core.init: Rosetta version exported from http://www.rosettacommons.org core.init: command: /home/dancebean/Cheng/rosetta_2014.30.57114_bundle/main/source/bin/loopmodel.linuxgccrelease @/mnt/hgfs/Cheng/test/ccd.options -database /home/dancebean/Cheng/rosetta_2014.30.57114_bundle/main/database core.init: 'RNG device' seed mode, using '/dev/urandom', seed=-50411027 seed_offset=0 real_seed=-50411027 core.init.random: RandomGenerator:init: Normal mode, seed=-50411027 RG_type=mt19937 protocols.loop_build.LoopBuild: ==== Loop protocol: ================================================= protocols.loop_build.LoopBuild: remodel quick_ccd protocols.loop_build.LoopBuild: intermedrelax no protocols.loop_build.LoopBuild: refine refine_kic protocols.loop_build.LoopBuild: relax fastrelax protocols.loops.loops_main: Frag libraries debug /mnt/hgfs/Cheng/test/aa4KMT_HC09_05.200_v1_3 9 core.io.fragments: reading fragments from file: /mnt/hgfs/Cheng/test/aa4KMT_HC09_05.200_v1_3 ... core.io.fragments: rosetta++ fileformat detected! Calling legacy reader... core.fragments.ConstantLengthFragSet: finished reading top 200 9mer fragments from file /mnt/hgfs/Cheng/test/aa4KMT_HC09_05.200_v1_3 protocols.loops.loops_main: Frag libraries debug /mnt/hgfs/Cheng/test/aa4KMT_HC03_05.200_v1_3 3 core.io.fragments: reading fragments from file: /mnt/hgfs/Cheng/test/aa4KMT_HC03_05.200_v1_3 ... core.io.fragments: rosetta++ fileformat detected! Calling legacy reader... core.fragments.ConstantLengthFragSet: finished reading top 200 3mer fragments from file /mnt/hgfs/Cheng/test/aa4KMT_HC03_05.200_v1_3 protocols.loops.loops_main: Frag libraries debug none 1 protocols.loops.loops_main: Set up 1-mer library from 3-mer library protocols.loops.loops_main: Fragment libraries: 1 135600 protocols.loops.loops_main: Fragment libraries: 3 45200 protocols.loops.loops_main: Fragment libraries: 9 44000 basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt basic.io.database: Database file opened: scoring/score_functions/hbonds/sp2_elec_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/sp2_elec_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/sp2_elec_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/rama/Rama_smooth_dyn.dat_ss_6.4 core.scoring.ScoreFunctionFactory: SCOREFUNCTION: talaris2013 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/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_pp protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs protocols.jd2.PDBJobInputter: pushed /mnt/hgfs/Cheng/test/4KMT_HC_native_442residue_FullAtom_no_loop.pdb nstruct index 1 protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: filling pose from PDB /mnt/hgfs/Cheng/test/4KMT_HC_native_442residue_FullAtom_no_loop.pdb core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 737 residue types core.io.pdb.file_data: Randomized: N SER 136 core.io.pdb.file_data: Randomized: CA SER 136 core.io.pdb.file_data: Randomized: C SER 136 core.io.pdb.file_data: Randomized: O SER 136 core.io.pdb.file_data: Randomized: CB SER 136 core.io.pdb.file_data: Randomized: OG SER 136 core.io.pdb.file_data: Randomized: H SER 136 core.io.pdb.file_data: Randomized: HA SER 136 core.io.pdb.file_data: Randomized: 1HB SER 136 core.io.pdb.file_data: Randomized: 2HB SER 136 core.io.pdb.file_data: Randomized: HG SER 136 core.io.pdb.file_data: Randomized: N THR 137 core.io.pdb.file_data: Randomized: CA THR 137 core.io.pdb.file_data: Randomized: C THR 137 core.io.pdb.file_data: Randomized: O THR 137 core.io.pdb.file_data: Randomized: CB THR 137 core.io.pdb.file_data: Randomized: OG1 THR 137 core.io.pdb.file_data: Randomized: CG2 THR 137 core.io.pdb.file_data: Randomized: H THR 137 core.io.pdb.file_data: Randomized: HA THR 137 core.io.pdb.file_data: Randomized: HB THR 137 core.io.pdb.file_data: Randomized: HG1 THR 137 core.io.pdb.file_data: Randomized: 1HG2 THR 137 core.io.pdb.file_data: Randomized: 2HG2 THR 137 core.io.pdb.file_data: Randomized: 3HG2 THR 137 core.io.pdb.file_data: Randomized: N SER 138 core.io.pdb.file_data: Randomized: CA SER 138 core.io.pdb.file_data: Randomized: C SER 138 core.io.pdb.file_data: Randomized: O SER 138 core.io.pdb.file_data: Randomized: CB SER 138 core.io.pdb.file_data: Randomized: OG SER 138 core.io.pdb.file_data: Randomized: H SER 138 core.io.pdb.file_data: Randomized: HA SER 138 core.io.pdb.file_data: Randomized: 1HB SER 138 core.io.pdb.file_data: Randomized: 2HB SER 138 core.io.pdb.file_data: Randomized: HG SER 138 core.io.pdb.file_data: Randomized: N GLY 139 core.io.pdb.file_data: Randomized: CA GLY 139 core.io.pdb.file_data: Randomized: C GLY 139 core.io.pdb.file_data: Randomized: O GLY 139 core.io.pdb.file_data: Randomized: H GLY 139 core.io.pdb.file_data: Randomized: 1HA GLY 139 core.io.pdb.file_data: Randomized: 2HA GLY 139 core.io.pdb.file_data: Randomized: N HIS 223 core.io.pdb.file_data: Randomized: CA HIS 223 core.io.pdb.file_data: Randomized: C HIS 223 core.io.pdb.file_data: Randomized: O HIS 223 core.io.pdb.file_data: Randomized: CB HIS 223 core.io.pdb.file_data: Randomized: CG HIS 223 core.io.pdb.file_data: Randomized: ND1 HIS 223 core.io.pdb.file_data: Randomized: CD2 HIS 223 core.io.pdb.file_data: Randomized: CE1 HIS 223 core.io.pdb.file_data: Randomized: NE2 HIS 223 core.io.pdb.file_data: Randomized: H HIS 223 core.io.pdb.file_data: Randomized: HA HIS 223 core.io.pdb.file_data: Randomized: 1HB HIS 223 core.io.pdb.file_data: Randomized: 2HB HIS 223 core.io.pdb.file_data: Randomized: HD2 HIS 223 core.io.pdb.file_data: Randomized: HE1 HIS 223 core.io.pdb.file_data: Randomized: HE2 HIS 223 core.io.pdb.file_data: Randomized: N HIS 224 core.io.pdb.file_data: Randomized: CA HIS 224 core.io.pdb.file_data: Randomized: C HIS 224 core.io.pdb.file_data: Randomized: O HIS 224 core.io.pdb.file_data: Randomized: CB HIS 224 core.io.pdb.file_data: Randomized: CG HIS 224 core.io.pdb.file_data: Randomized: ND1 HIS 224 core.io.pdb.file_data: Randomized: CD2 HIS 224 core.io.pdb.file_data: Randomized: CE1 HIS 224 core.io.pdb.file_data: Randomized: NE2 HIS 224 core.io.pdb.file_data: Randomized: H HIS 224 core.io.pdb.file_data: Randomized: HA HIS 224 core.io.pdb.file_data: Randomized: 1HB HIS 224 core.io.pdb.file_data: Randomized: 2HB HIS 224 core.io.pdb.file_data: Randomized: HD2 HIS 224 core.io.pdb.file_data: Randomized: HE1 HIS 224 core.io.pdb.file_data: Randomized: HE2 HIS 224 core.io.pdb.file_data: Randomized: N HIS 225 core.io.pdb.file_data: Randomized: CA HIS 225 core.io.pdb.file_data: Randomized: C HIS 225 core.io.pdb.file_data: Randomized: O HIS 225 core.io.pdb.file_data: Randomized: CB HIS 225 core.io.pdb.file_data: Randomized: CG HIS 225 core.io.pdb.file_data: Randomized: ND1 HIS 225 core.io.pdb.file_data: Randomized: CD2 HIS 225 core.io.pdb.file_data: Randomized: CE1 HIS 225 core.io.pdb.file_data: Randomized: NE2 HIS 225 core.io.pdb.file_data: Randomized: H HIS 225 core.io.pdb.file_data: Randomized: HA HIS 225 core.io.pdb.file_data: Randomized: 1HB HIS 225 core.io.pdb.file_data: Randomized: 2HB HIS 225 core.io.pdb.file_data: Randomized: HD2 HIS 225 core.io.pdb.file_data: Randomized: HE1 HIS 225 core.io.pdb.file_data: Randomized: HE2 HIS 225 core.io.pdb.file_data: Randomized: N HIS 226 core.io.pdb.file_data: Randomized: CA HIS 226 core.io.pdb.file_data: Randomized: C HIS 226 core.io.pdb.file_data: Randomized: O HIS 226 core.io.pdb.file_data: Randomized: CB HIS 226 core.io.pdb.file_data: Randomized: CG HIS 226 core.io.pdb.file_data: Randomized: ND1 HIS 226 core.io.pdb.file_data: Randomized: CD2 HIS 226 core.io.pdb.file_data: Randomized: CE1 HIS 226 core.io.pdb.file_data: Randomized: NE2 HIS 226 core.io.pdb.file_data: Randomized: H HIS 226 core.io.pdb.file_data: Randomized: HA HIS 226 core.io.pdb.file_data: Randomized: 1HB HIS 226 core.io.pdb.file_data: Randomized: 2HB HIS 226 core.io.pdb.file_data: Randomized: HD2 HIS 226 core.io.pdb.file_data: Randomized: HE1 HIS 226 core.io.pdb.file_data: Randomized: HE2 HIS 226 core.io.pdb.file_data: Randomized: N HIS 227 core.io.pdb.file_data: Randomized: CA HIS 227 core.io.pdb.file_data: Randomized: C HIS 227 core.io.pdb.file_data: Randomized: O HIS 227 core.io.pdb.file_data: Randomized: CB HIS 227 core.io.pdb.file_data: Randomized: CG HIS 227 core.io.pdb.file_data: Randomized: ND1 HIS 227 core.io.pdb.file_data: Randomized: CD2 HIS 227 core.io.pdb.file_data: Randomized: CE1 HIS 227 core.io.pdb.file_data: Randomized: NE2 HIS 227 core.io.pdb.file_data: Randomized: H HIS 227 core.io.pdb.file_data: Randomized: HA HIS 227 core.io.pdb.file_data: Randomized: 1HB HIS 227 core.io.pdb.file_data: Randomized: 2HB HIS 227 core.io.pdb.file_data: Randomized: HD2 HIS 227 core.io.pdb.file_data: Randomized: HE1 HIS 227 core.io.pdb.file_data: Randomized: HE2 HIS 227 core.io.pdb.file_data: Randomized: N HIS 228 core.io.pdb.file_data: Randomized: CA HIS 228 core.io.pdb.file_data: Randomized: C HIS 228 core.io.pdb.file_data: Randomized: O HIS 228 core.io.pdb.file_data: Randomized: OXT HIS 228 core.io.pdb.file_data: Randomized: CB HIS 228 core.io.pdb.file_data: Randomized: CG HIS 228 core.io.pdb.file_data: Randomized: ND1 HIS 228 core.io.pdb.file_data: Randomized: CD2 HIS 228 core.io.pdb.file_data: Randomized: CE1 HIS 228 core.io.pdb.file_data: Randomized: NE2 HIS 228 core.io.pdb.file_data: Randomized: H HIS 228 core.io.pdb.file_data: Randomized: HA HIS 228 core.io.pdb.file_data: Randomized: 1HB HIS 228 core.io.pdb.file_data: Randomized: 2HB HIS 228 core.io.pdb.file_data: Randomized: HD2 HIS 228 core.io.pdb.file_data: Randomized: HE1 HIS 228 core.io.pdb.file_data: Randomized: HE2 HIS 228 core.conformation.Conformation: Found disulfide between residues 22 96 core.conformation.Conformation: current variant for 22 CYS core.conformation.Conformation: current variant for 96 CYS core.conformation.Conformation: current variant for 22 CYD core.conformation.Conformation: current variant for 96 CYD core.conformation.Conformation: Found disulfide between residues 146 202 core.conformation.Conformation: current variant for 146 CYS core.conformation.Conformation: current variant for 202 CYS core.conformation.Conformation: current variant for 146 CYD core.conformation.Conformation: current variant for 202 CYD core.pack.task: Packer task: initialize from command line() core.pose.util: Cannot open psipred_ss2 file tt protocols.loops.loops_main: can not open DSSP file tt protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... protocols.loop_build.LoopBuildMover: Annotated sequence of pose: E[GLU:NtermProteinFull]VQLVQSGAEVKKPGESLKISC[CYD]KGSGYSFTSYWIGWVRQMPGKGLEWMGIIYPGDSDTRYSPSFQGQVTISADKSISTAYLQWSSLKASDTAMYYC[CYD]ARYDGIYGELDFWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGC[CYD]LVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYIC[CYD]NVNHKPSNTKVDKKVEPKSCHHHHHH[HIS:CtermProteinFull] protocols.looprelax: ==== Loop protocol: ================================================= protocols.looprelax: remodel quick_ccd protocols.looprelax: intermedrelax no protocols.looprelax: refine refine_kic protocols.looprelax: relax fastrelax protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... core.chemical.ResidueTypeSet: Finished initializing centroid residue type set. Created 1010 residue types protocols.looprelax: ==================================================================================== protocols.looprelax: === protocols.looprelax: === Remodel protocols.looprelax: === protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD: ALL_LOOPS:LOOP begin end cut skip_rate extended protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD: LOOP 222 228 228 0 1 protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD: protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD: SELECTEDLOOPS:LOOP begin end cut skip_rate extended protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD: LOOP 222 228 228 0 1 protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD: protocols.loops.loops_main: Pose fold tree FOLD_TREE EDGE 1 221 -1 EDGE 221 228 -1 protocols.loops.loops_main: protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD: Setting extended torsions: LOOP 222 228 228 0 1 protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD: Building Loop: LOOP 222 228 228 0 1 protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD: Building Loop attempt: 0 protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD: ***** CCD CLOSURE ***** protocols.loops.loops_main: Pose fold tree FOLD_TREE EDGE 1 221 -1 EDGE 221 228 -1 protocols.loops.loops_main: protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD: Number of cycles: cycles2 and cycles3 2 35 protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD: vdw hbond_sr_bb hbond_lr_bb pair rama env cbeta rg chainbreak protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD: 395.129 3.243 -12.748 -66.731 6.282 -5.183 -45.159 82.224 433.201 0.000 protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD: 394.111 3.243 -13.398 -66.731 6.328 -5.181 -45.531 82.213 433.168 0.000 protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD: FragCount: 210 protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD: Looptime 8 protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD: ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ vdw 1.000 3.243 3.243 hbond_sr_bb 1.000 -13.398 -13.398 hbond_lr_bb 1.000 -66.731 -66.731 pair 1.000 6.328 6.328 rama 0.100 -51.814 -5.181 env 1.000 -45.531 -45.531 cbeta 1.000 82.213 82.213 rg 2.000 216.584 433.168 chainbreak 3.333 0.000 0.000 --------------------------------------------------- Total weighted score: 394.111 ------------------------- protocols.moves.TrialCounter: QuickCCD trials= 210; accepts= 0.7238; energy_drop/trial= 0.00239 protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD: result of loop closure:0 success, 3 failure 0 protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD: Loopstat: 222 228 222 228 7 time 8.0 0 time 0.0 394.111 ext protocols::checkpoint: Deleting checkpoints of Remodel protocols.looprelax: Buildtime: 8 protocols.looprelax: FOLD_TREE EDGE 1 228 -1 protocols.looprelax: protocols.looprelax: ==================================================================================== protocols.looprelax: === protocols.looprelax: === Fullatom protocols.looprelax: === protocols.looprelax: Annotated sequence before fa switch: E[GLU:NtermProteinFull]VQLVQSGAEVKKPGESLKISC[CYD]KGSGYSFTSYWIGWVRQMPGKGLEWMGIIYPGDSDTRYSPSFQGQVTISADKSISTAYLQWSSLKASDTAMYYC[CYD]ARYDGIYGELDFWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGC[CYD]LVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYIC[CYD]NVNHKPSNTKVDKKVEPKSCHHHHHH[HIS:CtermProteinFull] protocols.looprelax: Repacking required protocols.looprelax: Detecting disulfides protocols.looprelax: Annotated sequence before repack: E[GLU:NtermProteinFull]VQLVQSGAEVKKPGESLKISC[CYD]KGSGYSFTSYWIGWVRQMPGKGLEWMGIIYPGDSDTRYSPSFQGQVTISADKSISTAYLQWSSLKASDTAMYYC[CYD]ARYDGIYGELDFWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGC[CYD]LVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYIC[CYD]NVNHKPSNTKVDKKVEPKSCHHHHHH[HIS:CtermProteinFull] core.conformation.Conformation: Found disulfide between residues 22 96 core.conformation.Conformation: current variant for 22 CYD core.conformation.Conformation: current variant for 96 CYD core.conformation.Conformation: current variant for 22 CYD core.conformation.Conformation: current variant for 96 CYD core.conformation.Conformation: Found disulfide between residues 146 202 core.conformation.Conformation: current variant for 146 CYD core.conformation.Conformation: current variant for 202 CYD core.conformation.Conformation: current variant for 146 CYD core.conformation.Conformation: current variant for 202 CYD core.pack.task: Packer task: initialize from command line() protocols.looprelax: 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000disabling minimization on disulfide residue 22 protocols.looprelax: disabling minimization on disulfide residue 96 protocols.looprelax: disabling minimization on disulfide residue 146 protocols.looprelax: disabling minimization on disulfide residue 202 core.pack.dunbrack: Dunbrack 2010 library took 0.402304 seconds to load from binary core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.pack_rotamers: built 346 rotamers at 14 positions. core.pack.pack_rotamers: IG: 62184 bytes protocols.looprelax: -233.807 -745.626 62.502 401.771 1.503 -78.597 1.761 -15.675 -78.075 -18.266 -13.684 -1.463 -10.363 79.892 184.685 -25.076 20.904==================================================================================== protocols.looprelax: === protocols.looprelax: === Refine protocols.looprelax: === core.kinematics.FoldTree: FoldTree::reorder( 1 ) failed, new/old edge_list_ size mismatch core.kinematics.FoldTree: 4 3 core.kinematics.FoldTree: FOLD_TREE EDGE 221 228 -1 EDGE 221 228 1 EDGE 229 228 -1 EDGE 1 221 -1 protocols::checkpoint: Deleting checkpoints of Loopbuild protocols.jd2.JobDistributor: [ERROR] Exception caught by JobDistributor for job 4KMT_HC_native_442residue_FullAtom_no_loop_0001Unable to reorder the FoldTree for this loops set! protocols.jd2.JobDistributor: protocols.jd2.JobDistributor: 4KMT_HC_native_442residue_FullAtom_no_loop_0001 reported failure and will NOT retry protocols.jd2.JobDistributor: no more batches to process... protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 18 seconds