core.init: Mini-Rosetta version 43134M from https://svn.rosettacommons.org/source/trunk/mini core.init: command: ../../bin/AbinitioRelax.linuxgccrelease @flags core.init: 'RNG device' seed mode, using '/dev/urandom', seed=-540226944 seed_offset=0 real_seed=-540226944 core.init.random: RandomGenerator:init: Normal mode, seed=-540226944 RG_type=mt19937 core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 4101 residue types core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU_p:NtermProteinFull 1 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU_p:NtermProteinFull 1 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU_p:NtermProteinFull 1 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU_p:NtermProteinFull 1 core.pack.task: Packer task: initialize from command line() core.pack.pack_missing_sidechains: packing residue number 1 because of missing atom number 6 atom name CG 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: pdb_pair_stats_fine basic.io.database: Database file opened: scoring/score_functions/hbonds/standard_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/standard_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/standard_params/HBEval.csv basic.io.database: Database file opened: env_log.txt basic.io.database: Database file opened: cbeta_den.txt basic.io.database: Database file opened: pair_log.txt basic.io.database: Database file opened: cenpack_log.txt basic.io.database: Database file opened: env_log.txt basic.io.database: Database file opened: cbeta_den.txt basic.io.database: Database file opened: pair_log.txt basic.io.database: Database file opened: cenpack_log.txt basic.io.database: Database file opened: CEN6_mem_env_log.txt basic.io.database: Database file opened: CEN10_mem_env_log.txt basic.io.database: Database file opened: memcbeta_den.txt basic.io.database: Database file opened: mem_pair_log.txt basic.io.database: Database file opened: P_AA basic.io.database: Database file opened: P_AA_n basic.io.database: Database file opened: P_AA_pp basic.io.database: Database file opened: Rama_smooth_dyn.dat_ss_6.4 core.pack.dunbrack: Dunbrack library took 0.06 seconds to load from binary core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.pack_rotamers: built 13 rotamers at 1 positions. core.pack.pack_rotamers: IG: 840 bytes core.chemical.ResidueTypeSet: Finished initializing centroid residue type set. Created 1202 residue types protocols.abinitio.AbrelaxApplication: read fasta sequence: 117 residues EQVNELKEKGNKALSVGNIDDALQCYSEAIKLDPHNHVLYSNRSAAYAKKGDYQKAYEDGCKTVDLKPDWGKGYSRKAAALEFLNRFEEAKRTYEEGLKHEANNPQLKEGLQNMEAR core.conformation.Conformation: [ WARNING ] missing heavyatom: CG on residue GLU_p:NtermProteinFull 1 core.conformation.Conformation: [ WARNING ] missing heavyatom: CD on residue GLU_p:NtermProteinFull 1 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE1 on residue GLU_p:NtermProteinFull 1 core.conformation.Conformation: [ WARNING ] missing heavyatom: OE2 on residue GLU_p:NtermProteinFull 1 core.pack.task: Packer task: initialize from command line() core.pack.pack_missing_sidechains: packing residue number 1 because of missing atom number 6 atom name CG core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.pack_rotamers: built 13 rotamers at 1 positions. core.pack.pack_rotamers: IG: 840 bytes core.io.fragments: reading fragments from file: ./input_files/aa1elwA09_05.200_v1_3 ... core.io.fragments: rosetta++ fileformat detected! Calling legacy reader... core.fragments.ConstantLengthFragSet: finished reading top 25 9mer fragments from file ./input_files/aa1elwA09_05.200_v1_3 core.io.fragments: reading fragments from file: ./input_files/aa1elwA03_05.200_v1_3 ... core.io.fragments: rosetta++ fileformat detected! Calling legacy reader... core.fragments.ConstantLengthFragSet: finished reading top 200 3mer fragments from file ./input_files/aa1elwA03_05.200_v1_3 core.fragment: compute strand/loop fractions for 117 residues... protocols.abinitio.AbrelaxApplication: run ClassicAbinitio..... basic.io.database: Database file opened: env_log.txt basic.io.database: Database file opened: cbeta_den.txt basic.io.database: Database file opened: pair_log.txt basic.io.database: Database file opened: cenpack_log.txt basic.io.database: Database file opened: phi.theta.36.HS.resmooth basic.io.database: Database file opened: phi.theta.36.SS.resmooth core.scoring.ScoreFunctionFactory: SCOREFUNCTION: standard core.scoring.ScoreFunctionFactory: SCOREFUNCTION PATCH: score12 protocols.jobdist.JobDistributors: Looking for an available job: 1 1 1 protocols.relax.ClassicRelax: Setting up default relax setting protocols::checkpoint: Deleting checkpoints of ClassicRelax protocols.abinitio: =================================================================== Stage 1 Folding with score0 for max of 20000 protocols.abinitio: Replaced extended chain after 95 cycles. protocols.moves.MonteCarlo: ClassicFragmentM trials= 95; accepts= 0.7474; energy_drop/trial= 0.01215 protocols.abinitio: ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ vdw 0.100 11.539 1.154 --------------------------------------------------- Total weighted score: 1.154 =================================================================== Stage 2 Folding with score1 for 20000 protocols.moves.MonteCarlo: ClassicFragmentM trials= 20000; accepts= 0.4688; energy_drop/trial= -0.00117 protocols.abinitio: ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ vdw 1.000 0.961 0.961 pair 1.000 -3.636 -3.636 env 1.000 -18.210 -18.210 hs_pair 1.000 0.000 0.000 ss_pair 0.300 0.000 0.000 sheet 1.000 0.000 0.000 --------------------------------------------------- Total weighted score: -20.885 =================================================================== Stage 3 Folding with score2 and score5 for 20000 protocols.moves.MonteCarlo: ClassicFragmentM trials= 200000; accepts= 0.3878; energy_drop/trial= 0.00103 protocols.abinitio: ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ vdw 1.000 0.000 0.000 cenpack 0.500 -18.416 -9.208 pair 1.000 -4.176 -4.176 env 1.000 -22.501 -22.501 cbeta 0.250 23.131 5.783 hs_pair 1.000 0.000 0.000 ss_pair 1.000 0.000 0.000 sheet 1.000 0.000 0.000 --------------------------------------------------- Total weighted score: -30.103 =================================================================== Stage 4 Folding with score3 for 40000 protocols.moves.MonteCarlo: ClassicFragmentM trials= 40000; accepts= 0.2631; energy_drop/trial= 0.00140 protocols.moves.MonteCarlo: SmoothFragmentMo trials= 80000; accepts= 0.2988; energy_drop/trial= 0.00116 protocols.abinitio: ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ vdw 1.000 0.515 0.515 cenpack 1.000 -24.995 -24.995 pair 1.000 -4.497 -4.497 env 1.000 -19.582 -19.582 cbeta 1.000 22.769 22.769 rg 1.500 15.096 22.644 hs_pair 1.000 0.000 0.000 ss_pair 1.000 0.000 0.000 rsigma 1.000 0.000 0.000 sheet 1.000 0.000 0.000 --------------------------------------------------- Total weighted score: -3.147 =================================================================== Finished Abinitio protocols.filters.AbinitioBaseFilter: apply filter: RGFilter protocols.filters.AbinitioBaseFilter: apply filter: Contact-Order Filter protocols.filters.AbinitioBaseFilter: apply filter: SheetFilter protocols.abinitio.AbrelaxApplication: passed all filters core.scoring.ScoreFunctionFactory: SCOREFUNCTION: standard core.scoring.ScoreFunctionFactory: SCOREFUNCTION PATCH: score12 core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.pack_rotamers: built 1093 rotamers at 117 positions. core.pack.pack_rotamers: IG: 845356 bytes core.scoring.ScoreFunctionFactory: SCOREFUNCTION: standard core.scoring.ScoreFunctionFactory: SCOREFUNCTION PATCH: score12 protocols.relax.FastRelax: ================== Using default script ================== core.pack.task: Packer task: initialize from command line() protocols.relax.FastRelax: CMD: repeat 72.0617 0 0 0.44 core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.pack_rotamers: built 1270 rotamers at 117 positions. core.pack.pack_rotamers: IG: 1004756 bytes protocols.relax.FastRelax: CMD: ramp_repack_min -281.658 1.17642 1.17642 0.0088 core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.pack_rotamers: built 1167 rotamers at 117 positions. core.pack.pack_rotamers: IG: 896816 bytes protocols.relax.FastRelax: CMD: ramp_repack_min -240.401 2.31525 2.31525 0.11 core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.pack_rotamers: built 1139 rotamers at 117 positions. core.pack.pack_rotamers: IG: 815752 bytes protocols.relax.FastRelax: CMD: ramp_repack_min -223.363 2.61765 2.61765 0.242 core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.pack_rotamers: built 1120 rotamers at 117 positions. core.pack.pack_rotamers: IG: 783420 bytes protocols.relax.FastRelax: CMD: ramp_repack_min -240.274 3.43774 3.43774 0.44 protocols.relax.FastRelax: MRP: 0 -240.274 -240.274 3.43774 3.43774 protocols.relax.FastRelax: CMD: accept_to_best -240.274 3.43774 3.43774 0.44 protocols.relax.FastRelax: CMD: endrepeat -240.274 3.43774 3.43774 0.44 core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.pack_rotamers: built 1319 rotamers at 117 positions. core.pack.pack_rotamers: IG: 1057648 bytes protocols.relax.FastRelax: CMD: ramp_repack_min -327.979 3.17596 3.17596 0.0088 core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.pack_rotamers: built 1173 rotamers at 117 positions. core.pack.pack_rotamers: IG: 910512 bytes protocols.relax.FastRelax: CMD: ramp_repack_min -281.927 3.69218 3.69218 0.11 core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.pack_rotamers: built 1147 rotamers at 117 positions. core.pack.pack_rotamers: IG: 828976 bytes protocols.relax.FastRelax: CMD: ramp_repack_min -259.218 3.67522 3.67522 0.242 core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.pack_rotamers: built 1148 rotamers at 117 positions. core.pack.pack_rotamers: IG: 814096 bytes protocols.relax.FastRelax: CMD: ramp_repack_min -250.613 4.04484 4.04484 0.44 protocols.relax.FastRelax: MRP: 1 -250.613 -250.613 4.04484 4.04484 protocols.relax.FastRelax: CMD: accept_to_best -250.613 4.04484 4.04484 0.44 protocols.relax.FastRelax: CMD: endrepeat -250.613 4.04484 4.04484 0.44 core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.pack_rotamers: built 1342 rotamers at 117 positions. core.pack.pack_rotamers: IG: 1084188 bytes protocols.relax.FastRelax: CMD: ramp_repack_min -330.533 3.4605 3.4605 0.0088 core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.pack_rotamers: built 1186 rotamers at 117 positions. core.pack.pack_rotamers: IG: 905240 bytes protocols.relax.FastRelax: CMD: ramp_repack_min -286.036 3.96093 3.96093 0.11 core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.pack_rotamers: built 1176 rotamers at 117 positions. core.pack.pack_rotamers: IG: 864736 bytes protocols.relax.FastRelax: CMD: ramp_repack_min -265.659 4.05099 4.05099 0.242 core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.pack_rotamers: built 1160 rotamers at 117 positions. core.pack.pack_rotamers: IG: 829344 bytes protocols.relax.FastRelax: CMD: ramp_repack_min -255.63 3.87089 3.87089 0.44 protocols.relax.FastRelax: MRP: 2 -255.63 -255.63 3.87089 3.87089 protocols.relax.FastRelax: CMD: accept_to_best -255.63 3.87089 3.87089 0.44 protocols.relax.FastRelax: CMD: endrepeat -255.63 3.87089 3.87089 0.44 core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.pack_rotamers: built 1343 rotamers at 117 positions. core.pack.pack_rotamers: IG: 1117224 bytes protocols.relax.FastRelax: CMD: ramp_repack_min -327.302 3.91581 3.91581 0.0088 core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.pack_rotamers: built 1192 rotamers at 117 positions. core.pack.pack_rotamers: IG: 905160 bytes protocols.relax.FastRelax: CMD: ramp_repack_min -293.967 3.89599 3.89599 0.11 core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.pack_rotamers: built 1170 rotamers at 117 positions. core.pack.pack_rotamers: IG: 860040 bytes protocols.relax.FastRelax: CMD: ramp_repack_min -273.322 4.00523 4.00523 0.242 core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.pack_rotamers: built 1150 rotamers at 117 positions. core.pack.pack_rotamers: IG: 819180 bytes protocols.relax.FastRelax: CMD: ramp_repack_min -258.208 3.56834 3.56834 0.44 protocols.relax.FastRelax: MRP: 3 -258.208 -258.208 3.56834 3.56834 protocols.relax.FastRelax: CMD: accept_to_best -258.208 3.56834 3.56834 0.44 protocols.relax.FastRelax: CMD: endrepeat -258.208 3.56834 3.56834 0.44 core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.pack_rotamers: built 1367 rotamers at 117 positions. core.pack.pack_rotamers: IG: 1145788 bytes protocols.relax.FastRelax: CMD: ramp_repack_min -336.332 3.62396 3.62396 0.0088 core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.pack_rotamers: built 1207 rotamers at 117 positions. core.pack.pack_rotamers: IG: 931996 bytes protocols.relax.FastRelax: CMD: ramp_repack_min -299.038 3.55535 3.55535 0.11 core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.pack_rotamers: built 1165 rotamers at 117 positions. core.pack.pack_rotamers: IG: 861716 bytes protocols.relax.FastRelax: CMD: ramp_repack_min -279.293 3.71527 3.71527 0.242 core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.pack_rotamers: built 1151 rotamers at 117 positions. core.pack.pack_rotamers: IG: 832672 bytes protocols.relax.FastRelax: CMD: ramp_repack_min -265.246 3.58111 3.58111 0.44 protocols.relax.FastRelax: MRP: 4 -265.246 -265.246 3.58111 3.58111 protocols.relax.FastRelax: CMD: accept_to_best -265.246 3.58111 3.58111 0.44 protocols.relax.FastRelax: CMD: endrepeat -265.246 3.58111 3.58111 0.44 protocols::checkpoint: Deleting checkpoints of FastRelax protocols::checkpoint: Deleting checkpoints of FastRelax protocols.abinitio.AbrelaxApplication: Finished _0001 in 470 seconds. protocols::checkpoint: Deleting checkpoints of ClassicAbinitio protocols::checkpoint: Deleting checkpoints of Abrelax protocols::checkpoint: Deleting checkpoints of ClassicAbinitio protocols::checkpoint: Deleting checkpoints of Abrelax