core.init: Rosetta version exported from http://www.rosettacommons.org core.init: command: /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/source/bin/score_jd2.linuxgccrelease -database /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database -in:file:l /mnt/hgfs/Mutagenesis_Rosetta/4KMT/2.0_Relax/20141007/list_of_pdbs_5.txt -out:file:scorefile /mnt/hgfs/Mutagenesis_Rosetta/4KMT/2.0_Relax/20141007/total_score_5.sc core.init: 'RNG device' seed mode, using '/dev/urandom', seed=256607794 seed_offset=0 real_seed=256607794 core.init.random: RandomGenerator:init: Normal mode, seed=256607794 RG_type=mt19937 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/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 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.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs protocols.jd2.PDBJobInputter: pushed /mnt/hgfs/Mutagenesis_Rosetta/4KMT/2.0_Relax/20141007/4KMT_clean_0001.pdb nstruct index 1 protocols.jd2.PDBJobInputter: pushed /mnt/hgfs/Mutagenesis_Rosetta/4KMT/2.0_Relax/20141007/4KMT_clean_0002.pdb nstruct index 1 protocols.jd2.PDBJobInputter: pushed /mnt/hgfs/Mutagenesis_Rosetta/4KMT/2.0_Relax/20141007/4KMT_clean_0003.pdb nstruct index 1 protocols.jd2.PDBJobInputter: pushed /mnt/hgfs/Mutagenesis_Rosetta/4KMT/2.0_Relax/20141007/4KMT_clean_0004.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/Mutagenesis_Rosetta/4KMT/2.0_Relax/20141007/4KMT_clean_0001.pdb core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 899 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() core.pack.dunbrack: Dunbrack 2010 library took 0.585026 seconds to load from binary protocols.jd2.JobDistributor: 4KMT_clean_0001_0001 reported success in 6 seconds protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: filling pose from PDB /mnt/hgfs/Mutagenesis_Rosetta/4KMT/2.0_Relax/20141007/4KMT_clean_0002.pdb 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.jd2.JobDistributor: 4KMT_clean_0002_0001 reported success in 3 seconds protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: filling pose from PDB /mnt/hgfs/Mutagenesis_Rosetta/4KMT/2.0_Relax/20141007/4KMT_clean_0003.pdb 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.jd2.JobDistributor: 4KMT_clean_0003_0001 reported success in 4 seconds protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: filling pose from PDB /mnt/hgfs/Mutagenesis_Rosetta/4KMT/2.0_Relax/20141007/4KMT_clean_0004.pdb 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.jd2.JobDistributor: 4KMT_clean_0004_0001 reported success in 4 seconds protocols.jd2.JobDistributor: no more batches to process... protocols.jd2.JobDistributor: 4 jobs considered, 4 jobs attempted in 18 seconds