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