core.init: Rosetta version exported from http://www.rosettacommons.org
core.init: command: ../../../../main/source/bin/rosetta_scripts.linuxgccrelease -parser:protocol mutation_script_new.xml -s ../starting_files/4apx_temp-ConformerNew-noGOL-noMES-noCL-1.pdb -ignore_unrecognized_res -restore_pre_talaris_2013_behavior -nstruct 1 -database ../../../../main/database -override_rsd_type_limit -overwrite -out:path:pdb ../output_files -out:path:score ../output_files
core.init: 'RNG device' seed mode, using '/dev/urandom', seed=-135269029 seed_offset=0 real_seed=-135269029
core.init.random: RandomGenerator:init: Normal mode, seed=-135269029 RG_type=mt19937
protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter
protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs
protocols.jd2.PDBJobInputter: pushed ../starting_files/4apx_temp-ConformerNew-noGOL-noMES-noCL-1.pdb nstruct index 1
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ...
protocols.jd2.JobDistributor: Parser is present. Input mover will be overwritten with whatever the parser creates.
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from PDB ../starting_files/4apx_temp-ConformerNew-noGOL-noMES-noCL-1.pdb
core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 6242 residue types
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue GLU:CtermProteinFull 208
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue HIS:CtermProteinFull 450
core.conformation.Conformation: Found disulfide between residues 224 312
core.conformation.Conformation: current variant for 224 CYS
core.conformation.Conformation: current variant for 312 CYS
core.conformation.Conformation: current variant for 224 CYD
core.conformation.Conformation: current variant for 312 CYD
core.pack.task: Packer task: initialize from command line()
protocols.rosetta_scripts.RosettaScriptsParser: dock_design_filename=mutation_script_new.xml
protocols.rosetta_scripts.RosettaScriptsParser: Parsed script:
protocols.rosetta_scripts.RosettaScriptsParser: tag is deprecated; please use instead.
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: pre_talaris_2013_standard.wts
core.scoring.ScoreFunctionFactory: SCOREFUNCTION PATCH: score12
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/PairEPotential/pdb_pair_stats_fine
basic.io.database: Database file opened: scoring/score_functions/hbonds/score12_params/HBPoly1D.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/score12_params/HBFadeIntervals.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/score12_params/HBEval.csv
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
basic.io.database: Database file opened: scoring/score_functions/rama/Rama_smooth_dyn.dat_ss_6.4
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.
core.scoring.etable: Using alternate parameters: LJ_RADIUS_SOFT in Etable construction.
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/InterchainPotential/interchain_env_log.txt
basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_pair_log.txt
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
protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "repack_only" of type RestrictToRepacking
protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "resfile_mut" of type ReadResfile
protocols.simple_filters.DdgFilter: ddg filter with threshold 1000 repeats=3 and scorefxn score12 over jump 1extreme_value_removal: 0 and repack 1
protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "dg_wt" of type Ddg
protocols.simple_filters.DdgFilter: ddg filter with threshold 1000 repeats=3 and scorefxn score12 over jump 1extreme_value_removal: 0 and repack 1
protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "dg_mut" of type Ddg
protocols.relax.FastRelax: ================== Using default script ==================
protocols.relax.FastRelax: ================== Using default script ==================
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "relax" of type FastRelax
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "ddg_calc" of type ddG
protocols.RosettaScripts.util: Object pack reading the following task_operations: Adding the following task operations
repack_only
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "pack" of type PackRotamersMover
protocols.RosettaScripts.util: Object mut_and_pack reading the following task_operations: Adding the following task operations
resfile_mut
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "mut_and_pack" of type PackRotamersMover
protocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following movers and filters
protocols.rosetta_scripts.ParsedProtocol: added mover "relax" with filter "true_filter"
protocols.rosetta_scripts.ParsedProtocol: added mover "pack" with filter "true_filter"
protocols.rosetta_scripts.ParsedProtocol: added mover "ddg_calc" with filter "true_filter"
protocols.rosetta_scripts.ParsedProtocol: added mover "mut_and_pack" with filter "true_filter"
protocols.rosetta_scripts.ParsedProtocol: added mover "ddg_calc" with filter "true_filter"
protocols::checkpoint: Deleting checkpoints of FastRelax
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from saved copy ../starting_files/4apx_temp-ConformerNew-noGOL-noMES-noCL-1.pdb
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER FastRelax - relax=======================
basic.io.database: Database file opened: scoring/score_functions/disulfides/fa_SS_distance_score
core.pack.dunbrack: Dunbrack library took 0.02 seconds to load from binary
protocols.relax.FastRelax: CMD: repeat -562.572 0 0 0.44
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 3922 rotamers at 454 positions.
core.pack.pack_rotamers: IG: 3231716 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min -1388.93 2.61149 2.61149 0.0088
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 3284 rotamers at 454 positions.
core.pack.pack_rotamers: IG: 2851008 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min -1178.22 1.7654 1.7654 0.11
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 3272 rotamers at 454 positions.
core.pack.pack_rotamers: IG: 2666232 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min -1082.83 1.43623 1.43623 0.242
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 3252 rotamers at 454 positions.
core.pack.pack_rotamers: IG: 2595600 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min -1006.25 1.27445 1.27445 0.44
protocols.relax.FastRelax: MRP: 0 -1006.25 -1006.25 1.27445 1.27445
protocols.relax.FastRelax: CMD: accept_to_best -1006.25 1.27445 1.27445 0.44
protocols.relax.FastRelax: CMD: endrepeat -1006.25 1.27445 1.27445 0.44
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 3878 rotamers at 454 positions.
core.pack.pack_rotamers: IG: 3310348 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min -1416.07 3.20721 3.20721 0.0088
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 3211 rotamers at 454 positions.
core.pack.pack_rotamers: IG: 2808084 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min -1189.84 2.45054 2.45054 0.11
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 3232 rotamers at 454 positions.
core.pack.pack_rotamers: IG: 2632320 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min -1098.52 1.81126 1.81126 0.242
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 3221 rotamers at 454 positions.
core.pack.pack_rotamers: IG: 2546104 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min -1008.29 1.72249 1.72249 0.44
protocols.relax.FastRelax: MRP: 1 -1008.29 -1008.29 1.72249 1.72249
protocols.relax.FastRelax: CMD: accept_to_best -1008.29 1.72249 1.72249 0.44
protocols.relax.FastRelax: CMD: endrepeat -1008.29 1.72249 1.72249 0.44
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 3846 rotamers at 454 positions.
core.pack.pack_rotamers: IG: 3252212 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min -1430.47 3.33925 3.33925 0.0088
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 3182 rotamers at 454 positions.
core.pack.pack_rotamers: IG: 2782244 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min -1195.97 2.34443 2.34443 0.11
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 3214 rotamers at 454 positions.
core.pack.pack_rotamers: IG: 2590032 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min -1101.99 1.82668 1.82668 0.242
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 3211 rotamers at 454 positions.
core.pack.pack_rotamers: IG: 2531820 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min -1018.02 1.42514 1.42514 0.44
protocols.relax.FastRelax: MRP: 2 -1018.02 -1018.02 1.42514 1.42514
protocols.relax.FastRelax: CMD: accept_to_best -1018.02 1.42514 1.42514 0.44
protocols.relax.FastRelax: CMD: endrepeat -1018.02 1.42514 1.42514 0.44
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 3838 rotamers at 454 positions.
core.pack.pack_rotamers: IG: 3259924 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min -1427.46 3.15115 3.15115 0.0088
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 3179 rotamers at 454 positions.
core.pack.pack_rotamers: IG: 2764576 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min -1191.88 2.28054 2.28054 0.11
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 3245 rotamers at 454 positions.
core.pack.pack_rotamers: IG: 2631692 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min -1101.6 1.97898 1.97898 0.242
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 3170 rotamers at 454 positions.
core.pack.pack_rotamers: IG: 2503340 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min -1021.95 2.06025 2.06025 0.44
protocols.relax.FastRelax: MRP: 3 -1021.95 -1021.95 2.06025 2.06025
protocols.relax.FastRelax: CMD: accept_to_best -1021.95 2.06025 2.06025 0.44
protocols.relax.FastRelax: CMD: endrepeat -1021.95 2.06025 2.06025 0.44
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 3836 rotamers at 454 positions.
core.pack.pack_rotamers: IG: 3256768 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min -1428.99 3.19946 3.19946 0.0088
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 3189 rotamers at 454 positions.
core.pack.pack_rotamers: IG: 2802952 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min -1196.6 2.37998 2.37998 0.11
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 3216 rotamers at 454 positions.
core.pack.pack_rotamers: IG: 2604700 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min -1103.99 2.31019 2.31019 0.242
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 3177 rotamers at 454 positions.
core.pack.pack_rotamers: IG: 2522624 bytes
protocols.relax.FastRelax: CMD: ramp_repack_min -1018.44 2.26069 2.26069 0.44
protocols.relax.FastRelax: MRP: 4 -1018.44 -1021.95 2.06025 2.06025
protocols.relax.FastRelax: CMD: accept_to_best -1018.44 2.26069 2.26069 0.44
protocols.relax.FastRelax: CMD: endrepeat -1018.44 2.26069 2.26069 0.44
protocols::checkpoint: Deleting checkpoints of FastRelax
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER =======================
protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER =======================
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER PackRotamersMover - pack=======================
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 2827 rotamers at 454 positions.
core.pack.pack_rotamers: IG: 2302736 bytes
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER =======================
protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER =======================
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER ddG - ddg_calc=======================
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 185 rotamers at 24 positions.
core.pack.pack_rotamers: IG: 101756 bytes
protocols.moves.RigidBodyMover: Translate: Jump (before): RT -0.703902 0.0589134 -0.70785 0.305808 -0.874328 -0.376871 -0.641096 -0.481747 0.597425 9.7683 -4.58338 5.36682
protocols.moves.RigidBodyMover: Translate: Jump (after): RT -0.703902 0.0589134 -0.70785 0.305808 -0.874328 -0.376871 -0.641096 -0.481747 0.597425 -571.792 343.18 -730.057
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 183 rotamers at 24 positions.
core.pack.pack_rotamers: IG: 94860 bytes
protocols.protein_interface_design.movers.ddG: -----------------------------------------
Scores Wghtd.Score
-----------------------------------------
fa_atr -1.860
fa_rep 0.146
fa_sol 0.979
fa_intra_rep 0.000
fa_pair 0.374
hbond_sr_bb 0.000
hbond_lr_bb 0.000
hbond_bb_sc -0.285
hbond_sc -0.029
dslf_ss_dst 0.000
dslf_cs_ang 0.000
dslf_ca_dih 0.000
rama 0.000
omega 0.000
fa_dun 0.000
p_aa_pp 0.000
ref 0.000
-----------------------------------------
Sum ddg: -0.676022
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER =======================
protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER =======================
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER PackRotamersMover - mut_and_pack=======================
core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph
core.pack.pack_rotamers: built 12135 rotamers at 454 positions.
core.pack.pack_rotamers: IG: 23477844 bytes
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER =======================
protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER =======================
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER ddG - ddg_calc=======================
core.pack.task: Packer task: initialize from command line()
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 183 rotamers at 24 positions.
core.pack.pack_rotamers: IG: 101004 bytes
protocols.moves.RigidBodyMover: Translate: Jump (before): RT -0.703902 0.0589134 -0.70785 0.305808 -0.874328 -0.376871 -0.641096 -0.481747 0.597425 9.7683 -4.58338 5.36682
protocols.moves.RigidBodyMover: Translate: Jump (after): RT -0.703902 0.0589134 -0.70785 0.305808 -0.874328 -0.376871 -0.641096 -0.481747 0.597425 -571.878 343.125 -730.015
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
core.pack.pack_rotamers: built 181 rotamers at 24 positions.
core.pack.pack_rotamers: IG: 94108 bytes
protocols.protein_interface_design.movers.ddG: -----------------------------------------
Scores Wghtd.Score
-----------------------------------------
fa_atr -1.860
fa_rep 0.146
fa_sol 0.979
fa_intra_rep 0.000
fa_pair 0.374
hbond_sr_bb 0.000
hbond_lr_bb 0.000
hbond_bb_sc -0.285
hbond_sc -0.029
dslf_ss_dst 0.000
dslf_cs_ang 0.000
dslf_ss_dih 0.000
dslf_ca_dih 0.000
rama 0.000
omega 0.000
fa_dun 0.000
p_aa_pp 0.000
ref 0.000
-----------------------------------------
Sum ddg: -0.67683
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER =======================
protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER =======================
protocols.rosetta_scripts.ParsedProtocol: setting status to success
protocols.rosetta_scripts.ParsedProtocol.REPORT: ============Begin report for ==================
protocols.rosetta_scripts.ParsedProtocol.REPORT: ============End report for ==================
protocols.rosetta_scripts.ParsedProtocol.REPORT: ============Begin report for ==================
protocols.rosetta_scripts.ParsedProtocol.REPORT: ============End report for ==================
protocols.rosetta_scripts.ParsedProtocol.REPORT: ============Begin report for ==================
protocols.rosetta_scripts.ParsedProtocol.REPORT: ============End report for ==================
protocols.rosetta_scripts.ParsedProtocol.REPORT: ============Begin report for ==================
protocols.rosetta_scripts.ParsedProtocol.REPORT: ============End report for ==================
protocols.rosetta_scripts.ParsedProtocol.REPORT: ============Begin report for ==================
protocols.rosetta_scripts.ParsedProtocol.REPORT: ============End report for ==================
protocols.jd2.JobDistributor: 4apx_temp-ConformerNew-noGOL-noMES-noCL-1_0001 reported success in 1153 seconds
protocols.jd2.JobDistributor: no more batches to process...
protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 1153 seconds
protocols::checkpoint: Deleting checkpoints of FastRelax