Branch: rosetta:commits 「revision: №20468」
Test: linux.gcc.python312.PyRosetta.unit
SubTest: T220_AtomAtomPairEnergies
SubTest files: 「file-system-view」
Daemon: hojo-2    
State: T220_AtomAtomPairEnergies

core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+4.HEAD.cb14ed8 cb14ed864b1605487800375e6021640c6086314f git@github.com:RosettaCommons/rosetta.git 2024-09-07T16:54:30 core.init: Rosetta extras: [] core.init: command: PyRosetta -ex1 -ex2aro -constant_seed -database /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.17/gcc-4.8.5/python-3.12/minsizerel/build/pyrosetta/database basic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 2.12 seconds. core.import_pose.import_pose: File '../test/data/test_dock.pdb' automatically determined to be of type PDB core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom O in residue 13 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 36 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 36 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 36 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CA in residue 77 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom O in residue 77 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OG in residue 77 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 79 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 79 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 79 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 87 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 87 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 87 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 87 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 93 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 93 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 93 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 116 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 116 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OE1 in residue 116 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CZ in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH1 in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH2 in residue 145 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom N in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CA in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom C in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom O in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 149 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom N in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CA in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom C in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom O in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OD1 in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom ND2 in residue 150 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CZ in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH1 in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NH2 in residue 154 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 169 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 169 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 169 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 170 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 170 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 170 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 203 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG1 in residue 227 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OE1 in residue 239 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE2 in residue 239 E. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NZ in residue 8 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CB in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom ND1 in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD2 in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CE1 in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom NE2 in residue 28 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CG in residue 49 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom CD2 in residue 49 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom OD1 in residue 50 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] PDB reader is ignoring atom ND2 in residue 50 I. Pass flag -ignore_zero_occupancy false to change this behavior core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] skipping pdb residue b/c it's missing too many mainchain atoms: 77 E SER SER core.io.pose_from_sfr.PoseFromSFRBuilder: missing: CA core.conformation.Conformation: [ WARNING ] missing heavyatom: O on residue LEU 13 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 34 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 34 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 34 core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue GLU 75. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 75 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 76 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 76 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 76 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 84 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 84 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 84 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 84 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 90 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 90 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 90 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLN 113 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLN 113 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN 113 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue ARG 142 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 142 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 142 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 142 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 142 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 142 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue ARG 147 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE on residue ARG 147 core.conformation.Conformation: [ WARNING ] missing heavyatom: CZ on residue ARG 147 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH1 on residue ARG 147 core.conformation.Conformation: [ WARNING ] missing heavyatom: NH2 on residue ARG 147 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 162 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 162 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 162 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 163 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 163 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 163 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue LYS 196 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS 196 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS 196 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS 196 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS 196 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG1 on residue VAL 220 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLN 232 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue GLN 232 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue LYS:NtermProteinFull 239 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue LYS:NtermProteinFull 239 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue LYS:NtermProteinFull 239 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE on residue LYS:NtermProteinFull 239 core.conformation.Conformation: [ WARNING ] missing heavyatom: NZ on residue LYS:NtermProteinFull 239 core.conformation.Conformation: [ WARNING ] missing heavyatom: CB on residue HIS 259 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue HIS 259 core.conformation.Conformation: [ WARNING ] missing heavyatom: ND1 on residue HIS 259 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue HIS 259 core.conformation.Conformation: [ WARNING ] missing heavyatom: CE1 on residue HIS 259 core.conformation.Conformation: [ WARNING ] missing heavyatom: NE2 on residue HIS 259 core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue TYR 280 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD2 on residue TYR 280 core.conformation.Conformation: [ WARNING ] missing heavyatom: OD1 on residue ASN 281 core.conformation.Conformation: [ WARNING ] missing heavyatom: ND2 on residue ASN 281 core.conformation.Conformation: [ WARNING ] Failed to find a residue connection for residue 74 with connection point 2 core.conformation.Conformation: [ WARNING ] Failed to find a residue connection for residue 75 with connection point 1 core.conformation.Conformation: Found disulfide between residues 1 119 core.conformation.Conformation: Found disulfide between residues 40 56 core.conformation.Conformation: Found disulfide between residues 133 194 core.conformation.Conformation: Found disulfide between residues 161 175 core.conformation.Conformation: Found disulfide between residues 184 213 core.pack.pack_missing_sidechains: packing residue number 34 because of missing atom number 7 atom name CD core.pack.pack_missing_sidechains: packing residue number 76 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 84 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 90 because of missing atom number 7 atom name CD core.pack.pack_missing_sidechains: packing residue number 113 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 142 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 147 because of missing atom number 7 atom name CD core.pack.pack_missing_sidechains: packing residue number 162 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 163 because of missing atom number 7 atom name CD core.pack.pack_missing_sidechains: packing residue nu┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2024 [Rosetta devel 2024.35.post.dev+4.HEAD.cb14ed864b1605487800375e6021640c6086314f 2024-09-07T16:54:30] retrieved from: git@github.com:RosettaCommons/rosetta.git Printing individual energies: res-res atr score emap: -2.5584311767440906 res-res atr score pairwise: -2.5584311767440906 res-res rep score emap: 3.515015877828057 res-res rep score pairwise: 3.515015877828057 res-res solv score emap: 0.7697815585356838 res-res solv score pairwise: 0.7697815585356838 Checking if scores match... Score did match, yay... mber 196 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 220 because of missing atom number 6 atom name CG1 core.pack.pack_missing_sidechains: packing residue number 232 because of missing atom number 8 atom name OE1 core.pack.pack_missing_sidechains: packing residue number 239 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 259 because of missing atom number 5 atom name CB core.pack.pack_missing_sidechains: packing residue number 280 because of missing atom number 6 atom name CG core.pack.pack_missing_sidechains: packing residue number 281 because of missing atom number 7 atom name OD1 core.pack.task: Packer task: initialize from command line() core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat core.scoring.elec.util: Read 40 countpair representative atoms core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true. core.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated. core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.17/gcc-4.8.5/python-3.12/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.17/gcc-4.8.5/python-3.12/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.25 seconds to load from binary core.pack.pack_rotamers: built 238 rotamers at 16 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph Finished T220_AtomAtomPairEnergies in 0:00:11.075959