Branch: rosetta:commits 「revision: №20469」
Test: linux.clang.python310.PyRosetta.unit
SubTest: T500_Packing
SubTest files: 「file-system-view」
Daemon: hojo-3    
State: T500_Packing

core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: 2024.35.post.dev+5.HEAD.c9abca8 c9abca83f0a4dd927aceaa98f4ceeb8708e10f37 git@github.com:RosettaCommons/rosetta.git 2024-09-07T17:30:08 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/clang-3.4.2/python-3.10/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 1.13 seconds. core.import_pose.import_pose: File '../test/data/test_in.pdb' automatically determined to be of type PDB 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 core.pack.task: Packer task: initialize from command line() 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/clang-3.4.2/python-3.10/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/clang-3.4.2/python-3.10/minsizerel/build/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.31 seconds to load from binary core.pack.pack_rotamers: built 2848 rotamers at 115 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.pack_rotamers: built 1023 rotamers at 6 positions. core.pack.interaction_graph┌──────────────────────────────────────────────────────────────────────────────┐ │ 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+5.HEAD.c9abca83f0a4dd927aceaa98f4ceeb8708e10f37 2024-09-07T17:30:08] retrieved from: git@github.com:RosettaCommons/rosetta.git Packing and Design ---------------------------------------------- mover: PackRotamersMover #Packer_Task Threads to request: ALL AVAILABLE resid pack? design? allowed_aas 1 TRUE FALSE ASP:NtermProteinFull 2 TRUE FALSE ALA 3 TRUE FALSE ILE 4 TRUE FALSE THR 5 FALSE FALSE 6 TRUE FALSE HIS,HIS_D 7 TRUE FALSE SER 8 TRUE FALSE ILE 9 TRUE FALSE LEU 10 TRUE FALSE ASP 11 TRUE FALSE TRP 12 TRUE FALSE ILE 13 TRUE FALSE GLU 14 TRUE FALSE ASP 15 TRUE FALSE ASN 16 TRUE FALSE LEU 17 TRUE FALSE GLU 18 TRUE FALSE SER 19 TRUE FALSE PRO 20 TRUE FALSE LEU 21 TRUE FALSE SER 22 TRUE FALSE LEU 23 TRUE FALSE GLU 24 TRUE FALSE LYS 25 TRUE FALSE VAL 26 TRUE FALSE SER 27 TRUE FALSE GLU 28 TRUE FALSE ARG 29 TRUE FALSE SER 30 TRUE FALSE GLY 31 TRUE FALSE TYR 32 TRUE FALSE SER 33 TRUE FALSE LYS 34 TRUE FALSE TRP 35 TRUE FALSE HIS,HIS_D 36 TRUE FALSE LEU 37 TRUE FALSE GLN 38 TRUE FALSE ARG 39 TRUE FALSE MET 40 TRUE FALSE PHE 41 TRUE FALSE LYS 42 TRUE FALSE LYS 43 TRUE FALSE GLU 44 TRUE FALSE THR 45 TRUE FALSE GLY 46 TRUE FALSE HIS,HIS_D 47 TRUE FALSE SER 48 TRUE FALSE LEU 49 TRUE FALSE GLY 50 TRUE FALSE GLN 51 TRUE FALSE TYR 52 TRUE FALSE ILE 53 TRUE FALSE ARG 54 TRUE FALSE SER 55 TRUE FALSE ARG 56 TRUE FALSE LYS 57 TRUE FALSE MET 58 TRUE FALSE THR 59 TRUE FALSE GLU 60 TRUE FALSE ILE 61 TRUE FALSE ALA 62 TRUE FALSE GLN 63 TRUE FALSE LYS 64 TRUE FALSE LEU 65 TRUE FALSE LYS 66 TRUE FALSE GLU 67 TRUE FALSE SER 68 TRUE FALSE ASN 69 TRUE FALSE GLU 70 TRUE FALSE PRO 71 TRUE FALSE ILE 72 TRUE FALSE LEU 73 TRUE FALSE TYR 74 TRUE FALSE LEU 75 TRUE FALSE ALA 76 TRUE FALSE GLU 77 TRUE FALSE ARG 78 TRUE FALSE TYR 79 TRUE FALSE GLY 80 TRUE FALSE PHE 81 TRUE FALSE GLU 82 TRUE FALSE SER 83 TRUE FALSE GLN 84 TRUE FALSE GLN 85 TRUE FALSE THR 86 TRUE FALSE LEU 87 TRUE FALSE THR 88 TRUE FALSE ARG 89 TRUE FALSE THR 90 TRUE FALSE PHE 91 TRUE FALSE LYS 92 TRUE FALSE ASN 93 TRUE FALSE TYR 94 TRUE FALSE PHE 95 TRUE FALSE ASP 96 TRUE FALSE VAL 97 TRUE FALSE PRO 98 TRUE FALSE PRO 99 TRUE FALSE HIS,HIS_D 100 TRUE FALSE LYS 101 TRUE FALSE TYR 102 TRUE FALSE ARG 103 TRUE FALSE MET 104 TRUE FALSE THR 105 TRUE FALSE ASN 106 TRUE FALSE MET 107 TRUE FALSE GLN 108 TRUE FALSE GLY 109 TRUE FALSE GLU 110 TRUE FALSE SER 111 TRUE FALSE ARG 112 TRUE FALSE PHE 113 TRUE FALSE LEU 114 TRUE FALSE HIS,HIS_D 115 TRUE FALSE PRO 116 TRUE FALSE LEU:CtermProteinFull Mover name: PackRotamersMover, Mover type: PackRotamersMover, Mover current tag:NoTag Score function: ref2015 #Packer_Task Threads to request: ALL AVAILABLE resid pack? design? allowed_aas 1 TRUE TRUE ALA:NtermProteinFull,CYS:NtermProteinFull,ASP:NtermProteinFull,GLU:NtermProteinFull,PHE:NtermProteinFull,GLY:NtermProteinFull,HIS:NtermProteinFull,HIS_D:NtermProteinFull,ILE:NtermProteinFull,LYS:NtermProteinFull,LEU:NtermProteinFull,MET:NtermProteinFull,ASN:NtermProteinFull,PRO:NtermProteinFull,GLN:NtermProteinFull,ARG:NtermProteinFull,SER:NtermProteinFull,THR:NtermProteinFull,VAL:NtermProteinFull,TRP:NtermProteinFull,TYR:NtermProteinFull 2 TRUE TRUE ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR 3 TRUE TRUE ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR 4 TRUE TRUE ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR 5 TRUE TRUE ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR 6 TRUE TRUE ALA,CYS,ASP,GLU,PHE,GLY,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,PRO,GLN,ARG,SER,THR,VAL,TRP,TYR 7 FALSE FALSE 8 FALSE FALSE 9 FALSE FALSE 10 FALSE FALSE 11 FALSE FALSE 12 FALSE FALSE 13 FALSE FALSE 14 FALSE FALSE 15 FALSE FALSE 16 FALSE FALSE 17 FALSE FALSE 18 FALSE FALSE 19 FALSE FALSE 20 FALSE FALSE 21 FALSE FALSE 22 FALSE FALSE 23 FALSE FALSE 24 FALSE FALSE 25 FALSE FALSE 26 FALSE FALSE 27 FALSE FALSE 28 FALSE FALSE 29 FALSE FALSE 30 FALSE FALSE 31 FALSE FALSE 32 FALSE FALSE 33 FALSE FALSE 34 FALSE FALSE 35 FALSE FALSE 36 FALSE FALSE 37 FALSE FALSE 38 FALSE FALSE 39 FALSE FALSE 40 FALSE FALSE 41 FALSE FALSE 42 FALSE FALSE 43 FALSE FALSE 44 FALSE FALSE 45 FALSE FALSE 46 FALSE FALSE 47 FALSE FALSE 48 FALSE FALSE 49 FALSE FALSE 50 FALSE FALSE 51 FALSE FALSE 52 FALSE FALSE 53 FALSE FALSE 54 FALSE FALSE 55 FALSE FALSE 56 FALSE FALSE 57 FALSE FALSE 58 FALSE FALSE 59 FALSE FALSE 60 FALSE FALSE 61 FALSE FALSE 62 FALSE FALSE 63 FALSE FALSE 64 FALSE FALSE 65 FALSE FALSE 66 FALSE FALSE 67 FALSE FALSE 68 FALSE FALSE 69 FALSE FALSE 70 FALSE FALSE 71 FALSE FALSE 72 FALSE FALSE 73 FALSE FALSE 74 FALSE FALSE 75 FALSE FALSE 76 FALSE FALSE 77 FALSE FALSE 78 FALSE FALSE 79 FALSE FALSE 80 FALSE FALSE 81 FALSE FALSE 82 FALSE FALSE 83 FALSE FALSE 84 FALSE FALSE 85 FALSE FALSE 86 FALSE FALSE 87 FALSE FALSE 88 FALSE FALSE 89 FALSE FALSE 90 FALSE FALSE 91 FALSE FALSE 92 FALSE FALSE 93 FALSE FALSE 94 FALSE FALSE 95 FALSE FALSE 96 FALSE FALSE 97 FALSE FALSE 98 FALSE FALSE 99 FALSE FALSE 100 FALSE FALSE 101 FALSE FALSE 102 FALSE FALSE 103 FALSE FALSE 104 FALSE FALSE 105 FALSE FALSE 106 FALSE FALSE 107 FALSE FALSE 108 FALSE FALSE 109 FALSE FALSE 110 FALSE FALSE 111 FALSE FALSE 112 FALSE FALSE 113 FALSE FALSE 114 FALSE FALSE 115 FALSE FALSE 116 FALSE FALSE GGGG .interaction_graph_factory: Instantiating PDInteractionGraph core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 2822 rotamers at 115 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph protocols.minimization_packing.PackRotamersMover: [ WARNING ] undefined ScoreFunction -- creating a default one core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.pack.pack_rotamers: built 4 rotamers at 4 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph Finished T500_Packing in 0:00:18.529507