core.init: Rosetta version exported from http://www.rosettacommons.org core.init: command: /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/source/bin/minirosetta.linuxgccrelease @/home/lanselibai/Cheng/20150121_minirosetta/input/comparative_model_4KMT_to_C226S.options -database /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database core.init: 'RNG device' seed mode, using '/dev/urandom', seed=-2133849879 seed_offset=0 real_seed=-2133849879 core.init.random: RandomGenerator:init: Normal mode, seed=-2133849879 RG_type=mt19937 protocols.loops.loops_main: Frag libraries debug /home/lanselibai/Cheng/20150121_minirosetta/input/aaC226S_09_05.200_v1_3 9 core.io.fragments: reading fragments from file: /home/lanselibai/Cheng/20150121_minirosetta/input/aaC226S_09_05.200_v1_3 ... core.io.fragments: rosetta++ fileformat detected! Calling legacy reader... core.fragments.ConstantLengthFragSet: finished reading top 200 9mer fragments from file /home/lanselibai/Cheng/20150121_minirosetta/input/aaC226S_09_05.200_v1_3 protocols.loops.loops_main: Frag libraries debug /home/lanselibai/Cheng/20150121_minirosetta/input/aaC226S_03_05.200_v1_3 3 core.io.fragments: reading fragments from file: /home/lanselibai/Cheng/20150121_minirosetta/input/aaC226S_03_05.200_v1_3 ... core.io.fragments: rosetta++ fileformat detected! Calling legacy reader... core.fragments.ConstantLengthFragSet: finished reading top 200 3mer fragments from file /home/lanselibai/Cheng/20150121_minirosetta/input/aaC226S_03_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 264000 protocols.loops.loops_main: Fragment libraries: 3 88000 protocols.loops.loops_main: Fragment libraries: 9 86800 core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 737 residue types core.conformation.Conformation: Found disulfide between residues 23 88 core.conformation.Conformation: current variant for 23 CYS core.conformation.Conformation: current variant for 88 CYS core.conformation.Conformation: current variant for 23 CYD core.conformation.Conformation: current variant for 88 CYD core.conformation.Conformation: Found disulfide between residues 134 194 core.conformation.Conformation: current variant for 134 CYS core.conformation.Conformation: current variant for 194 CYS core.conformation.Conformation: current variant for 134 CYD core.conformation.Conformation: current variant for 194 CYD core.conformation.Conformation: Found disulfide between residues 214 432 core.conformation.Conformation: current variant for 214 CYS core.conformation.Conformation: current variant for 432 CYS core.conformation.Conformation: current variant for 214 CYD core.conformation.Conformation: current variant for 432 CYD core.conformation.Conformation: Found disulfide between residues 236 310 core.conformation.Conformation: current variant for 236 CYS core.conformation.Conformation: current variant for 310 CYS core.conformation.Conformation: current variant for 236 CYD core.conformation.Conformation: current variant for 310 CYD core.conformation.Conformation: Found disulfide between residues 356 412 core.conformation.Conformation: current variant for 356 CYS core.conformation.Conformation: current variant for 412 CYS core.conformation.Conformation: current variant for 356 CYD core.conformation.Conformation: current variant for 412 CYD core.pack.task: Packer task: initialize from command line() protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... protocols.comparative_modeling.threading: skipping atom,position HG ,23 because template doesn't have atom HG . protocols.comparative_modeling.threading: skipping atom,position HG ,88 because template doesn't have atom HG . protocols.comparative_modeling.threading: skipping atom,position HG ,134 because template doesn't have atom HG . protocols.comparative_modeling.threading: skipping atom,position HG ,194 because template doesn't have atom HG . protocols.comparative_modeling.threading: skipping atom,position HG ,214 because template doesn't have atom HG . protocols.comparative_modeling.threading: skipping atom,position H ,215 because template doesn't have atom H . protocols.comparative_modeling.threading: skipping atom,position 1HA ,223 because template doesn't have atom 1HA . protocols.comparative_modeling.threading: skipping atom,position 2HA ,223 because template doesn't have atom 2HA . protocols.comparative_modeling.threading: skipping atom,position 1HA ,224 because template doesn't have atom 1HA . protocols.comparative_modeling.threading: skipping atom,position 2HA ,224 because template doesn't have atom 2HA . protocols.comparative_modeling.threading: skipping atom,position 1HA ,230 because template doesn't have atom 1HA . protocols.comparative_modeling.threading: skipping atom,position 2HA ,230 because template doesn't have atom 2HA . protocols.comparative_modeling.threading: skipping atom,position HG ,236 because template doesn't have atom HG . protocols.comparative_modeling.threading: skipping atom,position CB ,238 because template doesn't have atom CB . protocols.comparative_modeling.threading: skipping atom,position HA ,238 because template doesn't have atom HA . protocols.comparative_modeling.threading: skipping atom,position CB ,249 because template doesn't have atom CB . protocols.comparative_modeling.threading: skipping atom,position HA ,249 because template doesn't have atom HA . protocols.comparative_modeling.threading: skipping atom,position CB ,263 because template doesn't have atom CB . protocols.comparative_modeling.threading: skipping atom,position HA ,263 because template doesn't have atom HA . protocols.comparative_modeling.threading: skipping atom,position H ,267 because template doesn't have atom H . protocols.comparative_modeling.threading: skipping atom,position 1HA ,269 because template doesn't have atom 1HA . protocols.comparative_modeling.threading: skipping atom,position 2HA ,269 because template doesn't have atom 2HA . protocols.comparative_modeling.threading: skipping atom,position H ,276 because template doesn't have atom H . protocols.comparative_modeling.threading: skipping atom,position HG ,310 because template doesn't have atom HG . protocols.comparative_modeling.threading: skipping atom,position CB ,315 because template doesn't have atom CB . protocols.comparative_modeling.threading: skipping atom,position HA ,315 because template doesn't have atom HA . protocols.comparative_modeling.threading: skipping atom,position HG ,358 because template doesn't have atom HG . protocols.comparative_modeling.threading: skipping atom,position HG ,414 because template doesn't have atom HG . protocols.comparative_modeling.threading: skipping atom,position HG ,434 because template doesn't have atom HG . protocols.loops.Loop: Autoset cut_ for loop 317 318 as 317. protocols.loops.Loop: Autoset cut_ for loop 347 352 as 348. protocols.loops.Loop: Autoset cut_ for loop 434 442 as 442. protocols.threading: loops to be rebuilt are: protocols.threading: 0x13f20780 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.looprelax: ==== Loop protocol: ================================================= protocols.looprelax: remodel quick_ccd protocols.looprelax: intermedrelax no protocols.looprelax: refine refine_ccd 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: === Initial Building 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 317 318 317 0 1 protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD: LOOP 347 352 348 0 1 protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD: LOOP 434 442 442 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 317 318 317 0 1 protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD: LOOP 347 352 348 0 1 protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD: LOOP 434 442 442 0 1 protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD: protocols.loops.loops_main: Pose fold tree FOLD_TREE EDGE 1 316 -1 EDGE 316 317 -1 EDGE 316 319 1 EDGE 319 318 -1 EDGE 319 442 -1 protocols.loops.loops_main: protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD: Setting extended torsions: LOOP 317 318 317 0 1 protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD: Building Loop: LOOP 317 318 317 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 1 316 -1 EDGE 316 317 -1 EDGE 316 319 1 EDGE 319 318 -1 EDGE 319 442 -1 protocols.loops.loops_main: protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD: Number of cycles: cycles2 and cycles3 2 15 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: 724.414 577.206 -23.791 -130.817 -70.332 -12.593 -121.205 155.253 50.913 299.779 protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD: 522.226 576.739 -23.791 -130.817 -68.725 -11.649 -120.651 155.359 50.914 94.847 protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD: FragCount: 90 protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD: Looptime 7 protocols.loops.loop_mover.perturb.LoopMover_Perturb_QuickCCD: ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ vdw 1.000 576.773 576.773 hbond_sr_bb 1.000 -23.791 -23.791 hbond_lr_bb 1.000 -130.817 -130.817 pair 1.000 -68.724 -68.724 rama 0.100 -117.635 -11.764 env