Vpmg_setPart:  actual minima = (12.822, -45.153, 9.545)\n Vpmg_setPart:  actual maxima = (36.822, -21.153, 33.545)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 2.434258164340E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.930000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.610000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 37.837\n Vpbe_ctor2:  solute dimensions = 60.969 x 56.587 x 62.12\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -1790,31 +1790,31 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 2.101408\n+Vacc_SASA: Time elapsed: 2.147917\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.665903e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.622373e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.956400e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.797500e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.371281e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.366523e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.477811e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.089600e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.976616e-02\n Vprtstp: contraction number = 8.976616e-02\n Vprtstp: iteration = 2\n@@ -1834,30 +1834,30 @@\n Vprtstp: contraction number = 1.851080e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.610068e-06\n Vprtstp: contraction number = 2.038795e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 3.565510e-07\n Vprtstp: contraction number = 2.214509e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.388395e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.626270e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.227068e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.421085e+01\n Vpmg_setPart:  lower corner = (-6.031, -67.507, -7.978)\n Vpmg_setPart:  upper corner = (63.969, 2.493, 62.022)\n Vpmg_setPart:  actual minima = (-6.031, -67.507, -7.978)\n Vpmg_setPart:  actual maxima = (63.969, 2.493, 62.022)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.493215172512E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 8.206000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.860000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 37.837\n Vpbe_ctor2:  solute dimensions = 60.969 x 56.587 x 62.12\n Vpbe_ctor2:  solute charge = 1\n@@ -1905,29 +1905,29 @@\n VPMG::extEnergy: extQfEnergy = 120027 kT\n VPMG::extEnergy: extDiEnergy = 58911 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 2.281701\n+Vacc_SASA: Time elapsed: 2.193990\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.885918e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.793129e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.399700e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 4.041000e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.524764e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.263446e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.872421e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.359910e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.180177e-01\n Vprtstp: contraction number = 1.180177e-01\n Vprtstp: iteration = 2\n@@ -1947,38 +1947,38 @@\n Vprtstp: contraction number = 1.739107e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.163103e-06\n Vprtstp: contraction number = 1.834388e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.205019e-07\n Vprtstp: contraction number = 1.895807e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.004027e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.249137e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.108995e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.290688e+01\n Vpmg_setPart:  lower corner = (12.822, -45.153, 9.545)\n Vpmg_setPart:  upper corner = (36.822, -21.153, 33.545)\n Vpmg_setPart:  actual minima = (12.822, -45.153, 9.545)\n Vpmg_setPart:  actual maxima = (36.822, -21.153, 33.545)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 2.519180536568E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.240000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.940000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 2.175410e+02\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.573922e+02\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 06:47:49 2025\n+# Creation Date and Time:  Tue Jan  9 04:50:13 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path bx6_7_lig_apbs.pqr\n@@ -2314,31 +2314,31 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.170757\n+Vacc_SASA: Time elapsed: 0.091884\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.454910e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.854100e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.825100e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.351400e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.332744e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.301340e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.932395e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.877642e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.599213e-01\n Vprtstp: contraction number = 1.599213e-01\n Vprtstp: iteration = 2\n@@ -2367,30 +2367,30 @@\n Vprtstp: contraction number = 2.963523e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.017970e-06\n Vprtstp: contraction number = 2.969958e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.027030e-07\n Vprtstp: contraction number = 2.973596e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.555095e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.772132e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.170524e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.399531e+01\n Vpmg_setPart:  lower corner = (-6.031, -67.507, -7.978)\n Vpmg_setPart:  upper corner = (63.969, 2.493, 62.022)\n Vpmg_setPart:  actual minima = (-6.031, -67.507, -7.978)\n Vpmg_setPart:  actual maxima = (63.969, 2.493, 62.022)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.810710599589E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.698100e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.700000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 10.66\n Vpbe_ctor2:  solute dimensions = 17.188 x 12.75 x 15.33\n Vpbe_ctor2:  solute charge = 1.11022e-16\n@@ -2438,29 +2438,29 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.127039 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.135252\n+Vacc_SASA: Time elapsed: 0.103151\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.076500e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.134452e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.160200e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.193500e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.464648e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.444238e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.241158e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.835042e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.128592e-01\n Vprtstp: contraction number = 2.128592e-01\n Vprtstp: iteration = 2\n@@ -2492,30 +2492,30 @@\n Vprtstp: contraction number = 3.367480e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 1.365284e-06\n Vprtstp: contraction number = 3.379196e-01\n Vprtstp: iteration = 12\n Vprtstp: relative residual = 4.626034e-07\n Vprtstp: contraction number = 3.388332e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 4.791672e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 5.054814e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.462660e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.710325e+01\n Vpmg_setPart:  lower corner = (12.822, -45.153, 9.545)\n Vpmg_setPart:  upper corner = (36.822, -21.153, 33.545)\n Vpmg_setPart:  actual minima = (12.822, -45.153, 9.545)\n Vpmg_setPart:  actual maxima = (36.822, -21.153, 33.545)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 8.488596110069E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.200000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.800000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 37.837\n Vpbe_ctor2:  solute dimensions = 60.969 x 56.587 x 62.12\n Vpbe_ctor2:  solute charge = 1\n@@ -2538,31 +2538,31 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.552247\n+Vacc_SASA: Time elapsed: 1.564319\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.949016e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.784793e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 4.769500e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 4.388000e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.200739e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.284294e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.578689e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.802134e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.008467e-01\n Vprtstp: contraction number = 1.008467e-01\n Vprtstp: iteration = 2\n@@ -2591,32 +2591,32 @@\n Vprtstp: contraction number = 4.011046e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.434965e-06\n Vprtstp: contraction number = 4.261259e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 6.351498e-07\n Vprtstp: contraction number = 4.426237e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 4.377900e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.614289e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.050632e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.257336e+01\n Vpmg_setPart:  lower corner = (-6.031, -67.507, -7.978)\n Vpmg_setPart:  upper corner = (63.969, 2.493, 62.022)\n Vpmg_setPart:  actual minima = (-6.031, -67.507, -7.978)\n Vpmg_setPart:  actual maxima = (63.969, 2.493, 62.022)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.502732517701E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.860000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.100000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 37.837\n Vpbe_ctor2:  solute dimensions = 60.969 x 56.587 x 62.12\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -2662,29 +2662,29 @@\n VPMG::extEnergy: extQfEnergy = 122258 kT\n VPMG::extEnergy: extDiEnergy = 60015.6 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.440138\n+Vacc_SASA: Time elapsed: 1.542972\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.101843e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.173699e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 3.970000e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 3.917800e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.348950e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.113148e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.452554e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.138370e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.444678e-01\n Vprtstp: contraction number = 1.444678e-01\n Vprtstp: iteration = 2\n@@ -2713,32 +2713,32 @@\n Vprtstp: contraction number = 3.502797e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.520619e-06\n Vprtstp: contraction number = 3.554465e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 5.554489e-07\n Vprtstp: contraction number = 3.652782e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 4.671693e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.918270e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.298641e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.490405e+01\n Vpmg_setPart:  lower corner = (12.822, -45.153, 9.545)\n Vpmg_setPart:  upper corner = (36.822, -21.153, 33.545)\n Vpmg_setPart:  actual minima = (12.822, -45.153, 9.545)\n Vpmg_setPart:  actual maxima = (36.822, -21.153, 33.545)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 2.462158714651E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.390000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.710000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 37.837\n Vpbe_ctor2:  solute dimensions = 60.969 x 56.587 x 62.12\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -2759,31 +2759,31 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.529749\n+Vacc_SASA: Time elapsed: 1.530874\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.766627e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.764529e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.748600e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.894200e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.376140e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.226754e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.974404e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.518081e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.951095e-02\n Vprtstp: contraction number = 9.951095e-02\n Vprtstp: iteration = 2\n@@ -2812,32 +2812,32 @@\n Vprtstp: contraction number = 3.973081e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.298337e-06\n Vprtstp: contraction number = 4.223462e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 5.734047e-07\n Vprtstp: contraction number = 4.416455e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 4.488696e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 4.738401e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.091267e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.298782e+01\n Vpmg_setPart:  lower corner = (-6.031, -67.507, -7.978)\n Vpmg_setPart:  upper corner = (63.969, 2.493, 62.022)\n Vpmg_setPart:  actual minima = (-6.031, -67.507, -7.978)\n Vpmg_setPart:  actual maxima = (63.969, 2.493, 62.022)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.522103263384E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.270000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.290000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 37.837\n Vpbe_ctor2:  solute dimensions = 60.969 x 56.587 x 62.12\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -2883,29 +2883,29 @@\n VPMG::extEnergy: extQfEnergy = 122254 kT\n VPMG::extEnergy: extDiEnergy = 60014.8 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.528279\n+Vacc_SASA: Time elapsed: 1.555947\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.977019e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.060270e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 4.376200e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.600300e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.250165e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.246745e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.476484e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.880868e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.413483e-01\n Vprtstp: contraction number = 1.413483e-01\n Vprtstp: iteration = 2\n@@ -2934,38 +2934,38 @@\n Vprtstp: contraction number = 3.543205e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.106047e-06\n Vprtstp: contraction number = 3.675340e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 4.216013e-07\n Vprtstp: contraction number = 3.811783e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.540590e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.767860e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.159559e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.375512e+01\n Vpmg_setPart:  lower corner = (12.822, -45.153, 9.545)\n Vpmg_setPart:  upper corner = (36.822, -21.153, 33.545)\n Vpmg_setPart:  actual minima = (12.822, -45.153, 9.545)\n Vpmg_setPart:  actual maxima = (36.822, -21.153, 33.545)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 2.548006855100E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.750000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.420000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 2.833611e+02\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 2.199776e+02\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 06:48:25 2025\n+# Creation Date and Time:  Tue Jan  9 04:51:01 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path bx6_7_lig_apbs.pqr\n@@ -3301,31 +3301,31 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.177982\n+Vacc_SASA: Time elapsed: 0.107722\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.288146e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.084934e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.875100e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.219100e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.395049e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.158805e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.557595e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.055248e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.452175e-01\n Vprtstp: contraction number = 1.452175e-01\n Vprtstp: iteration = 2\n@@ -3345,30 +3345,30 @@\n Vprtstp: contraction number = 1.752116e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.443360e-06\n Vprtstp: contraction number = 1.802654e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 4.491907e-07\n Vprtstp: contraction number = 1.838414e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.136332e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.351562e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.258974e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.446077e+01\n Vpmg_setPart:  lower corner = (-6.031, -67.507, -7.978)\n Vpmg_setPart:  upper corner = (63.969, 2.493, 62.022)\n Vpmg_setPart:  actual minima = (-6.031, -67.507, -7.978)\n Vpmg_setPart:  actual maxima = (63.969, 2.493, 62.022)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.816452194100E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.000000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.600000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 10.66\n Vpbe_ctor2:  solute dimensions = 17.188 x 12.75 x 15.33\n Vpbe_ctor2:  solute charge = 1.11022e-16\n@@ -3416,29 +3416,29 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.133537 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.133426\n+Vacc_SASA: Time elapsed: 0.194189\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.852641e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.667978e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.623800e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.316800e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.392899e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.291604e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.920579e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.958590e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.775500e-01\n Vprtstp: contraction number = 1.775500e-01\n Vprtstp: iteration = 2\n@@ -3458,32 +3458,32 @@\n Vprtstp: contraction number = 1.827663e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.496113e-06\n Vprtstp: contraction number = 1.891043e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 6.759954e-07\n Vprtstp: contraction number = 1.933563e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.787907e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.018549e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.436642e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.644036e+01\n Vpmg_setPart:  lower corner = (12.822, -45.153, 9.545)\n Vpmg_setPart:  upper corner = (36.822, -21.153, 33.545)\n Vpmg_setPart:  actual minima = (12.822, -45.153, 9.545)\n Vpmg_setPart:  actual maxima = (36.822, -21.153, 33.545)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 8.493961459749E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.600000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.400000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 37.837\n Vpbe_ctor2:  solute dimensions = 60.969 x 56.587 x 62.12\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -3504,31 +3504,31 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.678014\n+Vacc_SASA: Time elapsed: 1.553954\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.325817e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.135037e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.541900e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 4.309600e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.360407e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.113479e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.267256e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.896733e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.789951e-02\n Vprtstp: contraction number = 8.789951e-02\n Vprtstp: iteration = 2\n@@ -3545,30 +3545,30 @@\n Vprtstp: contraction number = 1.398889e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 4.364929e-06\n Vprtstp: contraction number = 1.509054e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 8.472971e-07\n Vprtstp: contraction number = 1.941148e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.356203e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.561259e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.948350e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.121231e+01\n Vpmg_setPart:  lower corner = (-6.031, -67.507, -7.978)\n Vpmg_setPart:  upper corner = (63.969, 2.493, 62.022)\n Vpmg_setPart:  actual minima = (-6.031, -67.507, -7.978)\n Vpmg_setPart:  actual maxima = (63.969, 2.493, 62.022)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.503907197961E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.686000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.850000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 37.837\n Vpbe_ctor2:  solute dimensions = 60.969 x 56.587 x 62.12\n Vpbe_ctor2:  solute charge = 1\n@@ -3616,29 +3616,29 @@\n VPMG::extEnergy: extQfEnergy = 122356 kT\n VPMG::extEnergy: extDiEnergy = 60065 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.539488\n+Vacc_SASA: Time elapsed: 1.523659\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.598972e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.637244e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 4.674400e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 3.938900e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.366105e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.098543e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.022020e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.399276e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.361361e-01\n Vprtstp: contraction number = 1.361361e-01\n Vprtstp: iteration = 2\n@@ -3658,30 +3658,30 @@\n Vprtstp: contraction number = 1.780896e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.357861e-06\n Vprtstp: contraction number = 1.814853e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.460991e-07\n Vprtstp: contraction number = 1.812402e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.353298e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.569412e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.158343e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.339076e+01\n Vpmg_setPart:  lower corner = (12.822, -45.153, 9.545)\n Vpmg_setPart:  upper corner = (36.822, -21.153, 33.545)\n Vpmg_setPart:  actual minima = (12.822, -45.153, 9.545)\n Vpmg_setPart:  actual maxima = (36.822, -21.153, 33.545)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 2.463376211100E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.860000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.000000e-04\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 37.837\n Vpbe_ctor2:  solute dimensions = 60.969 x 56.587 x 62.12\n Vpbe_ctor2:  solute charge = 1\n@@ -3704,31 +3704,31 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.547180\n+Vacc_SASA: Time elapsed: 1.468511\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.099194e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.116880e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.835900e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.921500e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.727510e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.256352e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.417569e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.107827e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.694592e-02\n Vprtstp: contraction number = 8.694592e-02\n Vprtstp: iteration = 2\n@@ -3745,30 +3745,30 @@\n Vprtstp: contraction number = 1.389852e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 4.160523e-06\n Vprtstp: contraction number = 1.496124e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 8.105844e-07\n Vprtstp: contraction number = 1.948275e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.119627e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.398246e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.242590e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.431043e+01\n Vpmg_setPart:  lower corner = (-6.031, -67.507, -7.978)\n Vpmg_setPart:  upper corner = (63.969, 2.493, 62.022)\n Vpmg_setPart:  actual minima = (-6.031, -67.507, -7.978)\n Vpmg_setPart:  actual maxima = (63.969, 2.493, 62.022)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.523234125638E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.870000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.683000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 37.837\n Vpbe_ctor2:  solute dimensions = 60.969 x 56.587 x 62.12\n Vpbe_ctor2:  solute charge = 1\n@@ -3816,29 +3816,29 @@\n VPMG::extEnergy: extQfEnergy = 122353 kT\n VPMG::extEnergy: extDiEnergy = 60064.1 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 1.493200\n+Vacc_SASA: Time elapsed: 1.575086\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.299393e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.346527e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (097, 097, 097)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 4.472700e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 4.013700e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (049, 049, 049)\n Vbuildops: Galer: (025, 025, 025)\n Vbuildops: Galer: (013, 013, 013)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.377705e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.174599e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.787001e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.385253e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.348493e-01\n Vprtstp: contraction number = 1.348493e-01\n Vprtstp: iteration = 2\n@@ -3858,28 +3858,28 @@\n Vprtstp: contraction number = 1.735657e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.117086e-06\n Vprtstp: contraction number = 1.891826e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.184693e-07\n Vprtstp: contraction number = 1.955708e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.185797e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.407237e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.404962e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.587036e+01\n Vpmg_setPart:  lower corner = (12.822, -45.153, 9.545)\n Vpmg_setPart:  upper corner = (36.822, -21.153, 33.545)\n Vpmg_setPart:  actual minima = (12.822, -45.153, 9.545)\n Vpmg_setPart:  actual maxima = (36.822, -21.153, 33.545)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 2.549194232887E+05 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.500000e-04\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.919000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 2.108606e+02\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.628646e+02\n"}, {"source1": "./usr/share/apbs/examples/point-pmf/io.mc", "source2": "./usr/share/apbs/examples/point-pmf/io.mc", "unified_diff": "@@ -1,10 +1,10 @@\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 06:48:57 2025\n+# Creation Date and Time:  Tue Jan  9 04:51:40 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path mol0.pqr\n@@ -184,28 +184,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.397330e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.163240e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 4.225700e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.513000e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.186774e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.219340e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.655427e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.118261e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.117158e-01\n Vprtstp: contraction number = 1.117158e-01\n Vprtstp: iteration = 2\n@@ -222,33 +222,33 @@\n Vprtstp: contraction number = 1.067217e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.472908e-06\n Vprtstp: contraction number = 1.074130e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.590269e-07\n Vprtstp: contraction number = 1.079680e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.781007e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.021494e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.126324e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.315241e+01\n Vpmg_setPart:  lower corner = (-6.72, -6.72, -6.72)\n Vpmg_setPart:  upper corner = (6.72, 6.72, 6.72)\n Vpmg_setPart:  actual minima = (-6.72, -6.72, -6.72)\n Vpmg_setPart:  actual maxima = (6.72, 6.72, 6.72)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 7.887170085535E+01 kT\n Vpmg_qmEnergy:  Zero energy for zero ionic strength!\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.475000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.489000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 0\n Vpbe_ctor2:  solute dimensions = 0 x 0 x 0\n Vpbe_ctor2:  solute charge = 1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -269,28 +269,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.457650e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.745680e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.101400e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.357630e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.490371e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.053870e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.370662e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.566564e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.116487e-01\n Vprtstp: contraction number = 1.116487e-01\n Vprtstp: iteration = 2\n@@ -307,31 +307,31 @@\n Vprtstp: contraction number = 1.068390e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.476968e-06\n Vprtstp: contraction number = 1.075610e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.596976e-07\n Vprtstp: contraction number = 1.081253e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.729516e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.010397e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.181046e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.376674e+01\n Vpmg_setPart:  lower corner = (-6.72, -6.72, -6.72)\n Vpmg_setPart:  upper corner = (6.72, 6.72, 6.72)\n Vpmg_setPart:  actual minima = (-6.72, -6.72, -6.72)\n Vpmg_setPart:  actual maxima = (6.72, 6.72, 6.72)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 7.241648379021E+01 kT\n Vpmg_qmEnergy:  Zero energy for zero ionic strength!\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 8.450000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.488000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 0.5\n Vpbe_ctor2:  solute dimensions = 1 x 0 x 0\n Vpbe_ctor2:  solute charge = 2\n@@ -354,28 +354,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.767170e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.898040e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 4.414500e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.406900e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.480372e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.057567e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.404292e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.982304e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.110273e-01\n Vprtstp: contraction number = 1.110273e-01\n Vprtstp: iteration = 2\n@@ -392,39 +392,39 @@\n Vprtstp: contraction number = 1.067630e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.464818e-06\n Vprtstp: contraction number = 1.074713e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.582462e-07\n Vprtstp: contraction number = 1.080314e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.281055e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.544601e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.855731e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.057062e+01\n Vpmg_setPart:  lower corner = (-6.72, -6.72, -6.72)\n Vpmg_setPart:  upper corner = (6.72, 6.72, 6.72)\n Vpmg_setPart:  actual minima = (-6.72, -6.72, -6.72)\n Vpmg_setPart:  actual maxima = (6.72, 6.72, 6.72)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.660589930493E+02 kT\n Vpmg_qmEnergy:  Zero energy for zero ionic strength!\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.182000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.242000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 9.706544e+01\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 6.853215e+01\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 06:49:06 2025\n+# Creation Date and Time:  Tue Jan  9 04:51:52 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path mol0.pqr\n@@ -604,28 +604,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.089490e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.732730e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.395220e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.449480e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.207314e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.623840e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.775409e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.228344e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.117158e-01\n Vprtstp: contraction number = 1.117158e-01\n Vprtstp: iteration = 2\n@@ -642,31 +642,31 @@\n Vprtstp: contraction number = 1.067217e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.472908e-06\n Vprtstp: contraction number = 1.074130e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.590269e-07\n Vprtstp: contraction number = 1.079680e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.141108e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.396713e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.441291e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.645753e+01\n Vpmg_setPart:  lower corner = (-6.72, -6.72, -6.72)\n Vpmg_setPart:  upper corner = (6.72, 6.72, 6.72)\n Vpmg_setPart:  actual minima = (-6.72, -6.72, -6.72)\n Vpmg_setPart:  actual maxima = (6.72, 6.72, 6.72)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 7.887170085535E+01 kT\n Vpmg_qmEnergy:  Zero energy for zero ionic strength!\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.844000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.475000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 0\n Vpbe_ctor2:  solute dimensions = 0 x 0 x 0\n Vpbe_ctor2:  solute charge = 1\n@@ -689,28 +689,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.791070e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.107360e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.445920e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.437310e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.047245e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.185678e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.819603e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.932212e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.115116e-01\n Vprtstp: contraction number = 1.115116e-01\n Vprtstp: iteration = 2\n@@ -727,31 +727,31 @@\n Vprtstp: contraction number = 1.068563e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.477070e-06\n Vprtstp: contraction number = 1.075813e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.597562e-07\n Vprtstp: contraction number = 1.081575e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.161040e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.517085e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.202133e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.431149e+01\n Vpmg_setPart:  lower corner = (-6.72, -6.72, -6.72)\n Vpmg_setPart:  upper corner = (6.72, 6.72, 6.72)\n Vpmg_setPart:  actual minima = (-6.72, -6.72, -6.72)\n Vpmg_setPart:  actual maxima = (6.72, 6.72, 6.72)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 8.209948502984E+01 kT\n Vpmg_qmEnergy:  Zero energy for zero ionic strength!\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.221500e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.076000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 1\n Vpbe_ctor2:  solute dimensions = 2 x 0 x 0\n Vpbe_ctor2:  solute charge = 2\n@@ -774,28 +774,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.510700e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.306000e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.303890e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.229030e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.959949e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.147604e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.394512e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.372790e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.112280e-01\n Vprtstp: contraction number = 1.112280e-01\n Vprtstp: iteration = 2\n@@ -812,39 +812,39 @@\n Vprtstp: contraction number = 1.067265e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.466596e-06\n Vprtstp: contraction number = 1.074314e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.583845e-07\n Vprtstp: contraction number = 1.079946e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.053172e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.423009e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.098009e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.296047e+01\n Vpmg_setPart:  lower corner = (-6.72, -6.72, -6.72)\n Vpmg_setPart:  upper corner = (6.72, 6.72, 6.72)\n Vpmg_setPart:  actual minima = (-6.72, -6.72, -6.72)\n Vpmg_setPart:  actual maxima = (6.72, 6.72, 6.72)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.681569832028E+02 kT\n Vpmg_qmEnergy:  Zero energy for zero ionic strength!\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.546000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.128000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.046093e+02\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 7.483428e+01\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 06:49:15 2025\n+# Creation Date and Time:  Tue Jan  9 04:52:04 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path mol0.pqr\n@@ -1024,28 +1024,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.326250e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.881070e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.533900e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.793000e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.365808e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.396740e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.723998e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.181477e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.117158e-01\n Vprtstp: contraction number = 1.117158e-01\n Vprtstp: iteration = 2\n@@ -1062,31 +1062,31 @@\n Vprtstp: contraction number = 1.067217e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.472908e-06\n Vprtstp: contraction number = 1.074130e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.590269e-07\n Vprtstp: contraction number = 1.079680e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.181460e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.429333e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.122899e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.321199e+01\n Vpmg_setPart:  lower corner = (-6.72, -6.72, -6.72)\n Vpmg_setPart:  upper corner = (6.72, 6.72, 6.72)\n Vpmg_setPart:  actual minima = (-6.72, -6.72, -6.72)\n Vpmg_setPart:  actual maxima = (6.72, 6.72, 6.72)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 7.887170085535E+01 kT\n Vpmg_qmEnergy:  Zero energy for zero ionic strength!\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.076100e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.627000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 0\n Vpbe_ctor2:  solute dimensions = 0 x 0 x 0\n Vpbe_ctor2:  solute charge = 1\n@@ -1109,28 +1109,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.516100e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.720510e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 4.783200e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.433720e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.540107e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.779590e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.786358e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.566269e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.122494e-01\n Vprtstp: contraction number = 1.122494e-01\n Vprtstp: iteration = 2\n@@ -1147,31 +1147,31 @@\n Vprtstp: contraction number = 1.068256e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.484900e-06\n Vprtstp: contraction number = 1.075504e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.605755e-07\n Vprtstp: contraction number = 1.081389e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.194661e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.492919e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.005064e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.195687e+01\n Vpmg_setPart:  lower corner = (-6.72, -6.72, -6.72)\n Vpmg_setPart:  upper corner = (6.72, 6.72, 6.72)\n Vpmg_setPart:  actual minima = (-6.72, -6.72, -6.72)\n Vpmg_setPart:  actual maxima = (6.72, 6.72, 6.72)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.079207063662E+02 kT\n Vpmg_qmEnergy:  Zero energy for zero ionic strength!\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.344000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.245000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 1.5\n Vpbe_ctor2:  solute dimensions = 3 x 0 x 0\n Vpbe_ctor2:  solute charge = 2\n@@ -1194,28 +1194,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.129130e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.131770e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.002760e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.095320e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 2.277998e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.149831e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.396214e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.813329e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.117126e-01\n Vprtstp: contraction number = 1.117126e-01\n Vprtstp: iteration = 2\n@@ -1232,39 +1232,39 @@\n Vprtstp: contraction number = 1.067223e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.472511e-06\n Vprtstp: contraction number = 1.074345e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.590395e-07\n Vprtstp: contraction number = 1.080057e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.351064e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.725506e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.053480e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.266777e+01\n Vpmg_setPart:  lower corner = (-6.72, -6.72, -6.72)\n Vpmg_setPart:  upper corner = (6.72, 6.72, 6.72)\n Vpmg_setPart:  actual minima = (-6.72, -6.72, -6.72)\n Vpmg_setPart:  actual maxima = (6.72, 6.72, 6.72)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.915601904303E+02 kT\n Vpmg_qmEnergy:  Zero energy for zero ionic strength!\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.355000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.391000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.076335e+02\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 6.879520e+01\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 06:49:24 2025\n+# Creation Date and Time:  Tue Jan  9 04:52:16 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path mol0.pqr\n@@ -1444,28 +1444,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.062520e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.278640e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.952400e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.061200e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.170760e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.050517e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.691459e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.245659e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.117158e-01\n Vprtstp: contraction number = 1.117158e-01\n Vprtstp: iteration = 2\n@@ -1482,31 +1482,31 @@\n Vprtstp: contraction number = 1.067217e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.472908e-06\n Vprtstp: contraction number = 1.074130e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.590269e-07\n Vprtstp: contraction number = 1.079680e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.190653e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.438250e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.227005e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.437759e+01\n Vpmg_setPart:  lower corner = (-6.72, -6.72, -6.72)\n Vpmg_setPart:  upper corner = (6.72, 6.72, 6.72)\n Vpmg_setPart:  actual minima = (-6.72, -6.72, -6.72)\n Vpmg_setPart:  actual maxima = (6.72, 6.72, 6.72)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 7.887170085535E+01 kT\n Vpmg_qmEnergy:  Zero energy for zero ionic strength!\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.472000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.548000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 0\n Vpbe_ctor2:  solute dimensions = 0 x 0 x 0\n Vpbe_ctor2:  solute charge = 1\n@@ -1529,28 +1529,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.893820e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.888860e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.487660e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.516280e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.514555e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.166723e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.789191e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.715257e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.115116e-01\n Vprtstp: contraction number = 1.115116e-01\n Vprtstp: iteration = 2\n@@ -1567,31 +1567,31 @@\n Vprtstp: contraction number = 1.068563e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.477070e-06\n Vprtstp: contraction number = 1.075813e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.597562e-07\n Vprtstp: contraction number = 1.081575e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.387738e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.682703e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 1.961145e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.195399e+01\n Vpmg_setPart:  lower corner = (-6.72, -6.72, -6.72)\n Vpmg_setPart:  upper corner = (6.72, 6.72, 6.72)\n Vpmg_setPart:  actual minima = (-6.72, -6.72, -6.72)\n Vpmg_setPart:  actual maxima = (6.72, 6.72, 6.72)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 8.209948502984E+01 kT\n Vpmg_qmEnergy:  Zero energy for zero ionic strength!\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.105000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.739000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 2\n Vpbe_ctor2:  solute dimensions = 4 x 0 x 0\n Vpbe_ctor2:  solute charge = 2\n@@ -1614,28 +1614,28 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.869910e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.821400e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.133930e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.227210e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.333969e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.222741e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.484655e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.935728e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.113661e-01\n Vprtstp: contraction number = 1.113661e-01\n Vprtstp: iteration = 2\n@@ -1652,29 +1652,29 @@\n Vprtstp: contraction number = 1.067553e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.470482e-06\n Vprtstp: contraction number = 1.074604e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.588507e-07\n Vprtstp: contraction number = 1.080263e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.235081e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.499431e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.291852e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.515746e+01\n Vpmg_setPart:  lower corner = (-6.72, -6.72, -6.72)\n Vpmg_setPart:  upper corner = (6.72, 6.72, 6.72)\n Vpmg_setPart:  actual minima = (-6.72, -6.72, -6.72)\n Vpmg_setPart:  actual maxima = (6.72, 6.72, 6.72)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.645453654146E+02 kT\n Vpmg_qmEnergy:  Zero energy for zero ionic strength!\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.098000e-03\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.108000e-03\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.073875e+02\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 7.248689e+01\n"}, {"source1": "./usr/share/apbs/examples/protein-rna/io.mc", "source2": "./usr/share/apbs/examples/protein-rna/io.mc", "unified_diff": "@@ -1,10 +1,10 @@\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 06:50:01 2025\n+# Creation Date and Time:  Tue Jan  9 04:53:07 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path model_outNB.pqr\n@@ -274,151 +274,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.644551\n+Vacc_SASA: Time elapsed: 0.610876\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.814533e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.654368e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 6.333400e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.117800e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.204867e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.561930e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.190440e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.751071e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 3489953.107213\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.666212e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.831188e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.541420e+05\n Vprtstp: contraction number = 4.541420e+05\n Vnewton: Attempting damping, relres = 0.152961\n Vnewton: Attempting damping, relres = 0.557868\n Vnewton: Damping accepted, relres = 0.152961\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.529613e-01\n Vprtstp: contraction number = 1.529613e-01\n Vnewton: Using errtol_s: 533827.862441\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.589971e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.052399e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.616204e+04\n Vprtstp: contraction number = 7.616204e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.889845e-02\n Vprtstp: contraction number = 1.889265e-01\n Vnewton: Using errtol_s: 100854.249053\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.724518e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.619493e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.621156e+04\n Vprtstp: contraction number = 1.621156e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 6.485254e-03\n Vprtstp: contraction number = 2.244153e-01\n Vnewton: Using errtol_s: 22633.233232\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.219938e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.499741e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.163481e+03\n Vprtstp: contraction number = 4.163481e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.448984e-03\n Vprtstp: contraction number = 2.234275e-01\n Vnewton: Using errtol_s: 5056.886378\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.372761e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.945436e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.135331e+03\n Vprtstp: contraction number = 1.135331e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.105204e-04\n Vprtstp: contraction number = 2.143021e-01\n Vnewton: Using errtol_s: 1083.701574\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.158181e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.219300e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.001303e+02\n Vprtstp: contraction number = 3.001303e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 7.746175e-05\n Vprtstp: contraction number = 2.494579e-01\n Vnewton: Using errtol_s: 270.337872\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.400781e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.550817e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.503484e+01\n Vprtstp: contraction number = 8.503484e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.192913e-05\n Vprtstp: contraction number = 2.830962e-01\n Vnewton: Using errtol_s: 76.531632\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.628432e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.090808e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.526272e+01\n Vprtstp: contraction number = 2.526272e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 6.514831e-06\n Vprtstp: contraction number = 2.970857e-01\n Vnewton: Using errtol_s: 22.736454\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.823852e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.242967e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.640103e+00\n Vprtstp: contraction number = 7.640103e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 1.970254e-06\n Vprtstp: contraction number = 3.024259e-01\n Vnewton: Using errtol_s: 6.876093\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.018661e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.378237e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.337433e+00\n Vprtstp: contraction number = 2.337433e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 6.027844e-07\n Vprtstp: contraction number = 3.059426e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.136673e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.150021e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.467237e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.477817e+02\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -428,17 +428,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 6.965827433401E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.569434563500E+04 kT\n Vpmg_energy:  dielEnergy = 1.283478359962E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.548900e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.343770e-01\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 25.8477\n Vpbe_ctor2:  solute dimensions = 26.666 x 32.3234 x 48.3902\n Vpbe_ctor2:  solute charge = -14\n Vpbe_ctor2:  bulk ionic strength = 0.025\n Vpbe_ctor2:  xkappa = 0.0514861\n@@ -485,160 +485,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.194992 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.555414\n+Vacc_SASA: Time elapsed: 0.612033\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.684571e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.592961e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.062500e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.875500e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.083349e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.127536e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.198300e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.526403e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 3601925.484823\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.222186e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.547246e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.484865e+05\n Vprtstp: contraction number = 5.484865e+05\n Vnewton: Attempting damping, relres = 0.170948\n Vnewton: Attempting damping, relres = 0.567920\n Vnewton: Damping accepted, relres = 0.170948\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.709480e-01\n Vprtstp: contraction number = 1.709480e-01\n Vnewton: Using errtol_s: 615741.974888\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.405602e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.724208e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.034638e+05\n Vprtstp: contraction number = 1.034638e+05\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 3.462084e-02\n Vprtstp: contraction number = 2.025226e-01\n Vnewton: Using errtol_s: 124701.671212\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.593757e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.900586e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.424561e+04\n Vprtstp: contraction number = 2.424561e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 8.233375e-03\n Vprtstp: contraction number = 2.378156e-01\n Vnewton: Using errtol_s: 29656.002425\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.788852e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.068748e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.562093e+03\n Vprtstp: contraction number = 6.562093e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.983416e-03\n Vprtstp: contraction number = 2.408995e-01\n Vnewton: Using errtol_s: 7144.117639\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.978912e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.215149e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.862413e+03\n Vprtstp: contraction number = 1.862413e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.794286e-04\n Vprtstp: contraction number = 2.417186e-01\n Vnewton: Using errtol_s: 1726.865972\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.214382e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.358442e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.263950e+02\n Vprtstp: contraction number = 5.263950e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.315588e-04\n Vprtstp: contraction number = 2.744075e-01\n Vnewton: Using errtol_s: 473.865007\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.461765e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.516967e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.568838e+02\n Vprtstp: contraction number = 1.568838e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.920007e-05\n Vprtstp: contraction number = 2.979661e-01\n Vnewton: Using errtol_s: 141.195715\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.720841e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.659890e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.889017e+01\n Vprtstp: contraction number = 4.889017e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.221601e-05\n Vprtstp: contraction number = 3.116325e-01\n Vnewton: Using errtol_s: 44.001172\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.965488e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.797692e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.562922e+01\n Vprtstp: contraction number = 1.562922e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.905217e-06\n Vprtstp: contraction number = 3.196802e-01\n Vnewton: Using errtol_s: 14.066301\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.212251e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.934875e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.094993e+00\n Vprtstp: contraction number = 5.094993e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.273067e-06\n Vprtstp: contraction number = 3.259914e-01\n Vnewton: Using errtol_s: 4.585493\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.462327e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.074660e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.686155e+00\n Vprtstp: contraction number = 1.686155e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 4.213135e-07\n Vprtstp: contraction number = 3.309436e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.504510e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.516511e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.690821e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.703796e+02\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -648,17 +648,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 6.946137752289E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.954048421546E+04 kT\n Vpmg_energy:  dielEnergy = 1.475783126623E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.461400e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.705700e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vnm_tstart: starting timer 27 (Setup timer)..\n@@ -685,151 +685,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.325217\n+Vacc_SASA: Time elapsed: 0.357363\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.068678e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.915630e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.949700e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.850900e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.213327e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.032713e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.740900e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.253609e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 990625.209730\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.770546e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.275465e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.350454e+05\n Vprtstp: contraction number = 1.350454e+05\n Vnewton: Attempting damping, relres = 0.127353\n Vnewton: Attempting damping, relres = 0.559577\n Vnewton: Damping accepted, relres = 0.127353\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.273531e-01\n Vprtstp: contraction number = 1.273531e-01\n Vnewton: Using errtol_s: 126159.215622\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.972832e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.430389e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.277893e+04\n Vprtstp: contraction number = 2.277893e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.085042e-02\n Vprtstp: contraction number = 1.637213e-01\n Vnewton: Using errtol_s: 20654.953727\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.156462e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.561836e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.649050e+03\n Vprtstp: contraction number = 4.649050e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 4.224159e-03\n Vprtstp: contraction number = 2.025935e-01\n Vnewton: Using errtol_s: 4184.558722\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.338925e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.688356e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.091881e+03\n Vprtstp: contraction number = 1.091881e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 9.919956e-04\n Vprtstp: contraction number = 2.348386e-01\n Vnewton: Using errtol_s: 982.695801\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.521576e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.798511e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.793836e+02\n Vprtstp: contraction number = 2.793836e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 2.538250e-04\n Vprtstp: contraction number = 2.558731e-01\n Vnewton: Using errtol_s: 251.445454\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.674535e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.912525e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.524959e+01\n Vprtstp: contraction number = 7.524959e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 6.836556e-05\n Vprtstp: contraction number = 2.693413e-01\n Vnewton: Using errtol_s: 67.724647\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.866267e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.022508e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.096668e+01\n Vprtstp: contraction number = 2.096668e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.904859e-05\n Vprtstp: contraction number = 2.786284e-01\n Vnewton: Using errtol_s: 18.870009\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.037090e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.130504e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.985543e+00\n Vprtstp: contraction number = 5.985543e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 5.437969e-06\n Vprtstp: contraction number = 2.854789e-01\n Vnewton: Using errtol_s: 5.386989\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.192887e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.230260e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.740420e+00\n Vprtstp: contraction number = 1.740420e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 1.581202e-06\n Vprtstp: contraction number = 2.907706e-01\n Vnewton: Using errtol_s: 1.566378\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.380568e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.335287e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.132173e-01\n Vprtstp: contraction number = 5.132173e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 4.662667e-07\n Vprtstp: contraction number = 2.948812e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.816374e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.829304e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.172765e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.184184e+02\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -839,15 +839,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.196703875366E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 6.838438031793E+03 kT\n Vpmg_energy:  dielEnergy = 3.417360829181E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.409300e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.102200e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 19.3778\n Vpbe_ctor2:  solute dimensions = 19.082 x 18.3114 x 35.7654\n Vpbe_ctor2:  solute charge = 4\n@@ -896,149 +896,149 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.017697 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.276170\n+Vacc_SASA: Time elapsed: 0.336654\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.712640e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.599750e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.136300e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.706200e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.342785e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.987120e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.583254e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.448529e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1033125.204115\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.615678e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.469076e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.675387e+05\n Vprtstp: contraction number = 1.675387e+05\n Vnewton: Attempting damping, relres = 0.150147\n Vnewton: Attempting damping, relres = 0.571307\n Vnewton: Damping accepted, relres = 0.150147\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.501469e-01\n Vprtstp: contraction number = 1.501469e-01\n Vnewton: Using errtol_s: 155120.525305\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.828343e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.592552e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.209762e+04\n Vprtstp: contraction number = 3.209762e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.810624e-02\n Vprtstp: contraction number = 1.871917e-01\n Vnewton: Using errtol_s: 29037.270087\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.016697e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.700509e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.331420e+03\n Vprtstp: contraction number = 7.331420e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 6.387218e-03\n Vprtstp: contraction number = 2.272526e-01\n Vnewton: Using errtol_s: 6598.796330\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.211918e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.811432e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.824095e+03\n Vprtstp: contraction number = 1.824095e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.589055e-03\n Vprtstp: contraction number = 2.487867e-01\n Vnewton: Using errtol_s: 1641.692880\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.399654e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.925143e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.792383e+02\n Vprtstp: contraction number = 4.792383e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.174858e-04\n Vprtstp: contraction number = 2.627258e-01\n Vnewton: Using errtol_s: 431.315051\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.584671e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.037257e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.310006e+02\n Vprtstp: contraction number = 1.310006e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.141203e-04\n Vprtstp: contraction number = 2.733515e-01\n Vnewton: Using errtol_s: 117.900599\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.763371e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.148998e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.696481e+01\n Vprtstp: contraction number = 3.696481e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.220165e-05\n Vprtstp: contraction number = 2.821727e-01\n Vnewton: Using errtol_s: 33.268335\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.906459e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.262341e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.072629e+01\n Vprtstp: contraction number = 1.072629e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 9.344133e-06\n Vprtstp: contraction number = 2.901756e-01\n Vnewton: Using errtol_s: 9.653659\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.088631e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.370688e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.196371e+00\n Vprtstp: contraction number = 3.196371e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.784497e-06\n Vprtstp: contraction number = 2.979941e-01\n Vnewton: Using errtol_s: 2.876734\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.272443e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.480628e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.745912e-01\n Vprtstp: contraction number = 9.745912e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 8.490085e-07\n Vprtstp: contraction number = 3.049056e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.872322e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.887760e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.132328e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.144731e+02\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -1048,17 +1048,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.190473517167E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 8.070936043953E+03 kT\n Vpmg_energy:  dielEnergy = 4.033615774534E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.108100e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.136000e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vnm_tstart: starting timer 27 (Setup timer)..\n@@ -1085,151 +1085,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.425202\n+Vacc_SASA: Time elapsed: 0.446495\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.282363e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.206894e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.522200e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.751400e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.244732e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.296750e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.496028e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.618309e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 3098216.768197\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.525296e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.639307e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.288533e+05\n Vprtstp: contraction number = 4.288533e+05\n Vnewton: Attempting damping, relres = 0.287242\n Vnewton: Attempting damping, relres = 0.564665\n Vnewton: Damping accepted, relres = 0.287242\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.872423e-01\n Vprtstp: contraction number = 2.872423e-01\n Vnewton: Using errtol_s: 889939.028652\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.701138e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.772544e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.459682e+04\n Vprtstp: contraction number = 8.459682e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 7.479655e-02\n Vprtstp: contraction number = 2.603953e-01\n Vnewton: Using errtol_s: 231735.935287\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.942174e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.970644e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.140926e+04\n Vprtstp: contraction number = 2.140926e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.197950e-02\n Vprtstp: contraction number = 2.938571e-01\n Vnewton: Using errtol_s: 68097.244831\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.203917e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.127040e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.306461e+03\n Vprtstp: contraction number = 6.306461e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 6.113198e-03\n Vprtstp: contraction number = 2.781319e-01\n Vnewton: Using errtol_s: 18940.013709\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.426830e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.252207e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.039254e+03\n Vprtstp: contraction number = 2.039254e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 1.310252e-03\n Vprtstp: contraction number = 2.143317e-01\n Vnewton: Using errtol_s: 4059.444466\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.620767e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.369946e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.729156e+02\n Vprtstp: contraction number = 5.729156e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.010708e-04\n Vprtstp: contraction number = 1.534596e-01\n Vnewton: Using errtol_s: 622.960837\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.809082e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.497692e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.140542e+02\n Vprtstp: contraction number = 1.140542e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.330907e-05\n Vprtstp: contraction number = 1.656585e-01\n Vnewton: Using errtol_s: 103.198728\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.996197e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.637251e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.743226e+01\n Vprtstp: contraction number = 2.743226e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 7.968958e-06\n Vprtstp: contraction number = 2.392429e-01\n Vnewton: Using errtol_s: 24.689560\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.017281e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.756813e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.960222e+00\n Vprtstp: contraction number = 7.960222e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.312364e-06\n Vprtstp: contraction number = 2.901714e-01\n Vnewton: Using errtol_s: 7.164205\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.034648e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.862348e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.414518e+00\n Vprtstp: contraction number = 2.414518e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 7.013925e-07\n Vprtstp: contraction number = 3.033227e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.003829e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.017052e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.339661e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.350276e+02\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -1239,15 +1239,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.097220464694E+01 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.877310278267E+04 kT\n Vpmg_energy:  dielEnergy = 9.366275092847E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.811700e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.109740e-01\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 20.7943\n Vpbe_ctor2:  solute dimensions = 25.3482 x 27.3592 x 40.136\n Vpbe_ctor2:  solute charge = -18\n@@ -1296,160 +1296,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.182726 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.443767\n+Vacc_SASA: Time elapsed: 0.419838\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.347369e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.231069e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.960000e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.794900e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.292192e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.920910e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.052949e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.984412e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 3179322.196917\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.056032e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.004900e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.157153e+05\n Vprtstp: contraction number = 5.157153e+05\n Vnewton: Attempting damping, relres = 0.300823\n Vnewton: Attempting damping, relres = 0.575285\n Vnewton: Damping accepted, relres = 0.300823\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.008234e-01\n Vprtstp: contraction number = 3.008234e-01\n Vnewton: Using errtol_s: 956414.609494\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.078876e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.134503e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.112831e+05\n Vprtstp: contraction number = 1.112831e+05\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 7.919694e-02\n Vprtstp: contraction number = 2.632672e-01\n Vnewton: Using errtol_s: 251792.580740\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.103442e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.322213e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.912764e+04\n Vprtstp: contraction number = 2.912764e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.322957e-02\n Vprtstp: contraction number = 2.933140e-01\n Vnewton: Using errtol_s: 73854.286564\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.128949e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.491254e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.683374e+03\n Vprtstp: contraction number = 8.683374e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 6.478032e-03\n Vprtstp: contraction number = 2.788701e-01\n Vnewton: Using errtol_s: 20595.750772\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.149820e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.635241e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.778111e+03\n Vprtstp: contraction number = 2.778111e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 1.439717e-03\n Vprtstp: contraction number = 2.222460e-01\n Vnewton: Using errtol_s: 4577.322906\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.169949e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.772726e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.948966e+02\n Vprtstp: contraction number = 7.948966e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.541519e-04\n Vprtstp: contraction number = 1.765291e-01\n Vnewton: Using errtol_s: 808.030623\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.189386e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.883063e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.884080e+02\n Vprtstp: contraction number = 1.884080e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 5.345432e-05\n Vprtstp: contraction number = 2.103243e-01\n Vnewton: Using errtol_s: 169.948515\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.209562e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.995137e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.248467e+01\n Vprtstp: contraction number = 5.248467e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.485742e-05\n Vprtstp: contraction number = 2.779462e-01\n Vnewton: Using errtol_s: 47.236538\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.229339e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.106665e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.636645e+01\n Vprtstp: contraction number = 1.636645e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 4.633006e-06\n Vprtstp: contraction number = 3.118310e-01\n Vnewton: Using errtol_s: 14.729818\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.248360e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.221405e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.289991e+00\n Vprtstp: contraction number = 5.289991e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.497487e-06\n Vprtstp: contraction number = 3.232214e-01\n Vnewton: Using errtol_s: 4.760992\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.266996e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.335764e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.736329e+00\n Vprtstp: contraction number = 1.736329e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 4.915187e-07\n Vprtstp: contraction number = 3.282291e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.310919e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.326273e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.454461e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.466410e+02\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -1459,29 +1459,29 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.094905051954E+01 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.139048085008E+04 kT\n Vpmg_energy:  dielEnergy = 1.067494556843E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.436600e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 9.348800e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.285390e+03\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 8.455423e+02\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 06:52:05 2025\n+# Creation Date and Time:  Tue Jan  9 04:55:41 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path model_outNB.pqr\n@@ -1751,151 +1751,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.606782\n+Vacc_SASA: Time elapsed: 0.588409\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.759270e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.592729e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.551900e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.806800e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.029434e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.088114e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.925298e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.841064e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2974958.994733\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.243342e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.042561e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.870275e+05\n Vprtstp: contraction number = 3.870275e+05\n Vnewton: Attempting damping, relres = 0.153059\n Vnewton: Attempting damping, relres = 0.557808\n Vnewton: Damping accepted, relres = 0.153059\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.530588e-01\n Vprtstp: contraction number = 1.530588e-01\n Vnewton: Using errtol_s: 455343.743026\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.733387e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.002578e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.695400e+04\n Vprtstp: contraction number = 6.695400e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.920739e-02\n Vprtstp: contraction number = 1.908246e-01\n Vnewton: Using errtol_s: 86890.793846\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.042141e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.647171e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.482146e+04\n Vprtstp: contraction number = 1.482146e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 6.545819e-03\n Vprtstp: contraction number = 2.241151e-01\n Vnewton: Using errtol_s: 19473.541826\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.640054e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.348151e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.884267e+03\n Vprtstp: contraction number = 3.884267e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.453691e-03\n Vprtstp: contraction number = 2.220793e-01\n Vnewton: Using errtol_s: 4324.671146\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.978627e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.953820e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.057768e+03\n Vprtstp: contraction number = 1.057768e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.284783e-04\n Vprtstp: contraction number = 2.259615e-01\n Vnewton: Using errtol_s: 977.209364\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.220727e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.309427e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.866048e+02\n Vprtstp: contraction number = 2.866048e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 8.672414e-05\n Vprtstp: contraction number = 2.640179e-01\n Vnewton: Using errtol_s: 258.000773\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.455011e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.731182e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.283684e+01\n Vprtstp: contraction number = 8.283684e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.506027e-05\n Vprtstp: contraction number = 2.889653e-01\n Vnewton: Using errtol_s: 74.553271\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.664202e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.102532e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.472736e+01\n Vprtstp: contraction number = 2.472736e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 7.480652e-06\n Vprtstp: contraction number = 2.985065e-01\n Vnewton: Using errtol_s: 22.254632\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.881104e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.246141e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.490971e+00\n Vprtstp: contraction number = 7.490971e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.266207e-06\n Vprtstp: contraction number = 3.029425e-01\n Vnewton: Using errtol_s: 6.741874\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.117912e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.389873e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.293363e+00\n Vprtstp: contraction number = 2.293363e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 6.938001e-07\n Vprtstp: contraction number = 3.061503e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.301313e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.312636e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.490204e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.502337e+02\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -1905,17 +1905,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 7.155593608885E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.568720386421E+04 kT\n Vpmg_energy:  dielEnergy = 1.283293314758E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.185030e-01\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.789000e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 25.8477\n Vpbe_ctor2:  solute dimensions = 26.666 x 32.3234 x 48.3902\n Vpbe_ctor2:  solute charge = -14\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.0728124\n@@ -1962,160 +1962,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.103051 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.597491\n+Vacc_SASA: Time elapsed: 0.582791\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.751305e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.605345e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.347100e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.941600e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.276720e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.016867e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.363992e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.547753e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 3077114.923847\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.392131e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.567754e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.742704e+05\n Vprtstp: contraction number = 4.742704e+05\n Vnewton: Attempting damping, relres = 0.172865\n Vnewton: Attempting damping, relres = 0.568730\n Vnewton: Damping accepted, relres = 0.172865\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.728651e-01\n Vprtstp: contraction number = 1.728651e-01\n Vnewton: Using errtol_s: 531925.831070\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.645104e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.725175e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.143761e+04\n Vprtstp: contraction number = 9.143761e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 3.526713e-02\n Vprtstp: contraction number = 2.040153e-01\n Vnewton: Using errtol_s: 108521.009470\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.870578e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.878227e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.196947e+04\n Vprtstp: contraction number = 2.196947e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 8.376912e-03\n Vprtstp: contraction number = 2.375275e-01\n Vnewton: Using errtol_s: 25776.719868\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.120488e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.025463e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.034692e+03\n Vprtstp: contraction number = 6.034692e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.018356e-03\n Vprtstp: contraction number = 2.409428e-01\n Vnewton: Using errtol_s: 6210.714220\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.356921e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.177696e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.718760e+03\n Vprtstp: contraction number = 1.718760e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.089360e-04\n Vprtstp: contraction number = 2.521537e-01\n Vnewton: Using errtol_s: 1566.054712\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.601806e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.327979e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.951703e+02\n Vprtstp: contraction number = 4.951703e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.448376e-04\n Vprtstp: contraction number = 2.845889e-01\n Vnewton: Using errtol_s: 445.681818\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.852739e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.479150e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.503700e+02\n Vprtstp: contraction number = 1.503700e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.398054e-05\n Vprtstp: contraction number = 3.036542e-01\n Vnewton: Using errtol_s: 135.333176\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.057246e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.673264e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.725124e+01\n Vprtstp: contraction number = 4.725124e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.382013e-05\n Vprtstp: contraction number = 3.142328e-01\n Vnewton: Using errtol_s: 42.526127\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.300144e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.844870e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.517823e+01\n Vprtstp: contraction number = 1.517823e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 4.439356e-06\n Vprtstp: contraction number = 3.212239e-01\n Vnewton: Using errtol_s: 13.660408\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.538217e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.995113e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.961627e+00\n Vprtstp: contraction number = 4.961627e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.451185e-06\n Vprtstp: contraction number = 3.268910e-01\n Vnewton: Using errtol_s: 4.465464\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.769805e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.152356e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.644451e+00\n Vprtstp: contraction number = 1.644451e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 4.809720e-07\n Vprtstp: contraction number = 3.314339e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.637973e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.651742e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.745371e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.756695e+02\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -2125,15 +2125,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 7.136719459534E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.953334472721E+04 kT\n Vpmg_energy:  dielEnergy = 1.475599755841E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.317800e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.664200e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n@@ -2162,151 +2162,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.388595\n+Vacc_SASA: Time elapsed: 0.336712\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.051302e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.016097e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.353600e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.063300e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.354416e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.051851e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.045090e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.330986e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 847635.298627\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.075642e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.355909e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.156652e+05\n Vprtstp: contraction number = 1.156652e+05\n Vnewton: Attempting damping, relres = 0.129563\n Vnewton: Attempting damping, relres = 0.559453\n Vnewton: Damping accepted, relres = 0.129563\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.295633e-01\n Vprtstp: contraction number = 1.295633e-01\n Vnewton: Using errtol_s: 109822.397033\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.273907e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.507222e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.025826e+04\n Vprtstp: contraction number = 2.025826e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.180592e-02\n Vprtstp: contraction number = 1.683033e-01\n Vnewton: Using errtol_s: 18483.468929\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.435686e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.617808e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.307643e+03\n Vprtstp: contraction number = 4.307643e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 4.574915e-03\n Vprtstp: contraction number = 2.098015e-01\n Vnewton: Using errtol_s: 3877.859579\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.613257e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.732242e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.042197e+03\n Vprtstp: contraction number = 1.042197e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.106587e-03\n Vprtstp: contraction number = 2.418813e-01\n Vnewton: Using errtol_s: 937.981802\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.785037e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.838980e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.719312e+02\n Vprtstp: contraction number = 2.719312e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 2.887307e-04\n Vprtstp: contraction number = 2.609201e-01\n Vnewton: Using errtol_s: 244.738306\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.966007e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.951258e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.411670e+01\n Vprtstp: contraction number = 7.411670e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 7.869545e-05\n Vprtstp: contraction number = 2.725566e-01\n Vnewton: Using errtol_s: 66.705044\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.136604e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.071287e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.079247e+01\n Vprtstp: contraction number = 2.079247e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.207697e-05\n Vprtstp: contraction number = 2.805368e-01\n Vnewton: Using errtol_s: 18.713222\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.316859e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.178896e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.958188e+00\n Vprtstp: contraction number = 5.958188e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 6.326270e-06\n Vprtstp: contraction number = 2.865551e-01\n Vnewton: Using errtol_s: 5.362370\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.481453e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.296391e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.735927e+00\n Vprtstp: contraction number = 1.735927e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 1.843168e-06\n Vprtstp: contraction number = 2.913515e-01\n Vnewton: Using errtol_s: 1.562335\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.643802e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.405655e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.124069e-01\n Vprtstp: contraction number = 5.124069e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 5.440621e-07\n Vprtstp: contraction number = 2.951777e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.755644e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.770136e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.175366e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.186759e+02\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -2316,17 +2316,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.454852948136E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 6.836680918650E+03 kT\n Vpmg_energy:  dielEnergy = 3.416367945808E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.212140e-01\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.052730e-01\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 19.3778\n Vpbe_ctor2:  solute dimensions = 19.082 x 18.3114 x 35.7654\n Vpbe_ctor2:  solute charge = 4\n Vpbe_ctor2:  bulk ionic strength = 0.05\n Vpbe_ctor2:  xkappa = 0.0728124\n@@ -2373,149 +2373,149 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0108218 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.382740\n+Vacc_SASA: Time elapsed: 0.376790\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.473260e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.918880e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 6.092400e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.060800e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.347476e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.080722e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.829057e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.530718e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 886073.910303\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.858269e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.550415e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.444647e+05\n Vprtstp: contraction number = 1.444647e+05\n Vnewton: Attempting damping, relres = 0.152834\n Vnewton: Attempting damping, relres = 0.571521\n Vnewton: Damping accepted, relres = 0.152834\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.528340e-01\n Vprtstp: contraction number = 1.528340e-01\n Vnewton: Using errtol_s: 135422.205259\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.052063e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.689865e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.834174e+04\n Vprtstp: contraction number = 2.834174e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.906007e-02\n Vprtstp: contraction number = 1.901414e-01\n Vnewton: Using errtol_s: 25749.370228\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.242469e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.808713e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.624232e+03\n Vprtstp: contraction number = 6.624232e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 6.729649e-03\n Vprtstp: contraction number = 2.315772e-01\n Vnewton: Using errtol_s: 5962.966787\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.445126e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.922778e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.678296e+03\n Vprtstp: contraction number = 1.678296e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.704684e-03\n Vprtstp: contraction number = 2.533095e-01\n Vnewton: Using errtol_s: 1510.476086\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.649103e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.038180e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.484576e+02\n Vprtstp: contraction number = 4.484576e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.555067e-04\n Vprtstp: contraction number = 2.672089e-01\n Vnewton: Using errtol_s: 403.612606\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.830485e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.155128e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.244400e+02\n Vprtstp: contraction number = 1.244400e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.263959e-04\n Vprtstp: contraction number = 2.774841e-01\n Vnewton: Using errtol_s: 111.996087\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.012103e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.269825e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.556127e+01\n Vprtstp: contraction number = 3.556127e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.612018e-05\n Vprtstp: contraction number = 2.857702e-01\n Vnewton: Using errtol_s: 32.005148\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.179668e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.386680e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.042544e+01\n Vprtstp: contraction number = 1.042544e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.058929e-05\n Vprtstp: contraction number = 2.931684e-01\n Vnewton: Using errtol_s: 9.382897\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.356581e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.501195e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.131407e+00\n Vprtstp: contraction number = 3.131407e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.180622e-06\n Vprtstp: contraction number = 3.003620e-01\n Vnewton: Using errtol_s: 2.818266\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.549003e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.624584e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.605131e-01\n Vprtstp: contraction number = 9.605131e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 9.756091e-07\n Vprtstp: contraction number = 3.067353e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.881207e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.897511e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.207769e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.221130e+02\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -2525,15 +2525,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.447897988359E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 8.069186882543E+03 kT\n Vpmg_energy:  dielEnergy = 4.032629667471E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.036630e-01\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.965100e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n@@ -2562,151 +2562,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.415188\n+Vacc_SASA: Time elapsed: 0.366952\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.264344e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.233277e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.328800e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.760100e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.324946e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.472080e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.752104e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.776376e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2425643.021917\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.780601e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.796854e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.395849e+05\n Vprtstp: contraction number = 3.395849e+05\n Vnewton: Attempting damping, relres = 0.271218\n Vnewton: Attempting damping, relres = 0.565917\n Vnewton: Damping accepted, relres = 0.271218\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.712177e-01\n Vprtstp: contraction number = 2.712177e-01\n Vnewton: Using errtol_s: 657877.293778\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.975016e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.918963e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.802706e+04\n Vprtstp: contraction number = 6.802706e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 6.815619e-02\n Vprtstp: contraction number = 2.512970e-01\n Vnewton: Using errtol_s: 165322.578504\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.231690e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.076844e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.706699e+04\n Vprtstp: contraction number = 1.706699e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.896759e-02\n Vprtstp: contraction number = 2.782960e-01\n Vnewton: Using errtol_s: 46008.609864\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.475264e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.229089e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.017255e+03\n Vprtstp: contraction number = 5.017255e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 4.765082e-03\n Vprtstp: contraction number = 2.512223e-01\n Vnewton: Using errtol_s: 11558.387363\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.679836e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.368452e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.518068e+03\n Vprtstp: contraction number = 1.518068e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 8.818480e-04\n Vprtstp: contraction number = 1.850646e-01\n Vnewton: Using errtol_s: 2139.048483\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.875174e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.488530e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.762132e+02\n Vprtstp: contraction number = 3.762132e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.458866e-04\n Vprtstp: contraction number = 1.654328e-01\n Vnewton: Using errtol_s: 353.868838\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.005169e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.621523e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.902937e+01\n Vprtstp: contraction number = 8.902937e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.304341e-05\n Vprtstp: contraction number = 2.265007e-01\n Vnewton: Using errtol_s: 80.151522\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.022839e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.735345e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.527505e+01\n Vprtstp: contraction number = 2.527505e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 9.377960e-06\n Vprtstp: contraction number = 2.838073e-01\n Vnewton: Using errtol_s: 22.747583\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.039519e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.849146e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.628220e+00\n Vprtstp: contraction number = 7.628220e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.830342e-06\n Vprtstp: contraction number = 3.018078e-01\n Vnewton: Using errtol_s: 6.865399\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.059188e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.968779e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.330827e+00\n Vprtstp: contraction number = 2.330827e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 8.648198e-07\n Vprtstp: contraction number = 3.055531e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.002865e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.016968e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.291339e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.301502e+02\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -2716,15 +2716,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.060833611390E+01 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.876241790075E+04 kT\n Vpmg_energy:  dielEnergy = 9.364173698262E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.941500e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.075400e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 20.7943\n Vpbe_ctor2:  solute dimensions = 25.3482 x 27.3592 x 40.136\n Vpbe_ctor2:  solute charge = -18\n@@ -2773,160 +2773,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0855205 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.437772\n+Vacc_SASA: Time elapsed: 0.439798\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.199266e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.131352e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 7.514000e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.815300e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.358210e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.799200e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.078079e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.092175e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2500270.754638\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.079960e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.112936e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.160810e+05\n Vprtstp: contraction number = 4.160810e+05\n Vnewton: Attempting damping, relres = 0.288431\n Vnewton: Attempting damping, relres = 0.577725\n Vnewton: Damping accepted, relres = 0.288431\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.884309e-01\n Vprtstp: contraction number = 2.884309e-01\n Vnewton: Using errtol_s: 721155.339967\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.100923e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.249079e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.034405e+04\n Vprtstp: contraction number = 9.034405e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 7.349134e-02\n Vprtstp: contraction number = 2.547970e-01\n Vnewton: Using errtol_s: 183748.247493\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.126348e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.440279e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.360950e+04\n Vprtstp: contraction number = 2.360950e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 2.053916e-02\n Vprtstp: contraction number = 2.794773e-01\n Vnewton: Using errtol_s: 51353.458771\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.151672e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.594101e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.072490e+03\n Vprtstp: contraction number = 7.072490e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 5.268603e-03\n Vprtstp: contraction number = 2.565150e-01\n Vnewton: Using errtol_s: 13172.933437\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.174627e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.732275e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.172100e+03\n Vprtstp: contraction number = 2.172100e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 1.067554e-03\n Vprtstp: contraction number = 2.026257e-01\n Vnewton: Using errtol_s: 2669.175106\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.194416e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.853343e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.851792e+02\n Vprtstp: contraction number = 5.851792e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.156116e-04\n Vprtstp: contraction number = 2.019677e-01\n Vnewton: Using errtol_s: 539.087280\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.213627e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.992226e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.590368e+02\n Vprtstp: contraction number = 1.590368e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 5.725368e-05\n Vprtstp: contraction number = 2.655409e-01\n Vnewton: Using errtol_s: 143.149712\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.233881e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.100122e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.862838e+01\n Vprtstp: contraction number = 4.862838e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.750434e-05\n Vprtstp: contraction number = 3.057329e-01\n Vnewton: Using errtol_s: 43.765584\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.254827e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.215881e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.560157e+01\n Vprtstp: contraction number = 1.560157e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.615959e-06\n Vprtstp: contraction number = 3.208324e-01\n Vnewton: Using errtol_s: 14.041419\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.275325e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.335451e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.091636e+00\n Vprtstp: contraction number = 5.091636e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.832791e-06\n Vprtstp: contraction number = 3.263540e-01\n Vnewton: Using errtol_s: 4.582473\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.294847e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.479403e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.679382e+00\n Vprtstp: contraction number = 1.679382e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 6.045119e-07\n Vprtstp: contraction number = 3.298314e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.335475e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.348042e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.497054e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.508812e+02\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -2936,29 +2936,29 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.058843361489E+01 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.137979732190E+04 kT\n Vpmg_energy:  dielEnergy = 1.067286106944E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.657840e-01\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.597000e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.313197e+03\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 8.605478e+02\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 06:54:08 2025\n+# Creation Date and Time:  Tue Jan  9 04:58:11 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path model_outNB.pqr\n@@ -3228,151 +3228,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.592413\n+Vacc_SASA: Time elapsed: 0.596033\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.683325e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.550851e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.489600e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.822300e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.173509e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.652190e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.047658e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.678958e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2729151.378915\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.871288e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.642716e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.548080e+05\n Vprtstp: contraction number = 3.548080e+05\n Vnewton: Attempting damping, relres = 0.149964\n Vnewton: Attempting damping, relres = 0.557619\n Vnewton: Damping accepted, relres = 0.149964\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.499638e-01\n Vprtstp: contraction number = 1.499638e-01\n Vnewton: Using errtol_s: 409273.850655\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.042687e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.986442e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.220624e+04\n Vprtstp: contraction number = 6.220624e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.835999e-02\n Vprtstp: contraction number = 1.891123e-01\n Vnewton: Using errtol_s: 77398.710345\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.553283e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.615257e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.402989e+04\n Vprtstp: contraction number = 1.402989e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 6.278471e-03\n Vprtstp: contraction number = 2.213848e-01\n Vnewton: Using errtol_s: 17134.898633\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.027011e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.489232e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.695573e+03\n Vprtstp: contraction number = 3.695573e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.396538e-03\n Vprtstp: contraction number = 2.224328e-01\n Vnewton: Using errtol_s: 3811.362986\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.059234e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.995521e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.003191e+03\n Vprtstp: contraction number = 1.003191e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.340894e-04\n Vprtstp: contraction number = 2.392269e-01\n Vnewton: Using errtol_s: 911.780505\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.281660e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.503269e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.777519e+02\n Vprtstp: contraction number = 2.777519e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 9.159963e-05\n Vprtstp: contraction number = 2.741770e-01\n Vnewton: Using errtol_s: 249.989261\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.480822e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.030925e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.121282e+01\n Vprtstp: contraction number = 8.121282e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.678181e-05\n Vprtstp: contraction number = 2.923790e-01\n Vnewton: Using errtol_s: 73.091601\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.721983e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.191881e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.430204e+01\n Vprtstp: contraction number = 2.430204e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.014155e-06\n Vprtstp: contraction number = 2.992388e-01\n Vnewton: Using errtol_s: 21.871842\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.965778e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.366580e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.369042e+00\n Vprtstp: contraction number = 7.369042e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.430110e-06\n Vprtstp: contraction number = 3.032272e-01\n Vnewton: Using errtol_s: 6.632138\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.205529e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.541306e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.256893e+00\n Vprtstp: contraction number = 2.256893e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 7.442621e-07\n Vprtstp: contraction number = 3.062668e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.393668e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.406980e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.677224e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.688141e+02\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -3382,17 +3382,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 7.061471335399E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.568309380303E+04 kT\n Vpmg_energy:  dielEnergy = 1.283186160859E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.083790e-01\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.339700e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 25.8477\n Vpbe_ctor2:  solute dimensions = 26.666 x 32.3234 x 48.3902\n Vpbe_ctor2:  solute charge = -14\n Vpbe_ctor2:  bulk ionic strength = 0.075\n Vpbe_ctor2:  xkappa = 0.0891766\n@@ -3439,160 +3439,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0651756 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.587191\n+Vacc_SASA: Time elapsed: 0.565886\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.640358e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.579532e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.817100e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.905300e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.536154e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 8.925530e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.459327e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.731940e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2820294.276955\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.489561e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.752710e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.376310e+05\n Vprtstp: contraction number = 4.376310e+05\n Vnewton: Attempting damping, relres = 0.171074\n Vnewton: Attempting damping, relres = 0.569073\n Vnewton: Damping accepted, relres = 0.171074\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.710740e-01\n Vprtstp: contraction number = 1.710740e-01\n Vnewton: Using errtol_s: 482478.932943\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.712974e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.928616e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.516733e+04\n Vprtstp: contraction number = 8.516733e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 3.468956e-02\n Vprtstp: contraction number = 2.027752e-01\n Vnewton: Using errtol_s: 97834.754534\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.911137e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.111172e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.072493e+04\n Vprtstp: contraction number = 2.072493e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 8.178682e-03\n Vprtstp: contraction number = 2.357678e-01\n Vnewton: Using errtol_s: 23066.288642\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.155294e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.265209e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.715545e+03\n Vprtstp: contraction number = 5.715545e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.982874e-03\n Vprtstp: contraction number = 2.424442e-01\n Vnewton: Using errtol_s: 5592.288694\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.405594e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.422641e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.627358e+03\n Vprtstp: contraction number = 1.627358e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.213861e-04\n Vprtstp: contraction number = 2.629446e-01\n Vnewton: Using errtol_s: 1470.462342\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.627741e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.590538e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.759299e+02\n Vprtstp: contraction number = 4.759299e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.518795e-04\n Vprtstp: contraction number = 2.912995e-01\n Vnewton: Using errtol_s: 428.344902\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.863441e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.749506e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.460718e+02\n Vprtstp: contraction number = 1.460718e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.661385e-05\n Vprtstp: contraction number = 3.069133e-01\n Vnewton: Using errtol_s: 131.464764\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.063041e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.901586e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.608450e+01\n Vprtstp: contraction number = 4.608450e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.470629e-05\n Vprtstp: contraction number = 3.154918e-01\n Vnewton: Using errtol_s: 41.476059\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.272645e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.052267e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.483594e+01\n Vprtstp: contraction number = 1.483594e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 4.734380e-06\n Vprtstp: contraction number = 3.219290e-01\n Vnewton: Using errtol_s: 13.352345\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.477370e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.190703e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.855098e+00\n Vprtstp: contraction number = 4.855098e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.549338e-06\n Vprtstp: contraction number = 3.272525e-01\n Vnewton: Using errtol_s: 4.369588\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.684375e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.342555e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.609852e+00\n Vprtstp: contraction number = 1.609852e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 5.137291e-07\n Vprtstp: contraction number = 3.315798e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.422620e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.439357e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.771812e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.782488e+02\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -3602,17 +3602,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 7.043656925356E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.952923600964E+04 kT\n Vpmg_energy:  dielEnergy = 1.475493408028E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.455320e-01\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.540220e-01\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vnm_tstart: starting timer 27 (Setup timer)..\n@@ -3639,151 +3639,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.365132\n+Vacc_SASA: Time elapsed: 0.360604\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.782640e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.083380e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.356400e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.712200e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.238289e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 8.960610e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.924101e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.538353e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 782805.209515\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.950304e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.558640e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.066964e+05\n Vprtstp: contraction number = 1.066964e+05\n Vnewton: Attempting damping, relres = 0.130466\n Vnewton: Attempting damping, relres = 0.559276\n Vnewton: Damping accepted, relres = 0.130466\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.304657e-01\n Vprtstp: contraction number = 1.304657e-01\n Vnewton: Using errtol_s: 102129.196068\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.124876e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.684735e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.906966e+04\n Vprtstp: contraction number = 1.906966e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.228836e-02\n Vprtstp: contraction number = 1.708370e-01\n Vnewton: Using errtol_s: 17447.447142\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.285690e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.795523e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.144180e+03\n Vprtstp: contraction number = 4.144180e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 4.766221e-03\n Vprtstp: contraction number = 2.138435e-01\n Vnewton: Using errtol_s: 3731.022666\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.453047e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.905042e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.018149e+03\n Vprtstp: contraction number = 1.018149e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.170583e-03\n Vprtstp: contraction number = 2.455999e-01\n Vnewton: Using errtol_s: 916.338711\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.619728e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.012133e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.682787e+02\n Vprtstp: contraction number = 2.682787e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.084434e-04\n Vprtstp: contraction number = 2.634955e-01\n Vnewton: Using errtol_s: 241.451081\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.796255e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.130399e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.355327e+01\n Vprtstp: contraction number = 7.355327e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 8.456504e-05\n Vprtstp: contraction number = 2.741672e-01\n Vnewton: Using errtol_s: 66.197957\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.969222e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.242394e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.070399e+01\n Vprtstp: contraction number = 2.070399e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.380361e-05\n Vprtstp: contraction number = 2.814829e-01\n Vnewton: Using errtol_s: 18.633591\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.131327e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.349696e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.943814e+00\n Vprtstp: contraction number = 5.943814e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 6.833671e-06\n Vprtstp: contraction number = 2.870855e-01\n Vnewton: Using errtol_s: 5.349433\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.297612e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.467201e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.733432e+00\n Vprtstp: contraction number = 1.733432e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 1.992946e-06\n Vprtstp: contraction number = 2.916363e-01\n Vnewton: Using errtol_s: 1.560089\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.470649e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.573322e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.119221e-01\n Vprtstp: contraction number = 5.119221e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 5.885626e-07\n Vprtstp: contraction number = 2.953228e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.710386e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.724765e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.133010e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.143966e+02\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -3793,15 +3793,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.580382874271E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 6.835549724492E+03 kT\n Vpmg_energy:  dielEnergy = 3.415749841387E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.925000e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.040100e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 19.3778\n Vpbe_ctor2:  solute dimensions = 19.082 x 18.3114 x 35.7654\n Vpbe_ctor2:  solute charge = 4\n@@ -3850,160 +3850,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00827481 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.347604\n+Vacc_SASA: Time elapsed: 0.375670\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.551190e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.203390e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 6.761200e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.860900e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.262441e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.776280e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.660816e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.694452e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 817942.139336\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.689663e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.712642e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.333917e+05\n Vprtstp: contraction number = 1.333917e+05\n Vnewton: Attempting damping, relres = 0.153834\n Vnewton: Attempting damping, relres = 0.571434\n Vnewton: Damping accepted, relres = 0.153834\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.538338e-01\n Vprtstp: contraction number = 1.538338e-01\n Vnewton: Using errtol_s: 125827.150717\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.895553e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.834974e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.649228e+04\n Vprtstp: contraction number = 2.649228e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.948474e-02\n Vprtstp: contraction number = 1.916662e-01\n Vnewton: Using errtol_s: 24116.815003\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.082843e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.949313e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.270875e+03\n Vprtstp: contraction number = 6.270875e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 6.901762e-03\n Vprtstp: contraction number = 2.340791e-01\n Vnewton: Using errtol_s: 5645.242129\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.254710e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.085528e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.605106e+03\n Vprtstp: contraction number = 1.605106e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.766147e-03\n Vprtstp: contraction number = 2.558981e-01\n Vnewton: Using errtol_s: 1444.606457\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.436693e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.197530e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.329441e+02\n Vprtstp: contraction number = 4.329441e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.763791e-04\n Vprtstp: contraction number = 2.697278e-01\n Vnewton: Using errtol_s: 389.650539\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.618263e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.321371e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.211228e+02\n Vprtstp: contraction number = 1.211228e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.332742e-04\n Vprtstp: contraction number = 2.797649e-01\n Vnewton: Using errtol_s: 109.010550\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.803234e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.439029e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.484891e+01\n Vprtstp: contraction number = 3.484891e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.834504e-05\n Vprtstp: contraction number = 2.877155e-01\n Vnewton: Using errtol_s: 31.364026\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.978383e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.569664e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.027201e+01\n Vprtstp: contraction number = 1.027201e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.130252e-05\n Vprtstp: contraction number = 2.947583e-01\n Vnewton: Using errtol_s: 9.244807\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.156904e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.699180e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.098070e+00\n Vprtstp: contraction number = 3.098070e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.408876e-06\n Vprtstp: contraction number = 3.016032e-01\n Vnewton: Using errtol_s: 2.788263\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.345065e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.849332e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.532281e-01\n Vprtstp: contraction number = 9.532281e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.048858e-06\n Vprtstp: contraction number = 3.076845e-01\n Vnewton: Using errtol_s: 0.857905\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.525676e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.989352e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.981595e-01\n Vprtstp: contraction number = 2.981595e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.280716e-07\n Vprtstp: contraction number = 3.127892e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.030991e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.046328e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.412868e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.424919e+02\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -4013,17 +4013,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.573110826930E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 8.068060919052E+03 kT\n Vpmg_energy:  dielEnergy = 4.032015460715E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.075600e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.066600e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vnm_tstart: starting timer 27 (Setup timer)..\n@@ -4050,151 +4050,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.440861\n+Vacc_SASA: Time elapsed: 0.373931\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.331892e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.240166e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.862400e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.065500e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.234282e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.079112e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.734045e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.146574e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2117741.361264\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.759082e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.167086e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.981667e+05\n Vprtstp: contraction number = 2.981667e+05\n Vnewton: Attempting damping, relres = 0.251946\n Vnewton: Attempting damping, relres = 0.566227\n Vnewton: Damping accepted, relres = 0.251946\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.519462e-01\n Vprtstp: contraction number = 2.519462e-01\n Vnewton: Using errtol_s: 533556.965989\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.901895e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.292267e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.927315e+04\n Vprtstp: contraction number = 5.927315e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 6.069562e-02\n Vprtstp: contraction number = 2.409070e-01\n Vnewton: Using errtol_s: 128537.620946\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.102838e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.460821e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.480174e+04\n Vprtstp: contraction number = 1.480174e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.600227e-02\n Vprtstp: contraction number = 2.636478e-01\n Vnewton: Using errtol_s: 33888.662126\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.283950e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.624497e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.318636e+03\n Vprtstp: contraction number = 4.318636e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 3.683613e-03\n Vprtstp: contraction number = 2.301932e-01\n Vnewton: Using errtol_s: 7800.938716\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.431273e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.754958e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.240563e+03\n Vprtstp: contraction number = 1.240563e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 6.541706e-04\n Vprtstp: contraction number = 1.775894e-01\n Vnewton: Using errtol_s: 1385.364119\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.574120e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.882267e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.070828e+02\n Vprtstp: contraction number = 3.070828e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.315622e-04\n Vprtstp: contraction number = 2.011130e-01\n Vnewton: Using errtol_s: 278.614703\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.712284e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.005558e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.245841e+01\n Vprtstp: contraction number = 8.245841e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.504428e-05\n Vprtstp: contraction number = 2.663704e-01\n Vnewton: Using errtol_s: 74.214712\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.838700e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.124435e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.449789e+01\n Vprtstp: contraction number = 2.449789e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.041114e-05\n Vprtstp: contraction number = 2.970854e-01\n Vnewton: Using errtol_s: 22.048109\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.967147e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.250654e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.450269e+00\n Vprtstp: contraction number = 7.450269e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.166223e-06\n Vprtstp: contraction number = 3.041187e-01\n Vnewton: Using errtol_s: 6.705242\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.011067e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.377482e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.280137e+00\n Vprtstp: contraction number = 2.280137e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 9.690153e-07\n Vprtstp: contraction number = 3.060477e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.505500e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.518674e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.337854e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.349384e+02\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -4204,15 +4204,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.019051099333E+01 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.875636108518E+04 kT\n Vpmg_energy:  dielEnergy = 9.362891956470E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 8.102300e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.726500e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 20.7943\n Vpbe_ctor2:  solute dimensions = 25.3482 x 27.3592 x 40.136\n Vpbe_ctor2:  solute charge = -18\n@@ -4261,160 +4261,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0483679 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.429582\n+Vacc_SASA: Time elapsed: 0.400113\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.326833e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.137935e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.367900e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.815700e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.141712e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.054583e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.026673e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.510059e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2182522.884057\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.029442e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.531059e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.686053e+05\n Vprtstp: contraction number = 3.686053e+05\n Vnewton: Attempting damping, relres = 0.272056\n Vnewton: Attempting damping, relres = 0.578831\n Vnewton: Damping accepted, relres = 0.272056\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.720560e-01\n Vprtstp: contraction number = 2.720560e-01\n Vnewton: Using errtol_s: 593768.373592\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.043730e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.675298e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.934239e+04\n Vprtstp: contraction number = 7.934239e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 6.680635e-02\n Vprtstp: contraction number = 2.455611e-01\n Vnewton: Using errtol_s: 145806.393631\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.061973e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.854296e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.075932e+04\n Vprtstp: contraction number = 2.075932e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.784022e-02\n Vprtstp: contraction number = 2.670438e-01\n Vnewton: Using errtol_s: 38936.692163\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.079864e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.040283e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.202423e+03\n Vprtstp: contraction number = 6.202423e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 4.287010e-03\n Vprtstp: contraction number = 2.403003e-01\n Vnewton: Using errtol_s: 9356.498262\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.095149e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.176078e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.844032e+03\n Vprtstp: contraction number = 1.844032e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 8.713644e-04\n Vprtstp: contraction number = 2.032569e-01\n Vnewton: Using errtol_s: 1901.772758\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.110207e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.296886e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.035865e+02\n Vprtstp: contraction number = 5.035865e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.084187e-04\n Vprtstp: contraction number = 2.391867e-01\n Vnewton: Using errtol_s: 454.878668\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.124187e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.427647e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.482404e+02\n Vprtstp: contraction number = 1.482404e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 6.113004e-05\n Vprtstp: contraction number = 2.933039e-01\n Vnewton: Using errtol_s: 133.417702\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.138835e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.554177e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.685160e+01\n Vprtstp: contraction number = 4.685160e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.932006e-05\n Vprtstp: contraction number = 3.160485e-01\n Vnewton: Using errtol_s: 42.166463\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.154178e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.671395e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.516259e+01\n Vprtstp: contraction number = 1.516259e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 6.252549e-06\n Vprtstp: contraction number = 3.236300e-01\n Vnewton: Using errtol_s: 13.646331\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.170541e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.791114e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.968000e+00\n Vprtstp: contraction number = 4.968000e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 2.048639e-06\n Vprtstp: contraction number = 3.276485e-01\n Vnewton: Using errtol_s: 4.471200\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.186348e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.911990e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.642278e+00\n Vprtstp: contraction number = 1.642278e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 6.772208e-07\n Vprtstp: contraction number = 3.305711e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.743709e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.756120e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.506541e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.519284e+02\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -4424,29 +4424,29 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.017305990862E+01 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.137374131733E+04 kT\n Vpmg_energy:  dielEnergy = 1.067158704261E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.676400e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.636100e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.202858e+03\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 9.032803e+02\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 06:56:19 2025\n+# Creation Date and Time:  Tue Jan  9 05:01:00 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path model_outNB.pqr\n@@ -4716,151 +4716,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.644661\n+Vacc_SASA: Time elapsed: 0.588391\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.664150e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.624759e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.434900e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.918400e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.198324e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.434310e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.101279e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.719086e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2581577.235420\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.761272e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.702835e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.353899e+05\n Vprtstp: contraction number = 3.353899e+05\n Vnewton: Attempting damping, relres = 0.146634\n Vnewton: Attempting damping, relres = 0.557407\n Vnewton: Damping accepted, relres = 0.146634\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.466339e-01\n Vprtstp: contraction number = 1.466339e-01\n Vnewton: Using errtol_s: 378546.858038\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.373989e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.999423e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.923639e+04\n Vprtstp: contraction number = 5.923639e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.740677e-02\n Vprtstp: contraction number = 1.869061e-01\n Vnewton: Using errtol_s: 70752.704235\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.217567e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.536797e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.351296e+04\n Vprtstp: contraction number = 1.351296e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 6.004523e-03\n Vprtstp: contraction number = 2.190890e-01\n Vnewton: Using errtol_s: 15501.138648\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.945806e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.049256e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.562530e+03\n Vprtstp: contraction number = 3.562530e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.351206e-03\n Vprtstp: contraction number = 2.250314e-01\n Vnewton: Using errtol_s: 3488.243698\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.674207e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.521783e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.669348e+02\n Vprtstp: contraction number = 9.669348e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.383252e-04\n Vprtstp: contraction number = 2.503875e-01\n Vnewton: Using errtol_s: 873.412615\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.340079e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.307879e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.719290e+02\n Vprtstp: contraction number = 2.719290e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 9.480245e-05\n Vprtstp: contraction number = 2.802110e-01\n Vnewton: Using errtol_s: 244.739841\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.112740e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.009859e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.995844e+01\n Vprtstp: contraction number = 7.995844e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.787545e-05\n Vprtstp: contraction number = 2.940373e-01\n Vnewton: Using errtol_s: 71.962638\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.292937e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.175314e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.395977e+01\n Vprtstp: contraction number = 2.395977e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.352954e-06\n Vprtstp: contraction number = 2.996527e-01\n Vnewton: Using errtol_s: 21.563797\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.471553e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.331207e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.269734e+00\n Vprtstp: contraction number = 7.269734e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.534405e-06\n Vprtstp: contraction number = 3.034141e-01\n Vnewton: Using errtol_s: 6.542761\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.666707e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.473718e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.227052e+00\n Vprtstp: contraction number = 2.227052e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 7.764038e-07\n Vprtstp: contraction number = 3.063457e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.774308e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.788269e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.579395e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.589972e+02\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -4870,17 +4870,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 6.906130010441E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.568022982352E+04 kT\n Vpmg_energy:  dielEnergy = 1.283111172254E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.599600e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.286500e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 25.8477\n Vpbe_ctor2:  solute dimensions = 26.666 x 32.3234 x 48.3902\n Vpbe_ctor2:  solute charge = -14\n Vpbe_ctor2:  bulk ionic strength = 0.1\n Vpbe_ctor2:  xkappa = 0.102972\n@@ -4927,160 +4927,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.046103 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.505630\n+Vacc_SASA: Time elapsed: 0.581174\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.661716e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.683950e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.308900e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.094900e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.641916e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.087257e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.841801e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.637292e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2663765.095172\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.874047e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.661040e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.151111e+05\n Vprtstp: contraction number = 4.151111e+05\n Vnewton: Attempting damping, relres = 0.168665\n Vnewton: Attempting damping, relres = 0.569219\n Vnewton: Damping accepted, relres = 0.168665\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.686646e-01\n Vprtstp: contraction number = 1.686646e-01\n Vnewton: Using errtol_s: 449282.900987\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.081644e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.835212e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.120110e+04\n Vprtstp: contraction number = 8.120110e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 3.393027e-02\n Vprtstp: contraction number = 2.011700e-01\n Vnewton: Using errtol_s: 90382.255629\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.274846e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.999018e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.991839e+04\n Vprtstp: contraction number = 1.991839e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.954387e-03\n Vprtstp: contraction number = 2.344334e-01\n Vnewton: Using errtol_s: 21188.618171\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.470745e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.163331e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.497898e+03\n Vprtstp: contraction number = 5.497898e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.952447e-03\n Vprtstp: contraction number = 2.454554e-01\n Vnewton: Using errtol_s: 5200.860154\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.660566e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.313413e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.566684e+03\n Vprtstp: contraction number = 1.566684e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.300165e-04\n Vprtstp: contraction number = 2.714627e-01\n Vnewton: Using errtol_s: 1411.839327\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.867776e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.462961e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.634720e+02\n Vprtstp: contraction number = 4.634720e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.565934e-04\n Vprtstp: contraction number = 2.954500e-01\n Vnewton: Using errtol_s: 417.127917\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.059508e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.608130e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.430369e+02\n Vprtstp: contraction number = 1.430369e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.832756e-05\n Vprtstp: contraction number = 3.086182e-01\n Vnewton: Using errtol_s: 128.733272\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.259440e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.789022e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.523062e+01\n Vprtstp: contraction number = 4.523062e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.528197e-05\n Vprtstp: contraction number = 3.162164e-01\n Vnewton: Using errtol_s: 40.707568\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.460341e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.936374e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.458043e+01\n Vprtstp: contraction number = 1.458043e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 4.926255e-06\n Vprtstp: contraction number = 3.223574e-01\n Vnewton: Using errtol_s: 13.122387\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.671788e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.071599e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.774711e+00\n Vprtstp: contraction number = 4.774711e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.613220e-06\n Vprtstp: contraction number = 3.274740e-01\n Vnewton: Using errtol_s: 4.297240\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.861729e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.237037e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.583552e+00\n Vprtstp: contraction number = 1.583552e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 5.350309e-07\n Vprtstp: contraction number = 3.316539e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.203699e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.221562e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.734026e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.746038e+02\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -5090,15 +5090,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 6.889253587078E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.952637303887E+04 kT\n Vpmg_energy:  dielEnergy = 1.475418891145E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.326540e-01\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.304900e-01\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n@@ -5127,151 +5127,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.369506\n+Vacc_SASA: Time elapsed: 0.366865\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.071215e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.334200e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.254200e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.919200e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.450950e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.804490e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.085193e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.407754e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 745120.170523\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.107455e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.427007e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.014015e+05\n Vprtstp: contraction number = 1.014015e+05\n Vnewton: Attempting damping, relres = 0.130811\n Vnewton: Attempting damping, relres = 0.559104\n Vnewton: Damping accepted, relres = 0.130811\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.308109e-01\n Vprtstp: contraction number = 1.308109e-01\n Vnewton: Using errtol_s: 97469.809951\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.262875e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.547255e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.835986e+04\n Vprtstp: contraction number = 1.835986e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.256558e-02\n Vprtstp: contraction number = 1.725054e-01\n Vnewton: Using errtol_s: 16814.071331\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.403858e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.680293e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.045264e+03\n Vprtstp: contraction number = 4.045264e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 4.887910e-03\n Vprtstp: contraction number = 2.166091e-01\n Vnewton: Using errtol_s: 3642.080543\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.546017e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.800580e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.003527e+03\n Vprtstp: contraction number = 1.003527e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.212126e-03\n Vprtstp: contraction number = 2.479845e-01\n Vnewton: Using errtol_s: 903.179662\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.695116e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.909516e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.660395e+02\n Vprtstp: contraction number = 2.660395e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.213385e-04\n Vprtstp: contraction number = 2.651031e-01\n Vnewton: Using errtol_s: 239.435768\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.852056e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.018215e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.320387e+01\n Vprtstp: contraction number = 7.320387e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 8.841996e-05\n Vprtstp: contraction number = 2.751615e-01\n Vnewton: Using errtol_s: 65.883497\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.014111e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.123322e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.064818e+01\n Vprtstp: contraction number = 2.064818e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.494009e-05\n Vprtstp: contraction number = 2.820641e-01\n Vnewton: Using errtol_s: 18.583367\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.170653e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.224579e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.934502e+00\n Vprtstp: contraction number = 5.934502e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 7.168040e-06\n Vprtstp: contraction number = 2.874103e-01\n Vnewton: Using errtol_s: 5.341051\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.326582e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.330500e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.731750e+00\n Vprtstp: contraction number = 1.731750e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.091710e-06\n Vprtstp: contraction number = 2.918105e-01\n Vnewton: Using errtol_s: 1.558575\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.491114e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.433463e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.115793e-01\n Vprtstp: contraction number = 5.115793e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 6.179156e-07\n Vprtstp: contraction number = 2.954117e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.546707e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.557488e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.116566e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.127758e+02\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -5281,15 +5281,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.655453691226E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 6.834706672328E+03 kT\n Vpmg_energy:  dielEnergy = 3.415300525959E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.828000e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.612100e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 19.3778\n Vpbe_ctor2:  solute dimensions = 19.082 x 18.3114 x 35.7654\n Vpbe_ctor2:  solute charge = 4\n@@ -5338,160 +5338,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00688905 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.345113\n+Vacc_SASA: Time elapsed: 0.384736\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.598060e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.902170e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.561300e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 6.758500e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.117577e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.054880e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.655862e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.548001e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 777935.905465\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.679633e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.566978e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.267239e+05\n Vprtstp: contraction number = 1.267239e+05\n Vnewton: Attempting damping, relres = 0.154165\n Vnewton: Attempting damping, relres = 0.571273\n Vnewton: Damping accepted, relres = 0.154165\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.541646e-01\n Vprtstp: contraction number = 1.541646e-01\n Vnewton: Using errtol_s: 119930.213668\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.843156e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.695047e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.535999e+04\n Vprtstp: contraction number = 2.535999e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.969700e-02\n Vprtstp: contraction number = 1.926317e-01\n Vnewton: Using errtol_s: 23102.366146\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.009145e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.803601e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.051917e+03\n Vprtstp: contraction number = 6.051917e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.003479e-03\n Vprtstp: contraction number = 2.358312e-01\n Vnewton: Using errtol_s: 5448.257890\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.190273e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.915758e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.559687e+03\n Vprtstp: contraction number = 1.559687e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.804429e-03\n Vprtstp: contraction number = 2.576475e-01\n Vnewton: Using errtol_s: 1403.729913\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.360460e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.029485e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.232949e+02\n Vprtstp: contraction number = 4.232949e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.897143e-04\n Vprtstp: contraction number = 2.713957e-01\n Vnewton: Using errtol_s: 380.966319\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.531259e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.140156e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.190545e+02\n Vprtstp: contraction number = 1.190545e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.377351e-04\n Vprtstp: contraction number = 2.812561e-01\n Vnewton: Using errtol_s: 107.149093\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.698919e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.253260e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.440341e+01\n Vprtstp: contraction number = 3.440341e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.980158e-05\n Vprtstp: contraction number = 2.889719e-01\n Vnewton: Using errtol_s: 30.963075\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.865863e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.394128e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.017569e+01\n Vprtstp: contraction number = 1.017569e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.177234e-05\n Vprtstp: contraction number = 2.957757e-01\n Vnewton: Using errtol_s: 9.158125\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.040305e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.544730e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.077041e+00\n Vprtstp: contraction number = 3.077041e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.559852e-06\n Vprtstp: contraction number = 3.023913e-01\n Vnewton: Using errtol_s: 2.769337\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.214262e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.663911e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.486014e-01\n Vprtstp: contraction number = 9.486014e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.097444e-06\n Vprtstp: contraction number = 3.082837e-01\n Vnewton: Using errtol_s: 0.853741\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.380857e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.781417e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.971293e-01\n Vprtstp: contraction number = 2.971293e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.437512e-07\n Vprtstp: contraction number = 3.132288e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.893918e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.907201e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.339797e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.353049e+02\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -5501,15 +5501,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.647978359783E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 8.067221403363E+03 kT\n Vpmg_energy:  dielEnergy = 4.031568484712E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.079370e-01\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.603100e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n@@ -5538,162 +5538,162 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.448434\n+Vacc_SASA: Time elapsed: 0.384957\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.288565e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.179121e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.677700e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.959700e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.335430e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.606950e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.592210e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.925503e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1939359.308692\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.622414e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.944289e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.739516e+05\n Vprtstp: contraction number = 2.739516e+05\n Vnewton: Attempting damping, relres = 0.235690\n Vnewton: Attempting damping, relres = 0.566181\n Vnewton: Damping accepted, relres = 0.235690\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.356901e-01\n Vprtstp: contraction number = 2.356901e-01\n Vnewton: Using errtol_s: 457087.767732\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.819423e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.068775e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.385706e+04\n Vprtstp: contraction number = 5.385706e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 5.455782e-02\n Vprtstp: contraction number = 2.314812e-01\n Vnewton: Using errtol_s: 105807.213748\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.073729e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.222526e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.345524e+04\n Vprtstp: contraction number = 1.345524e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.370821e-02\n Vprtstp: contraction number = 2.512602e-01\n Vnewton: Using errtol_s: 26585.137711\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.307018e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.355782e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.888746e+03\n Vprtstp: contraction number = 3.888746e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.963355e-03\n Vprtstp: contraction number = 2.161738e-01\n Vnewton: Using errtol_s: 5747.009743\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.508171e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.469104e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.082322e+03\n Vprtstp: contraction number = 1.082322e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.510650e-04\n Vprtstp: contraction number = 1.859598e-01\n Vnewton: Using errtol_s: 1068.713018\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.694702e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.578303e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.783449e+02\n Vprtstp: contraction number = 2.783449e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.293604e-04\n Vprtstp: contraction number = 2.347461e-01\n Vnewton: Using errtol_s: 250.876218\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.883085e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.705563e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.935007e+01\n Vprtstp: contraction number = 7.935007e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.682419e-05\n Vprtstp: contraction number = 2.846636e-01\n Vnewton: Using errtol_s: 71.415338\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.074016e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.810948e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.391930e+01\n Vprtstp: contraction number = 2.391930e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.110025e-05\n Vprtstp: contraction number = 3.014391e-01\n Vnewton: Using errtol_s: 21.527377\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.256234e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.921913e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.292472e+00\n Vprtstp: contraction number = 7.292472e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.384223e-06\n Vprtstp: contraction number = 3.048781e-01\n Vnewton: Using errtol_s: 6.563225\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.438783e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.034658e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.233482e+00\n Vprtstp: contraction number = 2.233482e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.036494e-06\n Vprtstp: contraction number = 3.062723e-01\n Vnewton: Using errtol_s: 2.010134\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.629138e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.150142e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.858053e-01\n Vprtstp: contraction number = 6.858053e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.182622e-07\n Vprtstp: contraction number = 3.070566e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.201915e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.216572e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.338225e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.349204e+02\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -5703,17 +5703,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 9.820035378222E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.875217906563E+04 kT\n Vpmg_energy:  dielEnergy = 9.361966912953E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.664000e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 9.732400e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 20.7943\n Vpbe_ctor2:  solute dimensions = 25.3482 x 27.3592 x 40.136\n Vpbe_ctor2:  solute charge = -18\n Vpbe_ctor2:  bulk ionic strength = 0.1\n Vpbe_ctor2:  xkappa = 0.102972\n@@ -5760,160 +5760,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0305183 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.255723\n+Vacc_SASA: Time elapsed: 0.456816\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.381488e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.213805e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.486300e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.814900e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.308610e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.000935e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.823337e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.290003e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1996023.779999\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.854379e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.307285e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.403294e+05\n Vprtstp: contraction number = 3.403294e+05\n Vnewton: Attempting damping, relres = 0.257870\n Vnewton: Attempting damping, relres = 0.579346\n Vnewton: Damping accepted, relres = 0.257870\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.578703e-01\n Vprtstp: contraction number = 2.578703e-01\n Vnewton: Using errtol_s: 514715.207917\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.005635e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.435987e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.253173e+04\n Vprtstp: contraction number = 7.253173e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 6.121431e-02\n Vprtstp: contraction number = 2.373841e-01\n Vnewton: Using errtol_s: 122185.216313\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.030589e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.593836e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.904030e+04\n Vprtstp: contraction number = 1.904030e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.572892e-02\n Vprtstp: contraction number = 2.569484e-01\n Vnewton: Using errtol_s: 31395.299569\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.054124e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.739987e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.659593e+03\n Vprtstp: contraction number = 5.659593e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 3.629998e-03\n Vprtstp: contraction number = 2.307850e-01\n Vnewton: Using errtol_s: 7245.562904\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.075664e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.861345e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.651310e+03\n Vprtstp: contraction number = 1.651310e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 7.856291e-04\n Vprtstp: contraction number = 2.164268e-01\n Vnewton: Using errtol_s: 1568.134340\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.093757e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.985722e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.661219e+02\n Vprtstp: contraction number = 4.661219e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.102913e-04\n Vprtstp: contraction number = 2.676725e-01\n Vnewton: Using errtol_s: 419.746448\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.113352e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.103468e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.425822e+02\n Vprtstp: contraction number = 1.425822e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 6.428993e-05\n Vprtstp: contraction number = 3.057184e-01\n Vnewton: Using errtol_s: 128.324228\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.132362e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.221144e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.557507e+01\n Vprtstp: contraction number = 4.557507e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.054964e-05\n Vprtstp: contraction number = 3.196401e-01\n Vnewton: Using errtol_s: 41.017570\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.150969e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.333600e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.480670e+01\n Vprtstp: contraction number = 1.480670e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 6.676290e-06\n Vprtstp: contraction number = 3.248860e-01\n Vnewton: Using errtol_s: 13.326033\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.169774e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.450406e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.862220e+00\n Vprtstp: contraction number = 4.862220e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 2.192358e-06\n Vprtstp: contraction number = 3.283797e-01\n Vnewton: Using errtol_s: 4.375998\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.189150e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.572109e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.609470e+00\n Vprtstp: contraction number = 1.609470e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 7.257041e-07\n Vprtstp: contraction number = 3.310154e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.250401e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.265141e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.394304e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.406401e+02\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -5923,29 +5923,29 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 9.804365657787E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.136955879048E+04 kT\n Vpmg_energy:  dielEnergy = 1.067066513912E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 9.791100e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.519560e-01\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.209196e+03\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 8.698813e+02\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 06:58:28 2025\n+# Creation Date and Time:  Tue Jan  9 05:03:30 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path model_outNB.pqr\n@@ -6215,151 +6215,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.600829\n+Vacc_SASA: Time elapsed: 0.580110\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.671802e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.581675e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.809500e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.854300e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.256599e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.478640e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.104558e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.687358e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2482316.849131\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.070624e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.712533e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.222887e+05\n Vprtstp: contraction number = 3.222887e+05\n Vnewton: Attempting damping, relres = 0.143642\n Vnewton: Attempting damping, relres = 0.557204\n Vnewton: Damping accepted, relres = 0.143642\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.436423e-01\n Vprtstp: contraction number = 1.436423e-01\n Vnewton: Using errtol_s: 356565.753990\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.959093e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.069032e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.719340e+04\n Vprtstp: contraction number = 5.719340e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.655317e-02\n Vprtstp: contraction number = 1.848561e-01\n Vnewton: Using errtol_s: 65913.370564\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.547388e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.641471e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.314754e+04\n Vprtstp: contraction number = 1.314754e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 5.777425e-03\n Vprtstp: contraction number = 2.175795e-01\n Vnewton: Using errtol_s: 14341.400512\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.000249e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.146373e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.464763e+03\n Vprtstp: contraction number = 3.464763e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.322569e-03\n Vprtstp: contraction number = 2.289202e-01\n Vnewton: Using errtol_s: 3283.035896\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.015999e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.623720e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.430238e+02\n Vprtstp: contraction number = 9.430238e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.423711e-04\n Vprtstp: contraction number = 2.588682e-01\n Vnewton: Using errtol_s: 849.873571\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.224679e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.121614e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.680844e+02\n Vprtstp: contraction number = 2.680844e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 9.719850e-05\n Vprtstp: contraction number = 2.838981e-01\n Vnewton: Using errtol_s: 241.277472\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.444878e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.535865e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.904724e+01\n Vprtstp: contraction number = 7.904724e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.865974e-05\n Vprtstp: contraction number = 2.948578e-01\n Vnewton: Using errtol_s: 71.142545\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.658768e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.092916e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.370878e+01\n Vprtstp: contraction number = 2.370878e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.595964e-06\n Vprtstp: contraction number = 2.999317e-01\n Vnewton: Using errtol_s: 21.337905\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.869817e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.255759e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.196546e+00\n Vprtstp: contraction number = 7.196546e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.609212e-06\n Vprtstp: contraction number = 3.035392e-01\n Vnewton: Using errtol_s: 6.476891\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.097883e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.415619e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.205063e+00\n Vprtstp: contraction number = 2.205063e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 7.994776e-07\n Vprtstp: contraction number = 3.064057e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.272731e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.286704e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.519936e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.530672e+02\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -6369,15 +6369,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 6.741026947407E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.567804611788E+04 kT\n Vpmg_energy:  dielEnergy = 1.283053686435E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.380100e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.882500e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 25.8477\n Vpbe_ctor2:  solute dimensions = 26.666 x 32.3234 x 48.3902\n Vpbe_ctor2:  solute charge = -14\n@@ -6426,160 +6426,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0353875 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.549230\n+Vacc_SASA: Time elapsed: 0.580133\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.623544e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.505084e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.272300e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.963000e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.036443e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.011754e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.333359e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.576040e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2557475.753383\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.359012e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.596312e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.996924e+05\n Vprtstp: contraction number = 3.996924e+05\n Vnewton: Attempting damping, relres = 0.166335\n Vnewton: Attempting damping, relres = 0.569269\n Vnewton: Damping accepted, relres = 0.166335\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.663353e-01\n Vprtstp: contraction number = 1.663353e-01\n Vnewton: Using errtol_s: 425398.550037\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.576010e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.765874e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.844641e+04\n Vprtstp: contraction number = 7.844641e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 3.321581e-02\n Vprtstp: contraction number = 1.996918e-01\n Vnewton: Using errtol_s: 84948.619306\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.759885e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.915590e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.934802e+04\n Vprtstp: contraction number = 1.934802e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.763061e-03\n Vprtstp: contraction number = 2.337159e-01\n Vnewton: Using errtol_s: 19853.840744\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.986292e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.070553e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.339655e+03\n Vprtstp: contraction number = 5.339655e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.934926e-03\n Vprtstp: contraction number = 2.492478e-01\n Vnewton: Using errtol_s: 4948.526141\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.225621e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.220227e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.525404e+03\n Vprtstp: contraction number = 1.525404e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.370526e-04\n Vprtstp: contraction number = 2.775572e-01\n Vnewton: Using errtol_s: 1373.498967\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.464301e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.366137e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.551328e+02\n Vprtstp: contraction number = 4.551328e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.601661e-04\n Vprtstp: contraction number = 2.982316e-01\n Vnewton: Using errtol_s: 409.620859\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.715570e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.512887e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.409185e+02\n Vprtstp: contraction number = 1.409185e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.959057e-05\n Vprtstp: contraction number = 3.096197e-01\n Vnewton: Using errtol_s: 126.826691\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.956727e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.664959e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.462999e+01\n Vprtstp: contraction number = 4.462999e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.570572e-05\n Vprtstp: contraction number = 3.167077e-01\n Vnewton: Using errtol_s: 40.166995\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.197528e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.816228e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.440051e+01\n Vprtstp: contraction number = 1.440051e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.067675e-06\n Vprtstp: contraction number = 3.226643e-01\n Vnewton: Using errtol_s: 12.960456\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.440747e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.966242e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.718013e+00\n Vprtstp: contraction number = 4.718013e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.660314e-06\n Vprtstp: contraction number = 3.276283e-01\n Vnewton: Using errtol_s: 4.246212\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.691598e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.116403e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.564985e+00\n Vprtstp: contraction number = 1.564985e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 5.507330e-07\n Vprtstp: contraction number = 3.317042e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.588674e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.601110e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.677942e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.690306e+02\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -6589,15 +6589,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 6.724934425703E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.952419017164E+04 kT\n Vpmg_energy:  dielEnergy = 1.475361712291E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.508040e-01\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.873700e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n@@ -6626,151 +6626,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.360090\n+Vacc_SASA: Time elapsed: 0.369400\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.221700e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.431430e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.771700e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 8.376600e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.126236e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.161090e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.959820e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.290261e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 720364.541598\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.986820e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.311158e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.787737e+04\n Vprtstp: contraction number = 9.787737e+04\n Vnewton: Attempting damping, relres = 0.130881\n Vnewton: Attempting damping, relres = 0.558946\n Vnewton: Damping accepted, relres = 0.130881\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.308815e-01\n Vprtstp: contraction number = 1.308815e-01\n Vnewton: Using errtol_s: 94282.387082\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.173536e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.451202e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.788353e+04\n Vprtstp: contraction number = 1.788353e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.273611e-02\n Vprtstp: contraction number = 1.737152e-01\n Vnewton: Using errtol_s: 16378.286782\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.340393e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.564748e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.978150e+03\n Vprtstp: contraction number = 3.978150e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 4.972005e-03\n Vprtstp: contraction number = 2.186832e-01\n Vnewton: Using errtol_s: 3581.655852\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.515955e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.681040e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.935846e+02\n Vprtstp: contraction number = 9.935846e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.241360e-03\n Vprtstp: contraction number = 2.496698e-01\n Vnewton: Using errtol_s: 894.231472\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.694612e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.782031e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.645071e+02\n Vprtstp: contraction number = 2.645071e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.304670e-04\n Vprtstp: contraction number = 2.662137e-01\n Vnewton: Using errtol_s: 238.056677\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.862543e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.889214e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.296267e+01\n Vprtstp: contraction number = 7.296267e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 9.115721e-05\n Vprtstp: contraction number = 2.758437e-01\n Vnewton: Using errtol_s: 65.666425\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.029344e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.992460e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.060915e+01\n Vprtstp: contraction number = 2.060915e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.574840e-05\n Vprtstp: contraction number = 2.824615e-01\n Vnewton: Using errtol_s: 18.548236\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.200178e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.094492e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.927860e+00\n Vprtstp: contraction number = 5.927860e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 7.406076e-06\n Vprtstp: contraction number = 2.876324e-01\n Vnewton: Using errtol_s: 5.335074\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.359443e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.205507e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.730517e+00\n Vprtstp: contraction number = 1.730517e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.162052e-06\n Vprtstp: contraction number = 2.919295e-01\n Vnewton: Using errtol_s: 1.557466\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.528294e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.322085e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.113205e-01\n Vprtstp: contraction number = 5.113205e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 6.388271e-07\n Vprtstp: contraction number = 2.954726e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.721377e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.734744e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.148234e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.159297e+02\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -6780,15 +6780,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.705203011942E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 6.834032014754E+03 kT\n Vpmg_energy:  dielEnergy = 3.414947804784E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 9.740600e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.042600e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 19.3778\n Vpbe_ctor2:  solute dimensions = 19.082 x 18.3114 x 35.7654\n Vpbe_ctor2:  solute charge = 4\n@@ -6837,160 +6837,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0059523 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.382298\n+Vacc_SASA: Time elapsed: 0.374608\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.036636e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.098450e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 7.633100e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.801600e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.311360e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.081570e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.709818e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.462060e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 751497.765770\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.735230e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.482124e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.222283e+05\n Vprtstp: contraction number = 1.222283e+05\n Vnewton: Attempting damping, relres = 0.154183\n Vnewton: Attempting damping, relres = 0.571098\n Vnewton: Damping accepted, relres = 0.154183\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.541833e-01\n Vprtstp: contraction number = 1.541833e-01\n Vnewton: Using errtol_s: 115868.383651\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.898003e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.627832e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.458734e+04\n Vprtstp: contraction number = 2.458734e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.980652e-02\n Vprtstp: contraction number = 1.933188e-01\n Vnewton: Using errtol_s: 22399.536309\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.088315e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.768118e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.900997e+03\n Vprtstp: contraction number = 5.900997e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.069086e-03\n Vprtstp: contraction number = 2.371657e-01\n Vnewton: Using errtol_s: 5312.402554\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.274628e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.904184e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.528364e+03\n Vprtstp: contraction number = 1.528364e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.830398e-03\n Vprtstp: contraction number = 2.589300e-01\n Vnewton: Using errtol_s: 1375.540379\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.454796e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.020961e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.166306e+02\n Vprtstp: contraction number = 4.166306e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.989616e-04\n Vprtstp: contraction number = 2.725973e-01\n Vnewton: Using errtol_s: 374.968546\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.638768e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.129110e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.176231e+02\n Vprtstp: contraction number = 1.176231e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.408665e-04\n Vprtstp: contraction number = 2.823194e-01\n Vnewton: Using errtol_s: 105.860894\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.818381e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.245520e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.409436e+01\n Vprtstp: contraction number = 3.409436e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.083170e-05\n Vprtstp: contraction number = 2.898609e-01\n Vnewton: Using errtol_s: 30.684933\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.996611e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.347672e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.010867e+01\n Vprtstp: contraction number = 1.010867e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.210623e-05\n Vprtstp: contraction number = 2.964909e-01\n Vnewton: Using errtol_s: 9.097804\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.173345e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.480920e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.062356e+00\n Vprtstp: contraction number = 3.062356e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.667504e-06\n Vprtstp: contraction number = 3.029435e-01\n Vnewton: Using errtol_s: 2.756121\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.355690e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.609332e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.453520e-01\n Vprtstp: contraction number = 9.453520e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.132162e-06\n Vprtstp: contraction number = 3.087009e-01\n Vnewton: Using errtol_s: 0.850817\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.544169e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.731938e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.964013e-01\n Vprtstp: contraction number = 2.964013e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.549727e-07\n Vprtstp: contraction number = 3.135354e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.001170e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.017168e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.378632e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.391635e+02\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -7000,17 +7000,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.697571697895E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 8.066549555181E+03 kT\n Vpmg_energy:  dielEnergy = 4.031217527268E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 9.177700e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.859200e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vnm_tstart: starting timer 27 (Setup timer)..\n@@ -7037,162 +7037,162 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.436336\n+Vacc_SASA: Time elapsed: 0.415225\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.334645e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.255551e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.577700e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.415100e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.134330e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.701850e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.752375e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.879190e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1823063.193603\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.779488e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.901222e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.580519e+05\n Vprtstp: contraction number = 2.580519e+05\n Vnewton: Attempting damping, relres = 0.222567\n Vnewton: Attempting damping, relres = 0.565989\n Vnewton: Damping accepted, relres = 0.222567\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.225671e-01\n Vprtstp: contraction number = 2.225671e-01\n Vnewton: Using errtol_s: 405753.919509\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.970748e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.048333e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.022631e+04\n Vprtstp: contraction number = 5.022631e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 4.970113e-02\n Vprtstp: contraction number = 2.233085e-01\n Vnewton: Using errtol_s: 90608.292404\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.226428e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.202306e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.257885e+04\n Vprtstp: contraction number = 1.257885e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.198700e-02\n Vprtstp: contraction number = 2.411816e-01\n Vnewton: Using errtol_s: 21853.051255\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.434250e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.329569e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.600602e+03\n Vprtstp: contraction number = 3.600602e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.500944e-03\n Vprtstp: contraction number = 2.086381e-01\n Vnewton: Using errtol_s: 4559.378536\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.625867e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.439080e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.867332e+02\n Vprtstp: contraction number = 9.867332e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.056164e-04\n Vprtstp: contraction number = 2.021702e-01\n Vnewton: Using errtol_s: 921.770690\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.802824e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.559566e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.646218e+02\n Vprtstp: contraction number = 2.646218e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.306754e-04\n Vprtstp: contraction number = 2.584478e-01\n Vnewton: Using errtol_s: 238.229561\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.987684e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.674653e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.765679e+01\n Vprtstp: contraction number = 7.765679e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.833723e-05\n Vprtstp: contraction number = 2.933775e-01\n Vnewton: Using errtol_s: 69.891187\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.016448e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.781319e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.351839e+01\n Vprtstp: contraction number = 2.351839e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.161043e-05\n Vprtstp: contraction number = 3.028501e-01\n Vnewton: Using errtol_s: 21.166555\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.034447e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.890212e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.178418e+00\n Vprtstp: contraction number = 7.178418e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.543803e-06\n Vprtstp: contraction number = 3.052257e-01\n Vnewton: Using errtol_s: 6.460576\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.054398e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.007053e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.199458e+00\n Vprtstp: contraction number = 2.199458e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.085817e-06\n Vprtstp: contraction number = 3.063988e-01\n Vnewton: Using errtol_s: 1.979513\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.072123e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.103829e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.755609e-01\n Vprtstp: contraction number = 6.755609e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.335073e-07\n Vprtstp: contraction number = 3.071488e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.118300e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.130575e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.326409e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.337108e+02\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -7202,17 +7202,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 9.498944659129E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.874900883074E+04 kT\n Vpmg_energy:  dielEnergy = 9.361242882871E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.436300e-01\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.775700e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 20.7943\n Vpbe_ctor2:  solute dimensions = 25.3482 x 27.3592 x 40.136\n Vpbe_ctor2:  solute charge = -18\n Vpbe_ctor2:  bulk ionic strength = 0.125\n Vpbe_ctor2:  xkappa = 0.115127\n@@ -7259,160 +7259,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0207746 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.442952\n+Vacc_SASA: Time elapsed: 0.447605\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.416133e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.222732e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.188000e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.781300e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.297690e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.402650e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.090240e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.230245e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1873431.596335\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.093423e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.251825e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.215071e+05\n Vprtstp: contraction number = 3.215071e+05\n Vnewton: Attempting damping, relres = 0.246235\n Vnewton: Attempting damping, relres = 0.579562\n Vnewton: Damping accepted, relres = 0.246235\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.462348e-01\n Vprtstp: contraction number = 2.462348e-01\n Vnewton: Using errtol_s: 461304.132219\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.114110e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.388061e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.793925e+04\n Vprtstp: contraction number = 6.793925e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 5.674078e-02\n Vprtstp: contraction number = 2.304336e-01\n Vnewton: Using errtol_s: 106299.974305\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.139709e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.535951e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.790128e+04\n Vprtstp: contraction number = 1.790128e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.413343e-02\n Vprtstp: contraction number = 2.490877e-01\n Vnewton: Using errtol_s: 26478.015957\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.162792e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.681523e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.289572e+03\n Vprtstp: contraction number = 5.289572e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 3.207748e-03\n Vprtstp: contraction number = 2.269618e-01\n Vnewton: Using errtol_s: 6009.496862\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.184006e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.814753e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.531645e+03\n Vprtstp: contraction number = 1.531645e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 7.505521e-04\n Vprtstp: contraction number = 2.339810e-01\n Vnewton: Using errtol_s: 1406.107935\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.203352e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.926660e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.459814e+02\n Vprtstp: contraction number = 4.459814e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.142740e-04\n Vprtstp: contraction number = 2.854885e-01\n Vnewton: Using errtol_s: 401.427706\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.221525e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.042183e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.392761e+02\n Vprtstp: contraction number = 1.392761e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 6.690856e-05\n Vprtstp: contraction number = 3.122570e-01\n Vnewton: Using errtol_s: 125.348607\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.241474e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.155420e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.474617e+01\n Vprtstp: contraction number = 4.474617e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.149615e-05\n Vprtstp: contraction number = 3.212765e-01\n Vnewton: Using errtol_s: 40.271562\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.261771e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.281738e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.457086e+01\n Vprtstp: contraction number = 1.457086e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 6.999869e-06\n Vprtstp: contraction number = 3.256337e-01\n Vnewton: Using errtol_s: 13.113776\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.281485e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.407939e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.791596e+00\n Vprtstp: contraction number = 4.791596e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 2.301892e-06\n Vprtstp: contraction number = 3.288478e-01\n Vnewton: Using errtol_s: 4.312437\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.301678e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.542161e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.587543e+00\n Vprtstp: contraction number = 1.587543e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 7.626585e-07\n Vprtstp: contraction number = 3.313182e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.291817e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.306942e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.431040e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.442161e+02\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -7422,29 +7422,29 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 9.484583962909E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.136638905481E+04 kT\n Vpmg_energy:  dielEnergy = 1.066994369938E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 8.203800e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.591200e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.320956e+03\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 8.676252e+02\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 07:00:33 2025\n+# Creation Date and Time:  Tue Jan  9 05:06:03 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path model_outNB.pqr\n@@ -7714,151 +7714,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.635825\n+Vacc_SASA: Time elapsed: 0.596201\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.714345e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.591268e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.116300e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.854000e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.163484e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.087798e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.007403e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.827168e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2410732.356899\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.807730e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.727014e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.128143e+05\n Vprtstp: contraction number = 3.128143e+05\n Vnewton: Attempting damping, relres = 0.141068\n Vnewton: Attempting damping, relres = 0.557017\n Vnewton: Damping accepted, relres = 0.141068\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.410683e-01\n Vprtstp: contraction number = 1.410683e-01\n Vnewton: Using errtol_s: 340078.014247\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.027104e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.053611e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.570013e+04\n Vprtstp: contraction number = 5.570013e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.582927e-02\n Vprtstp: contraction number = 1.830975e-01\n Vnewton: Using errtol_s: 62267.446259\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.521833e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.701067e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.287475e+04\n Vprtstp: contraction number = 1.287475e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 5.599207e-03\n Vprtstp: contraction number = 2.167776e-01\n Vnewton: Using errtol_s: 13498.190114\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.011971e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.538831e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.390785e+03\n Vprtstp: contraction number = 3.390785e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.306467e-03\n Vprtstp: contraction number = 2.333308e-01\n Vnewton: Using errtol_s: 3149.543372\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.044542e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.182049e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.269338e+02\n Vprtstp: contraction number = 9.269338e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.462424e-04\n Vprtstp: contraction number = 2.650218e-01\n Vnewton: Using errtol_s: 834.697770\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.272035e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.917704e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.654672e+02\n Vprtstp: contraction number = 2.654672e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 9.910734e-05\n Vprtstp: contraction number = 2.862369e-01\n Vnewton: Using errtol_s: 238.921266\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.501343e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.036998e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.840492e+01\n Vprtstp: contraction number = 7.840492e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.927096e-05\n Vprtstp: contraction number = 2.953460e-01\n Vnewton: Using errtol_s: 70.564451\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.732190e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.173398e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.353183e+01\n Vprtstp: contraction number = 2.353183e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.785152e-06\n Vprtstp: contraction number = 3.001320e-01\n Vnewton: Using errtol_s: 21.178651\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.978836e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.319017e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.144902e+00\n Vprtstp: contraction number = 7.144902e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.667410e-06\n Vprtstp: contraction number = 3.036271e-01\n Vnewton: Using errtol_s: 6.430412\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.178940e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.480648e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.189586e+00\n Vprtstp: contraction number = 2.189586e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 8.174393e-07\n Vprtstp: contraction number = 3.064543e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.377856e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.390456e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.608992e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.620995e+02\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -7868,17 +7868,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 6.581693957245E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.567629004923E+04 kT\n Vpmg_energy:  dielEnergy = 1.283007133277E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.946200e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.291400e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 25.8477\n Vpbe_ctor2:  solute dimensions = 26.666 x 32.3234 x 48.3902\n Vpbe_ctor2:  solute charge = -14\n Vpbe_ctor2:  bulk ionic strength = 0.15\n Vpbe_ctor2:  xkappa = 0.126115\n@@ -7925,160 +7925,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0289035 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.619440\n+Vacc_SASA: Time elapsed: 0.511935\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.803044e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.411351e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.359800e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.896200e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.264501e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.004692e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.440999e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.665242e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2480363.897694\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.469004e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.689079e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.884147e+05\n Vprtstp: contraction number = 3.884147e+05\n Vnewton: Attempting damping, relres = 0.164249\n Vnewton: Attempting damping, relres = 0.569268\n Vnewton: Damping accepted, relres = 0.164249\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.642495e-01\n Vprtstp: contraction number = 1.642495e-01\n Vnewton: Using errtol_s: 407398.416424\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.738552e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.878881e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.641742e+04\n Vprtstp: contraction number = 7.641742e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 3.259356e-02\n Vprtstp: contraction number = 1.984394e-01\n Vnewton: Using errtol_s: 80843.885291\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.011847e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.068850e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.892121e+04\n Vprtstp: contraction number = 1.892121e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.611596e-03\n Vprtstp: contraction number = 2.335307e-01\n Vnewton: Using errtol_s: 18879.528241\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.275845e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.253047e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.219825e+03\n Vprtstp: contraction number = 5.219825e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.927310e-03\n Vprtstp: contraction number = 2.532071e-01\n Vnewton: Using errtol_s: 4780.429766\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.524038e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.425072e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.496544e+03\n Vprtstp: contraction number = 1.496544e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.431250e-04\n Vprtstp: contraction number = 2.818047e-01\n Vnewton: Using errtol_s: 1347.147545\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.771410e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.609801e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.492633e+02\n Vprtstp: contraction number = 4.492633e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.630155e-04\n Vprtstp: contraction number = 3.001437e-01\n Vnewton: Using errtol_s: 404.337796\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.019399e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.789714e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.394005e+02\n Vprtstp: contraction number = 1.394005e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 5.058149e-05\n Vprtstp: contraction number = 3.102863e-01\n Vnewton: Using errtol_s: 125.460496\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.250555e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.968137e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.420063e+01\n Vprtstp: contraction number = 4.420063e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.603820e-05\n Vprtstp: contraction number = 3.170765e-01\n Vnewton: Using errtol_s: 39.780577\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.469963e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.144660e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.427219e+01\n Vprtstp: contraction number = 1.427219e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.178663e-06\n Vprtstp: contraction number = 3.228955e-01\n Vnewton: Using errtol_s: 12.844969\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.710128e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.329218e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.677701e+00\n Vprtstp: contraction number = 4.677701e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.697304e-06\n Vprtstp: contraction number = 3.277495e-01\n Vnewton: Using errtol_s: 4.209931\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.961703e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.530884e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.551790e+00\n Vprtstp: contraction number = 1.551790e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 5.630670e-07\n Vprtstp: contraction number = 3.317420e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.764170e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.777871e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.053048e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.065535e+02\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -8088,15 +8088,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 6.566249593084E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.952243483734E+04 kT\n Vpmg_energy:  dielEnergy = 1.475315373786E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.006900e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.825500e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n@@ -8125,151 +8125,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.328165\n+Vacc_SASA: Time elapsed: 0.361324\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.151389e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.638970e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.044300e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.998700e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.283401e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.052407e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.247362e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.754569e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 702833.844391\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.273647e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.777059e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.535199e+04\n Vprtstp: contraction number = 9.535199e+04\n Vnewton: Attempting damping, relres = 0.130807\n Vnewton: Attempting damping, relres = 0.558803\n Vnewton: Damping accepted, relres = 0.130807\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.308068e-01\n Vprtstp: contraction number = 1.308068e-01\n Vnewton: Using errtol_s: 91935.456218\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.455263e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.932659e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.754021e+04\n Vprtstp: contraction number = 1.754021e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.284568e-02\n Vprtstp: contraction number = 1.746521e-01\n Vnewton: Using errtol_s: 16056.717423\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.625629e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.069241e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.929316e+03\n Vprtstp: contraction number = 3.929316e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 5.033389e-03\n Vprtstp: contraction number = 2.203212e-01\n Vnewton: Using errtol_s: 3537.635824\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.804380e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.194406e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.863417e+02\n Vprtstp: contraction number = 9.863417e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.263048e-03\n Vprtstp: contraction number = 2.509340e-01\n Vnewton: Using errtol_s: 887.712932\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.978523e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.327926e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.633855e+02\n Vprtstp: contraction number = 2.633855e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.372735e-04\n Vprtstp: contraction number = 2.670314e-01\n Vnewton: Using errtol_s: 237.047224\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.141948e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.458205e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.278494e+01\n Vprtstp: contraction number = 7.278494e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 9.320334e-05\n Vprtstp: contraction number = 2.763435e-01\n Vnewton: Using errtol_s: 65.506461\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.317592e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.585940e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.058009e+01\n Vprtstp: contraction number = 2.058009e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.635343e-05\n Vprtstp: contraction number = 2.827520e-01\n Vnewton: Using errtol_s: 18.522083\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.492558e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.719612e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.922842e+00\n Vprtstp: contraction number = 5.922842e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 7.584378e-06\n Vprtstp: contraction number = 2.877947e-01\n Vnewton: Using errtol_s: 5.330558\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.659445e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.854564e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.729569e+00\n Vprtstp: contraction number = 1.729569e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.214765e-06\n Vprtstp: contraction number = 2.920167e-01\n Vnewton: Using errtol_s: 1.556612\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.838059e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.974514e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.111172e-01\n Vprtstp: contraction number = 5.111172e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 6.545011e-07\n Vprtstp: contraction number = 2.955171e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.745948e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.759576e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.322237e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.333795e+02\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -8279,15 +8279,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.740193498696E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 6.833468589698E+03 kT\n Vpmg_energy:  dielEnergy = 3.414657798024E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.335700e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.684000e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 19.3778\n Vpbe_ctor2:  solute dimensions = 19.082 x 18.3114 x 35.7654\n Vpbe_ctor2:  solute charge = 4\n@@ -8336,160 +8336,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00524143 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.353924\n+Vacc_SASA: Time elapsed: 0.333273\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.021598e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.547350e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.960900e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.422100e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.846690e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.001555e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.017471e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.099397e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 732702.640135\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.045207e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.120915e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.189776e+05\n Vprtstp: contraction number = 1.189776e+05\n Vnewton: Attempting damping, relres = 0.154045\n Vnewton: Attempting damping, relres = 0.570927\n Vnewton: Damping accepted, relres = 0.154045\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.540451e-01\n Vprtstp: contraction number = 1.540451e-01\n Vnewton: Using errtol_s: 112869.287383\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.246727e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.265299e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.402351e+04\n Vprtstp: contraction number = 2.402351e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.986126e-02\n Vprtstp: contraction number = 1.938474e-01\n Vnewton: Using errtol_s: 21879.422460\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.451862e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.407672e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.789967e+03\n Vprtstp: contraction number = 5.789967e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.113936e-03\n Vprtstp: contraction number = 2.382330e-01\n Vnewton: Using errtol_s: 5212.399665\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.636124e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.544706e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.505316e+03\n Vprtstp: contraction number = 1.505316e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.849041e-03\n Vprtstp: contraction number = 2.599182e-01\n Vnewton: Using errtol_s: 1354.797457\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.840145e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.680000e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.117226e+02\n Vprtstp: contraction number = 4.117226e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.057322e-04\n Vprtstp: contraction number = 2.735105e-01\n Vnewton: Using errtol_s: 370.551343\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.025558e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.810966e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.165670e+02\n Vprtstp: contraction number = 1.165670e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.431828e-04\n Vprtstp: contraction number = 2.831198e-01\n Vnewton: Using errtol_s: 104.910419\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.196901e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.955368e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.386584e+01\n Vprtstp: contraction number = 3.386584e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.159841e-05\n Vprtstp: contraction number = 2.905266e-01\n Vnewton: Using errtol_s: 30.479265\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.392934e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.096237e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.005899e+01\n Vprtstp: contraction number = 1.005899e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.235575e-05\n Vprtstp: contraction number = 2.970246e-01\n Vnewton: Using errtol_s: 9.053091\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.575602e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.224747e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.051439e+00\n Vprtstp: contraction number = 3.051439e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.748171e-06\n Vprtstp: contraction number = 3.033544e-01\n Vnewton: Using errtol_s: 2.746295\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.755620e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.375848e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.429257e-01\n Vprtstp: contraction number = 9.429257e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.158223e-06\n Vprtstp: contraction number = 3.090102e-01\n Vnewton: Using errtol_s: 0.848633\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.944548e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.508992e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.958550e-01\n Vprtstp: contraction number = 2.958550e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.634073e-07\n Vprtstp: contraction number = 3.137628e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.099327e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.112168e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.522745e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.535465e+02\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -8499,15 +8499,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.732432041867E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 8.065988471810E+03 kT\n Vpmg_energy:  dielEnergy = 4.030928944477E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 8.579700e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.427600e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n@@ -8536,162 +8536,162 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.434321\n+Vacc_SASA: Time elapsed: 0.398715\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.353715e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.166137e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.860500e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.882500e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.116454e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.141280e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.157204e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.659698e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1741500.081736\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.184037e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.679520e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.468341e+05\n Vprtstp: contraction number = 2.468341e+05\n Vnewton: Attempting damping, relres = 0.211968\n Vnewton: Attempting damping, relres = 0.565739\n Vnewton: Damping accepted, relres = 0.211968\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.119682e-01\n Vprtstp: contraction number = 2.119682e-01\n Vnewton: Using errtol_s: 369142.647388\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.374153e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.815226e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.765545e+04\n Vprtstp: contraction number = 4.765545e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 4.585316e-02\n Vprtstp: contraction number = 2.163209e-01\n Vnewton: Using errtol_s: 79853.288161\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.627662e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.995207e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.196657e+04\n Vprtstp: contraction number = 1.196657e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.069307e-02\n Vprtstp: contraction number = 2.332024e-01\n Vnewton: Using errtol_s: 18621.978068\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.834355e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.143068e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.396204e+03\n Vprtstp: contraction number = 3.396204e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.206422e-03\n Vprtstp: contraction number = 2.063414e-01\n Vnewton: Using errtol_s: 3842.484890\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.002551e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.278441e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.262198e+02\n Vprtstp: contraction number = 9.262198e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.857523e-04\n Vprtstp: contraction number = 2.201538e-01\n Vnewton: Using errtol_s: 845.937714\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.020236e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.413448e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.568315e+02\n Vprtstp: contraction number = 2.568315e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.327389e-04\n Vprtstp: contraction number = 2.732646e-01\n Vnewton: Using errtol_s: 231.164809\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.038048e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.549181e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.648381e+01\n Vprtstp: contraction number = 7.648381e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.952654e-05\n Vprtstp: contraction number = 2.977766e-01\n Vnewton: Using errtol_s: 68.835472\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.056265e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.684294e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.321302e+01\n Vprtstp: contraction number = 2.321302e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.199639e-05\n Vprtstp: contraction number = 3.035022e-01\n Vnewton: Using errtol_s: 20.891720\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.075290e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.815423e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.089761e+00\n Vprtstp: contraction number = 7.089761e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.663959e-06\n Vprtstp: contraction number = 3.054217e-01\n Vnewton: Using errtol_s: 6.380785\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.093239e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.944417e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.172932e+00\n Vprtstp: contraction number = 2.172932e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.122962e-06\n Vprtstp: contraction number = 3.064887e-01\n Vnewton: Using errtol_s: 1.955639\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.111318e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.063982e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.675659e-01\n Vprtstp: contraction number = 6.675659e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.449953e-07\n Vprtstp: contraction number = 3.072190e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.122347e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.134221e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.506509e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.516598e+02\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -8701,15 +8701,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 9.219214525491E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.874647090507E+04 kT\n Vpmg_energy:  dielEnergy = 9.360649736533E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.257000e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.540000e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 20.7943\n Vpbe_ctor2:  solute dimensions = 25.3482 x 27.3592 x 40.136\n Vpbe_ctor2:  solute charge = -18\n@@ -8758,160 +8758,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0149776 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.448323\n+Vacc_SASA: Time elapsed: 0.443820\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.395065e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.240102e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.673800e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.766100e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.220886e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.957090e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.130940e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.191394e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1787000.080841\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.133856e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.212338e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.080871e+05\n Vprtstp: contraction number = 3.080871e+05\n Vnewton: Attempting damping, relres = 0.236727\n Vnewton: Attempting damping, relres = 0.579616\n Vnewton: Damping accepted, relres = 0.236727\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.367272e-01\n Vprtstp: contraction number = 2.367272e-01\n Vnewton: Using errtol_s: 423031.456074\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.155435e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.356052e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.466075e+04\n Vprtstp: contraction number = 6.466075e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 5.316615e-02\n Vprtstp: contraction number = 2.245883e-01\n Vnewton: Using errtol_s: 95007.918174\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.180830e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.543551e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.709590e+04\n Vprtstp: contraction number = 1.709590e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.292750e-02\n Vprtstp: contraction number = 2.431528e-01\n Vnewton: Using errtol_s: 23101.438026\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.203035e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.726640e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.023315e+03\n Vprtstp: contraction number = 5.023315e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.939979e-03\n Vprtstp: contraction number = 2.274206e-01\n Vnewton: Using errtol_s: 5253.742566\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.224366e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.872124e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.453031e+03\n Vprtstp: contraction number = 1.453031e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 7.371716e-04\n Vprtstp: contraction number = 2.507404e-01\n Vnewton: Using errtol_s: 1317.325709\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.243395e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.003680e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.332970e+02\n Vprtstp: contraction number = 4.332970e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.182303e-04\n Vprtstp: contraction number = 2.960373e-01\n Vnewton: Using errtol_s: 389.977573\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.260676e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.149494e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.367395e+02\n Vprtstp: contraction number = 1.367395e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 6.886719e-05\n Vprtstp: contraction number = 3.155711e-01\n Vnewton: Using errtol_s: 123.065671\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.279837e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.282292e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.406045e+01\n Vprtstp: contraction number = 4.406045e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.219049e-05\n Vprtstp: contraction number = 3.222216e-01\n Vnewton: Using errtol_s: 39.654416\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.298615e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.404795e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.437042e+01\n Vprtstp: contraction number = 1.437042e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 7.237482e-06\n Vprtstp: contraction number = 3.261524e-01\n Vnewton: Using errtol_s: 12.933382\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.317904e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.545566e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.730536e+00\n Vprtstp: contraction number = 4.730536e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 2.382475e-06\n Vprtstp: contraction number = 3.291856e-01\n Vnewton: Using errtol_s: 4.257482\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.336634e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.698340e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.568402e+00\n Vprtstp: contraction number = 1.568402e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 7.899057e-07\n Vprtstp: contraction number = 3.315484e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.234717e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.250299e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.609234e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.620646e+02\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -8921,29 +8921,29 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 9.205829898099E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.136385155975E+04 kT\n Vpmg_energy:  dielEnergy = 1.066935223116E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.920800e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.218300e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.355856e+03\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 9.815894e+02\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 07:02:39 2025\n+# Creation Date and Time:  Tue Jan  9 05:09:22 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path model_outNB.pqr\n@@ -9213,151 +9213,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.594154\n+Vacc_SASA: Time elapsed: 0.606917\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.701600e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.654636e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.011500e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.025400e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.144536e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.404080e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.990706e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.749729e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2356583.284651\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.483028e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.698206e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.056288e+05\n Vprtstp: contraction number = 3.056288e+05\n Vnewton: Attempting damping, relres = 0.138875\n Vnewton: Attempting damping, relres = 0.556850\n Vnewton: Damping accepted, relres = 0.138875\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.388745e-01\n Vprtstp: contraction number = 1.388745e-01\n Vnewton: Using errtol_s: 327269.333015\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.592745e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.986277e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.456208e+04\n Vprtstp: contraction number = 5.456208e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.522390e-02\n Vprtstp: contraction number = 1.816309e-01\n Vnewton: Using errtol_s: 59442.210907\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.086582e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.500638e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.266310e+04\n Vprtstp: contraction number = 1.266310e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 5.461794e-03\n Vprtstp: contraction number = 2.165325e-01\n Vnewton: Using errtol_s: 12871.173067\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.546133e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.050285e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.333848e+03\n Vprtstp: contraction number = 3.333848e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.298357e-03\n Vprtstp: contraction number = 2.377162e-01\n Vnewton: Using errtol_s: 3059.685767\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.884377e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.504578e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.158069e+02\n Vprtstp: contraction number = 9.158069e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.498387e-04\n Vprtstp: contraction number = 2.694473e-01\n Vnewton: Using errtol_s: 824.424114\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.219894e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.027256e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.635874e+02\n Vprtstp: contraction number = 2.635874e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.006665e-04\n Vprtstp: contraction number = 2.877513e-01\n Vnewton: Using errtol_s: 237.229108\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.446677e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.435853e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.793651e+01\n Vprtstp: contraction number = 7.793651e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.976465e-05\n Vprtstp: contraction number = 2.956757e-01\n Vnewton: Using errtol_s: 70.142875\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.702170e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.087437e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.340231e+01\n Vprtstp: contraction number = 2.340231e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.937548e-06\n Vprtstp: contraction number = 3.002739e-01\n Vnewton: Using errtol_s: 21.062077\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.955383e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.220375e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.107171e+00\n Vprtstp: contraction number = 7.107171e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.714292e-06\n Vprtstp: contraction number = 3.036953e-01\n Vnewton: Using errtol_s: 6.396454\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.226662e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.349007e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.178301e+00\n Vprtstp: contraction number = 2.178301e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 8.319126e-07\n Vprtstp: contraction number = 3.064934e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.425759e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.438312e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.449538e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.460115e+02\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -9367,15 +9367,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 6.432923079367E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.567482695315E+04 kT\n Vpmg_energy:  dielEnergy = 1.282968021669E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.182300e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.387500e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 25.8477\n Vpbe_ctor2:  solute dimensions = 26.666 x 32.3234 x 48.3902\n Vpbe_ctor2:  solute charge = -14\n@@ -9424,160 +9424,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.024752 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.576365\n+Vacc_SASA: Time elapsed: 0.588476\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.721276e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.566248e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.316300e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.942700e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.335011e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.000452e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.488337e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.505663e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2421825.168549\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.520702e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.529371e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.797843e+05\n Vprtstp: contraction number = 3.797843e+05\n Vnewton: Attempting damping, relres = 0.162423\n Vnewton: Attempting damping, relres = 0.569239\n Vnewton: Damping accepted, relres = 0.162423\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.624227e-01\n Vprtstp: contraction number = 1.624227e-01\n Vnewton: Using errtol_s: 393359.388162\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.778925e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.718512e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.485976e+04\n Vprtstp: contraction number = 7.485976e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 3.206345e-02\n Vprtstp: contraction number = 1.974075e-01\n Vnewton: Using errtol_s: 77652.078067\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.060064e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.872787e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.858810e+04\n Vprtstp: contraction number = 1.858810e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.494162e-03\n Vprtstp: contraction number = 2.337291e-01\n Vnewton: Using errtol_s: 18149.549466\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.331988e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.019107e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.126907e+03\n Vprtstp: contraction number = 5.126907e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.925418e-03\n Vprtstp: contraction number = 2.569223e-01\n Vnewton: Using errtol_s: 4663.024844\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.581675e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.171034e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.475836e+03\n Vprtstp: contraction number = 1.475836e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.485012e-04\n Vprtstp: contraction number = 2.848739e-01\n Vnewton: Using errtol_s: 1328.373956\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.828402e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.343460e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.449115e+02\n Vprtstp: contraction number = 4.449115e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.653385e-04\n Vprtstp: contraction number = 3.014369e-01\n Vnewton: Using errtol_s: 400.420960\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.079253e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.506023e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.382677e+02\n Vprtstp: contraction number = 1.382677e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 5.138313e-05\n Vprtstp: contraction number = 3.107753e-01\n Vnewton: Using errtol_s: 124.440953\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.330891e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.656735e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.388153e+01\n Vprtstp: contraction number = 4.388153e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.630728e-05\n Vprtstp: contraction number = 3.173665e-01\n Vnewton: Using errtol_s: 39.493386\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.592420e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.807797e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.417721e+01\n Vprtstp: contraction number = 1.417721e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.268543e-06\n Vprtstp: contraction number = 3.230792e-01\n Vnewton: Using errtol_s: 12.759491\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.850255e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.979703e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.647969e+00\n Vprtstp: contraction number = 4.647969e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.727281e-06\n Vprtstp: contraction number = 3.278479e-01\n Vnewton: Using errtol_s: 4.183172\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.110458e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.128456e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.542077e+00\n Vprtstp: contraction number = 1.542077e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 5.730676e-07\n Vprtstp: contraction number = 3.317744e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.845416e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.859936e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.754913e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.766830e+02\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -9587,15 +9587,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 6.418015826462E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.952097240352E+04 kT\n Vpmg_energy:  dielEnergy = 1.475276420502E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.404870e-01\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.117680e-01\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n@@ -9624,151 +9624,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.383887\n+Vacc_SASA: Time elapsed: 0.382715\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.011788e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.333250e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.610800e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.999200e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.067712e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.974320e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.370692e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.298591e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 689766.139707\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.399240e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.320598e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.344903e+04\n Vprtstp: contraction number = 9.344903e+04\n Vnewton: Attempting damping, relres = 0.130653\n Vnewton: Attempting damping, relres = 0.558674\n Vnewton: Damping accepted, relres = 0.130653\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.306530e-01\n Vprtstp: contraction number = 1.306530e-01\n Vnewton: Using errtol_s: 90120.018484\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.567895e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.435637e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.728022e+04\n Vprtstp: contraction number = 1.728022e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.291797e-02\n Vprtstp: contraction number = 1.754110e-01\n Vnewton: Using errtol_s: 15808.042794\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.744165e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.538548e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.892059e+03\n Vprtstp: contraction number = 3.892059e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 5.080008e-03\n Vprtstp: contraction number = 2.216604e-01\n Vnewton: Using errtol_s: 3504.017199\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.919492e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.653280e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.808109e+02\n Vprtstp: contraction number = 9.808109e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.279760e-03\n Vprtstp: contraction number = 2.519209e-01\n Vnewton: Using errtol_s: 882.735296\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.097159e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.755823e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.625258e+02\n Vprtstp: contraction number = 2.625258e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.425414e-04\n Vprtstp: contraction number = 2.676606e-01\n Vnewton: Using errtol_s: 236.273473\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.273005e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.874911e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.264793e+01\n Vprtstp: contraction number = 7.264793e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 9.479032e-05\n Vprtstp: contraction number = 2.767266e-01\n Vnewton: Using errtol_s: 65.383155\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.463652e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.013738e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.055752e+01\n Vprtstp: contraction number = 2.055752e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.682325e-05\n Vprtstp: contraction number = 2.829746e-01\n Vnewton: Using errtol_s: 18.501770\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.653792e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.124223e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.918897e+00\n Vprtstp: contraction number = 5.918897e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 7.722918e-06\n Vprtstp: contraction number = 2.879188e-01\n Vnewton: Using errtol_s: 5.327008\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.832028e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.228118e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.728813e+00\n Vprtstp: contraction number = 1.728813e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.255738e-06\n Vprtstp: contraction number = 2.920837e-01\n Vnewton: Using errtol_s: 1.555932\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.013674e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.329323e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.109531e-01\n Vprtstp: contraction number = 5.109531e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 6.666866e-07\n Vprtstp: contraction number = 2.955514e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.806532e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.818894e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.134382e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.146266e+02\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -9778,17 +9778,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.765725415923E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 6.832984433292E+03 kT\n Vpmg_energy:  dielEnergy = 3.414411854652E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.506700e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.223500e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 19.3778\n Vpbe_ctor2:  solute dimensions = 19.082 x 18.3114 x 35.7654\n Vpbe_ctor2:  solute charge = 4\n Vpbe_ctor2:  bulk ionic strength = 0.175\n Vpbe_ctor2:  xkappa = 0.13622\n@@ -9835,160 +9835,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00466833 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.228082\n+Vacc_SASA: Time elapsed: 0.370178\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.171811e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.335370e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.755200e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.900200e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.321273e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 8.777220e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.203820e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.453998e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 718654.980128\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.234876e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.473832e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.165117e+05\n Vprtstp: contraction number = 1.165117e+05\n Vnewton: Attempting damping, relres = 0.153827\n Vnewton: Attempting damping, relres = 0.570766\n Vnewton: Damping accepted, relres = 0.153827\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.538266e-01\n Vprtstp: contraction number = 1.538266e-01\n Vnewton: Using errtol_s: 110548.228061\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.444775e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.601048e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.359273e+04\n Vprtstp: contraction number = 2.359273e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.988514e-02\n Vprtstp: contraction number = 1.942782e-01\n Vnewton: Using errtol_s: 21477.106835\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.629781e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.713175e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.704562e+03\n Vprtstp: contraction number = 5.704562e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.145907e-03\n Vprtstp: contraction number = 2.391124e-01\n Vnewton: Using errtol_s: 5135.441496\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.818433e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.818239e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.487585e+03\n Vprtstp: contraction number = 1.487585e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.862980e-03\n Vprtstp: contraction number = 2.607059e-01\n Vnewton: Using errtol_s: 1338.839679\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.008462e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.943597e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.079440e+02\n Vprtstp: contraction number = 4.079440e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.108858e-04\n Vprtstp: contraction number = 2.742305e-01\n Vnewton: Using errtol_s: 367.150629\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.193406e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.052081e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.157528e+02\n Vprtstp: contraction number = 1.157528e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.449619e-04\n Vprtstp: contraction number = 2.837461e-01\n Vnewton: Using errtol_s: 104.177567\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.378618e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.160023e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.368933e+01\n Vprtstp: contraction number = 3.368933e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.219048e-05\n Vprtstp: contraction number = 2.910454e-01\n Vnewton: Using errtol_s: 30.320401\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.576016e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.267741e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.002053e+01\n Vprtstp: contraction number = 1.002053e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.254910e-05\n Vprtstp: contraction number = 2.974392e-01\n Vnewton: Using errtol_s: 9.018476\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.770676e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.380967e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.042966e+00\n Vprtstp: contraction number = 3.042966e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.810826e-06\n Vprtstp: contraction number = 3.036732e-01\n Vnewton: Using errtol_s: 2.738669\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.965041e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.500546e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.410367e-01\n Vprtstp: contraction number = 9.410367e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.178497e-06\n Vprtstp: contraction number = 3.092499e-01\n Vnewton: Using errtol_s: 0.846933\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.164141e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.611066e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.954277e-01\n Vprtstp: contraction number = 2.954277e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.699758e-07\n Vprtstp: contraction number = 3.139386e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.132447e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.146573e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.256083e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.267457e+02\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -9998,17 +9998,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.757851015992E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 8.065506328732E+03 kT\n Vpmg_energy:  dielEnergy = 4.030684199537E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 8.365500e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.161900e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vnm_tstart: starting timer 27 (Setup timer)..\n@@ -10035,162 +10035,162 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.467155\n+Vacc_SASA: Time elapsed: 0.364100\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.331882e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.187092e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.176500e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.663700e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.403304e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.585920e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.382081e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.747418e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1681345.800904\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.413361e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.768517e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.385175e+05\n Vprtstp: contraction number = 2.385175e+05\n Vnewton: Attempting damping, relres = 0.203314\n Vnewton: Attempting damping, relres = 0.565471\n Vnewton: Damping accepted, relres = 0.203314\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.033139e-01\n Vprtstp: contraction number = 2.033139e-01\n Vnewton: Using errtol_s: 341841.011255\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.611662e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.898251e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.575913e+04\n Vprtstp: contraction number = 4.575913e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 4.277261e-02\n Vprtstp: contraction number = 2.103772e-01\n Vnewton: Using errtol_s: 71915.546235\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.862462e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.041477e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.151626e+04\n Vprtstp: contraction number = 1.151626e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 9.711565e-03\n Vprtstp: contraction number = 2.270510e-01\n Vnewton: Using errtol_s: 16328.498943\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.007433e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.169309e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.244716e+03\n Vprtstp: contraction number = 3.244716e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.018619e-03\n Vprtstp: contraction number = 2.078572e-01\n Vnewton: Using errtol_s: 3393.995992\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.025567e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.290423e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.861858e+02\n Vprtstp: contraction number = 8.861858e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.771677e-04\n Vprtstp: contraction number = 2.363833e-01\n Vnewton: Using errtol_s: 802.283944\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.044907e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.401505e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.516488e+02\n Vprtstp: contraction number = 2.516488e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.347069e-04\n Vprtstp: contraction number = 2.823051e-01\n Vnewton: Using errtol_s: 226.488825\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.064298e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.521971e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.546930e+01\n Vprtstp: contraction number = 7.546930e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.039764e-05\n Vprtstp: contraction number = 2.998929e-01\n Vnewton: Using errtol_s: 67.922396\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.082818e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.633690e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.293241e+01\n Vprtstp: contraction number = 2.293241e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.227539e-05\n Vprtstp: contraction number = 3.038640e-01\n Vnewton: Using errtol_s: 20.639168\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.100825e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.738207e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.006994e+00\n Vprtstp: contraction number = 7.006994e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.750742e-06\n Vprtstp: contraction number = 3.055499e-01\n Vnewton: Using errtol_s: 6.306295\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.120449e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.834882e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.148054e+00\n Vprtstp: contraction number = 2.148054e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.149822e-06\n Vprtstp: contraction number = 3.065586e-01\n Vnewton: Using errtol_s: 1.933249\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.141012e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.936647e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.600422e-01\n Vprtstp: contraction number = 6.600422e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.533110e-07\n Vprtstp: contraction number = 3.072745e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.206677e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.221446e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.286737e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.297337e+02\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -10200,17 +10200,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 8.973061479643E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.874436395142E+04 kT\n Vpmg_energy:  dielEnergy = 9.360148310218E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.741000e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.493320e-01\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 20.7943\n Vpbe_ctor2:  solute dimensions = 25.3482 x 27.3592 x 40.136\n Vpbe_ctor2:  solute charge = -18\n Vpbe_ctor2:  bulk ionic strength = 0.175\n Vpbe_ctor2:  xkappa = 0.13622\n@@ -10257,160 +10257,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.011302 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.442240\n+Vacc_SASA: Time elapsed: 0.445099\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.263283e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.220142e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.083600e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.766300e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.208906e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.620730e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.161642e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.060539e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1723046.376364\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.164490e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.081863e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.980547e+05\n Vprtstp: contraction number = 2.980547e+05\n Vnewton: Attempting damping, relres = 0.228891\n Vnewton: Attempting damping, relres = 0.579579\n Vnewton: Damping accepted, relres = 0.228891\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.288909e-01\n Vprtstp: contraction number = 2.288909e-01\n Vnewton: Using errtol_s: 394389.718028\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.186140e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.234233e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.222537e+04\n Vprtstp: contraction number = 6.222537e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 5.028364e-02\n Vprtstp: contraction number = 2.196838e-01\n Vnewton: Using errtol_s: 86641.047132\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.212743e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.416336e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.649630e+04\n Vprtstp: contraction number = 1.649630e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.200939e-02\n Vprtstp: contraction number = 2.388330e-01\n Vnewton: Using errtol_s: 20692.741964\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.234201e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.579235e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.824465e+03\n Vprtstp: contraction number = 4.824465e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.771121e-03\n Vprtstp: contraction number = 2.307461e-01\n Vnewton: Using errtol_s: 4774.769213\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.254328e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.734472e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.399802e+03\n Vprtstp: contraction number = 1.399802e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 7.332377e-04\n Vprtstp: contraction number = 2.645997e-01\n Vnewton: Using errtol_s: 1263.402543\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.274511e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.867053e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.245121e+02\n Vprtstp: contraction number = 4.245121e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.217376e-04\n Vprtstp: contraction number = 3.024089e-01\n Vnewton: Using errtol_s: 382.064121\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.293862e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.976779e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.346888e+02\n Vprtstp: contraction number = 1.346888e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 7.035216e-05\n Vprtstp: contraction number = 3.172767e-01\n Vnewton: Using errtol_s: 121.220033\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.312997e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.094538e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.348380e+01\n Vprtstp: contraction number = 4.348380e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.271293e-05\n Vprtstp: contraction number = 3.228462e-01\n Vnewton: Using errtol_s: 39.135424\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.333929e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.221998e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.419901e+01\n Vprtstp: contraction number = 1.419901e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 7.416577e-06\n Vprtstp: contraction number = 3.265355e-01\n Vnewton: Using errtol_s: 12.779106\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.353166e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.352302e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.677787e+00\n Vprtstp: contraction number = 4.677787e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 2.443352e-06\n Vprtstp: contraction number = 3.294447e-01\n Vnewton: Using errtol_s: 4.210009\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.372107e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.506784e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.551755e+00\n Vprtstp: contraction number = 1.551755e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 8.105291e-07\n Vprtstp: contraction number = 3.317283e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.271320e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.285706e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.547562e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.559298e+02\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -10420,29 +10420,29 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 8.960413626041E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.136174499148E+04 kT\n Vpmg_energy:  dielEnergy = 1.066885194167E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.268790e-01\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.721900e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.390196e+03\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 8.625015e+02\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 07:04:44 2025\n+# Creation Date and Time:  Tue Jan  9 05:12:00 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path model_outNB.pqr\n@@ -10712,151 +10712,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.624834\n+Vacc_SASA: Time elapsed: 0.598271\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.669152e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.606298e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.902100e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.937100e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.091833e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.383830e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.889422e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.700026e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2314164.846818\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.832641e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.879945e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.999858e+05\n Vprtstp: contraction number = 2.999858e+05\n Vnewton: Attempting damping, relres = 0.137001\n Vnewton: Attempting damping, relres = 0.556699\n Vnewton: Damping accepted, relres = 0.137001\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.370010e-01\n Vprtstp: contraction number = 1.370010e-01\n Vnewton: Using errtol_s: 317042.938668\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.697300e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.189211e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.366653e+04\n Vprtstp: contraction number = 5.366653e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.471777e-02\n Vprtstp: contraction number = 1.804203e-01\n Vnewton: Using errtol_s: 57200.987288\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.235488e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.883375e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.249422e+04\n Vprtstp: contraction number = 1.249422e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 5.356401e-03\n Vprtstp: contraction number = 2.167025e-01\n Vnewton: Using errtol_s: 12395.595920\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.715632e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.478026e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.289496e+03\n Vprtstp: contraction number = 3.289496e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.295127e-03\n Vprtstp: contraction number = 2.417905e-01\n Vnewton: Using errtol_s: 2997.137107\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.002625e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.929427e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.079428e+02\n Vprtstp: contraction number = 9.079428e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.531481e-04\n Vprtstp: contraction number = 2.726745e-01\n Vnewton: Using errtol_s: 817.243005\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.229485e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.572126e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.621817e+02\n Vprtstp: contraction number = 2.621817e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.019650e-04\n Vprtstp: contraction number = 2.887315e-01\n Vnewton: Using errtol_s: 235.963838\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.457095e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.020635e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.758363e+01\n Vprtstp: contraction number = 7.758363e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.017299e-05\n Vprtstp: contraction number = 2.959152e-01\n Vnewton: Using errtol_s: 69.825280\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.690453e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.155770e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.330457e+01\n Vprtstp: contraction number = 2.330457e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 9.063361e-06\n Vprtstp: contraction number = 3.003799e-01\n Vnewton: Using errtol_s: 20.974111\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.941507e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.298375e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.078759e+00\n Vprtstp: contraction number = 7.078759e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.752995e-06\n Vprtstp: contraction number = 3.037499e-01\n Vnewton: Using errtol_s: 6.370884\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.182016e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.443864e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.169820e+00\n Vprtstp: contraction number = 2.169820e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 8.438628e-07\n Vprtstp: contraction number = 3.065254e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.388665e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.400942e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.550770e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.561343e+02\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -10866,17 +10866,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 6.295748470746E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.567357663948E+04 kT\n Vpmg_energy:  dielEnergy = 1.282934286498E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.481140e-01\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.664200e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 25.8477\n Vpbe_ctor2:  solute dimensions = 26.666 x 32.3234 x 48.3902\n Vpbe_ctor2:  solute charge = -14\n Vpbe_ctor2:  bulk ionic strength = 0.2\n Vpbe_ctor2:  xkappa = 0.145625\n@@ -10923,160 +10923,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0219675 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.580554\n+Vacc_SASA: Time elapsed: 0.576409\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.704924e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.479584e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.968300e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.975500e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.268478e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.521910e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.451175e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.605469e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2375881.010490\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.479732e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.623575e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.729565e+05\n Vprtstp: contraction number = 3.729565e+05\n Vnewton: Attempting damping, relres = 0.160831\n Vnewton: Attempting damping, relres = 0.569195\n Vnewton: Damping accepted, relres = 0.160831\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.608306e-01\n Vprtstp: contraction number = 1.608306e-01\n Vnewton: Using errtol_s: 382114.425441\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.743254e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.781393e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.362534e+04\n Vprtstp: contraction number = 7.362534e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 3.161380e-02\n Vprtstp: contraction number = 1.965658e-01\n Vnewton: Using errtol_s: 75110.631839\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.017622e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.951936e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.832017e+04\n Vprtstp: contraction number = 1.832017e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.403849e-03\n Vprtstp: contraction number = 2.341967e-01\n Vnewton: Using errtol_s: 17590.663892\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.277959e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.118427e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.053669e+03\n Vprtstp: contraction number = 5.053669e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.926673e-03\n Vprtstp: contraction number = 2.602258e-01\n Vnewton: Using errtol_s: 4577.545268\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.539943e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.268604e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.460468e+03\n Vprtstp: contraction number = 1.460468e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.532624e-04\n Vprtstp: contraction number = 2.871595e-01\n Vnewton: Using errtol_s: 1314.485731\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.811295e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.429418e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.415879e+02\n Vprtstp: contraction number = 4.415879e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.672767e-04\n Vprtstp: contraction number = 3.023461e-01\n Vnewton: Using errtol_s: 397.429641\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.080749e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.585868e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.374012e+02\n Vprtstp: contraction number = 1.374012e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 5.204853e-05\n Vprtstp: contraction number = 3.111522e-01\n Vnewton: Using errtol_s: 123.661104\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.358431e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.743698e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.363894e+01\n Vprtstp: contraction number = 4.363894e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.653073e-05\n Vprtstp: contraction number = 3.176023e-01\n Vnewton: Using errtol_s: 39.275049\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.642772e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.903641e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.410540e+01\n Vprtstp: contraction number = 1.410540e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.343223e-06\n Vprtstp: contraction number = 3.232297e-01\n Vnewton: Using errtol_s: 12.694863\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.900588e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.066777e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.625592e+00\n Vprtstp: contraction number = 4.625592e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.752206e-06\n Vprtstp: contraction number = 3.279305e-01\n Vnewton: Using errtol_s: 4.163033\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.156754e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.224183e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.534788e+00\n Vprtstp: contraction number = 1.534788e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 5.813881e-07\n Vprtstp: contraction number = 3.318035e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.944364e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.958467e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.767209e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.778326e+02\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -11086,15 +11086,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 6.281289332707E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.951972269789E+04 kT\n Vpmg_energy:  dielEnergy = 1.475242807069E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.932700e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.100700e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n@@ -11123,151 +11123,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.354146\n+Vacc_SASA: Time elapsed: 0.374632\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.089009e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.829000e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 6.108800e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.107970e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.516133e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.407600e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.440099e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.409475e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 679651.374556\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.476232e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.429993e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.196081e+04\n Vprtstp: contraction number = 9.196081e+04\n Vnewton: Attempting damping, relres = 0.130456\n Vnewton: Attempting damping, relres = 0.558557\n Vnewton: Damping accepted, relres = 0.130456\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.304558e-01\n Vprtstp: contraction number = 1.304558e-01\n Vnewton: Using errtol_s: 88664.431621\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.664904e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.551386e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.707604e+04\n Vprtstp: contraction number = 1.707604e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.296641e-02\n Vprtstp: contraction number = 1.760475e-01\n Vnewton: Using errtol_s: 15609.155466\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.840016e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.655081e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.862634e+03\n Vprtstp: contraction number = 3.862634e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 5.116511e-03\n Vprtstp: contraction number = 2.227823e-01\n Vnewton: Using errtol_s: 3477.443419\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.025197e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.759630e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.764405e+02\n Vprtstp: contraction number = 9.764405e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.293019e-03\n Vprtstp: contraction number = 2.527150e-01\n Vnewton: Using errtol_s: 878.801976\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.211910e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.862100e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.618442e+02\n Vprtstp: contraction number = 2.618442e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.467366e-04\n Vprtstp: contraction number = 2.681606e-01\n Vnewton: Using errtol_s: 235.660041\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.398524e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.970214e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.253883e+01\n Vprtstp: contraction number = 7.253883e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 9.605654e-05\n Vprtstp: contraction number = 2.770303e-01\n Vnewton: Using errtol_s: 65.284962\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.575753e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.082616e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.053942e+01\n Vprtstp: contraction number = 2.053942e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.719848e-05\n Vprtstp: contraction number = 2.831507e-01\n Vnewton: Using errtol_s: 18.485484\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.751315e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.196918e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.915703e+00\n Vprtstp: contraction number = 5.915703e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 7.833623e-06\n Vprtstp: contraction number = 2.880170e-01\n Vnewton: Using errtol_s: 5.324133\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.936104e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.298162e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.728194e+00\n Vprtstp: contraction number = 1.728194e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.288489e-06\n Vprtstp: contraction number = 2.921367e-01\n Vnewton: Using errtol_s: 1.555375\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.110550e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.406994e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.108177e-01\n Vprtstp: contraction number = 5.108177e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 6.764290e-07\n Vprtstp: contraction number = 2.955789e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.835363e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.852159e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.102627e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.114678e+02\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -11277,15 +11277,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.784786682149E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 6.832559781230E+03 kT\n Vpmg_energy:  dielEnergy = 3.414198595280E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.510700e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.696000e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 19.3778\n Vpbe_ctor2:  solute dimensions = 19.082 x 18.3114 x 35.7654\n Vpbe_ctor2:  solute charge = 4\n@@ -11334,160 +11334,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00419075 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.274767\n+Vacc_SASA: Time elapsed: 0.390990\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.662310e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.120230e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.680900e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 6.344200e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.114486e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.471930e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.299208e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.535340e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 707760.874892\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.326611e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.557839e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.145732e+05\n Vprtstp: contraction number = 1.145732e+05\n Vnewton: Attempting damping, relres = 0.153567\n Vnewton: Attempting damping, relres = 0.570617\n Vnewton: Damping accepted, relres = 0.153567\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.535669e-01\n Vprtstp: contraction number = 1.535669e-01\n Vnewton: Using errtol_s: 108688.631756\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.521391e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.695061e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.325223e+04\n Vprtstp: contraction number = 2.325223e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.989096e-02\n Vprtstp: contraction number = 1.946446e-01\n Vnewton: Using errtol_s: 21155.653880\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.731563e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.813655e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.636674e+03\n Vprtstp: contraction number = 5.636674e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.169438e-03\n Vprtstp: contraction number = 2.398530e-01\n Vnewton: Using errtol_s: 5074.248008\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.926464e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.927216e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.473491e+03\n Vprtstp: contraction number = 1.473491e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.873734e-03\n Vprtstp: contraction number = 2.613502e-01\n Vnewton: Using errtol_s: 1326.155494\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.112032e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.050479e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.049387e+02\n Vprtstp: contraction number = 4.049387e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.149280e-04\n Vprtstp: contraction number = 2.748139e-01\n Vnewton: Using errtol_s: 364.445920\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.306135e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.156962e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.151043e+02\n Vprtstp: contraction number = 1.151043e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.463685e-04\n Vprtstp: contraction number = 2.842504e-01\n Vnewton: Using errtol_s: 103.593915\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.494728e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.272893e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.354853e+01\n Vprtstp: contraction number = 3.354853e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.266085e-05\n Vprtstp: contraction number = 2.914619e-01\n Vnewton: Using errtol_s: 30.193683\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.697295e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.401631e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.989786e+00\n Vprtstp: contraction number = 9.989786e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.270317e-05\n Vprtstp: contraction number = 2.977712e-01\n Vnewton: Using errtol_s: 8.990808\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.885453e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.518608e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.036177e+00\n Vprtstp: contraction number = 3.036177e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.860851e-06\n Vprtstp: contraction number = 3.039281e-01\n Vnewton: Using errtol_s: 2.732559\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.072324e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.636846e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.395196e-01\n Vprtstp: contraction number = 9.395196e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.194708e-06\n Vprtstp: contraction number = 3.094416e-01\n Vnewton: Using errtol_s: 0.845568\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.266143e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.743934e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.950830e-01\n Vprtstp: contraction number = 2.950830e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.752323e-07\n Vprtstp: contraction number = 3.140786e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.140878e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.154412e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.306174e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.318299e+02\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -11497,17 +11497,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.776812399064E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 8.065083445518E+03 kT\n Vpmg_energy:  dielEnergy = 4.030471976313E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.849100e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.555300e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vnm_tstart: starting timer 27 (Setup timer)..\n@@ -11534,162 +11534,162 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.479040\n+Vacc_SASA: Time elapsed: 0.440903\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.314316e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.223884e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.454700e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.809100e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.698633e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.032755e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.488528e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.879344e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1635307.042590\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.523933e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.898627e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.321219e+05\n Vprtstp: contraction number = 2.321219e+05\n Vnewton: Attempting damping, relres = 0.196154\n Vnewton: Attempting damping, relres = 0.565205\n Vnewton: Damping accepted, relres = 0.196154\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.961538e-01\n Vprtstp: contraction number = 1.961538e-01\n Vnewton: Using errtol_s: 320771.668801\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.732009e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.018385e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.431372e+04\n Vprtstp: contraction number = 4.431372e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 4.027511e-02\n Vprtstp: contraction number = 2.053242e-01\n Vnewton: Using errtol_s: 65862.177446\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.979098e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.162315e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.117167e+04\n Vprtstp: contraction number = 1.117167e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 8.959711e-03\n Vprtstp: contraction number = 2.224627e-01\n Vnewton: Using errtol_s: 14651.878140\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.017453e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.290484e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.129072e+03\n Vprtstp: contraction number = 3.129072e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.898262e-03\n Vprtstp: contraction number = 2.118664e-01\n Vnewton: Using errtol_s: 3104.240662\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.036764e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.401788e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.589092e+02\n Vprtstp: contraction number = 8.589092e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.739068e-04\n Vprtstp: contraction number = 2.496530e-01\n Vnewton: Using errtol_s: 774.983094\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.056606e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.526033e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.479971e+02\n Vprtstp: contraction number = 2.479971e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.364875e-04\n Vprtstp: contraction number = 2.880050e-01\n Vnewton: Using errtol_s: 223.198993\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.077235e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.665502e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.463517e+01\n Vprtstp: contraction number = 7.463517e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.107588e-05\n Vprtstp: contraction number = 3.009497e-01\n Vnewton: Using errtol_s: 67.171671\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.096489e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.800202e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.269594e+01\n Vprtstp: contraction number = 2.269594e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.249083e-05\n Vprtstp: contraction number = 3.040916e-01\n Vnewton: Using errtol_s: 20.426343\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.116066e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.933315e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.936769e+00\n Vprtstp: contraction number = 6.936769e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.817688e-06\n Vprtstp: contraction number = 3.056392e-01\n Vnewton: Using errtol_s: 6.243092\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.135234e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.061663e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.126909e+00\n Vprtstp: contraction number = 2.126909e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.170556e-06\n Vprtstp: contraction number = 3.066138e-01\n Vnewton: Using errtol_s: 1.914218\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.153789e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.181243e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.536389e-01\n Vprtstp: contraction number = 6.536389e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.597337e-07\n Vprtstp: contraction number = 3.073187e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.214263e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.232744e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.426338e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.437560e+02\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -11699,15 +11699,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 8.754232717219E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.874256879798E+04 kT\n Vpmg_energy:  dielEnergy = 9.359714713535E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.600400e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.190690e-01\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 20.7943\n Vpbe_ctor2:  solute dimensions = 25.3482 x 27.3592 x 40.136\n Vpbe_ctor2:  solute charge = -18\n@@ -11756,160 +11756,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00885234 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.389160\n+Vacc_SASA: Time elapsed: 0.416341\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.285496e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.187043e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.878300e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.790900e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.246295e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.060016e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.173064e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.332523e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1674007.100681\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.175990e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.355715e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.902880e+05\n Vprtstp: contraction number = 2.902880e+05\n Vnewton: Attempting damping, relres = 0.222356\n Vnewton: Attempting damping, relres = 0.579491\n Vnewton: Damping accepted, relres = 0.222356\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.223561e-01\n Vprtstp: contraction number = 2.223561e-01\n Vnewton: Using errtol_s: 372225.695633\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.196329e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.505269e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.035839e+04\n Vprtstp: contraction number = 6.035839e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 4.793121e-02\n Vprtstp: contraction number = 2.155606e-01\n Vnewton: Using errtol_s: 80237.189117\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.222242e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.674993e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.603151e+04\n Vprtstp: contraction number = 1.603151e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.130393e-02\n Vprtstp: contraction number = 2.358364e-01\n Vnewton: Using errtol_s: 18922.853010\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.243976e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.819785e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.671524e+03\n Vprtstp: contraction number = 4.671524e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.665747e-03\n Vprtstp: contraction number = 2.358248e-01\n Vnewton: Using errtol_s: 4462.478601\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.263944e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.946994e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.362565e+03\n Vprtstp: contraction number = 1.362565e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 7.334180e-04\n Vprtstp: contraction number = 2.751267e-01\n Vnewton: Using errtol_s: 1227.746995\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.281981e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.076244e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.182590e+02\n Vprtstp: contraction number = 4.182590e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.248702e-04\n Vprtstp: contraction number = 3.066058e-01\n Vnewton: Using errtol_s: 376.434346\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.302901e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.201996e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.331321e+02\n Vprtstp: contraction number = 1.331321e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 7.157615e-05\n Vprtstp: contraction number = 3.182998e-01\n Vnewton: Using errtol_s: 119.818985\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.323580e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.315312e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.304104e+01\n Vprtstp: contraction number = 4.304104e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.314025e-05\n Vprtstp: contraction number = 3.232955e-01\n Vnewton: Using errtol_s: 38.736937\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.342883e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.441691e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.406731e+01\n Vprtstp: contraction number = 1.406731e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 7.563038e-06\n Vprtstp: contraction number = 3.268348e-01\n Vnewton: Using errtol_s: 12.660580\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.362803e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.561809e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.637253e+00\n Vprtstp: contraction number = 4.637253e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 2.493136e-06\n Vprtstp: contraction number = 3.296474e-01\n Vnewton: Using errtol_s: 4.173527\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.383006e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.692677e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.538961e+00\n Vprtstp: contraction number = 1.538961e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 8.273947e-07\n Vprtstp: contraction number = 3.318691e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.276853e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.290988e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.468788e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.481860e+02\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -11919,29 +11919,29 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 8.742146487539E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.135995019180E+04 kT\n Vpmg_energy:  dielEnergy = 1.066841914089E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.161810e-01\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.717600e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.402434e+03\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 8.816229e+02\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 07:06:49 2025\n+# Creation Date and Time:  Tue Jan  9 05:14:34 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path model_outNB.pqr\n@@ -12211,151 +12211,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.553408\n+Vacc_SASA: Time elapsed: 0.647565\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.682350e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.706646e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.720300e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.610800e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.132339e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.767140e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.933087e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.833131e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2280031.151733\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.560153e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.078231e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.954329e+05\n Vprtstp: contraction number = 2.954329e+05\n Vnewton: Attempting damping, relres = 0.135391\n Vnewton: Attempting damping, relres = 0.556564\n Vnewton: Damping accepted, relres = 0.135391\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.353914e-01\n Vprtstp: contraction number = 1.353914e-01\n Vnewton: Using errtol_s: 308696.705205\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.947794e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.267138e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.294410e+04\n Vprtstp: contraction number = 5.294410e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.429290e-02\n Vprtstp: contraction number = 1.794272e-01\n Vnewton: Using errtol_s: 55388.580044\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.654383e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.949318e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.235644e+04\n Vprtstp: contraction number = 1.235644e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 5.275732e-03\n Vprtstp: contraction number = 2.171717e-01\n Vnewton: Using errtol_s: 12028.832542\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.240643e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.707775e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.254639e+03\n Vprtstp: contraction number = 3.254639e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.294905e-03\n Vprtstp: contraction number = 2.454457e-01\n Vnewton: Using errtol_s: 2952.424699\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.061384e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.134711e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.022338e+02\n Vprtstp: contraction number = 9.022338e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.561621e-04\n Vprtstp: contraction number = 2.750487e-01\n Vnewton: Using errtol_s: 812.060580\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.300607e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.584907e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.611146e+02\n Vprtstp: contraction number = 2.611146e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.030702e-04\n Vprtstp: contraction number = 2.893914e-01\n Vnewton: Using errtol_s: 235.003369\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.533849e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.006475e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.731468e+01\n Vprtstp: contraction number = 7.731468e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.051854e-05\n Vprtstp: contraction number = 2.960946e-01\n Vnewton: Using errtol_s: 69.583224\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.780289e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.163514e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.323028e+01\n Vprtstp: contraction number = 2.323028e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 9.169724e-06\n Vprtstp: contraction number = 3.004640e-01\n Vnewton: Using errtol_s: 20.907256\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.016202e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.316822e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.057246e+00\n Vprtstp: contraction number = 7.057246e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.785717e-06\n Vprtstp: contraction number = 3.037951e-01\n Vnewton: Using errtol_s: 6.351522\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.260304e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.454729e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.163411e+00\n Vprtstp: contraction number = 2.163411e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 8.539662e-07\n Vprtstp: contraction number = 3.065517e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.461156e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.473352e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.587771e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.598629e+02\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -12365,15 +12365,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 6.169811385763E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.567248755988E+04 kT\n Vpmg_energy:  dielEnergy = 1.282904610946E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 9.001500e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.156380e-01\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 25.8477\n Vpbe_ctor2:  solute dimensions = 26.666 x 32.3234 x 48.3902\n Vpbe_ctor2:  solute charge = -14\n@@ -12422,160 +12422,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0200222 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.623916\n+Vacc_SASA: Time elapsed: 0.596108\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.665937e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.604540e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.811800e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.861900e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.210831e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.571210e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.522686e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.645369e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2338884.582029\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.552367e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.664947e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.674153e+05\n Vprtstp: contraction number = 3.674153e+05\n Vnewton: Attempting damping, relres = 0.159441\n Vnewton: Attempting damping, relres = 0.569142\n Vnewton: Damping accepted, relres = 0.159441\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.594406e-01\n Vprtstp: contraction number = 1.594406e-01\n Vnewton: Using errtol_s: 372913.066228\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.810948e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.855930e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.262273e+04\n Vprtstp: contraction number = 7.262273e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 3.123186e-02\n Vprtstp: contraction number = 1.958841e-01\n Vnewton: Using errtol_s: 73047.725996\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.068286e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.035700e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.810013e+04\n Vprtstp: contraction number = 1.810013e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.334559e-03\n Vprtstp: contraction number = 2.348422e-01\n Vnewton: Using errtol_s: 17154.687500\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.334616e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.202866e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.995290e+03\n Vprtstp: contraction number = 4.995290e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.929832e-03\n Vprtstp: contraction number = 2.631149e-01\n Vnewton: Using errtol_s: 4513.654553\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.608729e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.377592e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.448761e+03\n Vprtstp: contraction number = 1.448761e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.574979e-04\n Vprtstp: contraction number = 2.888841e-01\n Vnewton: Using errtol_s: 1303.923175\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.869370e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.528631e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.389996e+02\n Vprtstp: contraction number = 4.389996e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.689267e-04\n Vprtstp: contraction number = 3.030087e-01\n Vnewton: Using errtol_s: 395.100089\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.125665e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.709579e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.367279e+02\n Vprtstp: contraction number = 1.367279e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 5.261275e-05\n Vprtstp: contraction number = 3.114531e-01\n Vnewton: Using errtol_s: 123.055159\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.376808e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.907248e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.345198e+01\n Vprtstp: contraction number = 4.345198e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.672027e-05\n Vprtstp: contraction number = 3.177988e-01\n Vnewton: Using errtol_s: 39.106785\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.585156e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.066366e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.405050e+01\n Vprtstp: contraction number = 1.405050e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.406615e-06\n Vprtstp: contraction number = 3.233569e-01\n Vnewton: Using errtol_s: 12.645449\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.852396e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.223605e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.608577e+00\n Vprtstp: contraction number = 4.608577e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.773375e-06\n Vprtstp: contraction number = 3.280010e-01\n Vnewton: Using errtol_s: 4.147720\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.113274e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.386579e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.529264e+00\n Vprtstp: contraction number = 1.529264e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 5.884589e-07\n Vprtstp: contraction number = 3.318299e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.834231e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.847748e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.897603e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.908884e+02\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -12585,17 +12585,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 6.155729316700E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.951863418321E+04 kT\n Vpmg_energy:  dielEnergy = 1.475213228301E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.929400e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.148670e-01\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vnm_tstart: starting timer 27 (Setup timer)..\n@@ -12622,151 +12622,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.331823\n+Vacc_SASA: Time elapsed: 0.378625\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.169867e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.024100e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.669000e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.337690e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.448951e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 7.831530e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.398256e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.576826e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 671593.797102\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.429855e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.596036e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.076362e+04\n Vprtstp: contraction number = 9.076362e+04\n Vnewton: Attempting damping, relres = 0.130235\n Vnewton: Attempting damping, relres = 0.558450\n Vnewton: Damping accepted, relres = 0.130235\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.302353e-01\n Vprtstp: contraction number = 1.302353e-01\n Vnewton: Using errtol_s: 87465.248573\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.631078e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.726606e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.691112e+04\n Vprtstp: contraction number = 1.691112e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.299894e-02\n Vprtstp: contraction number = 1.765952e-01\n Vnewton: Using errtol_s: 15445.947049\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.819602e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.840344e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.838772e+03\n Vprtstp: contraction number = 3.838772e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 5.145781e-03\n Vprtstp: contraction number = 2.237399e-01\n Vnewton: Using errtol_s: 3455.874833\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.012727e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.954974e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.728949e+02\n Vprtstp: contraction number = 9.728949e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.303780e-03\n Vprtstp: contraction number = 2.533688e-01\n Vnewton: Using errtol_s: 875.610893\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.201794e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.070501e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.612895e+02\n Vprtstp: contraction number = 2.612895e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.501534e-04\n Vprtstp: contraction number = 2.685677e-01\n Vnewton: Using errtol_s: 235.160844\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.377957e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.176717e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.244969e+01\n Vprtstp: contraction number = 7.244969e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 9.708955e-05\n Vprtstp: contraction number = 2.772772e-01\n Vnewton: Using errtol_s: 65.204742\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.568986e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.298834e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.052456e+01\n Vprtstp: contraction number = 2.052456e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.750488e-05\n Vprtstp: contraction number = 2.832939e-01\n Vnewton: Using errtol_s: 18.472107\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.757446e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.435172e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.913055e+00\n Vprtstp: contraction number = 5.913055e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 7.924060e-06\n Vprtstp: contraction number = 2.880965e-01\n Vnewton: Using errtol_s: 5.321750\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.904822e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.562271e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.727677e+00\n Vprtstp: contraction number = 1.727677e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.315252e-06\n Vprtstp: contraction number = 2.921800e-01\n Vnewton: Using errtol_s: 1.554909\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.066215e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.704126e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.107037e-01\n Vprtstp: contraction number = 5.107037e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 6.843918e-07\n Vprtstp: contraction number = 2.956014e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.834285e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.849787e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.247391e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.257715e+02\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -12776,15 +12776,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.799206762061E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 6.832181524092E+03 kT\n Vpmg_energy:  dielEnergy = 3.414010557344E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 8.892000e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.430050e-01\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 19.3778\n Vpbe_ctor2:  solute dimensions = 19.082 x 18.3114 x 35.7654\n Vpbe_ctor2:  solute charge = 4\n@@ -12833,160 +12833,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00378487 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.379157\n+Vacc_SASA: Time elapsed: 0.340497\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.878370e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.881130e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.367100e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 8.061300e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.185891e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.150482e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.259488e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.849438e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 699069.872719\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.290297e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.872398e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.130075e+05\n Vprtstp: contraction number = 1.130075e+05\n Vnewton: Attempting damping, relres = 0.153289\n Vnewton: Attempting damping, relres = 0.570479\n Vnewton: Damping accepted, relres = 0.153289\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.532887e-01\n Vprtstp: contraction number = 1.532887e-01\n Vnewton: Using errtol_s: 107159.480370\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.506748e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.998153e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.297596e+04\n Vprtstp: contraction number = 2.297596e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.988594e-02\n Vprtstp: contraction number = 1.949651e-01\n Vnewton: Using errtol_s: 20892.361484\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.698678e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.116254e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.581341e+03\n Vprtstp: contraction number = 5.581341e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.187204e-03\n Vprtstp: contraction number = 2.404878e-01\n Vnewton: Using errtol_s: 5024.357995\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.901600e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.225318e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.462004e+03\n Vprtstp: contraction number = 1.462004e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.882240e-03\n Vprtstp: contraction number = 2.618876e-01\n Vnewton: Using errtol_s: 1315.817196\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.093671e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.344790e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.024878e+02\n Vprtstp: contraction number = 4.024878e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.181744e-04\n Vprtstp: contraction number = 2.752967e-01\n Vnewton: Using errtol_s: 362.240101\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.293810e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.470158e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.145747e+02\n Vprtstp: contraction number = 1.145747e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.475065e-04\n Vprtstp: contraction number = 2.846658e-01\n Vnewton: Using errtol_s: 103.117357\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.494994e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.603637e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.343339e+01\n Vprtstp: contraction number = 3.343339e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.304299e-05\n Vprtstp: contraction number = 2.918040e-01\n Vnewton: Using errtol_s: 30.090059\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.689122e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.723354e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.964601e+00\n Vprtstp: contraction number = 9.964601e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.282868e-05\n Vprtstp: contraction number = 2.980433e-01\n Vnewton: Using errtol_s: 8.968142\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.883093e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.854058e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.030606e+00\n Vprtstp: contraction number = 3.030606e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.901677e-06\n Vprtstp: contraction number = 3.041372e-01\n Vnewton: Using errtol_s: 2.727545\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.071554e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.970982e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.382714e-01\n Vprtstp: contraction number = 9.382714e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.207954e-06\n Vprtstp: contraction number = 3.095986e-01\n Vnewton: Using errtol_s: 0.844444\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.269144e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.078328e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.947982e-01\n Vprtstp: contraction number = 2.947982e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.795306e-07\n Vprtstp: contraction number = 3.141929e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.193235e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.207978e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.327526e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.341554e+02\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -12996,15 +12996,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.791143336195E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 8.064706767372E+03 kT\n Vpmg_energy:  dielEnergy = 4.030284850929E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 8.931800e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.096800e-01\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n@@ -13033,162 +13033,162 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.454738\n+Vacc_SASA: Time elapsed: 0.427891\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.341880e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.118227e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.236500e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.740700e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.111537e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.984390e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.493665e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.218308e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1599051.147684\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.520657e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.237474e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.270628e+05\n Vprtstp: contraction number = 2.270628e+05\n Vnewton: Attempting damping, relres = 0.190153\n Vnewton: Attempting damping, relres = 0.564950\n Vnewton: Damping accepted, relres = 0.190153\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.901527e-01\n Vprtstp: contraction number = 1.901527e-01\n Vnewton: Using errtol_s: 304063.886192\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.687610e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.365467e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.318204e+04\n Vprtstp: contraction number = 4.318204e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 3.822370e-02\n Vprtstp: contraction number = 2.010158e-01\n Vnewton: Using errtol_s: 61121.655411\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.876259e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.514028e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.090069e+04\n Vprtstp: contraction number = 1.090069e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 8.378283e-03\n Vprtstp: contraction number = 2.191908e-01\n Vnewton: Using errtol_s: 13397.302580\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.001178e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.641984e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.039014e+03\n Vprtstp: contraction number = 3.039014e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.821126e-03\n Vprtstp: contraction number = 2.173626e-01\n Vnewton: Using errtol_s: 2912.073157\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.014667e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.763022e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.399695e+02\n Vprtstp: contraction number = 8.399695e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.733052e-04\n Vprtstp: contraction number = 2.598970e-01\n Vnewton: Using errtol_s: 756.839199\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.029894e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.891521e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.453869e+02\n Vprtstp: contraction number = 2.453869e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.381125e-04\n Vprtstp: contraction number = 2.918043e-01\n Vnewton: Using errtol_s: 220.848913\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.043556e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.009483e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.399321e+01\n Vprtstp: contraction number = 7.399321e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.164589e-05\n Vprtstp: contraction number = 3.015360e-01\n Vnewton: Using errtol_s: 66.593908\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.056701e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.129338e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.251212e+01\n Vprtstp: contraction number = 2.251212e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.267058e-05\n Vprtstp: contraction number = 3.042457e-01\n Vnewton: Using errtol_s: 20.260912\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.069961e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.248889e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.882100e+00\n Vprtstp: contraction number = 6.882100e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.873479e-06\n Vprtstp: contraction number = 3.057064e-01\n Vnewton: Using errtol_s: 6.193891\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.082894e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.368097e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.110443e+00\n Vprtstp: contraction number = 2.110443e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.187828e-06\n Vprtstp: contraction number = 3.066568e-01\n Vnewton: Using errtol_s: 1.899398\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.097644e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.477847e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.486511e-01\n Vprtstp: contraction number = 6.486511e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.650828e-07\n Vprtstp: contraction number = 3.073531e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.601693e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.613641e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.357157e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.368850e+02\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -13198,15 +13198,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 8.557875288957E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.874100920803E+04 kT\n Vpmg_energy:  dielEnergy = 9.359333289528E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.591700e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.256900e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 20.7943\n Vpbe_ctor2:  solute dimensions = 25.3482 x 27.3592 x 40.136\n Vpbe_ctor2:  solute charge = -18\n@@ -13255,160 +13255,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00715191 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.432345\n+Vacc_SASA: Time elapsed: 0.449545\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.315770e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.178747e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.603200e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 6.765100e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.087722e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.032760e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.112274e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.600108e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1635353.597903\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.114373e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.621350e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.841111e+05\n Vprtstp: contraction number = 2.841111e+05\n Vnewton: Attempting damping, relres = 0.216841\n Vnewton: Attempting damping, relres = 0.579374\n Vnewton: Damping accepted, relres = 0.216841\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.168415e-01\n Vprtstp: contraction number = 2.168415e-01\n Vnewton: Using errtol_s: 354612.472828\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.132516e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.762772e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.888895e+04\n Vprtstp: contraction number = 5.888895e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 4.598888e-02\n Vprtstp: contraction number = 2.120853e-01\n Vnewton: Using errtol_s: 75208.075023\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.152590e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.936327e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.566082e+04\n Vprtstp: contraction number = 1.566082e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.075687e-02\n Vprtstp: contraction number = 2.339015e-01\n Vnewton: Using errtol_s: 17591.280350\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.171771e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.068483e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.551176e+03\n Vprtstp: contraction number = 4.551176e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.599859e-03\n Vprtstp: contraction number = 2.416930e-01\n Vnewton: Using errtol_s: 4251.688603\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.186118e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.187928e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.335913e+03\n Vprtstp: contraction number = 1.335913e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 7.355871e-04\n Vprtstp: contraction number = 2.829335e-01\n Vnewton: Using errtol_s: 1202.945014\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.199861e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.316364e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.136155e+02\n Vprtstp: contraction number = 4.136155e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.276295e-04\n Vprtstp: contraction number = 3.094528e-01\n Vnewton: Using errtol_s: 372.254692\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.215661e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.452408e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.319427e+02\n Vprtstp: contraction number = 1.319427e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 7.261334e-05\n Vprtstp: contraction number = 3.189980e-01\n Vnewton: Using errtol_s: 118.748486\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.231990e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.572690e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.270247e+01\n Vprtstp: contraction number = 4.270247e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.350087e-05\n Vprtstp: contraction number = 3.236440e-01\n Vnewton: Using errtol_s: 38.432230\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.247718e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.703576e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.396688e+01\n Vprtstp: contraction number = 1.396688e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 7.686528e-06\n Vprtstp: contraction number = 3.270742e-01\n Vnewton: Using errtol_s: 12.570191\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.262211e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.836415e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.606421e+00\n Vprtstp: contraction number = 4.606421e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 2.535096e-06\n Vprtstp: contraction number = 3.298104e-01\n Vnewton: Using errtol_s: 4.145779\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.276337e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.959488e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.529247e+00\n Vprtstp: contraction number = 1.529247e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 8.416053e-07\n Vprtstp: contraction number = 3.319816e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.767939e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.780447e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.470067e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.481300e+02\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -13418,29 +13418,29 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 8.546220466896E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.135839093340E+04 kT\n Vpmg_energy:  dielEnergy = 1.066803828890E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.773600e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.137000e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.290794e+03\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 9.085409e+02\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 07:09:01 2025\n+# Creation Date and Time:  Tue Jan  9 05:17:19 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path model_outNB.pqr\n@@ -13710,151 +13710,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.575609\n+Vacc_SASA: Time elapsed: 0.584598\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.561194e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.590726e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.147500e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.786900e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.000260e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.001382e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.787355e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.727118e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2251971.697064\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.956200e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.670401e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.916802e+05\n Vprtstp: contraction number = 2.916802e+05\n Vnewton: Attempting damping, relres = 0.133998\n Vnewton: Attempting damping, relres = 0.556443\n Vnewton: Damping accepted, relres = 0.133998\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.339981e-01\n Vprtstp: contraction number = 1.339981e-01\n Vnewton: Using errtol_s: 301759.930673\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.376806e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.029298e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.235007e+04\n Vprtstp: contraction number = 5.235007e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.393476e-02\n Vprtstp: contraction number = 1.786201e-01\n Vnewton: Using errtol_s: 53900.402880\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.279487e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.582196e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.224190e+04\n Vprtstp: contraction number = 1.224190e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 5.213784e-03\n Vprtstp: contraction number = 2.178331e-01\n Vnewton: Using errtol_s: 11741.294295\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.807120e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.069328e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.226956e+03\n Vprtstp: contraction number = 3.226956e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.296373e-03\n Vprtstp: contraction number = 2.486433e-01\n Vnewton: Using errtol_s: 2919.394410\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.374871e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.471305e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.979745e+02\n Vprtstp: contraction number = 8.979745e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.588880e-04\n Vprtstp: contraction number = 2.768402e-01\n Vnewton: Using errtol_s: 808.205614\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.104083e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.957402e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.602996e+02\n Vprtstp: contraction number = 2.602996e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.040288e-04\n Vprtstp: contraction number = 2.898642e-01\n Vnewton: Using errtol_s: 234.269873\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.080874e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.346718e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.710898e+01\n Vprtstp: contraction number = 7.710898e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.081659e-05\n Vprtstp: contraction number = 2.962314e-01\n Vnewton: Using errtol_s: 69.398097\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.262606e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.069003e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.317379e+01\n Vprtstp: contraction number = 2.317379e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 9.261402e-06\n Vprtstp: contraction number = 3.005329e-01\n Vnewton: Using errtol_s: 20.856415\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.452038e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.229310e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.040959e+00\n Vprtstp: contraction number = 7.040959e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.813918e-06\n Vprtstp: contraction number = 3.038328e-01\n Vnewton: Using errtol_s: 6.336864\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.622542e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.382147e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.158573e+00\n Vprtstp: contraction number = 2.158573e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 8.626731e-07\n Vprtstp: contraction number = 3.065736e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.753068e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.765415e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.476473e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.487460e+02\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -13864,15 +13864,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 6.054258370854E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.567152466024E+04 kT\n Vpmg_energy:  dielEnergy = 1.282878106932E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.391500e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.888700e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 25.8477\n Vpbe_ctor2:  solute dimensions = 26.666 x 32.3234 x 48.3902\n Vpbe_ctor2:  solute charge = -14\n@@ -13921,160 +13921,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0186115 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.619691\n+Vacc_SASA: Time elapsed: 0.593304\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.626604e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.564233e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.968100e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.201700e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.061412e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.062309e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.810786e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.533066e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2308477.613734\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.835230e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.552659e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.628256e+05\n Vprtstp: contraction number = 3.628256e+05\n Vnewton: Attempting damping, relres = 0.158221\n Vnewton: Attempting damping, relres = 0.569085\n Vnewton: Damping accepted, relres = 0.158221\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.582211e-01\n Vprtstp: contraction number = 1.582211e-01\n Vnewton: Using errtol_s: 365249.935342\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.066498e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.728002e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.179371e+04\n Vprtstp: contraction number = 7.179371e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 3.090684e-02\n Vprtstp: contraction number = 1.953395e-01\n Vnewton: Using errtol_s: 71347.745828\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.298633e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.892318e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.791601e+04\n Vprtstp: contraction number = 1.791601e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.281434e-03\n Vprtstp: contraction number = 2.355930e-01\n Vnewton: Using errtol_s: 16809.026903\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.537355e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.056844e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.947991e+03\n Vprtstp: contraction number = 4.947991e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.933961e-03\n Vprtstp: contraction number = 2.656017e-01\n Vnewton: Using errtol_s: 4464.506758\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.766054e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.216662e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.439628e+03\n Vprtstp: contraction number = 1.439628e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.612744e-04\n Vprtstp: contraction number = 2.902201e-01\n Vnewton: Using errtol_s: 1295.689464\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.010587e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.358408e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.369472e+02\n Vprtstp: contraction number = 4.369472e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.703516e-04\n Vprtstp: contraction number = 3.035087e-01\n Vnewton: Using errtol_s: 393.252962\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.266790e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.513993e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.361967e+02\n Vprtstp: contraction number = 1.361967e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 5.309866e-05\n Vprtstp: contraction number = 3.117003e-01\n Vnewton: Using errtol_s: 122.577063\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.529633e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.660303e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.330599e+01\n Vprtstp: contraction number = 4.330599e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.688359e-05\n Vprtstp: contraction number = 3.179665e-01\n Vnewton: Using errtol_s: 38.975398\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.789430e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.807234e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.400799e+01\n Vprtstp: contraction number = 1.400799e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.461259e-06\n Vprtstp: contraction number = 3.234655e-01\n Vnewton: Using errtol_s: 12.607195\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.050623e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.965470e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.595493e+00\n Vprtstp: contraction number = 4.595493e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.791632e-06\n Vprtstp: contraction number = 3.280621e-01\n Vnewton: Using errtol_s: 4.135943\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.305688e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.121703e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.525032e+00\n Vprtstp: contraction number = 1.525032e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 5.945603e-07\n Vprtstp: contraction number = 3.318539e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.742959e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.755291e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.711772e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.723880e+02\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -14084,15 +14084,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 6.040496519362E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.951767181280E+04 kT\n Vpmg_energy:  dielEnergy = 1.475186803356E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.504900e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.323300e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n@@ -14121,151 +14121,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.389152\n+Vacc_SASA: Time elapsed: 0.342535\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.190063e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.633350e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.747200e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.009800e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.290407e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 8.963250e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.595614e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.281333e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 665026.668065\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.626399e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.303452e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.977874e+04\n Vprtstp: contraction number = 8.977874e+04\n Vnewton: Attempting damping, relres = 0.130004\n Vnewton: Attempting damping, relres = 0.558352\n Vnewton: Damping accepted, relres = 0.130004\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.300040e-01\n Vprtstp: contraction number = 1.300040e-01\n Vnewton: Using errtol_s: 86456.120106\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.826312e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.438533e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.677494e+04\n Vprtstp: contraction number = 1.677494e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.302058e-02\n Vprtstp: contraction number = 1.770760e-01\n Vnewton: Using errtol_s: 15309.299757\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.009270e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.548084e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.819009e+03\n Vprtstp: contraction number = 3.819009e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 5.169720e-03\n Vprtstp: contraction number = 2.245695e-01\n Vnewton: Using errtol_s: 3438.001701\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.174474e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.670142e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.699577e+02\n Vprtstp: contraction number = 9.699577e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.312680e-03\n Vprtstp: contraction number = 2.539171e-01\n Vnewton: Using errtol_s: 872.967407\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.353110e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.779388e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.608286e+02\n Vprtstp: contraction number = 2.608286e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.529874e-04\n Vprtstp: contraction number = 2.689059e-01\n Vnewton: Using errtol_s: 234.746058\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.530133e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.888461e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.237536e+01\n Vprtstp: contraction number = 7.237536e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 9.794772e-05\n Vprtstp: contraction number = 2.774822e-01\n Vnewton: Using errtol_s: 65.137847\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.705868e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.995863e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.051211e+01\n Vprtstp: contraction number = 2.051211e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.775964e-05\n Vprtstp: contraction number = 2.834128e-01\n Vnewton: Using errtol_s: 18.460901\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.890877e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.098995e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.910817e+00\n Vprtstp: contraction number = 5.910817e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 7.999282e-06\n Vprtstp: contraction number = 2.881623e-01\n Vnewton: Using errtol_s: 5.319736\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.065651e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.203418e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.727236e+00\n Vprtstp: contraction number = 1.727236e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.337519e-06\n Vprtstp: contraction number = 2.922161e-01\n Vnewton: Using errtol_s: 1.554512\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.235370e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.308142e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.106059e-01\n Vprtstp: contraction number = 5.106059e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 6.910179e-07\n Vprtstp: contraction number = 2.956203e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.805090e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.819121e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.118525e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.128763e+02\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -14275,15 +14275,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.810176987891E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 6.831840502654E+03 kT\n Vpmg_energy:  dielEnergy = 3.413842577574E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.726600e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.086300e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 19.3778\n Vpbe_ctor2:  solute dimensions = 19.082 x 18.3114 x 35.7654\n Vpbe_ctor2:  solute charge = 4\n@@ -14332,160 +14332,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00343543 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.316406\n+Vacc_SASA: Time elapsed: 0.381538\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.036591e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 8.884490e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.934300e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.883300e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.221830e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.067426e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.426086e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.423420e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 691979.805773\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.456605e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.442291e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.117154e+05\n Vprtstp: contraction number = 1.117154e+05\n Vnewton: Attempting damping, relres = 0.153004\n Vnewton: Attempting damping, relres = 0.570353\n Vnewton: Damping accepted, relres = 0.153004\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.530041e-01\n Vprtstp: contraction number = 1.530041e-01\n Vnewton: Using errtol_s: 105875.763511\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.668202e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.584303e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.274708e+04\n Vprtstp: contraction number = 2.274708e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.987439e-02\n Vprtstp: contraction number = 1.952522e-01\n Vnewton: Using errtol_s: 20672.472417\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.855219e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.706514e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.535330e+03\n Vprtstp: contraction number = 5.535330e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.200880e-03\n Vprtstp: contraction number = 2.410386e-01\n Vnewton: Using errtol_s: 4982.863785\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.041191e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.819899e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.452451e+03\n Vprtstp: contraction number = 1.452451e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.889102e-03\n Vprtstp: contraction number = 2.623432e-01\n Vnewton: Using errtol_s: 1307.220185\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.231994e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.929589e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.004485e+02\n Vprtstp: contraction number = 4.004485e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.208313e-04\n Vprtstp: contraction number = 2.757032e-01\n Vnewton: Using errtol_s: 360.404730\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.428832e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.040300e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.141337e+02\n Vprtstp: contraction number = 1.141337e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.484443e-04\n Vprtstp: contraction number = 2.850142e-01\n Vnewton: Using errtol_s: 102.720463\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.624462e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.152226e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.333734e+01\n Vprtstp: contraction number = 3.333734e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.335909e-05\n Vprtstp: contraction number = 2.920899e-01\n Vnewton: Using errtol_s: 30.003614\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.822628e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.261885e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.943557e+00\n Vprtstp: contraction number = 9.943557e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.293275e-05\n Vprtstp: contraction number = 2.982708e-01\n Vnewton: Using errtol_s: 8.949202\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.022168e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.367230e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.025944e+00\n Vprtstp: contraction number = 3.025944e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.935591e-06\n Vprtstp: contraction number = 3.043120e-01\n Vnewton: Using errtol_s: 2.723350\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.220313e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.474388e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.372238e-01\n Vprtstp: contraction number = 9.372238e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.218968e-06\n Vprtstp: contraction number = 3.097294e-01\n Vnewton: Using errtol_s: 0.843501\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.422083e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.582703e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.945582e-01\n Vprtstp: contraction number = 2.945582e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.831071e-07\n Vprtstp: contraction number = 3.142880e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.177553e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.191527e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.252563e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.265786e+02\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -14495,17 +14495,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.802033666464E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 8.064367172760E+03 kT\n Vpmg_energy:  dielEnergy = 4.030117685645E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.527100e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.135410e-01\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vnm_tstart: starting timer 27 (Setup timer)..\n@@ -14532,162 +14532,162 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.334751\n+Vacc_SASA: Time elapsed: 0.424891\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.194762e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.219640e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.573100e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.820200e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.198608e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.620350e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.641551e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.715203e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1569842.241791\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.670609e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.734852e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.229696e+05\n Vprtstp: contraction number = 2.229696e+05\n Vnewton: Attempting damping, relres = 0.185061\n Vnewton: Attempting damping, relres = 0.564709\n Vnewton: Damping accepted, relres = 0.185061\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.850613e-01\n Vprtstp: contraction number = 1.850613e-01\n Vnewton: Using errtol_s: 290517.094461\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.876813e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.862554e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.227646e+04\n Vprtstp: contraction number = 4.227646e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 3.651895e-02\n Vprtstp: contraction number = 1.973343e-01\n Vnewton: Using errtol_s: 57328.986523\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.115281e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.003398e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.068153e+04\n Vprtstp: contraction number = 1.068153e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.924548e-03\n Vprtstp: contraction number = 2.169982e-01\n Vnewton: Using errtol_s: 12440.289572\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.321497e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.124560e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.967582e+03\n Vprtstp: contraction number = 2.967582e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.771235e-03\n Vprtstp: contraction number = 2.235125e-01\n Vnewton: Using errtol_s: 2780.560196\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.515349e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.227926e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.265098e+02\n Vprtstp: contraction number = 8.265098e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.740960e-04\n Vprtstp: contraction number = 2.676640e-01\n Vnewton: Using errtol_s: 744.255948\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.701924e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.343441e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.434115e+02\n Vprtstp: contraction number = 2.434115e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.395496e-04\n Vprtstp: contraction number = 2.943487e-01\n Vnewton: Using errtol_s: 219.070780\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.886596e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.467295e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.348771e+01\n Vprtstp: contraction number = 7.348771e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.213095e-05\n Vprtstp: contraction number = 3.019068e-01\n Vnewton: Using errtol_s: 66.138952\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.008536e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.584998e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.236672e+01\n Vprtstp: contraction number = 2.236672e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.282298e-05\n Vprtstp: contraction number = 3.043600e-01\n Vnewton: Using errtol_s: 20.130053\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.028071e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.699158e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.838847e+00\n Vprtstp: contraction number = 6.838847e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.920752e-06\n Vprtstp: contraction number = 3.057599e-01\n Vnewton: Using errtol_s: 6.154962\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.045971e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.808048e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.097413e+00\n Vprtstp: contraction number = 2.097413e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.202459e-06\n Vprtstp: contraction number = 3.066910e-01\n Vnewton: Using errtol_s: 1.887672\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.064671e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.907041e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.447028e-01\n Vprtstp: contraction number = 6.447028e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.696120e-07\n Vprtstp: contraction number = 3.073800e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.166612e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.180174e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.281577e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.292828e+02\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -14697,15 +14697,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 8.380223605804E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.873963354108E+04 kT\n Vpmg_energy:  dielEnergy = 9.358993220617E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 9.813000e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.869000e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 20.7943\n Vpbe_ctor2:  solute dimensions = 25.3482 x 27.3592 x 40.136\n Vpbe_ctor2:  solute charge = -18\n@@ -14754,160 +14754,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00593059 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.466785\n+Vacc_SASA: Time elapsed: 0.427944\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.290226e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.159472e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.035000e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.760600e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.257033e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.647470e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.083815e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.021969e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1604207.937715\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.086830e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.040536e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.790911e+05\n Vprtstp: contraction number = 2.790911e+05\n Vnewton: Attempting damping, relres = 0.212135\n Vnewton: Attempting damping, relres = 0.579242\n Vnewton: Damping accepted, relres = 0.212135\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.121354e-01\n Vprtstp: contraction number = 2.121354e-01\n Vnewton: Using errtol_s: 340309.311873\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.103630e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.180772e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.770596e+04\n Vprtstp: contraction number = 5.770596e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 4.436697e-02\n Vprtstp: contraction number = 2.091445e-01\n Vnewton: Using errtol_s: 71173.837804\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.121803e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.361011e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.535772e+04\n Vprtstp: contraction number = 1.535772e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 1.032915e-02\n Vprtstp: contraction number = 2.328117e-01\n Vnewton: Using errtol_s: 16570.101449\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.139375e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.484361e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.454547e+03\n Vprtstp: contraction number = 4.454547e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.558458e-03\n Vprtstp: contraction number = 2.476930e-01\n Vnewton: Using errtol_s: 4104.298326\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.158942e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.622580e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.316329e+03\n Vprtstp: contraction number = 1.316329e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 7.386763e-04\n Vprtstp: contraction number = 2.887193e-01\n Vnewton: Using errtol_s: 1184.990339\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.177944e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.750125e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.099732e+02\n Vprtstp: contraction number = 4.099732e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.300054e-04\n Vprtstp: contraction number = 3.113751e-01\n Vnewton: Using errtol_s: 368.976439\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.191770e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.889347e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.309902e+02\n Vprtstp: contraction number = 1.309902e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 7.348872e-05\n Vprtstp: contraction number = 3.195087e-01\n Vnewton: Using errtol_s: 117.891195\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.204182e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.027737e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.243118e+01\n Vprtstp: contraction number = 4.243118e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.380494e-05\n Vprtstp: contraction number = 3.239264e-01\n Vnewton: Using errtol_s: 38.188070\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.221064e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.149668e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.388647e+01\n Vprtstp: contraction number = 1.388647e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 7.790652e-06\n Vprtstp: contraction number = 3.272704e-01\n Vnewton: Using errtol_s: 12.497826\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.236840e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.263153e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.581763e+00\n Vprtstp: contraction number = 4.581763e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 2.570482e-06\n Vprtstp: contraction number = 3.299443e-01\n Vnewton: Using errtol_s: 4.123587\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.253295e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.371525e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.521483e+00\n Vprtstp: contraction number = 1.521483e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 8.535894e-07\n Vprtstp: contraction number = 3.320737e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.850544e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.865478e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.473071e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.484713e+02\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -14917,29 +14917,29 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 8.368902130517E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.135701558187E+04 kT\n Vpmg_energy:  dielEnergy = 1.066769863960E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.832200e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.723900e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.270711e+03\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 8.510253e+02\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 07:11:21 2025\n+# Creation Date and Time:  Tue Jan  9 05:20:02 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path model_outNB.pqr\n@@ -15209,151 +15209,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.629434\n+Vacc_SASA: Time elapsed: 0.609068\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.590959e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.632426e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.772900e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.962800e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.086733e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.105759e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.832811e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.867220e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2228500.711111\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.154783e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.355263e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.885324e+05\n Vprtstp: contraction number = 2.885324e+05\n Vnewton: Attempting damping, relres = 0.132783\n Vnewton: Attempting damping, relres = 0.556333\n Vnewton: Damping accepted, relres = 0.132783\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.327828e-01\n Vprtstp: contraction number = 1.327828e-01\n Vnewton: Using errtol_s: 295906.495800\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.205679e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.049958e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.185298e+04\n Vprtstp: contraction number = 5.185298e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.363031e-02\n Vprtstp: contraction number = 1.779622e-01\n Vnewton: Using errtol_s: 52660.160944\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.164454e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.544910e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.214543e+04\n Vprtstp: contraction number = 1.214543e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 5.166063e-03\n Vprtstp: contraction number = 2.186202e-01\n Vnewton: Using errtol_s: 11512.574293\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.165134e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.953032e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.204841e+03\n Vprtstp: contraction number = 3.204841e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.298834e-03\n Vprtstp: contraction number = 2.514166e-01\n Vnewton: Using errtol_s: 2894.452376\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.761170e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.380512e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.947420e+02\n Vprtstp: contraction number = 8.947420e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.613575e-04\n Vprtstp: contraction number = 2.782168e-01\n Vnewton: Using errtol_s: 805.285400\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.770893e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.846433e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.596666e+02\n Vprtstp: contraction number = 2.596666e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.048688e-04\n Vprtstp: contraction number = 2.902078e-01\n Vnewton: Using errtol_s: 233.700117\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.149550e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.235713e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.695052e+01\n Vprtstp: contraction number = 7.695052e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.107716e-05\n Vprtstp: contraction number = 2.963434e-01\n Vnewton: Using errtol_s: 69.255484\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.328711e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.068199e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.313064e+01\n Vprtstp: contraction number = 2.313064e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 9.341518e-06\n Vprtstp: contraction number = 3.005911e-01\n Vnewton: Using errtol_s: 20.817580\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.515197e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.199790e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.028571e+00\n Vprtstp: contraction number = 7.028571e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.838551e-06\n Vprtstp: contraction number = 3.038640e-01\n Vnewton: Using errtol_s: 6.325714\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.713516e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.342569e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.154905e+00\n Vprtstp: contraction number = 2.154905e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 8.702776e-07\n Vprtstp: contraction number = 3.065922e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.834975e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.846943e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.454026e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.466002e+02\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -15363,17 +15363,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 5.948103828558E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.567066305004E+04 kT\n Vpmg_energy:  dielEnergy = 1.282854148760E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 8.188000e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.956700e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 25.8477\n Vpbe_ctor2:  solute dimensions = 26.666 x 32.3234 x 48.3902\n Vpbe_ctor2:  solute charge = -14\n Vpbe_ctor2:  bulk ionic strength = 0.275\n Vpbe_ctor2:  xkappa = 0.17076\n@@ -15420,160 +15420,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0175518 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.611741\n+Vacc_SASA: Time elapsed: 0.556148\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.429071e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.555859e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.211600e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.919800e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.005260e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.069316e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.892404e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.512550e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2283064.573073\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.911515e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.537373e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.589605e+05\n Vprtstp: contraction number = 3.589605e+05\n Vnewton: Attempting damping, relres = 0.157146\n Vnewton: Attempting damping, relres = 0.569027\n Vnewton: Damping accepted, relres = 0.157146\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.571455e-01\n Vprtstp: contraction number = 1.571455e-01\n Vnewton: Using errtol_s: 358773.390898\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.085587e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.715090e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.109555e+04\n Vprtstp: contraction number = 7.109555e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 3.062803e-02\n Vprtstp: contraction number = 1.949023e-01\n Vnewton: Using errtol_s: 69925.774403\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.271745e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.905939e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.775956e+04\n Vprtstp: contraction number = 1.775956e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.240527e-03\n Vprtstp: contraction number = 2.364020e-01\n Vnewton: Using errtol_s: 16530.590965\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.442458e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.109815e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.909187e+03\n Vprtstp: contraction number = 4.909187e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.938451e-03\n Vprtstp: contraction number = 2.677224e-01\n Vnewton: Using errtol_s: 4425.608962\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.649994e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.292196e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.432328e+03\n Vprtstp: contraction number = 1.432328e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.646405e-04\n Vprtstp: contraction number = 2.912844e-01\n Vnewton: Using errtol_s: 1289.110788\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.851741e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.444564e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.352860e+02\n Vprtstp: contraction number = 4.352860e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.715930e-04\n Vprtstp: contraction number = 3.038977e-01\n Vnewton: Using errtol_s: 391.757810\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.034614e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.597583e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.357704e+02\n Vprtstp: contraction number = 1.357704e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 5.352166e-05\n Vprtstp: contraction number = 3.119106e-01\n Vnewton: Using errtol_s: 122.193412\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.223395e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.765823e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.319013e+01\n Vprtstp: contraction number = 4.319013e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.702585e-05\n Vprtstp: contraction number = 3.181115e-01\n Vnewton: Using errtol_s: 38.871124\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.454268e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.955750e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.397456e+01\n Vprtstp: contraction number = 1.397456e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.508868e-06\n Vprtstp: contraction number = 3.235590e-01\n Vnewton: Using errtol_s: 12.577101\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.648836e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.109827e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.585274e+00\n Vprtstp: contraction number = 4.585274e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.807547e-06\n Vprtstp: contraction number = 3.281159e-01\n Vnewton: Using errtol_s: 4.126746\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.806332e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.254371e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.521742e+00\n Vprtstp: contraction number = 1.521742e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 5.998813e-07\n Vprtstp: contraction number = 3.318759e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.082776e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.095694e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.901902e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.914569e+02\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -15583,17 +15583,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 5.934616474565E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.951681070136E+04 kT\n Vpmg_energy:  dielEnergy = 1.475162911234E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 8.765200e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.564500e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vnm_tstart: starting timer 27 (Setup timer)..\n@@ -15620,151 +15620,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.387009\n+Vacc_SASA: Time elapsed: 0.301153\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.065807e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.005240e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.184000e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.833800e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.379965e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.037190e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.019387e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.451308e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 659573.848020\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.045408e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.471535e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.895379e+04\n Vprtstp: contraction number = 8.895379e+04\n Vnewton: Attempting damping, relres = 0.129769\n Vnewton: Attempting damping, relres = 0.558262\n Vnewton: Damping accepted, relres = 0.129769\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.297694e-01\n Vprtstp: contraction number = 1.297694e-01\n Vnewton: Using errtol_s: 85592.483355\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.189718e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.598421e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.666045e+04\n Vprtstp: contraction number = 1.666045e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.303462e-02\n Vprtstp: contraction number = 1.775043e-01\n Vnewton: Using errtol_s: 15193.035895\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.340645e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.741157e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.802357e+03\n Vprtstp: contraction number = 3.802357e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 5.189623e-03\n Vprtstp: contraction number = 2.252966e-01\n Vnewton: Using errtol_s: 3422.939434\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.491828e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.845394e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.674822e+02\n Vprtstp: contraction number = 9.674822e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.320155e-03\n Vprtstp: contraction number = 2.543835e-01\n Vnewton: Using errtol_s: 870.739405\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.618156e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.942531e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.604392e+02\n Vprtstp: contraction number = 2.604392e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.553742e-04\n Vprtstp: contraction number = 2.691914e-01\n Vnewton: Using errtol_s: 234.395549\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.753105e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.042099e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.231232e+01\n Vprtstp: contraction number = 7.231232e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 9.867144e-05\n Vprtstp: contraction number = 2.776550e-01\n Vnewton: Using errtol_s: 65.081104\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.873148e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.152243e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.050149e+01\n Vprtstp: contraction number = 2.050149e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.797465e-05\n Vprtstp: contraction number = 2.835131e-01\n Vnewton: Using errtol_s: 18.451347\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.003853e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.279866e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.908895e+00\n Vprtstp: contraction number = 5.908895e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.062791e-06\n Vprtstp: contraction number = 2.882178e-01\n Vnewton: Using errtol_s: 5.318006\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.131737e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.399051e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.726854e+00\n Vprtstp: contraction number = 1.726854e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.356322e-06\n Vprtstp: contraction number = 2.922465e-01\n Vnewton: Using errtol_s: 1.554169\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.254030e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.531759e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.105208e-01\n Vprtstp: contraction number = 5.105208e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 6.966145e-07\n Vprtstp: contraction number = 2.956364e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.345331e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.359865e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.171771e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.183015e+02\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -15774,17 +15774,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.818510917310E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 6.831530055588E+03 kT\n Vpmg_energy:  dielEnergy = 3.413690932719E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.322400e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.452100e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 19.3778\n Vpbe_ctor2:  solute dimensions = 19.082 x 18.3114 x 35.7654\n Vpbe_ctor2:  solute charge = 4\n Vpbe_ctor2:  bulk ionic strength = 0.275\n Vpbe_ctor2:  xkappa = 0.17076\n@@ -15831,160 +15831,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00313173 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.337236\n+Vacc_SASA: Time elapsed: 0.383279\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.140080e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.104480e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.280300e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.727600e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.049917e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.012926e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.388165e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.645907e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 686089.077180\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.408807e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.666179e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.106303e+05\n Vprtstp: contraction number = 1.106303e+05\n Vnewton: Attempting damping, relres = 0.152721\n Vnewton: Attempting damping, relres = 0.570236\n Vnewton: Damping accepted, relres = 0.152721\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.527207e-01\n Vprtstp: contraction number = 1.527207e-01\n Vnewton: Using errtol_s: 104780.035977\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.545017e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.798849e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.255423e+04\n Vprtstp: contraction number = 2.255423e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.985893e-02\n Vprtstp: contraction number = 1.955132e-01\n Vnewton: Using errtol_s: 20485.884926\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.689657e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.919049e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.496448e+03\n Vprtstp: contraction number = 5.496448e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.211588e-03\n Vprtstp: contraction number = 2.415220e-01\n Vnewton: Using errtol_s: 4947.791442\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.832101e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.039442e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.444377e+03\n Vprtstp: contraction number = 1.444377e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.894730e-03\n Vprtstp: contraction number = 2.627341e-01\n Vnewton: Using errtol_s: 1299.953373\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.968090e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.147447e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.987236e+02\n Vprtstp: contraction number = 3.987236e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.230404e-04\n Vprtstp: contraction number = 2.760502e-01\n Vnewton: Using errtol_s: 358.852327\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.094830e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.252181e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.137605e+02\n Vprtstp: contraction number = 1.137605e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.492292e-04\n Vprtstp: contraction number = 2.853110e-01\n Vnewton: Using errtol_s: 102.384499\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.230926e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.367140e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.325592e+01\n Vprtstp: contraction number = 3.325592e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.362456e-05\n Vprtstp: contraction number = 2.923327e-01\n Vnewton: Using errtol_s: 29.930336\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.375437e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.491860e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.925690e+00\n Vprtstp: contraction number = 9.925690e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.302035e-05\n Vprtstp: contraction number = 2.984638e-01\n Vnewton: Using errtol_s: 8.933121\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.509087e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.606264e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.021979e+00\n Vprtstp: contraction number = 3.021979e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.964181e-06\n Vprtstp: contraction number = 3.044603e-01\n Vnewton: Using errtol_s: 2.719781\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.642879e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.723523e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.363300e-01\n Vprtstp: contraction number = 9.363300e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.228262e-06\n Vprtstp: contraction number = 3.098400e-01\n Vnewton: Using errtol_s: 0.842697\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.795883e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.830196e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.943527e-01\n Vprtstp: contraction number = 2.943527e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.861268e-07\n Vprtstp: contraction number = 3.143685e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.543872e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.557075e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.305231e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.317514e+02\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -15994,15 +15994,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.810295872225E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 8.064058027536E+03 kT\n Vpmg_energy:  dielEnergy = 4.029966775084E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.210200e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 9.355900e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n@@ -16031,162 +16031,162 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.421333\n+Vacc_SASA: Time elapsed: 0.440393\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.165554e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.184862e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.349500e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.973300e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.281215e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.003415e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.973027e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.989639e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1545868.713233\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.001667e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.008799e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.195959e+05\n Vprtstp: contraction number = 2.195959e+05\n Vnewton: Attempting damping, relres = 0.180695\n Vnewton: Attempting damping, relres = 0.564482\n Vnewton: Damping accepted, relres = 0.180695\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.806948e-01\n Vprtstp: contraction number = 1.806948e-01\n Vnewton: Using errtol_s: 279330.491277\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.152815e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.143823e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.153850e+04\n Vprtstp: contraction number = 4.153850e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 3.508737e-02\n Vprtstp: contraction number = 1.941803e-01\n Vnewton: Using errtol_s: 54240.471315\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.322327e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.301127e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.050009e+04\n Vprtstp: contraction number = 1.050009e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.567269e-03\n Vprtstp: contraction number = 2.156693e-01\n Vnewton: Using errtol_s: 11698.005091\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.479639e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.423407e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.909851e+03\n Vprtstp: contraction number = 2.909851e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.738825e-03\n Vprtstp: contraction number = 2.297824e-01\n Vnewton: Using errtol_s: 2687.995161\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.631171e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.536169e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.166574e+02\n Vprtstp: contraction number = 8.166574e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.755829e-04\n Vprtstp: contraction number = 2.735082e-01\n Vnewton: Using errtol_s: 735.188760\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.787818e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.641289e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.418263e+02\n Vprtstp: contraction number = 2.418263e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.407907e-04\n Vprtstp: contraction number = 2.960382e-01\n Vnewton: Using errtol_s: 217.643927\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.941500e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.748170e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.307074e+01\n Vprtstp: contraction number = 7.307074e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.254157e-05\n Vprtstp: contraction number = 3.021618e-01\n Vnewton: Using errtol_s: 65.763679\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.089309e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.858076e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.224627e+01\n Vprtstp: contraction number = 2.224627e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.295171e-05\n Vprtstp: contraction number = 3.044484e-01\n Vnewton: Using errtol_s: 20.021644\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.254601e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.978338e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.802985e+00\n Vprtstp: contraction number = 6.802985e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.960677e-06\n Vprtstp: contraction number = 3.058034e-01\n Vnewton: Using errtol_s: 6.122687\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.409922e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.098582e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.086607e+00\n Vprtstp: contraction number = 2.086607e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.214816e-06\n Vprtstp: contraction number = 3.067192e-01\n Vnewton: Using errtol_s: 1.877946\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.559160e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.207756e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.414261e-01\n Vprtstp: contraction number = 6.414261e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.734363e-07\n Vprtstp: contraction number = 3.074016e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.723237e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.737325e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.319451e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.331046e+02\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -16196,15 +16196,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 8.218327471785E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.873840524527E+04 kT\n Vpmg_energy:  dielEnergy = 9.358686721845E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.527200e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.687700e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 20.7943\n Vpbe_ctor2:  solute dimensions = 25.3482 x 27.3592 x 40.136\n Vpbe_ctor2:  solute charge = -18\n@@ -16253,160 +16253,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00502725 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.440476\n+Vacc_SASA: Time elapsed: 0.432643\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.269390e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.250212e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.130900e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.727800e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.106179e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.819100e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.723353e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.335286e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1578654.561343\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.748291e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.358138e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.749391e+05\n Vprtstp: contraction number = 2.749391e+05\n Vnewton: Attempting damping, relres = 0.208079\n Vnewton: Attempting damping, relres = 0.579104\n Vnewton: Damping accepted, relres = 0.208079\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.080792e-01\n Vprtstp: contraction number = 2.080792e-01\n Vnewton: Using errtol_s: 328485.121608\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.922427e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.499371e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.673641e+04\n Vprtstp: contraction number = 5.673641e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 4.299902e-02\n Vprtstp: contraction number = 2.066474e-01\n Vnewton: Using errtol_s: 67880.597256\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.131038e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.657323e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.510541e+04\n Vprtstp: contraction number = 1.510541e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 9.991987e-03\n Vprtstp: contraction number = 2.323771e-01\n Vnewton: Using errtol_s: 15773.896333\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.302234e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.782173e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.375823e+03\n Vprtstp: contraction number = 4.375823e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.532644e-03\n Vprtstp: contraction number = 2.534675e-01\n Vnewton: Using errtol_s: 3998.170369\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.473617e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.902912e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.301537e+03\n Vprtstp: contraction number = 1.301537e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 7.421078e-04\n Vprtstp: contraction number = 2.930170e-01\n Vnewton: Using errtol_s: 1171.531808\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.642088e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.009308e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.070189e+02\n Vprtstp: contraction number = 4.070189e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.320441e-04\n Vprtstp: contraction number = 3.126824e-01\n Vnewton: Using errtol_s: 366.317427\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.783670e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.122103e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.302066e+02\n Vprtstp: contraction number = 1.302066e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 7.423158e-05\n Vprtstp: contraction number = 3.199029e-01\n Vnewton: Using errtol_s: 117.186019\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.928322e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.250716e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.220788e+01\n Vprtstp: contraction number = 4.220788e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.406296e-05\n Vprtstp: contraction number = 3.241606e-01\n Vnewton: Using errtol_s: 37.987094\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.008928e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.366387e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.382030e+01\n Vprtstp: contraction number = 1.382030e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 7.879032e-06\n Vprtstp: contraction number = 3.274341e-01\n Vnewton: Using errtol_s: 12.438270\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.022846e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.494108e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.561479e+00\n Vprtstp: contraction number = 4.561479e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 2.600526e-06\n Vprtstp: contraction number = 3.300565e-01\n Vnewton: Using errtol_s: 4.105331\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.037829e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.648583e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.515099e+00\n Vprtstp: contraction number = 1.515099e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 8.637667e-07\n Vprtstp: contraction number = 3.321508e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.798379e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.811012e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.424972e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.436714e+02\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -16416,29 +16416,29 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 8.207264728497E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.135578758917E+04 kT\n Vpmg_energy:  dielEnergy = 1.066739245337E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.459600e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 2.221060e-01\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.054003e+03\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 8.776415e+02\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 07:13:54 2025\n+# Creation Date and Time:  Tue Jan  9 05:22:37 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path model_outNB.pqr\n@@ -16708,151 +16708,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.638571\n+Vacc_SASA: Time elapsed: 0.572269\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.576944e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.540833e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.928400e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.802100e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.099903e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.663140e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.852425e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.662846e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2208581.508242\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.124112e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.763106e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.858538e+05\n Vprtstp: contraction number = 2.858538e+05\n Vnewton: Attempting damping, relres = 0.131715\n Vnewton: Attempting damping, relres = 0.556234\n Vnewton: Damping accepted, relres = 0.131715\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.317149e-01\n Vprtstp: contraction number = 1.317149e-01\n Vnewton: Using errtol_s: 290903.178824\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.626940e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.065655e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.143090e+04\n Vprtstp: contraction number = 5.143090e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.336960e-02\n Vprtstp: contraction number = 1.774256e-01\n Vnewton: Using errtol_s: 51613.668608\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.714838e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.705169e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.206326e+04\n Vprtstp: contraction number = 1.206326e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 5.129225e-03\n Vprtstp: contraction number = 2.194828e-01\n Vnewton: Using errtol_s: 11328.310511\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.931022e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.278582e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.187128e+03\n Vprtstp: contraction number = 3.187128e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.301872e-03\n Vprtstp: contraction number = 2.538146e-01\n Vnewton: Using errtol_s: 2875.290058\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.155448e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.822505e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.922285e+02\n Vprtstp: contraction number = 8.922285e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.635897e-04\n Vprtstp: contraction number = 2.792822e-01\n Vnewton: Using errtol_s: 803.017471\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.113943e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.245489e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.591681e+02\n Vprtstp: contraction number = 2.591681e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.056114e-04\n Vprtstp: contraction number = 2.904687e-01\n Vnewton: Using errtol_s: 233.251428\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.313203e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.762451e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.682702e+01\n Vprtstp: contraction number = 7.682702e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.130712e-05\n Vprtstp: contraction number = 2.964369e-01\n Vnewton: Using errtol_s: 69.144331\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.522048e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.129803e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.309726e+01\n Vprtstp: contraction number = 2.309726e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 9.412165e-06\n Vprtstp: contraction number = 3.006398e-01\n Vnewton: Using errtol_s: 20.787535\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.730014e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.280065e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.019037e+00\n Vprtstp: contraction number = 7.019037e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.860267e-06\n Vprtstp: contraction number = 3.038904e-01\n Vnewton: Using errtol_s: 6.317133\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.957143e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.421042e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.152093e+00\n Vprtstp: contraction number = 2.152093e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 8.769810e-07\n Vprtstp: contraction number = 3.066081e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.144579e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.156913e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.529221e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.540084e+02\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -16862,17 +16862,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 5.850378362352E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.566988443868E+04 kT\n Vpmg_energy:  dielEnergy = 1.282832279800E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.012000e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.226430e-01\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 25.8477\n Vpbe_ctor2:  solute dimensions = 26.666 x 32.3234 x 48.3902\n Vpbe_ctor2:  solute charge = -14\n Vpbe_ctor2:  bulk ionic strength = 0.3\n Vpbe_ctor2:  xkappa = 0.178353\n@@ -16919,160 +16919,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0167285 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.628745\n+Vacc_SASA: Time elapsed: 0.583848\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.758923e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.567681e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.483000e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.220900e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.245172e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.113390e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.205511e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.586552e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2261526.211377\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.230412e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.611903e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.556600e+05\n Vprtstp: contraction number = 3.556600e+05\n Vnewton: Attempting damping, relres = 0.156191\n Vnewton: Attempting damping, relres = 0.568968\n Vnewton: Damping accepted, relres = 0.156191\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.561910e-01\n Vprtstp: contraction number = 1.561910e-01\n Vnewton: Using errtol_s: 353229.985787\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.442207e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.813942e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.049885e+04\n Vprtstp: contraction number = 7.049885e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 3.038701e-02\n Vprtstp: contraction number = 1.945503e-01\n Vnewton: Using errtol_s: 68721.012670\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.683896e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.976297e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.762526e+04\n Vprtstp: contraction number = 1.762526e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.209079e-03\n Vprtstp: contraction number = 2.372422e-01\n Vnewton: Using errtol_s: 16303.521422\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.927754e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.141331e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.877060e+03\n Vprtstp: contraction number = 4.877060e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.943013e-03\n Vprtstp: contraction number = 2.695230e-01\n Vnewton: Using errtol_s: 4394.173812\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.162436e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.296297e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.426343e+03\n Vprtstp: contraction number = 1.426343e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.676342e-04\n Vprtstp: contraction number = 2.921413e-01\n Vnewton: Using errtol_s: 1283.719712\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.391325e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.445606e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.339166e+02\n Vprtstp: contraction number = 4.339166e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.726822e-04\n Vprtstp: contraction number = 3.042139e-01\n Vnewton: Using errtol_s: 390.525321\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.627261e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.591737e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.354221e+02\n Vprtstp: contraction number = 1.354221e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 5.389279e-05\n Vprtstp: contraction number = 3.120924e-01\n Vnewton: Using errtol_s: 121.879967\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.860181e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.747735e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.309648e+01\n Vprtstp: contraction number = 4.309648e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.715074e-05\n Vprtstp: contraction number = 3.182380e-01\n Vnewton: Using errtol_s: 38.786838\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.089032e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.903943e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.394777e+01\n Vprtstp: contraction number = 1.394777e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.550675e-06\n Vprtstp: contraction number = 3.236406e-01\n Vnewton: Using errtol_s: 12.552997\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.321067e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.045014e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.577150e+00\n Vprtstp: contraction number = 4.577150e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.821529e-06\n Vprtstp: contraction number = 3.281635e-01\n Vnewton: Using errtol_s: 4.119435\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.506749e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.200088e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.519139e+00\n Vprtstp: contraction number = 1.519139e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 6.045585e-07\n Vprtstp: contraction number = 3.318962e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.510099e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.524061e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.757097e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.769715e+02\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -17082,15 +17082,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 5.837128515027E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.951603256216E+04 kT\n Vpmg_energy:  dielEnergy = 1.475141098473E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.608520e-01\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.693800e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n@@ -17119,151 +17119,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.371252\n+Vacc_SASA: Time elapsed: 0.346724\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.593750e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.061164e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.093700e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.855100e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.110916e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.033581e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.753803e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.380140e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 654975.595106\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.779814e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.398094e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.825232e+04\n Vprtstp: contraction number = 8.825232e+04\n Vnewton: Attempting damping, relres = 0.129536\n Vnewton: Attempting damping, relres = 0.558179\n Vnewton: Damping accepted, relres = 0.129536\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.295360e-01\n Vprtstp: contraction number = 1.295360e-01\n Vnewton: Using errtol_s: 84842.899807\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.948348e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.515152e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.656273e+04\n Vprtstp: contraction number = 1.656273e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.304324e-02\n Vprtstp: contraction number = 1.778907e-01\n Vnewton: Using errtol_s: 15092.761763\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.103121e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.625580e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.788125e+03\n Vprtstp: contraction number = 3.788125e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 5.206395e-03\n Vprtstp: contraction number = 2.259402e-01\n Vnewton: Using errtol_s: 3410.061436\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.267360e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.738492e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.653659e+02\n Vprtstp: contraction number = 9.653659e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.326515e-03\n Vprtstp: contraction number = 2.547856e-01\n Vnewton: Using errtol_s: 868.834666\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.430957e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.844582e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.601053e+02\n Vprtstp: contraction number = 2.601053e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.574104e-04\n Vprtstp: contraction number = 2.694357e-01\n Vnewton: Using errtol_s: 234.095066\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.586388e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.975147e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.225806e+01\n Vprtstp: contraction number = 7.225806e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 9.928962e-05\n Vprtstp: contraction number = 2.778029e-01\n Vnewton: Using errtol_s: 65.032277\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.749354e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.097032e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.049231e+01\n Vprtstp: contraction number = 2.049231e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.815843e-05\n Vprtstp: contraction number = 2.835989e-01\n Vnewton: Using errtol_s: 18.443082\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.896562e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.248179e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.907221e+00\n Vprtstp: contraction number = 5.907221e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.117095e-06\n Vprtstp: contraction number = 2.882652e-01\n Vnewton: Using errtol_s: 5.316499\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.062970e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.413998e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.726518e+00\n Vprtstp: contraction number = 1.726518e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.372403e-06\n Vprtstp: contraction number = 2.922725e-01\n Vnewton: Using errtol_s: 1.553866\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.249005e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.547799e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.104456e-01\n Vprtstp: contraction number = 5.104456e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 7.014018e-07\n Vprtstp: contraction number = 2.956503e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.652196e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.665216e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.273284e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.284338e+02\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -17273,15 +17273,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.824785455447E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 6.831245180939E+03 kT\n Vpmg_energy:  dielEnergy = 3.413552848131E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 8.427200e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 9.890700e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 19.3778\n Vpbe_ctor2:  solute dimensions = 19.082 x 18.3114 x 35.7654\n Vpbe_ctor2:  solute charge = 4\n@@ -17330,160 +17330,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00286585 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.404136\n+Vacc_SASA: Time elapsed: 0.353575\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.713560e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.021480e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.455400e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.592300e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.012108e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.303055e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.430691e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.680132e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 681119.647673\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.457669e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.703134e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.097058e+05\n Vprtstp: contraction number = 1.097058e+05\n Vnewton: Attempting damping, relres = 0.152443\n Vnewton: Attempting damping, relres = 0.570128\n Vnewton: Damping accepted, relres = 0.152443\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.524432e-01\n Vprtstp: contraction number = 1.524432e-01\n Vnewton: Using errtol_s: 103832.028377\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.627707e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.856776e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.238938e+04\n Vprtstp: contraction number = 2.238938e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.984124e-02\n Vprtstp: contraction number = 1.957533e-01\n Vnewton: Using errtol_s: 20325.457528\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.795149e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.992365e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.463136e+03\n Vprtstp: contraction number = 5.463136e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.220083e-03\n Vprtstp: contraction number = 2.419498e-01\n Vnewton: Using errtol_s: 4917.740487\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.971979e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.114312e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.437458e+03\n Vprtstp: contraction number = 1.437458e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.899412e-03\n Vprtstp: contraction number = 2.630734e-01\n Vnewton: Using errtol_s: 1293.726521\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.150416e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.294332e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.972446e+02\n Vprtstp: contraction number = 3.972446e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.249023e-04\n Vprtstp: contraction number = 2.763499e-01\n Vnewton: Using errtol_s: 357.521241\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.317823e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.462532e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.134401e+02\n Vprtstp: contraction number = 1.134401e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.498946e-04\n Vprtstp: contraction number = 2.855667e-01\n Vnewton: Using errtol_s: 102.096166\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.489636e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.592028e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.318595e+01\n Vprtstp: contraction number = 3.318595e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.385040e-05\n Vprtstp: contraction number = 2.925415e-01\n Vnewton: Using errtol_s: 29.867366\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.664730e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.713752e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.910309e+00\n Vprtstp: contraction number = 9.910309e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.309503e-05\n Vprtstp: contraction number = 2.986296e-01\n Vnewton: Using errtol_s: 8.919279\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.847076e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.884140e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.018558e+00\n Vprtstp: contraction number = 3.018558e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.988583e-06\n Vprtstp: contraction number = 3.045877e-01\n Vnewton: Using errtol_s: 2.716702\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.054989e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.035516e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.355568e-01\n Vprtstp: contraction number = 9.355568e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.236201e-06\n Vprtstp: contraction number = 3.099350e-01\n Vnewton: Using errtol_s: 0.842001\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.243719e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.227248e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.941742e-01\n Vprtstp: contraction number = 2.941742e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.887082e-07\n Vprtstp: contraction number = 3.144376e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.989977e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.002962e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.696091e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.711858e+02\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -17493,17 +17493,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.816506018339E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 8.063774350048E+03 kT\n Vpmg_energy:  dielEnergy = 4.029829357702E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.109300e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.177520e-01\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vnm_tstart: starting timer 27 (Setup timer)..\n@@ -17530,162 +17530,162 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.398589\n+Vacc_SASA: Time elapsed: 0.423841\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.322217e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.312812e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.061400e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.714700e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.294149e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.005421e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.462566e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.413871e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1525884.348969\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.492527e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.430497e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.167719e+05\n Vprtstp: contraction number = 2.167719e+05\n Vnewton: Attempting damping, relres = 0.176913\n Vnewton: Attempting damping, relres = 0.564272\n Vnewton: Damping accepted, relres = 0.176913\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.769126e-01\n Vprtstp: contraction number = 1.769126e-01\n Vnewton: Using errtol_s: 269948.173272\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.686898e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.586766e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.092694e+04\n Vprtstp: contraction number = 4.092694e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 3.387341e-02\n Vprtstp: contraction number = 1.914697e-01\n Vnewton: Using errtol_s: 51686.903490\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.872425e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.804634e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.034780e+04\n Vprtstp: contraction number = 1.034780e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.283807e-03\n Vprtstp: contraction number = 2.150302e-01\n Vnewton: Using errtol_s: 11114.247135\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.025551e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.992081e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.862719e+03\n Vprtstp: contraction number = 2.862719e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.717625e-03\n Vprtstp: contraction number = 2.358142e-01\n Vnewton: Using errtol_s: 2620.897639\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.164059e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.156886e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.092476e+02\n Vprtstp: contraction number = 8.092476e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.773796e-04\n Vprtstp: contraction number = 2.779300e-01\n Vnewton: Using errtol_s: 728.426056\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.304520e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.334439e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.405150e+02\n Vprtstp: contraction number = 2.405150e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.418612e-04\n Vprtstp: contraction number = 2.971664e-01\n Vnewton: Using errtol_s: 216.463714\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.434446e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.514195e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.272000e+01\n Vprtstp: contraction number = 7.272000e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.289186e-05\n Vprtstp: contraction number = 3.023510e-01\n Vnewton: Using errtol_s: 65.448016\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.579122e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.691631e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.214460e+01\n Vprtstp: contraction number = 2.214460e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.306137e-05\n Vprtstp: contraction number = 3.045186e-01\n Vnewton: Using errtol_s: 19.930141\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.726846e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.855261e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.772692e+00\n Vprtstp: contraction number = 6.772692e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.994682e-06\n Vprtstp: contraction number = 3.058394e-01\n Vnewton: Using errtol_s: 6.095423\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.847934e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.029822e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.077475e+00\n Vprtstp: contraction number = 2.077475e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.225341e-06\n Vprtstp: contraction number = 3.067429e-01\n Vnewton: Using errtol_s: 1.869728\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.000094e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.196020e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.386558e-01\n Vprtstp: contraction number = 6.386558e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.766932e-07\n Vprtstp: contraction number = 3.074192e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.666105e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.679778e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.908130e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.918847e+02\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -17695,15 +17695,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 8.069846752513E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.873729752993E+04 kT\n Vpmg_energy:  dielEnergy = 9.358408005729E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.634700e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 8.219600e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 20.7943\n Vpbe_ctor2:  solute dimensions = 25.3482 x 27.3592 x 40.136\n Vpbe_ctor2:  solute charge = -18\n@@ -17752,160 +17752,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00434174 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.433532\n+Vacc_SASA: Time elapsed: 0.421674\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.271427e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.379295e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.885800e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.869000e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.159801e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.219620e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.015556e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.350621e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1557370.209900\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.018214e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.379612e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.714539e+05\n Vprtstp: contraction number = 2.714539e+05\n Vnewton: Attempting damping, relres = 0.204551\n Vnewton: Attempting damping, relres = 0.578965\n Vnewton: Damping accepted, relres = 0.204551\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.045506e-01\n Vprtstp: contraction number = 2.045506e-01\n Vnewton: Using errtol_s: 318560.936336\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.033774e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.585214e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.592903e+04\n Vprtstp: contraction number = 5.592903e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 4.183467e-02\n Vprtstp: contraction number = 2.045200e-01\n Vnewton: Using errtol_s: 65152.068354\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.053187e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.811322e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.489191e+04\n Vprtstp: contraction number = 1.489191e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 9.724338e-03\n Vprtstp: contraction number = 2.324469e-01\n Vnewton: Using errtol_s: 15144.393716\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.070171e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.002786e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.311238e+03\n Vprtstp: contraction number = 4.311238e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.516326e-03\n Vprtstp: contraction number = 2.587658e-01\n Vnewton: Using errtol_s: 3918.850513\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.085620e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.184235e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.290056e+03\n Vprtstp: contraction number = 1.290056e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 7.455704e-04\n Vprtstp: contraction number = 2.962933e-01\n Vnewton: Using errtol_s: 1161.129054\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.098450e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.350203e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.045979e+02\n Vprtstp: contraction number = 4.045979e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.338163e-04\n Vprtstp: contraction number = 3.136073e-01\n Vnewton: Using errtol_s: 364.138497\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.116501e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.516005e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.295599e+02\n Vprtstp: contraction number = 1.295599e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 7.487232e-05\n Vprtstp: contraction number = 3.202186e-01\n Vnewton: Using errtol_s: 116.603918\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.132398e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.715298e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.202377e+01\n Vprtstp: contraction number = 4.202377e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.428543e-05\n Vprtstp: contraction number = 3.243579e-01\n Vnewton: Using errtol_s: 37.821402\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.146101e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.901681e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.376584e+01\n Vprtstp: contraction number = 1.376584e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 7.955244e-06\n Vprtstp: contraction number = 3.275727e-01\n Vnewton: Using errtol_s: 12.389260\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.162828e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.008961e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.544810e+00\n Vprtstp: contraction number = 4.544810e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 2.626434e-06\n Vprtstp: contraction number = 3.301512e-01\n Vnewton: Using errtol_s: 4.090329\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.177279e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.028415e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.509859e+00\n Vprtstp: contraction number = 1.509859e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 8.725435e-07\n Vprtstp: contraction number = 3.322161e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.759846e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.773210e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.102240e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.115299e+02\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -17915,29 +17915,29 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 8.058985499757E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.135468016715E+04 kT\n Vpmg_energy:  dielEnergy = 1.066711397255E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.076200e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 8.715200e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.193408e+03\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.046582e+03\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 07:16:11 2025\n+# Creation Date and Time:  Tue Jan  9 05:24:46 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path model_outNB.pqr\n@@ -18207,151 +18207,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.615505\n+Vacc_SASA: Time elapsed: 0.556298\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.668514e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.608706e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.208100e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.813300e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.139722e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.066453e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.043553e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.795864e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2191468.217175\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.420323e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.375472e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.835462e+05\n Vprtstp: contraction number = 2.835462e+05\n Vnewton: Attempting damping, relres = 0.130770\n Vnewton: Attempting damping, relres = 0.556143\n Vnewton: Damping accepted, relres = 0.130770\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.307700e-01\n Vprtstp: contraction number = 1.307700e-01\n Vnewton: Using errtol_s: 286578.355364\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.384099e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.894220e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.106806e+04\n Vprtstp: contraction number = 5.106806e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.314467e-02\n Vprtstp: contraction number = 1.769876e-01\n Vnewton: Using errtol_s: 50720.810223\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.375329e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.754289e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.199262e+04\n Vprtstp: contraction number = 1.199262e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 5.100754e-03\n Vprtstp: contraction number = 2.203857e-01\n Vnewton: Using errtol_s: 11178.140515\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.174231e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.463208e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.172798e+03\n Vprtstp: contraction number = 3.172798e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.305202e-03\n Vprtstp: contraction number = 2.558841e-01\n Vnewton: Using errtol_s: 2860.308039\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.193384e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.817854e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.902300e+02\n Vprtstp: contraction number = 8.902300e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.656064e-04\n Vprtstp: contraction number = 2.801149e-01\n Vnewton: Using errtol_s: 801.214793\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.783375e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.122707e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.587695e+02\n Vprtstp: contraction number = 2.587695e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.062725e-04\n Vprtstp: contraction number = 2.906745e-01\n Vnewton: Using errtol_s: 232.892741\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.151586e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.349992e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.672901e+01\n Vprtstp: contraction number = 7.672901e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.151135e-05\n Vprtstp: contraction number = 2.965147e-01\n Vnewton: Using errtol_s: 69.056118\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.310706e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.592468e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.307099e+01\n Vprtstp: contraction number = 2.307099e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 9.474878e-06\n Vprtstp: contraction number = 3.006815e-01\n Vnewton: Using errtol_s: 20.763894\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.485424e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.781831e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.011582e+00\n Vprtstp: contraction number = 7.011582e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.879541e-06\n Vprtstp: contraction number = 3.039133e-01\n Vnewton: Using errtol_s: 6.310424\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.641114e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.949134e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.149903e+00\n Vprtstp: contraction number = 2.149903e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 8.829299e-07\n Vprtstp: contraction number = 3.066217e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.753366e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.766662e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.137333e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.148896e+02\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -18361,17 +18361,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 5.760186349323E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.566917500477E+04 kT\n Vpmg_energy:  dielEnergy = 1.282812157004E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.236500e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 9.761500e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 25.8477\n Vpbe_ctor2:  solute dimensions = 26.666 x 32.3234 x 48.3902\n Vpbe_ctor2:  solute charge = -14\n Vpbe_ctor2:  bulk ionic strength = 0.325\n Vpbe_ctor2:  xkappa = 0.185636\n@@ -18418,160 +18418,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0160678 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.637200\n+Vacc_SASA: Time elapsed: 0.597844\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.679311e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.697147e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.375200e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.226800e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.556610e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.118250e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.812757e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.196363e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2243053.741102\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.834638e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.223889e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.528083e+05\n Vprtstp: contraction number = 3.528083e+05\n Vnewton: Attempting damping, relres = 0.155339\n Vnewton: Attempting damping, relres = 0.568910\n Vnewton: Damping accepted, relres = 0.155339\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.553392e-01\n Vprtstp: contraction number = 1.553392e-01\n Vnewton: Using errtol_s: 348434.112950\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.030433e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.437289e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.998444e+04\n Vprtstp: contraction number = 6.998444e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 3.017800e-02\n Vprtstp: contraction number = 1.942717e-01\n Vnewton: Using errtol_s: 67690.878524\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.223838e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.685684e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.750872e+04\n Vprtstp: contraction number = 1.750872e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.184752e-03\n Vprtstp: contraction number = 2.380791e-01\n Vnewton: Using errtol_s: 16115.784303\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.393233e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.945863e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.850206e+03\n Vprtstp: contraction number = 4.850206e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.947538e-03\n Vprtstp: contraction number = 2.710655e-01\n Vnewton: Using errtol_s: 4368.432326\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.588671e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.184361e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.421336e+03\n Vprtstp: contraction number = 1.421336e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.702989e-04\n Vprtstp: contraction number = 2.928307e-01\n Vnewton: Using errtol_s: 1279.211122\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.786209e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.417397e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.327691e+02\n Vprtstp: contraction number = 4.327691e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.736439e-04\n Vprtstp: contraction number = 3.044787e-01\n Vnewton: Using errtol_s: 389.492590\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.973278e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.610684e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.351326e+02\n Vprtstp: contraction number = 1.351326e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 5.422045e-05\n Vprtstp: contraction number = 3.122508e-01\n Vnewton: Using errtol_s: 121.619374\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.193831e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.816931e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.301940e+01\n Vprtstp: contraction number = 4.301940e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.726105e-05\n Vprtstp: contraction number = 3.183495e-01\n Vnewton: Using errtol_s: 38.717465\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.404012e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.043629e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.392593e+01\n Vprtstp: contraction number = 1.392593e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.587625e-06\n Vprtstp: contraction number = 3.237129e-01\n Vnewton: Using errtol_s: 12.533342\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.574532e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.212821e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.570574e+00\n Vprtstp: contraction number = 4.570574e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.833891e-06\n Vprtstp: contraction number = 3.282059e-01\n Vnewton: Using errtol_s: 4.113517\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.762679e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.475224e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.517041e+00\n Vprtstp: contraction number = 1.517041e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 6.086957e-07\n Vprtstp: contraction number = 3.319148e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.112079e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.122768e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.496575e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.508767e+02\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -18581,17 +18581,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 5.747143888593E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.951532357684E+04 kT\n Vpmg_energy:  dielEnergy = 1.475121024223E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.420200e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.052170e-01\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vnm_tstart: starting timer 27 (Setup timer)..\n@@ -18618,151 +18618,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.381448\n+Vacc_SASA: Time elapsed: 0.330829\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.430690e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.350530e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.974100e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.939900e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.197679e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.213658e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.965083e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.730059e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 651047.049796\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.990918e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.756042e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.764819e+04\n Vprtstp: contraction number = 8.764819e+04\n Vnewton: Attempting damping, relres = 0.129306\n Vnewton: Attempting damping, relres = 0.558102\n Vnewton: Damping accepted, relres = 0.129306\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.293065e-01\n Vprtstp: contraction number = 1.293065e-01\n Vnewton: Using errtol_s: 84184.596649\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.161409e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.937963e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.647823e+04\n Vprtstp: contraction number = 1.647823e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.304786e-02\n Vprtstp: contraction number = 1.782421e-01\n Vnewton: Using errtol_s: 15005.240621\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.307055e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.104052e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.775815e+03\n Vprtstp: contraction number = 3.775815e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 5.220699e-03\n Vprtstp: contraction number = 2.265156e-01\n Vnewton: Using errtol_s: 3398.920946\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.440119e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.252115e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.635341e+02\n Vprtstp: contraction number = 9.635341e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.331987e-03\n Vprtstp: contraction number = 2.551357e-01\n Vnewton: Using errtol_s: 867.186094\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.555895e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.414733e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.598155e+02\n Vprtstp: contraction number = 2.598155e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.591665e-04\n Vprtstp: contraction number = 2.696472e-01\n Vnewton: Using errtol_s: 233.834272\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.670058e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.517388e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.221080e+01\n Vprtstp: contraction number = 7.221080e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 9.982341e-05\n Vprtstp: contraction number = 2.779308e-01\n Vnewton: Using errtol_s: 64.989737\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.800460e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.682244e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.048426e+01\n Vprtstp: contraction number = 2.048426e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.831721e-05\n Vprtstp: contraction number = 2.836731e-01\n Vnewton: Using errtol_s: 18.435838\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.929362e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.834476e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.905744e+00\n Vprtstp: contraction number = 5.905744e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.164034e-06\n Vprtstp: contraction number = 2.883064e-01\n Vnewton: Using errtol_s: 5.315170\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.041189e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.983953e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.726219e+00\n Vprtstp: contraction number = 1.726219e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.386306e-06\n Vprtstp: contraction number = 2.922949e-01\n Vnewton: Using errtol_s: 1.553597\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.180406e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.151267e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.103781e-01\n Vprtstp: contraction number = 5.103781e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 7.055409e-07\n Vprtstp: contraction number = 2.956624e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.339327e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.353048e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.547469e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.561396e+02\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -18772,15 +18772,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.829422361663E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 6.830982023597E+03 kT\n Vpmg_energy:  dielEnergy = 3.413426199926E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.891100e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.990900e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 19.3778\n Vpbe_ctor2:  solute dimensions = 19.082 x 18.3114 x 35.7654\n Vpbe_ctor2:  solute charge = 4\n@@ -18829,160 +18829,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00263165 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.359883\n+Vacc_SASA: Time elapsed: 0.381184\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.558270e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.943910e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.718300e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.142700e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.327710e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.238605e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.326516e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.302994e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 676873.511924\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.347006e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.335089e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.089080e+05\n Vprtstp: contraction number = 1.089080e+05\n Vnewton: Attempting damping, relres = 0.152173\n Vnewton: Attempting damping, relres = 0.570027\n Vnewton: Damping accepted, relres = 0.152173\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.521734e-01\n Vprtstp: contraction number = 1.521734e-01\n Vnewton: Using errtol_s: 103002.176045\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.479469e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.543517e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.224678e+04\n Vprtstp: contraction number = 2.224678e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.982235e-02\n Vprtstp: contraction number = 1.959760e-01\n Vnewton: Using errtol_s: 20185.957327\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.614082e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.724609e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.434268e+03\n Vprtstp: contraction number = 5.434268e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.226895e-03\n Vprtstp: contraction number = 2.423315e-01\n Vnewton: Using errtol_s: 4891.693818\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.756032e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.865890e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.431460e+03\n Vprtstp: contraction number = 1.431460e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.903352e-03\n Vprtstp: contraction number = 2.633707e-01\n Vnewton: Using errtol_s: 1288.328715\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.884684e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.985154e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.959616e+02\n Vprtstp: contraction number = 3.959616e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.264891e-04\n Vprtstp: contraction number = 2.766115e-01\n Vnewton: Using errtol_s: 356.366550\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.013630e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.096322e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.131619e+02\n Vprtstp: contraction number = 1.131619e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.504650e-04\n Vprtstp: contraction number = 2.857895e-01\n Vnewton: Using errtol_s: 101.845804\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.148981e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.244446e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.312512e+01\n Vprtstp: contraction number = 3.312512e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.404458e-05\n Vprtstp: contraction number = 2.927230e-01\n Vnewton: Using errtol_s: 29.812613\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.300750e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.416240e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.896913e+00\n Vprtstp: contraction number = 9.896913e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.315936e-05\n Vprtstp: contraction number = 2.987736e-01\n Vnewton: Using errtol_s: 8.907223\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.458866e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.550834e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.015572e+00\n Vprtstp: contraction number = 3.015572e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 4.009634e-06\n Vprtstp: contraction number = 3.046983e-01\n Vnewton: Using errtol_s: 2.714015\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.613131e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.687534e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.348798e-01\n Vprtstp: contraction number = 9.348798e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.243056e-06\n Vprtstp: contraction number = 3.100174e-01\n Vnewton: Using errtol_s: 0.841392\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.756344e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.830337e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.940173e-01\n Vprtstp: contraction number = 2.940173e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.909380e-07\n Vprtstp: contraction number = 3.144974e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.549754e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.561405e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.664244e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.678486e+02\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -18992,17 +18992,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.821085170706E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 8.063512300781E+03 kT\n Vpmg_energy:  dielEnergy = 4.029703319589E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.302400e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.033600e-01\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 4.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vnm_tstart: starting timer 27 (Setup timer)..\n@@ -19029,162 +19029,162 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.448370\n+Vacc_SASA: Time elapsed: 0.435627\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.266826e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.178306e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.615500e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.891200e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.177453e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.260829e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.920047e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.010368e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1509004.572180\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.946087e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.040691e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.143767e+05\n Vprtstp: contraction number = 2.143767e+05\n Vnewton: Attempting damping, relres = 0.173607\n Vnewton: Attempting damping, relres = 0.564075\n Vnewton: Damping accepted, relres = 0.173607\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.736069e-01\n Vprtstp: contraction number = 1.736069e-01\n Vnewton: Using errtol_s: 261973.588074\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.122883e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.231456e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.041338e+04\n Vprtstp: contraction number = 4.041338e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 3.283481e-02\n Vprtstp: contraction number = 1.891331e-01\n Vnewton: Using errtol_s: 49547.880487\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.273367e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.437509e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.021814e+04\n Vprtstp: contraction number = 1.021814e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.057379e-03\n Vprtstp: contraction number = 2.149359e-01\n Vnewton: Using errtol_s: 10649.617829\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.418082e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.609106e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.824157e+03\n Vprtstp: contraction number = 2.824157e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.703748e-03\n Vprtstp: contraction number = 2.414137e-01\n Vnewton: Using errtol_s: 2570.963479\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.550348e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.775424e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.035455e+02\n Vprtstp: contraction number = 8.035455e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.792870e-04\n Vprtstp: contraction number = 2.813133e-01\n Vnewton: Using errtol_s: 723.246303\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.671998e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.940849e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.394281e+02\n Vprtstp: contraction number = 2.394281e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.427997e-04\n Vprtstp: contraction number = 2.979420e-01\n Vnewton: Using errtol_s: 215.485426\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.812732e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.122171e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.242618e+01\n Vprtstp: contraction number = 7.242618e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.319641e-05\n Vprtstp: contraction number = 3.024964e-01\n Vnewton: Using errtol_s: 65.183576\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.955700e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.298753e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.205930e+01\n Vprtstp: contraction number = 2.205930e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.315660e-05\n Vprtstp: contraction number = 3.045762e-01\n Vnewton: Using errtol_s: 19.853369\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.088574e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.434036e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.747262e+00\n Vprtstp: contraction number = 6.747262e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 4.024200e-06\n Vprtstp: contraction number = 3.058693e-01\n Vnewton: Using errtol_s: 6.072536\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.221689e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.571325e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.069809e+00\n Vprtstp: contraction number = 2.069809e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.234475e-06\n Vprtstp: contraction number = 3.067629e-01\n Vnewton: Using errtol_s: 1.862829\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.354685e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.731978e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.363291e-01\n Vprtstp: contraction number = 6.363291e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.795192e-07\n Vprtstp: contraction number = 3.074337e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.574807e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.587439e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.866524e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.881001e+02\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -19194,15 +19194,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 7.932901630700E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.873629019341E+04 kT\n Vpmg_energy:  dielEnergy = 9.358152654068E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.057400e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.809000e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 20.7943\n Vpbe_ctor2:  solute dimensions = 25.3482 x 27.3592 x 40.136\n Vpbe_ctor2:  solute charge = -18\n@@ -19251,160 +19251,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00380956 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.451730\n+Vacc_SASA: Time elapsed: 0.439266\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.365035e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.227891e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.327200e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.045900e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.718200e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.106638e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.521312e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.903076e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1539412.424593\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.546447e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.927182e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.684916e+05\n Vprtstp: contraction number = 2.684916e+05\n Vnewton: Attempting damping, relres = 0.201455\n Vnewton: Attempting damping, relres = 0.578827\n Vnewton: Damping accepted, relres = 0.201455\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.014550e-01\n Vprtstp: contraction number = 2.014550e-01\n Vnewton: Using errtol_s: 310122.358535\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.704289e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.011558e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.524646e+04\n Vprtstp: contraction number = 5.524646e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 4.083558e-02\n Vprtstp: contraction number = 2.027032e-01\n Vnewton: Using errtol_s: 62862.800070\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.886162e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.033003e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.470940e+04\n Vprtstp: contraction number = 1.470940e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 9.510864e-03\n Vprtstp: contraction number = 2.329063e-01\n Vnewton: Using errtol_s: 14641.142976\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.038407e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.051289e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.258026e+03\n Vprtstp: contraction number = 4.258026e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.506079e-03\n Vprtstp: contraction number = 2.634965e-01\n Vnewton: Using errtol_s: 3857.889813\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.194568e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.069081e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.281004e+03\n Vprtstp: contraction number = 1.281004e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 7.489530e-04\n Vprtstp: contraction number = 2.988545e-01\n Vnewton: Using errtol_s: 1152.947571\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.342987e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.088029e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.026096e+02\n Vprtstp: contraction number = 4.026096e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.353814e-04\n Vprtstp: contraction number = 3.142806e-01\n Vnewton: Using errtol_s: 362.348997\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.485998e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.105590e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.290278e+02\n Vprtstp: contraction number = 1.290278e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 7.543469e-05\n Vprtstp: contraction number = 3.204786e-01\n Vnewton: Using errtol_s: 116.125091\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.628502e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.118843e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.187301e+01\n Vprtstp: contraction number = 4.187301e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.448058e-05\n Vprtstp: contraction number = 3.245269e-01\n Vnewton: Using errtol_s: 37.685715\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.773370e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.135364e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.372141e+01\n Vprtstp: contraction number = 1.372141e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 8.022069e-06\n Vprtstp: contraction number = 3.276911e-01\n Vnewton: Using errtol_s: 12.349273\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.913214e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.151568e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.531250e+00\n Vprtstp: contraction number = 4.531250e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 2.649144e-06\n Vprtstp: contraction number = 3.302320e-01\n Vnewton: Using errtol_s: 4.078125\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.005104e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.168414e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.505606e+00\n Vprtstp: contraction number = 1.505606e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 8.802356e-07\n Vprtstp: contraction number = 3.322717e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.667764e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.679166e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.924995e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.937489e+02\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -19414,29 +19414,29 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 7.922197679692E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.135367311591E+04 kT\n Vpmg_energy:  dielEnergy = 1.066685879920E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.734500e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.367200e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.020847e+03\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.184134e+03\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 07:18:52 2025\n+# Creation Date and Time:  Tue Jan  9 05:26:40 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path model_outNB.pqr\n@@ -19706,151 +19706,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.648621\n+Vacc_SASA: Time elapsed: 0.541813\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.638175e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.541833e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.616200e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.991700e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.171909e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.046770e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.005605e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.570737e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2152094.716706\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.025222e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.240978e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.782066e+05\n Vprtstp: contraction number = 2.782066e+05\n Vnewton: Attempting damping, relres = 0.128497\n Vnewton: Attempting damping, relres = 0.555913\n Vnewton: Damping accepted, relres = 0.128497\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.284973e-01\n Vprtstp: contraction number = 1.284973e-01\n Vnewton: Using errtol_s: 276538.353939\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.476474e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.269882e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.023327e+04\n Vprtstp: contraction number = 5.023327e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.262924e-02\n Vprtstp: contraction number = 1.761067e-01\n Vnewton: Using errtol_s: 48700.264198\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.301903e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.474150e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.183043e+04\n Vprtstp: contraction number = 1.183043e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 5.048628e-03\n Vprtstp: contraction number = 2.231020e-01\n Vnewton: Using errtol_s: 10865.126461\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.020265e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.598974e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.142996e+03\n Vprtstp: contraction number = 3.142996e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.315159e-03\n Vprtstp: contraction number = 2.604983e-01\n Vnewton: Using errtol_s: 2830.346955\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.960899e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.515838e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.861041e+02\n Vprtstp: contraction number = 8.861041e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.705677e-04\n Vprtstp: contraction number = 2.817665e-01\n Vnewton: Using errtol_s: 797.496893\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.734234e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.020763e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.579465e+02\n Vprtstp: contraction number = 2.579465e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.078726e-04\n Vprtstp: contraction number = 2.911008e-01\n Vnewton: Using errtol_s: 232.151972\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.159507e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.215760e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.653069e+01\n Vprtstp: contraction number = 7.653069e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.200493e-05\n Vprtstp: contraction number = 2.966920e-01\n Vnewton: Using errtol_s: 68.877633\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.333161e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.385960e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.301874e+01\n Vprtstp: contraction number = 2.301874e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 9.626375e-06\n Vprtstp: contraction number = 3.007779e-01\n Vnewton: Using errtol_s: 20.716870\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.515615e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.569114e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.996910e+00\n Vprtstp: contraction number = 6.996910e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.926088e-06\n Vprtstp: contraction number = 3.039658e-01\n Vnewton: Using errtol_s: 6.297219\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.703842e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.753888e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.145621e+00\n Vprtstp: contraction number = 2.145621e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 8.972926e-07\n Vprtstp: contraction number = 3.066526e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.838102e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.851364e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.907279e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.917286e+02\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -19860,17 +19860,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 5.527227679472E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.566736557939E+04 kT\n Vpmg_energy:  dielEnergy = 1.282759892518E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.693200e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.087200e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 25.8477\n Vpbe_ctor2:  solute dimensions = 26.666 x 32.3234 x 48.3902\n Vpbe_ctor2:  solute charge = -14\n Vpbe_ctor2:  bulk ionic strength = 0.4\n Vpbe_ctor2:  xkappa = 0.205945\n@@ -19917,160 +19917,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0146503 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.613317\n+Vacc_SASA: Time elapsed: 0.570384\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.679521e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.573043e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.162800e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.603700e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.070433e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.255830e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.898451e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.963275e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2200727.622444\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.919505e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.987831e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.461855e+05\n Vprtstp: contraction number = 3.461855e+05\n Vnewton: Attempting damping, relres = 0.153259\n Vnewton: Attempting damping, relres = 0.568747\n Vnewton: Damping accepted, relres = 0.153259\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.532593e-01\n Vprtstp: contraction number = 1.532593e-01\n Vnewton: Using errtol_s: 337281.994589\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.117657e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.183699e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.878964e+04\n Vprtstp: contraction number = 6.878964e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.969348e-02\n Vprtstp: contraction number = 1.937467e-01\n Vnewton: Using errtol_s: 65347.260012\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.309879e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.360986e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.723760e+04\n Vprtstp: contraction number = 1.723760e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.139932e-03\n Vprtstp: contraction number = 2.404545e-01\n Vnewton: Using errtol_s: 15713.045576\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.510858e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.545259e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.791285e+03\n Vprtstp: contraction number = 4.791285e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.959957e-03\n Vprtstp: contraction number = 2.745064e-01\n Vnewton: Using errtol_s: 4313.331787\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.702381e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.733622e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.410218e+03\n Vprtstp: contraction number = 1.410218e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.767187e-04\n Vprtstp: contraction number = 2.942507e-01\n Vnewton: Using errtol_s: 1269.200854\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.872497e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.920539e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.302153e+02\n Vprtstp: contraction number = 4.302153e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.759391e-04\n Vprtstp: contraction number = 3.050692e-01\n Vnewton: Using errtol_s: 387.194118\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.078938e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.105312e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.344961e+02\n Vprtstp: contraction number = 1.344961e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 5.500295e-05\n Vprtstp: contraction number = 3.126248e-01\n Vnewton: Using errtol_s: 121.046502\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.289587e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.284939e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.285292e+01\n Vprtstp: contraction number = 4.285292e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.752495e-05\n Vprtstp: contraction number = 3.186183e-01\n Vnewton: Using errtol_s: 38.567632\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.492020e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.474570e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.387951e+01\n Vprtstp: contraction number = 1.387951e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.676104e-06\n Vprtstp: contraction number = 3.238871e-01\n Vnewton: Using errtol_s: 12.491560\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.656299e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.654205e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.556799e+00\n Vprtstp: contraction number = 4.556799e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.863529e-06\n Vprtstp: contraction number = 3.283112e-01\n Vnewton: Using errtol_s: 4.101119\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.839855e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.844289e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.512689e+00\n Vprtstp: contraction number = 1.512689e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 6.186225e-07\n Vprtstp: contraction number = 3.319630e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.143794e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.155879e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.057252e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.070877e+02\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -20080,15 +20080,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 5.514675732237E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.951351537778E+04 kT\n Vpmg_energy:  dielEnergy = 1.475068873214E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.052300e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.364100e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n@@ -20117,151 +20117,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.339332\n+Vacc_SASA: Time elapsed: 0.352828\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.160170e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.054150e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.225800e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.534400e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.126736e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.119994e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.082491e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.062363e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 642085.519744\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.105681e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.088176e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.625055e+04\n Vprtstp: contraction number = 8.625055e+04\n Vnewton: Attempting damping, relres = 0.128656\n Vnewton: Attempting damping, relres = 0.557901\n Vnewton: Damping accepted, relres = 0.128656\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.286562e-01\n Vprtstp: contraction number = 1.286562e-01\n Vnewton: Using errtol_s: 82608.252849\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.259535e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.233405e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.628118e+04\n Vprtstp: contraction number = 1.628118e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.304734e-02\n Vprtstp: contraction number = 1.791390e-01\n Vnewton: Using errtol_s: 14798.361839\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.374424e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.356470e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.747143e+03\n Vprtstp: contraction number = 3.747143e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 5.253150e-03\n Vprtstp: contraction number = 2.279287e-01\n Vnewton: Using errtol_s: 3372.971529\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.502286e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.474696e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.592593e+02\n Vprtstp: contraction number = 9.592593e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.344585e-03\n Vprtstp: contraction number = 2.559579e-01\n Vnewton: Using errtol_s: 863.338654\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.625593e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.602383e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.591357e+02\n Vprtstp: contraction number = 2.591357e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.632264e-04\n Vprtstp: contraction number = 2.701401e-01\n Vnewton: Using errtol_s: 233.222386\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.752728e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.731541e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.209902e+01\n Vprtstp: contraction number = 7.209902e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.010600e-04\n Vprtstp: contraction number = 2.782286e-01\n Vnewton: Using errtol_s: 64.889141\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.872212e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.858906e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.046499e+01\n Vprtstp: contraction number = 2.046499e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.868541e-05\n Vprtstp: contraction number = 2.838455e-01\n Vnewton: Using errtol_s: 18.418489\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.015688e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.986511e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.902147e+00\n Vprtstp: contraction number = 5.902147e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.272935e-06\n Vprtstp: contraction number = 2.884022e-01\n Vnewton: Using errtol_s: 5.311932\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.146007e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.108513e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.725476e+00\n Vprtstp: contraction number = 1.725476e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.418570e-06\n Vprtstp: contraction number = 2.923472e-01\n Vnewton: Using errtol_s: 1.552929\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.267661e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.228594e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.102067e-01\n Vprtstp: contraction number = 5.102067e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 7.151478e-07\n Vprtstp: contraction number = 2.956904e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.299105e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.311660e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.278329e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.290873e+02\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -20271,15 +20271,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.836319274152E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 6.830295346260E+03 kT\n Vpmg_energy:  dielEnergy = 3.413099848091E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.217500e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.145600e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 19.3778\n Vpbe_ctor2:  solute dimensions = 19.082 x 18.3114 x 35.7654\n Vpbe_ctor2:  solute charge = 4\n@@ -20328,160 +20328,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00207488 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.285086\n+Vacc_SASA: Time elapsed: 0.305020\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.020810e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.491490e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.343400e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.226200e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.113883e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.046815e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.405471e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.363670e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 667195.414501\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.430392e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.387085e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.070575e+05\n Vprtstp: contraction number = 1.070575e+05\n Vnewton: Attempting damping, relres = 0.151420\n Vnewton: Attempting damping, relres = 0.569765\n Vnewton: Damping accepted, relres = 0.151420\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.514203e-01\n Vprtstp: contraction number = 1.514203e-01\n Vnewton: Using errtol_s: 101026.941605\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.586775e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.540136e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.191459e+04\n Vprtstp: contraction number = 2.191459e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.976400e-02\n Vprtstp: contraction number = 1.965654e-01\n Vnewton: Using errtol_s: 19858.405232\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.751202e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.677107e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.366842e+03\n Vprtstp: contraction number = 5.366842e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.240542e-03\n Vprtstp: contraction number = 2.432651e-01\n Vnewton: Using errtol_s: 4830.856278\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.899723e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.808804e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.417443e+03\n Vprtstp: contraction number = 1.417443e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.912054e-03\n Vprtstp: contraction number = 2.640761e-01\n Vnewton: Using errtol_s: 1275.713735\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.048378e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.951097e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.929589e+02\n Vprtstp: contraction number = 3.929589e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.300759e-04\n Vprtstp: contraction number = 2.772285e-01\n Vnewton: Using errtol_s: 353.664179\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.183038e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.089420e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.125096e+02\n Vprtstp: contraction number = 1.125096e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.517678e-04\n Vprtstp: contraction number = 2.863133e-01\n Vnewton: Using errtol_s: 101.258773\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.333773e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.224946e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.298207e+01\n Vprtstp: contraction number = 3.298207e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.449052e-05\n Vprtstp: contraction number = 2.931486e-01\n Vnewton: Using errtol_s: 29.683870\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.501793e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.351427e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.865288e+00\n Vprtstp: contraction number = 9.865288e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.330759e-05\n Vprtstp: contraction number = 2.991106e-01\n Vnewton: Using errtol_s: 8.878760\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.653148e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.477339e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.008494e+00\n Vprtstp: contraction number = 3.008494e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 4.058248e-06\n Vprtstp: contraction number = 3.049575e-01\n Vnewton: Using errtol_s: 2.707645\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.797249e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.601826e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.332652e-01\n Vprtstp: contraction number = 9.332652e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.258910e-06\n Vprtstp: contraction number = 3.102101e-01\n Vnewton: Using errtol_s: 0.839939\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.922525e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.723919e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.936402e-01\n Vprtstp: contraction number = 2.936402e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.961001e-07\n Vprtstp: contraction number = 3.146374e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.651633e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.665168e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.475318e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.487663e+02\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -20491,17 +20491,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.827843084018E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 8.062828524213E+03 kT\n Vpmg_energy:  dielEnergy = 4.029378526105E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.142700e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.097800e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vnm_tstart: starting timer 27 (Setup timer)..\n@@ -20528,162 +20528,162 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.426468\n+Vacc_SASA: Time elapsed: 0.431566\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.255124e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.258298e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.144600e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.465100e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.156358e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.055287e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.101076e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.880905e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1471319.117079\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.126878e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.904237e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.089888e+05\n Vprtstp: contraction number = 2.089888e+05\n Vnewton: Attempting damping, relres = 0.165808\n Vnewton: Attempting damping, relres = 0.563564\n Vnewton: Damping accepted, relres = 0.165808\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.658082e-01\n Vprtstp: contraction number = 1.658082e-01\n Vnewton: Using errtol_s: 243956.756463\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.282061e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.049443e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.927783e+04\n Vprtstp: contraction number = 3.927783e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 3.048323e-02\n Vprtstp: contraction number = 1.838464e-01\n Vnewton: Using errtol_s: 44850.563282\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.431804e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.197497e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.923271e+03\n Vprtstp: contraction number = 9.923271e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 6.609400e-03\n Vprtstp: contraction number = 2.168208e-01\n Vnewton: Using errtol_s: 9724.536863\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.578480e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.351529e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.744656e+03\n Vprtstp: contraction number = 2.744656e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.685430e-03\n Vprtstp: contraction number = 2.550050e-01\n Vnewton: Using errtol_s: 2479.805360\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.710028e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.492117e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.927726e+02\n Vprtstp: contraction number = 7.927726e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.849448e-04\n Vprtstp: contraction number = 2.877276e-01\n Vnewton: Using errtol_s: 713.508521\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.869687e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.642644e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.371902e+02\n Vprtstp: contraction number = 2.371902e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.450884e-04\n Vprtstp: contraction number = 2.991854e-01\n Vnewton: Using errtol_s: 213.471337\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.010763e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.780766e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.181744e+01\n Vprtstp: contraction number = 7.181744e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.393045e-05\n Vprtstp: contraction number = 3.027840e-01\n Vnewton: Using errtol_s: 64.635706\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.162145e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.926705e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.188269e+01\n Vprtstp: contraction number = 2.188269e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.338555e-05\n Vprtstp: contraction number = 3.046988e-01\n Vnewton: Using errtol_s: 19.694422\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.307228e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.059477e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.694672e+00\n Vprtstp: contraction number = 6.694672e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 4.095104e-06\n Vprtstp: contraction number = 3.059346e-01\n Vnewton: Using errtol_s: 6.025205\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.458606e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.192407e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.053963e+00\n Vprtstp: contraction number = 2.053963e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.256401e-06\n Vprtstp: contraction number = 3.068056e-01\n Vnewton: Using errtol_s: 1.848567\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.605935e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.353372e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.315192e-01\n Vprtstp: contraction number = 6.315192e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.862977e-07\n Vprtstp: contraction number = 3.074637e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.637777e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.650545e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.613098e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.624510e+02\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -20693,17 +20693,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 7.577297422192E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.873373018987E+04 kT\n Vpmg_energy:  dielEnergy = 9.357495652952E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.457100e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.290400e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-05\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 20.7943\n Vpbe_ctor2:  solute dimensions = 25.3482 x 27.3592 x 40.136\n Vpbe_ctor2:  solute charge = -18\n Vpbe_ctor2:  bulk ionic strength = 0.4\n Vpbe_ctor2:  xkappa = 0.205945\n@@ -20750,160 +20750,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00276825 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.425211\n+Vacc_SASA: Time elapsed: 0.440359\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.264695e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.196095e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.553600e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.325100e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.053976e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.106777e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.765544e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.520546e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1499432.159358\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.784930e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.544907e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.618100e+05\n Vprtstp: contraction number = 2.618100e+05\n Vnewton: Attempting damping, relres = 0.194105\n Vnewton: Attempting damping, relres = 0.578438\n Vnewton: Damping accepted, relres = 0.194105\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.941047e-01\n Vprtstp: contraction number = 1.941047e-01\n Vnewton: Using errtol_s: 291046.875702\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.960846e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.713353e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.372130e+04\n Vprtstp: contraction number = 5.372130e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 3.856178e-02\n Vprtstp: contraction number = 1.986648e-01\n Vnewton: Using errtol_s: 57820.773992\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.130534e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.890410e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.429172e+04\n Vprtstp: contraction number = 1.429172e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 9.088822e-03\n Vprtstp: contraction number = 2.356951e-01\n Vnewton: Using errtol_s: 13628.071398\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.299112e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.060566e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.146951e+03\n Vprtstp: contraction number = 4.146951e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.494923e-03\n Vprtstp: contraction number = 2.745046e-01\n Vnewton: Using errtol_s: 3740.967765\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.439196e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.219513e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.262928e+03\n Vprtstp: contraction number = 1.262928e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 7.580508e-04\n Vprtstp: contraction number = 3.038374e-01\n Vnewton: Using errtol_s: 1136.645774\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.591946e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.389696e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.984728e+02\n Vprtstp: contraction number = 3.984728e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.391744e-04\n Vprtstp: contraction number = 3.155124e-01\n Vnewton: Using errtol_s: 358.625830\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.739319e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.553053e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.279297e+02\n Vprtstp: contraction number = 1.279297e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 7.678689e-05\n Vprtstp: contraction number = 3.210497e-01\n Vnewton: Using errtol_s: 115.136728\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.911610e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.705732e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.156614e+01\n Vprtstp: contraction number = 4.156614e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.494913e-05\n Vprtstp: contraction number = 3.249140e-01\n Vnewton: Using errtol_s: 37.409531\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.005520e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.878791e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.363199e+01\n Vprtstp: contraction number = 1.363199e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 8.182289e-06\n Vprtstp: contraction number = 3.279589e-01\n Vnewton: Using errtol_s: 12.268788\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.021683e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.004767e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.504209e+00\n Vprtstp: contraction number = 4.504209e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 2.703549e-06\n Vprtstp: contraction number = 3.304147e-01\n Vnewton: Using errtol_s: 4.053788\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.035619e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.020541e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.497181e+00\n Vprtstp: contraction number = 1.497181e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 8.986490e-07\n Vprtstp: contraction number = 3.323961e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.750394e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.763463e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.835286e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.848708e+02\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -20913,29 +20913,29 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 7.566888561677E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.135111393094E+04 kT\n Vpmg_energy:  dielEnergy = 1.066620211340E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.394300e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.202500e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 4.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.053371e+03\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.037536e+03\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 07:21:41 2025\n+# Creation Date and Time:  Tue Jan  9 05:31:44 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path model_outNB.pqr\n@@ -21205,151 +21205,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.619944\n+Vacc_SASA: Time elapsed: 0.642297\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.655585e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.733493e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.793100e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 8.076900e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.143241e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.214863e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.951410e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.251132e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2117021.813584\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.289584e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.992772e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.733993e+05\n Vprtstp: contraction number = 2.733993e+05\n Vnewton: Attempting damping, relres = 0.126346\n Vnewton: Attempting damping, relres = 0.555677\n Vnewton: Damping accepted, relres = 0.126346\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.263459e-01\n Vprtstp: contraction number = 1.263459e-01\n Vnewton: Using errtol_s: 267477.104304\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.388180e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.790805e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.948638e+04\n Vprtstp: contraction number = 4.948638e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.218275e-02\n Vprtstp: contraction number = 1.755716e-01\n Vnewton: Using errtol_s: 46961.371226\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.662217e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.895766e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.168877e+04\n Vprtstp: contraction number = 1.168877e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 5.021324e-03\n Vprtstp: contraction number = 2.263616e-01\n Vnewton: Using errtol_s: 10630.252373\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.512661e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.855376e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.120176e+03\n Vprtstp: contraction number = 3.120176e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.326708e-03\n Vprtstp: contraction number = 2.642148e-01\n Vnewton: Using errtol_s: 2808.669489\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.128583e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.862615e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.828690e+02\n Vprtstp: contraction number = 8.828690e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.753310e-04\n Vprtstp: contraction number = 2.829040e-01\n Vnewton: Using errtol_s: 794.583820\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.002826e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.077379e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.573077e+02\n Vprtstp: contraction number = 2.573077e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.093881e-04\n Vprtstp: contraction number = 2.914445e-01\n Vnewton: Using errtol_s: 231.577068\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.174283e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.279836e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.638166e+01\n Vprtstp: contraction number = 7.638166e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.247180e-05\n Vprtstp: contraction number = 2.968494e-01\n Vnewton: Using errtol_s: 68.743505\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.374876e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.491203e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.298047e+01\n Vprtstp: contraction number = 2.298047e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 9.769584e-06\n Vprtstp: contraction number = 3.008636e-01\n Vnewton: Using errtol_s: 20.682422\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.563724e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.675532e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.986364e+00\n Vprtstp: contraction number = 6.986364e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.970082e-06\n Vprtstp: contraction number = 3.040131e-01\n Vnewton: Using errtol_s: 6.287728\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.772300e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.859809e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.142572e+00\n Vprtstp: contraction number = 2.142572e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 9.108619e-07\n Vprtstp: contraction number = 3.066791e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.912180e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.924697e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.013344e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.027924e+02\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -21359,17 +21359,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 5.282938613188E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.566547142826E+04 kT\n Vpmg_energy:  dielEnergy = 1.282703574681E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.140480e-01\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.127400e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 4.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 5.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 25.8477\n Vpbe_ctor2:  solute dimensions = 26.666 x 32.3234 x 48.3902\n Vpbe_ctor2:  solute charge = -14\n Vpbe_ctor2:  bulk ionic strength = 0.5\n Vpbe_ctor2:  xkappa = 0.230253\n@@ -21416,160 +21416,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0133684 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.631175\n+Vacc_SASA: Time elapsed: 0.642160\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.658073e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.768346e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.485800e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 6.953300e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.166316e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.262127e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.973108e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.079725e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2163354.564593\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.998736e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.104492e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.401998e+05\n Vprtstp: contraction number = 3.401998e+05\n Vnewton: Attempting damping, relres = 0.151250\n Vnewton: Attempting damping, relres = 0.568556\n Vnewton: Damping accepted, relres = 0.151250\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.512496e-01\n Vprtstp: contraction number = 1.512496e-01\n Vnewton: Using errtol_s: 327206.577099\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.201950e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.330720e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.770698e+04\n Vprtstp: contraction number = 6.770698e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.926462e-02\n Vprtstp: contraction number = 1.934856e-01\n Vnewton: Using errtol_s: 63309.757927\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.402774e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.531884e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.699399e+04\n Vprtstp: contraction number = 1.699399e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.115656e-03\n Vprtstp: contraction number = 2.431487e-01\n Vnewton: Using errtol_s: 15393.687585\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.590941e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.749738e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.742003e+03\n Vprtstp: contraction number = 4.742003e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.972961e-03\n Vprtstp: contraction number = 2.772704e-01\n Vnewton: Using errtol_s: 4268.214485\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.764518e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.947018e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.400571e+03\n Vprtstp: contraction number = 1.400571e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.826678e-04\n Vprtstp: contraction number = 2.953265e-01\n Vnewton: Using errtol_s: 1260.517005\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.937514e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.144198e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.279978e+02\n Vprtstp: contraction number = 4.279978e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.780560e-04\n Vprtstp: contraction number = 3.055876e-01\n Vnewton: Using errtol_s: 385.198337\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.132665e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.347233e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.339544e+02\n Vprtstp: contraction number = 1.339544e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 5.572782e-05\n Vprtstp: contraction number = 3.129791e-01\n Vnewton: Using errtol_s: 120.559033\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.328001e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.561588e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.271452e+01\n Vprtstp: contraction number = 4.271452e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.777012e-05\n Vprtstp: contraction number = 3.188734e-01\n Vnewton: Using errtol_s: 38.443069\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.533801e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.776135e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.384186e+01\n Vprtstp: contraction number = 1.384186e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.758498e-06\n Vprtstp: contraction number = 3.240551e-01\n Vnewton: Using errtol_s: 12.457672\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.733675e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.992963e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.545889e+00\n Vprtstp: contraction number = 4.545889e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.891183e-06\n Vprtstp: contraction number = 3.284161e-01\n Vnewton: Using errtol_s: 4.091300\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.907701e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.197245e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.509299e+00\n Vprtstp: contraction number = 1.509299e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 6.278996e-07\n Vprtstp: contraction number = 3.320141e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.112614e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.125558e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.331427e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.346720e+02\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -21579,17 +21579,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 5.270848264537E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.951162263981E+04 kT\n Vpmg_energy:  dielEnergy = 1.475012659776E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.901600e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.969210e-01\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vnm_tstart: starting timer 27 (Setup timer)..\n@@ -21616,151 +21616,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.322522\n+Vacc_SASA: Time elapsed: 0.353500\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.094137e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.021225e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.434100e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.082470e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.235002e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.308238e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.127463e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.460713e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 634193.792999\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.152432e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.485131e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.499222e+04\n Vprtstp: contraction number = 8.499222e+04\n Vnewton: Attempting damping, relres = 0.127890\n Vnewton: Attempting damping, relres = 0.557688\n Vnewton: Damping accepted, relres = 0.127890\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.278898e-01\n Vprtstp: contraction number = 1.278898e-01\n Vnewton: Using errtol_s: 81106.914272\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.293484e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.640921e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.610090e+04\n Vprtstp: contraction number = 1.610090e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.303084e-02\n Vprtstp: contraction number = 1.800835e-01\n Vnewton: Using errtol_s: 14606.018111\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.424701e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.788447e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.721077e+03\n Vprtstp: contraction number = 3.721077e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 5.281325e-03\n Vprtstp: contraction number = 2.293153e-01\n Vnewton: Using errtol_s: 3349.383286\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.575517e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.923028e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.553498e+02\n Vprtstp: contraction number = 9.553498e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.355768e-03\n Vprtstp: contraction number = 2.567099e-01\n Vnewton: Using errtol_s: 859.819863\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.705591e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.064050e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.585067e+02\n Vprtstp: contraction number = 2.585067e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.668537e-04\n Vprtstp: contraction number = 2.705873e-01\n Vnewton: Using errtol_s: 232.656331\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.837701e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.217766e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.199407e+01\n Vprtstp: contraction number = 7.199407e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.021686e-04\n Vprtstp: contraction number = 2.784995e-01\n Vnewton: Using errtol_s: 64.794682\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.968198e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.363559e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.044636e+01\n Vprtstp: contraction number = 2.044636e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.901594e-05\n Vprtstp: contraction number = 2.840006e-01\n Vnewton: Using errtol_s: 18.401729\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.097118e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.531465e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.898540e+00\n Vprtstp: contraction number = 5.898540e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.370763e-06\n Vprtstp: contraction number = 2.884884e-01\n Vnewton: Using errtol_s: 5.308686\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.227065e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.671134e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.724703e+00\n Vprtstp: contraction number = 1.724703e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.447569e-06\n Vprtstp: contraction number = 2.923949e-01\n Vnewton: Using errtol_s: 1.552233\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.349367e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.815174e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.100216e-01\n Vprtstp: contraction number = 5.100216e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 7.237842e-07\n Vprtstp: contraction number = 2.957156e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.341357e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.354706e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.475312e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.491491e+02\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -21770,17 +21770,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.835376083091E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 6.829553004280E+03 kT\n Vpmg_energy:  dielEnergy = 3.412753768634E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.479700e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.988300e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 19.3778\n Vpbe_ctor2:  solute dimensions = 19.082 x 18.3114 x 35.7654\n Vpbe_ctor2:  solute charge = 4\n Vpbe_ctor2:  bulk ionic strength = 0.5\n Vpbe_ctor2:  xkappa = 0.230253\n@@ -21827,160 +21827,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00156468 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.424090\n+Vacc_SASA: Time elapsed: 0.268013\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.528550e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.141800e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.406800e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 6.896400e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.223952e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.417533e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.494988e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.963581e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 658696.826144\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.517738e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.991084e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.053855e+05\n Vprtstp: contraction number = 1.053855e+05\n Vnewton: Attempting damping, relres = 0.150549\n Vnewton: Attempting damping, relres = 0.569486\n Vnewton: Damping accepted, relres = 0.150549\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.505490e-01\n Vprtstp: contraction number = 1.505490e-01\n Vnewton: Using errtol_s: 99166.139789\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.669618e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.159513e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.161238e+04\n Vprtstp: contraction number = 2.161238e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.969136e-02\n Vprtstp: contraction number = 1.972206e-01\n Vnewton: Using errtol_s: 19557.601485\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.803727e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.317939e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.305338e+03\n Vprtstp: contraction number = 5.305338e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.249717e-03\n Vprtstp: contraction number = 2.441693e-01\n Vnewton: Using errtol_s: 4775.365541\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.943229e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.477403e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.404636e+03\n Vprtstp: contraction number = 1.404636e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.919225e-03\n Vprtstp: contraction number = 2.647311e-01\n Vnewton: Using errtol_s: 1264.187582\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.080670e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.646216e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.902078e+02\n Vprtstp: contraction number = 3.902078e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.331561e-04\n Vprtstp: contraction number = 2.777976e-01\n Vnewton: Using errtol_s: 351.188214\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.221384e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.809285e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.119096e+02\n Vprtstp: contraction number = 1.119096e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.529061e-04\n Vprtstp: contraction number = 2.867943e-01\n Vnewton: Using errtol_s: 100.718769\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.366614e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.952958e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.284972e+01\n Vprtstp: contraction number = 3.284972e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.488371e-05\n Vprtstp: contraction number = 2.935377e-01\n Vnewton: Using errtol_s: 29.564758\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.510030e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.108047e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.835792e+00\n Vprtstp: contraction number = 9.835792e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.343898e-05\n Vprtstp: contraction number = 2.994178e-01\n Vnewton: Using errtol_s: 8.852214\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.650803e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.273128e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.001834e+00\n Vprtstp: contraction number = 3.001834e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 4.101508e-06\n Vprtstp: contraction number = 3.051949e-01\n Vnewton: Using errtol_s: 2.701650\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.793694e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.441580e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.317265e-01\n Vprtstp: contraction number = 9.317265e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.273050e-06\n Vprtstp: contraction number = 3.103858e-01\n Vnewton: Using errtol_s: 0.838554\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.930807e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.602932e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.932750e-01\n Vprtstp: contraction number = 2.932750e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 4.007117e-07\n Vprtstp: contraction number = 3.147651e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.569967e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.585074e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.792491e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.810119e+02\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -21990,17 +21990,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.826778540566E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 8.062089331006E+03 kT\n Vpmg_energy:  dielEnergy = 4.029034062463E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.260000e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.098000e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vnm_tstart: starting timer 27 (Setup timer)..\n@@ -22027,162 +22027,162 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.481330\n+Vacc_SASA: Time elapsed: 0.470585\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.227606e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.364310e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.237500e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 6.588900e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.117549e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.509498e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.105465e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.812474e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1439349.266881\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.125348e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.841657e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.043544e+05\n Vprtstp: contraction number = 2.043544e+05\n Vnewton: Attempting damping, relres = 0.158631\n Vnewton: Attempting damping, relres = 0.563029\n Vnewton: Damping accepted, relres = 0.158631\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.586310e-01\n Vprtstp: contraction number = 1.586310e-01\n Vnewton: Using errtol_s: 228325.431602\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.282036e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.032944e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.831785e+04\n Vprtstp: contraction number = 3.831785e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.847279e-02\n Vprtstp: contraction number = 1.794907e-01\n Vnewton: Using errtol_s: 40982.294833\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.438871e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.213354e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.668291e+03\n Vprtstp: contraction number = 9.668291e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 6.314045e-03\n Vprtstp: contraction number = 2.217571e-01\n Vnewton: Using errtol_s: 9088.116327\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.582380e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.370448e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.688849e+03\n Vprtstp: contraction number = 2.688849e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.683268e-03\n Vprtstp: contraction number = 2.665910e-01\n Vnewton: Using errtol_s: 2422.810315\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.734569e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.520119e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.856129e+02\n Vprtstp: contraction number = 7.856129e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.912324e-04\n Vprtstp: contraction number = 2.918326e-01\n Vnewton: Using errtol_s: 707.055007\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.884650e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.676867e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.356112e+02\n Vprtstp: contraction number = 2.356112e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.473237e-04\n Vprtstp: contraction number = 2.999062e-01\n Vnewton: Using errtol_s: 212.050207\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.032461e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.842552e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.139103e+01\n Vprtstp: contraction number = 7.139103e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.463957e-05\n Vprtstp: contraction number = 3.030034e-01\n Vnewton: Using errtol_s: 64.251934\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.185269e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.023361e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.175983e+01\n Vprtstp: contraction number = 2.175983e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.360604e-05\n Vprtstp: contraction number = 3.047978e-01\n Vnewton: Using errtol_s: 19.583846\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.341005e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.189615e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.658230e+00\n Vprtstp: contraction number = 6.658230e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 4.163275e-06\n Vprtstp: contraction number = 3.059873e-01\n Vnewton: Using errtol_s: 5.992407\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.513879e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.356642e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.042996e+00\n Vprtstp: contraction number = 2.042996e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.277450e-06\n Vprtstp: contraction number = 3.068378e-01\n Vnewton: Using errtol_s: 1.838697\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.691061e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.528743e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.281914e-01\n Vprtstp: contraction number = 6.281914e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.927971e-07\n Vprtstp: contraction number = 3.074853e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.737426e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.749633e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.862471e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.880212e+02\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -22192,17 +22192,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 7.196840922494E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.873106662838E+04 kT\n Vpmg_energy:  dielEnergy = 9.356799948261E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.646000e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.110000e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 20.7943\n Vpbe_ctor2:  solute dimensions = 25.3482 x 27.3592 x 40.136\n Vpbe_ctor2:  solute charge = -18\n Vpbe_ctor2:  bulk ionic strength = 0.5\n Vpbe_ctor2:  xkappa = 0.230253\n@@ -22249,160 +22249,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00202496 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.475260\n+Vacc_SASA: Time elapsed: 0.443049\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.210917e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.285740e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.334400e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 6.593800e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.149581e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.215830e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.870113e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.704368e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1465724.452340\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.896340e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.732234e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.560590e+05\n Vprtstp: contraction number = 2.560590e+05\n Vnewton: Attempting damping, relres = 0.187284\n Vnewton: Attempting damping, relres = 0.577996\n Vnewton: Damping accepted, relres = 0.187284\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.872842e-01\n Vprtstp: contraction number = 1.872842e-01\n Vnewton: Using errtol_s: 274507.063571\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.108817e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.905090e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.241855e+04\n Vprtstp: contraction number = 5.241855e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 3.660510e-02\n Vprtstp: contraction number = 1.954521e-01\n Vnewton: Using errtol_s: 53652.984086\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.329280e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.007570e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.392830e+04\n Vprtstp: contraction number = 1.392830e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 8.808972e-03\n Vprtstp: contraction number = 2.406488e-01\n Vnewton: Using errtol_s: 12911.525544\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.524253e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.024478e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.064869e+03\n Vprtstp: contraction number = 4.064869e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.497826e-03\n Vprtstp: contraction number = 2.835548e-01\n Vnewton: Using errtol_s: 3661.124985\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.725164e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.041076e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.249555e+03\n Vprtstp: contraction number = 1.249555e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 7.672679e-04\n Vprtstp: contraction number = 3.071743e-01\n Vnewton: Using errtol_s: 1124.603371\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.932752e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.058933e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.953417e+02\n Vprtstp: contraction number = 3.953417e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.427522e-04\n Vprtstp: contraction number = 3.163852e-01\n Vnewton: Using errtol_s: 355.807819\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.012766e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.076314e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.271192e+02\n Vprtstp: contraction number = 1.271192e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 7.805515e-05\n Vprtstp: contraction number = 3.215425e-01\n Vnewton: Using errtol_s: 114.407339\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.033508e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.095605e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.134607e+01\n Vprtstp: contraction number = 4.134607e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.538777e-05\n Vprtstp: contraction number = 3.252542e-01\n Vnewton: Using errtol_s: 37.211468\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.054191e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.114284e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.356940e+01\n Vprtstp: contraction number = 1.356940e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 8.332028e-06\n Vprtstp: contraction number = 3.281907e-01\n Vnewton: Using errtol_s: 12.212457\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.074281e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.132586e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.485660e+00\n Vprtstp: contraction number = 4.485660e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 2.754334e-06\n Vprtstp: contraction number = 3.305718e-01\n Vnewton: Using errtol_s: 4.037094\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.095914e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.150053e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.491490e+00\n Vprtstp: contraction number = 1.491490e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 9.158205e-07\n Vprtstp: contraction number = 3.325017e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.270678e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.284557e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.967885e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.983024e+02\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -22412,29 +22412,29 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 7.186606092212E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.134845139455E+04 kT\n Vpmg_energy:  dielEnergy = 1.066550655218E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.707800e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.333500e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.115415e+03\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.169379e+03\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 07:24:05 2025\n+# Creation Date and Time:  Tue Jan  9 05:37:11 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path model_outNB.pqr\n@@ -22704,151 +22704,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.589594\n+Vacc_SASA: Time elapsed: 0.618612\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.625437e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.777625e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.892200e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 1.203610e-01\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.086203e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.307321e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.902251e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.431707e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2093191.031761\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.611815e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.130327e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.700910e+05\n Vprtstp: contraction number = 2.700910e+05\n Vnewton: Attempting damping, relres = 0.124805\n Vnewton: Attempting damping, relres = 0.555496\n Vnewton: Damping accepted, relres = 0.124805\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.248046e-01\n Vprtstp: contraction number = 1.248046e-01\n Vnewton: Using errtol_s: 261239.913592\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.140691e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.031173e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.897400e+04\n Vprtstp: contraction number = 4.897400e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.189435e-02\n Vprtstp: contraction number = 1.754290e-01\n Vnewton: Using errtol_s: 45829.056358\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.614808e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.254843e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.159488e+04\n Vprtstp: contraction number = 1.159488e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 5.014196e-03\n Vprtstp: contraction number = 2.290178e-01\n Vnewton: Using errtol_s: 10495.669115\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.216314e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.450454e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.106549e+03\n Vprtstp: contraction number = 3.106549e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.335806e-03\n Vprtstp: contraction number = 2.664048e-01\n Vnewton: Using errtol_s: 2796.096256\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.081910e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.603756e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.808235e+02\n Vprtstp: contraction number = 8.808235e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.787243e-04\n Vprtstp: contraction number = 2.835176e-01\n Vnewton: Using errtol_s: 792.742402\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.292196e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.206566e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.569082e+02\n Vprtstp: contraction number = 2.569082e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.104617e-04\n Vprtstp: contraction number = 2.916679e-01\n Vnewton: Using errtol_s: 231.217496\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.537049e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.443491e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.629035e+01\n Vprtstp: contraction number = 7.629035e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.280223e-05\n Vprtstp: contraction number = 2.969556e-01\n Vnewton: Using errtol_s: 68.661328\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.793989e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.657481e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.295748e+01\n Vprtstp: contraction number = 2.295748e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 9.870924e-06\n Vprtstp: contraction number = 3.009224e-01\n Vnewton: Using errtol_s: 20.661731\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.052961e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.887684e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.980126e+00\n Vprtstp: contraction number = 6.980126e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.001214e-06\n Vprtstp: contraction number = 3.040459e-01\n Vnewton: Using errtol_s: 6.282114\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.315629e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.093243e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.140783e+00\n Vprtstp: contraction number = 2.140783e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 9.204627e-07\n Vprtstp: contraction number = 3.066968e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.514974e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.527431e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.271884e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.287882e+02\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -22858,15 +22858,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 5.091310515028E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.566396275850E+04 kT\n Vpmg_energy:  dielEnergy = 1.282657451494E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 8.001300e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.004800e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 25.8477\n Vpbe_ctor2:  solute dimensions = 26.666 x 32.3234 x 48.3902\n Vpbe_ctor2:  solute charge = -14\n@@ -22915,160 +22915,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0123549 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.580030\n+Vacc_SASA: Time elapsed: 0.659016\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.598104e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.739433e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.227800e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.846800e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.212734e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.153967e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.575574e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.338360e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2138246.077963\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.604766e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.364393e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.360784e+05\n Vprtstp: contraction number = 3.360784e+05\n Vnewton: Attempting damping, relres = 0.149785\n Vnewton: Attempting damping, relres = 0.568394\n Vnewton: Damping accepted, relres = 0.149785\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.497849e-01\n Vprtstp: contraction number = 1.497849e-01\n Vnewton: Using errtol_s: 320277.019000\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.874196e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.613785e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.696106e+04\n Vprtstp: contraction number = 6.696106e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.898319e-02\n Vprtstp: contraction number = 1.934987e-01\n Vnewton: Using errtol_s: 61973.189490\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.149608e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.834531e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.682773e+04\n Vprtstp: contraction number = 1.682773e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.107594e-03\n Vprtstp: contraction number = 2.452316e-01\n Vnewton: Using errtol_s: 15197.785187\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.402297e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.057593e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.709721e+03\n Vprtstp: contraction number = 4.709721e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.982435e-03\n Vprtstp: contraction number = 2.789179e-01\n Vnewton: Using errtol_s: 4238.934308\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.665720e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.270565e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.393997e+03\n Vprtstp: contraction number = 1.393997e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.867426e-04\n Vprtstp: contraction number = 2.959706e-01\n Vnewton: Using errtol_s: 1254.599967\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.925613e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.509215e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.264850e+02\n Vprtstp: contraction number = 4.264850e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.795101e-04\n Vprtstp: contraction number = 3.059436e-01\n Vnewton: Using errtol_s: 383.836806\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.195007e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.726157e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.335898e+02\n Vprtstp: contraction number = 1.335898e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 5.622871e-05\n Vprtstp: contraction number = 3.132342e-01\n Vnewton: Using errtol_s: 120.230819\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.452872e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.937930e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.262294e+01\n Vprtstp: contraction number = 4.262294e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.794024e-05\n Vprtstp: contraction number = 3.190584e-01\n Vnewton: Using errtol_s: 38.360650\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.703391e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.163174e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.381744e+01\n Vprtstp: contraction number = 1.381744e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.815841e-06\n Vprtstp: contraction number = 3.241785e-01\n Vnewton: Using errtol_s: 12.435699\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.963666e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.386702e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.538963e+00\n Vprtstp: contraction number = 4.538963e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.910476e-06\n Vprtstp: contraction number = 3.284952e-01\n Vnewton: Using errtol_s: 4.085067\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.224155e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.613472e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.507189e+00\n Vprtstp: contraction number = 1.507189e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 6.343844e-07\n Vprtstp: contraction number = 3.320557e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.886877e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.900929e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.486841e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.500472e+02\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -23078,15 +23078,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 5.079562127761E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.951011518926E+04 kT\n Vpmg_energy:  dielEnergy = 1.474966609512E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.188130e-01\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.162200e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n@@ -23115,151 +23115,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.360401\n+Vacc_SASA: Time elapsed: 0.380451\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.069313e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.152006e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.226900e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 7.786700e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.238038e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.456742e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.503842e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.871757e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 628877.747769\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.533063e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.903850e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.412647e+04\n Vprtstp: contraction number = 8.412647e+04\n Vnewton: Attempting damping, relres = 0.127232\n Vnewton: Attempting damping, relres = 0.557518\n Vnewton: Damping accepted, relres = 0.127232\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.272321e-01\n Vprtstp: contraction number = 1.272321e-01\n Vnewton: Using errtol_s: 80013.454014\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.729350e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.090181e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.597434e+04\n Vprtstp: contraction number = 1.597434e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.300878e-02\n Vprtstp: contraction number = 1.808409e-01\n Vnewton: Using errtol_s: 14469.707458\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.917679e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.242364e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.702955e+03\n Vprtstp: contraction number = 3.702955e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 5.299891e-03\n Vprtstp: contraction number = 2.303422e-01\n Vnewton: Using errtol_s: 3332.983791\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.110504e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.402373e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.526036e+02\n Vprtstp: contraction number = 9.526036e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.363298e-03\n Vprtstp: contraction number = 2.572314e-01\n Vnewton: Using errtol_s: 857.348085\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.285322e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.558600e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.580584e+02\n Vprtstp: contraction number = 2.580584e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.693131e-04\n Vprtstp: contraction number = 2.708968e-01\n Vnewton: Using errtol_s: 232.252814\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.461563e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.735620e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.191756e+01\n Vprtstp: contraction number = 7.191756e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.029227e-04\n Vprtstp: contraction number = 2.786869e-01\n Vnewton: Using errtol_s: 64.725819\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.643426e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.900293e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.043225e+01\n Vprtstp: contraction number = 2.043225e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.924102e-05\n Vprtstp: contraction number = 2.841066e-01\n Vnewton: Using errtol_s: 18.389029\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.817013e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.076942e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.895681e+00\n Vprtstp: contraction number = 5.895681e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.437431e-06\n Vprtstp: contraction number = 2.885477e-01\n Vnewton: Using errtol_s: 5.306113\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.986418e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.222940e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.724061e+00\n Vprtstp: contraction number = 1.724061e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.467339e-06\n Vprtstp: contraction number = 2.924277e-01\n Vnewton: Using errtol_s: 1.551655\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.162268e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.372736e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.098608e-01\n Vprtstp: contraction number = 5.098608e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 7.296724e-07\n Vprtstp: contraction number = 2.957325e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.809438e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.822691e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.634890e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.651410e+02\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -23269,15 +23269,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.828142417011E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 6.828945138010E+03 kT\n Vpmg_energy:  dielEnergy = 3.412475614010E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 9.992900e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.231300e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 19.3778\n Vpbe_ctor2:  solute dimensions = 19.082 x 18.3114 x 35.7654\n Vpbe_ctor2:  solute charge = 4\n@@ -23326,160 +23326,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0012176 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.396629\n+Vacc_SASA: Time elapsed: 0.375142\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.748860e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.837290e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 6.478900e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.707700e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.188549e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.195992e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.339834e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.532495e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 653003.444935\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.364245e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.559755e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.042328e+05\n Vprtstp: contraction number = 1.042328e+05\n Vnewton: Attempting damping, relres = 0.149810\n Vnewton: Attempting damping, relres = 0.569263\n Vnewton: Damping accepted, relres = 0.149810\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.498099e-01\n Vprtstp: contraction number = 1.498099e-01\n Vnewton: Using errtol_s: 97826.408096\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.511554e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.767848e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.140231e+04\n Vprtstp: contraction number = 2.140231e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.962843e-02\n Vprtstp: contraction number = 1.977735e-01\n Vnewton: Using errtol_s: 19347.468430\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.672171e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.933074e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.262567e+03\n Vprtstp: contraction number = 5.262567e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.253840e-03\n Vprtstp: contraction number = 2.448270e-01\n Vnewton: Using errtol_s: 4736.782334\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.836091e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.101482e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.395696e+03\n Vprtstp: contraction number = 1.395696e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.923638e-03\n Vprtstp: contraction number = 2.651889e-01\n Vnewton: Using errtol_s: 1256.142167\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.989957e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.249329e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.882795e+02\n Vprtstp: contraction number = 3.882795e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.351469e-04\n Vprtstp: contraction number = 2.781952e-01\n Vnewton: Using errtol_s: 349.452740\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.167497e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.408474e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.114868e+02\n Vprtstp: contraction number = 1.114868e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.536566e-04\n Vprtstp: contraction number = 2.871297e-01\n Vnewton: Using errtol_s: 100.338262\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.356278e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.562049e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.275571e+01\n Vprtstp: contraction number = 3.275571e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.514547e-05\n Vprtstp: contraction number = 2.938077e-01\n Vnewton: Using errtol_s: 29.480150\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.539581e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.732879e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.814633e+00\n Vprtstp: contraction number = 9.814633e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.352699e-05\n Vprtstp: contraction number = 2.996311e-01\n Vnewton: Using errtol_s: 8.833170\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.720830e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.892988e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.996998e+00\n Vprtstp: contraction number = 2.996998e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 4.130604e-06\n Vprtstp: contraction number = 3.053602e-01\n Vnewton: Using errtol_s: 2.697298\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.901675e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.051579e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.305904e-01\n Vprtstp: contraction number = 9.305904e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.282583e-06\n Vprtstp: contraction number = 3.105075e-01\n Vnewton: Using errtol_s: 0.837531\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.084293e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.217786e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.929997e-01\n Vprtstp: contraction number = 2.929997e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 4.038259e-07\n Vprtstp: contraction number = 3.148535e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.918598e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.933500e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.819987e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.835026e+02\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -23489,15 +23489,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.819478148872E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 8.061484049390E+03 kT\n Vpmg_energy:  dielEnergy = 4.028757163114E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.106300e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.595000e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n@@ -23526,162 +23526,162 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.410334\n+Vacc_SASA: Time elapsed: 0.425584\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.317023e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.229342e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.118100e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.208400e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.385779e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.159464e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.302083e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.393907e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1418682.220089\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.334838e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.423036e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.013102e+05\n Vprtstp: contraction number = 2.013102e+05\n Vnewton: Attempting damping, relres = 0.153624\n Vnewton: Attempting damping, relres = 0.562616\n Vnewton: Damping accepted, relres = 0.153624\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.536244e-01\n Vprtstp: contraction number = 1.536244e-01\n Vnewton: Using errtol_s: 217944.143405\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.486983e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.602427e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.768720e+04\n Vprtstp: contraction number = 3.768720e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.718554e-02\n Vprtstp: contraction number = 1.769611e-01\n Vnewton: Using errtol_s: 38567.641801\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.638289e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.779030e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.503404e+03\n Vprtstp: contraction number = 9.503404e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 6.173770e-03\n Vprtstp: contraction number = 2.270976e-01\n Vnewton: Using errtol_s: 8758.617788\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.788057e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.939376e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.660166e+03\n Vprtstp: contraction number = 2.660166e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.688330e-03\n Vprtstp: contraction number = 2.734683e-01\n Vnewton: Using errtol_s: 2395.204376\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.931836e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.092459e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.818054e+02\n Vprtstp: contraction number = 7.818054e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.959721e-04\n Vprtstp: contraction number = 2.937648e-01\n Vnewton: Using errtol_s: 703.626776\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.008366e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.243738e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.347603e+02\n Vprtstp: contraction number = 2.347603e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.489300e-04\n Vprtstp: contraction number = 3.002790e-01\n Vnewton: Using errtol_s: 211.284321\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.025914e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.395827e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.116445e+01\n Vprtstp: contraction number = 7.116445e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.514613e-05\n Vprtstp: contraction number = 3.031366e-01\n Vnewton: Using errtol_s: 64.048016\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.043727e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.545014e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.169522e+01\n Vprtstp: contraction number = 2.169522e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.376326e-05\n Vprtstp: contraction number = 3.048603e-01\n Vnewton: Using errtol_s: 19.525698\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.062097e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.711602e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.639132e+00\n Vprtstp: contraction number = 6.639132e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 4.211809e-06\n Vprtstp: contraction number = 3.060182e-01\n Vnewton: Using errtol_s: 5.975219\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.080613e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.867167e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.037255e+00\n Vprtstp: contraction number = 2.037255e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.292417e-06\n Vprtstp: contraction number = 3.068556e-01\n Vnewton: Using errtol_s: 1.833530\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.098581e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.002159e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.264492e-01\n Vprtstp: contraction number = 6.264492e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 3.974141e-07\n Vprtstp: contraction number = 3.074967e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.839240e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.853835e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.760245e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.773155e+02\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -23691,15 +23691,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 6.888929472568E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.872895947241E+04 kT\n Vpmg_energy:  dielEnergy = 9.356241018508E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.740300e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.771200e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 20.7943\n Vpbe_ctor2:  solute dimensions = 25.3482 x 27.3592 x 40.136\n Vpbe_ctor2:  solute charge = -18\n@@ -23748,160 +23748,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00159488 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.441542\n+Vacc_SASA: Time elapsed: 0.411326\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.355737e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.172303e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.766200e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.565500e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.254092e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.158535e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.116937e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.018175e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1444108.030883\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.119835e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.020715e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.522925e+05\n Vprtstp: contraction number = 2.522925e+05\n Vnewton: Attempting damping, relres = 0.182497\n Vnewton: Attempting damping, relres = 0.577636\n Vnewton: Damping accepted, relres = 0.182497\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.824967e-01\n Vprtstp: contraction number = 1.824967e-01\n Vnewton: Using errtol_s: 263544.898395\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.137999e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.038260e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.156495e+04\n Vprtstp: contraction number = 5.156495e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 3.534743e-02\n Vprtstp: contraction number = 1.936881e-01\n Vnewton: Using errtol_s: 51045.503065\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.154872e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.056325e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.369160e+04\n Vprtstp: contraction number = 1.369160e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 8.672608e-03\n Vprtstp: contraction number = 2.453533e-01\n Vnewton: Using errtol_s: 12524.182385\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.170205e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.073627e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.019157e+03\n Vprtstp: contraction number = 4.019157e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.505566e-03\n Vprtstp: contraction number = 2.889057e-01\n Vnewton: Using errtol_s: 3618.307619\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.186120e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.090522e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.241608e+03\n Vprtstp: contraction number = 1.241608e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 7.737990e-04\n Vprtstp: contraction number = 3.088321e-01\n Vnewton: Using errtol_s: 1117.449365\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.202576e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.106426e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.934907e+02\n Vprtstp: contraction number = 3.934907e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.452323e-04\n Vprtstp: contraction number = 3.169199e-01\n Vnewton: Using errtol_s: 354.141922\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.220726e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.124144e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.266527e+02\n Vprtstp: contraction number = 1.266527e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 7.893280e-05\n Vprtstp: contraction number = 3.218695e-01\n Vnewton: Using errtol_s: 113.987497\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.239376e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.140650e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.122303e+01\n Vprtstp: contraction number = 4.122303e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.569111e-05\n Vprtstp: contraction number = 3.254807e-01\n Vnewton: Using errtol_s: 37.100733\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.258966e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.156418e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.353532e+01\n Vprtstp: contraction number = 1.353532e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 8.435513e-06\n Vprtstp: contraction number = 3.283437e-01\n Vnewton: Using errtol_s: 12.181792\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.278581e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.175628e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.475781e+00\n Vprtstp: contraction number = 4.475781e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 2.789406e-06\n Vprtstp: contraction number = 3.306741e-01\n Vnewton: Using errtol_s: 4.028203\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.298400e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.195224e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.488509e+00\n Vprtstp: contraction number = 1.488509e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 9.276717e-07\n Vprtstp: contraction number = 3.325696e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.005530e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.018889e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.931362e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.945938e+02\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -23911,29 +23911,29 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 6.878772494899E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.134634520141E+04 kT\n Vpmg_energy:  dielEnergy = 1.066494761685E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.049290e-01\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.338800e-01\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.319167e+03\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.213318e+03\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 07:26:14 2025\n+# Creation Date and Time:  Tue Jan  9 05:43:32 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path model_outNB.pqr\n@@ -24203,151 +24203,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.585980\n+Vacc_SASA: Time elapsed: 0.621030\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.609438e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.677372e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.770300e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 6.844000e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 9.541390e-01\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.183155e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.762129e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.100646e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2075985.759525\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.337873e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.494743e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.676742e+05\n Vprtstp: contraction number = 2.676742e+05\n Vnewton: Attempting damping, relres = 0.123645\n Vnewton: Attempting damping, relres = 0.555352\n Vnewton: Damping accepted, relres = 0.123645\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.236446e-01\n Vprtstp: contraction number = 1.236446e-01\n Vnewton: Using errtol_s: 256684.416130\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.873294e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.709473e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.859973e+04\n Vprtstp: contraction number = 4.859973e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.169836e-02\n Vprtstp: contraction number = 1.754897e-01\n Vnewton: Using errtol_s: 45045.483798\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.540769e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.112988e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.152870e+04\n Vprtstp: contraction number = 1.152870e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 5.014779e-03\n Vprtstp: contraction number = 2.311133e-01\n Vnewton: Using errtol_s: 10410.609915\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.093352e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.288827e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.097422e+03\n Vprtstp: contraction number = 3.097422e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.342870e-03\n Vprtstp: contraction number = 2.677824e-01\n Vnewton: Using errtol_s: 2787.778355\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.072996e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.497787e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.793803e+02\n Vprtstp: contraction number = 8.793803e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.812374e-04\n Vprtstp: contraction number = 2.838975e-01\n Vnewton: Using errtol_s: 791.443333\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.325229e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.156464e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.566243e+02\n Vprtstp: contraction number = 2.566243e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.112541e-04\n Vprtstp: contraction number = 2.918238e-01\n Vnewton: Using errtol_s: 230.962017\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.590088e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.356638e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.622598e+01\n Vprtstp: contraction number = 7.622598e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.304618e-05\n Vprtstp: contraction number = 2.970332e-01\n Vnewton: Using errtol_s: 68.603390\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.845498e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.558320e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.294139e+01\n Vprtstp: contraction number = 2.294139e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 9.945756e-06\n Vprtstp: contraction number = 3.009654e-01\n Vnewton: Using errtol_s: 20.647248\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.062099e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.759223e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.975781e+00\n Vprtstp: contraction number = 6.975781e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.024203e-06\n Vprtstp: contraction number = 3.040697e-01\n Vnewton: Using errtol_s: 6.278203\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.284557e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.964229e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.139542e+00\n Vprtstp: contraction number = 2.139542e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 9.275536e-07\n Vprtstp: contraction number = 3.067101e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.500941e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.512138e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.123769e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.137558e+02\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -24357,15 +24357,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 4.936418090820E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.566271448852E+04 kT\n Vpmg_energy:  dielEnergy = 1.282618425876E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.492700e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.093200e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 25.8477\n Vpbe_ctor2:  solute dimensions = 26.666 x 32.3234 x 48.3902\n Vpbe_ctor2:  solute charge = -14\n@@ -24414,160 +24414,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0114665 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.541850\n+Vacc_SASA: Time elapsed: 0.600503\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.589418e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.684534e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 3.935500e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 6.491400e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.056078e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.152985e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.558225e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.185740e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2120327.174672\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.579318e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.212137e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.330788e+05\n Vprtstp: contraction number = 3.330788e+05\n Vnewton: Attempting damping, relres = 0.148670\n Vnewton: Attempting damping, relres = 0.568259\n Vnewton: Damping accepted, relres = 0.148670\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.486698e-01\n Vprtstp: contraction number = 1.486698e-01\n Vnewton: Using errtol_s: 315228.684259\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.834268e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.445089e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.641464e+04\n Vprtstp: contraction number = 6.641464e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.878895e-02\n Vprtstp: contraction number = 1.936435e-01\n Vnewton: Using errtol_s: 61041.990934\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.093990e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.668804e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.670744e+04\n Vprtstp: contraction number = 1.670744e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.105637e-03\n Vprtstp: contraction number = 2.468182e-01\n Vnewton: Using errtol_s: 15066.274957\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.328322e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.881513e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.686665e+03\n Vprtstp: contraction number = 4.686665e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.989361e-03\n Vprtstp: contraction number = 2.799694e-01\n Vnewton: Using errtol_s: 4218.095910\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.583010e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.089027e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.389137e+03\n Vprtstp: contraction number = 1.389137e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.896382e-04\n Vprtstp: contraction number = 2.963958e-01\n Vnewton: Using errtol_s: 1250.225849\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.835068e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.282733e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.253662e+02\n Vprtstp: contraction number = 4.253662e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.805523e-04\n Vprtstp: contraction number = 3.062086e-01\n Vnewton: Using errtol_s: 382.829903\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.118131e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.492449e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.333214e+02\n Vprtstp: contraction number = 1.333214e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 5.659001e-05\n Vprtstp: contraction number = 3.134273e-01\n Vnewton: Using errtol_s: 119.989327\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.412608e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.686638e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.255612e+01\n Vprtstp: contraction number = 4.255612e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.806349e-05\n Vprtstp: contraction number = 3.191993e-01\n Vnewton: Using errtol_s: 38.300511\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.673870e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.893708e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.379985e+01\n Vprtstp: contraction number = 1.379985e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.857525e-06\n Vprtstp: contraction number = 3.242742e-01\n Vnewton: Using errtol_s: 12.419869\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.936762e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.102306e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.534043e+00\n Vprtstp: contraction number = 4.534043e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.924533e-06\n Vprtstp: contraction number = 3.285573e-01\n Vnewton: Using errtol_s: 4.080639\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.202631e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.315810e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.505713e+00\n Vprtstp: contraction number = 1.505713e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 6.391193e-07\n Vprtstp: contraction number = 3.320906e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.902539e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.915164e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.313130e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.326480e+02\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -24577,15 +24577,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 4.924946278586E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.950886798741E+04 kT\n Vpmg_energy:  dielEnergy = 1.474927636785E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.253890e-01\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.361600e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n@@ -24614,151 +24614,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.374954\n+Vacc_SASA: Time elapsed: 0.349288\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.098428e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.281250e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.886100e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.651400e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.486664e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.261806e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.502929e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.540845e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 625058.556229\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.534963e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.567377e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.349434e+04\n Vprtstp: contraction number = 8.349434e+04\n Vnewton: Attempting damping, relres = 0.126666\n Vnewton: Attempting damping, relres = 0.557380\n Vnewton: Damping accepted, relres = 0.126666\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.266665e-01\n Vprtstp: contraction number = 1.266665e-01\n Vnewton: Using errtol_s: 79173.978566\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.750525e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.726592e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.587988e+04\n Vprtstp: contraction number = 1.587988e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.298610e-02\n Vprtstp: contraction number = 1.814695e-01\n Vnewton: Using errtol_s: 14367.659528\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.953177e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.873387e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.689543e+03\n Vprtstp: contraction number = 3.689543e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 5.312865e-03\n Vprtstp: contraction number = 2.311338e-01\n Vnewton: Using errtol_s: 3320.851989\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.151304e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.027192e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.505518e+02\n Vprtstp: contraction number = 9.505518e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.368674e-03\n Vprtstp: contraction number = 2.576150e-01\n Vnewton: Using errtol_s: 855.501271\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.343445e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.174330e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.577170e+02\n Vprtstp: contraction number = 2.577170e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.710781e-04\n Vprtstp: contraction number = 2.711224e-01\n Vnewton: Using errtol_s: 231.945545\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.531584e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.310138e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.185767e+01\n Vprtstp: contraction number = 7.185767e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.034654e-04\n Vprtstp: contraction number = 2.788237e-01\n Vnewton: Using errtol_s: 64.671921\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.730181e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.443985e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.042074e+01\n Vprtstp: contraction number = 2.042074e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.940311e-05\n Vprtstp: contraction number = 2.841831e-01\n Vnewton: Using errtol_s: 18.378664\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.921667e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.581687e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.893233e+00\n Vprtstp: contraction number = 5.893233e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.485461e-06\n Vprtstp: contraction number = 2.885906e-01\n Vnewton: Using errtol_s: 5.303910\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.119944e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.720541e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.723486e+00\n Vprtstp: contraction number = 1.723486e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.481587e-06\n Vprtstp: contraction number = 2.924517e-01\n Vnewton: Using errtol_s: 1.551137\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.293763e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.855193e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.097109e-01\n Vprtstp: contraction number = 5.097109e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 7.339149e-07\n Vprtstp: contraction number = 2.957442e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.946420e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.962849e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.445075e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.459172e+02\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -24768,15 +24768,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.817512164844E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 6.828431655726E+03 kT\n Vpmg_energy:  dielEnergy = 3.412244339074E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 7.941600e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.341700e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 19.3778\n Vpbe_ctor2:  solute dimensions = 19.082 x 18.3114 x 35.7654\n Vpbe_ctor2:  solute charge = 4\n@@ -24825,160 +24825,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.000971631 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.387196\n+Vacc_SASA: Time elapsed: 0.347527\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.134013e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.441840e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.348300e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.711600e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.366256e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.185776e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.478976e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.011042e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 648940.820048\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.510662e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.037478e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.033896e+05\n Vprtstp: contraction number = 1.033896e+05\n Vnewton: Attempting damping, relres = 0.149178\n Vnewton: Attempting damping, relres = 0.569081\n Vnewton: Damping accepted, relres = 0.149178\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.491779e-01\n Vprtstp: contraction number = 1.491779e-01\n Vnewton: Using errtol_s: 96807.596825\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.718500e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.190896e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.124753e+04\n Vprtstp: contraction number = 2.124753e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.957488e-02\n Vprtstp: contraction number = 1.982525e-01\n Vnewton: Using errtol_s: 19192.349469\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.917356e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.341765e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.231045e+03\n Vprtstp: contraction number = 5.231045e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.255435e-03\n Vprtstp: contraction number = 2.453242e-01\n Vnewton: Using errtol_s: 4708.348197\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.096259e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.477981e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.389072e+03\n Vprtstp: contraction number = 1.389072e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.926494e-03\n Vprtstp: contraction number = 2.655242e-01\n Vnewton: Using errtol_s: 1250.180442\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.268083e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.611574e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.868439e+02\n Vprtstp: contraction number = 3.868439e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.365061e-04\n Vprtstp: contraction number = 2.784884e-01\n Vnewton: Using errtol_s: 348.160728\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.441337e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.766845e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.111703e+02\n Vprtstp: contraction number = 1.111703e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.541795e-04\n Vprtstp: contraction number = 2.873769e-01\n Vnewton: Using errtol_s: 100.053355\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.586184e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.925072e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.268464e+01\n Vprtstp: contraction number = 3.268464e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.532954e-05\n Vprtstp: contraction number = 2.940050e-01\n Vnewton: Using errtol_s: 29.416189\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.727259e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.073904e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.798450e+00\n Vprtstp: contraction number = 9.798450e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.358923e-05\n Vprtstp: contraction number = 2.997875e-01\n Vnewton: Using errtol_s: 8.818606\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.878624e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.221232e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.993247e+00\n Vprtstp: contraction number = 2.993247e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 4.151261e-06\n Vprtstp: contraction number = 3.054817e-01\n Vnewton: Using errtol_s: 2.693923\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.015742e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.383434e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.296932e-01\n Vprtstp: contraction number = 9.296932e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.289368e-06\n Vprtstp: contraction number = 3.105968e-01\n Vnewton: Using errtol_s: 0.836724\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.202034e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.536325e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.927772e-01\n Vprtstp: contraction number = 2.927772e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 4.060455e-07\n Vprtstp: contraction number = 3.149181e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.857060e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.873251e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.672644e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.687612e+02\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -24988,17 +24988,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.808821595407E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 8.060972751461E+03 kT\n Vpmg_energy:  dielEnergy = 4.028526891385E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 6.102700e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.187500e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vnm_tstart: starting timer 27 (Setup timer)..\n@@ -25025,162 +25025,162 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.452446\n+Vacc_SASA: Time elapsed: 0.417566\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.303231e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.223716e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.660700e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.243900e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.226345e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.115848e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.380923e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.723844e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1404398.831107\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.403524e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.749932e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.991752e+05\n Vprtstp: contraction number = 1.991752e+05\n Vnewton: Attempting damping, relres = 0.149937\n Vnewton: Attempting damping, relres = 0.562289\n Vnewton: Damping accepted, relres = 0.149937\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.499366e-01\n Vprtstp: contraction number = 1.499366e-01\n Vnewton: Using errtol_s: 210570.777586\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.574269e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.913499e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.724441e+04\n Vprtstp: contraction number = 3.724441e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.631656e-02\n Vprtstp: contraction number = 1.755180e-01\n Vnewton: Using errtol_s: 36958.952617\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.744973e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.068354e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.392042e+03\n Vprtstp: contraction number = 9.392042e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 6.102282e-03\n Vprtstp: contraction number = 2.318799e-01\n Vnewton: Using errtol_s: 8570.037199\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.893634e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.213718e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.643900e+03\n Vprtstp: contraction number = 2.643900e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.694653e-03\n Vprtstp: contraction number = 2.777081e-01\n Vnewton: Using errtol_s: 2379.968912\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.003859e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.358956e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.795002e+02\n Vprtstp: contraction number = 7.795002e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 4.995386e-04\n Vprtstp: contraction number = 2.947734e-01\n Vnewton: Using errtol_s: 701.551412\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.021133e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.512042e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.342462e+02\n Vprtstp: contraction number = 2.342462e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.501153e-04\n Vprtstp: contraction number = 3.005079e-01\n Vnewton: Using errtol_s: 210.821708\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.036219e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.665231e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.102938e+01\n Vprtstp: contraction number = 7.102938e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.551873e-05\n Vprtstp: contraction number = 3.032252e-01\n Vnewton: Using errtol_s: 63.926447\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.049501e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.819288e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.165701e+01\n Vprtstp: contraction number = 2.165701e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.387876e-05\n Vprtstp: contraction number = 3.049021e-01\n Vnewton: Using errtol_s: 19.491311\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.065689e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.970159e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.627865e+00\n Vprtstp: contraction number = 6.627865e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 4.247425e-06\n Vprtstp: contraction number = 3.060378e-01\n Vnewton: Using errtol_s: 5.965078\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.082614e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.126162e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.033869e+00\n Vprtstp: contraction number = 2.033869e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.303392e-06\n Vprtstp: contraction number = 3.068664e-01\n Vnewton: Using errtol_s: 1.830482\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.100041e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.290129e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.254212e-01\n Vprtstp: contraction number = 6.254212e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 4.007972e-07\n Vprtstp: contraction number = 3.075032e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.761047e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.774407e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.715299e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.727837e+02\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -25190,15 +25190,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 6.631424094606E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.872722745686E+04 kT\n Vpmg_energy:  dielEnergy = 9.355776117184E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.701000e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.412000e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 20.7943\n Vpbe_ctor2:  solute dimensions = 25.3482 x 27.3592 x 40.136\n Vpbe_ctor2:  solute charge = -18\n@@ -25247,160 +25247,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00130951 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.385406\n+Vacc_SASA: Time elapsed: 0.439332\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.395494e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.355925e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.748600e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 6.213800e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.234237e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.373491e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.117059e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.468612e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1429289.662203\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.119451e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.494623e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.496624e+05\n Vprtstp: contraction number = 2.496624e+05\n Vnewton: Attempting damping, relres = 0.178955\n Vnewton: Attempting damping, relres = 0.577343\n Vnewton: Damping accepted, relres = 0.178955\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.789551e-01\n Vprtstp: contraction number = 1.789551e-01\n Vnewton: Using errtol_s: 255778.622825\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.135479e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.671182e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.096661e+04\n Vprtstp: contraction number = 5.096661e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 3.449699e-02\n Vprtstp: contraction number = 1.927690e-01\n Vnewton: Using errtol_s: 49306.188432\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.151753e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.843068e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.352983e+04\n Vprtstp: contraction number = 1.352983e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 8.601027e-03\n Vprtstp: contraction number = 2.493269e-01\n Vnewton: Using errtol_s: 12293.359097\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.167409e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.001740e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.990835e+03\n Vprtstp: contraction number = 3.990835e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.513298e-03\n Vprtstp: contraction number = 2.922090e-01\n Vnewton: Using errtol_s: 3592.230783\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.184798e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.020758e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.236351e+03\n Vprtstp: contraction number = 1.236351e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 7.785110e-04\n Vprtstp: contraction number = 3.097567e-01\n Vnewton: Using errtol_s: 1112.717700\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.200844e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.038109e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.922762e+02\n Vprtstp: contraction number = 3.922762e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.470100e-04\n Vprtstp: contraction number = 3.172852e-01\n Vnewton: Using errtol_s: 353.048870\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.217919e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.053729e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.263525e+02\n Vprtstp: contraction number = 1.263525e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 7.956210e-05\n Vprtstp: contraction number = 3.221007e-01\n Vnewton: Using errtol_s: 113.717282\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.232045e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.069815e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.114546e+01\n Vprtstp: contraction number = 4.114546e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.590862e-05\n Vprtstp: contraction number = 3.256402e-01\n Vnewton: Using errtol_s: 37.030918\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.246731e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.087652e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.351428e+01\n Vprtstp: contraction number = 1.351428e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 8.509716e-06\n Vprtstp: contraction number = 3.284512e-01\n Vnewton: Using errtol_s: 12.162848\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.261440e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.107515e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.469783e+00\n Vprtstp: contraction number = 4.469783e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 2.814548e-06\n Vprtstp: contraction number = 3.307453e-01\n Vnewton: Using errtol_s: 4.022804\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.275957e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.126187e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.486721e+00\n Vprtstp: contraction number = 1.486721e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 9.361638e-07\n Vprtstp: contraction number = 3.326161e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.726164e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.739741e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.948837e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.964507e+02\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -25410,29 +25410,29 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 6.621321814807E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.134461409198E+04 kT\n Vpmg_energy:  dielEnergy = 1.066448263473E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.491700e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.235200e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.291488e+03\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.143614e+03\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 07:28:36 2025\n+# Creation Date and Time:  Tue Jan  9 05:51:30 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path model_outNB.pqr\n@@ -25702,151 +25702,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.635208\n+Vacc_SASA: Time elapsed: 0.644152\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.678624e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.624521e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.297300e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 6.294200e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.256577e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.224481e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.103561e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.160271e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2063009.659222\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.428119e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.044219e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.658306e+05\n Vprtstp: contraction number = 2.658306e+05\n Vnewton: Attempting damping, relres = 0.122739\n Vnewton: Attempting damping, relres = 0.555235\n Vnewton: Damping accepted, relres = 0.122739\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.227391e-01\n Vprtstp: contraction number = 1.227391e-01\n Vnewton: Using errtol_s: 253211.880914\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.615469e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.157522e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.831485e+04\n Vprtstp: contraction number = 4.831485e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.156033e-02\n Vprtstp: contraction number = 1.756599e-01\n Vnewton: Using errtol_s: 44479.169236\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.582480e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.409533e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.148001e+04\n Vprtstp: contraction number = 1.148001e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 5.018325e-03\n Vprtstp: contraction number = 2.327573e-01\n Vnewton: Using errtol_s: 10352.852780\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.419293e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.757075e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.090763e+03\n Vprtstp: contraction number = 3.090763e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.348386e-03\n Vprtstp: contraction number = 2.686924e-01\n Vnewton: Using errtol_s: 2781.733245\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.253310e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.468191e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.782780e+02\n Vprtstp: contraction number = 8.782780e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.831544e-04\n Vprtstp: contraction number = 2.841578e-01\n Vnewton: Using errtol_s: 790.451228\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.012528e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.126852e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.564053e+02\n Vprtstp: contraction number = 2.564053e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.118584e-04\n Vprtstp: contraction number = 2.919407e-01\n Vnewton: Using errtol_s: 230.764871\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.200638e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.309734e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.617617e+01\n Vprtstp: contraction number = 7.617617e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 3.323230e-05\n Vprtstp: contraction number = 2.970927e-01\n Vnewton: Using errtol_s: 68.558559\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.386908e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.490799e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.292888e+01\n Vprtstp: contraction number = 2.292888e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.000286e-05\n Vprtstp: contraction number = 3.009981e-01\n Vnewton: Using errtol_s: 20.635996\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.583184e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.672212e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.972403e+00\n Vprtstp: contraction number = 6.972403e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 3.041752e-06\n Vprtstp: contraction number = 3.040882e-01\n Vnewton: Using errtol_s: 6.275163\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.775587e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.860817e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.138578e+00\n Vprtstp: contraction number = 2.138578e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 9.329670e-07\n Vprtstp: contraction number = 3.067203e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.946766e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.960590e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.996570e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.011511e+02\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -25856,15 +25856,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 4.808172570835E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.566165331536E+04 kT\n Vpmg_energy:  dielEnergy = 1.282584652691E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.004700e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.105700e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 25.8477\n Vpbe_ctor2:  solute dimensions = 26.666 x 32.3234 x 48.3902\n Vpbe_ctor2:  solute charge = -14\n@@ -25913,160 +25913,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.0106595 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.599560\n+Vacc_SASA: Time elapsed: 0.617722\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.691828e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.708489e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.466200e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.971600e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.294919e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.169308e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.009786e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.059948e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 2106967.008420\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.032790e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.084039e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.308151e+05\n Vprtstp: contraction number = 3.308151e+05\n Vnewton: Attempting damping, relres = 0.147795\n Vnewton: Attempting damping, relres = 0.568147\n Vnewton: Damping accepted, relres = 0.147795\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.477951e-01\n Vprtstp: contraction number = 1.477951e-01\n Vnewton: Using errtol_s: 311399.390533\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.239225e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.309503e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.599748e+04\n Vprtstp: contraction number = 6.599748e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.864948e-02\n Vprtstp: contraction number = 1.938459e-01\n Vnewton: Using errtol_s: 60363.499136\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.433753e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.513926e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.661676e+04\n Vprtstp: contraction number = 1.661676e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.106188e-03\n Vprtstp: contraction number = 2.480390e-01\n Vnewton: Using errtol_s: 14972.503442\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.633733e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.689462e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.669116e+03\n Vprtstp: contraction number = 4.669116e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.994461e-03\n Vprtstp: contraction number = 2.806653e-01\n Vnewton: Using errtol_s: 4202.262595\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.823744e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.887759e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.385353e+03\n Vprtstp: contraction number = 1.385353e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.917609e-04\n Vprtstp: contraction number = 2.967022e-01\n Vnewton: Using errtol_s: 1246.820661\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.027984e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.087055e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.244924e+02\n Vprtstp: contraction number = 4.244924e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.813239e-04\n Vprtstp: contraction number = 3.064141e-01\n Vnewton: Using errtol_s: 382.043458\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.210372e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.296985e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.331120e+02\n Vprtstp: contraction number = 1.331120e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 5.685939e-05\n Vprtstp: contraction number = 3.135792e-01\n Vnewton: Using errtol_s: 119.800865\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.385394e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.488459e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.250410e+01\n Vprtstp: contraction number = 4.250410e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.815581e-05\n Vprtstp: contraction number = 3.193107e-01\n Vnewton: Using errtol_s: 38.253693\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.587175e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.673021e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.378625e+01\n Vprtstp: contraction number = 1.378625e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 5.888858e-06\n Vprtstp: contraction number = 3.243511e-01\n Vnewton: Using errtol_s: 12.407629\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.781644e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.879854e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.530276e+00\n Vprtstp: contraction number = 4.530276e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.935127e-06\n Vprtstp: contraction number = 3.286082e-01\n Vnewton: Using errtol_s: 4.077249\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.975225e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.079139e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.504596e+00\n Vprtstp: contraction number = 1.504596e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 6.426945e-07\n Vprtstp: contraction number = 3.321201e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.139051e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.153144e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 2.191757e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.205089e+02\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -26076,15 +26076,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 4.796939220773E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.950780776080E+04 kT\n Vpmg_energy:  dielEnergy = 1.474893902492E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.743900e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.132200e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n@@ -26113,151 +26113,151 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.389237\n+Vacc_SASA: Time elapsed: 0.348328\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.985530e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.003411e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.243400e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.933600e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.249000e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.282366e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.191854e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.294627e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 622184.484743\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.217656e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.322343e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 8.301310e+04\n Vprtstp: contraction number = 8.301310e+04\n Vnewton: Attempting damping, relres = 0.126177\n Vnewton: Attempting damping, relres = 0.557265\n Vnewton: Damping accepted, relres = 0.126177\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.261770e-01\n Vprtstp: contraction number = 1.261770e-01\n Vnewton: Using errtol_s: 78505.344097\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.419939e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.495021e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.580629e+04\n Vprtstp: contraction number = 1.580629e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.296474e-02\n Vprtstp: contraction number = 1.820042e-01\n Vnewton: Using errtol_s: 14288.305999\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.615204e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.630365e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.679149e+03\n Vprtstp: contraction number = 3.679149e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 5.322303e-03\n Vprtstp: contraction number = 2.317597e-01\n Vnewton: Using errtol_s: 3311.454085\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.808434e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.765468e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.489453e+02\n Vprtstp: contraction number = 9.489453e+02\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.372672e-03\n Vprtstp: contraction number = 2.579095e-01\n Vnewton: Using errtol_s: 854.055318\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.986485e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.893872e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.574445e+02\n Vprtstp: contraction number = 2.574445e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 3.723980e-04\n Vprtstp: contraction number = 2.712942e-01\n Vnewton: Using errtol_s: 231.700267\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.163448e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.027802e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.180833e+01\n Vprtstp: contraction number = 7.180833e+01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.038719e-04\n Vprtstp: contraction number = 2.789272e-01\n Vnewton: Using errtol_s: 64.627514\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.351349e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.168462e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.041084e+01\n Vprtstp: contraction number = 2.041084e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.952461e-05\n Vprtstp: contraction number = 2.842404e-01\n Vnewton: Using errtol_s: 18.369753\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.536896e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.324740e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.891035e+00\n Vprtstp: contraction number = 5.891035e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 8.521479e-06\n Vprtstp: contraction number = 2.886229e-01\n Vnewton: Using errtol_s: 5.301932\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.711862e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.461019e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.722947e+00\n Vprtstp: contraction number = 1.722947e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 2.492271e-06\n Vprtstp: contraction number = 2.924694e-01\n Vnewton: Using errtol_s: 1.550653\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.890382e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.592260e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.095658e-01\n Vprtstp: contraction number = 5.095658e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 7.370953e-07\n Vprtstp: contraction number = 2.957524e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.840259e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.854178e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.416131e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.430241e+02\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -26267,15 +26267,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.805001041922E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 6.827988101886E+03 kT\n Vpmg_energy:  dielEnergy = 3.412047294485E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.260100e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.573000e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 19.3778\n Vpbe_ctor2:  solute dimensions = 19.082 x 18.3114 x 35.7654\n Vpbe_ctor2:  solute charge = 4\n@@ -26324,160 +26324,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.000791536 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.347566\n+Vacc_SASA: Time elapsed: 0.363559\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.012492e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 9.797270e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.367100e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 6.111400e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.091335e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.187892e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.056110e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.736530e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 645906.037357\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.080633e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.757389e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.027473e+05\n Vprtstp: contraction number = 1.027473e+05\n Vnewton: Attempting damping, relres = 0.148634\n Vnewton: Attempting damping, relres = 0.568930\n Vnewton: Damping accepted, relres = 0.148634\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.486339e-01\n Vprtstp: contraction number = 1.486339e-01\n Vnewton: Using errtol_s: 96003.523693\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.246398e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.907512e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.112857e+04\n Vprtstp: contraction number = 2.112857e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.952923e-02\n Vprtstp: contraction number = 1.986709e-01\n Vnewton: Using errtol_s: 19073.107408\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.394908e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.062129e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.206787e+03\n Vprtstp: contraction number = 5.206787e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 7.255653e-03\n Vprtstp: contraction number = 2.457109e-01\n Vnewton: Using errtol_s: 4686.469778\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.566250e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.206395e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.383944e+03\n Vprtstp: contraction number = 1.383944e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.928400e-03\n Vprtstp: contraction number = 2.657790e-01\n Vnewton: Using errtol_s: 1245.565289\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.712154e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.370230e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.857274e+02\n Vprtstp: contraction number = 3.857274e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.374712e-04\n Vprtstp: contraction number = 2.787135e-01\n Vnewton: Using errtol_s: 347.155903\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.862489e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.548459e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.109221e+02\n Vprtstp: contraction number = 1.109221e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.545581e-04\n Vprtstp: contraction number = 2.875654e-01\n Vnewton: Using errtol_s: 99.830021\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.994445e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.704147e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.262844e+01\n Vprtstp: contraction number = 3.262844e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.546421e-05\n Vprtstp: contraction number = 2.941561e-01\n Vnewton: Using errtol_s: 29.365605\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.132975e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 6.874096e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.785490e+00\n Vprtstp: contraction number = 9.785490e+00\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.363502e-05\n Vprtstp: contraction number = 2.999067e-01\n Vnewton: Using errtol_s: 8.806942\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.287237e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.026094e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.990197e+00\n Vprtstp: contraction number = 2.990197e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 4.166516e-06\n Vprtstp: contraction number = 3.055746e-01\n Vnewton: Using errtol_s: 2.691178\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.463755e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.182625e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.289503e-01\n Vprtstp: contraction number = 9.289503e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.294392e-06\n Vprtstp: contraction number = 3.106652e-01\n Vnewton: Using errtol_s: 0.836055\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.612278e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.337573e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.925887e-01\n Vprtstp: contraction number = 2.925887e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 4.076906e-07\n Vprtstp: contraction number = 3.149670e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.686162e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.698985e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.733000e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.747721e+02\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -26487,17 +26487,17 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 1.796314557167E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 8.060531082527E+03 kT\n Vpmg_energy:  dielEnergy = 4.028330665485E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.408800e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.279600e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vnm_tstart: starting timer 27 (Setup timer)..\n@@ -26524,162 +26524,162 @@\n Vpmp_ctor2:  Using meth = 1, mgsolv = 0\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.350537\n+Vacc_SASA: Time elapsed: 0.342356\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.359858e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.222029e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.321800e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 5.775300e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.318308e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.229310e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.788343e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.513155e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1394036.370554\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.819887e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.539027e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.976078e+05\n Vprtstp: contraction number = 1.976078e+05\n Vnewton: Attempting damping, relres = 0.147111\n Vnewton: Attempting damping, relres = 0.562025\n Vnewton: Damping accepted, relres = 0.147111\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.471110e-01\n Vprtstp: contraction number = 1.471110e-01\n Vnewton: Using errtol_s: 205078.018083\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.975561e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.700171e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.691787e+04\n Vprtstp: contraction number = 3.691787e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 2.570682e-02\n Vprtstp: contraction number = 1.747444e-01\n Vnewton: Using errtol_s: 35836.239165\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.121489e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.853913e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 9.313783e+03\n Vprtstp: contraction number = 9.313783e+03\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 6.063883e-03\n Vprtstp: contraction number = 2.358862e-01\n Vnewton: Using errtol_s: 8453.273025\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.289230e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.999578e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.633660e+03\n Vprtstp: contraction number = 2.633660e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 1.700470e-03\n Vprtstp: contraction number = 2.804259e-01\n Vnewton: Using errtol_s: 2370.516473\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.456619e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.170362e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.779603e+02\n Vprtstp: contraction number = 7.779603e+02\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 5.022576e-04\n Vprtstp: contraction number = 2.953640e-01\n Vnewton: Using errtol_s: 700.165343\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.623188e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.321214e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.339032e+02\n Vprtstp: contraction number = 2.339032e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.510097e-04\n Vprtstp: contraction number = 3.006618e-01\n Vnewton: Using errtol_s: 210.512957\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.777203e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.471299e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 7.094002e+01\n Vprtstp: contraction number = 7.094002e+01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 4.579940e-05\n Vprtstp: contraction number = 3.032879e-01\n Vnewton: Using errtol_s: 63.846030\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.917500e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.618065e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.163184e+01\n Vprtstp: contraction number = 2.163184e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 1.396567e-05\n Vprtstp: contraction number = 3.049313e-01\n Vnewton: Using errtol_s: 19.468652\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.063762e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.762000e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.620444e+00\n Vprtstp: contraction number = 6.620444e+00\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 4.274207e-06\n Vprtstp: contraction number = 3.060510e-01\n Vnewton: Using errtol_s: 5.958400\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.207472e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.907716e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.031637e+00\n Vprtstp: contraction number = 2.031637e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 1.311640e-06\n Vprtstp: contraction number = 3.068733e-01\n Vnewton: Using errtol_s: 1.828474\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.344633e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.074946e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 6.247427e-01\n Vprtstp: contraction number = 6.247427e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 4.033384e-07\n Vprtstp: contraction number = 3.075070e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.681373e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.695298e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.700248e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.713925e+02\n Vpmg_setPart:  lower corner = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  upper corner = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  actual minima = (-8.8441, -22.1914, -32.8742)\n Vpmg_setPart:  actual maxima = (36.4881, 32.7584, 49.3892)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -26689,15 +26689,15 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 6.410814502422E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 1.872576445438E+04 kT\n Vpmg_energy:  dielEnergy = 9.355379703968E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 8.770000e-02\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.948800e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 20.7943\n Vpbe_ctor2:  solute dimensions = 25.3482 x 27.3592 x 40.136\n Vpbe_ctor2:  solute charge = -18\n@@ -26746,160 +26746,160 @@\n VPMG::extEnergy: extQfEnergy = 0 kT\n VPMG::extEnergy: extDiEnergy = 0.00110224 kT\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline2...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.425850\n+Vacc_SASA: Time elapsed: 0.445550\n Vpmg_fillco:  done filling coefficient arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.369890e+00\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 1.249678e+00\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vnewdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 097, 129)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 4.246600e-02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: fine problem setup).  CPU TIME = 6.083700e-02\n Vnm_tstart: starting timer 30 (Vnewdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 049, 065)\n Vbuildops: Galer: (017, 025, 033)\n Vbuildops: Galer: (009, 013, 017)\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.097030e+00\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: coarse problem setup).  CPU TIME = 1.060610e+00\n Vnm_tstart: starting timer 30 (Vnewdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.496866e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.240488e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vnewton: Damping enabled\n Vnewton: Using errtol_s: 1418623.682815\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.523404e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.263658e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.477376e+05\n Vprtstp: contraction number = 2.477376e+05\n Vnewton: Attempting damping, relres = 0.176231\n Vnewton: Attempting damping, relres = 0.577102\n Vnewton: Damping accepted, relres = 0.176231\n Vnewton: Damping disabled\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.762312e-01\n Vprtstp: contraction number = 1.762312e-01\n Vnewton: Using errtol_s: 250005.771686\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.690557e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.431661e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 5.052668e+04\n Vprtstp: contraction number = 5.052668e+04\n Vprtstp: iteration = 2\n Vprtstp: relative residual = 3.389791e-02\n Vprtstp: contraction number = 1.923491e-01\n Vnewton: Using errtol_s: 48088.378660\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.855703e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.607311e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.341451e+04\n Vprtstp: contraction number = 1.341451e+04\n Vprtstp: iteration = 3\n Vprtstp: relative residual = 8.561128e-03\n Vprtstp: contraction number = 2.525562e-01\n Vnewton: Using errtol_s: 12145.019085\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.004040e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.767654e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.971688e+03\n Vprtstp: contraction number = 3.971688e+03\n Vprtstp: iteration = 4\n Vprtstp: relative residual = 2.519877e-03\n Vprtstp: contraction number = 2.943394e-01\n Vnewton: Using errtol_s: 3574.757814\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.018756e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.916743e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.232605e+03\n Vprtstp: contraction number = 1.232605e+03\n Vprtstp: iteration = 5\n Vprtstp: relative residual = 7.819875e-04\n Vprtstp: contraction number = 3.103276e-01\n Vnewton: Using errtol_s: 1109.346049\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.034748e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.007606e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 3.914134e+02\n Vprtstp: contraction number = 3.914134e+02\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 2.483197e-04\n Vprtstp: contraction number = 3.175495e-01\n Vnewton: Using errtol_s: 352.272271\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.050207e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.024096e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.261412e+02\n Vprtstp: contraction number = 1.261412e+02\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 8.002626e-05\n Vprtstp: contraction number = 3.222710e-01\n Vnewton: Using errtol_s: 113.527152\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.067952e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.040690e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.109151e+01\n Vprtstp: contraction number = 4.109151e+01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 2.606919e-05\n Vprtstp: contraction number = 3.257579e-01\n Vnewton: Using errtol_s: 36.982365\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.086004e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.056443e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.349979e+01\n Vprtstp: contraction number = 1.349979e+01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 8.564509e-06\n Vprtstp: contraction number = 3.285300e-01\n Vnewton: Using errtol_s: 12.149816\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.107308e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.072345e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 4.465689e+00\n Vprtstp: contraction number = 4.465689e+00\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 2.833112e-06\n Vprtstp: contraction number = 3.307968e-01\n Vnewton: Using errtol_s: 4.019120\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.127591e+03\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.087980e+03\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.485509e+00\n Vprtstp: contraction number = 1.485509e+00\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 9.424331e-07\n Vprtstp: contraction number = 3.326494e-01\n-Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.984930e+02\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.996718e+02\n+Vnm_tstop: stopping timer 30 (Vnewdrv2: solve).  CPU TIME = 1.785369e+02\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 1.798746e+02\n Vpmg_setPart:  lower corner = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  upper corner = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  actual minima = (-8.8441, -20.8782, -25.9376)\n Vpmg_setPart:  actual maxima = (36.4881, 31.4452, 42.4526)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -26909,19 +26909,19 @@\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating full PBE energy\n Vpmg_qmEnergy:  Calculating nonlinear energy\n Vpmg_energy:  qmEnergy = 6.400773657781E+00 kT\n Vpmg_qfEnergyVolume:  Calculating energy\n Vpmg_energy:  qfEnergy = 2.134315194179E+04 kT\n Vpmg_energy:  dielEnergy = 1.066408609760E+04 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 1.040180e-01\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.246000e-02\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.200000e-05\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n Vgrid_writeDX:  Opening virtual socket...\n Vgrid_writeDX:  Writing to virtual socket...\n Vgrid_writeDX:  Writing comments for ASC format.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.149767e+03\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.104362e+03\n"}, {"source1": "./usr/share/apbs/examples/solv/io.mc", "source2": "./usr/share/apbs/examples/solv/io.mc", "unified_diff": "@@ -1,10 +1,10 @@\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 06:49:34 2025\n+# Creation Date and Time:  Tue Jan  9 04:52:28 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path methanol.pqr\n@@ -245,32 +245,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000524\n+Vacc_SASA: Time elapsed: 0.000432\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.520200e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 2.514630e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 7.241900e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.091700e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.248786e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.244671e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.760435e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.733450e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.930795e-01\n Vprtstp: contraction number = 2.930795e-01\n Vprtstp: iteration = 2\n@@ -299,30 +299,30 @@\n Vprtstp: contraction number = 3.064107e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 2.158998e-06\n Vprtstp: contraction number = 3.114698e-01\n Vprtstp: iteration = 11\n Vprtstp: relative residual = 6.836605e-07\n Vprtstp: contraction number = 3.166565e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 5.010855e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 5.260524e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.737629e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.984595e+01\n Vpmg_setPart:  lower corner = (-7.69135, -8, -8.2417)\n Vpmg_setPart:  upper corner = (8.30865, 8, 7.7583)\n Vpmg_setPart:  actual minima = (-7.69135, -8, -8.2417)\n Vpmg_setPart:  actual maxima = (8.30865, 8, 7.7583)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.481476875907E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.300000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.400000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 2.83039\n Vpbe_ctor2:  solute dimensions = 3.775 x 3.775 x 4.8153\n Vpbe_ctor2:  solute charge = 5.55112e-17\n@@ -345,32 +345,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000879\n+Vacc_SASA: Time elapsed: 0.000436\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.445680e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 3.795640e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 6.134400e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.586920e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.710692e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.417570e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.653892e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.303106e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.518468e-01\n Vprtstp: contraction number = 1.518468e-01\n Vprtstp: iteration = 2\n@@ -387,30 +387,30 @@\n Vprtstp: contraction number = 1.057725e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.782567e-06\n Vprtstp: contraction number = 1.074900e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.936135e-07\n Vprtstp: contraction number = 1.086150e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.293411e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.600569e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.550959e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.802467e+01\n Vpmg_setPart:  lower corner = (-7.69135, -8, -8.2417)\n Vpmg_setPart:  upper corner = (8.30865, 8, 7.7583)\n Vpmg_setPart:  actual minima = (-7.69135, -8, -8.2417)\n Vpmg_setPart:  actual maxima = (8.30865, 8, 7.7583)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.510541428496E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.600000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.400000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 2.54275\n Vpbe_ctor2:  solute dimensions = 3.775 x 3.775 x 4.733\n Vpbe_ctor2:  solute charge = -1\n@@ -433,32 +433,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000272\n+Vacc_SASA: Time elapsed: 0.000253\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.268590e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.471640e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.226700e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 9.994400e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.665451e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.104070e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 9.303667e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.104284e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.228747e-01\n Vprtstp: contraction number = 1.228747e-01\n Vprtstp: iteration = 2\n@@ -484,32 +484,32 @@\n Vprtstp: contraction number = 3.196112e-01\n Vprtstp: iteration = 9\n Vprtstp: relative residual = 1.915327e-06\n Vprtstp: contraction number = 3.214910e-01\n Vprtstp: iteration = 10\n Vprtstp: relative residual = 6.179105e-07\n Vprtstp: contraction number = 3.226135e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 4.763906e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 5.063456e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.710745e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.913475e+01\n Vpmg_setPart:  lower corner = (-8, -8, -8.12785)\n Vpmg_setPart:  upper corner = (8, 8, 7.87215)\n Vpmg_setPart:  actual minima = (-8, -8, -8.12785)\n Vpmg_setPart:  actual maxima = (8, 8, 7.87215)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 2.191047608004E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.300000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 5.400000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 2.54275\n Vpbe_ctor2:  solute dimensions = 3.775 x 3.775 x 4.733\n Vpbe_ctor2:  solute charge = -1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -530,32 +530,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000276\n+Vacc_SASA: Time elapsed: 0.000250\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.322290e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 4.897050e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.440820e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.440970e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.806550e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.235381e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.443473e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.010012e+02\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.134958e-01\n Vprtstp: contraction number = 1.134958e-01\n Vprtstp: iteration = 2\n@@ -572,16 +572,16 @@\n Vprtstp: contraction number = 1.069805e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.498256e-06\n Vprtstp: contraction number = 1.078455e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.625625e-07\n Vprtstp: contraction number = 1.085012e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.985623e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.295233e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.280558e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.514559e+01\n Vpmg_setPart:  lower corner = (-8, -8, -8.12785)\n Vpmg_setPart:  upper corner = (8, 8, 7.87215)\n Vpmg_setPart:  actual minima = (-8, -8, -8.12785)\n Vpmg_setPart:  actual maxima = (8, 8, 7.87215)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n@@ -596,18 +596,18 @@\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.743328e+02\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.238985e+02\n ##############################################################################\n # MC-shell I/O capture file.\n-# Creation Date and Time:  Sun Feb  9 06:49:49 2025\n+# Creation Date and Time:  Tue Jan  9 04:52:49 2024\n \n ##############################################################################\n Hello world from PE 0\n Vnm_tstart: starting timer 26 (APBS WALL CLOCK)..\n NOsh_parseInput:  Starting file parsing...\n NOsh: Parsing READ section\n NOsh: Storing molecule 0 path methanol.pqr\n@@ -848,32 +848,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000604\n+Vacc_SASA: Time elapsed: 0.000452\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.510330e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.120520e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 5.822100e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 4.035900e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.282714e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.035005e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.213074e+00\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 2.604565e+00\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 2.392714e-01\n Vprtstp: contraction number = 2.392714e-01\n Vprtstp: iteration = 2\n@@ -893,30 +893,30 @@\n Vprtstp: contraction number = 1.556589e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 2.217054e-06\n Vprtstp: contraction number = 1.639311e-01\n Vprtstp: iteration = 8\n Vprtstp: relative residual = 3.821154e-07\n Vprtstp: contraction number = 1.723528e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.473206e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.718366e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.561608e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.769584e+01\n Vpmg_setPart:  lower corner = (-7.69135, -8, -8.2417)\n Vpmg_setPart:  upper corner = (8.30865, 8, 7.7583)\n Vpmg_setPart:  actual minima = (-7.69135, -8, -8.2417)\n Vpmg_setPart:  actual maxima = (8.30865, 8, 7.7583)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.481634746029E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.500000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.500000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 2.83039\n Vpbe_ctor2:  solute dimensions = 3.775 x 3.775 x 4.8153\n Vpbe_ctor2:  solute charge = 5.55112e-17\n@@ -939,32 +939,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000370\n+Vacc_SASA: Time elapsed: 0.000350\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.990140e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.966520e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 9.232300e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 2.193280e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.475553e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.208159e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 4.145223e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 3.117917e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.514442e-01\n Vprtstp: contraction number = 1.514442e-01\n Vprtstp: iteration = 2\n@@ -981,32 +981,32 @@\n Vprtstp: contraction number = 1.045560e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.694780e-06\n Vprtstp: contraction number = 1.061179e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.817099e-07\n Vprtstp: contraction number = 1.072174e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.027582e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.299800e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.543611e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.773007e+01\n Vpmg_setPart:  lower corner = (-7.69135, -8, -8.2417)\n Vpmg_setPart:  upper corner = (8.30865, 8, 7.7583)\n Vpmg_setPart:  actual minima = (-7.69135, -8, -8.2417)\n Vpmg_setPart:  actual maxima = (8.30865, 8, 7.7583)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 1.511763544580E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.600000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.300000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 1.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 2.54275\n Vpbe_ctor2:  solute dimensions = 3.775 x 3.775 x 4.733\n Vpbe_ctor2:  solute charge = -1\n Vpbe_ctor2:  bulk ionic strength = 0\n Vpbe_ctor2:  xkappa = 0\n@@ -1027,32 +1027,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000294\n+Vacc_SASA: Time elapsed: 0.000273\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 7.139530e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 6.690930e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.546410e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 9.867300e-02\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 9.916590e-01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.245711e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 7.447185e+01\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 5.950005e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.159916e-01\n Vprtstp: contraction number = 1.159916e-01\n Vprtstp: iteration = 2\n@@ -1069,30 +1069,30 @@\n Vprtstp: contraction number = 1.378576e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 3.539643e-06\n Vprtstp: contraction number = 1.515814e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 5.760895e-07\n Vprtstp: contraction number = 1.627536e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.766753e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.964757e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.262693e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.481891e+01\n Vpmg_setPart:  lower corner = (-8, -8, -8.12785)\n Vpmg_setPart:  upper corner = (8, 8, 7.87215)\n Vpmg_setPart:  actual minima = (-8, -8, -8.12785)\n Vpmg_setPart:  actual maxima = (8, 8, 7.87215)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 2.192183682119E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 3.500000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.000000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n Vnm_tstart: starting timer 27 (Setup timer)..\n Setting up PBE object...\n Vpbe_ctor2:  solute radius = 2.54275\n Vpbe_ctor2:  solute dimensions = 3.775 x 3.775 x 4.733\n Vpbe_ctor2:  solute charge = -1\n@@ -1115,32 +1115,32 @@\n Vpmp_ctor2:  Using meth = 2, mgsolv = 1\n Setting PDE center to local center...\n Vpmg_fillco:  filling in source term.\n fillcoCharge:  Calling fillcoChargeSpline1...\n Vpmg_fillco:  filling in source term.\n Vpmg_fillco:  marking ion and solvent accessibility.\n fillcoCoef:  Calling fillcoCoefMol...\n-Vacc_SASA: Time elapsed: 0.000245\n+Vacc_SASA: Time elapsed: 0.000251\n Vpmg_fillco:  done filling coefficient arrays\n Vpmg_fillco:  filling boundary arrays\n Vpmg_fillco:  done filling boundary arrays\n-Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.886100e-01\n+Vnm_tstop: stopping timer 27 (Setup timer).  CPU TIME = 5.497640e-01\n Vnm_tstart: starting timer 28 (Solver timer)..\n Vnm_tstart: starting timer 30 (Vmgdrv2: fine problem setup)..\n Vbuildops: Fine: (065, 065, 065)\n Vbuildops: Operator stencil (lev, numdia) = (1, 4)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 8.918700e-02\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: fine problem setup).  CPU TIME = 1.178100e-01\n Vnm_tstart: starting timer 30 (Vmgdrv2: coarse problem setup)..\n Vbuildops: Galer: (033, 033, 033)\n Vbuildops: Galer: (017, 017, 017)\n Vbuildops: Galer: (009, 009, 009)\n Vbuildops: Galer: (005, 005, 005)\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.526349e+00\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: coarse problem setup).  CPU TIME = 1.287407e+00\n Vnm_tstart: starting timer 30 (Vmgdrv2: solve)..\n-Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 1.053488e+02\n+Vnm_tstop: stopping timer 40 (MG iteration).  CPU TIME = 8.511866e+01\n Vprtstp: iteration = 0\n Vprtstp: relative residual = 1.000000e+00\n Vprtstp: contraction number = 1.000000e+00\n Vprtstp: iteration = 1\n Vprtstp: relative residual = 1.128724e-01\n Vprtstp: contraction number = 1.128724e-01\n Vprtstp: iteration = 2\n@@ -1157,32 +1157,32 @@\n Vprtstp: contraction number = 1.067766e-01\n Vprtstp: iteration = 6\n Vprtstp: relative residual = 1.477665e-06\n Vprtstp: contraction number = 1.075719e-01\n Vprtstp: iteration = 7\n Vprtstp: relative residual = 1.598211e-07\n Vprtstp: contraction number = 1.081578e-01\n-Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 3.214967e+01\n-Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 3.471839e+01\n+Vnm_tstop: stopping timer 30 (Vmgdrv2: solve).  CPU TIME = 2.114409e+01\n+Vnm_tstop: stopping timer 28 (Solver timer).  CPU TIME = 2.351789e+01\n Vpmg_setPart:  lower corner = (-8, -8, -8.12785)\n Vpmg_setPart:  upper corner = (8, 8, 7.87215)\n Vpmg_setPart:  actual minima = (-8, -8, -8.12785)\n Vpmg_setPart:  actual maxima = (8, 8, 7.87215)\n Vpmg_setPart:  bflag[FRONT] = 0\n Vpmg_setPart:  bflag[BACK] = 0\n Vpmg_setPart:  bflag[LEFT] = 0\n Vpmg_setPart:  bflag[RIGHT] = 0\n Vpmg_setPart:  bflag[UP] = 0\n Vpmg_setPart:  bflag[DOWN] = 0\n Vnm_tstart: starting timer 29 (Energy timer)..\n Vpmg_energy:  calculating only q-phi energy\n Vpmg_energy:  qfEnergy = 2.505883286802E+03 kT\n-Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.100000e-05\n+Vnm_tstop: stopping timer 29 (Energy timer).  CPU TIME = 4.700000e-05\n Vnm_tstart: starting timer 30 (Force timer)..\n-Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 2.000000e-06\n+Vnm_tstop: stopping timer 30 (Force timer).  CPU TIME = 3.000000e-06\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n printEnergy:  Performing global reduction (sum)\n Vcom_reduce:  Not compiled with MPI, doing simple copy.\n-Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.376312e+02\n+Vnm_tstop: stopping timer 26 (APBS WALL CLOCK).  CPU TIME = 1.063989e+02\n"}]}]}]}]}