{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "\n", "*This notebook contains material from [PyRosetta](https://RosettaCommons.github.io/PyRosetta.notebooks);\n", "content is available [on Github](https://github.com/RosettaCommons/PyRosetta.notebooks.git).*" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "\n", "< [Ligand Refinement in PyRosetta (a.k.a. High-Resolution Local Docking) Using the `ligand.wts` Scorefunction](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/08.00-Ligand-Docking-PyRosetta.ipynb) | [Contents](toc.ipynb) | [Index](index.ipynb) | [`GALigandDock` Protocol with `pyrosetta.distributed` Using the `beta_cart.wts` Scorefunction](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/08.02-Ligand-Docking-pyrosetta.distributed.ipynb) >

\"Open" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "# Global Ligand Docking using `XMLObjects` Using the `ref2015.wts` Scorefunction" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "*Warning*: This notebook uses `pyrosetta.distributed.viewer` code, which runs in `jupyter notebook` and might not run if you're using `jupyterlab`." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "*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. " ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [ { "data": { "text/html": [ "" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "import logging\n", "logging.basicConfig(level=logging.INFO)\n", "import matplotlib\n", "%matplotlib inline\n", "import os\n", "import pandas as pd\n", "import pyrosetta\n", "import pyrosetta.distributed.viewer as viewer\n", "import seaborn\n", "seaborn.set()\n", "import sys\n", "\n", "!pip install pyrosettacolabsetup\n", "import pyrosettacolabsetup; pyrosettacolabsetup.install_pyrosetta()\n", "import pyrosetta; pyrosetta.init()\n" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "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`." ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "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}\n", "INFO:pyrosetta.rosetta:Found rosetta database at: /mnt/home/klimaj/git/Rosetta/main/source/src/python/PyRosetta/src/pyrosetta/database; using it....\n", "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\n", "(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\n", "INFO:rosetta:core.init: {0} Checking for fconfig files in pwd and ./rosetta/flags\n", "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\n", "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\n", "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\n", "INFO:rosetta:basic.random.init_random_generator: {0} RandomGenerator:init: Normal mode, seed=-2105863589 RG_type=mt19937\n", "INFO:rosetta:core.chemical.GlobalResidueTypeSet: {0} Finished initializing fa_standard residue type set. Created 981 residue types\n", "INFO:rosetta:core.chemical.GlobalResidueTypeSet: {0} Total time to initialize 1.97866 seconds.\n", "INFO:rosetta:core.import_pose.import_pose: {0} File 'inputs/test_lig.pdb' automatically determined to be of type PDB\n", "INFO:rosetta:core.scoring.etable: {0} Starting energy table calculation\n", "INFO:rosetta:core.scoring.etable: {0} smooth_etable: changing atr/rep split to bottom of energy well\n", "INFO:rosetta:core.scoring.etable: {0} smooth_etable: spline smoothing lj etables (maxdis = 6)\n", "INFO:rosetta:core.scoring.etable: {0} smooth_etable: spline smoothing solvation etables (max_dis = 6)\n", "INFO:rosetta:core.scoring.etable: {0} Finished calculating energy tables.\n", "INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv\n", "INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv\n", "INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv\n", "INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv\n", "INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv\n", "INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/rama/fd/all.ramaProb\n", "INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb\n", "INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt\n", "INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt\n", "INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt\n", "INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt\n", "INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/P_AA_pp/P_AA\n", "INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/P_AA_pp/P_AA_n\n", "INFO:rosetta:core.scoring.P_AA: {0} shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated.\n", "INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop\n" ] } ], "source": [ "ligand_params = \"inputs/TPA.am1-bcc.fa.params\"\n", "flags = f\"\"\"\n", "-ignore_unrecognized_res 1\n", "-extra_res_fa {ligand_params}\n", "\"\"\"\n", "pyrosetta.distributed.init(flags)\n", "pose = pyrosetta.io.pose_from_file(filename=\"inputs/test_lig.pdb\")\n", "scorefxn = pyrosetta.create_score_function(\"ref2015\")" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Ligand docking using `XmlObjects`:" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "INFO:rosetta:protocols.rosetta_scripts.RosettaScriptsParser: {0} Generating XML Schema for rosetta_scripts...\n", "INFO:rosetta:protocols.rosetta_scripts.RosettaScriptsParser: {0} ...done\n", "INFO:rosetta:protocols.rosetta_scripts.RosettaScriptsParser: {0} Initializing schema validator...\n", "INFO:rosetta:protocols.rosetta_scripts.RosettaScriptsParser: {0} ...done\n", "INFO:rosetta:protocols.rosetta_scripts.RosettaScriptsParser: {0} Validating input script...\n", "INFO:rosetta:protocols.rosetta_scripts.RosettaScriptsParser: {0} ...done\n", "INFO:rosetta:protocols.rosetta_scripts.RosettaScriptsParser: {0} Parsed script:\n", "\n", "\t\n", "\t\t\n", "\t\n", "\t\n", "\t\t\n", "\t\n", "\t\n", "\t\t\n", "\t\n", "\t\n", "\t\t\n", "\t\n", "\t\n", "\t\t\n", "\t\t\n", "\t\t\n", "\t\n", "\t\n", "\t\t\n", "\t\t\n", "\t\t\n", "\t\n", "\t\n", "\t\t\n", "\t\t\n", "\t\n", "\t\n", "\t\t\n", "\t\t\n", "\t\t\n", "\t\t\n", "\t\n", "\t\n", "\t\t\n", "\t\t\n", "\t\n", "\t\n", "\t\t\n", "\t\t\n", "\t\t\n", "\t\t\n", "\t\t\n", "\t\t\n", "\t\n", "\n", "INFO:rosetta:core.scoring.ScoreFunctionFactory: {0} SCOREFUNCTION: ref2015\n", "INFO:rosetta:core.scoring.etable: {0} Starting energy table calculation\n", "INFO:rosetta:core.scoring.etable: {0} smooth_etable: changing atr/rep split to bottom of energy well\n", "INFO:rosetta:core.scoring.etable: {0} smooth_etable: spline smoothing lj etables (maxdis = 6)\n", "INFO:rosetta:core.scoring.etable: {0} smooth_etable: spline smoothing solvation etables (max_dis = 6)\n", "INFO:rosetta:core.scoring.etable: {0} Finished calculating energy tables.\n", "INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine\n", "INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/InterchainPotential/interchain_env_log.txt\n", "INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/InterchainPotential/interchain_pair_log.txt\n", "INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt\n", "INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt\n", "INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt\n", "INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt\n", "INFO:rosetta:core.scoring.ramachandran: {0} shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated.\n", "INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb\n", "INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/rama/flat/avg_L_rama.dat\n", "INFO:rosetta:core.scoring.ramachandran: {0} Reading custom Ramachandran table from scoring/score_functions/rama/flat/avg_L_rama.dat.\n", "INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/rama/flat/sym_all_rama.dat\n", "INFO:rosetta:core.scoring.ramachandran: {0} Reading custom Ramachandran table from scoring/score_functions/rama/flat/sym_all_rama.dat.\n", "INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/rama/flat/sym_G_rama.dat\n", "INFO:rosetta:core.scoring.ramachandran: {0} Reading custom Ramachandran table from scoring/score_functions/rama/flat/sym_G_rama.dat.\n", "INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/rama/flat/sym_P_rama.dat\n", "INFO:rosetta:core.scoring.ramachandran: {0} Reading custom Ramachandran table from scoring/score_functions/rama/flat/sym_P_rama.dat.\n", "INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/rama/flat/avg_L_rama_str.dat\n", "INFO:rosetta:core.scoring.ramachandran: {0} Reading custom Ramachandran table from scoring/score_functions/rama/flat/avg_L_rama_str.dat.\n", "INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/rama/flat/sym_all_rama_str.dat\n", "INFO:rosetta:core.scoring.ramachandran: {0} Reading custom Ramachandran table from scoring/score_functions/rama/flat/sym_all_rama_str.dat.\n", "INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/rama/flat/sym_G_rama_str.dat\n", "INFO:rosetta:core.scoring.ramachandran: {0} Reading custom Ramachandran table from scoring/score_functions/rama/flat/sym_G_rama_str.dat.\n", "INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/rama/flat/sym_P_rama_str.dat\n", "INFO:rosetta:core.scoring.ramachandran: {0} Reading custom Ramachandran table from scoring/score_functions/rama/flat/sym_P_rama_str.dat.\n", "INFO:rosetta:protocols.jd2.parser.ScoreFunctionLoader: {0} defined score function \"fa_standard\" with weights \"ref2015.wts\"\n", "INFO:rosetta:core.select.residue_selector.util: {0} Found residue selector chX\n", "INFO:rosetta:core.select.residue_selector.util: {0} Found residue selector chX\n", "INFO:rosetta:core.pose.ref_pose: {0} Loading PDB: store_native\n", "INFO:rosetta:core.simple_metrics.metrics.RMSDMetric: {0} Loaded reference pose: store_native with 0 residues\n", "INFO:rosetta:core.pose.ref_pose: {0} Loading PDB: store_native\n", "INFO:rosetta:protocols.rosetta_scripts.RosettaScriptsParser: {0} Defined mover named \"spm\" of type SavePoseMover\n", "INFO:rosetta:protocols.rosetta_scripts.RosettaScriptsParser: {0} Defined mover named \"transform\" of type Transform\n", "INFO:rosetta:protocols.rosetta_scripts.RosettaScriptsParser: {0} Defined mover named \"high_res_docker\" of type HighResDocker\n", "INFO:rosetta:protocols.rosetta_scripts.RosettaScriptsParser: {0} Defined mover named \"final\" of type FinalMinimizer\n", "INFO:rosetta:protocols.rosetta_scripts.RosettaScriptsParser: {0} Defined filter named \"interfE\" of type LigInterfaceEnergy\n", "INFO:rosetta:protocols.rosetta_scripts.RosettaScriptsParser: {0} Defined filter named \"rmsd_chX\" of type SimpleMetricFilter\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} ParsedProtocol mover with the following movers and filters\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} added mover \"spm\" with filter \"true_filter\"\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} added mover \"transform\" with filter \"true_filter\"\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} added mover \"high_res_docker\" with filter \"true_filter\"\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} added mover \"final\" with filter \"true_filter\"\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} added mover \"NULL_MOVER\" with filter \"interfE\"\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} added mover \"NULL_MOVER\" with filter \"rmsd_chX\"\n" ] } ], "source": [ "xml = pyrosetta.rosetta.protocols.rosetta_scripts.XmlObjects.create_from_string(\"\"\"\n", "\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "\n", "\"\"\").get_mover(\"ParsedProtocol\")" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Produce 5 global ligand docking trajectories using `PyJobDistributor`:" ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER SavePoseMover - spm=======================\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER Transform - transform=======================\n", "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\n", "INFO:rosetta:protocols.qsar.scoring_grid.GridManager: {0} No conformation matching hash: 4dc5d457f2bb8b129abbf363feeefd56e18fe3d2 Updating grid and adding it to the cache\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Working on decoy: test_lig_XMLObjects_1.pdb\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "INFO:rosetta:protocols.ligand_docking.Transform: {0} Considering 9 conformers during sampling\n", "INFO:rosetta:protocols.ligand_docking.Transform: {0} percent acceptance: 1433 0.5732 1067\n", "INFO:rosetta:protocols.ligand_docking.Transform: {0} Moves rejected for being outside of grid: 1063 0.4252\n", "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.\n", "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.\n", "INFO:rosetta:protocols.evaluation.ChiWellRmsdEvaluatorCreator: {0} Evaluation Creator active ...\n", "INFO:rosetta:protocols.ligand_docking.Transform: {0} Accepted pose with grid score: -34\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER HighResDocker - high_res_docker=======================\n", "INFO:rosetta:basic.io.database: {0} Database file opened: scoring/score_functions/elec_cp_reps.dat\n", "INFO:rosetta:core.scoring.elec.util: {0} Read 40 countpair representative atoms\n", "INFO:rosetta:core.pack.dunbrack.RotamerLibrary: {0} shapovalov_lib_fixes_enable option is true.\n", "INFO:rosetta:core.pack.dunbrack.RotamerLibrary: {0} shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated.\n", "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\n", "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'.\n", "INFO:rosetta:core.pack.dunbrack.RotamerLibrary: {0} Dunbrack 2010 library took 0.442342 seconds to load from binary\n", "INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()\n", "INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA\n", "INFO:rosetta:core.pack.pack_rotamers: {0} built 2057 rotamers at 69 positions.\n", "INFO:rosetta:core.pack.interaction_graph.interaction_graph_factory: {0} Instantiating DensePDInteractionGraph\n", "INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()\n", "INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA\n", "INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()\n", "INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA\n", "INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()\n", "INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA\n", "INFO:rosetta:core.pack.pack_rotamers: {0} built 1986 rotamers at 66 positions.\n", "INFO:rosetta:core.pack.interaction_graph.interaction_graph_factory: {0} Instantiating DensePDInteractionGraph\n", "INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()\n", "INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA\n", "INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()\n", "INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA\n", "INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()\n", "INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA\n", "INFO:rosetta:core.pack.pack_rotamers: {0} built 1987 rotamers at 66 positions.\n", "INFO:rosetta:core.pack.interaction_graph.interaction_graph_factory: {0} Instantiating DensePDInteractionGraph\n", "INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()\n", "INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA\n", "INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()\n", "INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA\n", "INFO:rosetta:protocols.moves.MonteCarlo: {0} MonteCarlo:: last_accepted_score,lowest_score: 1600.31 1600.31\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER FinalMinimizer - final=======================\n", "INFO:rosetta:protocols.ligand_docking.ligand_options.FinalMinimizer: {0} Energy prior to minimizing: 1600.31\n", "INFO:rosetta:protocols.ligand_docking.ligand_options.FinalMinimizer: {0} Energy after minimizing: 1456.97\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN FILTER interfE=======================\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================END FILTER interfE=======================\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN FILTER rmsd_chX=======================\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================END FILTER rmsd_chX=======================\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} setting status to success\n", "INFO:rosetta:protocols.enzdes.EnzFilters: {0} Calculated Interface Energy is before cst correction is:-28.1887\n", "INFO:rosetta:protocols.enzdes.EnzFilters: {0} Calculated Interface Energy is -28.2764\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} ============Begin report for interfE==================\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} \n", " chain res AA total contact fa_atr fa_rep hb_bb_sc hb_sc fa_sol fa_dun fa_pair\n", " E 48 THR -2.417 -3.119 -6.763 1.021 -0.993 -0.583 4.200 0.450 0.000\n", " E 49 LEU -6.543 -7.144 -9.186 0.803 0.000 0.000 1.238 0.075 0.000\n", " E 50 GLY -2.059 -0.700 -4.684 0.811 0.000 0.000 3.173 0.000 0.000\n", " E 51 THR -1.979 -1.965 -4.199 0.355 0.000 0.000 1.879 0.099 0.000\n", " E 52 GLY -0.176 0.969 -2.910 0.272 0.000 0.000 3.608 0.000 0.000\n", " E 53 SER -2.735 0.784 -3.306 0.162 -0.931 -0.328 5.188 0.270 0.000\n", " E 54 PHE 0.876 -1.600 -6.411 0.658 -0.411 0.000 4.564 2.876 0.000\n", " E 55 GLY -1.377 0.007 -2.945 0.151 -0.511 0.000 3.312 0.000 0.000\n", " E 56 ARG -1.088 -1.522 -6.706 0.518 0.000 -0.357 5.024 2.218 0.000\n", " E 57 VAL -6.165 -4.674 -9.023 1.013 0.000 0.000 3.336 0.060 0.000\n", " E 58 MET -2.147 -3.447 -9.067 1.359 0.000 0.000 4.260 1.512 0.000\n", " E 59 LEU -5.857 -5.463 -8.600 1.494 0.000 0.000 1.643 0.422 0.000\n", " E 69 TYR -0.690 -4.729 -9.958 1.822 0.000 -0.419 3.827 2.872 0.000\n", " E 70 ALA -2.410 -3.401 -6.353 0.516 0.000 0.000 2.437 0.000 0.000\n", " E 71 MET -2.666 -6.202 -9.279 1.245 0.000 0.000 1.832 1.710 0.000\n", " E 72 LYS -4.477 0.903 -7.895 0.904 0.000 -0.646 8.540 1.037 0.000\n", " E 74 LEU -1.722 -2.492 -6.620 1.523 0.000 0.000 2.605 0.910 0.000\n", " E 78 LYS -3.043 -0.299 -6.728 0.818 -0.861 0.000 6.473 1.565 0.000\n", " E 82 LEU -0.419 -2.208 -5.790 0.787 -0.503 0.000 3.298 1.863 0.000\n", " E 84 GLN -4.641 -2.305 -7.459 0.571 -0.503 -0.725 5.810 2.196 0.000\n", " E 87 HIS -0.886 -1.113 -7.215 0.802 0.000 -0.725 6.025 2.189 0.000\n", " E 91 GLU -3.591 0.525 -8.598 0.855 0.000 -0.646 8.914 2.849 0.000\n", " E 104 VAL -2.234 -4.151 -6.001 0.510 0.000 0.000 1.340 0.567 0.000\n", " E 105 LYS -0.037 0.469 -4.287 0.256 0.000 0.000 4.501 1.138 0.000\n", " E 106 LEU -4.116 -5.203 -7.960 1.520 0.000 0.000 1.237 0.385 0.000\n", " E 118 MET -1.417 -4.497 -8.675 1.533 0.000 0.000 2.646 1.986 0.000\n", " E 119 VAL -4.636 -4.850 -8.706 2.116 0.000 0.000 1.741 0.110 0.000\n", " E 120 MET -3.844 -4.911 -9.727 0.778 0.000 0.000 4.038 1.848 0.000\n", " E 121 GLU -1.310 -0.462 -4.028 0.206 0.000 0.000 3.360 2.373 0.000\n", " E 122 TYR -4.442 -6.152 -8.669 0.525 -0.330 0.000 2.322 2.406 0.000\n", " E 123 VAL -2.182 -4.170 -6.584 0.877 0.000 0.000 1.537 0.017 0.000\n", " E 124 ALA -2.617 -2.974 -3.698 0.205 -0.799 0.000 1.318 0.000 0.000\n", " E 125 GLY -1.329 -0.985 -4.236 0.734 -0.556 0.000 3.073 0.000 0.000\n", " E 126 GLY -3.437 -0.662 -4.172 0.426 0.000 0.000 3.085 0.000 0.000\n", " E 127 GLU -2.925 1.039 -6.871 1.447 0.000 -0.564 7.027 2.748 0.000\n", " E 129 PHE -0.241 -1.619 -8.049 1.213 0.000 0.000 5.216 1.387 0.000\n", " E 130 SER -0.329 0.469 -3.921 0.233 0.000 0.000 4.157 1.080 0.000\n", " E 165 ARG -0.333 -2.149 -8.747 1.746 -1.333 -0.520 6.705 3.113 0.000\n", " E 166 ASP 0.543 1.140 -5.401 0.991 -0.482 -0.630 6.663 2.948 0.000\n", " E 168 LYS -3.030 1.904 -9.478 2.652 0.000 -0.673 9.403 1.179 0.000\n", " E 169 PRO -3.490 -1.704 -7.718 2.992 0.000 0.000 3.023 0.065 0.000\n", " E 170 GLU -1.311 0.098 -6.086 0.567 0.000 0.000 5.616 2.716 0.000\n", " E 171 ASN -4.392 -0.202 -7.832 0.790 -0.482 -0.245 7.566 1.695 0.000\n", " E 172 LEU -5.886 -6.302 -8.858 1.341 0.000 0.000 1.215 0.637 0.000\n", " E 173 LEU -5.721 -5.168 -9.243 1.134 0.000 0.000 2.941 0.551 0.000\n", " E 181 GLN -1.309 -2.677 -7.989 0.498 -0.630 0.000 5.444 4.290 0.000\n", " E 182 VAL -4.450 -4.501 -6.797 0.742 0.000 0.000 1.553 0.074 0.000\n", " E 183 THR -3.797 -3.976 -6.762 0.572 -0.795 -0.657 3.666 2.388 0.000\n", " E 184 ASP 4.753 2.582 -5.326 0.990 -0.699 -0.245 7.861 2.374 0.000\n", " E 185 PHE -0.523 -6.075 -8.430 1.314 0.000 0.000 1.042 3.227 0.000\n", " E 186 GLY 1.335 0.780 -3.222 0.783 -0.148 0.000 3.367 0.000 0.000\n", " E 187 PHE -2.917 -3.863 -7.082 0.523 -0.834 0.000 3.529 1.619 0.000\n", " E 200 GLY -2.562 -1.246 -2.623 0.242 0.000 0.000 1.135 0.000 0.000\n", " E 201 THR 3.537 1.468 -6.014 3.466 0.000 -0.914 4.930 0.030 0.000\n", " E 204 TYR -2.788 -4.504 -9.457 1.975 0.000 -0.471 3.449 2.682 0.000\n", " E 324 THR -1.583 -0.856 -4.823 1.003 0.000 -0.765 3.730 0.002 0.000\n", " E 327 PHE -3.412 -4.721 -8.228 0.931 0.000 0.000 2.576 1.602 0.000\n", " E 328 ASP -0.300 0.147 -2.732 0.306 -0.583 0.000 3.155 2.607 0.000\n", " E 330 TYR -1.936 -2.871 -6.672 0.840 0.000 0.000 2.960 1.343 0.000\n", " X 1 TPA -8.279 1.922 -19.728 1.307 -1.854 -1.938 24.135 0.000 0.000\n", "============End report for interfE==================\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} ============Begin report for rmsd_chX==================\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} ============End report for rmsd_chX==================\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER SavePoseMover - spm=======================\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER Transform - transform=======================\n", "INFO:rosetta:protocols.qsar.scoring_grid.GridManager: {0} Found a conformation matching hash: 4dc5d457f2bb8b129abbf363feeefd56e18fe3d2 Loading from grid cache\n", "INFO:rosetta:protocols.ligand_docking.Transform: {0} Considering 9 conformers during sampling\n", "INFO:rosetta:protocols.ligand_docking.Transform: {0} percent acceptance: 1353 0.5412 1147\n", "INFO:rosetta:protocols.ligand_docking.Transform: {0} Moves rejected for being outside of grid: 1144 0.4576\n", "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.\n", "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.\n", "INFO:rosetta:protocols.ligand_docking.Transform: {0} Accepted pose with grid score: -20\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER HighResDocker - high_res_docker=======================\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Working on decoy: test_lig_XMLObjects_2.pdb\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()\n", "INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA\n", "INFO:rosetta:core.pack.pack_rotamers: {0} built 1285 rotamers at 47 positions.\n", "INFO:rosetta:core.pack.interaction_graph.interaction_graph_factory: {0} Instantiating DensePDInteractionGraph\n", "INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()\n", "INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA\n", "INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()\n", "INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA\n", "INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()\n", "INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA\n", "INFO:rosetta:core.pack.pack_rotamers: {0} built 700 rotamers at 25 positions.\n", "INFO:rosetta:core.pack.interaction_graph.interaction_graph_factory: {0} Instantiating DensePDInteractionGraph\n", "INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()\n", "INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA\n", "INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()\n", "INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA\n", "INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()\n", "INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA\n", "INFO:rosetta:core.pack.pack_rotamers: {0} built 749 rotamers at 28 positions.\n", "INFO:rosetta:core.pack.interaction_graph.interaction_graph_factory: {0} Instantiating DensePDInteractionGraph\n", "INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()\n", "INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA\n", "INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()\n", "INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA\n", "INFO:rosetta:protocols.moves.MonteCarlo: {0} MonteCarlo:: last_accepted_score,lowest_score: 1700.33 1699.91\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER FinalMinimizer - final=======================\n", "INFO:rosetta:protocols.ligand_docking.ligand_options.FinalMinimizer: {0} Energy prior to minimizing: 1699.91\n", "INFO:rosetta:protocols.ligand_docking.ligand_options.FinalMinimizer: {0} Energy after minimizing: 1642.36\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN FILTER interfE=======================\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================END FILTER interfE=======================\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN FILTER rmsd_chX=======================\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================END FILTER rmsd_chX=======================\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} setting status to success\n", "INFO:rosetta:protocols.enzdes.EnzFilters: {0} Calculated Interface Energy is before cst correction is:-9.16448\n", "INFO:rosetta:protocols.enzdes.EnzFilters: {0} Calculated Interface Energy is -9.16449\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} ============Begin report for interfE==================\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} \n", " chain res AA total contact fa_atr fa_rep hb_bb_sc hb_sc fa_sol fa_dun fa_pair\n", " E 50 GLY -2.296 -0.757 -3.364 0.450 0.000 0.000 2.158 0.000 0.000\n", " E 51 THR -1.745 -2.048 -3.708 0.328 0.000 0.000 1.332 0.201 0.000\n", " E 52 GLY -0.743 0.562 -2.039 0.177 0.000 0.000 2.424 0.000 0.000\n", " E 53 SER -2.328 0.986 -2.794 0.138 -0.642 -0.323 4.606 0.459 0.000\n", " E 54 PHE 1.582 -2.847 -4.806 0.484 0.000 0.000 1.476 3.029 0.000\n", " E 55 GLY 2.725 -0.245 -2.547 0.231 0.000 0.000 2.070 0.000 0.000\n", " E 56 ARG -0.269 -0.805 -5.369 0.636 0.000 0.000 3.929 2.112 0.000\n", " E 78 LYS 20.730 0.029 -6.578 0.992 -1.154 0.000 6.769 25.465 0.000\n", " E 129 PHE -0.876 -1.288 -8.575 1.275 0.000 0.000 6.012 1.430 0.000\n", " E 165 ARG -0.079 -2.045 -8.668 1.792 -1.201 -0.529 6.560 2.703 0.000\n", " E 166 ASP 1.767 1.464 -5.566 1.647 -0.551 -0.792 6.725 3.451 0.000\n", " E 168 LYS 1.055 2.719 -10.010 2.216 0.000 0.000 10.513 3.967 0.000\n", " E 170 GLU 1.793 1.101 -6.604 0.571 0.000 0.000 7.135 3.642 0.000\n", " E 171 ASN -2.146 1.006 -7.524 1.171 -0.551 -0.170 8.080 2.803 0.000\n", " E 184 ASP 2.815 1.050 -4.320 0.764 -0.801 0.000 5.407 2.996 0.000\n", " E 187 PHE -0.381 -3.856 -7.494 1.055 -0.702 0.000 3.285 3.732 0.000\n", " E 200 GLY -0.160 0.327 -2.553 1.984 0.000 0.000 0.896 0.000 0.000\n", " E 201 THR 0.282 0.738 -5.717 2.727 0.000 -0.622 4.349 0.045 0.000\n", " E 202 PRO -2.553 -1.789 -5.301 1.953 0.000 0.000 1.559 1.056 0.000\n", " E 203 GLU -1.442 -1.872 -5.333 0.519 0.000 0.000 2.943 3.079 0.000\n", " E 204 TYR -3.817 -5.068 -9.444 1.464 0.000 -0.772 3.684 2.401 0.000\n", " E 243 PRO -1.520 -0.674 -5.010 1.704 0.000 0.000 2.632 0.092 0.000\n", " E 328 ASP -1.224 0.218 -2.808 0.180 -0.812 0.000 3.658 2.781 0.000\n", " E 330 TYR -2.065 -3.112 -6.174 0.461 0.000 0.000 2.601 1.424 0.000\n", " E 331 GLU -0.535 0.167 -1.627 0.081 0.000 0.000 1.713 2.598 0.000\n", " E 333 GLU 1.144 1.728 -3.952 0.965 -0.181 0.000 4.897 3.221 0.000\n", " X 1 TPA 2.588 2.692 -2.422 0.013 -0.350 -0.323 5.773 0.000 0.000\n", "============End report for interfE==================\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} ============Begin report for rmsd_chX==================\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} ============End report for rmsd_chX==================\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER SavePoseMover - spm=======================\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER Transform - transform=======================\n", "INFO:rosetta:protocols.qsar.scoring_grid.GridManager: {0} Found a conformation matching hash: 4dc5d457f2bb8b129abbf363feeefd56e18fe3d2 Loading from grid cache\n", "INFO:rosetta:protocols.ligand_docking.Transform: {0} Considering 9 conformers during sampling\n", "INFO:rosetta:protocols.ligand_docking.Transform: {0} percent acceptance: 1374 0.5496 1126\n", "INFO:rosetta:protocols.ligand_docking.Transform: {0} Moves rejected for being outside of grid: 1125 0.45\n", "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.\n", "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.\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "INFO:rosetta:protocols.ligand_docking.Transform: {0} Accepted pose with grid score: -20\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER HighResDocker - high_res_docker=======================\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Working on decoy: test_lig_XMLObjects_3.pdb\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()\n", "INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA\n", "INFO:rosetta:core.pack.pack_rotamers: {0} built 1342 rotamers at 48 positions.\n", "INFO:rosetta:core.pack.interaction_graph.interaction_graph_factory: {0} Instantiating DensePDInteractionGraph\n", "INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()\n", "INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA\n", "INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()\n", "INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA\n", "INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()\n", "INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA\n", "INFO:rosetta:core.pack.pack_rotamers: {0} built 1163 rotamers at 42 positions.\n", "INFO:rosetta:core.pack.interaction_graph.interaction_graph_factory: {0} Instantiating DensePDInteractionGraph\n", "INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()\n", "INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA\n", "INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()\n", "INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA\n", "INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()\n", "INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA\n", "INFO:rosetta:core.pack.pack_rotamers: {0} built 1167 rotamers at 43 positions.\n", "INFO:rosetta:core.pack.interaction_graph.interaction_graph_factory: {0} Instantiating DensePDInteractionGraph\n", "INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()\n", "INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA\n", "INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()\n", "INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA\n", "INFO:rosetta:protocols.moves.MonteCarlo: {0} MonteCarlo:: last_accepted_score,lowest_score: 1686.12 1686.12\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER FinalMinimizer - final=======================\n", "INFO:rosetta:protocols.ligand_docking.ligand_options.FinalMinimizer: {0} Energy prior to minimizing: 1686.12\n", "INFO:rosetta:protocols.ligand_docking.ligand_options.FinalMinimizer: {0} Energy after minimizing: 1591.67\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN FILTER interfE=======================\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================END FILTER interfE=======================\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN FILTER rmsd_chX=======================\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================END FILTER rmsd_chX=======================\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} setting status to success\n", "INFO:rosetta:protocols.enzdes.EnzFilters: {0} Calculated Interface Energy is before cst correction is:2.79191\n", "INFO:rosetta:protocols.enzdes.EnzFilters: {0} Calculated Interface Energy is 2.54229\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} ============Begin report for interfE==================\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} \n", " chain res AA total contact fa_atr fa_rep hb_bb_sc hb_sc fa_sol fa_dun fa_pair\n", " E 48 THR -2.568 -2.644 -6.709 1.086 -0.720 -0.458 4.157 0.516 0.000\n", " E 49 LEU -5.507 -6.602 -7.780 0.585 0.000 0.000 0.593 0.203 0.000\n", " E 50 GLY -2.529 -0.930 -4.443 0.883 0.000 0.000 2.630 0.000 0.000\n", " E 51 THR 0.706 -1.417 -4.608 0.553 0.000 0.000 2.638 0.461 0.000\n", " E 52 GLY 0.587 0.625 -1.602 0.166 0.000 0.000 2.060 0.000 0.000\n", " E 53 SER -0.679 -0.364 -2.358 0.195 -0.261 0.000 2.060 1.040 0.000\n", " E 54 PHE 2.458 -2.900 -5.225 0.622 0.000 0.000 1.703 3.540 0.000\n", " E 55 GLY 9.392 -0.410 -2.625 0.249 0.000 0.000 1.967 0.000 0.000\n", " E 56 ARG -1.234 -1.626 -6.936 0.600 0.000 -0.322 5.031 2.663 0.000\n", " E 57 VAL -4.318 -3.181 -6.370 0.670 0.000 0.000 2.519 0.027 0.000\n", " E 72 LYS -3.991 -0.900 -7.739 1.305 0.000 -0.642 6.177 1.612 0.000\n", " E 126 GLY -3.003 -0.605 -4.369 0.381 0.000 0.000 3.383 0.000 0.000\n", " E 127 GLU -0.249 -0.078 -7.265 1.183 0.000 -0.388 6.391 4.655 0.000\n", " E 128 MET -4.301 -5.412 -9.602 0.969 0.000 0.000 3.221 1.982 0.000\n", " E 129 PHE -0.264 -0.947 -9.168 1.249 0.000 0.000 6.972 1.906 0.000\n", " E 130 SER -0.959 0.198 -4.887 0.318 0.000 -0.388 5.155 0.650 0.000\n", " E 133 ARG -0.063 -0.981 -5.668 0.330 0.000 -0.987 5.343 3.519 0.000\n", " E 134 ARG 3.262 0.797 -3.061 0.638 0.000 0.000 3.220 2.070 0.000\n", " E 168 LYS 3.329 4.262 -9.570 4.595 0.000 -0.171 9.408 3.034 0.000\n", " E 169 PRO -0.923 -0.402 -7.917 4.430 0.000 0.000 3.085 0.402 0.000\n", " E 170 GLU 4.451 1.155 -7.463 1.622 -0.296 0.000 7.292 6.067 0.000\n", " E 171 ASN -3.417 -0.606 -7.327 0.614 -0.584 0.000 6.690 1.525 0.000\n", " E 172 LEU -6.024 -6.343 -8.757 1.260 0.000 0.000 1.154 0.693 0.000\n", " E 173 LEU -4.450 -4.174 -8.186 1.308 0.000 0.000 2.704 0.778 0.000\n", " E 183 THR -1.365 -2.833 -5.282 0.387 -0.365 0.000 2.426 1.430 0.000\n", " E 184 ASP 2.686 0.881 -4.167 0.374 -0.792 0.000 5.465 3.613 0.000\n", " E 201 THR 0.998 0.304 -4.625 1.925 0.000 -0.539 3.543 0.074 0.000\n", " E 202 PRO -0.038 -1.535 -4.797 1.704 0.000 0.000 1.557 1.410 0.000\n", " E 203 GLU 0.951 -1.048 -5.555 0.460 0.000 0.000 4.046 2.504 0.000\n", " E 204 TYR 1.143 -3.667 -10.113 2.033 0.000 0.000 4.413 2.503 0.000\n", " E 235 TYR 0.109 -1.418 -6.762 2.623 0.000 0.000 2.721 1.597 0.000\n", " E 236 PRO 7.370 -0.861 -6.286 2.169 0.000 0.000 3.256 3.299 0.000\n", " E 239 PHE -0.312 -2.086 -4.550 0.764 0.000 0.000 1.700 1.078 0.000\n", " E 241 ASP -0.399 -0.142 -1.859 0.136 0.000 0.000 1.582 1.900 0.000\n", " E 243 PRO -1.533 -0.702 -5.038 1.698 0.000 0.000 2.638 0.096 0.000\n", " E 327 PHE -3.273 -4.278 -7.562 0.650 0.000 0.000 2.634 1.460 0.000\n", " E 328 ASP -0.363 -0.146 -2.248 0.086 -0.839 0.000 2.856 3.043 0.000\n", " E 329 ASP -2.612 0.083 -2.195 0.067 -0.839 -0.297 3.347 2.636 0.000\n", " E 330 TYR -1.929 -2.696 -7.460 0.824 0.000 -0.276 4.215 1.429 0.000\n", " X 1 TPA 7.066 4.327 -8.387 1.313 -0.296 -0.447 12.144 0.000 0.000\n", "============End report for interfE==================\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} ============Begin report for rmsd_chX==================\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} ============End report for rmsd_chX==================\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER SavePoseMover - spm=======================\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER Transform - transform=======================\n", "INFO:rosetta:protocols.qsar.scoring_grid.GridManager: {0} Found a conformation matching hash: 4dc5d457f2bb8b129abbf363feeefd56e18fe3d2 Loading from grid cache\n", "INFO:rosetta:protocols.ligand_docking.Transform: {0} Considering 9 conformers during sampling\n", "INFO:rosetta:protocols.ligand_docking.Transform: {0} percent acceptance: 1349 0.5396 1151\n", "INFO:rosetta:protocols.ligand_docking.Transform: {0} Moves rejected for being outside of grid: 1150 0.46\n", "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.\n", "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.\n", "INFO:rosetta:protocols.ligand_docking.Transform: {0} Accepted pose with grid score: -21\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER HighResDocker - high_res_docker=======================\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Working on decoy: test_lig_XMLObjects_0.pdb\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()\n", "INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA\n", "INFO:rosetta:core.pack.pack_rotamers: {0} built 1219 rotamers at 44 positions.\n", "INFO:rosetta:core.pack.interaction_graph.interaction_graph_factory: {0} Instantiating DensePDInteractionGraph\n", "INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()\n", "INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA\n", "INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()\n", "INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA\n", "INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()\n", "INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA\n", "INFO:rosetta:core.pack.pack_rotamers: {0} built 933 rotamers at 38 positions.\n", "INFO:rosetta:core.pack.interaction_graph.interaction_graph_factory: {0} Instantiating DensePDInteractionGraph\n", "INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()\n", "INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA\n", "INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()\n", "INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA\n", "INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()\n", "INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA\n", "INFO:rosetta:core.pack.pack_rotamers: {0} built 952 rotamers at 40 positions.\n", "INFO:rosetta:core.pack.interaction_graph.interaction_graph_factory: {0} Instantiating DensePDInteractionGraph\n", "INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()\n", "INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA\n", "INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()\n", "INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA\n", "INFO:rosetta:protocols.moves.MonteCarlo: {0} MonteCarlo:: last_accepted_score,lowest_score: 1611.25 1611.25\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER FinalMinimizer - final=======================\n", "INFO:rosetta:protocols.ligand_docking.ligand_options.FinalMinimizer: {0} Energy prior to minimizing: 1611.25\n", "INFO:rosetta:protocols.ligand_docking.ligand_options.FinalMinimizer: {0} Energy after minimizing: 1519.85\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN FILTER interfE=======================\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================END FILTER interfE=======================\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN FILTER rmsd_chX=======================\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================END FILTER rmsd_chX=======================\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} setting status to success\n", "INFO:rosetta:protocols.enzdes.EnzFilters: {0} Calculated Interface Energy is before cst correction is:-11.7332\n", "INFO:rosetta:protocols.enzdes.EnzFilters: {0} Calculated Interface Energy is -11.7982\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} ============Begin report for interfE==================\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} \n", " chain res AA total contact fa_atr fa_rep hb_bb_sc hb_sc fa_sol fa_dun fa_pair\n", " E 51 THR -1.563 -1.798 -2.919 0.245 0.000 0.000 0.876 0.153 0.000\n", " E 52 GLY 5.776 0.711 -2.165 0.054 0.000 0.000 2.822 0.000 0.000\n", " E 53 SER 7.427 0.446 -3.310 0.661 -0.525 -0.368 3.988 1.607 0.000\n", " E 54 PHE 6.186 -2.451 -5.163 0.674 0.000 0.000 2.038 3.284 0.000\n", " E 55 GLY -2.106 -0.347 -2.810 0.143 0.000 0.000 2.320 0.000 0.000\n", " E 56 ARG -1.271 -1.790 -6.885 0.415 0.000 -0.382 5.061 3.036 0.000\n", " E 78 LYS -1.823 -0.573 -6.139 0.645 -0.861 0.000 5.782 2.390 0.000\n", " E 82 LEU -2.364 -2.190 -5.796 0.810 -0.495 0.000 3.292 0.042 0.000\n", " E 165 ARG -2.459 -3.163 -8.056 0.915 -1.849 -0.595 6.421 2.208 0.000\n", " E 166 ASP -2.087 0.447 -4.710 0.538 -0.340 -0.944 5.903 2.476 0.000\n", " E 168 LYS -2.531 1.567 -9.979 2.888 0.000 -0.928 9.586 0.926 0.000\n", " E 170 GLU -1.701 0.172 -5.437 0.554 0.000 -0.258 5.313 2.644 0.000\n", " E 171 ASN -3.745 -0.489 -6.885 0.438 -0.340 -0.224 6.522 1.908 0.000\n", " E 184 ASP -0.614 0.819 -3.444 0.766 -0.357 -0.285 4.138 2.651 0.000\n", " E 187 PHE -0.373 -4.362 -7.258 0.696 -0.749 0.000 2.950 3.700 0.000\n", " E 198 LEU 1.834 -1.331 -2.905 0.752 0.000 0.000 0.823 0.576 0.000\n", " E 199 CYS 5.081 -3.481 -6.217 0.919 0.000 0.000 1.817 2.442 0.000\n", " E 200 GLY -2.235 -1.423 -2.525 0.108 0.000 0.000 0.995 0.000 0.000\n", " E 201 THR -2.011 -0.071 -5.331 1.734 0.000 -1.390 4.915 0.051 0.000\n", " E 202 PRO -3.321 -1.984 -5.694 1.727 0.000 0.000 1.982 1.019 0.000\n", " E 203 GLU -1.351 -1.740 -5.010 0.541 0.000 0.000 2.729 3.089 0.000\n", " E 204 TYR -3.569 -4.762 -8.961 1.374 0.000 -0.733 3.557 2.658 0.000\n", " E 205 LEU -2.973 -4.662 -6.935 0.899 0.000 0.000 1.374 0.956 0.000\n", " E 210 ILE 46.181 -3.743 -5.688 1.091 0.000 0.000 0.854 47.349 0.000\n", " E 242 GLN 0.549 0.380 -4.327 1.292 -0.244 0.000 3.659 2.465 0.000\n", " E 243 PRO -3.732 -1.299 -5.921 1.289 0.000 0.000 3.333 0.134 0.000\n", " E 244 ILE 1.292 -0.636 -4.342 0.600 0.000 0.000 3.106 0.133 0.000\n", " E 246 ILE -4.078 -3.923 -9.900 1.563 0.000 0.000 4.414 0.116 0.000\n", " E 247 TYR -1.044 -4.043 -10.503 2.098 0.000 0.000 4.362 3.693 0.000\n", " X 1 TPA 1.273 1.190 -4.233 0.213 -0.525 -0.368 6.102 0.000 0.000\n", "============End report for interfE==================\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} ============Begin report for rmsd_chX==================\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} ============End report for rmsd_chX==================\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER SavePoseMover - spm=======================\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER Transform - transform=======================\n", "INFO:rosetta:protocols.qsar.scoring_grid.GridManager: {0} Found a conformation matching hash: 4dc5d457f2bb8b129abbf363feeefd56e18fe3d2 Loading from grid cache\n", "INFO:rosetta:protocols.ligand_docking.Transform: {0} Considering 9 conformers during sampling\n", "INFO:rosetta:protocols.ligand_docking.Transform: {0} percent acceptance: 1363 0.5452 1137\n", "INFO:rosetta:protocols.ligand_docking.Transform: {0} Moves rejected for being outside of grid: 1136 0.4544\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "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.\n", "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.\n", "INFO:rosetta:protocols.ligand_docking.Transform: {0} Accepted pose with grid score: -20\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER HighResDocker - high_res_docker=======================\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Working on decoy: test_lig_XMLObjects_4.pdb\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()\n", "INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA\n", "INFO:rosetta:core.pack.pack_rotamers: {0} built 1013 rotamers at 35 positions.\n", "INFO:rosetta:core.pack.interaction_graph.interaction_graph_factory: {0} Instantiating DensePDInteractionGraph\n", "INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()\n", "INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA\n", "INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()\n", "INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA\n", "INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()\n", "INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA\n", "INFO:rosetta:core.pack.pack_rotamers: {0} built 959 rotamers at 33 positions.\n", "INFO:rosetta:core.pack.interaction_graph.interaction_graph_factory: {0} Instantiating DensePDInteractionGraph\n", "INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()\n", "INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA\n", "INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()\n", "INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA\n", "INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()\n", "INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA\n", "INFO:rosetta:core.pack.pack_rotamers: {0} built 990 rotamers at 36 positions.\n", "INFO:rosetta:core.pack.interaction_graph.interaction_graph_factory: {0} Instantiating DensePDInteractionGraph\n", "INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()\n", "INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA\n", "INFO:rosetta:core.pack.task: {0} Packer task: initialize from command line()\n", "INFO:rosetta:core.pack.rotamer_set.RotamerSet_: {0} Using simple Rotamer generation logic for TPA\n", "INFO:rosetta:protocols.moves.MonteCarlo: {0} MonteCarlo:: last_accepted_score,lowest_score: 1697.63 1697.63\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN MOVER FinalMinimizer - final=======================\n", "INFO:rosetta:protocols.ligand_docking.ligand_options.FinalMinimizer: {0} Energy prior to minimizing: 1697.63\n", "INFO:rosetta:protocols.ligand_docking.ligand_options.FinalMinimizer: {0} Energy after minimizing: 1628.15\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN FILTER interfE=======================\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================END FILTER interfE=======================\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================BEGIN FILTER rmsd_chX=======================\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} =======================END FILTER rmsd_chX=======================\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol: {0} setting status to success\n", "INFO:rosetta:protocols.enzdes.EnzFilters: {0} Calculated Interface Energy is before cst correction is:-14.9022\n", "INFO:rosetta:protocols.enzdes.EnzFilters: {0} Calculated Interface Energy is -15.1627\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} ============Begin report for interfE==================\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} \n", " chain res AA total contact fa_atr fa_rep hb_bb_sc hb_sc fa_sol fa_dun fa_pair\n", " E 50 GLY -2.600 -0.787 -3.367 0.435 0.000 0.000 2.145 0.000 0.000\n", " E 51 THR 7.583 -1.229 -2.633 0.172 0.000 0.000 1.232 0.037 0.000\n", " E 52 GLY 0.178 0.809 -2.585 0.425 0.000 0.000 2.969 0.000 0.000\n", " E 53 SER -3.224 0.460 -2.928 0.168 -1.012 -0.299 4.531 0.298 0.000\n", " E 54 PHE 2.350 -2.057 -4.940 0.813 0.000 0.000 2.070 3.101 0.000\n", " E 55 GLY -1.168 -0.190 -2.719 0.251 0.000 0.000 2.278 0.000 0.000\n", " E 56 ARG 0.113 -1.410 -6.148 0.773 0.000 -0.411 4.376 3.603 0.000\n", " E 127 GLU 5.674 0.265 -6.455 1.188 0.000 0.000 5.532 5.527 0.000\n", " E 129 PHE -2.187 -2.254 -9.665 1.325 0.000 0.000 6.085 1.411 0.000\n", " E 130 SER -0.490 0.509 -4.664 0.405 0.000 0.000 4.769 0.469 0.000\n", " E 133 ARG 1.166 -0.886 -5.718 0.435 0.000 -0.982 5.379 4.010 0.000\n", " E 134 ARG 3.354 1.267 -4.227 1.445 0.000 0.000 4.049 2.042 0.000\n", " E 165 ARG 0.630 -1.073 -8.797 2.914 -1.167 -0.506 6.483 2.654 0.000\n", " E 166 ASP 3.562 3.175 -4.858 3.206 -0.654 0.000 5.482 2.057 0.000\n", " E 168 LYS -0.694 2.273 -10.086 2.547 0.000 -1.344 11.157 2.410 0.000\n", " E 169 PRO -3.279 -2.341 -7.808 1.650 0.000 0.000 3.817 0.765 0.000\n", " E 170 GLU -0.540 1.225 -6.618 0.772 0.000 -0.226 7.296 4.054 0.000\n", " E 171 ASN -3.534 -0.548 -6.847 0.680 -0.654 0.000 6.273 1.839 0.000\n", " E 184 ASP 2.870 0.655 -4.090 0.497 -0.882 0.000 5.131 2.941 0.000\n", " E 187 PHE -0.138 -3.956 -7.393 0.944 -0.667 0.000 3.161 4.153 0.000\n", " E 199 CYS 6.887 -3.734 -6.109 0.820 0.000 0.000 1.555 1.717 0.000\n", " E 200 GLY -1.379 -0.992 -2.480 0.181 0.000 0.000 1.308 0.000 0.000\n", " E 201 THR -0.477 1.709 -6.176 2.025 0.000 -0.856 6.715 0.233 0.000\n", " E 202 PRO -3.121 -1.733 -6.090 2.213 0.000 0.000 2.143 0.972 0.000\n", " E 203 GLU -1.709 -1.867 -5.405 0.573 0.000 0.000 2.965 3.113 0.000\n", " E 204 TYR -3.322 -4.715 -9.141 1.386 0.000 -0.746 3.786 2.709 0.000\n", " E 205 LEU -2.956 -4.722 -7.322 1.400 0.000 0.000 1.200 0.956 0.000\n", " E 235 TYR 0.122 -1.408 -6.782 2.630 0.000 0.000 2.743 1.616 0.000\n", " E 236 PRO 7.327 -0.974 -6.149 2.112 0.000 0.000 3.064 3.290 0.000\n", " E 239 PHE -0.307 -2.076 -4.537 0.748 0.000 0.000 1.713 1.082 0.000\n", " E 243 PRO -1.686 -0.869 -5.261 1.702 0.000 0.000 2.690 0.096 0.000\n", " E 327 PHE -2.893 -4.383 -8.065 0.694 0.000 0.000 2.989 1.670 0.000\n", " E 328 ASP -1.274 -0.065 -3.252 0.186 -1.244 0.000 4.244 2.773 0.000\n", " E 329 ASP -0.818 -0.140 -2.374 0.113 -0.738 0.000 2.859 2.979 0.000\n", " E 330 TYR -1.763 -2.681 -6.591 0.659 0.000 0.000 3.251 1.362 0.000\n", " X 1 TPA -1.690 3.484 -7.017 0.166 -0.759 -1.336 12.431 0.000 0.000\n", "============End report for interfE==================\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} ============Begin report for rmsd_chX==================\n", "INFO:rosetta:protocols.rosetta_scripts.ParsedProtocol.REPORT: {0} ============End report for rmsd_chX==================\n" ] } ], "source": [ "if not os.getenv(\"DEBUG\"):\n", " working_dir = os.getcwd()\n", " output_dir = \"outputs\"\n", " if not os.path.exists(output_dir):\n", " os.mkdir(output_dir)\n", " os.chdir(output_dir)\n", "\n", " jd = pyrosetta.toolbox.py_jobdistributor.PyJobDistributor(pdb_name=\"test_lig_XMLObjects\",\n", " nstruct=5,\n", " scorefxn=scorefxn)\n", " jd.native_pose = pose\n", " df = pd.DataFrame()\n", " while not jd.job_complete:\n", " test_pose = pose.clone()\n", " xml.apply(test_pose)\n", " test_df = pd.DataFrame.from_records(dict(test_pose.scores), index=[jd.current_name])\n", " df = df.append(test_df)\n", " jd.output_decoy(test_pose)\n", " os.chdir(working_dir)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Now that we have sampled some global ligand docking trajectories, let's plot the ligand binding energy landscape:" ] }, { "cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "" ] }, "execution_count": 5, "metadata": {}, "output_type": "execute_result" }, { "data": { "image/png": "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\n", "text/plain": [ "

" ] }, "metadata": { "needs_background": "light" }, "output_type": "display_data" } ], "source": [ "#Skip for tests (as DF is not present)\n", "if not os.getenv(\"DEBUG\"):\n", " matplotlib.rcParams['figure.figsize'] = [12.0, 8.0]\n", " seaborn.scatterplot(x=\"rmsd_chX\", y=\"interfE\", data=df)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "We can check which `.pdb` file has the lowest `interfE` score:" ] }, { "cell_type": "code", "execution_count": 6, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
\n", "\n", "\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
dslf_fa13fa_atrfa_dunfa_elecfa_intra_repfa_intra_sol_xover4fa_repfa_solhbond_bb_schbond_lr_bb...interfElk_ball_wtdomegap_aa_pppro_closerama_preprorefrmsd_chXtotal_scoreyhh_planarity
test_lig_XMLObjects_1.pdb0.0-2141.7902472839.589602-505.3031611549.88806890.3946841355.5383971338.970707-52.121705-49.476625...-28.276440-50.97489516.443889-84.49347591.445419117.82268081.746340.6314871456.9713391.100056
test_lig_XMLObjects_4.pdb0.0-2117.5112393002.017883-484.3953731575.12687191.6686371434.2391511329.615403-48.468502-47.234071...-15.162686-49.593810-1.135463-85.51854768.279343118.63633881.7463411.4350351628.1461630.366937
test_lig_XMLObjects_0.pdb0.0-2101.6347822881.724947-484.0219721552.93793990.9575711395.9670001307.276630-48.113076-47.985689...-11.798166-48.713822-0.016234-86.66521673.794018111.03581881.7463418.7233891519.8469380.360842
test_lig_XMLObjects_2.pdb0.0-2108.1991962995.956828-483.6972061572.75451491.5833221441.9948181317.274987-47.207246-47.496493...-9.164489-48.3985683.595816-82.20558373.140703122.27093381.7463413.2370481642.3566140.294935
test_lig_XMLObjects_3.pdb0.0-2114.3632492941.806947-471.4618451563.09211090.7728941426.5949931318.093586-47.347564-48.064493...2.542285-49.7043184.201275-83.26199968.786798117.52252281.746349.7905561591.6724710.122519
\n", "

5 rows × 22 columns

\n", "
" ], "text/plain": [ " dslf_fa13 fa_atr fa_dun fa_elec \\\n", "test_lig_XMLObjects_1.pdb 0.0 -2141.790247 2839.589602 -505.303161 \n", "test_lig_XMLObjects_4.pdb 0.0 -2117.511239 3002.017883 -484.395373 \n", "test_lig_XMLObjects_0.pdb 0.0 -2101.634782 2881.724947 -484.021972 \n", "test_lig_XMLObjects_2.pdb 0.0 -2108.199196 2995.956828 -483.697206 \n", "test_lig_XMLObjects_3.pdb 0.0 -2114.363249 2941.806947 -471.461845 \n", "\n", " fa_intra_rep fa_intra_sol_xover4 fa_rep \\\n", "test_lig_XMLObjects_1.pdb 1549.888068 90.394684 1355.538397 \n", "test_lig_XMLObjects_4.pdb 1575.126871 91.668637 1434.239151 \n", "test_lig_XMLObjects_0.pdb 1552.937939 90.957571 1395.967000 \n", "test_lig_XMLObjects_2.pdb 1572.754514 91.583322 1441.994818 \n", "test_lig_XMLObjects_3.pdb 1563.092110 90.772894 1426.594993 \n", "\n", " fa_sol hbond_bb_sc hbond_lr_bb ... \\\n", "test_lig_XMLObjects_1.pdb 1338.970707 -52.121705 -49.476625 ... \n", "test_lig_XMLObjects_4.pdb 1329.615403 -48.468502 -47.234071 ... \n", "test_lig_XMLObjects_0.pdb 1307.276630 -48.113076 -47.985689 ... \n", "test_lig_XMLObjects_2.pdb 1317.274987 -47.207246 -47.496493 ... \n", "test_lig_XMLObjects_3.pdb 1318.093586 -47.347564 -48.064493 ... \n", "\n", " interfE lk_ball_wtd omega p_aa_pp \\\n", "test_lig_XMLObjects_1.pdb -28.276440 -50.974895 16.443889 -84.493475 \n", "test_lig_XMLObjects_4.pdb -15.162686 -49.593810 -1.135463 -85.518547 \n", "test_lig_XMLObjects_0.pdb -11.798166 -48.713822 -0.016234 -86.665216 \n", "test_lig_XMLObjects_2.pdb -9.164489 -48.398568 3.595816 -82.205583 \n", "test_lig_XMLObjects_3.pdb 2.542285 -49.704318 4.201275 -83.261999 \n", "\n", " pro_close rama_prepro ref rmsd_chX \\\n", "test_lig_XMLObjects_1.pdb 91.445419 117.822680 81.74634 0.631487 \n", "test_lig_XMLObjects_4.pdb 68.279343 118.636338 81.74634 11.435035 \n", "test_lig_XMLObjects_0.pdb 73.794018 111.035818 81.74634 18.723389 \n", "test_lig_XMLObjects_2.pdb 73.140703 122.270933 81.74634 13.237048 \n", "test_lig_XMLObjects_3.pdb 68.786798 117.522522 81.74634 9.790556 \n", "\n", " total_score yhh_planarity \n", "test_lig_XMLObjects_1.pdb 1456.971339 1.100056 \n", "test_lig_XMLObjects_4.pdb 1628.146163 0.366937 \n", "test_lig_XMLObjects_0.pdb 1519.846938 0.360842 \n", "test_lig_XMLObjects_2.pdb 1642.356614 0.294935 \n", "test_lig_XMLObjects_3.pdb 1591.672471 0.122519 \n", "\n", "[5 rows x 22 columns]" ] }, "execution_count": 6, "metadata": {}, "output_type": "execute_result" } ], "source": [ "#Skip for tests\n", "if not os.getenv(\"DEBUG\"):\n", " df.sort_values(by=\"interfE\")" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Let's take a look at the pose with the lowest `interfE` value that was generated:" ] }, { "cell_type": "code", "execution_count": 8, "metadata": {}, "outputs": [ { "data": { "application/3dmoljs_load.v0": "
\n

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

\n
\n", "text/html": [ "
\n", "

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

\n", "
\n", "" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "#Skip for tests\n", "if not os.getenv(\"DEBUG\"):\n", " lowest_energy_pdb_filename = os.path.join(\"expected_outputs\", df.sort_values(by=\"interfE\").head(1).index[0])\n", " test_pose = pyrosetta.io.pose_from_file(filename=lowest_energy_pdb_filename)\n", "\n", " chE = pyrosetta.rosetta.core.select.residue_selector.ChainSelector(\"E\")\n", "\n", " view = viewer.init(test_pose)\n", " view.add(viewer.setStyle())\n", " view.add(viewer.setStyle(command=({\"hetflag\": True}, {\"stick\": {\"colorscheme\": \"brownCarbon\", \"radius\": 0.2}})))\n", " view.add(viewer.setSurface(residue_selector=chE, opacity=0.7, color='white'))\n", " view.add(viewer.setHydrogenBonds())\n", " view()" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "*Exercise:*\n", "\n", "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\n", "\n", "*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." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "***\n", "*Restart Jupyter Notebook kernel to properly re-initialize PyRosetta*\n", "***" ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [ { "data": { "text/html": [ "" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "import glob\n", "import logging\n", "logging.basicConfig(level=logging.INFO)\n", "import matplotlib\n", "%matplotlib inline\n", "import os\n", "import pandas as pd\n", "import pyrosetta\n", "import pyrosetta.distributed.viewer as viewer\n", "import seaborn\n", "seaborn.set()\n", "import sys\n", "\n", "!pip install pyrosettacolabsetup\n", "import pyrosettacolabsetup; pyrosettacolabsetup.install_pyrosetta()\n", "import pyrosetta; pyrosetta.init()\n" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "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}\n", "INFO:pyrosetta.rosetta:Found rosetta database at: /mnt/home/klimaj/git/Rosetta/main/source/src/python/PyRosetta/src/pyrosetta/database; using it....\n", "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\n", "(C) Copyright Rosetta Commons Member Institutions. Created in JHU by Sergey Lyskov and PyRosetta Team.\n" ] }, { "data": { "image/png": "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\n", "text/plain": [ "
" ] }, "metadata": { "needs_background": "light" }, "output_type": "display_data" } ], "source": [ "if not os.getenv(\"DEBUG\"):\n", " pdb_filenames = glob.glob(\"expected_outputs/test_lig_XMLObjects*.pdb\")\n", " ligand_params = \"inputs/TPA.am1-bcc.fa.params\"\n", " native_pdb_filename = \"expected_outputs/test_lig_XMLObjects_1.pdb\"\n", "\n", " flags = f\"\"\"\n", " -extra_res_fa {ligand_params} \n", " -in:file:native {native_pdb_filename}\n", " -ignore_unrecognized_res 1 \n", " -mute all\n", " \"\"\"\n", " pyrosetta.distributed.init(flags)\n", " scorefxn = pyrosetta.create_score_function(\"ref2015\")\n", "\n", " xml = pyrosetta.rosetta.protocols.rosetta_scripts.XmlObjects.create_from_string(\"\"\"\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \"\"\").get_mover(\"ParsedProtocol\")\n", "\n", " df = pd.DataFrame()\n", " for pdb_filename in pdb_filenames:\n", " test_pose = pyrosetta.io.pose_from_file(filename=pdb_filename)\n", " xml.apply(test_pose)\n", " test_df = pd.DataFrame.from_records(dict(test_pose.scores), index=[pdb_filename.split(\"/\")[-1]])\n", " df = df.append(test_df)\n", "\n", " matplotlib.rcParams['figure.figsize'] = [12.0, 8.0]\n", " seaborn.scatterplot(x=\"rmsd_chX\", y=\"interfE\", data=df)" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [] }, { "cell_type": "markdown", "metadata": {}, "source": [ "\n", "< [Ligand Refinement in PyRosetta (a.k.a. High-Resolution Local Docking) Using the `ligand.wts` Scorefunction](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/08.00-Ligand-Docking-PyRosetta.ipynb) | [Contents](toc.ipynb) | [Index](index.ipynb) | [`GALigandDock` Protocol with `pyrosetta.distributed` Using the `beta_cart.wts` Scorefunction](http://nbviewer.jupyter.org/github/RosettaCommons/PyRosetta.notebooks/blob/master/notebooks/08.02-Ligand-Docking-pyrosetta.distributed.ipynb) >

\"Open" ] } ], "metadata": { "kernelspec": { "display_name": "Python 3", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.6.1" }, "toc": { "base_numbering": 1, "nav_menu": {}, "number_sections": true, "sideBar": true, "skip_h1_title": false, "title_cell": "Table of Contents", "title_sidebar": "Contents", "toc_cell": false, "toc_position": {}, "toc_section_display": true, "toc_window_display": false } }, "nbformat": 4, "nbformat_minor": 2 }