core.init: Checking for fconfig files in pwd and ./rosetta/flags
core.init: Rosetta version: rosetta.source.release-210 r210 2019.06+release.4d8c807 4d8c8074e4eab340e5d26c0069d807aa5a8d6978 https://www.rosettacommons.org 2019-02-08T21:17:06.810779
core.init: command: rosetta_scripts.macosclangrelease -l list -ex1 -ex2 -use_input_sc -parser:protocol motifgrat_sc.xml -script_vars context=context.pdb motif=motif.pdb rmsd=5 NCrmsd=5 clash=50 hotspots=1:4:8:10,1:4:6,1:3,2:3:4 delta=0:0,0:0,2:0,1:2 independent=0
core.init: 'RNG device' seed mode, using '/dev/urandom', seed=750879612 seed_offset=0 real_seed=750879612
core.init.random: RandomGenerator:init: Normal mode, seed=750879612 RG_type=mt19937
core.init: found database environment variable ROSETTA3_DB: /Users/dcoelho/Programs/rosetta-3.10/main/database
protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter
protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1a0k_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1a1x_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1a58_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1aa2_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1aaj_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1acf_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1ad6_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1agi_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1ahq_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1am2_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1amx_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1anu_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1aqt_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1ax8_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1ayd_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1ayi_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1az5_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1b0x_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1b1j_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1b1u_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1b7j_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1b8k_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1b9w_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1bbc_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1bd8_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1bea_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1bfg_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1bj7_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1bk7_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1bm8_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1box_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1br9_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1buo_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1bv1_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1byl_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1bz4_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1c25_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1c26_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1c2a_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1c44_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1c76_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1cdy_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1cew_I.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1chd_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1cm3_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1cqa_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1cqy_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1csp_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1cuj_A.pdb nstruct index 1
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protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1df4_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1dhn_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1dol_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1dsl_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1dto_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1dun_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1dvo_A.pdb nstruct index 1
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protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1eic_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1enh_A.pdb nstruct index 1
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protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1eoe_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1ep0_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1erv_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1et9_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1evs_A.pdb nstruct index 1
protocols.jd2.PDBJobInputter: pushed /Users/dcoelho/work/work/official-scaffolds/1ew3_A.pdb nstruct index 1
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protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ...
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from PDB /Users/dcoelho/work/work/official-scaffolds/1a0k_A.pdb
core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 696 residue types
core.chemical.GlobalResidueTypeSet: Total time to initialize 0.752862 seconds.
core.import_pose.import_pose: File '/Users/dcoelho/work/work/official-scaffolds/1a0k_A.pdb' automatically determined to be of type PDB
protocols.rosetta_scripts.RosettaScriptsParser: dock_design_filename=motifgrat_sc.xml
protocols.rosetta_scripts.RosettaScriptsParser: Variable substitution will occur with the following values: '%%NCrmsd%%'='5'; '%%clash%%'='50'; '%%context%%'='context.pdb'; '%%delta%%'='0:0,0:0,2:0,1:2'; '%%hotspots%%'='1:4:8:10,1:4:6,1:3,2:3:4'; '%%independent%%'='0'; '%%motif%%'='motif.pdb'; '%%rmsd%%'='5';
protocols.rosetta_scripts.RosettaScriptsParser: Substituted script:
protocols.rosetta_scripts.RosettaScriptsParser: Generating XML Schema for rosetta_scripts...
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Initializing schema validator...
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Validating input script...
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Parsed script:
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
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/ref2015_params/HBPoly1D.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv
basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb
basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt
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
core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop
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/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
core.scoring.ramachandran: shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated.
basic.io.database: Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb
protocols.jd2.parser.ScoreFunctionLoader: defined score function "ref15" with weights "ref2015.wts"
protocols.simple_filters.DdgFilter: ddg filter with threshold -15 repeats=1 and scorefxn commandline over jump 1extreme_value_removal: 0 and repack 1
protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "ddg" of type Ddg
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015
protocols.simple_filters.BuriedUnsatHbondFilter: WARNING! use_reporter_behavior=true, need to set one behavior to true; will use default report_all_heavy_atom_unsats:
protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "unsat" of type BuriedUnsatHbonds
protocols.simple_filters.ShapeComplementarityFilter: Structures with shape complementarity < 0.5, interface area < 0 A^2, median distance > 0 will be filtered.
protocols.simple_filters.ShapeComplementarityFilter: Ignoring residue range selection since residues2 is empty.
protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "Sc" of type ShapeComplementarity
protocols.motif_grafting.movers.MotifGraftMover: Reading XML parameters
protocols.motif_grafting.movers.MotifGraftMover: [ WARNING ] No only_allow_if_N_point_match_aa_identity option defined, the default "false" will be used
protocols.motif_grafting.movers.MotifGraftMover: [ WARNING ] No only_allow_if_C_point_match_aa_identity option defined, the default "false" will be used
protocols.motif_grafting.movers.MotifGraftMover: DONE reading XML parmeters
core.conformation.Conformation: Found disulfide between residues 11 42
core.conformation.Conformation: current variant for 11 CYS
core.conformation.Conformation: current variant for 42 CYS
core.conformation.Conformation: current variant for 11 CYD
core.conformation.Conformation: current variant for 42 CYD
core.conformation.Conformation: [ WARNING ] missing heavyatom: CO on residue LEU:AcetylatedNtermProteinFull 1
core.conformation.Conformation: [ WARNING ] missing heavyatom: OP1 on residue LEU:AcetylatedNtermProteinFull 1
core.conformation.Conformation: [ WARNING ] missing heavyatom: CP2 on residue LEU:AcetylatedNtermProteinFull 1
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue TYR:CtermProteinFull 10
core.conformation.Conformation: [ WARNING ] missing heavyatom: CO on residue PHE:AcetylatedNtermProteinFull 11
core.conformation.Conformation: [ WARNING ] missing heavyatom: OP1 on residue PHE:AcetylatedNtermProteinFull 11
core.conformation.Conformation: [ WARNING ] missing heavyatom: CP2 on residue PHE:AcetylatedNtermProteinFull 11
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue TYR:CtermProteinFull 16
core.conformation.Conformation: [ WARNING ] missing heavyatom: CO on residue ASN:AcetylatedNtermProteinFull 17
core.conformation.Conformation: [ WARNING ] missing heavyatom: OP1 on residue ASN:AcetylatedNtermProteinFull 17
core.conformation.Conformation: [ WARNING ] missing heavyatom: CP2 on residue ASN:AcetylatedNtermProteinFull 17
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue TYR:CtermProteinFull 19
core.conformation.Conformation: [ WARNING ] missing heavyatom: CO on residue GLU:AcetylatedNtermProteinFull 20
core.conformation.Conformation: [ WARNING ] missing heavyatom: OP1 on residue GLU:AcetylatedNtermProteinFull 20
core.conformation.Conformation: [ WARNING ] missing heavyatom: CP2 on residue GLU:AcetylatedNtermProteinFull 20
core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue VAL:CtermProteinFull 25
protocols.motif_grafting.movers.MotifGraftMover: RMSD tolerance settled to: 5
protocols.motif_grafting.movers.MotifGraftMover: N-/C-points RMSD tolerance settled to: 5
protocols.motif_grafting.movers.MotifGraftMover: Clash score cutoff settled to: 50
protocols.motif_grafting.movers.MotifGraftMover: Parsed combinatory size delta for fragment #1 = 0,0
protocols.motif_grafting.movers.MotifGraftMover: Parsed combinatory size delta for fragment #2 = 0,0
protocols.motif_grafting.movers.MotifGraftMover: Parsed combinatory size delta for fragment #3 = 2,0
protocols.motif_grafting.movers.MotifGraftMover: Parsed combinatory size delta for fragment #4 = 1,2
protocols.motif_grafting.movers.MotifGraftMover: [ WARNING ] No max_fragment_replacement_size defined, assuming that each motif fragment can replace a fragment of any size in the scaffold
protocols.motif_grafting.movers.MotifGraftMover: Replacement size delta for fragment #1 set by default to: 0, 0
protocols.motif_grafting.movers.MotifGraftMover: Replacement size delta for fragment #2 set by default to: 0, 0
protocols.motif_grafting.movers.MotifGraftMover: Replacement size delta for fragment #3 set by default to: 0, 0
protocols.motif_grafting.movers.MotifGraftMover: Replacement size delta for fragment #4 set by default to: 0, 0
protocols.motif_grafting.movers.MotifGraftMover: Parsed hotspot at position: 1, for fragment #1
protocols.motif_grafting.movers.MotifGraftMover: Parsed hotspot at position: 4, for fragment #1
protocols.motif_grafting.movers.MotifGraftMover: Parsed hotspot at position: 8, for fragment #1
protocols.motif_grafting.movers.MotifGraftMover: Parsed hotspot at position: 10, for fragment #1
protocols.motif_grafting.movers.MotifGraftMover: Parsed hotspot at position: 1, for fragment #2
protocols.motif_grafting.movers.MotifGraftMover: Parsed hotspot at position: 4, for fragment #2
protocols.motif_grafting.movers.MotifGraftMover: Parsed hotspot at position: 6, for fragment #2
protocols.motif_grafting.movers.MotifGraftMover: Parsed hotspot at position: 1, for fragment #3
protocols.motif_grafting.movers.MotifGraftMover: Parsed hotspot at position: 3, for fragment #3
protocols.motif_grafting.movers.MotifGraftMover: Parsed hotspot at position: 2, for fragment #4
protocols.motif_grafting.movers.MotifGraftMover: Parsed hotspot at position: 3, for fragment #4
protocols.motif_grafting.movers.MotifGraftMover: Parsed hotspot at position: 4, for fragment #4
protocols.motif_grafting.movers.MotifGraftMover: [ WARNING ] You have enabled raft_only_hotspots_by_sidechain_replacement. Opposed to fragment grafting, this option will just copy the sidechains of the hotspots, not the backbone into the target scaffold. Use this option wisely (i.e. only under the assumption of a very low rmsd).
protocols.motif_grafting.movers.MotifGraftMover: [ WARNING ] Using Full Back Bone alignment OVERRIDES fragment_replacement_size_delta different to 0:0
protocols.motif_grafting.movers.MotifGraftMover: Replacement size delta for fragment #1 FORCED by full_motif_bb_alignment to: 0, 0
protocols.motif_grafting.movers.MotifGraftMover: Replacement size delta for fragment #2 FORCED by full_motif_bb_alignment to: 0, 0
protocols.motif_grafting.movers.MotifGraftMover: Replacement size delta for fragment #3 FORCED by full_motif_bb_alignment to: 0, 0
protocols.motif_grafting.movers.MotifGraftMover: Replacement size delta for fragment #4 FORCED by full_motif_bb_alignment to: 0, 0
protocols.motif_grafting.movers.MotifGraftMover: [ WARNING ] If the number of matches in a single pose is < nstruct, when all the matches are generated the mover will stop.
protocols.motif_grafting.movers.MotifGraftMover: DONE parsing global arguments
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "motif_grafting" of type MotifGraft
protocols.minimization_packing.MinMover: Setting min on jump 1
protocols.minimization_packing.MinMover: Options chi, bb: 1, 0 omega: 1
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "rb_min" of type MinMover
protocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following movers and filters
protocols.rosetta_scripts.ParsedProtocol: added mover "motif_grafting" with filter "true_filter"
protocols.rosetta_scripts.ParsedProtocol: added mover "rb_min" with filter "true_filter"
protocols.rosetta_scripts.ParsedProtocol: added mover "NULL_MOVER" with filter "unsat"
protocols.rosetta_scripts.ParsedProtocol: added mover "NULL_MOVER" with filter "ddg"
protocols.rosetta_scripts.ParsedProtocol: added mover "NULL_MOVER" with filter "Sc"
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from saved copy /Users/dcoelho/work/work/official-scaffolds/1a0k_A.pdb
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER MotifGraft - motif_grafting=======================
protocols.motif_grafting.movers.MotifGraftMover: Executing Motif Graft Mover
protocols.motif_grafting.movers.MotifGraftMover: Target scaffold size: 130
protocols.motif_grafting.movers.MotifGraftMover: Motif size: 25
protocols.motif_grafting.movers.MotifGraftMover: contextStructure size: 107
protocols.motif_grafting.movers.MotifGraftMover: Target scaffold numChains: 1
protocols.motif_grafting.movers.MotifGraftMover: Motif numChains: 4
protocols.motif_grafting.movers.MotifGraftMover: contextStructure numChains: 1
protocols.motif_grafting.movers.MotifGraftMover: Fragments combination to be tested: 1 10 11 16 17 19 20 25
protocols.motif_grafting.movers.MotifGraftMover: [ WARNING ] For this scaffold & fragment combination there are not fragments that pass the RMSD test.
protocols.motif_grafting.movers.MotifGraftMover: Fragments combination to be tested: 1 10 11 16 17 19 20 24
protocols.motif_grafting.movers.MotifGraftMover: [ WARNING ] For this scaffold & fragment combination there are not fragments that pass the RMSD test.
protocols.motif_grafting.movers.MotifGraftMover: Fragments combination to be tested: 1 10 11 16 17 19 20 23
protocols.motif_grafting.movers.MotifGraftMover: [ WARNING ] For this scaffold & fragment combination there are not fragments that pass the RMSD test.
protocols.motif_grafting.movers.MotifGraftMover: Fragments combination to be tested: 1 10 11 16 17 19 21 25
protocols.motif_grafting.movers.MotifGraftMover: [ WARNING ] For this scaffold & fragment combination there are not fragments that pass the RMSD test.
protocols.motif_grafting.movers.MotifGraftMover: Fragments combination to be tested: 1 10 11 16 17 19 21 24
protocols.motif_grafting.movers.MotifGraftMover: [ WARNING ] For this scaffold & fragment combination there are not fragments that pass the RMSD test.
protocols.motif_grafting.movers.MotifGraftMover: Fragments combination to be tested: 1 10 11 16 17 19 21 23
protocols.motif_grafting.movers.MotifGraftMover: [ WARNING ] For this scaffold & fragment combination there are not fragments that pass the RMSD test.
protocols.motif_grafting.movers.MotifGraftMover: Fragments combination to be tested: 1 10 11 16 18 19 20 25
protocols.motif_grafting.movers.MotifGraftMover: [ WARNING ] For this scaffold & fragment combination there are not fragments that pass the RMSD test.
protocols.motif_grafting.movers.MotifGraftMover: Fragments combination to be tested: 1 10 11 16 18 19 20 24
protocols.motif_grafting.movers.MotifGraftMover: [ WARNING ] For this scaffold & fragment combination there are not fragments that pass the RMSD test.
protocols.motif_grafting.movers.MotifGraftMover: Fragments combination to be tested: 1 10 11 16 18 19 20 23
protocols.motif_grafting.movers.MotifGraftMover: [ WARNING ] For this scaffold & fragment combination there are not fragments that pass the RMSD test.
protocols.motif_grafting.movers.MotifGraftMover: Fragments combination to be tested: 1 10 11 16 18 19 21 25
protocols.motif_grafting.movers.MotifGraftMover: [ WARNING ] For this scaffold & fragment combination there are not fragments that pass the RMSD test.
protocols.motif_grafting.movers.MotifGraftMover: Fragments combination to be tested: 1 10 11 16 18 19 21 24
protocols.motif_grafting.movers.MotifGraftMover: [ WARNING ] For this scaffold & fragment combination there are not fragments that pass the RMSD test.
protocols.motif_grafting.movers.MotifGraftMover: Fragments combination to be tested: 1 10 11 16 18 19 21 23
protocols.motif_grafting.movers.MotifGraftMover: [ WARNING ] For this scaffold & fragment combination there are not fragments that pass the RMSD test.
protocols.motif_grafting.movers.MotifGraftMover: Fragments combination to be tested: 1 10 11 16 19 19 20 25
protocols.motif_grafting.movers.MotifGraftMover: Using mutation mode for clash test, with the residue: GLY
protocols.motif_grafting.movers.MotifGraftMover: In the iteration 13,there are a total of: 1 fragments in the priority queue
protocols.motif_grafting.movers.MotifGraftMover: Fragments combination to be tested: 1 10 11 16 19 19 20 24
protocols.motif_grafting.movers.MotifGraftMover: Using mutation mode for clash test, with the residue: GLY
protocols.motif_grafting.movers.MotifGraftMover: In the iteration 14,there are a total of: 2 fragments in the priority queue
protocols.motif_grafting.movers.MotifGraftMover: Fragments combination to be tested: 1 10 11 16 19 19 20 23
protocols.motif_grafting.movers.MotifGraftMover: [ WARNING ] For this scaffold & fragment combination there are not fragments that pass the RMSD test.
protocols.motif_grafting.movers.MotifGraftMover: Fragments combination to be tested: 1 10 11 16 19 19 21 25
protocols.motif_grafting.movers.MotifGraftMover: [ WARNING ] For this scaffold & fragment combination there are not fragments that pass the RMSD test.
protocols.motif_grafting.movers.MotifGraftMover: Fragments combination to be tested: 1 10 11 16 19 19 21 24
protocols.motif_grafting.movers.MotifGraftMover: Using mutation mode for clash test, with the residue: GLY
protocols.motif_grafting.movers.MotifGraftMover: In the iteration 17,there are a total of: 4 fragments in the priority queue
protocols.motif_grafting.movers.MotifGraftMover: Fragments combination to be tested: 1 10 11 16 19 19 21 23
protocols.motif_grafting.movers.MotifGraftMover: [ WARNING ] For this scaffold & fragment combination there are not fragments that pass the RMSD test.
protocols.motif_grafting.movers.MotifGraftMover: After all the iterations there are a total of: 4 fragments in the priority queue
protocols.motif_grafting.movers.MotifGraftMover: Generated 4 results.
protocols.motif_grafting.movers.MotifGraftMover: Generating a epigraft structure with overal RMSD score: 4.16317, motif maxRMDS of: 0, and clash score of: 23
core.conformation.Residue: [ WARNING ] Residue connection id changed when creating a new residue at seqpos 23
core.conformation.Residue: [ WARNING ] ResConnID info stored on the connected residue (residue 24) is now out of date!
core.conformation.Residue: [ WARNING ] Connection atom name (in src): C
Segmentation fault: 11