This notebook contains material from PyRosetta; content is available on Github.

Global Ligand Docking using XMLObjects Using the ref2015.wts Scorefunction

Warning: This notebook uses pyrosetta.distributed.viewer code, which runs in jupyter notebook and might not run if you're using jupyterlab.

Note: This Jupyter notebook requires the PyRosetta distributed layer. Please make sure to activate the PyRosetta.notebooks conda environment before running this notebook. The kernel is set to use this environment.

In [1]:
import logging
logging.basicConfig(level=logging.INFO)
import matplotlib
%matplotlib inline
import os
import pandas as pd
import pyrosetta
import pyrosetta.distributed.viewer as viewer
import seaborn
seaborn.set()
import sys

# Notebook setup
import sys
if 'google.colab' in sys.modules:
   print("This Jupyter notebook uses parallelization and is therefore not set up for the Google Colab environment.")
   sys.exit(0)

Now we change the scorefunction to ref2015.wts, the weights of which were optimized on ligands with AM1-BCC partial charges generated with Amber's antechamber. Therefore, the Rosetta .params file should ideally also have AM1-BCC partial charges generated with antechamber.

In [2]:
ligand_params = "inputs/TPA.am1-bcc.fa.params"
flags = f"""
-ignore_unrecognized_res 1
-extra_res_fa {ligand_params}
"""
pyrosetta.distributed.init(flags)
pose = pyrosetta.io.pose_from_file(filename="inputs/test_lig.pdb")
scorefxn = pyrosetta.create_score_function("ref2015")
INFO:pyrosetta.distributed:maybe_init performing pyrosetta initialization: {'extra_options': '-ignore_unrecognized_res 1 -extra_res_fa inputs/TPA.am1-bcc.fa.params', 'silent': True}
INFO:pyrosetta.rosetta:Found rosetta database at: /mnt/home/klimaj/git/Rosetta/main/source/src/python/PyRosetta/src/pyrosetta/database; using it....
INFO:pyrosetta.rosetta:PyRosetta-4 2019 [Rosetta PyRosetta4.conda.linux.CentOS.python36.Release 2019.39+release.93456a567a8125cafdf7f8cb44400bc20b570d81 2019-09-26T14:24:44] retrieved from: http://www.pyrosetta.org
(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.
INFO:rosetta:core.init: {0} Checking for fconfig files in pwd and ./rosetta/flags
INFO:rosetta:core.init: {0} Rosetta version: PyRosetta4.conda.linux.CentOS.python36.Release r233 2019.39+release.93456a5 93456a567a8125cafdf7f8cb44400bc20b570d81 http://www.pyrosetta.org 2019-09-26T14:24:44
INFO:rosetta:core.init: {0} command: PyRosetta -ex1 -ex2aro -ignore_unrecognized_res 1 -extra_res_fa inputs/TPA.am1-bcc.fa.params -database /mnt/home/klimaj/git/Rosetta/main/source/src/python/PyRosetta/src/pyrosetta/database
INFO:rosetta:basic.random.init_random_generator: {0} 'RNG device' seed mode, using '/dev/urandom', seed=-2105863589 seed_offset=0 real_seed=-2105863589 thread_index=0
INFO:rosetta:basic.random.init_random_generator: {0} RandomGenerator:init: Normal mode, seed=-2105863589 RG_type=mt19937
INFO:rosetta:core.chemical.GlobalResidueTypeSet: {0} Finished initializing fa_standard residue type set.  Created 981 residue types
INFO:rosetta:core.chemical.GlobalResidueTypeSet: {0} Total time to initialize 1.97866 seconds.
INFO:rosetta:core.import_pose.import_pose: {0} File 'inputs/test_lig.pdb' automatically determined to be of type PDB
INFO:rosetta:core.scoring.etable: {0} Starting energy table calculation
INFO:rosetta:core.scoring.etable: {0} smooth_etable: changing atr/rep split to bottom of energy well
INFO:rosetta:core.scoring.etable: {0} smooth_etable: spline smoothing lj etables (maxdis = 6)
INFO:rosetta:core.scoring.etable: {0} smooth_etable: spline smoothing solvation etables (max_dis = 6)
INFO:rosetta:core.scoring.etable: {0} Finished calculating energy tables.
INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv
INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv
INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv
INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv
INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv
INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/rama/fd/all.ramaProb
INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb
INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt
INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt
INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt
INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt
INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/P_AA_pp/P_AA
INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/P_AA_pp/P_AA_n
INFO:rosetta:core.scoring.P_AA: {0} shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.
INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop

Ligand docking using XmlObjects:

In [3]:
xml = pyrosetta.rosetta.protocols.rosetta_scripts.XmlObjects.create_from_string("""
<ROSETTASCRIPTS>
  <SCOREFXNS>
    <ScoreFunction name="fa_standard" weights="ref2015.wts"/>
  </SCOREFXNS>
  <RESIDUE_SELECTORS>
    <Chain name="chX" chains="X"/>
  </RESIDUE_SELECTORS>
  <SIMPLE_METRICS>
    <RMSDMetric name="rmsd_chX" residue_selector="chX" reference_name="store_native" residue_selector_ref="chX" robust="true" rmsd_type="rmsd_all" />
  </SIMPLE_METRICS>
  <SCORINGGRIDS ligand_chain="X" width="25">
    <ClassicGrid grid_name="vdw" weight="1.0"/>
  </SCORINGGRIDS>
  <LIGAND_AREAS>
    <LigandArea name="docking_sidechain_X" chain="X" cutoff="6.0" add_nbr_radius="true" all_atom_mode="true" minimize_ligand="10"/>
    <LigandArea name="final_sidechain_X" chain="X" cutoff="6.0" add_nbr_radius="true" all_atom_mode="true"/>
    <LigandArea name="final_backbone_X" chain="X" cutoff="7.0" add_nbr_radius="false" all_atom_mode="true" Calpha_restraints="0.3"/>
  </LIGAND_AREAS>
  <INTERFACE_BUILDERS>
    <InterfaceBuilder name="side_chain_for_docking" ligand_areas="docking_sidechain_X"/>
    <InterfaceBuilder name="side_chain_for_final" ligand_areas="final_sidechain_X"/>
    <InterfaceBuilder name="backbone" ligand_areas="final_backbone_X" extension_window="3"/>
  </INTERFACE_BUILDERS>
  <MOVEMAP_BUILDERS>
    <MoveMapBuilder name="docking" sc_interface="side_chain_for_docking" minimize_water="true"/>
    <MoveMapBuilder name="final" sc_interface="side_chain_for_final" bb_interface="backbone" minimize_water="true"/>
  </MOVEMAP_BUILDERS>
  <MOVERS>
    <SavePoseMover name="spm" restore_pose="0" reference_name="store_native"/>
    <Transform name="transform" chain="X" box_size="20.0" move_distance="10" angle="360" initial_perturb="2" cycles="500" repeats="5" temperature="1000"/>
    <HighResDocker name="high_res_docker" cycles="9" repack_every_Nth="3" scorefxn="fa_standard" movemap_builder="docking"/>
    <FinalMinimizer name="final" scorefxn="fa_standard" movemap_builder="final"/>
  </MOVERS>
  <FILTERS>
      <LigInterfaceEnergy name="interfE" scorefxn="fa_standard" energy_cutoff="0.0" confidence="0"/>
      <SimpleMetricFilter name="rmsd_chX" metric="rmsd_chX" cutoff="999999." comparison_type="lt" confidence="0"/>
  </FILTERS>
  <PROTOCOLS>
    <Add mover="spm"/>
    <Add mover="transform"/>
    <Add mover="high_res_docker"/>
    <Add mover="final"/>
    <Add filter="interfE"/>
    <Add filter="rmsd_chX"/>
  </PROTOCOLS>
</ROSETTASCRIPTS>
""").get_mover("ParsedProtocol")
INFO:rosetta:protocols.rosetta_scripts.RosettaScriptsParser: {0} Generating XML Schema for rosetta_scripts...
INFO:rosetta:protocols.rosetta_scripts.RosettaScriptsParser: {0} ...done
INFO:rosetta:protocols.rosetta_scripts.RosettaScriptsParser: {0} Initializing schema validator...
INFO:rosetta:protocols.rosetta_scripts.RosettaScriptsParser: {0} ...done
INFO:rosetta:protocols.rosetta_scripts.RosettaScriptsParser: {0} Validating input script...
INFO:rosetta:protocols.rosetta_scripts.RosettaScriptsParser: {0} ...done
INFO:rosetta:protocols.rosetta_scripts.RosettaScriptsParser: {0} Parsed script:
<ROSETTASCRIPTS>
	<SCOREFXNS>
		<ScoreFunction name="fa_standard" weights="ref2015.wts"/>
	</SCOREFXNS>
	<RESIDUE_SELECTORS>
		<Chain chains="X" name="chX"/>
	</RESIDUE_SELECTORS>
	<SIMPLE_METRICS>
		<RMSDMetric name="rmsd_chX" reference_name="store_native" residue_selector="chX" residue_selector_ref="chX" rmsd_type="rmsd_all" robust="true"/>
	</SIMPLE_METRICS>
	<SCORINGGRIDS ligand_chain="X" width="25">
		<ClassicGrid grid_name="vdw" weight="1.0"/>
	</SCORINGGRIDS>
	<LIGAND_AREAS>
		<LigandArea add_nbr_radius="true" all_atom_mode="true" chain="X" cutoff="6.0" minimize_ligand="10" name="docking_sidechain_X"/>
		<LigandArea add_nbr_radius="true" all_atom_mode="true" chain="X" cutoff="6.0" name="final_sidechain_X"/>
		<LigandArea Calpha_restraints="0.3" add_nbr_radius="false" all_atom_mode="true" chain="X" cutoff="7.0" name="final_backbone_X"/>
	</LIGAND_AREAS>
	<INTERFACE_BUILDERS>
		<InterfaceBuilder ligand_areas="docking_sidechain_X" name="side_chain_for_docking"/>
		<InterfaceBuilder ligand_areas="final_sidechain_X" name="side_chain_for_final"/>
		<InterfaceBuilder extension_window="3" ligand_areas="final_backbone_X" name="backbone"/>
	</INTERFACE_BUILDERS>
	<MOVEMAP_BUILDERS>
		<MoveMapBuilder minimize_water="true" name="docking" sc_interface="side_chain_for_docking"/>
		<MoveMapBuilder bb_interface="backbone" minimize_water="true" name="final" sc_interface="side_chain_for_final"/>
	</MOVEMAP_BUILDERS>
	<MOVERS>
		<SavePoseMover name="spm" reference_name="store_native" restore_pose="0"/>
		<Transform angle="360" box_size="20.0" chain="X" cycles="500" initial_perturb="2" move_distance="10" name="transform" repeats="5" temperature="1000"/>
		<HighResDocker cycles="9" movemap_builder="docking" name="high_res_docker" repack_every_Nth="3" scorefxn="fa_standard"/>
		<FinalMinimizer movemap_builder="final" name="final" scorefxn="fa_standard"/>
	</MOVERS>
	<FILTERS>
		<LigInterfaceEnergy confidence="0" energy_cutoff="0.0" name="interfE" scorefxn="fa_standard"/>
		<SimpleMetricFilter comparison_type="lt" confidence="0" cutoff="999999." metric="rmsd_chX" name="rmsd_chX"/>
	</FILTERS>
	<PROTOCOLS>
		<Add mover="spm"/>
		<Add mover="transform"/>
		<Add mover="high_res_docker"/>
		<Add mover="final"/>
		<Add filter="interfE"/>
		<Add filter="rmsd_chX"/>
	</PROTOCOLS>
</ROSETTASCRIPTS>
INFO:rosetta:core.scoring.ScoreFunctionFactory: {0} SCOREFUNCTION: ref2015
INFO:rosetta:core.scoring.etable: {0} Starting energy table calculation
INFO:rosetta:core.scoring.etable: {0} smooth_etable: changing atr/rep split to bottom of energy well
INFO:rosetta:core.scoring.etable: {0} smooth_etable: spline smoothing lj etables (maxdis = 6)
INFO:rosetta:core.scoring.etable: {0} smooth_etable: spline smoothing solvation etables (max_dis = 6)
INFO:rosetta:core.scoring.etable: {0} Finished calculating energy tables.
INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine
INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/InterchainPotential/interchain_env_log.txt
INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/InterchainPotential/interchain_pair_log.txt
INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt
INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt
INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt
INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt
INFO:rosetta:core.scoring.ramachandran: {0} shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated.
INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb
INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/rama/flat/avg_L_rama.dat
INFO:rosetta:core.scoring.ramachandran: {0} Reading custom Ramachandran table from scoring/score_functions/rama/flat/avg_L_rama.dat.
INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/rama/flat/sym_all_rama.dat
INFO:rosetta:core.scoring.ramachandran: {0} Reading custom Ramachandran table from scoring/score_functions/rama/flat/sym_all_rama.dat.
INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/rama/flat/sym_G_rama.dat
INFO:rosetta:core.scoring.ramachandran: {0} Reading custom Ramachandran table from scoring/score_functions/rama/flat/sym_G_rama.dat.
INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/rama/flat/sym_P_rama.dat
INFO:rosetta:core.scoring.ramachandran: {0} Reading custom Ramachandran table from scoring/score_functions/rama/flat/sym_P_rama.dat.
INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/rama/flat/avg_L_rama_str.dat
INFO:rosetta:core.scoring.ramachandran: {0} Reading custom Ramachandran table from scoring/score_functions/rama/flat/avg_L_rama_str.dat.
INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/rama/flat/sym_all_rama_str.dat
INFO:rosetta:core.scoring.ramachandran: {0} Reading custom Ramachandran table from scoring/score_functions/rama/flat/sym_all_rama_str.dat.
INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/rama/flat/sym_G_rama_str.dat
INFO:rosetta:core.scoring.ramachandran: {0} Reading custom Ramachandran table from scoring/score_functions/rama/flat/sym_G_rama_str.dat.
INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/rama/flat/sym_P_rama_str.dat
INFO:rosetta:core.scoring.ramachandran: {0} Reading custom Ramachandran table from scoring/score_functions/rama/flat/sym_P_rama_str.dat.
INFO:rosetta:protocols.jd2.parser.ScoreFunctionLoader: {0} defined score function "fa_standard" with weights "ref2015.wts"
INFO:rosetta:core.select.residue_selector.util: {0} Found residue selector chX
INFO:rosetta:core.select.residue_selector.util: {0} Found residue selector chX
INFO:rosetta:core.pose.ref_pose: {0} Loading PDB: store_native
INFO:rosetta:core.simple_metrics.metrics.RMSDMetric: {0} Loaded reference pose: store_native with 0 residues
INFO:rosetta:core.pose.ref_pose: {0} Loading PDB: store_native
INFO:rosetta:protocols.rosetta_scripts.RosettaScriptsParser: {0} Defined mover named "spm" of type SavePoseMover
INFO:rosetta:protocols.rosetta_scripts.RosettaScriptsParser: {0} Defined mover named "transform" of type Transform
INFO:rosetta:protocols.rosetta_scripts.RosettaScriptsParser: {0} Defined mover named "high_res_docker" of type HighResDocker
INFO:rosetta:protocols.rosetta_scripts.RosettaScriptsParser: {0} Defined mover named "final" of type FinalMinimizer
INFO:rosetta:protocols.rosetta_scripts.RosettaScriptsParser: {0} Defined filter named "interfE" of type LigInterfaceEnergy
INFO:rosetta:protocols.rosetta_scripts.RosettaScriptsParser: {0} Defined filter named "rmsd_chX" of type SimpleMetricFilter
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} ParsedProtocol mover with the following movers and filters
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} added mover "spm" with filter "true_filter"
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} added mover "transform" with filter "true_filter"
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} added mover "high_res_docker" with filter "true_filter"
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} added mover "final" with filter "true_filter"
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} added mover "NULL_MOVER" with filter "interfE"
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} added mover "NULL_MOVER" with filter "rmsd_chX"

Produce 5 global ligand docking trajectories using PyJobDistributor:

In [4]:
if not os.getenv("DEBUG"):
    working_dir = os.getcwd()
    output_dir = "outputs"
    if not os.path.exists(output_dir):
        os.mkdir(output_dir)
    os.chdir(output_dir)

    jd = pyrosetta.toolbox.py_jobdistributor.PyJobDistributor(pdb_name="test_lig_XMLObjects",
                                                              nstruct=5,
                                                              scorefxn=scorefxn)
    jd.native_pose = pose
    df = pd.DataFrame()
    while not jd.job_complete:
        test_pose = pose.clone()
        xml.apply(test_pose)
        test_df = pd.DataFrame.from_records(dict(test_pose.scores), index=[jd.current_name])
        df = df.append(test_df)
        jd.output_decoy(test_pose)
    os.chdir(working_dir)
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER SavePoseMover - spm=======================
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER Transform - transform=======================
INFO:rosetta:protocols.qsar.scoring_grid.GridManager: {0} [ WARNING ] option -qsar:grid_dir is not set.  Use this flag to specify a directory to store scoring grids.  This will save you a huge amount of time
INFO:rosetta:protocols.qsar.scoring_grid.GridManager: {0} No conformation matching hash: 4dc5d457f2bb8b129abbf363feeefd56e18fe3d2 Updating grid and adding it to the cache
Working on decoy: test_lig_XMLObjects_1.pdb
INFO:rosetta:protocols.ligand_docking.Transform: {0} Considering 9 conformers during sampling
INFO:rosetta:protocols.ligand_docking.Transform: {0} percent acceptance: 1433 0.5732 1067
INFO:rosetta:protocols.ligand_docking.Transform: {0} Moves rejected for being outside of grid: 1063  0.4252
INFO:rosetta:protocols.ligand_docking.Transform: {0} [ WARNING ] A large number of moves were rejected for being outside the grid. You likely want to reexamine your settings.
INFO:rosetta:protocols.ligand_docking.Transform: {0} [ WARNING ]     For the current settings, a grid size of at least 259.2    and a box size of at least 243.2 are recommended.
INFO:rosetta:protocols.evaluation.ChiWellRmsdEvaluatorCreator: {0} Evaluation Creator active ...
INFO:rosetta:protocols.ligand_docking.Transform: {0} Accepted pose with grid score: -34
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER HighResDocker - high_res_docker=======================
INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/elec_cp_reps.dat
INFO:rosetta:core.scoring.elec.util: {0} Read 40 countpair representative atoms
INFO:rosetta:core.pack.dunbrack.RotamerLibrary: {0} shapovalov_lib_fixes_enable option is true.
INFO:rosetta:core.pack.dunbrack.RotamerLibrary: {0} shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.
INFO:rosetta:core.pack.dunbrack.RotamerLibrary: {0} Binary rotamer library selected: /mnt/home/klimaj/git/Rosetta/main/source/src/python/PyRosetta/src/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin
INFO:rosetta:core.pack.dunbrack.RotamerLibrary: {0} Using Dunbrack library binary file '/mnt/home/klimaj/git/Rosetta/main/source/src/python/PyRosetta/src/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'.
INFO:rosetta:core.pack.dunbrack.RotamerLibrary: {0} Dunbrack 2010 library took 0.442342 seconds to load from binary
INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()
INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA
INFO:rosetta:core.pack.pack_rotamers: {0} built 2057 rotamers at 69 positions.
INFO:rosetta:core.pack.interaction_graph.interaction_graph_factory: {0} Instantiating DensePDInteractionGraph
INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()
INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA
INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()
INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA
INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()
INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA
INFO:rosetta:core.pack.pack_rotamers: {0} built 1986 rotamers at 66 positions.
INFO:rosetta:core.pack.interaction_graph.interaction_graph_factory: {0} Instantiating DensePDInteractionGraph
INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()
INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA
INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()
INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA
INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()
INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA
INFO:rosetta:core.pack.pack_rotamers: {0} built 1987 rotamers at 66 positions.
INFO:rosetta:core.pack.interaction_graph.interaction_graph_factory: {0} Instantiating DensePDInteractionGraph
INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()
INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA
INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()
INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA
INFO:rosetta:protocols.moves.MonteCarlo: {0} MonteCarlo:: last_accepted_score,lowest_score: 1600.31 1600.31
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER FinalMinimizer - final=======================
INFO:rosetta:protocols.ligand_docking.ligand_options.FinalMinimizer: {0} Energy prior to minimizing: 1600.31
INFO:rosetta:protocols.ligand_docking.ligand_options.FinalMinimizer: {0} Energy after minimizing: 1456.97
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN FILTER interfE=======================
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================END FILTER interfE=======================
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN FILTER rmsd_chX=======================
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================END FILTER rmsd_chX=======================
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} setting status to success
INFO:rosetta:protocols.enzdes.EnzFilters: {0} Calculated Interface Energy is before cst correction is:-28.1887
INFO:rosetta:protocols.enzdes.EnzFilters: {0} Calculated Interface Energy is -28.2764
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} ============Begin report for interfE==================
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} 
    chain      res       AA    total  contact   fa_atr   fa_rep hb_bb_sc    hb_sc   fa_sol   fa_dun  fa_pair
        E       48      THR   -2.417    -3.119    -6.763     1.021    -0.993    -0.583     4.200     0.450     0.000
        E       49      LEU   -6.543    -7.144    -9.186     0.803     0.000     0.000     1.238     0.075     0.000
        E       50      GLY   -2.059    -0.700    -4.684     0.811     0.000     0.000     3.173     0.000     0.000
        E       51      THR   -1.979    -1.965    -4.199     0.355     0.000     0.000     1.879     0.099     0.000
        E       52      GLY   -0.176     0.969    -2.910     0.272     0.000     0.000     3.608     0.000     0.000
        E       53      SER   -2.735     0.784    -3.306     0.162    -0.931    -0.328     5.188     0.270     0.000
        E       54      PHE    0.876    -1.600    -6.411     0.658    -0.411     0.000     4.564     2.876     0.000
        E       55      GLY   -1.377     0.007    -2.945     0.151    -0.511     0.000     3.312     0.000     0.000
        E       56      ARG   -1.088    -1.522    -6.706     0.518     0.000    -0.357     5.024     2.218     0.000
        E       57      VAL   -6.165    -4.674    -9.023     1.013     0.000     0.000     3.336     0.060     0.000
        E       58      MET   -2.147    -3.447    -9.067     1.359     0.000     0.000     4.260     1.512     0.000
        E       59      LEU   -5.857    -5.463    -8.600     1.494     0.000     0.000     1.643     0.422     0.000
        E       69      TYR   -0.690    -4.729    -9.958     1.822     0.000    -0.419     3.827     2.872     0.000
        E       70      ALA   -2.410    -3.401    -6.353     0.516     0.000     0.000     2.437     0.000     0.000
        E       71      MET   -2.666    -6.202    -9.279     1.245     0.000     0.000     1.832     1.710     0.000
        E       72      LYS   -4.477     0.903    -7.895     0.904     0.000    -0.646     8.540     1.037     0.000
        E       74      LEU   -1.722    -2.492    -6.620     1.523     0.000     0.000     2.605     0.910     0.000
        E       78      LYS   -3.043    -0.299    -6.728     0.818    -0.861     0.000     6.473     1.565     0.000
        E       82      LEU   -0.419    -2.208    -5.790     0.787    -0.503     0.000     3.298     1.863     0.000
        E       84      GLN   -4.641    -2.305    -7.459     0.571    -0.503    -0.725     5.810     2.196     0.000
        E       87      HIS   -0.886    -1.113    -7.215     0.802     0.000    -0.725     6.025     2.189     0.000
        E       91      GLU   -3.591     0.525    -8.598     0.855     0.000    -0.646     8.914     2.849     0.000
        E      104      VAL   -2.234    -4.151    -6.001     0.510     0.000     0.000     1.340     0.567     0.000
        E      105      LYS   -0.037     0.469    -4.287     0.256     0.000     0.000     4.501     1.138     0.000
        E      106      LEU   -4.116    -5.203    -7.960     1.520     0.000     0.000     1.237     0.385     0.000
        E      118      MET   -1.417    -4.497    -8.675     1.533     0.000     0.000     2.646     1.986     0.000
        E      119      VAL   -4.636    -4.850    -8.706     2.116     0.000     0.000     1.741     0.110     0.000
        E      120      MET   -3.844    -4.911    -9.727     0.778     0.000     0.000     4.038     1.848     0.000
        E      121      GLU   -1.310    -0.462    -4.028     0.206     0.000     0.000     3.360     2.373     0.000
        E      122      TYR   -4.442    -6.152    -8.669     0.525    -0.330     0.000     2.322     2.406     0.000
        E      123      VAL   -2.182    -4.170    -6.584     0.877     0.000     0.000     1.537     0.017     0.000
        E      124      ALA   -2.617    -2.974    -3.698     0.205    -0.799     0.000     1.318     0.000     0.000
        E      125      GLY   -1.329    -0.985    -4.236     0.734    -0.556     0.000     3.073     0.000     0.000
        E      126      GLY   -3.437    -0.662    -4.172     0.426     0.000     0.000     3.085     0.000     0.000
        E      127      GLU   -2.925     1.039    -6.871     1.447     0.000    -0.564     7.027     2.748     0.000
        E      129      PHE   -0.241    -1.619    -8.049     1.213     0.000     0.000     5.216     1.387     0.000
        E      130      SER   -0.329     0.469    -3.921     0.233     0.000     0.000     4.157     1.080     0.000
        E      165      ARG   -0.333    -2.149    -8.747     1.746    -1.333    -0.520     6.705     3.113     0.000
        E      166      ASP    0.543     1.140    -5.401     0.991    -0.482    -0.630     6.663     2.948     0.000
        E      168      LYS   -3.030     1.904    -9.478     2.652     0.000    -0.673     9.403     1.179     0.000
        E      169      PRO   -3.490    -1.704    -7.718     2.992     0.000     0.000     3.023     0.065     0.000
        E      170      GLU   -1.311     0.098    -6.086     0.567     0.000     0.000     5.616     2.716     0.000
        E      171      ASN   -4.392    -0.202    -7.832     0.790    -0.482    -0.245     7.566     1.695     0.000
        E      172      LEU   -5.886    -6.302    -8.858     1.341     0.000     0.000     1.215     0.637     0.000
        E      173      LEU   -5.721    -5.168    -9.243     1.134     0.000     0.000     2.941     0.551     0.000
        E      181      GLN   -1.309    -2.677    -7.989     0.498    -0.630     0.000     5.444     4.290     0.000
        E      182      VAL   -4.450    -4.501    -6.797     0.742     0.000     0.000     1.553     0.074     0.000
        E      183      THR   -3.797    -3.976    -6.762     0.572    -0.795    -0.657     3.666     2.388     0.000
        E      184      ASP    4.753     2.582    -5.326     0.990    -0.699    -0.245     7.861     2.374     0.000
        E      185      PHE   -0.523    -6.075    -8.430     1.314     0.000     0.000     1.042     3.227     0.000
        E      186      GLY    1.335     0.780    -3.222     0.783    -0.148     0.000     3.367     0.000     0.000
        E      187      PHE   -2.917    -3.863    -7.082     0.523    -0.834     0.000     3.529     1.619     0.000
        E      200      GLY   -2.562    -1.246    -2.623     0.242     0.000     0.000     1.135     0.000     0.000
        E      201      THR    3.537     1.468    -6.014     3.466     0.000    -0.914     4.930     0.030     0.000
        E      204      TYR   -2.788    -4.504    -9.457     1.975     0.000    -0.471     3.449     2.682     0.000
        E      324      THR   -1.583    -0.856    -4.823     1.003     0.000    -0.765     3.730     0.002     0.000
        E      327      PHE   -3.412    -4.721    -8.228     0.931     0.000     0.000     2.576     1.602     0.000
        E      328      ASP   -0.300     0.147    -2.732     0.306    -0.583     0.000     3.155     2.607     0.000
        E      330      TYR   -1.936    -2.871    -6.672     0.840     0.000     0.000     2.960     1.343     0.000
        X        1      TPA   -8.279     1.922   -19.728     1.307    -1.854    -1.938    24.135     0.000     0.000
============End report for interfE==================
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} ============Begin report for rmsd_chX==================
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} ============End report for rmsd_chX==================
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER SavePoseMover - spm=======================
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER Transform - transform=======================
INFO:rosetta:protocols.qsar.scoring_grid.GridManager: {0} Found a conformation matching hash: 4dc5d457f2bb8b129abbf363feeefd56e18fe3d2 Loading from grid cache
INFO:rosetta:protocols.ligand_docking.Transform: {0} Considering 9 conformers during sampling
INFO:rosetta:protocols.ligand_docking.Transform: {0} percent acceptance: 1353 0.5412 1147
INFO:rosetta:protocols.ligand_docking.Transform: {0} Moves rejected for being outside of grid: 1144  0.4576
INFO:rosetta:protocols.ligand_docking.Transform: {0} [ WARNING ] A large number of moves were rejected for being outside the grid. You likely want to reexamine your settings.
INFO:rosetta:protocols.ligand_docking.Transform: {0} [ WARNING ]     For the current settings, a grid size of at least 252.4    and a box size of at least 236.4 are recommended.
INFO:rosetta:protocols.ligand_docking.Transform: {0} Accepted pose with grid score: -20
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER HighResDocker - high_res_docker=======================
Working on decoy: test_lig_XMLObjects_2.pdb
INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()
INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA
INFO:rosetta:core.pack.pack_rotamers: {0} built 1285 rotamers at 47 positions.
INFO:rosetta:core.pack.interaction_graph.interaction_graph_factory: {0} Instantiating DensePDInteractionGraph
INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()
INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA
INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()
INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA
INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()
INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA
INFO:rosetta:core.pack.pack_rotamers: {0} built 700 rotamers at 25 positions.
INFO:rosetta:core.pack.interaction_graph.interaction_graph_factory: {0} Instantiating DensePDInteractionGraph
INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()
INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA
INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()
INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA
INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()
INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA
INFO:rosetta:core.pack.pack_rotamers: {0} built 749 rotamers at 28 positions.
INFO:rosetta:core.pack.interaction_graph.interaction_graph_factory: {0} Instantiating DensePDInteractionGraph
INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()
INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA
INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()
INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA
INFO:rosetta:protocols.moves.MonteCarlo: {0} MonteCarlo:: last_accepted_score,lowest_score: 1700.33 1699.91
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER FinalMinimizer - final=======================
INFO:rosetta:protocols.ligand_docking.ligand_options.FinalMinimizer: {0} Energy prior to minimizing: 1699.91
INFO:rosetta:protocols.ligand_docking.ligand_options.FinalMinimizer: {0} Energy after minimizing: 1642.36
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN FILTER interfE=======================
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================END FILTER interfE=======================
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN FILTER rmsd_chX=======================
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================END FILTER rmsd_chX=======================
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} setting status to success
INFO:rosetta:protocols.enzdes.EnzFilters: {0} Calculated Interface Energy is before cst correction is:-9.16448
INFO:rosetta:protocols.enzdes.EnzFilters: {0} Calculated Interface Energy is -9.16449
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} ============Begin report for interfE==================
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} 
    chain      res       AA    total  contact   fa_atr   fa_rep hb_bb_sc    hb_sc   fa_sol   fa_dun  fa_pair
        E       50      GLY   -2.296    -0.757    -3.364     0.450     0.000     0.000     2.158     0.000     0.000
        E       51      THR   -1.745    -2.048    -3.708     0.328     0.000     0.000     1.332     0.201     0.000
        E       52      GLY   -0.743     0.562    -2.039     0.177     0.000     0.000     2.424     0.000     0.000
        E       53      SER   -2.328     0.986    -2.794     0.138    -0.642    -0.323     4.606     0.459     0.000
        E       54      PHE    1.582    -2.847    -4.806     0.484     0.000     0.000     1.476     3.029     0.000
        E       55      GLY    2.725    -0.245    -2.547     0.231     0.000     0.000     2.070     0.000     0.000
        E       56      ARG   -0.269    -0.805    -5.369     0.636     0.000     0.000     3.929     2.112     0.000
        E       78      LYS   20.730     0.029    -6.578     0.992    -1.154     0.000     6.769    25.465     0.000
        E      129      PHE   -0.876    -1.288    -8.575     1.275     0.000     0.000     6.012     1.430     0.000
        E      165      ARG   -0.079    -2.045    -8.668     1.792    -1.201    -0.529     6.560     2.703     0.000
        E      166      ASP    1.767     1.464    -5.566     1.647    -0.551    -0.792     6.725     3.451     0.000
        E      168      LYS    1.055     2.719   -10.010     2.216     0.000     0.000    10.513     3.967     0.000
        E      170      GLU    1.793     1.101    -6.604     0.571     0.000     0.000     7.135     3.642     0.000
        E      171      ASN   -2.146     1.006    -7.524     1.171    -0.551    -0.170     8.080     2.803     0.000
        E      184      ASP    2.815     1.050    -4.320     0.764    -0.801     0.000     5.407     2.996     0.000
        E      187      PHE   -0.381    -3.856    -7.494     1.055    -0.702     0.000     3.285     3.732     0.000
        E      200      GLY   -0.160     0.327    -2.553     1.984     0.000     0.000     0.896     0.000     0.000
        E      201      THR    0.282     0.738    -5.717     2.727     0.000    -0.622     4.349     0.045     0.000
        E      202      PRO   -2.553    -1.789    -5.301     1.953     0.000     0.000     1.559     1.056     0.000
        E      203      GLU   -1.442    -1.872    -5.333     0.519     0.000     0.000     2.943     3.079     0.000
        E      204      TYR   -3.817    -5.068    -9.444     1.464     0.000    -0.772     3.684     2.401     0.000
        E      243      PRO   -1.520    -0.674    -5.010     1.704     0.000     0.000     2.632     0.092     0.000
        E      328      ASP   -1.224     0.218    -2.808     0.180    -0.812     0.000     3.658     2.781     0.000
        E      330      TYR   -2.065    -3.112    -6.174     0.461     0.000     0.000     2.601     1.424     0.000
        E      331      GLU   -0.535     0.167    -1.627     0.081     0.000     0.000     1.713     2.598     0.000
        E      333      GLU    1.144     1.728    -3.952     0.965    -0.181     0.000     4.897     3.221     0.000
        X        1      TPA    2.588     2.692    -2.422     0.013    -0.350    -0.323     5.773     0.000     0.000
============End report for interfE==================
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} ============Begin report for rmsd_chX==================
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} ============End report for rmsd_chX==================
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER SavePoseMover - spm=======================
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER Transform - transform=======================
INFO:rosetta:protocols.qsar.scoring_grid.GridManager: {0} Found a conformation matching hash: 4dc5d457f2bb8b129abbf363feeefd56e18fe3d2 Loading from grid cache
INFO:rosetta:protocols.ligand_docking.Transform: {0} Considering 9 conformers during sampling
INFO:rosetta:protocols.ligand_docking.Transform: {0} percent acceptance: 1374 0.5496 1126
INFO:rosetta:protocols.ligand_docking.Transform: {0} Moves rejected for being outside of grid: 1125  0.45
INFO:rosetta:protocols.ligand_docking.Transform: {0} [ WARNING ] A large number of moves were rejected for being outside the grid. You likely want to reexamine your settings.
INFO:rosetta:protocols.ligand_docking.Transform: {0} [ WARNING ]     For the current settings, a grid size of at least 254.1    and a box size of at least 238.1 are recommended.
INFO:rosetta:protocols.ligand_docking.Transform: {0} Accepted pose with grid score: -20
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER HighResDocker - high_res_docker=======================
Working on decoy: test_lig_XMLObjects_3.pdb
INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()
INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA
INFO:rosetta:core.pack.pack_rotamers: {0} built 1342 rotamers at 48 positions.
INFO:rosetta:core.pack.interaction_graph.interaction_graph_factory: {0} Instantiating DensePDInteractionGraph
INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()
INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA
INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()
INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA
INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()
INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA
INFO:rosetta:core.pack.pack_rotamers: {0} built 1163 rotamers at 42 positions.
INFO:rosetta:core.pack.interaction_graph.interaction_graph_factory: {0} Instantiating DensePDInteractionGraph
INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()
INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA
INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()
INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA
INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()
INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA
INFO:rosetta:core.pack.pack_rotamers: {0} built 1167 rotamers at 43 positions.
INFO:rosetta:core.pack.interaction_graph.interaction_graph_factory: {0} Instantiating DensePDInteractionGraph
INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()
INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA
INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()
INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA
INFO:rosetta:protocols.moves.MonteCarlo: {0} MonteCarlo:: last_accepted_score,lowest_score: 1686.12 1686.12
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER FinalMinimizer - final=======================
INFO:rosetta:protocols.ligand_docking.ligand_options.FinalMinimizer: {0} Energy prior to minimizing: 1686.12
INFO:rosetta:protocols.ligand_docking.ligand_options.FinalMinimizer: {0} Energy after minimizing: 1591.67
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN FILTER interfE=======================
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================END FILTER interfE=======================
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN FILTER rmsd_chX=======================
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================END FILTER rmsd_chX=======================
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} setting status to success
INFO:rosetta:protocols.enzdes.EnzFilters: {0} Calculated Interface Energy is before cst correction is:2.79191
INFO:rosetta:protocols.enzdes.EnzFilters: {0} Calculated Interface Energy is 2.54229
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} ============Begin report for interfE==================
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} 
    chain      res       AA    total  contact   fa_atr   fa_rep hb_bb_sc    hb_sc   fa_sol   fa_dun  fa_pair
        E       48      THR   -2.568    -2.644    -6.709     1.086    -0.720    -0.458     4.157     0.516     0.000
        E       49      LEU   -5.507    -6.602    -7.780     0.585     0.000     0.000     0.593     0.203     0.000
        E       50      GLY   -2.529    -0.930    -4.443     0.883     0.000     0.000     2.630     0.000     0.000
        E       51      THR    0.706    -1.417    -4.608     0.553     0.000     0.000     2.638     0.461     0.000
        E       52      GLY    0.587     0.625    -1.602     0.166     0.000     0.000     2.060     0.000     0.000
        E       53      SER   -0.679    -0.364    -2.358     0.195    -0.261     0.000     2.060     1.040     0.000
        E       54      PHE    2.458    -2.900    -5.225     0.622     0.000     0.000     1.703     3.540     0.000
        E       55      GLY    9.392    -0.410    -2.625     0.249     0.000     0.000     1.967     0.000     0.000
        E       56      ARG   -1.234    -1.626    -6.936     0.600     0.000    -0.322     5.031     2.663     0.000
        E       57      VAL   -4.318    -3.181    -6.370     0.670     0.000     0.000     2.519     0.027     0.000
        E       72      LYS   -3.991    -0.900    -7.739     1.305     0.000    -0.642     6.177     1.612     0.000
        E      126      GLY   -3.003    -0.605    -4.369     0.381     0.000     0.000     3.383     0.000     0.000
        E      127      GLU   -0.249    -0.078    -7.265     1.183     0.000    -0.388     6.391     4.655     0.000
        E      128      MET   -4.301    -5.412    -9.602     0.969     0.000     0.000     3.221     1.982     0.000
        E      129      PHE   -0.264    -0.947    -9.168     1.249     0.000     0.000     6.972     1.906     0.000
        E      130      SER   -0.959     0.198    -4.887     0.318     0.000    -0.388     5.155     0.650     0.000
        E      133      ARG   -0.063    -0.981    -5.668     0.330     0.000    -0.987     5.343     3.519     0.000
        E      134      ARG    3.262     0.797    -3.061     0.638     0.000     0.000     3.220     2.070     0.000
        E      168      LYS    3.329     4.262    -9.570     4.595     0.000    -0.171     9.408     3.034     0.000
        E      169      PRO   -0.923    -0.402    -7.917     4.430     0.000     0.000     3.085     0.402     0.000
        E      170      GLU    4.451     1.155    -7.463     1.622    -0.296     0.000     7.292     6.067     0.000
        E      171      ASN   -3.417    -0.606    -7.327     0.614    -0.584     0.000     6.690     1.525     0.000
        E      172      LEU   -6.024    -6.343    -8.757     1.260     0.000     0.000     1.154     0.693     0.000
        E      173      LEU   -4.450    -4.174    -8.186     1.308     0.000     0.000     2.704     0.778     0.000
        E      183      THR   -1.365    -2.833    -5.282     0.387    -0.365     0.000     2.426     1.430     0.000
        E      184      ASP    2.686     0.881    -4.167     0.374    -0.792     0.000     5.465     3.613     0.000
        E      201      THR    0.998     0.304    -4.625     1.925     0.000    -0.539     3.543     0.074     0.000
        E      202      PRO   -0.038    -1.535    -4.797     1.704     0.000     0.000     1.557     1.410     0.000
        E      203      GLU    0.951    -1.048    -5.555     0.460     0.000     0.000     4.046     2.504     0.000
        E      204      TYR    1.143    -3.667   -10.113     2.033     0.000     0.000     4.413     2.503     0.000
        E      235      TYR    0.109    -1.418    -6.762     2.623     0.000     0.000     2.721     1.597     0.000
        E      236      PRO    7.370    -0.861    -6.286     2.169     0.000     0.000     3.256     3.299     0.000
        E      239      PHE   -0.312    -2.086    -4.550     0.764     0.000     0.000     1.700     1.078     0.000
        E      241      ASP   -0.399    -0.142    -1.859     0.136     0.000     0.000     1.582     1.900     0.000
        E      243      PRO   -1.533    -0.702    -5.038     1.698     0.000     0.000     2.638     0.096     0.000
        E      327      PHE   -3.273    -4.278    -7.562     0.650     0.000     0.000     2.634     1.460     0.000
        E      328      ASP   -0.363    -0.146    -2.248     0.086    -0.839     0.000     2.856     3.043     0.000
        E      329      ASP   -2.612     0.083    -2.195     0.067    -0.839    -0.297     3.347     2.636     0.000
        E      330      TYR   -1.929    -2.696    -7.460     0.824     0.000    -0.276     4.215     1.429     0.000
        X        1      TPA    7.066     4.327    -8.387     1.313    -0.296    -0.447    12.144     0.000     0.000
============End report for interfE==================
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} ============Begin report for rmsd_chX==================
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} ============End report for rmsd_chX==================
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER SavePoseMover - spm=======================
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER Transform - transform=======================
INFO:rosetta:protocols.qsar.scoring_grid.GridManager: {0} Found a conformation matching hash: 4dc5d457f2bb8b129abbf363feeefd56e18fe3d2 Loading from grid cache
INFO:rosetta:protocols.ligand_docking.Transform: {0} Considering 9 conformers during sampling
INFO:rosetta:protocols.ligand_docking.Transform: {0} percent acceptance: 1349 0.5396 1151
INFO:rosetta:protocols.ligand_docking.Transform: {0} Moves rejected for being outside of grid: 1150  0.46
INFO:rosetta:protocols.ligand_docking.Transform: {0} [ WARNING ] A large number of moves were rejected for being outside the grid. You likely want to reexamine your settings.
INFO:rosetta:protocols.ligand_docking.Transform: {0} [ WARNING ]     For the current settings, a grid size of at least 251.5    and a box size of at least 235.5 are recommended.
INFO:rosetta:protocols.ligand_docking.Transform: {0} Accepted pose with grid score: -21
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER HighResDocker - high_res_docker=======================
Working on decoy: test_lig_XMLObjects_0.pdb
INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()
INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA
INFO:rosetta:core.pack.pack_rotamers: {0} built 1219 rotamers at 44 positions.
INFO:rosetta:core.pack.interaction_graph.interaction_graph_factory: {0} Instantiating DensePDInteractionGraph
INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()
INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA
INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()
INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA
INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()
INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA
INFO:rosetta:core.pack.pack_rotamers: {0} built 933 rotamers at 38 positions.
INFO:rosetta:core.pack.interaction_graph.interaction_graph_factory: {0} Instantiating DensePDInteractionGraph
INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()
INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA
INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()
INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA
INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()
INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA
INFO:rosetta:core.pack.pack_rotamers: {0} built 952 rotamers at 40 positions.
INFO:rosetta:core.pack.interaction_graph.interaction_graph_factory: {0} Instantiating DensePDInteractionGraph
INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()
INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA
INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()
INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA
INFO:rosetta:protocols.moves.MonteCarlo: {0} MonteCarlo:: last_accepted_score,lowest_score: 1611.25 1611.25
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER FinalMinimizer - final=======================
INFO:rosetta:protocols.ligand_docking.ligand_options.FinalMinimizer: {0} Energy prior to minimizing: 1611.25
INFO:rosetta:protocols.ligand_docking.ligand_options.FinalMinimizer: {0} Energy after minimizing: 1519.85
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN FILTER interfE=======================
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================END FILTER interfE=======================
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN FILTER rmsd_chX=======================
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================END FILTER rmsd_chX=======================
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} setting status to success
INFO:rosetta:protocols.enzdes.EnzFilters: {0} Calculated Interface Energy is before cst correction is:-11.7332
INFO:rosetta:protocols.enzdes.EnzFilters: {0} Calculated Interface Energy is -11.7982
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} ============Begin report for interfE==================
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} 
    chain      res       AA    total  contact   fa_atr   fa_rep hb_bb_sc    hb_sc   fa_sol   fa_dun  fa_pair
        E       51      THR   -1.563    -1.798    -2.919     0.245     0.000     0.000     0.876     0.153     0.000
        E       52      GLY    5.776     0.711    -2.165     0.054     0.000     0.000     2.822     0.000     0.000
        E       53      SER    7.427     0.446    -3.310     0.661    -0.525    -0.368     3.988     1.607     0.000
        E       54      PHE    6.186    -2.451    -5.163     0.674     0.000     0.000     2.038     3.284     0.000
        E       55      GLY   -2.106    -0.347    -2.810     0.143     0.000     0.000     2.320     0.000     0.000
        E       56      ARG   -1.271    -1.790    -6.885     0.415     0.000    -0.382     5.061     3.036     0.000
        E       78      LYS   -1.823    -0.573    -6.139     0.645    -0.861     0.000     5.782     2.390     0.000
        E       82      LEU   -2.364    -2.190    -5.796     0.810    -0.495     0.000     3.292     0.042     0.000
        E      165      ARG   -2.459    -3.163    -8.056     0.915    -1.849    -0.595     6.421     2.208     0.000
        E      166      ASP   -2.087     0.447    -4.710     0.538    -0.340    -0.944     5.903     2.476     0.000
        E      168      LYS   -2.531     1.567    -9.979     2.888     0.000    -0.928     9.586     0.926     0.000
        E      170      GLU   -1.701     0.172    -5.437     0.554     0.000    -0.258     5.313     2.644     0.000
        E      171      ASN   -3.745    -0.489    -6.885     0.438    -0.340    -0.224     6.522     1.908     0.000
        E      184      ASP   -0.614     0.819    -3.444     0.766    -0.357    -0.285     4.138     2.651     0.000
        E      187      PHE   -0.373    -4.362    -7.258     0.696    -0.749     0.000     2.950     3.700     0.000
        E      198      LEU    1.834    -1.331    -2.905     0.752     0.000     0.000     0.823     0.576     0.000
        E      199      CYS    5.081    -3.481    -6.217     0.919     0.000     0.000     1.817     2.442     0.000
        E      200      GLY   -2.235    -1.423    -2.525     0.108     0.000     0.000     0.995     0.000     0.000
        E      201      THR   -2.011    -0.071    -5.331     1.734     0.000    -1.390     4.915     0.051     0.000
        E      202      PRO   -3.321    -1.984    -5.694     1.727     0.000     0.000     1.982     1.019     0.000
        E      203      GLU   -1.351    -1.740    -5.010     0.541     0.000     0.000     2.729     3.089     0.000
        E      204      TYR   -3.569    -4.762    -8.961     1.374     0.000    -0.733     3.557     2.658     0.000
        E      205      LEU   -2.973    -4.662    -6.935     0.899     0.000     0.000     1.374     0.956     0.000
        E      210      ILE   46.181    -3.743    -5.688     1.091     0.000     0.000     0.854    47.349     0.000
        E      242      GLN    0.549     0.380    -4.327     1.292    -0.244     0.000     3.659     2.465     0.000
        E      243      PRO   -3.732    -1.299    -5.921     1.289     0.000     0.000     3.333     0.134     0.000
        E      244      ILE    1.292    -0.636    -4.342     0.600     0.000     0.000     3.106     0.133     0.000
        E      246      ILE   -4.078    -3.923    -9.900     1.563     0.000     0.000     4.414     0.116     0.000
        E      247      TYR   -1.044    -4.043   -10.503     2.098     0.000     0.000     4.362     3.693     0.000
        X        1      TPA    1.273     1.190    -4.233     0.213    -0.525    -0.368     6.102     0.000     0.000
============End report for interfE==================
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} ============Begin report for rmsd_chX==================
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} ============End report for rmsd_chX==================
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER SavePoseMover - spm=======================
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER Transform - transform=======================
INFO:rosetta:protocols.qsar.scoring_grid.GridManager: {0} Found a conformation matching hash: 4dc5d457f2bb8b129abbf363feeefd56e18fe3d2 Loading from grid cache
INFO:rosetta:protocols.ligand_docking.Transform: {0} Considering 9 conformers during sampling
INFO:rosetta:protocols.ligand_docking.Transform: {0} percent acceptance: 1363 0.5452 1137
INFO:rosetta:protocols.ligand_docking.Transform: {0} Moves rejected for being outside of grid: 1136  0.4544
INFO:rosetta:protocols.ligand_docking.Transform: {0} [ WARNING ] A large number of moves were rejected for being outside the grid. You likely want to reexamine your settings.
INFO:rosetta:protocols.ligand_docking.Transform: {0} [ WARNING ]     For the current settings, a grid size of at least 253.2    and a box size of at least 237.2 are recommended.
INFO:rosetta:protocols.ligand_docking.Transform: {0} Accepted pose with grid score: -20
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER HighResDocker - high_res_docker=======================
Working on decoy: test_lig_XMLObjects_4.pdb
INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()
INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA
INFO:rosetta:core.pack.pack_rotamers: {0} built 1013 rotamers at 35 positions.
INFO:rosetta:core.pack.interaction_graph.interaction_graph_factory: {0} Instantiating DensePDInteractionGraph
INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()
INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA
INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()
INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA
INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()
INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA
INFO:rosetta:core.pack.pack_rotamers: {0} built 959 rotamers at 33 positions.
INFO:rosetta:core.pack.interaction_graph.interaction_graph_factory: {0} Instantiating DensePDInteractionGraph
INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()
INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA
INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()
INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA
INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()
INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA
INFO:rosetta:core.pack.pack_rotamers: {0} built 990 rotamers at 36 positions.
INFO:rosetta:core.pack.interaction_graph.interaction_graph_factory: {0} Instantiating DensePDInteractionGraph
INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()
INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA
INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()
INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA
INFO:rosetta:protocols.moves.MonteCarlo: {0} MonteCarlo:: last_accepted_score,lowest_score: 1697.63 1697.63
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER FinalMinimizer - final=======================
INFO:rosetta:protocols.ligand_docking.ligand_options.FinalMinimizer: {0} Energy prior to minimizing: 1697.63
INFO:rosetta:protocols.ligand_docking.ligand_options.FinalMinimizer: {0} Energy after minimizing: 1628.15
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN FILTER interfE=======================
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================END FILTER interfE=======================
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN FILTER rmsd_chX=======================
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================END FILTER rmsd_chX=======================
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} setting status to success
INFO:rosetta:protocols.enzdes.EnzFilters: {0} Calculated Interface Energy is before cst correction is:-14.9022
INFO:rosetta:protocols.enzdes.EnzFilters: {0} Calculated Interface Energy is -15.1627
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} ============Begin report for interfE==================
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} 
    chain      res       AA    total  contact   fa_atr   fa_rep hb_bb_sc    hb_sc   fa_sol   fa_dun  fa_pair
        E       50      GLY   -2.600    -0.787    -3.367     0.435     0.000     0.000     2.145     0.000     0.000
        E       51      THR    7.583    -1.229    -2.633     0.172     0.000     0.000     1.232     0.037     0.000
        E       52      GLY    0.178     0.809    -2.585     0.425     0.000     0.000     2.969     0.000     0.000
        E       53      SER   -3.224     0.460    -2.928     0.168    -1.012    -0.299     4.531     0.298     0.000
        E       54      PHE    2.350    -2.057    -4.940     0.813     0.000     0.000     2.070     3.101     0.000
        E       55      GLY   -1.168    -0.190    -2.719     0.251     0.000     0.000     2.278     0.000     0.000
        E       56      ARG    0.113    -1.410    -6.148     0.773     0.000    -0.411     4.376     3.603     0.000
        E      127      GLU    5.674     0.265    -6.455     1.188     0.000     0.000     5.532     5.527     0.000
        E      129      PHE   -2.187    -2.254    -9.665     1.325     0.000     0.000     6.085     1.411     0.000
        E      130      SER   -0.490     0.509    -4.664     0.405     0.000     0.000     4.769     0.469     0.000
        E      133      ARG    1.166    -0.886    -5.718     0.435     0.000    -0.982     5.379     4.010     0.000
        E      134      ARG    3.354     1.267    -4.227     1.445     0.000     0.000     4.049     2.042     0.000
        E      165      ARG    0.630    -1.073    -8.797     2.914    -1.167    -0.506     6.483     2.654     0.000
        E      166      ASP    3.562     3.175    -4.858     3.206    -0.654     0.000     5.482     2.057     0.000
        E      168      LYS   -0.694     2.273   -10.086     2.547     0.000    -1.344    11.157     2.410     0.000
        E      169      PRO   -3.279    -2.341    -7.808     1.650     0.000     0.000     3.817     0.765     0.000
        E      170      GLU   -0.540     1.225    -6.618     0.772     0.000    -0.226     7.296     4.054     0.000
        E      171      ASN   -3.534    -0.548    -6.847     0.680    -0.654     0.000     6.273     1.839     0.000
        E      184      ASP    2.870     0.655    -4.090     0.497    -0.882     0.000     5.131     2.941     0.000
        E      187      PHE   -0.138    -3.956    -7.393     0.944    -0.667     0.000     3.161     4.153     0.000
        E      199      CYS    6.887    -3.734    -6.109     0.820     0.000     0.000     1.555     1.717     0.000
        E      200      GLY   -1.379    -0.992    -2.480     0.181     0.000     0.000     1.308     0.000     0.000
        E      201      THR   -0.477     1.709    -6.176     2.025     0.000    -0.856     6.715     0.233     0.000
        E      202      PRO   -3.121    -1.733    -6.090     2.213     0.000     0.000     2.143     0.972     0.000
        E      203      GLU   -1.709    -1.867    -5.405     0.573     0.000     0.000     2.965     3.113     0.000
        E      204      TYR   -3.322    -4.715    -9.141     1.386     0.000    -0.746     3.786     2.709     0.000
        E      205      LEU   -2.956    -4.722    -7.322     1.400     0.000     0.000     1.200     0.956     0.000
        E      235      TYR    0.122    -1.408    -6.782     2.630     0.000     0.000     2.743     1.616     0.000
        E      236      PRO    7.327    -0.974    -6.149     2.112     0.000     0.000     3.064     3.290     0.000
        E      239      PHE   -0.307    -2.076    -4.537     0.748     0.000     0.000     1.713     1.082     0.000
        E      243      PRO   -1.686    -0.869    -5.261     1.702     0.000     0.000     2.690     0.096     0.000
        E      327      PHE   -2.893    -4.383    -8.065     0.694     0.000     0.000     2.989     1.670     0.000
        E      328      ASP   -1.274    -0.065    -3.252     0.186    -1.244     0.000     4.244     2.773     0.000
        E      329      ASP   -0.818    -0.140    -2.374     0.113    -0.738     0.000     2.859     2.979     0.000
        E      330      TYR   -1.763    -2.681    -6.591     0.659     0.000     0.000     3.251     1.362     0.000
        X        1      TPA   -1.690     3.484    -7.017     0.166    -0.759    -1.336    12.431     0.000     0.000
============End report for interfE==================
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} ============Begin report for rmsd_chX==================
INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} ============End report for rmsd_chX==================

Now that we have sampled some global ligand docking trajectories, let's plot the ligand binding energy landscape:

In [5]:
#Skip for tests (as DF is not present)
if not os.getenv("DEBUG"):
    matplotlib.rcParams['figure.figsize'] = [12.0, 8.0]
    seaborn.scatterplot(x="rmsd_chX", y="interfE", data=df)
Out[5]:
<matplotlib.axes._subplots.AxesSubplot at 0x7ffff5de1278>

We can check which .pdb file has the lowest interfE score:

In [6]:
#Skip for tests
if not os.getenv("DEBUG"):
    df.sort_values(by="interfE")
Out[6]:
dslf_fa13 fa_atr fa_dun fa_elec fa_intra_rep fa_intra_sol_xover4 fa_rep fa_sol hbond_bb_sc hbond_lr_bb ... interfE lk_ball_wtd omega p_aa_pp pro_close rama_prepro ref rmsd_chX total_score yhh_planarity
test_lig_XMLObjects_1.pdb 0.0 -2141.790247 2839.589602 -505.303161 1549.888068 90.394684 1355.538397 1338.970707 -52.121705 -49.476625 ... -28.276440 -50.974895 16.443889 -84.493475 91.445419 117.822680 81.74634 0.631487 1456.971339 1.100056
test_lig_XMLObjects_4.pdb 0.0 -2117.511239 3002.017883 -484.395373 1575.126871 91.668637 1434.239151 1329.615403 -48.468502 -47.234071 ... -15.162686 -49.593810 -1.135463 -85.518547 68.279343 118.636338 81.74634 11.435035 1628.146163 0.366937
test_lig_XMLObjects_0.pdb 0.0 -2101.634782 2881.724947 -484.021972 1552.937939 90.957571 1395.967000 1307.276630 -48.113076 -47.985689 ... -11.798166 -48.713822 -0.016234 -86.665216 73.794018 111.035818 81.74634 18.723389 1519.846938 0.360842
test_lig_XMLObjects_2.pdb 0.0 -2108.199196 2995.956828 -483.697206 1572.754514 91.583322 1441.994818 1317.274987 -47.207246 -47.496493 ... -9.164489 -48.398568 3.595816 -82.205583 73.140703 122.270933 81.74634 13.237048 1642.356614 0.294935
test_lig_XMLObjects_3.pdb 0.0 -2114.363249 2941.806947 -471.461845 1563.092110 90.772894 1426.594993 1318.093586 -47.347564 -48.064493 ... 2.542285 -49.704318 4.201275 -83.261999 68.786798 117.522522 81.74634 9.790556 1591.672471 0.122519

5 rows × 22 columns

Let's take a look at the pose with the lowest interfE value that was generated:

In [8]:
#Skip for tests
if not os.getenv("DEBUG"):
    lowest_energy_pdb_filename = os.path.join("expected_outputs", df.sort_values(by="interfE").head(1).index[0])
    test_pose = pyrosetta.io.pose_from_file(filename=lowest_energy_pdb_filename)

    chE = pyrosetta.rosetta.core.select.residue_selector.ChainSelector("E")

    view = viewer.init(test_pose)
    view.add(viewer.setStyle())
    view.add(viewer.setStyle(command=({"hetflag": True}, {"stick": {"colorscheme": "brownCarbon", "radius": 0.2}})))
    view.add(viewer.setSurface(residue_selector=chE, opacity=0.7, color='white'))
    view.add(viewer.setHydrogenBonds())
    view()

You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
jupyter labextension install jupyterlab_3dmol

Exercise:

Re-run the above example with more sampling. Pretend that you have done enough sampling (i.e. ~2,000-10,000 global ligand docking trajectories depending on the surface area of the protein) and that the decoy with the lowest interfE score is the "native" ligand binding mode. Re-plot the ligand binding energy landscape fixing that decoy to rmsd_chX=0.0

Hint: You have all of the decoys saved as .pdb files, so you need to re-score them using the command line flag -in:file:native specifying the .pdb file with the lowest interfE score, that way all rmsd_chX values correspond to the RMSD from that decoy, not the binding mode we started with above. Use the following cell to get started! The code below does not save the new scores to a scorefile, but if you would like to, make use of the pyrosetta.toolbox.py_jobdistributor.output_scorefile() function.


Restart Jupyter Notebook kernel to properly re-initialize PyRosetta


In [1]:
import glob
import logging
logging.basicConfig(level=logging.INFO)
import matplotlib
%matplotlib inline
import os
import pandas as pd
import pyrosetta
import pyrosetta.distributed.viewer as viewer
import seaborn
seaborn.set()
import sys

# Notebook setup
if 'google.colab' in sys.modules:
    !pip install pyrosettacolabsetup
    import pyrosettacolabsetup
    pyrosettacolabsetup.mount_pyrosetta_install()
    print ("Notebook is set for PyRosetta use in Colab.  Have fun!")
In [2]:
if not os.getenv("DEBUG"):
    pdb_filenames = glob.glob("expected_outputs/test_lig_XMLObjects*.pdb")
    ligand_params = "inputs/TPA.am1-bcc.fa.params"
    native_pdb_filename = "expected_outputs/test_lig_XMLObjects_1.pdb"

    flags = f"""
    -extra_res_fa {ligand_params} 
    -in:file:native {native_pdb_filename}
    -ignore_unrecognized_res 1 
    -mute all
    """
    pyrosetta.distributed.init(flags)
    scorefxn = pyrosetta.create_score_function("ref2015")

    xml = pyrosetta.rosetta.protocols.rosetta_scripts.XmlObjects.create_from_string("""
    <ROSETTASCRIPTS>
      <SCOREFXNS>
        <ScoreFunction name="fa_standard" weights="ref2015.wts"/>
      </SCOREFXNS>
      <RESIDUE_SELECTORS>
        <Chain name="chX" chains="X"/>
      </RESIDUE_SELECTORS>
      <SIMPLE_METRICS>
        <RMSDMetric name="rmsd_chX" use_native="true" residue_selector="chX" residue_selector_ref="chX" robust="true" rmsd_type="rmsd_all" />
      </SIMPLE_METRICS>
      <FILTERS>
          <LigInterfaceEnergy name="interfE" scorefxn="fa_standard" energy_cutoff="0.0" confidence="0"/>
          <SimpleMetricFilter name="rmsd_chX" metric="rmsd_chX" cutoff="999999." comparison_type="lt" confidence="0"/>
      </FILTERS>
      <PROTOCOLS>
        <Add filter="interfE"/>
        <Add filter="rmsd_chX"/>
      </PROTOCOLS>
    </ROSETTASCRIPTS>
    """).get_mover("ParsedProtocol")

    df = pd.DataFrame()
    for pdb_filename in pdb_filenames:
        test_pose = pyrosetta.io.pose_from_file(filename=pdb_filename)
        xml.apply(test_pose)
        test_df = pd.DataFrame.from_records(dict(test_pose.scores), index=[pdb_filename.split("/")[-1]])
        df = df.append(test_df)

    matplotlib.rcParams['figure.figsize'] = [12.0, 8.0]
    seaborn.scatterplot(x="rmsd_chX", y="interfE", data=df)
INFO:pyrosetta.distributed:maybe_init performing pyrosetta initialization: {'extra_options': '-extra_res_fa inputs/TPA.am1-bcc.fa.params -in:file:native expected_outputs/test_lig_XMLObjects_1.pdb -ignore_unrecognized_res 1 -mute all', 'silent': True}
INFO:pyrosetta.rosetta:Found rosetta database at: /mnt/home/klimaj/git/Rosetta/main/source/src/python/PyRosetta/src/pyrosetta/database; using it....
INFO:pyrosetta.rosetta:PyRosetta-4 2019 [Rosetta PyRosetta4.conda.linux.CentOS.python36.Release 2019.39+release.93456a567a8125cafdf7f8cb44400bc20b570d81 2019-09-26T14:24:44] retrieved from: http://www.pyrosetta.org
(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.
In [ ]: