core.init: Rosetta version unknown:exported  from http://www.rosettacommons.org
core.init: command: /home/lulab/Julian/rosetta_src_2016.28.58794_bundle/main/source/bin/rosetta_scripts.linuxgccrelease -s Mb_b5_0b.pdb -parser:protocol design.xml -extra_res_fa HEM.params
core.init: 'RNG device' seed mode, using '/dev/urandom', seed=-24789649 seed_offset=0 real_seed=-24789649
core.init.random: RandomGenerator:init: Normal mode, seed=-24789649 RG_type=mt19937
core.init: Resolved executable path: /home/lulab/Julian/rosetta_src_2016.28.58794_bundle/main/source/build/src/release/linux/3.2/64/x86/gcc/4.7/default/rosetta_scripts.default.linuxgccrelease
core.init: Looking for database based on location of executable: /home/lulab/Julian/rosetta_src_2016.28.58794_bundle/main/database/
protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter
protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs
protocols.jd2.PDBJobInputter: pushed Mb_b5_0b.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 Mb_b5_0b.pdb
core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set.  Created 388 residue types
core.chemical.ResidueTypeSet: Total time to initialize 0.9 seconds.
core.io.pose_from_sfr.chirality_resolution: Flipping atom xyz for  H21 and  H22 for residue HEM
protocols.rosetta_scripts.RosettaScriptsParser: dock_design_filename=design.xml
protocols.rosetta_scripts.RosettaScriptsParser: Parsed script:
<ROSETTASCRIPTS>
	<SCOREFXNS>
		<tala weights=talaris2014/>
		<tala_soft weights=soft_rep/>
	</SCOREFXNS>
	<RESIDUE_SELECTORS/>
	<TASKOPERATIONS>
		<RestrictResiduesToRepacking name=no_mutate_important residues=1,2,3,4,5/>
		<RestrictToInterface distance=8.0 jump=1 name=design_interface/>
	</TASKOPERATIONS>
	<FILTERS>
		<ShapeComplementarity min_sc=0.4 name=sc_filt/>
		<PackStat chain=0 name=pack_filt repeats=1 threshold=0.5/>
		<Sasa jump=1 name=sasa_filt threshold=400 upper_threshold=10000000000000/>
		<BuriedUnsatHbonds cutoff=50 jump_number=1 name=BUH_filt scorefxn=tala/>
		<ExposedHydrophobics name=expF_filt sasa_cutoff=20 threshold=-1/>
	</FILTERS>
	<MOVERS>
		<BackrubDD bbg_move_probability=0.0 interface_distance_cutoff=8.0 moves=1000 name=move_b5 partner1=0 partner2=1 sc_move_probability=0.25 scorefxn=tala small_move_probability=0.0/>
		<PackRotamersMover name=pack scorefxn=tala_soft task_operations=no_mutate_important,design_interface/>
		<FastDesign name=design ramp_down_constraints=true repeats=8 scorefxn=tala task_operations=no_mutate_important,design_interface/>
	</MOVERS>
	<APPLY_TO_POSE/>
	<PROTOCOLS>
		<Add mover=move_b5/>
		<Add mover=pack/>
		<Add mover=design/>
		<Add filter=sc_filt/>
		<Add filter=BUH_filt/>
		<Add filter=pack_filt/>
		<Add filter=expF_filt/>
		<Add filter=sasa_filt/>
	</PROTOCOLS>
	<OUTPUT/>
</ROSETTASCRIPTS>
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: talaris2014
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
basic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine
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.ScoreFunctionLoader: defined score function "tala" with weights "talaris2014"
defined score function "tala_soft" with weights "soft_rep"
protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "no_mutate_important" of type RestrictResiduesToRepacking
protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "design_interface" of type RestrictToInterface
protocols.simple_filters.ShapeComplementarityFilter: Structures with shape complementarity < 0.4, interface area < 0 A^2 will be filtered.
protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "sc_filt" of type ShapeComplementarity
protocols.filters.PackStatFilter: Structures with packstat score 0.5 will be filtred.
protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "pack_filt" of type PackStat
protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "sasa_filt" of type Sasa
protocols.simple_filters.BuriedUnsatHbondFilter: Buried Unsatisfied Hbond filter over jump number 1 with cutoff 50
protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "BUH_filt" of type BuriedUnsatHbonds
protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "expF_filt" of type ExposedHydrophobics
core.mm.MMBondAngleLibrary: MM bond angle sets added fully assigned: 588; wildcard: 0 and 1 virtual parameter.
protocols.protein_interface_design.BackrubDDMover: backrub mover over residues: 
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "move_b5" of type BackrubDD
protocols.RosettaScripts.util: Object pack reading the following task_operations: Adding the following task operations
no_mutate_important design_interface 
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "pack" of type PackRotamersMover
protocols.relax.FastRelax: ================== Using default script ==================
protocols.RosettaScripts.util: Object design reading the following task_operations: Adding the following task operations
no_mutate_important design_interface 
protocols.relax.FastRelax: ================== Using default script ==================
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "design" of type FastDesign
protocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following movers and filters
protocols.rosetta_scripts.ParsedProtocol: added mover "move_b5" with filter "true_filter"
protocols.rosetta_scripts.ParsedProtocol: added mover "pack" with filter "true_filter"
protocols.rosetta_scripts.ParsedProtocol: added mover "design" with filter "true_filter"
protocols.rosetta_scripts.ParsedProtocol: added mover "NULL_MOVER" with filter "sc_filt"
protocols.rosetta_scripts.ParsedProtocol: added mover "NULL_MOVER" with filter "BUH_filt"
protocols.rosetta_scripts.ParsedProtocol: added mover "NULL_MOVER" with filter "pack_filt"
protocols.rosetta_scripts.ParsedProtocol: added mover "NULL_MOVER" with filter "expF_filt"
protocols.rosetta_scripts.ParsedProtocol: added mover "NULL_MOVER" with filter "sasa_filt"
protocols::checkpoint: Deleting checkpoints of FastRelax
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from saved copy Mb_b5_0b.pdb
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER BackrubDD - move_b5=======================
core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/lulab/Julian/rosetta_src_2016.28.58794_bundle/main/database/rotamer/ExtendedOpt1-5/Dunbrack10.lib.bin'.
core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.58 seconds to load from binary
basic.io.database: Database file opened: sampling/branch_angle/branch_angle_1.txt
basic.io.database: Database file opened: sampling/branch_angle/branch_angle_2.txt
protocols.backrub.BackrubMover: Segment lengths: 3-34 atoms
protocols.backrub.BackrubMover: Main chain pivot atoms: CA
protocols.backrub.BackrubMover: Adding backrub segments for residues 1-241
protocols.backrub.BackrubMover: Total Segments Added: 2391
protocols.protein_interface_design.BackrubDDMover: Backrub Segments Added: 2391
Score After PDB Load:
protocols.protein_interface_design.BackrubDDMover: ------------------------------------------------------------
 Scores                       Weight   Raw Score Wghtd.Score
------------------------------------------------------------
 fa_atr                       1.000   -1342.264   -1342.264
 fa_rep                       0.550   29764.602   16370.531
 fa_sol                       0.938     810.901     760.219
 fa_intra_rep                 0.005     791.642       3.958
 mm_bend                      1.000     324.279     324.279
 fa_elec                      0.875    -134.131    -117.365
 pro_close                    1.250       1.771       2.213
 hbond_sr_bb                  1.170     -86.135    -100.778
 hbond_lr_bb                  1.170     -12.709     -14.870
 hbond_bb_sc                  1.170     -15.839     -18.532
 hbond_sc                     1.100     -18.390     -20.229
 dslf_fa13                    1.250       0.000       0.000
 rama                         0.250     -99.167     -24.792
 omega                        0.625      50.348      31.467
 fa_dun                       0.700     585.616     409.931
 p_aa_pp                      0.400     -58.447     -23.379
 yhh_planarity                0.625       0.900       0.563
 ref                          1.000     -11.728     -11.728
---------------------------------------------------
 Total weighted score:                    16229.226
Score After Branch Angle Optimization/Side Chain Idealization:
------------------------------------------------------------
 Scores                       Weight   Raw Score Wghtd.Score
------------------------------------------------------------
 fa_atr                       1.000   -1333.462   -1333.462
 fa_rep                       0.550   29462.868   16204.577
 fa_sol                       0.938     810.074     759.445
 fa_intra_rep                 0.005     875.050       4.375
 mm_bend                      1.000     141.883     141.883
 fa_elec                      0.875    -124.839    -109.234
 pro_close                    1.250       1.771       2.213
 hbond_sr_bb                  1.170     -86.135    -100.778
 hbond_lr_bb                  1.170     -12.709     -14.870
 hbond_bb_sc                  1.170     -13.977     -16.353
 hbond_sc                     1.100     -13.441     -14.785
 dslf_fa13                    1.250       0.000       0.000
 rama                         0.250     -99.167     -24.792
 omega                        0.625      50.348      31.467
 fa_dun                       0.700     585.616     409.931
 p_aa_pp                      0.400     -58.447     -23.379
 yhh_planarity                0.625       0.900       0.563
 ref                          1.000     -11.728     -11.728
---------------------------------------------------
 Total weighted score:                    15905.073
Running 1000 trials...
core.pack.task: Packer task: initialize from command line() 
protocols.moves.TrialCounter:      br_CA_CA_04 trials=     67;  accepts= 0.3284;  energy_drop/trial=  -3.70692
protocols.moves.TrialCounter:      br_CA_CA_07 trials=     74;  accepts= 0.4459;  energy_drop/trial= -17.18577
protocols.moves.TrialCounter:      br_CA_CA_10 trials=     59;  accepts= 0.3220;  energy_drop/trial=  -4.71764
protocols.moves.TrialCounter:      br_CA_CA_13 trials=     75;  accepts= 0.2000;  energy_drop/trial=  -5.02642
protocols.moves.TrialCounter:      br_CA_CA_16 trials=     60;  accepts= 0.2667;  energy_drop/trial= -21.71157
protocols.moves.TrialCounter:      br_CA_CA_19 trials=     74;  accepts= 0.3378;  energy_drop/trial= -11.04677
protocols.moves.TrialCounter:      br_CA_CA_22 trials=     68;  accepts= 0.3529;  energy_drop/trial= -18.14749
protocols.moves.TrialCounter:      br_CA_CA_25 trials=     80;  accepts= 0.2625;  energy_drop/trial= -21.36113
protocols.moves.TrialCounter:      br_CA_CA_28 trials=     51;  accepts= 0.2941;  energy_drop/trial= -20.34855
protocols.moves.TrialCounter:      br_CA_CA_31 trials=     56;  accepts= 0.1964;  energy_drop/trial=  -8.19174
protocols.moves.TrialCounter:      br_CA_CA_34 trials=     75;  accepts= 0.2800;  energy_drop/trial= -14.35806
protocols.moves.TrialCounter:       sc_chi_rot trials=    239;  accepts= 0.2594;  energy_drop/trial=  -4.75143
protocols.moves.TrialCounter:      sc_chi_unif trials=     22;  accepts= 0.0455;  energy_drop/trial=  -0.01662
protocols.protein_interface_design.BackrubDDMover: Last Score:
protocols.protein_interface_design.BackrubDDMover: ------------------------------------------------------------
 Scores                       Weight   Raw Score Wghtd.Score
------------------------------------------------------------
 fa_atr                       1.000   -1296.914   -1296.914
 fa_rep                       0.550    9428.505    5185.678
 fa_sol                       0.938     773.133     724.812
 fa_intra_rep                 0.005     872.068       4.360
 mm_bend                      1.000     147.695     147.695
 fa_elec                      0.875     -90.564     -79.243
 pro_close                    1.250       1.771       2.213
 hbond_sr_bb                  1.170     -76.532     -89.542
 hbond_lr_bb                  1.170      -9.104     -10.652
 hbond_bb_sc                  1.170      -8.492      -9.936
 hbond_sc                     1.100      -7.653      -8.418
 dslf_fa13                    1.250       0.000       0.000
 rama                         0.250     -80.339     -20.085
 omega                        0.625      50.348      31.467
 fa_dun                       0.700     581.841     407.289
 p_aa_pp                      0.400     -50.792     -20.317
 yhh_planarity                0.625       0.900       0.563
 ref                          1.000     -11.728     -11.728
---------------------------------------------------
 Total weighted score:                     4957.241
Low Score:
------------------------------------------------------------
 Scores                       Weight   Raw Score Wghtd.Score
------------------------------------------------------------
 fa_atr                       1.000   -1296.914   -1296.914
 fa_rep                       0.550    9428.505    5185.678
 fa_sol                       0.938     773.133     724.812
 fa_intra_rep                 0.005     872.068       4.360
 mm_bend                      1.000     147.695     147.695
 fa_elec                      0.875     -90.564     -79.243
 pro_close                    1.250       1.771       2.213
 hbond_sr_bb                  1.170     -76.532     -89.542
 hbond_lr_bb                  1.170      -9.104     -10.652
 hbond_bb_sc                  1.170      -8.492      -9.936
 hbond_sc                     1.100      -7.653      -8.418
 dslf_fa13                    1.250       0.000       0.000
 rama                         0.250     -80.339     -20.085
 omega                        0.625      50.348      31.467
 fa_dun                       0.700     581.841     407.289
 p_aa_pp                      0.400     -50.792     -20.317
 yhh_planarity                0.625       0.900       0.563
 ref                          1.000     -11.728     -11.728
---------------------------------------------------
 Total weighted score:                     4957.241
protocols.simple_moves.BBGaussianMover: Final factorA=0.5
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER =======================
protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER =======================
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER PackRotamersMover - pack=======================
Illegal instruction