core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: rosetta.binary.linux.release-315 r315 2022.12+release.a4d7970 a4d79705213bc2acd6b51e370eddbb2738df6866 https://www.rosettacommons.org 2022-03-22T15:27:26.590656 core.init: command: /home/newdisk1/rosetta.binary.linux.release-315/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease -parser:protocol /home/zhengjishen/Desktop/caolongxing_protocol/cao_2021_protocol/paper_interface_design.xml -beta_nov16 -in:file:silent /home/newdisk1/binder_design/pilot_splits/xah.silent -keep_input_scores False -silent_read_through_errors -out:file:silent out.silent -out:file:silent_struct_type binary -mute protocols.rosetta_scripts.ParsedProtocol.REPORT -parser:script_vars CAO_2021_PROTOCOL=/home/zhengjishen/Desktop/caolongxing_protocol/cao_2021_protocol @/home/newdisk1/binder_design/design.flags basic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-1477614056 seed_offset=0 real_seed=-1477614056 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-1477614056 RG_type=mt19937 core.init: Resolved executable path: /home/newdisk1/rosetta.binary.linux.release-315/main/source/build/src/release/linux/5.13/64/x86/gcc/9/hdf5/rosetta_scripts.hdf5.linuxgccrelease core.init: Looking for database based on location of executable: /home/newdisk1/rosetta.binary.linux.release-315/main/database/ core.io.silent.SilentFileData: Reading all structures from /home/newdisk1/binder_design/pilot_splits/xah.silent core.io.silent.SilentFileData: Finished reading 20 structures from /home/newdisk1/binder_design/pilot_splits/xah.silent protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 983 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.703869 seconds. core.conformation.Conformation: Found disulfide between residues 81 117 core.conformation.Conformation: current variant for 81 CYS core.conformation.Conformation: current variant for 117 CYS core.conformation.Conformation: current variant for 81 CYD core.conformation.Conformation: current variant for 117 CYD protocols.rosetta_scripts.RosettaScriptsParser: dock_design_filename=/home/zhengjishen/Desktop/caolongxing_protocol/cao_2021_protocol/paper_interface_design.xml protocols.rosetta_scripts.RosettaScriptsParser: Variable substitution will occur with the following values: '%%CAO_2021_PROTOCOL%%'='/home/zhengjishen/Desktop/caolongxing_protocol/cao_2021_protocol'; '%%patchdock_res%%'='4,5,8,12,13'; '%%runpsipred_single%%'='/home/zhengjishen/Desktop/psipred/runpsipred_single'; protocols.rosetta_scripts.RosettaScriptsParser: Substituted script: # Brian Coventry and Longxing Cao 2020 # Derived (20 versions later) from protocol by Franziska Seeger, TaYi Yu, and Danny Sahtoe # This file contains a lot of arbitrary decisions that may or may not actually improve binding # To this end, BC went through and labeled lines with # X / 3 where X refers to how important this is # # 0 / 3 -- truly arbitrary # # 1 / 3 -- might help # # 2 / 3 -- definitely helps # # 3 / 3 -- protocol relies on this # It's hard to experimentally test all parts of xmls, but hopefully these numbers will give you a guideline # as to what is arbitary and what is important # 0 / 3 -- beta_nov16 vs ref2015. Beta16 was touted as the best, unclear if it is. # Should sfxn_relax be a vanilla ScoreFunction? Open question -- required for StructProfileMover # 1 / 3 -- Early we thought these were key, unclear now # 2 / 3 -- approx works on the computer, however unclear # how much buns matter in real life # 1 / 3 -- seemed like a good idea at the time # 1 / 3 -- interface size. 8 - 12 seems reasonable # at 8, you have trouble with ARG and LYS though # These are the default paramters to the old TaskOperation LayerDesign # 2 / 3 -- This is 3 / 3 if you don't have approx, StructProfile, and sap Rosetta will put hydrophobics on your surface and polars in your core We do need core polars for interfaces though # 2 / 3 -- penalize TRP by 3. This leads to a reasonable number of TRP given everything else # 2 / 3 -- Rosetta loves MET, but the Bakerlab doesn't. # 2 / 3 -- Bad way to prevent totally hydrophobic interfaces. The SapConstraint is a much better method here, but we didn't develop it until after we finished these designs. See adjust_total_netcharge.xml for ideas on how to use it. # 2 / 3 -- You can get by without this, but it gives a massive increase to your success in experimental folding (and mismatch_probability) # 2 / 3 -- see approx comments above. With both enabled, this mostly serves to speed up packing # 3 / 3 -- Massive improvement. Without this, Rosetta leaves your interface full of holes where obvious things can go. Upweighting by 2 is also reasonable here. # 0 / 3 -- distance cutoff # 1 / 3 -- With this, you get to reuse minimized rotamers. This hasn't been tested # 1 / 3 -- Bakerlab folklore. Some people don't like this. # 2 / 3 -- This has been extensively tested. ex2 wastes time without improving results. ex2aro is hardly a slowdown and improves results. ex1 is a slowdown, but also improves results. Improved results are on the computer, not biochemically. # 1 / 3 -- For rifdock, we found it's better to allow the rifres to redesign. For motif graft, we haven't tested it as much, but with the complicated process that goes into picking the motif residues, we think it's probably better to keep them. (Motif picking is on fully relaxed structures whereas rifdock is very low res) # 1 / 3 -- Bakerlab folklore # 1 / 3 -- Bakerlab folklore # 2 / 3 -- This makes sense, don't drop PRO and GLY # 0 / 3 -- Honestly, this might even hurt, but it gives a massive 2-3x speedup # 1 / 3 -- bb min? We haven't tested it # 3 / 3 -- relax script. The rosettacon2018 relax script gives much better performance than the original FastRelax-based one. Newer ones likely work too. # 1 / 3 -- cartesian. Through much testing, cartesian artifically gives better numbers. However, controlled experiments will show that the sequences it produce do not have intrinsically better metrics. It's also way slower. # 0 / 3 -- min_type. We haven't tested this very much. # 1 / 3 -- old ref weights. It's just what we've always used. Our aa_comps are trained based on these. # 2 / 3 -- flexible binder backbone. We haven't explicitly tested this, but we feel it's important # 1 / 3 -- fixed target backbone. Cuts down on metric noise and prevents rosetta from doing bad things # 3 / 3 -- You absolutely must let the two proteins move relative to one another # 1 / 3 -- Do you even need to run FastRelax? We've never actually tested it. # apply sequence constraints # perform sequence optimization # calculate interface metrics protocols.rosetta_scripts.RosettaScriptsParser: Validating input script... protocols.rosetta_scripts.RosettaScriptsSchemaValidator: Generating XML Schema for rosetta_scripts... protocols.rosetta_scripts.RosettaScriptsSchemaValidator: ...done protocols.rosetta_scripts.RosettaScriptsSchemaValidator: Initializing schema validator... protocols.rosetta_scripts.RosettaScriptsSchemaValidator: ...done protocols.rosetta_scripts.RosettaScriptsParser: ...done protocols.rosetta_scripts.RosettaScriptsParser: Parsed script: core.scoring.ScoreFunctionFactory: SCOREFUNCTION: beta_nov16.wts 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_beta_nov2016/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/rama/fd_beta_nov2016/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 basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/hydroxyl_torsion_preference.txt 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 "sfxn" with weights "beta_nov16" protocols.jd2.parser.ScoreFunctionLoader: defined score function "sfxn_relax" with weights "beta_nov16" protocols.jd2.parser.ScoreFunctionLoader: setting sfxn_relax weight arg_cation_pi to 3 protocols.jd2.parser.ScoreFunctionLoader: setting sfxn_relax weight approximate_buried_unsat_penalty to 5 protocols.jd2.parser.ScoreFunctionLoader: defined score function "sfxn_design" with weights "beta_nov16" protocols.jd2.parser.ScoreFunctionLoader: setting sfxn_design weight res_type_constraint to 1.5 protocols.jd2.parser.ScoreFunctionLoader: setting sfxn_design weight aa_composition to 1 protocols.jd2.parser.ScoreFunctionLoader: setting sfxn_design weight arg_cation_pi to 3 protocols.jd2.parser.ScoreFunctionLoader: setting sfxn_design weight approximate_buried_unsat_penalty to 5 protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "PR_monomer_core_sel" of type SelectBySASA protocols.residue_selectors.TaskSelector: Adding task operation PR_monomer_core_sel core.select.residue_selector.LayerSelector: Setting LayerSelector to use sidechain neighbors to determine burial. core.select.residue_selector.LayerSelector: Set cutoffs for core and surface to 5.2 and 2, respectively, in LayerSelector. core.select.residue_selector.LayerSelector: Setting core=false boundary=false surface=true in LayerSelector. core.select.residue_selector.LayerSelector: Setting LayerSelector to use sidechain neighbors to determine burial. core.select.residue_selector.LayerSelector: Set cutoffs for core and surface to 5.2 and 2, respectively, in LayerSelector. core.select.residue_selector.LayerSelector: Setting LayerSelector to use sidechain neighbors to determine burial. core.select.residue_selector.LayerSelector: Set cutoffs for core and surface to 5.2 and 2, respectively, in LayerSelector. core.select.residue_selector.LayerSelector: Setting core=false boundary=true surface=false in LayerSelector. core.select.residue_selector.LayerSelector: Setting LayerSelector to use sidechain neighbors to determine burial. core.select.residue_selector.LayerSelector: Set cutoffs for core and surface to 5.2 and 2, respectively, in LayerSelector. core.select.residue_selector.LayerSelector: Setting LayerSelector to use sidechain neighbors to determine burial. core.select.residue_selector.LayerSelector: Set cutoffs for core and surface to 5.2 and 2, respectively, in LayerSelector. core.select.residue_selector.LayerSelector: Setting core=true boundary=false surface=false in LayerSelector. core.select.residue_selector.LayerSelector: Setting LayerSelector to use sidechain neighbors to determine burial. core.select.residue_selector.LayerSelector: Set cutoffs for core and surface to 5.2 and 2, respectively, in LayerSelector. core.select.residue_selector.PrimarySequenceNeighborhoodSelector: Using residue selector entire_helix core.select.residue_selector.PrimarySequenceNeighborhoodSelector: Using residue selector helix_cap protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "layer_design_F_boundary_M" of type DesignRestrictions protocols.aa_composition.AddCompositionConstraintMover: Read composition contraint from tags.Initialized AACompositionConstraint object from file contents: PENALTY_DEFINITION TYPE TRP ABSOLUTE 0 PENALTIES 0 3 DELTA_START 0 DELTA_END 1 BEFORE_FUNCTION CONSTANT AFTER_FUNCTION LINEAR END_PENALTY_DEFINITION protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "3trp" of type AddCompositionConstraintMover protocols.aa_composition.AddCompositionConstraintMover: Read composition contraint from tags.Initialized AACompositionConstraint object from file contents: PENALTY_DEFINITION TYPE MET ABSOLUTE 0 PENALTIES 0 2 DELTA_START 0 DELTA_END 1 BEFORE_FUNCTION CONSTANT AFTER_FUNCTION LINEAR END_PENALTY_DEFINITION protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "2met" of type AddCompositionConstraintMover protocols.aa_composition.AddCompositionConstraintMover: Read composition contraint from tags.Initialized AACompositionConstraint object from file contents: PENALTY_DEFINITION TYPE ASP GLU HIS LYS ASN GLN ARG SER THR TYR FRACT_DELTA_START -0.01 FRACT_DELTA_END 0.0 PENALTIES 0.1 0 FRACTION 0.30 BEFORE_FUNCTION QUADRATIC AFTER_FUNCTION CONSTANT END_PENALTY_DEFINITION protocols.aa_composition.AddCompositionConstraintMover: Set selector name to for_hydrophobic. protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "30_percent_polar" of type AddCompositionConstraintMover basic.io.database: Database file opened: scoring/score_functions/P_AA_SS_cen6/P_AA_SS_cen6.txt core.indexed_structure_store.H5FragmentStoreBackend: Loading backend: /home/zhengjishen/Desktop/ss_grouped_vall_all.h5 core.indexed_structure_store.FragmentStoreManager: database loaded! protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "genProfile" of type StructProfileMover protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "prune_buried_unsats" of type PruneBuriedUnsats protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "upweight_interface" of type ProteinProteinInterfaceUpweighter protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "pack_long" of type ProteinInterfaceDesign core.pack.task.operation.TaskOperation: TaskOperation::parse_tag method called with no effect for Tag with type IncludeCurrent. Probably due to (un/mis)implemented virtual method in derived class. protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "current" of type IncludeCurrent protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "limitchi2" of type LimitAromaChi2 protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "ex1_ex2" of type ExtraRotamersGeneric protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "restrict_target_not_interface" of type OperateOnResidueSubset protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "restrict_to_interface" of type OperateOnResidueSubset protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "restrict_target2repacking" of type OperateOnResidueSubset protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "restrict_hotspots2repacking" of type OperateOnResidueSubset protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "disallow_GLY" of type DisallowIfNonnative protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "disallow_PRO" of type DisallowIfNonnative protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "restrict_PRO_GLY" of type OperateOnResidueSubset protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "PR_monomer_core" of type SelectBySASA core.scoring.ScoreFunctionFactory: SCOREFUNCTION: beta_nov16.wts protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "chain1only" of type SwitchChainOrder core.pack.task.xml_util: Object min reading the following task_operations: Adding the following task operations pack_long protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "min" of type TaskAwareMinMover protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "clear_constraints" of type ClearConstraintsMover protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "interface_buried_sasa" of type Sasa protocols.simple_filters.DdgFilter: ddg filter with threshold -10 and threshold_min -999999 repeats=5 and scorefxn sfxn extreme_value_removal: 1 and repack 1 protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "ddg" of type Ddg protocols.simple_filters.ShapeComplementarityFilter: Structures with shape complementarity < 0.55, interface area < 0 A^2, median distance > 0 will be filtered. protocols.simple_filters.ShapeComplementarityFilter: Ignoring residue range selection since residues2 is empty. protocols.simple_filters.ShapeComplementarityFilter: Using Jump Selector to define surfaces. protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "interface_sc" of type ShapeComplementarity protocols.simple_filters.ScoreTypeFilter: ScoreType filter for score_type total_score with threshold 0. protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "total_score_MBF" of type ScoreType protocols.filters.Filter: Setting MoveBeforeFilter for mover 'chain1only' and filter 'total_score_MBF' protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "total_score_monomer" of type MoveBeforeFilter core.select.residue_selector.util: [ WARNING ] Selector name is empty! protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "res_count_MBF" of type ResidueCount protocols.filters.Filter: Setting MoveBeforeFilter for mover 'chain1only' and filter 'res_count_MBF' protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "res_count_monomer" of type MoveBeforeFilter protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "score_per_res" of type CalculatorFilter core.scoring.ScoreFunctionFactory: SCOREFUNCTION: beta_nov16.wts protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "buns_heavy_ball_1.1D" of type BuriedUnsatHbonds protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "contact_molecular_surface" of type ContactMolecularSurface protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "contact_patch" of type ContactMolecularSurface protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "contact_patch_apolar" of type ContactMolecularSurface protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "contact_patch_apolar_sq5" of type ContactMolecularSurface protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "pre_mismatch_probability" of type SSPrediction protocols.filters.Filter: Setting MoveBeforeFilter for mover 'chain1only' and filter 'pre_mismatch_probability' protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "mismatch_probability" of type MoveBeforeFilter core.select.residue_selector.util: [ WARNING ] Selector name is empty! protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "ss_sc_pre" of type SSShapeComplementarity protocols.filters.Filter: Setting MoveBeforeFilter for mover 'chain1only' and filter 'ss_sc_pre' protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "ss_sc" of type MoveBeforeFilter protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "contact_molecular_surface_ap_target" of type ContactMolecularSurface protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "contact_molec_sq5_ap_target" of type ContactMolecularSurface protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "contact_molecular_surface_apap_target" of type ContactMolecularSurface protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "contact_molec_sq5_apap_target" of type ContactMolecularSurface protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "contact_molecular_surface_ap_binder" of type ContactMolecularSurface protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "contact_molec_sq5_ap_binder" of type ContactMolecularSurface protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "contact_molecular_surface_apap_binder" of type ContactMolecularSurface protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "contact_molec_sq5_apap_binder" of type ContactMolecularSurface protocols.rosetta_scripts.RosettaScriptsParser: Defined filter named "timed" of type Time protocols.relax.RelaxScriptManager: Reading relax scripts list from database. core.scoring.ScoreFunctionFactory: SCOREFUNCTION: beta_nov16.wts protocols.relax.RelaxScriptManager: Looking for MonomerRelax2019.txt protocols.relax.RelaxScriptManager: ================== Reading script file: /home/newdisk1/rosetta.binary.linux.release-315/main/database/sampling/relax_scripts/MonomerRelax2019.txt ================== protocols.relax.RelaxScriptManager: repeat %%nrepeats%% protocols.relax.RelaxScriptManager: coord_cst_weight 1.0 protocols.relax.RelaxScriptManager: scale:fa_rep 0.040 protocols.relax.RelaxScriptManager: repack protocols.relax.RelaxScriptManager: scale:fa_rep 0.051 protocols.relax.RelaxScriptManager: min 0.01 protocols.relax.RelaxScriptManager: coord_cst_weight 0.5 protocols.relax.RelaxScriptManager: scale:fa_rep 0.265 protocols.relax.RelaxScriptManager: repack protocols.relax.RelaxScriptManager: scale:fa_rep 0.280 protocols.relax.RelaxScriptManager: min 0.01 protocols.relax.RelaxScriptManager: coord_cst_weight 0.0 protocols.relax.RelaxScriptManager: scale:fa_rep 0.559 protocols.relax.RelaxScriptManager: repack protocols.relax.RelaxScriptManager: scale:fa_rep 0.581 protocols.relax.RelaxScriptManager: min 0.01 protocols.relax.RelaxScriptManager: coord_cst_weight 0.0 protocols.relax.RelaxScriptManager: scale:fa_rep 1 protocols.relax.RelaxScriptManager: repack protocols.relax.RelaxScriptManager: min 0.00001 protocols.relax.RelaxScriptManager: accept_to_best protocols.relax.RelaxScriptManager: endrepeat core.pack.task.xml_util: Object FastDesign reading the following task_operations: Adding the following task operations current limitchi2 ex1_ex2 restrict_to_interface restrict_target2repacking restrict_hotspots2repacking disallow_GLY disallow_PRO PR_monomer_core upweight_interface restrict_PRO_GLY prune_buried_unsats layer_design_F_boundary_M protocols.relax.RelaxScriptManager: ================== Reading script file: /home/zhengjishen/Desktop/caolongxing_protocol/cao_2021_protocol/old_beta_16_ref.rosettacon2018.txt ================== protocols.relax.RelaxScriptManager: repeat %%nrepeats%% protocols.relax.RelaxScriptManager: reference 1.8394 3.6196 -2.3716 -2.7348 1.0402 0.8370 -0.4546 0.7329 -1.5107 0.1807 0.6092 -0.9369 -2.4119 -0.1884 -1.2888 -0.7783 -1.0874 1.9342 1.6906 1.2797 protocols.relax.RelaxScriptManager: ramp_repack_min 0.079 0.01 1.0 protocols.relax.RelaxScriptManager: reference 1.8394 3.6196 -2.3716 -2.7348 1.0402 0.8370 -0.4546 0.7329 -1.5107 0.1807 0.6092 -0.9369 -2.4119 -0.1884 -1.2888 -0.7783 -1.0874 1.9342 1.6906 1.2797 protocols.relax.RelaxScriptManager: ramp_repack_min 0.295 0.01 0.5 protocols.relax.RelaxScriptManager: reference 1.8394 3.6196 -2.3716 -2.7348 1.0402 0.8370 -0.4546 0.7329 -1.5107 0.1807 0.6092 -0.9369 -2.4119 -0.1884 -1.2888 -0.7783 -1.0874 1.9342 1.6906 1.2797 protocols.relax.RelaxScriptManager: ramp_repack_min 0.577 0.01 0.0 protocols.relax.RelaxScriptManager: reference 1.8394 3.6196 -2.3716 -2.7348 1.0402 0.8370 -0.4546 0.7329 -1.5107 0.1807 0.6092 -0.9369 -2.4119 -0.1884 -1.2888 -0.7783 -1.0874 1.9342 1.6906 1.2797 protocols.relax.RelaxScriptManager: ramp_repack_min 1 0.00001 0.0 protocols.relax.RelaxScriptManager: accept_to_best protocols.relax.RelaxScriptManager: endrepeat protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "FastDesign" of type FastDesign core.scoring.ScoreFunctionFactory: SCOREFUNCTION: beta_nov16.wts core.pack.task.xml_util: Object FastRelax reading the following task_operations: Adding the following task operations restrict_target_not_interface ex1_ex2 limitchi2 prune_buried_unsats core.select.movemap.util: Found MoveMapFactory MM protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "FastRelax" of type FastRelax protocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following settings protocols.rosetta_scripts.ParsedProtocol: Added filter "timed" protocols.rosetta_scripts.ParsedProtocol: Added mover "3trp" protocols.rosetta_scripts.ParsedProtocol: Added mover "2met" protocols.rosetta_scripts.ParsedProtocol: Added mover "30_percent_polar" protocols.rosetta_scripts.ParsedProtocol: Added mover "genProfile" protocols.rosetta_scripts.ParsedProtocol: Added mover "FastDesign" protocols.rosetta_scripts.ParsedProtocol: Added mover "FastDesign" protocols.rosetta_scripts.ParsedProtocol: Added mover "clear_constraints" protocols.rosetta_scripts.ParsedProtocol: Added mover "FastRelax" protocols.rosetta_scripts.ParsedProtocol: Added filter "interface_buried_sasa" protocols.rosetta_scripts.ParsedProtocol: Added filter "ddg" protocols.rosetta_scripts.ParsedProtocol: Added filter "interface_sc" protocols.rosetta_scripts.ParsedProtocol: Added filter "score_per_res" protocols.rosetta_scripts.ParsedProtocol: Added filter "buns_heavy_ball_1.1D" protocols.rosetta_scripts.ParsedProtocol: Added filter "mismatch_probability" protocols.rosetta_scripts.ParsedProtocol: Added filter "contact_molecular_surface" protocols.rosetta_scripts.ParsedProtocol: Added filter "contact_patch" protocols.rosetta_scripts.ParsedProtocol: Added filter "contact_patch_apolar" protocols.rosetta_scripts.ParsedProtocol: Added filter "contact_patch_apolar_sq5" protocols.rosetta_scripts.ParsedProtocol: Added filter "ss_sc" protocols.rosetta_scripts.ParsedProtocol: Added filter "contact_molecular_surface_ap_target" protocols.rosetta_scripts.ParsedProtocol: Added filter "contact_molec_sq5_ap_target" protocols.rosetta_scripts.ParsedProtocol: Added filter "contact_molecular_surface_apap_target" protocols.rosetta_scripts.ParsedProtocol: Added filter "contact_molec_sq5_apap_target" core.simple_metrics.util: Added simple metric SapScoreMetric. protocols.rosetta_scripts.ParsedProtocol: Added metrics: "sap_score" core.simple_metrics.util: Added simple metric SapScoreMetric. protocols.rosetta_scripts.ParsedProtocol: Added metrics: "sap_score_target" core.simple_metrics.util: Added simple metric CalculatorMetric. protocols.rosetta_scripts.ParsedProtocol: Added metrics: "binder_delta_sap" core.simple_metrics.util: Added simple metric CalculatorMetric. protocols.rosetta_scripts.ParsedProtocol: Added metrics: "target_delta_sap" protocols.rosetta_scripts.ParsedProtocol: Added filter "timed" core.conformation.Conformation: Found disulfide between residues 81 117 core.conformation.Conformation: current variant for 81 CYS core.conformation.Conformation: current variant for 117 CYS core.conformation.Conformation: current variant for 81 CYD core.conformation.Conformation: current variant for 117 CYD protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER timed======================= protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER timed======================= protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER AddCompositionConstraintMover - 3trp======================= protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER AddCompositionConstraintMover - 2met======================= protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER AddCompositionConstraintMover - 30_percent_polar======================= protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER StructProfileMover - genProfile======================= core.chemical.GlobalResidueTypeSet: Finished initializing centroid residue type set. Created 69 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.065538 seconds. basic.io.database: Database file opened: scoring/score_functions/SecondaryStructurePotential/phi.theta.36.HS.resmooth basic.io.database: Database file opened: scoring/score_functions/SecondaryStructurePotential/phi.theta.36.SS.resmooth protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER FastDesign - FastDesign======================= core.select.residue_selector.NeighborhoodResidueSelector: [ WARNING ] ################ Cloning pose and building neighbor graph ################ core.select.residue_selector.NeighborhoodResidueSelector: [ WARNING ] Ensure that pose is either scored or has update_residue_neighbors() called core.select.residue_selector.NeighborhoodResidueSelector: [ WARNING ] before using NeighborhoodResidueSelector for maximum performance! core.select.residue_selector.NeighborhoodResidueSelector: [ WARNING ] ########################################################################## core.select.residue_selector.NeighborhoodResidueSelector: [ WARNING ] ################ Cloning pose and building neighbor graph ################ core.select.residue_selector.NeighborhoodResidueSelector: [ WARNING ] Ensure that pose is either scored or has update_residue_neighbors() called core.select.residue_selector.NeighborhoodResidueSelector: [ WARNING ] before using NeighborhoodResidueSelector for maximum performance! core.select.residue_selector.NeighborhoodResidueSelector: [ WARNING ] ########################################################################## protocols.pack_interface.ProteinProteinInterfaceUpweighterTaskOperation: Packer Energies between the interface residues are upweighted by factor 3. core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] protocols.denovo_design.movers.FastDesign: #Packer_Task protocols.denovo_design.movers.FastDesign: protocols.denovo_design.movers.FastDesign: Threads to request: ALL AVAILABLE protocols.denovo_design.movers.FastDesign: protocols.denovo_design.movers.FastDesign: resid pack? design? allowed_aas protocols.denovo_design.movers.FastDesign: 1 FALSE FALSE protocols.denovo_design.movers.FastDesign: 2 FALSE FALSE protocols.denovo_design.movers.FastDesign: 3 FALSE FALSE protocols.denovo_design.movers.FastDesign: 4 FALSE FALSE protocols.denovo_design.movers.FastDesign: 5 FALSE FALSE protocols.denovo_design.movers.FastDesign: 6 FALSE FALSE protocols.denovo_design.movers.FastDesign: 7 FALSE FALSE protocols.denovo_design.movers.FastDesign: 8 FALSE FALSE protocols.denovo_design.movers.FastDesign: 9 FALSE FALSE protocols.denovo_design.movers.FastDesign: 10 FALSE FALSE protocols.denovo_design.movers.FastDesign: 11 FALSE FALSE protocols.denovo_design.movers.FastDesign: 12 FALSE FALSE protocols.denovo_design.movers.FastDesign: 13 TRUE TRUE ALA,ASP,GLU,PHE,HIS,HIS_D,ILE,LYS,LEU,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR protocols.denovo_design.movers.FastDesign: 14 TRUE TRUE ASP,ASN,SER,THR protocols.denovo_design.movers.FastDesign: 15 FALSE FALSE protocols.denovo_design.movers.FastDesign: 16 TRUE TRUE ALA,ASP,GLU,PHE,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR protocols.denovo_design.movers.FastDesign: 17 FALSE FALSE protocols.denovo_design.movers.FastDesign: 18 FALSE FALSE protocols.denovo_design.movers.FastDesign: 19 TRUE TRUE ALA,ASP,GLU,PHE,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR protocols.denovo_design.movers.FastDesign: 20 TRUE TRUE ALA,ASP,GLU,PHE,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR protocols.denovo_design.movers.FastDesign: 21 FALSE FALSE protocols.denovo_design.movers.FastDesign: 22 TRUE TRUE GLU,HIS,HIS_D,LYS,GLN,ARG protocols.denovo_design.movers.FastDesign: 23 TRUE TRUE ALA,ASP,GLU,PHE,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR protocols.denovo_design.movers.FastDesign: 24 FALSE FALSE protocols.denovo_design.movers.FastDesign: 25 FALSE FALSE protocols.denovo_design.movers.FastDesign: 26 TRUE TRUE GLU,HIS,HIS_D,LYS,GLN,ARG protocols.denovo_design.movers.FastDesign: 27 TRUE TRUE ALA,ASP,GLU,PHE,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR protocols.denovo_design.movers.FastDesign: 28 FALSE FALSE protocols.denovo_design.movers.FastDesign: 29 FALSE FALSE protocols.denovo_design.movers.FastDesign: 30 TRUE TRUE GLU,HIS,HIS_D,LYS,GLN,ARG protocols.denovo_design.movers.FastDesign: 31 FALSE FALSE protocols.denovo_design.movers.FastDesign: 32 TRUE TRUE ALA,ASP,GLU,PHE,HIS,HIS_D,ILE,LYS,LEU,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR protocols.denovo_design.movers.FastDesign: 33 TRUE TRUE ALA,ASP,GLU,PHE,HIS,HIS_D,ILE,LYS,LEU,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR protocols.denovo_design.movers.FastDesign: 34 FALSE FALSE protocols.denovo_design.movers.FastDesign: 35 FALSE FALSE protocols.denovo_design.movers.FastDesign: 36 TRUE TRUE GLU,HIS,HIS_D,LYS,GLN,ARG protocols.denovo_design.movers.FastDesign: 37 TRUE TRUE ALA,ASP,GLU,PHE,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR protocols.denovo_design.movers.FastDesign: 38 FALSE FALSE protocols.denovo_design.movers.FastDesign: 39 FALSE FALSE protocols.denovo_design.movers.FastDesign: 40 TRUE TRUE GLU,HIS,HIS_D,LYS,GLN,ARG protocols.denovo_design.movers.FastDesign: 41 TRUE TRUE ALA,ASP,GLU,PHE,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR protocols.denovo_design.movers.FastDesign: 42 FALSE FALSE protocols.denovo_design.movers.FastDesign: 43 TRUE TRUE GLU,HIS,HIS_D,LYS,GLN,ARG protocols.denovo_design.movers.FastDesign: 44 TRUE TRUE ALA,ASP,GLU,PHE,HIS,HIS_D,ILE,LEU,MET,ASN,GLN,SER,THR,VAL,TRP,TYR protocols.denovo_design.movers.FastDesign: 45 TRUE TRUE ALA,ASP,GLU,PHE,HIS,HIS_D,ILE,LEU,MET,ASN,GLN,SER,THR,VAL,TRP,TYR protocols.denovo_design.movers.FastDesign: 46 TRUE TRUE ALA,ASP,GLU,PHE,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR protocols.denovo_design.movers.FastDesign: 47 TRUE TRUE GLU,HIS,HIS_D,LYS,GLN,ARG protocols.denovo_design.movers.FastDesign: 48 TRUE TRUE ALA,ASP,GLU,PHE,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR protocols.denovo_design.movers.FastDesign: 49 FALSE FALSE protocols.denovo_design.movers.FastDesign: 50 FALSE FALSE protocols.denovo_design.movers.FastDesign: 51 FALSE FALSE protocols.denovo_design.movers.FastDesign: 52 FALSE FALSE protocols.denovo_design.movers.FastDesign: 53 FALSE FALSE protocols.denovo_design.movers.FastDesign: 54 FALSE FALSE protocols.denovo_design.movers.FastDesign: 55 FALSE FALSE protocols.denovo_design.movers.FastDesign: 56 FALSE FALSE protocols.denovo_design.movers.FastDesign: 57 FALSE FALSE protocols.denovo_design.movers.FastDesign: 58 FALSE FALSE protocols.denovo_design.movers.FastDesign: 59 FALSE FALSE protocols.denovo_design.movers.FastDesign: 60 FALSE FALSE protocols.denovo_design.movers.FastDesign: 61 FALSE FALSE protocols.denovo_design.movers.FastDesign: 62 FALSE FALSE protocols.denovo_design.movers.FastDesign: 63 FALSE FALSE protocols.denovo_design.movers.FastDesign: 64 FALSE FALSE protocols.denovo_design.movers.FastDesign: 65 FALSE FALSE protocols.denovo_design.movers.FastDesign: 66 FALSE FALSE protocols.denovo_design.movers.FastDesign: 67 TRUE FALSE LYS protocols.denovo_design.movers.FastDesign: 68 FALSE FALSE protocols.denovo_design.movers.FastDesign: 69 FALSE FALSE protocols.denovo_design.movers.FastDesign: 70 TRUE FALSE ILE protocols.denovo_design.movers.FastDesign: 71 TRUE FALSE GLU protocols.denovo_design.movers.FastDesign: 72 TRUE FALSE GLU protocols.denovo_design.movers.FastDesign: 73 TRUE FALSE LEU protocols.denovo_design.movers.FastDesign: 74 TRUE FALSE GLU protocols.denovo_design.movers.FastDesign: 75 FALSE FALSE protocols.denovo_design.movers.FastDesign: 76 TRUE FALSE ARG protocols.denovo_design.movers.FastDesign: 77 FALSE FALSE protocols.denovo_design.movers.FastDesign: 78 TRUE FALSE PHE protocols.denovo_design.movers.FastDesign: 79 FALSE FALSE protocols.denovo_design.movers.FastDesign: 80 TRUE FALSE ASN protocols.denovo_design.movers.FastDesign: 81 FALSE FALSE protocols.denovo_design.movers.FastDesign: 82 TRUE FALSE ASN protocols.denovo_design.movers.FastDesign: 83 TRUE FALSE THR protocols.denovo_design.movers.FastDesign: 84 FALSE FALSE protocols.denovo_design.movers.FastDesign: 85 FALSE FALSE protocols.denovo_design.movers.FastDesign: 86 FALSE FALSE protocols.denovo_design.movers.FastDesign: 87 FALSE FALSE protocols.denovo_design.movers.FastDesign: 88 FALSE FALSE protocols.denovo_design.movers.FastDesign: 89 FALSE FALSE protocols.denovo_design.movers.FastDesign: 90 FALSE FALSE protocols.denovo_design.movers.FastDesign: 91 FALSE FALSE protocols.denovo_design.movers.FastDesign: 92 FALSE FALSE protocols.denovo_design.movers.FastDesign: 93 FALSE FALSE protocols.denovo_design.movers.FastDesign: 94 FALSE FALSE protocols.denovo_design.movers.FastDesign: 95 FALSE FALSE protocols.denovo_design.movers.FastDesign: 96 TRUE FALSE LEU protocols.denovo_design.movers.FastDesign: 97 FALSE FALSE protocols.denovo_design.movers.FastDesign: 98 FALSE FALSE protocols.denovo_design.movers.FastDesign: 99 TRUE FALSE ILE protocols.denovo_design.movers.FastDesign: 100 TRUE FALSE THR protocols.denovo_design.movers.FastDesign: 101 TRUE FALSE ARG protocols.denovo_design.movers.FastDesign: 102 FALSE FALSE protocols.denovo_design.movers.FastDesign: 103 FALSE FALSE protocols.denovo_design.movers.FastDesign: 104 FALSE FALSE protocols.denovo_design.movers.FastDesign: 105 FALSE FALSE protocols.denovo_design.movers.FastDesign: 106 FALSE FALSE protocols.denovo_design.movers.FastDesign: 107 FALSE FALSE protocols.denovo_design.movers.FastDesign: 108 FALSE FALSE protocols.denovo_design.movers.FastDesign: 109 FALSE FALSE protocols.denovo_design.movers.FastDesign: 110 FALSE FALSE protocols.denovo_design.movers.FastDesign: 111 FALSE FALSE protocols.denovo_design.movers.FastDesign: 112 FALSE FALSE protocols.denovo_design.movers.FastDesign: 113 FALSE FALSE protocols.denovo_design.movers.FastDesign: 114 FALSE FALSE protocols.denovo_design.movers.FastDesign: 115 FALSE FALSE protocols.denovo_design.movers.FastDesign: 116 FALSE FALSE protocols.denovo_design.movers.FastDesign: 117 FALSE FALSE protocols.denovo_design.movers.FastDesign: 118 FALSE FALSE protocols.denovo_design.movers.FastDesign: 119 FALSE FALSE protocols.denovo_design.movers.FastDesign: 120 TRUE FALSE SER protocols.denovo_design.movers.FastDesign: 121 FALSE FALSE protocols.denovo_design.movers.FastDesign: 122 FALSE FALSE protocols.denovo_design.movers.FastDesign: 123 FALSE FALSE protocols.denovo_design.movers.FastDesign: 124 FALSE FALSE protocols.denovo_design.movers.FastDesign: 125 FALSE FALSE protocols.denovo_design.movers.FastDesign: 126 FALSE FALSE protocols.denovo_design.movers.FastDesign: 127 FALSE FALSE protocols.denovo_design.movers.FastDesign: 128 FALSE FALSE protocols.denovo_design.movers.FastDesign: 129 FALSE FALSE protocols.denovo_design.movers.FastDesign: 130 FALSE FALSE protocols.denovo_design.movers.FastDesign: 131 FALSE FALSE core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 93 edges requiring: 56088 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 98, box[ 98* 98* 93], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10160 bytes basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat core.scoring.elec.util: Read 40 countpair representative atoms core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true. core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /home/newdisk1/rosetta.binary.linux.release-315/main/database/rotamer/beta_nov2016/Dunbrack10.lib.bin core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/newdisk1/rosetta.binary.linux.release-315/main/database/rotamer/beta_nov2016/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.08775 seconds to load from binary core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 93 edges requiring: 56088 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 98, box[ 98* 98* 93], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10160 bytes protocols.relax.FastRelax: CMD: repeat 3512.75 0 0 0.55 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 93 edges requiring: 56088 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 98, box[ 98* 98* 93], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10160 bytes protocols.relax.FastRelax: CMD: reference 3512.17 0 0 0.55 protocols.pack_interface.ProteinProteinInterfaceUpweighterTaskOperation: Packer Energies between the interface residues are upweighted by factor 3. core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 93 edges requiring: 56088 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 98, box[ 98* 98* 93], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10160 bytes protocols.task_operations.PruneBuriedUnsatsOperation: Building hbond graph protocols.task_operations.PruneBuriedUnsatsOperation: Hbond graph has: 16817 edges requiring: 5942976 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 98, box[ 98* 98* 93], resolution 0.504 protocols.task_operations.PruneBuriedUnsatsOperation: Pruned 1225 / 8264 rotamers. core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 12717 edges requiring: 4458936 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 98, box[ 98* 98* 93], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 743600 bytes core.pack.pack_rotamers: built 7039 rotamers at 38 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.energy_methods.AACompositionEnergy: Cleaning up cached AACompositionEnergy data after packing. core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 92 edges requiring: 55968 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 98, box[ 98* 98* 93], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10240 bytes core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 92 edges requiring: 55968 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 98, box[ 98* 98* 93], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10240 bytes core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 92 edges requiring: 55968 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 98, box[ 98* 98* 93], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10240 bytes core.energy_methods.AACompositionEnergy: Disabling AACompositionEnergy during minimization. core.energy_methods.AACompositionEnergy: Re-enabling AACompositionEnergy following minimization. core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 90 edges requiring: 55848 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 98, box[ 97* 98* 92], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 9760 bytes protocols.relax.FastRelax: CMD: ramp_repack_min 116.593 0.381389 0.381389 0.04345 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 90 edges requiring: 55848 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 98, box[ 97* 98* 92], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 9760 bytes protocols.relax.FastRelax: CMD: reference 116.593 0.381389 0.381389 0.04345 protocols.pack_interface.ProteinProteinInterfaceUpweighterTaskOperation: Packer Energies between the interface residues are upweighted by factor 3. core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 90 edges requiring: 55848 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 98, box[ 97* 98* 92], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 9760 bytes protocols.task_operations.PruneBuriedUnsatsOperation: Building hbond graph protocols.task_operations.PruneBuriedUnsatsOperation: Hbond graph has: 9596 edges requiring: 4083896 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 98, box[ 97* 98* 92], resolution 0.504 protocols.task_operations.PruneBuriedUnsatsOperation: Pruned 832 / 6990 rotamers. core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 7589 edges requiring: 3275136 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 98, box[ 97* 98* 92], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 299680 bytes core.pack.pack_rotamers: built 6158 rotamers at 35 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.energy_methods.AACompositionEnergy: Cleaning up cached AACompositionEnergy data after packing. core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 92 edges requiring: 55880 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 98, box[ 97* 98* 92], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 9800 bytes core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 92 edges requiring: 55880 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 98, box[ 97* 98* 92], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 9800 bytes core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 92 edges requiring: 55880 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 98, box[ 97* 98* 92], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 9800 bytes core.energy_methods.AACompositionEnergy: Disabling AACompositionEnergy during minimization. core.energy_methods.AACompositionEnergy: Re-enabling AACompositionEnergy following minimization. core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 93 edges requiring: 55984 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 98, box[ 98* 98* 92], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10280 bytes protocols.relax.FastRelax: CMD: ramp_repack_min 178.234 0.293622 0.293622 0.16225 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 93 edges requiring: 55984 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 98, box[ 98* 98* 92], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10280 bytes protocols.relax.FastRelax: CMD: reference 178.234 0.293622 0.293622 0.16225 protocols.pack_interface.ProteinProteinInterfaceUpweighterTaskOperation: Packer Energies between the interface residues are upweighted by factor 3. core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 93 edges requiring: 55984 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 98, box[ 98* 98* 92], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10280 bytes protocols.task_operations.PruneBuriedUnsatsOperation: Building hbond graph protocols.task_operations.PruneBuriedUnsatsOperation: Hbond graph has: 8123 edges requiring: 3332416 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 98, box[ 98* 98* 92], resolution 0.504 protocols.task_operations.PruneBuriedUnsatsOperation: Pruned 823 / 6170 rotamers. core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 6619 edges requiring: 2898272 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 98, box[ 98* 98* 92], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 206480 bytes core.pack.pack_rotamers: built 5347 rotamers at 33 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.energy_methods.AACompositionEnergy: Cleaning up cached AACompositionEnergy data after packing. core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 93 edges requiring: 56056 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 98, box[ 98* 98* 92], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10280 bytes core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 93 edges requiring: 56056 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 98, box[ 98* 98* 92], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10280 bytes core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 93 edges requiring: 56056 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 98, box[ 98* 98* 92], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10280 bytes core.energy_methods.AACompositionEnergy: Disabling AACompositionEnergy during minimization. core.energy_methods.AACompositionEnergy: Re-enabling AACompositionEnergy following minimization. core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 93 edges requiring: 56056 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 99, box[ 99* 99* 91], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 9960 bytes protocols.relax.FastRelax: CMD: ramp_repack_min 214.984 0.320576 0.320576 0.31735 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 93 edges requiring: 56056 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 99, box[ 99* 99* 91], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 9960 bytes protocols.relax.FastRelax: CMD: reference 214.984 0.320576 0.320576 0.31735 protocols.pack_interface.ProteinProteinInterfaceUpweighterTaskOperation: Packer Energies between the interface residues are upweighted by factor 3. core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 93 edges requiring: 56056 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 99, box[ 99* 99* 91], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 9960 bytes protocols.task_operations.PruneBuriedUnsatsOperation: Building hbond graph protocols.task_operations.PruneBuriedUnsatsOperation: Hbond graph has: 7670 edges requiring: 3083912 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 99, box[ 99* 99* 91], resolution 0.504 protocols.task_operations.PruneBuriedUnsatsOperation: Pruned 868 / 5595 rotamers. core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 6120 edges requiring: 2630072 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 99, box[ 99* 99* 91], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 184000 bytes core.pack.pack_rotamers: built 4727 rotamers at 33 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.energy_methods.AACompositionEnergy: Cleaning up cached AACompositionEnergy data after packing. core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 94 edges requiring: 56192 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 99, box[ 99* 99* 91], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 9960 bytes core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 94 edges requiring: 56192 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 99, box[ 99* 99* 91], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 9960 bytes core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 94 edges requiring: 56192 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 99, box[ 99* 99* 91], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 9960 bytes core.energy_methods.AACompositionEnergy: Disabling AACompositionEnergy during minimization. core.energy_methods.AACompositionEnergy: Re-enabling AACompositionEnergy following minimization. core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 95 edges requiring: 56272 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 100, box[ 99*100* 94], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 9920 bytes protocols.relax.FastRelax: CMD: ramp_repack_min 241.727 0.406364 0.406364 0.55 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 95 edges requiring: 56272 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 100, box[ 99*100* 94], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 9920 bytes protocols.relax.FastRelax: MRP: 0 241.727 241.727 0.406364 0.406364 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 95 edges requiring: 56272 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 100, box[ 99*100* 94], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 9920 bytes protocols.relax.FastRelax: CMD: accept_to_best 241.727 0.406364 0.406364 0.55 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 95 edges requiring: 56272 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 100, box[ 99*100* 94], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 9920 bytes protocols.relax.FastRelax: CMD: endrepeat 241.727 0.406364 0.406364 0.55 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 95 edges requiring: 56272 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 100, box[ 99*100* 94], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 9920 bytes protocols::checkpoint: Deleting checkpoints of FastRelax core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 95 edges requiring: 56272 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 100, box[ 99*100* 94], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 9920 bytes protocols.denovo_design.movers.FastDesign: ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ fa_atr 1.000 -756.459 -756.459 fa_rep 0.550 171.272 94.200 fa_sol 1.000 553.780 553.780 fa_intra_atr_xover4 1.000 -46.557 -46.557 fa_intra_rep_xover4 0.550 43.439 23.892 fa_intra_sol_xover4 1.000 30.420 30.420 lk_ball 0.920 332.578 305.972 lk_ball_iso -0.380 803.977 -305.511 lk_ball_bridge -0.330 3.103 -1.024 lk_ball_bridge_uncpl -0.330 21.368 -7.051 fa_elec 1.000 -244.704 -244.704 fa_intra_elec 1.000 -26.922 -26.922 pro_close 1.250 0.467 0.583 arg_cation_pi 3.000 -0.793 -2.378 hbond_sr_bb 1.000 -59.636 -59.636 hbond_lr_bb 1.000 -34.069 -34.069 hbond_bb_sc 1.000 -17.269 -17.269 hbond_sc 1.000 -19.288 -19.288 approximate_buried_unsat_penalty 5.000 8.400 42.000 dslf_fa13 1.250 -0.655 -0.818 omega 0.480 33.458 16.060 fa_dun_dev 0.690 30.084 20.758 fa_dun_rot 0.760 104.318 79.282 fa_dun_semi 0.780 130.323 101.652 p_aa_pp 0.610 -55.382 -33.783 hxl_tors 1.000 28.340 28.340 ref 1.000 -50.510 -50.510 rama_prepro 0.500 61.424 30.712 res_type_constraint 1.500 342.752 514.128 aa_composition 1.000 7.000 7.000 --------------------------------------------------- Total weighted score: 242.798 protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER FastDesign - FastDesign======================= protocols.pack_interface.ProteinProteinInterfaceUpweighterTaskOperation: Packer Energies between the interface residues are upweighted by factor 3. core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] protocols.denovo_design.movers.FastDesign: #Packer_Task protocols.denovo_design.movers.FastDesign: protocols.denovo_design.movers.FastDesign: Threads to request: ALL AVAILABLE protocols.denovo_design.movers.FastDesign: protocols.denovo_design.movers.FastDesign: resid pack? design? allowed_aas protocols.denovo_design.movers.FastDesign: 1 FALSE FALSE protocols.denovo_design.movers.FastDesign: 2 FALSE FALSE protocols.denovo_design.movers.FastDesign: 3 FALSE FALSE protocols.denovo_design.movers.FastDesign: 4 FALSE FALSE protocols.denovo_design.movers.FastDesign: 5 FALSE FALSE protocols.denovo_design.movers.FastDesign: 6 FALSE FALSE protocols.denovo_design.movers.FastDesign: 7 FALSE FALSE protocols.denovo_design.movers.FastDesign: 8 FALSE FALSE protocols.denovo_design.movers.FastDesign: 9 FALSE FALSE protocols.denovo_design.movers.FastDesign: 10 FALSE FALSE protocols.denovo_design.movers.FastDesign: 11 FALSE FALSE protocols.denovo_design.movers.FastDesign: 12 FALSE FALSE protocols.denovo_design.movers.FastDesign: 13 FALSE FALSE protocols.denovo_design.movers.FastDesign: 14 TRUE TRUE ASP,ASN,SER,THR protocols.denovo_design.movers.FastDesign: 15 FALSE FALSE protocols.denovo_design.movers.FastDesign: 16 TRUE TRUE ALA,ASP,GLU,PHE,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR protocols.denovo_design.movers.FastDesign: 17 FALSE FALSE protocols.denovo_design.movers.FastDesign: 18 FALSE FALSE protocols.denovo_design.movers.FastDesign: 19 TRUE TRUE ALA,ASP,GLU,PHE,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR protocols.denovo_design.movers.FastDesign: 20 TRUE TRUE ALA,ASP,GLU,PHE,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR protocols.denovo_design.movers.FastDesign: 21 FALSE FALSE protocols.denovo_design.movers.FastDesign: 22 TRUE TRUE GLU,HIS,HIS_D,LYS,GLN,ARG protocols.denovo_design.movers.FastDesign: 23 TRUE TRUE ALA,ASP,GLU,PHE,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR protocols.denovo_design.movers.FastDesign: 24 FALSE FALSE protocols.denovo_design.movers.FastDesign: 25 FALSE FALSE protocols.denovo_design.movers.FastDesign: 26 TRUE TRUE GLU,HIS,HIS_D,LYS,GLN,ARG protocols.denovo_design.movers.FastDesign: 27 FALSE FALSE protocols.denovo_design.movers.FastDesign: 28 FALSE FALSE protocols.denovo_design.movers.FastDesign: 29 FALSE FALSE protocols.denovo_design.movers.FastDesign: 30 TRUE TRUE GLU,HIS,HIS_D,LYS,GLN,ARG protocols.denovo_design.movers.FastDesign: 31 FALSE FALSE protocols.denovo_design.movers.FastDesign: 32 TRUE TRUE ASP,GLU,HIS,HIS_D,LYS,ASN,GLN,ARG,SER,THR protocols.denovo_design.movers.FastDesign: 33 TRUE TRUE ALA,ASP,GLU,PHE,HIS,HIS_D,ILE,LYS,LEU,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR protocols.denovo_design.movers.FastDesign: 34 FALSE FALSE protocols.denovo_design.movers.FastDesign: 35 FALSE FALSE protocols.denovo_design.movers.FastDesign: 36 TRUE TRUE GLU,HIS,HIS_D,LYS,GLN,ARG protocols.denovo_design.movers.FastDesign: 37 TRUE TRUE ALA,ASP,GLU,PHE,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR protocols.denovo_design.movers.FastDesign: 38 FALSE FALSE protocols.denovo_design.movers.FastDesign: 39 FALSE FALSE protocols.denovo_design.movers.FastDesign: 40 TRUE TRUE GLU,HIS,HIS_D,LYS,GLN,ARG protocols.denovo_design.movers.FastDesign: 41 TRUE TRUE ALA,ASP,GLU,PHE,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR protocols.denovo_design.movers.FastDesign: 42 FALSE FALSE protocols.denovo_design.movers.FastDesign: 43 TRUE TRUE GLU,HIS,HIS_D,LYS,GLN,ARG protocols.denovo_design.movers.FastDesign: 44 TRUE TRUE ALA,ASP,GLU,PHE,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR protocols.denovo_design.movers.FastDesign: 45 FALSE FALSE protocols.denovo_design.movers.FastDesign: 46 TRUE TRUE ALA,ASP,GLU,PHE,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR protocols.denovo_design.movers.FastDesign: 47 TRUE TRUE GLU,HIS,HIS_D,LYS,GLN,ARG protocols.denovo_design.movers.FastDesign: 48 TRUE TRUE ALA,ASP,GLU,PHE,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR protocols.denovo_design.movers.FastDesign: 49 TRUE TRUE ALA,ASP,GLU,PHE,HIS,HIS_D,ILE,LYS,LEU,MET,ASN,GLN,ARG,SER,THR,VAL,TRP,TYR protocols.denovo_design.movers.FastDesign: 50 FALSE FALSE protocols.denovo_design.movers.FastDesign: 51 FALSE FALSE protocols.denovo_design.movers.FastDesign: 52 FALSE FALSE protocols.denovo_design.movers.FastDesign: 53 FALSE FALSE protocols.denovo_design.movers.FastDesign: 54 FALSE FALSE protocols.denovo_design.movers.FastDesign: 55 FALSE FALSE protocols.denovo_design.movers.FastDesign: 56 FALSE FALSE protocols.denovo_design.movers.FastDesign: 57 FALSE FALSE protocols.denovo_design.movers.FastDesign: 58 FALSE FALSE protocols.denovo_design.movers.FastDesign: 59 FALSE FALSE protocols.denovo_design.movers.FastDesign: 60 FALSE FALSE protocols.denovo_design.movers.FastDesign: 61 FALSE FALSE protocols.denovo_design.movers.FastDesign: 62 FALSE FALSE protocols.denovo_design.movers.FastDesign: 63 FALSE FALSE protocols.denovo_design.movers.FastDesign: 64 FALSE FALSE protocols.denovo_design.movers.FastDesign: 65 FALSE FALSE protocols.denovo_design.movers.FastDesign: 66 FALSE FALSE protocols.denovo_design.movers.FastDesign: 67 TRUE FALSE LYS protocols.denovo_design.movers.FastDesign: 68 FALSE FALSE protocols.denovo_design.movers.FastDesign: 69 FALSE FALSE protocols.denovo_design.movers.FastDesign: 70 TRUE FALSE ILE protocols.denovo_design.movers.FastDesign: 71 TRUE FALSE GLU protocols.denovo_design.movers.FastDesign: 72 TRUE FALSE GLU protocols.denovo_design.movers.FastDesign: 73 TRUE FALSE LEU protocols.denovo_design.movers.FastDesign: 74 TRUE FALSE GLU protocols.denovo_design.movers.FastDesign: 75 FALSE FALSE protocols.denovo_design.movers.FastDesign: 76 TRUE FALSE ARG protocols.denovo_design.movers.FastDesign: 77 FALSE FALSE protocols.denovo_design.movers.FastDesign: 78 FALSE FALSE protocols.denovo_design.movers.FastDesign: 79 FALSE FALSE protocols.denovo_design.movers.FastDesign: 80 TRUE FALSE ASN protocols.denovo_design.movers.FastDesign: 81 FALSE FALSE protocols.denovo_design.movers.FastDesign: 82 TRUE FALSE ASN protocols.denovo_design.movers.FastDesign: 83 TRUE FALSE THR protocols.denovo_design.movers.FastDesign: 84 FALSE FALSE protocols.denovo_design.movers.FastDesign: 85 FALSE FALSE protocols.denovo_design.movers.FastDesign: 86 FALSE FALSE protocols.denovo_design.movers.FastDesign: 87 FALSE FALSE protocols.denovo_design.movers.FastDesign: 88 FALSE FALSE protocols.denovo_design.movers.FastDesign: 89 FALSE FALSE protocols.denovo_design.movers.FastDesign: 90 FALSE FALSE protocols.denovo_design.movers.FastDesign: 91 FALSE FALSE protocols.denovo_design.movers.FastDesign: 92 FALSE FALSE protocols.denovo_design.movers.FastDesign: 93 FALSE FALSE protocols.denovo_design.movers.FastDesign: 94 FALSE FALSE protocols.denovo_design.movers.FastDesign: 95 FALSE FALSE protocols.denovo_design.movers.FastDesign: 96 TRUE FALSE LEU protocols.denovo_design.movers.FastDesign: 97 FALSE FALSE protocols.denovo_design.movers.FastDesign: 98 FALSE FALSE protocols.denovo_design.movers.FastDesign: 99 TRUE FALSE ILE protocols.denovo_design.movers.FastDesign: 100 TRUE FALSE THR protocols.denovo_design.movers.FastDesign: 101 TRUE FALSE ARG protocols.denovo_design.movers.FastDesign: 102 FALSE FALSE protocols.denovo_design.movers.FastDesign: 103 FALSE FALSE protocols.denovo_design.movers.FastDesign: 104 FALSE FALSE protocols.denovo_design.movers.FastDesign: 105 FALSE FALSE protocols.denovo_design.movers.FastDesign: 106 FALSE FALSE protocols.denovo_design.movers.FastDesign: 107 FALSE FALSE protocols.denovo_design.movers.FastDesign: 108 FALSE FALSE protocols.denovo_design.movers.FastDesign: 109 FALSE FALSE protocols.denovo_design.movers.FastDesign: 110 FALSE FALSE protocols.denovo_design.movers.FastDesign: 111 FALSE FALSE protocols.denovo_design.movers.FastDesign: 112 FALSE FALSE protocols.denovo_design.movers.FastDesign: 113 FALSE FALSE protocols.denovo_design.movers.FastDesign: 114 FALSE FALSE protocols.denovo_design.movers.FastDesign: 115 FALSE FALSE protocols.denovo_design.movers.FastDesign: 116 FALSE FALSE protocols.denovo_design.movers.FastDesign: 117 FALSE FALSE protocols.denovo_design.movers.FastDesign: 118 FALSE FALSE protocols.denovo_design.movers.FastDesign: 119 FALSE FALSE protocols.denovo_design.movers.FastDesign: 120 FALSE FALSE protocols.denovo_design.movers.FastDesign: 121 FALSE FALSE protocols.denovo_design.movers.FastDesign: 122 FALSE FALSE protocols.denovo_design.movers.FastDesign: 123 FALSE FALSE protocols.denovo_design.movers.FastDesign: 124 FALSE FALSE protocols.denovo_design.movers.FastDesign: 125 FALSE FALSE protocols.denovo_design.movers.FastDesign: 126 FALSE FALSE protocols.denovo_design.movers.FastDesign: 127 FALSE FALSE protocols.denovo_design.movers.FastDesign: 128 FALSE FALSE protocols.denovo_design.movers.FastDesign: 129 FALSE FALSE protocols.denovo_design.movers.FastDesign: 130 FALSE FALSE protocols.denovo_design.movers.FastDesign: 131 FALSE FALSE core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 95 edges requiring: 56272 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 100, box[ 99*100* 94], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 9920 bytes core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 95 edges requiring: 56272 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 100, box[ 99*100* 94], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 9920 bytes protocols.relax.FastRelax: CMD: repeat 242.798 0 0 0.55 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 95 edges requiring: 56272 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 100, box[ 99*100* 94], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 9920 bytes protocols.relax.FastRelax: CMD: reference 241.727 0 0 0.55 protocols.pack_interface.ProteinProteinInterfaceUpweighterTaskOperation: Packer Energies between the interface residues are upweighted by factor 3. core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 95 edges requiring: 56272 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 100, box[ 99*100* 94], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 9920 bytes protocols.task_operations.PruneBuriedUnsatsOperation: Building hbond graph protocols.task_operations.PruneBuriedUnsatsOperation: Hbond graph has: 14079 edges requiring: 4901024 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 100, box[ 99*100* 94], resolution 0.504 protocols.task_operations.PruneBuriedUnsatsOperation: Pruned 980 / 8055 rotamers. core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 11854 edges requiring: 4340296 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 100, box[ 99*100* 94], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 470040 bytes core.pack.pack_rotamers: built 7075 rotamers at 34 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.energy_methods.AACompositionEnergy: Cleaning up cached AACompositionEnergy data after packing. core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 97 edges requiring: 56888 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 100, box[ 99*100* 94], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10040 bytes core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 97 edges requiring: 56888 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 100, box[ 99*100* 94], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10040 bytes core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 97 edges requiring: 56888 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 100, box[ 99*100* 94], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10040 bytes core.energy_methods.AACompositionEnergy: Disabling AACompositionEnergy during minimization. core.energy_methods.AACompositionEnergy: Re-enabling AACompositionEnergy following minimization. core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 95 edges requiring: 56760 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 97, box[ 97* 97* 93], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10000 bytes protocols.relax.FastRelax: CMD: ramp_repack_min 103.745 0.454554 0.454554 0.04345 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 95 edges requiring: 56760 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 97, box[ 97* 97* 93], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10000 bytes protocols.relax.FastRelax: CMD: reference 103.745 0.454554 0.454554 0.04345 protocols.pack_interface.ProteinProteinInterfaceUpweighterTaskOperation: Packer Energies between the interface residues are upweighted by factor 3. core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 95 edges requiring: 56760 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 97, box[ 97* 97* 93], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10000 bytes protocols.task_operations.PruneBuriedUnsatsOperation: Building hbond graph protocols.task_operations.PruneBuriedUnsatsOperation: Hbond graph has: 6764 edges requiring: 3236152 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 97, box[ 97* 97* 93], resolution 0.504 protocols.task_operations.PruneBuriedUnsatsOperation: Pruned 917 / 6144 rotamers. core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 5577 edges requiring: 2801168 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 97, box[ 97* 97* 93], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 196440 bytes core.pack.pack_rotamers: built 5227 rotamers at 34 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.energy_methods.AACompositionEnergy: Cleaning up cached AACompositionEnergy data after packing. core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 95 edges requiring: 56608 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 97, box[ 97* 97* 93], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10000 bytes core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 95 edges requiring: 56608 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 97, box[ 97* 97* 93], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10000 bytes core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 95 edges requiring: 56608 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 97, box[ 97* 97* 93], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10000 bytes core.energy_methods.AACompositionEnergy: Disabling AACompositionEnergy during minimization. core.energy_methods.AACompositionEnergy: Re-enabling AACompositionEnergy following minimization. core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 94 edges requiring: 56536 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 98, box[ 98* 98* 93], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 9680 bytes protocols.relax.FastRelax: CMD: ramp_repack_min 153.336 0.280646 0.280646 0.16225 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 94 edges requiring: 56536 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 98, box[ 98* 98* 93], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 9680 bytes protocols.relax.FastRelax: CMD: reference 153.336 0.280646 0.280646 0.16225 protocols.pack_interface.ProteinProteinInterfaceUpweighterTaskOperation: Packer Energies between the interface residues are upweighted by factor 3. core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 94 edges requiring: 56536 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 98, box[ 98* 98* 93], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 9680 bytes protocols.task_operations.PruneBuriedUnsatsOperation: Building hbond graph protocols.task_operations.PruneBuriedUnsatsOperation: Hbond graph has: 8384 edges requiring: 3689328 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 98, box[ 98* 98* 93], resolution 0.504 protocols.task_operations.PruneBuriedUnsatsOperation: Pruned 695 / 6127 rotamers. core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 7208 edges requiring: 3001584 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 98, box[ 98* 98* 93], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 226960 bytes core.pack.pack_rotamers: built 5432 rotamers at 34 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.energy_methods.AACompositionEnergy: Cleaning up cached AACompositionEnergy data after packing. core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 95 edges requiring: 56768 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 98, box[ 98* 98* 93], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 9680 bytes core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 95 edges requiring: 56768 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 98, box[ 98* 98* 93], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 9680 bytes core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 95 edges requiring: 56768 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 98, box[ 98* 98* 93], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 9680 bytes core.energy_methods.AACompositionEnergy: Disabling AACompositionEnergy during minimization. core.energy_methods.AACompositionEnergy: Re-enabling AACompositionEnergy following minimization. core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 96 edges requiring: 56824 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 99, box[ 98* 99* 92], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 9880 bytes protocols.relax.FastRelax: CMD: ramp_repack_min 198.752 0.176053 0.176053 0.31735 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 96 edges requiring: 56824 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 99, box[ 98* 99* 92], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 9880 bytes protocols.relax.FastRelax: CMD: reference 198.752 0.176053 0.176053 0.31735 protocols.pack_interface.ProteinProteinInterfaceUpweighterTaskOperation: Packer Energies between the interface residues are upweighted by factor 3. core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.SecondaryStructureSelector: Using dssp for secondary structure: LHHHHHHHHHHHLLHHHHHHHHHHHHHHHHLLLLHHHHHHHHHHHHHHHLLHHHHHHHHHHHHHLLLLLEEEELLEEEEELLLLEEEEEELLLEEEHHHLEEEEEEHHHLLEEEEEELLEEEEEELLLLLL core.select.residue_selector.PrimarySequenceNeighborhoodSelector: ] core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 96 edges requiring: 56824 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 99, box[ 98* 99* 92], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 9880 bytes protocols.task_operations.PruneBuriedUnsatsOperation: Building hbond graph protocols.task_operations.PruneBuriedUnsatsOperation: Hbond graph has: 6326 edges requiring: 2952696 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 99, box[ 98* 99* 92], resolution 0.504 protocols.task_operations.PruneBuriedUnsatsOperation: Pruned 850 / 5585 rotamers. core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 5208 edges requiring: 2546344 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 99, box[ 98* 99* 92], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 137480 bytes core.pack.pack_rotamers: built 4735 rotamers at 34 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph core.energy_methods.AACompositionEnergy: Cleaning up cached AACompositionEnergy data after packing. core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 96 edges requiring: 56824 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 99, box[ 98* 99* 92], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 9880 bytes core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 96 edges requiring: 56824 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 99, box[ 98* 99* 92], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 9880 bytes core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 96 edges requiring: 56824 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 99, box[ 98* 99* 92], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 9880 bytes core.energy_methods.AACompositionEnergy: Disabling AACompositionEnergy during minimization. core.energy_methods.AACompositionEnergy: Re-enabling AACompositionEnergy following minimization. core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 96 edges requiring: 56824 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 101, box[ 98*101* 91], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10160 bytes protocols.relax.FastRelax: CMD: ramp_repack_min 225.715 0.264581 0.264581 0.55 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 96 edges requiring: 56824 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 101, box[ 98*101* 91], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10160 bytes protocols.relax.FastRelax: MRP: 0 225.715 225.715 0.264581 0.264581 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 96 edges requiring: 56824 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 101, box[ 98*101* 91], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10160 bytes protocols.relax.FastRelax: CMD: accept_to_best 225.715 0.264581 0.264581 0.55 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 96 edges requiring: 56824 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 101, box[ 98*101* 91], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10160 bytes protocols.relax.FastRelax: CMD: endrepeat 225.715 0.264581 0.264581 0.55 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 96 edges requiring: 56824 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 101, box[ 98*101* 91], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10160 bytes protocols::checkpoint: Deleting checkpoints of FastRelax core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 96 edges requiring: 56824 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 101, box[ 98*101* 91], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10160 bytes protocols.denovo_design.movers.FastDesign: ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ fa_atr 1.000 -762.201 -762.201 fa_rep 0.550 171.093 94.101 fa_sol 1.000 563.254 563.254 fa_intra_atr_xover4 1.000 -46.862 -46.862 fa_intra_rep_xover4 0.550 40.932 22.512 fa_intra_sol_xover4 1.000 31.108 31.108 lk_ball 0.920 333.446 306.770 lk_ball_iso -0.380 814.801 -309.624 lk_ball_bridge -0.330 2.967 -0.979 lk_ball_bridge_uncpl -0.330 20.413 -6.736 fa_elec 1.000 -245.798 -245.798 fa_intra_elec 1.000 -25.535 -25.535 pro_close 1.250 0.478 0.597 arg_cation_pi 3.000 -0.814 -2.441 hbond_sr_bb 1.000 -59.227 -59.227 hbond_lr_bb 1.000 -34.093 -34.093 hbond_bb_sc 1.000 -15.529 -15.529 hbond_sc 1.000 -25.190 -25.190 approximate_buried_unsat_penalty 5.000 5.000 25.000 dslf_fa13 1.250 -0.657 -0.821 omega 0.480 35.285 16.937 fa_dun_dev 0.690 31.321 21.611 fa_dun_rot 0.760 104.791 79.641 fa_dun_semi 0.780 130.641 101.900 p_aa_pp 0.610 -54.302 -33.124 hxl_tors 1.000 26.366 26.366 ref 1.000 -50.768 -50.768 rama_prepro 0.500 62.652 31.326 res_type_constraint 1.500 344.889 517.333 aa_composition 1.000 7.000 7.000 --------------------------------------------------- Total weighted score: 226.530 protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER ClearConstraintsMover - clear_constraints======================= protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER FastRelax - FastRelax======================= core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 96 edges requiring: 56824 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 101, box[ 98*101* 91], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10160 bytes core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 96 edges requiring: 56824 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 101, box[ 98*101* 91], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10160 bytes protocols.relax.FastRelax: CMD: repeat -297.804 0 0 0.55 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 96 edges requiring: 56824 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 101, box[ 98*101* 91], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10160 bytes protocols.relax.FastRelax: CMD: coord_cst_weight -297.804 0 0 0.55 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 96 edges requiring: 56824 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 101, box[ 98*101* 91], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10160 bytes protocols.relax.FastRelax: CMD: scale:fa_rep -388.141 0 0 0.022 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 96 edges requiring: 56824 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 101, box[ 98*101* 91], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10160 bytes protocols.task_operations.PruneBuriedUnsatsOperation: Building hbond graph protocols.task_operations.PruneBuriedUnsatsOperation: Hbond graph has: 2123 edges requiring: 1128520 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 101, box[ 98*101* 91], resolution 0.504 protocols.task_operations.PruneBuriedUnsatsOperation: Pruned 242 / 2006 rotamers. core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 1764 edges requiring: 922864 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 101, box[ 98*101* 91], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 30480 bytes core.pack.pack_rotamers: built 1764 rotamers at 87 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.energy_methods.AACompositionEnergy: Cleaning up cached AACompositionEnergy data after packing. core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 97 edges requiring: 56896 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 101, box[ 98*101* 91], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10160 bytes core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 97 edges requiring: 56896 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 101, box[ 98*101* 91], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10160 bytes protocols.relax.FastRelax: CMD: repack -392.672 0 0 0.022 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 97 edges requiring: 56896 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 101, box[ 98*101* 91], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10160 bytes protocols.relax.FastRelax: CMD: scale:fa_rep -390.534 0 0 0.02805 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 97 edges requiring: 56896 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 101, box[ 98*101* 91], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10160 bytes core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 97 edges requiring: 56896 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 101, box[ 98*101* 91], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10160 bytes core.energy_methods.AACompositionEnergy: Disabling AACompositionEnergy during minimization. core.energy_methods.AACompositionEnergy: Re-enabling AACompositionEnergy following minimization. core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 93 edges requiring: 56592 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 97, box[ 97* 97* 95], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10080 bytes protocols.relax.FastRelax: CMD: min -419.647 0.493352 0.493352 0.02805 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 93 edges requiring: 56592 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 97, box[ 97* 97* 95], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10080 bytes protocols.relax.FastRelax: CMD: coord_cst_weight -419.647 0.493352 0.493352 0.02805 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 93 edges requiring: 56592 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 97, box[ 97* 97* 95], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10080 bytes protocols.relax.FastRelax: CMD: scale:fa_rep -292.945 0.493352 0.493352 0.14575 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 93 edges requiring: 56592 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 97, box[ 97* 97* 95], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10080 bytes protocols.task_operations.PruneBuriedUnsatsOperation: Building hbond graph protocols.task_operations.PruneBuriedUnsatsOperation: Hbond graph has: 2640 edges requiring: 1176688 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 97, box[ 97* 97* 95], resolution 0.504 protocols.task_operations.PruneBuriedUnsatsOperation: Pruned 158 / 2006 rotamers. core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 2370 edges requiring: 1091328 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 97, box[ 97* 97* 95], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 49880 bytes core.pack.pack_rotamers: built 1848 rotamers at 88 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.energy_methods.AACompositionEnergy: Cleaning up cached AACompositionEnergy data after packing. core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 92 edges requiring: 56544 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 97, box[ 97* 97* 95], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10080 bytes core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 92 edges requiring: 56544 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 97, box[ 97* 97* 95], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10080 bytes protocols.relax.FastRelax: CMD: repack -302.658 0.493352 0.493352 0.14575 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 92 edges requiring: 56544 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 97, box[ 97* 97* 95], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10080 bytes protocols.relax.FastRelax: CMD: scale:fa_rep -294.892 0.493352 0.493352 0.154 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 92 edges requiring: 56544 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 97, box[ 97* 97* 95], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10080 bytes core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 92 edges requiring: 56544 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 97, box[ 97* 97* 95], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10080 bytes core.energy_methods.AACompositionEnergy: Disabling AACompositionEnergy during minimization. core.energy_methods.AACompositionEnergy: Re-enabling AACompositionEnergy following minimization. core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 95 edges requiring: 56744 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 98, box[ 98* 98* 94], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 9800 bytes protocols.relax.FastRelax: CMD: min -377.045 0.267693 0.267693 0.154 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 95 edges requiring: 56744 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 98, box[ 98* 98* 94], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 9800 bytes protocols.relax.FastRelax: CMD: coord_cst_weight -377.045 0.267693 0.267693 0.154 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 95 edges requiring: 56744 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 98, box[ 98* 98* 94], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 9800 bytes protocols.relax.FastRelax: CMD: scale:fa_rep -325.446 0.267693 0.267693 0.30745 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 95 edges requiring: 56744 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 98, box[ 98* 98* 94], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 9800 bytes protocols.task_operations.PruneBuriedUnsatsOperation: Building hbond graph protocols.task_operations.PruneBuriedUnsatsOperation: Hbond graph has: 2236 edges requiring: 1087104 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 98, box[ 98* 98* 94], resolution 0.504 protocols.task_operations.PruneBuriedUnsatsOperation: Pruned 138 / 1880 rotamers. core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 1998 edges requiring: 931712 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 98, box[ 98* 98* 94], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 37600 bytes core.pack.pack_rotamers: built 1742 rotamers at 88 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.energy_methods.AACompositionEnergy: Cleaning up cached AACompositionEnergy data after packing. core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 95 edges requiring: 56744 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 98, box[ 98* 98* 94], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 9800 bytes core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 95 edges requiring: 56744 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 98, box[ 98* 98* 94], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 9800 bytes protocols.relax.FastRelax: CMD: repack -325.717 0.267693 0.267693 0.30745 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 95 edges requiring: 56744 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 98, box[ 98* 98* 94], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 9800 bytes protocols.relax.FastRelax: CMD: scale:fa_rep -321.649 0.267693 0.267693 0.31955 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 95 edges requiring: 56744 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 98, box[ 98* 98* 94], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 9800 bytes core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 95 edges requiring: 56744 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 98, box[ 98* 98* 94], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 9800 bytes core.energy_methods.AACompositionEnergy: Disabling AACompositionEnergy during minimization. core.energy_methods.AACompositionEnergy: Re-enabling AACompositionEnergy following minimization. core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 96 edges requiring: 56824 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 99, box[ 99* 99* 93], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10160 bytes protocols.relax.FastRelax: CMD: min -318.916 0.156392 0.156392 0.31955 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 96 edges requiring: 56824 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 99, box[ 99* 99* 93], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10160 bytes protocols.relax.FastRelax: CMD: coord_cst_weight -318.916 0.156392 0.156392 0.31955 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 96 edges requiring: 56824 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 99, box[ 99* 99* 93], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10160 bytes protocols.relax.FastRelax: CMD: scale:fa_rep -264.22 0.156392 0.156392 0.55 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 96 edges requiring: 56824 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 99, box[ 99* 99* 93], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10160 bytes protocols.task_operations.PruneBuriedUnsatsOperation: Building hbond graph protocols.task_operations.PruneBuriedUnsatsOperation: Hbond graph has: 1985 edges requiring: 972288 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 99, box[ 99* 99* 93], resolution 0.504 protocols.task_operations.PruneBuriedUnsatsOperation: Pruned 186 / 1857 rotamers. core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 1733 edges requiring: 881536 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 99, box[ 99* 99* 93], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 26360 bytes core.pack.pack_rotamers: built 1671 rotamers at 88 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.energy_methods.AACompositionEnergy: Cleaning up cached AACompositionEnergy data after packing. core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 96 edges requiring: 56824 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 99, box[ 99* 99* 93], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10120 bytes core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 96 edges requiring: 56824 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 99, box[ 99* 99* 93], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10120 bytes protocols.relax.FastRelax: CMD: repack -268.882 0.156392 0.156392 0.55 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 96 edges requiring: 56824 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 99, box[ 99* 99* 93], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10120 bytes core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 96 edges requiring: 56824 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 99, box[ 99* 99* 93], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10120 bytes core.energy_methods.AACompositionEnergy: Disabling AACompositionEnergy during minimization. core.energy_methods.AACompositionEnergy: Re-enabling AACompositionEnergy following minimization. core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 97 edges requiring: 56896 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 100, box[ 98*100* 94], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10240 bytes protocols.relax.FastRelax: CMD: min -301.803 0.0541649 0.0541649 0.55 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 97 edges requiring: 56896 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 100, box[ 98*100* 94], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10240 bytes protocols.relax.FastRelax: MRP: 0 -301.803 -301.803 0.0541649 0.0541649 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 97 edges requiring: 56896 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 100, box[ 98*100* 94], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10240 bytes protocols.relax.FastRelax: CMD: accept_to_best -301.803 0.0541649 0.0541649 0.55 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 97 edges requiring: 56896 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 100, box[ 98*100* 94], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10240 bytes protocols.relax.FastRelax: CMD: endrepeat -301.803 0.0541649 0.0541649 0.55 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Building hbond graph core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Hbond graph has: 97 edges requiring: 56896 bytes core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 1. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 1 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.chemical.AtomICoor: [ WARNING ] IcoorAtomID::atom_id(): Cannot get atom_id for POLYMER_LOWER of residue LEU 66. Returning BOGUS ID instead. core.conformation.Residue: [ WARNING ] missing an atom: 66 H that depends on a nonexistent polymer connection! core.conformation.Residue: [ WARNING ] --> generating it using idealized coordinates. core.scoring.atomic_depth.AtomicDepth: actual boxlength 100, box[ 98*100* 94], resolution 0.504 core.pack.guidance_scoreterms.approximate_buried_unsat_penalty: Rough mem use: 10240 bytes protocols::checkpoint: Deleting checkpoints of FastRelax protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER interface_buried_sasa======================= protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER interface_buried_sasa======================= protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER ddg======================= protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER ddg======================= protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER interface_sc======================= protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER interface_sc======================= protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER score_per_res======================= protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER score_per_res======================= protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER buns_heavy_ball_1.1D======================= protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER buns_heavy_ball_1.1D======================= protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER mismatch_probability======================= protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER mismatch_probability======================= protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER contact_molecular_surface======================= protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER contact_molecular_surface======================= protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER contact_patch======================= protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER contact_patch======================= protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER contact_patch_apolar======================= protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER contact_patch_apolar======================= protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER contact_patch_apolar_sq5======================= protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER contact_patch_apolar_sq5======================= protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER ss_sc======================= protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER ss_sc======================= protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER contact_molecular_surface_ap_target======================= protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER contact_molecular_surface_ap_target======================= protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER contact_molec_sq5_ap_target======================= protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER contact_molec_sq5_ap_target======================= protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER contact_molecular_surface_apap_target======================= protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER contact_molecular_surface_apap_target======================= protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER contact_molec_sq5_apap_target======================= prosh: 1: /home/newdisk1/rosetta.binary.linux.release-315/main/source/external/DAlphaBall: not found tocols.rosetta_scripts.ParsedProtocol: =======================END FILTER contact_molec_sq5_apap_target======================= protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN METRIC sap_score======================= basic.io.database: Database file opened: scoring/score_functions/sap_sasa_calib.dat WARNING!! DALPHABALL output nan at index 128 DALPHABALL output indicies not matching! 1!=128 ERROR:: Exit from: src/core/scoring/packing/surf_vol.cc line: 164 protocols.rosetta_scripts.ParsedProtocol: [ ERROR ] Exception while processing procotol: File: src/core/scoring/packing/surf_vol.cc:164 [ ERROR ] UtilityExitException ERROR: protocols.jd2.JobDistributor: [ ERROR ] [ERROR] Exception caught by JobDistributor for job HHHH_bc_00797_000000001_0001 [ ERROR ]: Caught exception: File: src/core/scoring/packing/surf_vol.cc:164 [ ERROR ] UtilityExitException ERROR: AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS. protocols.jd2.JobDistributor: [ WARNING ] HHHH_bc_00797_000000001_0001 reported failure and will NOT retry