core.init: Checking for fconfig files in pwd and ./rosetta/flags 
core.init.score_function_corrections: [ WARNING ] Flag -beta_nov16 is set but either -weights are also specified or this is being used with the genpot score function.  Not changing input weights file!
core.init: Rosetta version: rosetta.binary.linux.release-247 r247 2020.08+release.cb1caba cb1cabafd7463ab703f6abf5efa33d2707b85924 https://www.rosettacommons.org 2020-02-21T14:46:08.581859
core.init: command: /home/ievab/software/rosetta_bin_linux_2020.08.61146_bundle/main/source/bin/rosetta_scripts.static.linuxgccrelease -database /home/ievab/software/rosetta_bin_linux_2020.08.61146_bundle/main/database/ -in::file::s initial_PM_LSU_210503_relax_0001.pdb -parser::protocol B_relax_density_PM_LSU_rRNA.xml -parser::script_vars densweight=100 -ignore_unrecognized_res -edensity::mapreso 2.8 -edensity::cryoem_scatterers -crystal_refine -out::suffix _relax100 -beta
basic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=496648747 seed_offset=0 real_seed=496648747
basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=496648747 RG_type=mt19937
protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter
protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs
protocols.jd2.PDBJobInputter: pushed initial_PM_LSU_210503_relax_0001.pdb nstruct index 1
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... 
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from PDB initial_PM_LSU_210503_relax_0001.pdb
core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set.  Created 1251 residue types
core.chemical.GlobalResidueTypeSet: Total time to initialize 1.16 seconds.
core.import_pose.import_pose: File 'initial_PM_LSU_210503_relax_0001.pdb' automatically determined to be of type PDB
core.io.pdb.HeaderInformation: [ WARNING ] Deposition day not in range [1, 31]: 0
core.io.pdb.HeaderInformation: [ WARNING ] Unrecognized month in HEADER deposition date             
core.io.util: Automatic glycan connection is activated.
core.io.util: Start reordering residues.
core.io.util: Corrected glycan residue order (internal numbering): []
core.io.util: 
core.io.pose_from_sfr.PoseFromSFRBuilder: Adding undetected upper terminus type to residue 5956,   52 I
core.io.pose_from_sfr.chirality_resolution: Flipping atom xyz for  H21 and  H22 for residue   G
core.io.pose_from_sfr.chirality_resolution: Flipping atom xyz for  H21 and  H22 for residue   G
core.io.pose_from_sfr.chirality_resolution: Number of flip-atom fixups exceeds output limit. Rerun with -show_all_fixes to show everything.
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] missing density found at residue (rosetta number) 378
core.io.pose_from_sfr.PoseFromSFRBuilder:  add lower variant 379
core.conformation.Residue: [ WARNING ] Residue connection id changed when creating a new residue at seqpos 379
core.conformation.Residue: [ WARNING ] ResConnID info stored on the connected residue (residue 0) is now out of date!
core.conformation.Residue: [ WARNING ] Connection atom name (in src):  O3'
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] missing density found at residue (rosetta number) 480
core.io.pose_from_sfr.PoseFromSFRBuilder:  add lower variant 481
core.conformation.Residue: [ WARNING ] Residue connection id changed when creating a new residue at seqpos 481
core.conformation.Residue: [ WARNING ] ResConnID info stored on the connected residue (residue 0) is now out of date!
core.conformation.Residue: [ WARNING ] Connection atom name (in src):  O3'
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] missing density found at residue (rosetta number) 546
core.io.pose_from_sfr.PoseFromSFRBuilder:  add lower variant 547
core.conformation.Residue: [ WARNING ] Residue connection id changed when creating a new residue at seqpos 547
core.conformation.Residue: [ WARNING ] ResConnID info stored on the connected residue (residue 0) is now out of date!
core.conformation.Residue: [ WARNING ] Connection atom name (in src):  O3'
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] missing density found at residue (rosetta number) 595
core.io.pose_from_sfr.PoseFromSFRBuilder:  add lower variant 596
core.conformation.Residue: [ WARNING ] Residue connection id changed when creating a new residue at seqpos 596
core.conformation.Residue: [ WARNING ] ResConnID info stored on the connected residue (residue 0) is now out of date!
core.conformation.Residue: [ WARNING ] Connection atom name (in src):  O3'
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] missing density found at residue (rosetta number) 628
core.io.pose_from_sfr.PoseFromSFRBuilder:  add lower variant 629
core.conformation.Residue: [ WARNING ] Residue connection id changed when creating a new residue at seqpos 629
core.conformation.Residue: [ WARNING ] ResConnID info stored on the connected residue (residue 0) is now out of date!
core.conformation.Residue: [ WARNING ] Connection atom name (in src):  O3'
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] missing density found at residue (rosetta number) 709
core.io.pose_from_sfr.PoseFromSFRBuilder:  add lower variant 710
core.conformation.Residue: [ WARNING ] Residue connection id changed when creating a new residue at seqpos 710
core.conformation.Residue: [ WARNING ] ResConnID info stored on the connected residue (residue 0) is now out of date!
core.conformation.Residue: [ WARNING ] Connection atom name (in src):  O3'
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] missing density found at residue (rosetta number) 1100
core.io.pose_from_sfr.PoseFromSFRBuilder:  add lower variant 1101
core.conformation.Residue: [ WARNING ] Residue connection id changed when creating a new residue at seqpos 1101
core.conformation.Residue: [ WARNING ] ResConnID info stored on the connected residue (residue 0) is now out of date!
core.conformation.Residue: [ WARNING ] Connection atom name (in src):  O3'
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] missing density found at residue (rosetta number) 2798
core.conformation.Residue: [ WARNING ] Residue connection id changed when creating a new residue at seqpos 2799
core.conformation.Residue: [ WARNING ] ResConnID info stored on the connected residue (residue 0) is now out of date!
core.conformation.Residue: [ WARNING ] Connection atom name (in src):  C  
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] missing density found at residue (rosetta number) 2864
core.conformation.Residue: [ WARNING ] Residue connection id changed when creating a new residue at seqpos 2865
core.conformation.Residue: [ WARNING ] ResConnID info stored on the connected residue (residue 0) is now out of date!
core.conformation.Residue: [ WARNING ] Connection atom name (in src):  C  
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] missing density found at residue (rosetta number) 3166
core.conformation.Residue: [ WARNING ] Residue connection id changed when creating a new residue at seqpos 3167
core.conformation.Residue: [ WARNING ] ResConnID info stored on the connected residue (residue 0) is now out of date!
core.conformation.Residue: [ WARNING ] Connection atom name (in src):  C  
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] missing density found at residue (rosetta number) 4786
core.conformation.Residue: [ WARNING ] Residue connection id changed when creating a new residue at seqpos 4787
core.conformation.Residue: [ WARNING ] ResConnID info stored on the connected residue (residue 0) is now out of date!
core.conformation.Residue: [ WARNING ] Connection atom name (in src):  C  
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] missing density found at residue (rosetta number) 5973
core.conformation.Residue: [ WARNING ] Residue connection id changed when creating a new residue at seqpos 5974
core.conformation.Residue: [ WARNING ] ResConnID info stored on the connected residue (residue 0) is now out of date!
core.conformation.Residue: [ WARNING ] Connection atom name (in src):  C  
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] missing density found at residue (rosetta number) 6262
core.conformation.Residue: [ WARNING ] Residue connection id changed when creating a new residue at seqpos 6263
core.conformation.Residue: [ WARNING ] ResConnID info stored on the connected residue (residue 0) is now out of date!
core.conformation.Residue: [ WARNING ] Connection atom name (in src):  C  
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] missing density found at residue (rosetta number) 6834
core.conformation.Residue: [ WARNING ] Residue connection id changed when creating a new residue at seqpos 6835
core.conformation.Residue: [ WARNING ] ResConnID info stored on the connected residue (residue 0) is now out of date!
core.conformation.Residue: [ WARNING ] Connection atom name (in src):  C  
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] missing density found at residue (rosetta number) 8792
core.conformation.Residue: [ WARNING ] Residue connection id changed when creating a new residue at seqpos 8793
core.conformation.Residue: [ WARNING ] ResConnID info stored on the connected residue (residue 0) is now out of date!
core.conformation.Residue: [ WARNING ] Connection atom name (in src):  C  
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] missing density found at residue (rosetta number) 9370
core.conformation.Residue: [ WARNING ] Residue connection id changed when creating a new residue at seqpos 9371
core.conformation.Residue: [ WARNING ] ResConnID info stored on the connected residue (residue 0) is now out of date!
core.conformation.Residue: [ WARNING ] Connection atom name (in src):  C  
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] missing density found at residue (rosetta number) 9403
core.conformation.Residue: [ WARNING ] Residue connection id changed when creating a new residue at seqpos 9404
core.conformation.Residue: [ WARNING ] ResConnID info stored on the connected residue (residue 0) is now out of date!
core.conformation.Residue: [ WARNING ] Connection atom name (in src):  C  
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] missing density found at residue (rosetta number) 9953
core.conformation.Residue: [ WARNING ] Residue connection id changed when creating a new residue at seqpos 9954
core.conformation.Residue: [ WARNING ] ResConnID info stored on the connected residue (residue 0) is now out of date!
core.conformation.Residue: [ WARNING ] Connection atom name (in src):  C  
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] missing density found at residue (rosetta number) 9973
core.conformation.Residue: [ WARNING ] Residue connection id changed when creating a new residue at seqpos 9974
core.conformation.Residue: [ WARNING ] ResConnID info stored on the connected residue (residue 0) is now out of date!
core.conformation.Residue: [ WARNING ] Connection atom name (in src):  C  
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] missing density found at residue (rosetta number) 10224
core.conformation.Residue: [ WARNING ] Residue connection id changed when creating a new residue at seqpos 10225
core.conformation.Residue: [ WARNING ] ResConnID info stored on the connected residue (residue 0) is now out of date!
core.conformation.Residue: [ WARNING ] Connection atom name (in src):  C  
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] missing density found at residue (rosetta number) 10239
core.conformation.Residue: [ WARNING ] Residue connection id changed when creating a new residue at seqpos 10240
core.conformation.Residue: [ WARNING ] ResConnID info stored on the connected residue (residue 0) is now out of date!
core.conformation.Residue: [ WARNING ] Connection atom name (in src):  C  
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] missing density found at residue (rosetta number) 10289
core.conformation.Residue: [ WARNING ] Residue connection id changed when creating a new residue at seqpos 10290
core.conformation.Residue: [ WARNING ] ResConnID info stored on the connected residue (residue 0) is now out of date!
core.conformation.Residue: [ WARNING ] Connection atom name (in src):  C  
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] missing density found at residue (rosetta number) 10561
core.conformation.Residue: [ WARNING ] Residue connection id changed when creating a new residue at seqpos 10562
core.conformation.Residue: [ WARNING ] ResConnID info stored on the connected residue (residue 0) is now out of date!
core.conformation.Residue: [ WARNING ] Connection atom name (in src):  C  
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] missing density found at residue (rosetta number) 10604
core.conformation.Residue: [ WARNING ] Residue connection id changed when creating a new residue at seqpos 10605
core.conformation.Residue: [ WARNING ] ResConnID info stored on the connected residue (residue 0) is now out of date!
core.conformation.Residue: [ WARNING ] Connection atom name (in src):  C  
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] missing density found at residue (rosetta number) 10608
core.conformation.Residue: [ WARNING ] Residue connection id changed when creating a new residue at seqpos 10609
core.conformation.Residue: [ WARNING ] ResConnID info stored on the connected residue (residue 0) is now out of date!
core.conformation.Residue: [ WARNING ] Connection atom name (in src):  C  
core.io.pose_from_sfr.PoseFromSFRBuilder: [ WARNING ] missing density found at residue (rosetta number) 10855
core.io.pose_from_sfr.PoseFromSFRBuilder:  add lower variant 10856
core.conformation.Residue: [ WARNING ] Residue connection id changed when creating a new residue at seqpos 10856
core.conformation.Residue: [ WARNING ] ResConnID info stored on the connected residue (residue 0) is now out of date!
core.conformation.Residue: [ WARNING ] Connection atom name (in src):  O3'
core.conformation.Conformation: Found disulfide between residues 6104 10724
core.conformation.Conformation: current variant for 6104 CYS
core.conformation.Conformation: current variant for 10724 CYS
core.conformation.Conformation: current variant for 6104 CYD
core.conformation.Conformation: current variant for 10724 CYD
protocols.rosetta_scripts.RosettaScriptsParser: dock_design_filename=B_relax_density_PM_LSU_rRNA.xml
protocols.rosetta_scripts.RosettaScriptsParser: Variable substitution will occur with the following values: '%%densweight%%'='100';  
protocols.rosetta_scripts.RosettaScriptsParser: Substituted script:
<ROSETTASCRIPTS>
 <SCOREFXNS>
 <ScoreFunction name="dens" weights="beta_cart">
 <Reweight scoretype="elec_dens_fast" weight="100"/>
 <Set scale_sc_dens_byres="R:0.76,K:0.76,E:0.76,D:0.76,M:0.76,C:0.81,Q:0.81,H:0.81,N:0.81,T:0.81,S:0.81,Y:0.88,W:0.88,A:0.88,F:0.88,P:0.88,I:0.88,L:0.88,V:0.88"/>
 </ScoreFunction>
 </SCOREFXNS>
 <MOVERS>
 <SetupForDensityScoring name="setupdens"/>
 <LoadDensityMap name="loaddens" mapfile="MERGED_hires_-55.mrc"/>
 <FastRelax name="relaxcart" scorefxn="dens" repeats="3" cartesian="1"/>
 </MOVERS>
 <PROTOCOLS>
 <Add mover="setupdens"/>
 <Add mover="loaddens"/>
 <Add mover="relaxcart"/>
 </PROTOCOLS>
 <OUTPUT scorefxn="dens"/>
</ROSETTASCRIPTS>
protocols.rosetta_scripts.RosettaScriptsParser: Generating XML Schema for rosetta_scripts...
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Initializing schema validator...
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Validating input script...
protocols.rosetta_scripts.RosettaScriptsParser: ...done
protocols.rosetta_scripts.RosettaScriptsParser: Parsed script:
<ROSETTASCRIPTS>
	<SCOREFXNS>
		<ScoreFunction name="dens" weights="beta_cart">
			<Reweight scoretype="elec_dens_fast" weight="100"/>
			<Set scale_sc_dens_byres="R:0.76,K:0.76,E:0.76,D:0.76,M:0.76,C:0.81,Q:0.81,H:0.81,N:0.81,T:0.81,S:0.81,Y:0.88,W:0.88,A:0.88,F:0.88,P:0.88,I:0.88,L:0.88,V:0.88"/>
		</ScoreFunction>
	</SCOREFXNS>
	<MOVERS>
		<SetupForDensityScoring name="setupdens"/>
		<LoadDensityMap mapfile="MERGED_hires_-55.mrc" name="loaddens"/>
		<FastRelax cartesian="1" name="relaxcart" repeats="3" scorefxn="dens"/>
	</MOVERS>
	<PROTOCOLS>
		<Add mover="setupdens"/>
		<Add mover="loaddens"/>
		<Add mover="relaxcart"/>
	</PROTOCOLS>
	<OUTPUT scorefxn="dens"/>
</ROSETTASCRIPTS>
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: beta_genpot.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
basic.io.database: Database file opened: scoring/score_functions/generic_potential/generic_bonded.round6p.txt
core.scoring.GenericBondedPotential: Added total 0 bond parameters corresponding to 0 unique bonds.
core.scoring.GenericBondedPotential: Added total 0 angle parameters corresponding to 0 unique angles.
core.scoring.GenericBondedPotential: Added total 263 torsion parameters corresponding to 1125696 unique torsions.
core.scoring.GenericBondedPotential: Added total 50 improper parameters corresponding to 437 unique impropers.
core.scoring.ScoreFunctionFactory: The -include_sugars flag was used with no sugar_bb weight set in the weights file.  Setting sugar_bb weight to 1.0 by default.
core.scoring.ScoringManager: Creating CHI Energy Function.
core.scoring.carbohydrates.CHIEnergyFunction: Setting up chi sampling
core.scoring.ScoringManager: Creating carbohydrate omega preferences function.
core.scoring.carbohydrates.OmegaPreferencesFunction: Setting up omega preference sampling
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
core.scoring.CartesianBondedEnergy: Initializing IdealParametersDatabase with default Ks=300 , 80 , 80 , 10 , 80
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-lengths.txt
core.scoring.CartesianBondedEnergy: Read 759 bb-independent lengths.
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-angles.txt
core.scoring.CartesianBondedEnergy: Read 1434 bb-independent angles.
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-torsions.txt
core.scoring.CartesianBondedEnergy: Read 1 bb-independent torsions.
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-improper.txt
core.scoring.CartesianBondedEnergy: Read 2202 bb-independent improper tors.
protocols.jd2.parser.ScoreFunctionLoader: defined score function "dens" with weights "beta_cart"
protocols.jd2.parser.ScoreFunctionLoader:  setting dens weight elec_dens_fast to 100
protocols.jd2.parser.ScoreFunctionLoader: User defined per-residue sidechain density reweighing: 
protocols.jd2.parser.ScoreFunctionLoader:    ALA 0.88
protocols.jd2.parser.ScoreFunctionLoader:    CYS 0.81
protocols.jd2.parser.ScoreFunctionLoader:    ASP 0.76
protocols.jd2.parser.ScoreFunctionLoader:    GLU 0.76
protocols.jd2.parser.ScoreFunctionLoader:    PHE 0.88
protocols.jd2.parser.ScoreFunctionLoader:    GLY 1
protocols.jd2.parser.ScoreFunctionLoader:    HIS 0.81
protocols.jd2.parser.ScoreFunctionLoader:    ILE 0.88
protocols.jd2.parser.ScoreFunctionLoader:    LYS 0.76
protocols.jd2.parser.ScoreFunctionLoader:    LEU 0.88
protocols.jd2.parser.ScoreFunctionLoader:    MET 0.76
protocols.jd2.parser.ScoreFunctionLoader:    ASN 0.81
protocols.jd2.parser.ScoreFunctionLoader:    PRO 0.88
protocols.jd2.parser.ScoreFunctionLoader:    GLN 0.81
protocols.jd2.parser.ScoreFunctionLoader:    ARG 0.76
protocols.jd2.parser.ScoreFunctionLoader:    SER 0.81
protocols.jd2.parser.ScoreFunctionLoader:    THR 0.81
protocols.jd2.parser.ScoreFunctionLoader:    VAL 0.88
protocols.jd2.parser.ScoreFunctionLoader:    TRP 0.88
protocols.jd2.parser.ScoreFunctionLoader:    TYR 0.88
protocols.electron_density.util: Parsing SetupForDensityScoringMover----
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "setupdens" of type SetupForDensityScoring
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "loaddens" of type LoadDensityMap
protocols.relax.RelaxScriptManager: Reading relax scripts list from database.
core.scoring.ScoreFunctionFactory: SCOREFUNCTION: beta_genpot.wts
core.scoring.ScoreFunctionFactory: The -include_sugars flag was used with no sugar_bb weight set in the weights file.  Setting sugar_bb weight to 1.0 by default.
protocols.relax.RelaxScriptManager: Looking for MonomerRelax2019.txt
protocols.relax.RelaxScriptManager: ================== Reading script file: /home/ievab/software/rosetta_bin_linux_2020.08.61146_bundle/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
protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "relaxcart" of type FastRelax
protocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following movers and filters
protocols.rosetta_scripts.ParsedProtocol: added mover "setupdens" with filter "true_filter"
protocols.rosetta_scripts.ParsedProtocol: added mover "loaddens" with filter "true_filter"
protocols.rosetta_scripts.ParsedProtocol: added mover "relaxcart" with filter "true_filter"
protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: filling pose from saved copy initial_PM_LSU_210503_relax_0001.pdb
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER SetupForDensityScoring - setupdens=======================
core.scoring.electron_density.ElectronDensity: Loading Density Map
core.scoring.electron_density.ElectronDensity: [ WARNING ] No density map specified
core.scoring.electron_density.ElectronDensity: Loading Density Map
core.scoring.electron_density.ElectronDensity: [ WARNING ] No density map specified
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER LoadDensityMap - loaddens=======================
core.scoring.electron_density.ElectronDensity: Loading Density Map
core.scoring.electron_density.ElectronDensity: Loading density mapMERGED_hires_-55.mrc
core.scoring.electron_density.ElectronDensity:  Setting resolution to 2.8A
core.scoring.electron_density.ElectronDensity:           atom mask to 3.2A
core.scoring.electron_density.ElectronDensity:             CA mask to 6A
core.scoring.electron_density.ElectronDensity:  Read density map'MERGED_hires_-55.mrc'
core.scoring.electron_density.ElectronDensity:      extent: 700 x 700 x 700
core.scoring.electron_density.ElectronDensity:      origin: 0 x 0 x 0
core.scoring.electron_density.ElectronDensity:   altorigin: 0 x 0 x 0
core.scoring.electron_density.ElectronDensity:        grid: 700 x 700 x 700
core.scoring.electron_density.ElectronDensity:     celldim: 592.392 x 592.392 x 592.392
core.scoring.electron_density.ElectronDensity:  cellangles: 90 x 90 x 90
core.scoring.electron_density.ElectronDensity:  voxel vol.: 0.606086
core.scoring.electron_density.ElectronDensity: Effective resolution = 2.8
protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER FastRelax - relaxcart=======================
core.scoring.CartesianBondedEnergy: Creating new peptide-bonded energy container (10899)
core.scoring.methods.GenericBondedEnergy: Creating new peptide-bonded energy container (10899)
basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat
core.scoring.elec.util: Read 40 countpair representative atoms
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: OP2,P,OP1 to DB with theta0 = 2.08673 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: OP2,P,O5' to DB with theta0 = 1.8867 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: OP1,P,O5' to DB with theta0 = 1.88998 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: P,O5',C5' to DB with theta0 = 2.11066 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: O5',C5',C4' to DB with theta0 = 1.94901 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: O5',C5',H5' to DB with theta0 = 1.90267 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: O5',C5',H5'' to DB with theta0 = 1.90359 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: C4',C5',H5' to DB with theta0 = 1.9023 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: C4',C5',H5'' to DB with theta0 = 1.9022 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: H5',C5',H5'' to DB with theta0 = 1.90362 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: C5',C4',O4' to DB with theta0 = 1.91901 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: C5',C4',C3' to DB with theta0 = 2.02725 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: C5',C4',H4' to DB with theta0 = 1.89907 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: O4',C4',C3' to DB with theta0 = 1.8157 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: O4',C4',H4' to DB with theta0 = 1.89908 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: C3',C4',H4' to DB with theta0 = 1.89949 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: C4',O4',C1' to DB with theta0 = 1.91833 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: C4',C3',O3' to DB with theta0 = 1.97258 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: C4',C3',C2' to DB with theta0 = 1.79042 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: C4',C3',H3' to DB with theta0 = 1.90628 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: O3',C3',C2' to DB with theta0 = 1.98365 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: O3',C3',H3' to DB with theta0 = 1.90475 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: C2',C3',H3' to DB with theta0 = 1.9022 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: O4',C1',C2' to DB with theta0 = 1.88039 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: O4',C1',N1 to DB with theta0 = 1.90642 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: O4',C1',H1' to DB with theta0 = 1.90178 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: C2',C1',N1 to DB with theta0 = 1.95988 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: C2',C1',H1' to DB with theta0 = 1.90614 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: N1,C1',H1' to DB with theta0 = 1.90833 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: C3',C2',C1' to DB with theta0 = 1.77378 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: C3',C2',O2' to DB with theta0 = 1.9414 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: C3',C2',H2' to DB with theta0 = 1.94627 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: C1',C2',O2' to DB with theta0 = 1.90105 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: C1',C2',H2' to DB with theta0 = 1.94467 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: O2',C2',H2' to DB with theta0 = 1.94919 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: C2',O2',HO2' to DB with theta0 = 1.90245 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: C1',N1,C2 to DB with theta0 = 2.04443 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: C1',N1,C6 to DB with theta0 = 2.13542 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: C2,N1,C6 to DB with theta0 = 2.10334 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: N1,C2,O2 to DB with theta0 = 2.14878 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: N1,C2,N3 to DB with theta0 = 2.00879 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: O2,C2,N3 to DB with theta0 = 2.12561 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: C2,N3,C4 to DB with theta0 = 2.21856 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: C2,N3,H3 to DB with theta0 = 2.03204 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: C4,N3,H3 to DB with theta0 = 2.03259 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: N3,C4,O4 to DB with theta0 = 2.08382 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: N3,C4,C5 to DB with theta0 = 2.00175 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: O4,C4,C5 to DB with theta0 = 2.19761 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: C4,C5,C6 to DB with theta0 = 2.08469 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: C4,C5,H5 to DB with theta0 = 2.0983 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: C6,C5,H5 to DB with theta0 = 2.10019 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: N1,C6,C5 to DB with theta0 = 2.14923 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: N1,C6,H6 to DB with theta0 = 2.07658 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: C5,C6,H6 to DB with theta0 = 2.05738 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined length URA: P,OP2, to DB with d0 = 1.48521 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length URA: P,OP1, to DB with d0 = 1.48501 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length URA: P,O5', to DB with d0 = 1.59292 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length URA: O5',C5', to DB with d0 = 1.41951 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length URA: C5',C4', to DB with d0 = 1.50883 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length URA: C5',H5', to DB with d0 = 0.980078 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length URA: C5',H5'', to DB with d0 = 0.97972 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length URA: C4',O4', to DB with d0 = 1.45162 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length URA: C4',C3', to DB with d0 = 1.52094 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length URA: C4',H4', to DB with d0 = 0.97953 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length URA: O4',C1', to DB with d0 = 1.413 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length URA: C3',O3', to DB with d0 = 1.41636 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length URA: C3',C2', to DB with d0 = 1.52322 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length URA: C3',H3', to DB with d0 = 0.979621 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length URA: C1',C2', to DB with d0 = 1.52997 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length URA: C1',N1, to DB with d0 = 1.48301 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length URA: C1',H1', to DB with d0 = 0.980531 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length URA: C2',O2', to DB with d0 = 1.42055 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length URA: C2',H2', to DB with d0 = 0.97975 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length URA: O2',HO2', to DB with d0 = 0.980453 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length URA: N1,C2, to DB with d0 = 1.3827 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length URA: N1,C6, to DB with d0 = 1.37885 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length URA: C2,O2, to DB with d0 = 1.21866 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length URA: C2,N3, to DB with d0 = 1.37331 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length URA: N3,C4, to DB with d0 = 1.37866 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length URA: N3,H3, to DB with d0 = 0.979691 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length URA: C4,O4, to DB with d0 = 1.23196 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length URA: C4,C5, to DB with d0 = 1.43123 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length URA: C5,C6, to DB with d0 = 1.33692 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length URA: C5,H5, to DB with d0 = 0.980186 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length URA: C6,H6, to DB with d0 = 0.979067 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: C3',O3',P to DB with theta0 = 2.09873 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: OP2,P,OP1 to DB with theta0 = 2.08783 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: OP2,P,O5' to DB with theta0 = 1.88536 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: OP1,P,O5' to DB with theta0 = 1.8849 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: P,O5',C5' to DB with theta0 = 2.10997 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: O5',C5',C4' to DB with theta0 = 1.94703 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: O5',C5',H5' to DB with theta0 = 1.90373 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: O5',C5',H5'' to DB with theta0 = 1.90293 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: C4',C5',H5' to DB with theta0 = 1.90358 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: C4',C5',H5'' to DB with theta0 = 1.90354 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: H5',C5',H5'' to DB with theta0 = 1.90259 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: C5',C4',O4' to DB with theta0 = 1.91616 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: C5',C4',C3' to DB with theta0 = 2.025 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: C5',C4',H4' to DB with theta0 = 1.90024 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: O4',C4',C3' to DB with theta0 = 1.81674 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: O4',C4',H4' to DB with theta0 = 1.90047 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: C3',C4',H4' to DB with theta0 = 1.90118 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: C4',O4',C1' to DB with theta0 = 1.91954 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: C4',C3',O3' to DB with theta0 = 1.97173 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: C4',C3',C2' to DB with theta0 = 1.7902 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: C4',C3',H3' to DB with theta0 = 1.90521 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: O3',C3',C2' to DB with theta0 = 1.98421 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: O3',C3',H3' to DB with theta0 = 1.90445 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: C2',C3',H3' to DB with theta0 = 1.90411 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: O4',C1',C2' to DB with theta0 = 1.87909 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: O4',C1',N9 to DB with theta0 = 1.89738 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: O4',C1',H1' to DB with theta0 = 1.909 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: C2',C1',N9 to DB with theta0 = 1.95696 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: C2',C1',H1' to DB with theta0 = 1.91034 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: N9,C1',H1' to DB with theta0 = 1.91038 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: C3',C2',C1' to DB with theta0 = 1.7716 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: C3',C2',O2' to DB with theta0 = 1.94212 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: C3',C2',H2' to DB with theta0 = 1.94613 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: C1',C2',O2' to DB with theta0 = 1.90135 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: C1',C2',H2' to DB with theta0 = 1.94491 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: O2',C2',H2' to DB with theta0 = 1.95 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: C2',O2',HO2' to DB with theta0 = 1.90242 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: C2,N1,C6 to DB with theta0 = 2.18216 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: C2,N1,H1 to DB with theta0 = 2.05294 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: C6,N1,H1 to DB with theta0 = 2.04808 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: N1,C2,N2 to DB with theta0 = 2.03069 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: N1,C2,N3 to DB with theta0 = 2.16319 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: N2,C2,N3 to DB with theta0 = 2.08931 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: C2,N2,H22 to DB with theta0 = 2.09388 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: C2,N2,H21 to DB with theta0 = 2.09769 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: H22,N2,H21 to DB with theta0 = 2.09161 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: C2,N3,C4 to DB with theta0 = 1.9543 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: N3,C4,C5 to DB with theta0 = 2.24531 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: N3,C4,N9 to DB with theta0 = 2.19874 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: C5,C4,N9 to DB with theta0 = 1.83913 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: C4,C5,C6 to DB with theta0 = 2.07336 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: C4,C5,N7 to DB with theta0 = 1.93418 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: C6,C5,N7 to DB with theta0 = 2.27565 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: N1,C6,C5 to DB with theta0 = 1.94804 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: N1,C6,O6 to DB with theta0 = 2.09178 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: C5,C6,O6 to DB with theta0 = 2.24336 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: C5,N7,C8 to DB with theta0 = 1.82062 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: N7,C8,N9 to DB with theta0 = 1.9752 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: N7,C8,H8 to DB with theta0 = 2.15279 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: N9,C8,H8 to DB with theta0 = 2.1552 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: C1',N9,C4 to DB with theta0 = 2.20653 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: C1',N9,C8 to DB with theta0 = 2.221 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: C4,N9,C8 to DB with theta0 = 1.85566 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined length RGU: P,OP2, to DB with d0 = 1.48501 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RGU: P,OP1, to DB with d0 = 1.48541 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RGU: P,O5', to DB with d0 = 1.59352 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RGU: O5',C5', to DB with d0 = 1.41971 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RGU: C5',C4', to DB with d0 = 1.50851 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RGU: C5',H5', to DB with d0 = 0.97973 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RGU: C5',H5'', to DB with d0 = 0.980373 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RGU: C4',O4', to DB with d0 = 1.45181 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RGU: C4',C3', to DB with d0 = 1.52136 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RGU: C4',H4', to DB with d0 = 0.980454 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RGU: O4',C1', to DB with d0 = 1.4122 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RGU: C3',O3', to DB with d0 = 1.41754 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RGU: C3',C2', to DB with d0 = 1.52242 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RGU: C3',H3', to DB with d0 = 0.979184 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RGU: C1',C2', to DB with d0 = 1.52903 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RGU: C1',N9, to DB with d0 = 1.47502 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RGU: C1',H1', to DB with d0 = 0.98014 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RGU: C2',O2', to DB with d0 = 1.42037 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RGU: C2',H2', to DB with d0 = 0.980352 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RGU: O2',HO2', to DB with d0 = 0.980099 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RGU: N1,C2, to DB with d0 = 1.37372 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RGU: N1,C6, to DB with d0 = 1.39165 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RGU: N1,H1, to DB with d0 = 0.979946 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RGU: C2,N2, to DB with d0 = 1.3414 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RGU: C2,N3, to DB with d0 = 1.32303 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RGU: N2,H22, to DB with d0 = 0.980508 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RGU: N2,H21, to DB with d0 = 0.97963 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RGU: N3,C4, to DB with d0 = 1.34955 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RGU: C4,C5, to DB with d0 = 1.37893 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RGU: C4,N9, to DB with d0 = 1.37548 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RGU: C5,C6, to DB with d0 = 1.41919 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RGU: C5,N7, to DB with d0 = 1.38741 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RGU: C6,O6, to DB with d0 = 1.23627 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RGU: N7,C8, to DB with d0 = 1.30555 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RGU: C8,N9, to DB with d0 = 1.37396 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RGU: C8,H8, to DB with d0 = 0.979762 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: C3',O3',P to DB with theta0 = 2.09705 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: OP2,P,O3' to DB with theta0 = 1.88545 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: OP1,P,O3' to DB with theta0 = 1.88608 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RGU: O5',P,O3' to DB with theta0 = 1.81561 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined length RGU: P,O3', to DB with d0 = 1.607 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: OP2,P,O3' to DB with theta0 = 1.88511 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: OP1,P,O3' to DB with theta0 = 1.8858 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle URA: O5',P,O3' to DB with theta0 = 1.8148 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined length URA: P,O3', to DB with d0 = 1.60707 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: OP2,P,OP1 to DB with theta0 = 2.08834 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: OP2,P,O5' to DB with theta0 = 1.8846 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: OP1,P,O5' to DB with theta0 = 1.8855 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: P,O5',C5' to DB with theta0 = 2.10985 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: O5',C5',C4' to DB with theta0 = 1.94701 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: O5',C5',H5' to DB with theta0 = 1.90344 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: O5',C5',H5'' to DB with theta0 = 1.90428 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: C4',C5',H5' to DB with theta0 = 1.90262 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: C4',C5',H5'' to DB with theta0 = 1.90347 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: H5',C5',H5'' to DB with theta0 = 1.90256 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: C5',C4',O4' to DB with theta0 = 1.91614 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: C5',C4',C3' to DB with theta0 = 2.02495 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: C5',C4',H4' to DB with theta0 = 1.9004 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: O4',C4',C3' to DB with theta0 = 1.81717 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: O4',C4',H4' to DB with theta0 = 1.90135 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: C3',C4',H4' to DB with theta0 = 1.89985 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: C4',O4',C1' to DB with theta0 = 1.91958 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: C4',C3',O3' to DB with theta0 = 1.97304 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: C4',C3',C2' to DB with theta0 = 1.7906 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: C4',C3',H3' to DB with theta0 = 1.90485 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: O3',C3',C2' to DB with theta0 = 1.98358 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: O3',C3',H3' to DB with theta0 = 1.90441 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: C2',C3',H3' to DB with theta0 = 1.90339 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: O4',C1',C2' to DB with theta0 = 1.87913 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: O4',C1',N9 to DB with theta0 = 1.89665 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: O4',C1',H1' to DB with theta0 = 1.91025 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: C2',C1',N9 to DB with theta0 = 1.95723 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: C2',C1',H1' to DB with theta0 = 1.9095 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: N9,C1',H1' to DB with theta0 = 1.91043 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: C3',C2',C1' to DB with theta0 = 1.77096 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: C3',C2',O2' to DB with theta0 = 1.94176 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: C3',C2',H2' to DB with theta0 = 1.94605 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: C1',C2',O2' to DB with theta0 = 1.9016 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: C1',C2',H2' to DB with theta0 = 1.94484 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: O2',C2',H2' to DB with theta0 = 1.95078 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: C2',O2',HO2' to DB with theta0 = 1.90171 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: C2,N1,C6 to DB with theta0 = 2.07054 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: N1,C2,N3 to DB with theta0 = 2.25453 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: N1,C2,H2 to DB with theta0 = 2.01442 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: N3,C2,H2 to DB with theta0 = 2.01424 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: C2,N3,C4 to DB with theta0 = 1.93192 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: N3,C4,C5 to DB with theta0 = 2.21323 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: N3,C4,N9 to DB with theta0 = 2.22268 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: C5,C4,N9 to DB with theta0 = 1.84728 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: C4,C5,C6 to DB with theta0 = 2.04153 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: C4,C5,N7 to DB with theta0 = 1.93186 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: C6,C5,N7 to DB with theta0 = 2.3098 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: N1,C6,C5 to DB with theta0 = 2.05462 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: N1,C6,N6 to DB with theta0 = 2.06996 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: C5,C6,N6 to DB with theta0 = 2.1586 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: C6,N6,H61 to DB with theta0 = 2.09404 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: C6,N6,H62 to DB with theta0 = 2.09514 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: H61,N6,H62 to DB with theta0 = 2.094 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: C5,N7,C8 to DB with theta0 = 1.81295 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: N7,C8,N9 to DB with theta0 = 1.98615 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: N7,C8,H8 to DB with theta0 = 2.14826 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: N9,C8,H8 to DB with theta0 = 2.14877 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: C1',N9,C4 to DB with theta0 = 2.20372 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: C1',N9,C8 to DB with theta0 = 2.23292 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: C4,N9,C8 to DB with theta0 = 1.84654 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined length RAD: P,OP2, to DB with d0 = 1.48447 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RAD: P,OP1, to DB with d0 = 1.48421 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RAD: P,O5', to DB with d0 = 1.59359 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RAD: O5',C5', to DB with d0 = 1.41985 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RAD: C5',C4', to DB with d0 = 1.50813 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RAD: C5',H5', to DB with d0 = 0.980229 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RAD: C5',H5'', to DB with d0 = 0.979487 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RAD: C4',O4', to DB with d0 = 1.45151 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RAD: C4',C3', to DB with d0 = 1.52109 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RAD: C4',H4', to DB with d0 = 0.980192 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RAD: O4',C1', to DB with d0 = 1.41273 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RAD: C3',O3', to DB with d0 = 1.41704 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RAD: C3',C2', to DB with d0 = 1.52312 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RAD: C3',H3', to DB with d0 = 0.980582 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RAD: C1',C2', to DB with d0 = 1.52938 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RAD: C1',N9, to DB with d0 = 1.4752 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RAD: C1',H1', to DB with d0 = 0.980688 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RAD: C2',O2', to DB with d0 = 1.42019 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RAD: C2',H2', to DB with d0 = 0.980264 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RAD: O2',HO2', to DB with d0 = 0.979717 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RAD: N1,C2, to DB with d0 = 1.33918 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RAD: N1,C6, to DB with d0 = 1.35039 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RAD: C2,N3, to DB with d0 = 1.33134 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RAD: C2,H2, to DB with d0 = 0.980369 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RAD: N3,C4, to DB with d0 = 1.34488 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RAD: C4,C5, to DB with d0 = 1.38238 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RAD: C4,N9, to DB with d0 = 1.37391 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RAD: C5,C6, to DB with d0 = 1.40621 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RAD: C5,N7, to DB with d0 = 1.3884 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RAD: C6,N6, to DB with d0 = 1.33484 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RAD: N6,H61, to DB with d0 = 0.980394 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RAD: N6,H62, to DB with d0 = 0.979816 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RAD: N7,C8, to DB with d0 = 1.31006 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RAD: C8,N9, to DB with d0 = 1.37315 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RAD: C8,H8, to DB with d0 = 0.980513 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: C3',O3',P to DB with theta0 = 2.09751 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: OP2,P,O3' to DB with theta0 = 1.88566 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: OP1,P,O3' to DB with theta0 = 1.8862 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RAD: O5',P,O3' to DB with theta0 = 1.81471 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined length RAD: P,O3', to DB with d0 = 1.60735 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: OP2,P,OP1 to DB with theta0 = 2.08734 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: OP2,P,O5' to DB with theta0 = 1.88598 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: OP1,P,O5' to DB with theta0 = 1.8846 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: P,O5',C5' to DB with theta0 = 2.11066 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: O5',C5',C4' to DB with theta0 = 1.94909 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: O5',C5',H5' to DB with theta0 = 1.90258 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: O5',C5',H5'' to DB with theta0 = 1.9026 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: C4',C5',H5' to DB with theta0 = 1.90309 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: C4',C5',H5'' to DB with theta0 = 1.90261 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: H5',C5',H5'' to DB with theta0 = 1.90341 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: C5',C4',O4' to DB with theta0 = 1.91837 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: C5',C4',C3' to DB with theta0 = 2.02711 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: C5',C4',H4' to DB with theta0 = 1.89834 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: O4',C4',C3' to DB with theta0 = 1.81561 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: O4',C4',H4' to DB with theta0 = 1.89965 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: C3',C4',H4' to DB with theta0 = 1.90063 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: C4',O4',C1' to DB with theta0 = 1.91827 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: C4',C3',O3' to DB with theta0 = 1.97125 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: C4',C3',C2' to DB with theta0 = 1.79019 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: C4',C3',H3' to DB with theta0 = 1.90715 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: O3',C3',C2' to DB with theta0 = 1.98335 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: O3',C3',H3' to DB with theta0 = 1.90443 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: C2',C3',H3' to DB with theta0 = 1.90366 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: O4',C1',C2' to DB with theta0 = 1.88047 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: O4',C1',N1 to DB with theta0 = 1.9061 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: O4',C1',H1' to DB with theta0 = 1.90022 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: C2',C1',N1 to DB with theta0 = 1.96021 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: C2',C1',H1' to DB with theta0 = 1.9056 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: N1,C1',H1' to DB with theta0 = 1.91024 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: C3',C2',C1' to DB with theta0 = 1.7732 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: C3',C2',O2' to DB with theta0 = 1.94167 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: C3',C2',H2' to DB with theta0 = 1.94486 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: C1',C2',O2' to DB with theta0 = 1.90184 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: C1',C2',H2' to DB with theta0 = 1.94521 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: O2',C2',H2' to DB with theta0 = 1.94955 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: C2',O2',HO2' to DB with theta0 = 1.90343 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: C1',N1,C2 to DB with theta0 = 2.06557 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: C1',N1,C6 to DB with theta0 = 2.12836 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: C2,N1,C6 to DB with theta0 = 2.08926 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: N1,C2,O2 to DB with theta0 = 2.08106 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: N1,C2,N3 to DB with theta0 = 2.08612 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: O2,C2,N3 to DB with theta0 = 2.116 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: C2,N3,C4 to DB with theta0 = 2.09574 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: N3,C4,N4 to DB with theta0 = 2.05939 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: N3,C4,C5 to DB with theta0 = 2.1254 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: N4,C4,C5 to DB with theta0 = 2.0984 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: C4,N4,H42 to DB with theta0 = 2.0937 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: C4,N4,H41 to DB with theta0 = 2.09435 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: H42,N4,H41 to DB with theta0 = 2.09513 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: C4,C5,C6 to DB with theta0 = 2.05277 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: C4,C5,H5 to DB with theta0 = 2.11515 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: C6,C5,H5 to DB with theta0 = 2.11526 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: N1,C6,C5 to DB with theta0 = 2.11709 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: N1,C6,H6 to DB with theta0 = 2.0918 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: C5,C6,H6 to DB with theta0 = 2.0743 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined length RCY: P,OP2, to DB with d0 = 1.48441 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RCY: P,OP1, to DB with d0 = 1.48514 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RCY: P,O5', to DB with d0 = 1.59298 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RCY: O5',C5', to DB with d0 = 1.41951 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RCY: C5',C4', to DB with d0 = 1.50943 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RCY: C5',H5', to DB with d0 = 0.97995 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RCY: C5',H5'', to DB with d0 = 0.979938 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RCY: C4',O4', to DB with d0 = 1.45115 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RCY: C4',C3', to DB with d0 = 1.5207 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RCY: C4',H4', to DB with d0 = 0.979517 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RCY: O4',C1', to DB with d0 = 1.41309 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RCY: C3',O3', to DB with d0 = 1.41719 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RCY: C3',C2', to DB with d0 = 1.52374 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RCY: C3',H3', to DB with d0 = 0.979894 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RCY: C1',C2', to DB with d0 = 1.53011 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RCY: C1',N1, to DB with d0 = 1.48393 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RCY: C1',H1', to DB with d0 = 0.979578 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RCY: C2',O2', to DB with d0 = 1.41996 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RCY: C2',H2', to DB with d0 = 0.979647 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RCY: O2',HO2', to DB with d0 = 0.979523 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RCY: N1,C2, to DB with d0 = 1.40049 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RCY: N1,C6, to DB with d0 = 1.37023 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RCY: C2,O2, to DB with d0 = 1.24072 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RCY: C2,N3, to DB with d0 = 1.35279 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RCY: N3,C4, to DB with d0 = 1.33277 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RCY: C4,N4, to DB with d0 = 1.33551 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RCY: C4,C5, to DB with d0 = 1.42342 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RCY: N4,H42, to DB with d0 = 0.979634 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RCY: N4,H41, to DB with d0 = 0.980164 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RCY: C5,C6, to DB with d0 = 1.33853 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RCY: C5,H5, to DB with d0 = 0.980188 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length RCY: C6,H6, to DB with d0 = 0.979345 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: C3',O3',P to DB with theta0 = 2.09772 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: OP2,P,O3' to DB with theta0 = 1.88648 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: OP1,P,O3' to DB with theta0 = 1.88525 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle RCY: O5',P,O3' to DB with theta0 = 1.81565 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined length RCY: P,O3', to DB with d0 = 1.60681 , Kd = 300
core.scoring.electron_density.ElectronDensity: Setting [kmin_,kmax_] to [0.062821,1.90674]
core.scoring.electron_density.ElectronDensity: Bin 1:  B(C/N/O/S)=5.41598 / 8.49828 / 10.6554 / 5.60835  sum=(0,0)
core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.
core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /home/ievab/software/rosetta_bin_linux_2020.08.61146_bundle/main/database/rotamer/beta_nov2016/Dunbrack10.lib.bin
core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/ievab/software/rosetta_bin_linux_2020.08.61146_bundle/main/database/rotamer/beta_nov2016/Dunbrack10.lib.bin'.
core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.16 seconds to load from binary
core.scoring.CartesianBondedEnergy: Adding undefined angle ZN: V1,ZN,V2 to DB with theta0 = 1.91114 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle ZN: V1,ZN,V3 to DB with theta0 = 1.91114 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle ZN: V1,ZN,V4 to DB with theta0 = 1.91114 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle ZN: V2,ZN,V3 to DB with theta0 = 1.91013 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle ZN: V2,ZN,V4 to DB with theta0 = 1.91013 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined angle ZN: V3,ZN,V4 to DB with theta0 = 1.91013 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined length ZN: ZN,V1, to DB with d0 = 2.2 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length ZN: ZN,V2, to DB with d0 = 2.2 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length ZN: ZN,V3, to DB with d0 = 2.2 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length ZN: ZN,V4, to DB with d0 = 2.2 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined angle VRT: X,ORIG,Y to DB with theta0 = 1.5708 , Ktheta = 80
core.scoring.CartesianBondedEnergy: Adding undefined length VRT: ORIG,X, to DB with d0 = 1 , Kd = 300
core.scoring.CartesianBondedEnergy: Adding undefined length VRT: ORIG,Y, to DB with d0 = 1 , Kd = 300
protocols.relax.FastRelax: CMD: repeat  -607381  0  0  0.55
protocols.relax.FastRelax: CMD: coord_cst_weight  -607381  0  0  0.55
protocols.relax.FastRelax: CMD: scale:fa_rep  -621676  0  0  0.022
core.pack.task: Packer task: initialize from command line() 
core.pack.pack_rotamers: built 186127 rotamers at 10899 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -628847  0  0  0.022
protocols.relax.FastRelax: CMD: scale:fa_rep  -628592  0  0  0.02805
core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 6104 BRANCH 1
core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 10724 BRANCH 1
core.optimization.LineMinimizer: [ ERROR ] Inaccurate G! step= 3.8147e-08 Deriv= -1.76896e+11 Finite Diff= 7.98464e+09
core.optimization.LineMinimizer: [ ERROR ] Inaccurate G! step= 4.64377e-09 Deriv= -1.76896e+11 Finite Diff= 6.01612e+08
core.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#1
protocols.relax.FastRelax: CMD: min  -628592  0  0  0.02805
protocols.relax.FastRelax: CMD: coord_cst_weight  -628592  0  0  0.02805
protocols.relax.FastRelax: CMD: scale:fa_rep  -623631  0  0  0.14575
core.pack.task: Packer task: initialize from command line() 
core.pack.pack_rotamers: built 169099 rotamers at 10899 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -624531  0  0  0.14575
protocols.relax.FastRelax: CMD: scale:fa_rep  -624282  0  0  0.154
core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 6104 BRANCH 1
core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 10724 BRANCH 1
core.optimization.LineMinimizer: [ ERROR ] Inaccurate G! step= 3.8147e-08 Deriv= -1.76896e+11 Finite Diff= 7.98431e+09
core.optimization.LineMinimizer: [ ERROR ] Inaccurate G! step= 4.64377e-09 Deriv= -1.76896e+11 Finite Diff= 6.01279e+08
core.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#1
protocols.relax.FastRelax: CMD: min  -624282  0  0  0.154
protocols.relax.FastRelax: CMD: coord_cst_weight  -624282  0  0  0.154
protocols.relax.FastRelax: CMD: scale:fa_rep  -619641  0  0  0.30745
core.pack.task: Packer task: initialize from command line() 
core.pack.pack_rotamers: built 161845 rotamers at 10899 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -619858  0  0  0.30745
protocols.relax.FastRelax: CMD: scale:fa_rep  -619521  0  0  0.31955
core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 6104 BRANCH 1
core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 10724 BRANCH 1
core.optimization.LineMinimizer: [ ERROR ] Inaccurate G! step= 3.8147e-08 Deriv= -1.76897e+11 Finite Diff= 7.98348e+09
core.optimization.LineMinimizer: [ ERROR ] Inaccurate G! step= 4.64375e-09 Deriv= -1.76897e+11 Finite Diff= 6.00427e+08
core.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#1
protocols.relax.FastRelax: CMD: min  -619521  0  0  0.31955
protocols.relax.FastRelax: CMD: coord_cst_weight  -619521  0  0  0.31955
protocols.relax.FastRelax: CMD: scale:fa_rep  -613095  0  0  0.55
core.pack.task: Packer task: initialize from command line() 
core.pack.pack_rotamers: built 155993 rotamers at 10899 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -613291  0  0  0.55
core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 6104 BRANCH 1
core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 10724 BRANCH 1
core.optimization.LineMinimizer: [ ERROR ] Inaccurate G! step= 3.8147e-08 Deriv= -1.769e+11 Finite Diff= 7.98155e+09
core.optimization.LineMinimizer: [ ERROR ] Inaccurate G! step= 4.64373e-09 Deriv= -1.769e+11 Finite Diff= 5.98444e+08
core.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#1
protocols.relax.FastRelax: CMD: min  -613291  0  0  0.55
protocols.relax.FastRelax: MRP: 0  -613291  -613291  0  0  
protocols.relax.FastRelax: CMD: accept_to_best  -613291  0  0  0.55
protocols.relax.FastRelax: CMD: endrepeat  -613291  0  0  0.55
protocols.relax.FastRelax: CMD: coord_cst_weight  -613291  0  0  0.55
protocols.relax.FastRelax: CMD: scale:fa_rep  -627235  0  0  0.022
core.pack.task: Packer task: initialize from command line() 
core.pack.pack_rotamers: built 186025 rotamers at 10899 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -628641  0  0  0.022
protocols.relax.FastRelax: CMD: scale:fa_rep  -628376  0  0  0.02805
core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 6104 BRANCH 1
core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 10724 BRANCH 1
core.optimization.LineMinimizer: [ ERROR ] Inaccurate G! step= 3.8147e-08 Deriv= -1.76896e+11 Finite Diff= 7.98462e+09
core.optimization.LineMinimizer: [ ERROR ] Inaccurate G! step= 4.64377e-09 Deriv= -1.76896e+11 Finite Diff= 6.01593e+08
core.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#1
protocols.relax.FastRelax: CMD: min  -628376  0  0  0.02805
protocols.relax.FastRelax: CMD: coord_cst_weight  -628376  0  0  0.02805
protocols.relax.FastRelax: CMD: scale:fa_rep  -623218  0  0  0.14575
core.pack.task: Packer task: initialize from command line() 
core.pack.pack_rotamers: built 169078 rotamers at 10899 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -624355  0  0  0.14575
protocols.relax.FastRelax: CMD: scale:fa_rep  -624107  0  0  0.154
core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 6104 BRANCH 1
core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 10724 BRANCH 1
core.optimization.LineMinimizer: [ ERROR ] Inaccurate G! step= 3.8147e-08 Deriv= -1.76896e+11 Finite Diff= 7.98429e+09
core.optimization.LineMinimizer: [ ERROR ] Inaccurate G! step= 4.64377e-09 Deriv= -1.76896e+11 Finite Diff= 6.01262e+08
core.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#1
protocols.relax.FastRelax: CMD: min  -624107  0  0  0.154
protocols.relax.FastRelax: CMD: coord_cst_weight  -624107  0  0  0.154
protocols.relax.FastRelax: CMD: scale:fa_rep  -619486  0  0  0.30745
core.pack.task: Packer task: initialize from command line() 
core.pack.pack_rotamers: built 161830 rotamers at 10899 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -619763  0  0  0.30745
protocols.relax.FastRelax: CMD: scale:fa_rep  -619431  0  0  0.31955
core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 6104 BRANCH 1
core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 10724 BRANCH 1
core.optimization.LineMinimizer: [ ERROR ] Inaccurate G! step= 3.8147e-08 Deriv= -1.76897e+11 Finite Diff= 7.98348e+09
core.optimization.LineMinimizer: [ ERROR ] Inaccurate G! step= 4.64375e-09 Deriv= -1.76897e+11 Finite Diff= 6.00429e+08
core.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#1
protocols.relax.FastRelax: CMD: min  -619431  0  0  0.31955
protocols.relax.FastRelax: CMD: coord_cst_weight  -619431  0  0  0.31955
protocols.relax.FastRelax: CMD: scale:fa_rep  -613107  0  0  0.55
core.pack.task: Packer task: initialize from command line() 
core.pack.pack_rotamers: built 155982 rotamers at 10899 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -613261  0  0  0.55
core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 6104 BRANCH 1
core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 10724 BRANCH 1
core.optimization.LineMinimizer: [ ERROR ] Inaccurate G! step= 3.8147e-08 Deriv= -1.769e+11 Finite Diff= 7.98156e+09
core.optimization.LineMinimizer: [ ERROR ] Inaccurate G! step= 4.64373e-09 Deriv= -1.769e+11 Finite Diff= 5.98446e+08
core.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#1
protocols.relax.FastRelax: CMD: min  -613261  0  0  0.55
protocols.relax.FastRelax: MRP: 1  -613261  -613291  0  0  
protocols.relax.FastRelax: CMD: accept_to_best  -613261  0  0  0.55
protocols.relax.FastRelax: CMD: endrepeat  -613261  0  0  0.55
protocols.relax.FastRelax: CMD: coord_cst_weight  -613261  0  0  0.55
protocols.relax.FastRelax: CMD: scale:fa_rep  -627194  0  0  0.022
core.pack.task: Packer task: initialize from command line() 
core.pack.pack_rotamers: built 186027 rotamers at 10899 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -628623  0  0  0.022
protocols.relax.FastRelax: CMD: scale:fa_rep  -628358  0  0  0.02805
core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 6104 BRANCH 1
core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 10724 BRANCH 1
core.optimization.LineMinimizer: [ ERROR ] Inaccurate G! step= 3.8147e-08 Deriv= -1.76896e+11 Finite Diff= 7.98462e+09
core.optimization.LineMinimizer: [ ERROR ] Inaccurate G! step= 4.64377e-09 Deriv= -1.76896e+11 Finite Diff= 6.01593e+08
core.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#1
protocols.relax.FastRelax: CMD: min  -628358  0  0  0.02805
protocols.relax.FastRelax: CMD: coord_cst_weight  -628358  0  0  0.02805
protocols.relax.FastRelax: CMD: scale:fa_rep  -623218  0  0  0.14575
core.pack.task: Packer task: initialize from command line() 
core.pack.pack_rotamers: built 169082 rotamers at 10899 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -624312  0  0  0.14575
protocols.relax.FastRelax: CMD: scale:fa_rep  -624064  0  0  0.154
core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 6104 BRANCH 1
core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 10724 BRANCH 1
core.optimization.LineMinimizer: [ ERROR ] Inaccurate G! step= 3.8147e-08 Deriv= -1.76896e+11 Finite Diff= 7.98429e+09
core.optimization.LineMinimizer: [ ERROR ] Inaccurate G! step= 4.64377e-09 Deriv= -1.76896e+11 Finite Diff= 6.01264e+08
core.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#1
protocols.relax.FastRelax: CMD: min  -624064  0  0  0.154
protocols.relax.FastRelax: CMD: coord_cst_weight  -624064  0  0  0.154
protocols.relax.FastRelax: CMD: scale:fa_rep  -619453  0  0  0.30745
core.pack.task: Packer task: initialize from command line() 
core.pack.pack_rotamers: built 161834 rotamers at 10899 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -619713  0  0  0.30745
protocols.relax.FastRelax: CMD: scale:fa_rep  -619382  0  0  0.31955
core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 6104 BRANCH 1
core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 10724 BRANCH 1
core.optimization.LineMinimizer: [ ERROR ] Inaccurate G! step= 3.8147e-08 Deriv= -1.76897e+11 Finite Diff= 7.98348e+09
core.optimization.LineMinimizer: [ ERROR ] Inaccurate G! step= 4.64375e-09 Deriv= -1.76897e+11 Finite Diff= 6.00426e+08
core.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#1
protocols.relax.FastRelax: CMD: min  -619382  0  0  0.31955
protocols.relax.FastRelax: CMD: coord_cst_weight  -619382  0  0  0.31955
protocols.relax.FastRelax: CMD: scale:fa_rep  -613072  0  0  0.55
core.pack.task: Packer task: initialize from command line() 
core.pack.pack_rotamers: built 155986 rotamers at 10899 positions.
core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph
protocols.relax.FastRelax: CMD: repack  -613226  0  0  0.55
core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 6104 BRANCH 1
core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 10724 BRANCH 1
core.optimization.LineMinimizer: [ ERROR ] Inaccurate G! step= 3.8147e-08 Deriv= -1.769e+11 Finite Diff= 7.98153e+09
core.optimization.LineMinimizer: [ ERROR ] Inaccurate G! step= 4.64373e-09 Deriv= -1.769e+11 Finite Diff= 5.98424e+08
core.optimization.Minimizer: Line search failed even after resetting Hessian; aborting at iter#1
protocols.relax.FastRelax: CMD: min  -613226  0  0  0.55
protocols.relax.FastRelax: MRP: 2  -613226  -613291  0  0  
protocols.relax.FastRelax: CMD: accept_to_best  -613226  0  0  0.55
protocols.relax.FastRelax: CMD: endrepeat  -613226  0  0  0.55
protocols::checkpoint: Deleting checkpoints of FastRelax
protocols.rosetta_scripts.ParsedProtocol: setting status to success
protocols.jd2.JobDistributor: initial_PM_LSU_210503_relax_0001_relax100_0001 reported success in 3883 seconds
protocols.jd2.JobDistributor: no more batches to process... 
protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 3888 seconds