ligand.wts
Scorefunction¶Warning: This notebook uses pyrosetta.distributed.viewer
code, which runs in jupyter notebook
and might not run if you're using jupyterlab
.
!pip install pyrosettacolabsetup
import pyrosettacolabsetup; pyrosettacolabsetup.install_pyrosetta()
import pyrosetta; pyrosetta.init()
import logging
logging.basicConfig(level=logging.INFO)
import os
import pyrosetta
import pyrosetta.distributed
import pyrosetta.distributed.viewer as viewer
Initialize PyRosetta and setup the input pose:
params_file = "inputs/TPA.gasteiger.fa.params"
flags = f"""
-extra_res_fa {params_file} # Provide a custom TPA .params file
-ignore_unrecognized_res 1
-mute all
"""
pyrosetta.distributed.init(flags)
pose = pyrosetta.io.pose_from_file("inputs/test_lig.pdb")
INFO:pyrosetta.distributed:maybe_init performing pyrosetta initialization: {'extra_options': '-extra_res_fa inputs/TPA.gasteiger.fa.params -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.
Before we perform ligand refinement, let's take a look at the input .pdb
file using the pyrosetta.distributed.viewer
macromolecular visualizer:
chE = pyrosetta.rosetta.core.select.residue_selector.ChainSelector("E")
view = viewer.init(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
Restart Jupyter Notebook kernel to properly re-initialize PyRosetta
!pip install pyrosettacolabsetup
import pyrosettacolabsetup; pyrosettacolabsetup.install_pyrosetta()
import pyrosetta; pyrosetta.init()
import logging
logging.basicConfig(level=logging.INFO)
import os
import pyrosetta
import pyrosetta.distributed
import pyrosetta.distributed.viewer as viewer
The following ligand refinement example was adapted from ~Rosetta/main/source/src/python/PyRosetta/src/demo/D120_Ligand_interface.py
:
def sample_ligand_interface(pdb_filename,
partners,
ligand_params=[""],
jobs=1,
job_output="ligand_output"):
"""
Performs ligand-protein docking using Rosetta fullatom docking
(DockingHighRes) on the ligand-protein complex in <pdb_filename>
using the relative chain <partners>. If the ligand parameters
(a .params file) are not defaultly loaded into PyRosetta,
<ligand_params> must supply the list of files including the ligand
parameters. <jobs> trajectories are performed with output
structures named <job_output>_(job#).pdb.
Note: Global docking, a problem solved by the Rosetta DockingProtocol,
requires interface detection and refinement as with other protocols,
these tasks are split into centroid (interface detection) and
high-resolution (interface refinement) methods without a centroid
representation, low-resolution ligand-protein prediction is not
possible and as such, only the high-resolution ligand-protein
interface refinement is available. If you add a perturbation or
randomization step, the high-resolution stages may fail. A perturbation
step CAN make this a global docking algorithm however the rigid-body
sampling preceding refinement requires extensive sampling to produce
accurate results and this algorithm spends most of its effort in
refinement (which may be useless for the predicted interface).
This script performs ligand-protein interface structure prediction but does NOT
perform global ligand-protein docking. Since there is no generic interface
detection, the input PDB file must have the ligand placed near the interface
that will be refined. If the DockMCMProtocol is applied to a pose
without placement near the interface, then the refinement may:
-waste steps sampling the wrong interface
-fail by predicting an incorrect interface very far from the true interface
-fail by separating the ligand from the protein (usually due to a clash)
DockMCMProtocol does not require an independent randomization or perturbation
step to "seed" its prediction.
Additional refinement steps may increase the accuracy of the predicted
conformation (see refinement.py). Drastic moves (large conformational changes)
should be avoided; if they precede the protocol, the problems above may occur,
if they succeed the protocol, the protocol results may be lost.
"""
# Declare working directory and output directory
working_dir = os.getcwd()
output_dir = "outputs"
if not os.path.exists(output_dir):
os.mkdir(output_dir)
# Initialize PyRosetta
pyrosetta.init()
# Create an empty pose from the desired PDB file
pose = pyrosetta.rosetta.core.pose.Pose()
# If the params list has contents, load .params files
# Note: this method of adding ligands to the ResidueTypeSet is unnecessary
# if you call pyrosetta.init("-extra_res_fa {}".format(ligand_params))
if len(ligand_params) != 0 and ligand_params[0] != "":
ligand_params = pyrosetta.Vector1(ligand_params)
res_set = pose.conformation().modifiable_residue_type_set_for_conf()
res_set.read_files_for_base_residue_types(ligand_params)
pose.conformation().reset_residue_type_set_for_conf(res_set)
# Load pdb_filename into pose
pyrosetta.io.pose_from_file(pose, pdb_filename)
# Setup the docking FoldTree
# the method setup_foldtree takes an input pose and sets its
# FoldTree to have jump 1 represent the relation between the two docking
# partners, the jump points are the residues closest to the centers of
# geometry for each partner with a cutpoint at the end of the chain,
# the second argument is a string specifying the relative chain orientation
# such as "A_B" of "LH_A", ONLY TWO BODY DOCKING is supported and the
# partners MUST have different chain IDs and be in the same pose (the
# same PDB), additional chains can be grouped with one of the partners,
# the "_" character specifies which bodies are separated
# the third argument...is currently unsupported but must be set (it is
# supposed to specify which jumps are movable, to support multibody
# docking...but Rosetta doesn't currently)
# the FoldTrees setup by this method are for TWO BODY docking ONLY!
dock_jump = 1 # jump number 1 is the inter-body jump
pyrosetta.rosetta.protocols.docking.setup_foldtree(pose,
partners,
pyrosetta.Vector1([dock_jump]))
# Create ScoreFunctions for centroid and fullatom docking
scorefxn = pyrosetta.create_score_function("ligand.wts")
# Setup the high resolution (fullatom) docking protocol using DockMCMProtocol.
docking = pyrosetta.rosetta.protocols.docking.DockMCMProtocol()
# Many of its options and settings can be set using the setter methods.
docking.set_scorefxn(scorefxn)
# Change directory temporarily for output
os.chdir(output_dir)
# Setup the PyJobDistributor
jd = pyrosetta.toolbox.py_jobdistributor.PyJobDistributor(job_output,
jobs, scorefxn,
compress=False)
# Set the native pose so that the output scorefile contains the pose rmsd metric
jd.native_pose = pose
# Optional: setup a PyMOLObserver
# pyrosetta.rosetta.protocols.moves.AddPyMOLObserver(test_pose, True)
# Perform protein-ligand docking
# counter = 0 # for pretty output to PyMOLObserver
while not jd.job_complete:
test_pose = pose.clone() # Reset test pose to original structure
# counter += 1 # Change the pose name, for pretty output to PyMOLObserver
# test_pose.pdb_info().name(job_output + '_' + str(counter))
# Perform docking and output to PyMOL:
docking.apply(test_pose)
# Write the decoy structure to disk:
jd.output_decoy(test_pose)
os.chdir(working_dir)
Let's test out the sample_ligand_interface
function (takes ~2 minutes with jobs=1
, which means nstruct is set to 1 in the PyJobDistributor
):
if not os.getenv("DEBUG"):
sample_ligand_interface("inputs/test_lig.pdb", "E_X",
ligand_params=["inputs/TPA.gasteiger.fa.params"],
jobs=1,
job_output="test_lig")
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 -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=1279767154 seed_offset=0 real_seed=1279767154 thread_index=0 INFO:rosetta:basic.random.init_random_generator: {0} RandomGenerator:init: Normal mode, seed=1279767154 RG_type=mt19937 INFO:rosetta:core.conformation.Conformation: {0} [ WARNING ] Attempted to determine the residue type set of an empty pose. INFO:rosetta:core.import_pose.import_pose: {0} File 'inputs/test_lig.pdb' automatically determined to be of type PDB
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.scoring.ScoreFunctionFactory: {0} SCOREFUNCTION: ref2015 INFO:rosetta:core.scoring.ScoreFunctionFactory: {0} SCOREFUNCTION: ref2015 INFO:rosetta:core.scoring.ScoreFunctionFactory: {0} SCOREFUNCTION: ref2015 INFO:rosetta:protocols.docking.DockMCMProtocol: {0} in DockMCMProtocol.apply
Working on decoy: test_lig_0.pdb
INFO:rosetta:protocols.docking.DockMCMProtocol: {0} Using the DockingTaskFactory. INFO:rosetta:protocols.docking.DockMCMCycle: {0} Setting up defaults for DockMCMCycle: INFO:rosetta:protocols.docking.DockMCMCycle: {0} //////////////////////////////////////////////////////////////////////////////// INFO:rosetta:protocols.docking.DockMCMCycle: {0} /// Dockable Jumps: 1 /// INFO:rosetta:protocols.docking.DockMCMCycle: {0} /// Translation: 0.1 /// INFO:rosetta:protocols.docking.DockMCMCycle: {0} /// Rotation: 5 /// INFO:rosetta:protocols.docking.DockMCMCycle: {0} /// Scorefunction: /// INFO:rosetta:protocols.docking.DockMCMCycle: {0} ScoreFunction::show(): weights: (fa_atr 0.8) (fa_rep 0.4) (fa_sol 0.6) (fa_elec 0.25) (pro_close 1) (fa_pair 0.8) (hbond_sr_bb 2) (hbond_lr_bb 2) (hbond_bb_sc 2) (hbond_sc 2) (dslf_ss_dst 0.5) (dslf_cs_ang 2) (dslf_ss_dih 5) (dslf_ca_dih 5) (atom_pair_constraint 1) (coordinate_constraint 1) (angle_constraint 1) (dihedral_constraint 1) (omega 0.5) (fa_dun 0.4) (p_aa_pp 0.5) (ref 1) (chainbreak 1) energy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: mhc_epitope_setup_files: INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: netcharge_setup_files: INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: aspartimide_penalty_value: 25 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT analytic_etable_evaluation: 1 EnergyMethodOptions::show: method_weights: ref 0.05 0.09 -0.65 -0.27 1.88 -0.55 1.17 -0.73 -0.42 -0.66 -0.29 -0.76 -0.33 -0.29 -0.77 0 -0.57 -0.57 2.88 0.81 EnergyMethodOptions::show: method_weights: free_res EnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: covalent_labeling_input: INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: covalent_labeling_fa_input: INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: exclude_monomer_fa_elec: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: elec_max_dis: 5.5 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: elec_min_dis: 1.6 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: elec_die: 10 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: elec_no_dis_dep_die: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: elec_sigmoidal_die: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: elec_sigmoidal_D: 80 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: elec_sigmoidal_D0: 6 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: elec_sigmoidal_S: 0.4 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: smooth_fa_elec: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: grpelec_fade_type: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: grpelec_fade_param1: 1 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: grpelec_fade_param2: 1 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: grpelec_fade_hbond: 0 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: grp_cpfxn: 1 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: grpelec_context_dependent: 0 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: use_polarization: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: use_gen_kirkwood: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: protein_dielectric: 1 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: water_dielectric: 78.3 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: exclude_DNA_DNA: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: exclude_intra_res_protein: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: count_pair_hybrid: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: count_pair_full: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: put_intra_into_total: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: eval_intrares_elec_ST_only: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: envsmooth_zero_negatives: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: pb_bound_tag: bound INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: pb_unbound_tag: unbound INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: ordered_wat_penalty: 1.221 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_ref_seq_length_: 9 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_term_length_: 3 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_scorecut_: 0 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_aa_matrix_: INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_list_defined_: 0 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_list_: INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_defined_: 0 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_: INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_rank_list_: INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_rank_defined_: 0 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_rank_: INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: hbnet_bonus_ramping_function_: "quadratic" INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: hbnet_max_network_size_: 0 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: bond_angle_central_atoms_to_score: INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: bond_angle_residue_type_param_set: none INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: exclude_DNA_DNA: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: exclude_intra_res_protein_: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: exclude_intra_res_RNA_: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: put_intra_into_total_: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: exclude_self_hbonds: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: use_hb_env_dep: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: use_hb_env_dep_DNA: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: smooth_hb_env_dep: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: bb_donor_acceptor_check: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: decompose_bb_hb_into_pair_energies: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: params_database_tag_: ref2015_params INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: use_sp2_chi_penalty_: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: sp2_BAH180_rise_: 0.75 INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: sp2_outer_width_: 0.357 INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: fade_energy_: 1 INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: exclude_ether_oxygens_: 0 INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: Mbhbond: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} HbondOptions::show: mphbond: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: hbond_energy_shift: 0 INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: water_hybrid_sf: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0 INFO:rosetta:protocols.docking.DockMCMCycle: {0} RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011 INFO:rosetta:protocols.docking.DockMCMCycle: {0} RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson INFO:rosetta:protocols.docking.DockMCMCycle: {0} RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat INFO:rosetta:protocols.docking.DockMCMCycle: {0} FreeDOF_Options::show: free_suite_bonus: -1 INFO:rosetta:protocols.docking.DockMCMCycle: {0} FreeDOF_Options::show: free_2HOprime_bonus: -0.5 INFO:rosetta:protocols.docking.DockMCMCycle: {0} FreeDOF_Options::show: free_sugar_bonus: -1 INFO:rosetta:protocols.docking.DockMCMCycle: {0} FreeDOF_Options::show: pack_phosphate_penalty: 0.25 INFO:rosetta:protocols.docking.DockMCMCycle: {0} FreeDOF_Options::show: free_side_chain_bonus: -0.5 INFO:rosetta:protocols.docking.DockMCMCycle: {0} INFO:rosetta:protocols.docking.DockMCMCycle: {0} INFO:rosetta:protocols.docking.DockMCMCycle: {0} /// Packing scorefunction: /// INFO:rosetta:protocols.docking.DockMCMCycle: {0} ScoreFunction::show(): weights: (fa_atr 1) (fa_rep 0.55) (fa_sol 1) (fa_intra_rep 0.005) (fa_intra_sol_xover4 1) (lk_ball_wtd 1) (fa_elec 1) (pro_close 1.25) (hbond_sr_bb 1) (hbond_lr_bb 1) (hbond_bb_sc 1) (hbond_sc 1) (dslf_fa13 1.25) (omega 0.4) (fa_dun 0.7) (p_aa_pp 0.6) (yhh_planarity 0.625) (ref 1) (rama_prepro 0.45) energy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: mhc_epitope_setup_files: INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: netcharge_setup_files: INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: aspartimide_penalty_value: 25 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT analytic_etable_evaluation: 1 EnergyMethodOptions::show: method_weights: ref 1.32468 3.25479 -2.14574 -2.72453 1.21829 0.79816 -0.30065 2.30374 -0.71458 1.66147 1.65735 -1.34026 -1.64321 -1.45095 -0.09474 -0.28969 1.15175 2.64269 2.26099 0.58223 EnergyMethodOptions::show: method_weights: free_res EnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: covalent_labeling_input: INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: covalent_labeling_fa_input: INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: exclude_monomer_fa_elec: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: elec_max_dis: 5.5 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: elec_min_dis: 1.6 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: elec_die: 10 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: elec_no_dis_dep_die: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: elec_sigmoidal_die: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: elec_sigmoidal_D: 80 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: elec_sigmoidal_D0: 6 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: elec_sigmoidal_S: 0.4 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: smooth_fa_elec: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: grpelec_fade_type: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: grpelec_fade_param1: 1 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: grpelec_fade_param2: 1 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: grpelec_fade_hbond: 0 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: grp_cpfxn: 1 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: grpelec_context_dependent: 0 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: use_polarization: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: use_gen_kirkwood: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: protein_dielectric: 1 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: water_dielectric: 78.3 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: exclude_DNA_DNA: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: exclude_intra_res_protein: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: count_pair_hybrid: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: count_pair_full: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: put_intra_into_total: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: eval_intrares_elec_ST_only: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: envsmooth_zero_negatives: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: pb_bound_tag: bound INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: pb_unbound_tag: unbound INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: ordered_wat_penalty: 1.221 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_ref_seq_length_: 9 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_term_length_: 3 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_scorecut_: 0 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_aa_matrix_: INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_list_defined_: 0 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_list_: INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_defined_: 0 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_: INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_rank_list_: INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_rank_defined_: 0 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_rank_: INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: hbnet_bonus_ramping_function_: "quadratic" INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: hbnet_max_network_size_: 0 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: bond_angle_central_atoms_to_score: INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: bond_angle_residue_type_param_set: none INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: exclude_DNA_DNA: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: exclude_intra_res_protein_: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: exclude_intra_res_RNA_: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: put_intra_into_total_: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: exclude_self_hbonds: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: use_hb_env_dep: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: use_hb_env_dep_DNA: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: smooth_hb_env_dep: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: bb_donor_acceptor_check: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: decompose_bb_hb_into_pair_energies: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: params_database_tag_: ref2015_params INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: use_sp2_chi_penalty_: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: sp2_BAH180_rise_: 0.75 INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: sp2_outer_width_: 0.357 INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: fade_energy_: 1 INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: exclude_ether_oxygens_: 0 INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: Mbhbond: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} HbondOptions::show: mphbond: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: hbond_energy_shift: 0 INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: water_hybrid_sf: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0 INFO:rosetta:protocols.docking.DockMCMCycle: {0} RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011 INFO:rosetta:protocols.docking.DockMCMCycle: {0} RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson INFO:rosetta:protocols.docking.DockMCMCycle: {0} RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat INFO:rosetta:protocols.docking.DockMCMCycle: {0} FreeDOF_Options::show: free_suite_bonus: -1 INFO:rosetta:protocols.docking.DockMCMCycle: {0} FreeDOF_Options::show: free_2HOprime_bonus: -0.5 INFO:rosetta:protocols.docking.DockMCMCycle: {0} FreeDOF_Options::show: free_sugar_bonus: -1 INFO:rosetta:protocols.docking.DockMCMCycle: {0} FreeDOF_Options::show: pack_phosphate_penalty: 0.25 INFO:rosetta:protocols.docking.DockMCMCycle: {0} FreeDOF_Options::show: free_side_chain_bonus: -0.5 INFO:rosetta:protocols.docking.DockMCMCycle: {0} INFO:rosetta:protocols.docking.DockMCMCycle: {0} INFO:rosetta:protocols.docking.DockMCMCycle: {0} //////////////////////////////////////////////////////////////////////////////// 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 964 rotamers at 39 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.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.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.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.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 985 rotamers at 39 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.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.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 985 rotamers at 39 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.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.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 985 rotamers at 39 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.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.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 985 rotamers at 39 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.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.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 985 rotamers at 39 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.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
CPU times: user 2min 10s, sys: 457 ms, total: 2min 10s Wall time: 2min 12s
Interpreting Results:
The PyJobDistributor
will output the lowest scoring pose for each trajectory
(as a .pdb
file), recording the score in outputs/<job_output>.fasc
. Generally,
the decoy generated with the lowest score contains the best prediction
for the protein-ligand conformation. PDB files produced from docking will contain
both docking partners in their predicted conformation. When inspecting these
PDB files (or the PyMOLObserver
output) be aware that PyMOL can introduce or
predict bonds that do not exist, particularly for close atoms. This rarely
occurs when using the PyMOLMover.keep_history feature (since PyRosetta will
sample some conformation space that has clashes).
The PyMOLObserver
will output a series of structures directly produced by the
DockingProtocol. Unfortunately, this may include intermediate structures that
do not yield any insight into the protocol performance. A LARGE number of
structures are output to PyMOL and your machine may have difficulty
loading all of these structures. If this occurs, try changing the
PyMOLObserver
keep_history to False or running the protocol without the
PyMOLObserver
.
Interface structure prediction is useful for considering what physical properties are important in the binding event and what conformational changes occur. Once experienced using PyRosetta, you can easily write scripts to investigate the Rosetta score terms and structural characteristics. There is no general interpretation of ligand-binding results. Although Rosetta score does not translate directly to physical meaning (it is not physical energy), splitting the docked partners and comparing the scores (after packing or refinement) can indicate the strength of the bonding interaction.
Restart Jupyter Notebook kernel to properly re-initialize PyRosetta
!pip install pyrosettacolabsetup
import pyrosettacolabsetup; pyrosettacolabsetup.install_pyrosetta()
import pyrosetta; pyrosetta.init()
import logging
logging.basicConfig(level=logging.INFO)
import os, sys
import pyrosetta
import pyrosetta.distributed
import pyrosetta.distributed.viewer as viewer
params_file = "inputs/TPA.gasteiger.fa.params"
flags = f"""
-extra_res_fa {params_file}
-ignore_unrecognized_res 1
-mute all
"""
pyrosetta.distributed.init(flags)
pose = pyrosetta.io.pose_from_file("expected_outputs/test_lig_0.pdb")
INFO:pyrosetta.distributed:maybe_init performing pyrosetta initialization: {'extra_options': '-extra_res_fa inputs/TPA.gasteiger.fa.params -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.
After ligand refinement has completed, let's take a look at the output .pdb
file using the py3Dmol
module:
chE = pyrosetta.rosetta.core.select.residue_selector.ChainSelector("E")
view = viewer.init(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
Coding challenge:
Below, write an alternate version of the function sample_ligand_interface
called ligand_refinement_from_command_line.py
with the following modifications:
pyrosetta.init()
method rather than by modification of the ResidueTypeSet
database.talaris2014
Run it from the command line (Note: the optparse
module has already been added for you).
Note: Notice that the first line of the following cell uses the ipython magic command %%file
which writes the remainder of the cell contents to the file outputs/ligand_refinement_from_command_line.py
:
%%file outputs/ligand_refinement_from_command_line.py
import optparse
import os
import pyrosetta
def sample_ligand_interface(pdb_filename,
partners,
ligand_params=[""],
jobs=1,
job_output="ligand_output"):
"""
Performs ligand-protein docking using Rosetta fullatom docking
(DockingHighRes) on the ligand-protein complex in <pdb_filename>
using the relative chain <partners>. If the ligand parameters
(a .params file) are not defaultly loaded into PyRosetta,
<ligand_params> must supply the list of files including the ligand
parameters. <jobs> trajectories are performed with output
structures named <job_output>_(job#).pdb.
Note: Global docking, a problem solved by the Rosetta DockingProtocol,
requires interface detection and refinement as with other protocols,
these tasks are split into centroid (interface detection) and
high-resolution (interface refinement) methods without a centroid
representation, low-resolution ligand-protein prediction is not
possible and as such, only the high-resolution ligand-protein
interface refinement is available. If you add a perturbation or
randomization step, the high-resolution stages may fail. A perturbation
step CAN make this a global docking algorithm however the rigid-body
sampling preceding refinement requires extensive sampling to produce
accurate results and this algorithm spends most of its effort in
refinement (which may be useless for the predicted interface).
This script performs ligand-protein interface structure prediction but does NOT
perform global ligand-protein docking. Since there is no generic interface
detection, the input PDB file must have the ligand placed near the interface
that will be refined. If the DockMCMProtocol is applied to a pose
without placement near the interface, then the refinement may:
-waste steps sampling the wrong interface
-fail by predicting an incorrect interface very far from the true interface
-fail by separating the ligand from the protein (usually due to a clash)
DockMCMProtocol does not require an independent randomization or perturbation
step to "seed" its prediction.
Additional refinement steps may increase the accuracy of the predicted
conformation (see refinement.py). Drastic moves (large conformational changes)
should be avoided; if they precede the protocol, the problems above may occur,
if they succeed the protocol, the protocol results may be lost.
"""
# Declare working directory and output directory
working_dir = os.getcwd()
output_dir = "outputs"
if not os.path.exists(output_dir):
os.mkdir(output_dir)
# Initialize PyRosetta
pyrosetta.init()
# Create an empty pose from the desired PDB file
pose = pyrosetta.rosetta.core.pose.Pose()
# If the params list has contents, load .params files
# Note: this method of adding ligands to the ResidueTypeSet is unnecessary
# if you call pyrosetta.init("-extra_res_fa {}".format(ligand_params))
if len(ligand_params) != 0 and ligand_params[0] != "":
ligand_params = pyrosetta.Vector1(ligand_params)
res_set = pose.conformation().modifiable_residue_type_set_for_conf()
res_set.read_files_for_base_residue_types(ligand_params)
pose.conformation().reset_residue_type_set_for_conf(res_set)
# Load pdb_filename into pose
pyrosetta.io.pose_from_file(pose, pdb_filename)
# Setup the docking FoldTree
# the method setup_foldtree takes an input pose and sets its
# FoldTree to have jump 1 represent the relation between the two docking
# partners, the jump points are the residues closest to the centers of
# geometry for each partner with a cutpoint at the end of the chain,
# the second argument is a string specifying the relative chain orientation
# such as "A_B" of "LH_A", ONLY TWO BODY DOCKING is supported and the
# partners MUST have different chain IDs and be in the same pose (the
# same PDB), additional chains can be grouped with one of the partners,
# the "_" character specifies which bodies are separated
# the third argument...is currently unsupported but must be set (it is
# supposed to specify which jumps are movable, to support multibody
# docking...but Rosetta doesn't currently)
# the FoldTrees setup by this method are for TWO BODY docking ONLY!
dock_jump = 1 # jump number 1 is the inter-body jump
pyrosetta.rosetta.protocols.docking.setup_foldtree(pose,
partners,
pyrosetta.Vector1([dock_jump]))
# Create a copy of the pose for testing
test_pose = pose.clone()
# Create ScoreFunctions for centroid and fullatom docking
scorefxn = pyrosetta.create_score_function("ligand")
# Setup the high resolution (fullatom) docking protocol using DockMCMProtocol.
docking = pyrosetta.rosetta.protocols.docking.DockMCMProtocol()
# Many of its options and settings can be set using the setter methods.
docking.set_scorefxn(scorefxn)
# Change directory temporarily for output
os.chdir(output_dir)
# Setup the PyJobDistributor
jd = pyrosetta.toolbox.py_jobdistributor.PyJobDistributor(job_output,
jobs, scorefxn,
compress=False)
# Set the native pose so that the output scorefile contains the pose rmsd metric
jd.native_pose = pose
# Optional: setup a PyMOLObserver
# pyrosetta.rosetta.protocols.moves.AddPyMOLObserver(test_pose, True)
# Perform protein-ligand docking
# counter = 0 # for pretty output to PyMOLObserver
while not jd.job_complete:
test_pose = pose.clone() # Reset test pose to original structure
# counter += 1 # Change the pose name, for pretty output to PyMOLObserver
# test_pose.pdb_info().name(job_output + '_' + str(counter))
docking.apply(test_pose) # Perform docking and output to PyMOL
# Write the decoy structure to disc
jd.output_decoy(test_pose)
os.chdir(working_dir)
if __name__ == "__main__":
# Declare parser object for managing input options
parser = optparse.OptionParser()
parser.add_option("--pdb_filename",
dest="pdb_filename",
help="The PDB file containing the ligand and protein to dock.")
parser.add_option("--partners",
dest="partners",
default = "A_X",
help="The relative chain partners for docking.")
parser.add_option("--ligand_params",
dest="ligand_params",
help="The ligand residue parameter file.")
parser.add_option("--jobs",
dest="jobs",
default="1",
help="The number of jobs (trajectories) to perform.")
parser.add_option("--job_output",
dest="job_output",
default = "ligand_output",
help="The name preceding all output, output PDB files and scorefile.")
(options, args) = parser.parse_args()
# Catch input erros
if not options.pdb_filename:
parser.error("pdb_filename not given!")
if not options.ligand_params:
parser.error("ligand_params not given!")
# Run ligand refinement protocol
sample_ligand_interface(pdb_filename=options.pdb_filename,
partners=options.partners,
ligand_params=options.ligand_params.split(","),
jobs=int(options.jobs),
job_output=options.job_output)
Overwriting outputs/ligand_refinement_from_command_line.py
Run outputs/ligand_refinement_from_command_line.py
from the command line within this Jupyter Notebook!
pdb_filename = "inputs/test_lig.pdb"
params_file = "inputs/TPA.gasteiger.fa.params"
if not os.getenv("DEBUG"):
%run expected_outputs/ligand_refinement_from_command_line.py \
--pdb_filename {pdb_filename} \
--ligand_params {params_file} \
--partners E_X \
--jobs 1 \
--job_output test_lig_command_line
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.
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.scoring.ScoreFunctionFactory: {0} SCOREFUNCTION: ref2015 INFO:rosetta:core.scoring.ScoreFunctionFactory: {0} SCOREFUNCTION: ref2015 INFO:rosetta:core.scoring.ScoreFunctionFactory: {0} SCOREFUNCTION: ref2015 INFO:rosetta:protocols.docking.DockMCMProtocol: {0} in DockMCMProtocol.apply
Working on decoy: test_lig_command_line_0.pdb
INFO:rosetta:protocols.docking.DockMCMProtocol: {0} Using the DockingTaskFactory. INFO:rosetta:protocols.docking.DockMCMCycle: {0} Setting up defaults for DockMCMCycle: INFO:rosetta:protocols.docking.DockMCMCycle: {0} //////////////////////////////////////////////////////////////////////////////// INFO:rosetta:protocols.docking.DockMCMCycle: {0} /// Dockable Jumps: 1 /// INFO:rosetta:protocols.docking.DockMCMCycle: {0} /// Translation: 0.1 /// INFO:rosetta:protocols.docking.DockMCMCycle: {0} /// Rotation: 5 /// INFO:rosetta:protocols.docking.DockMCMCycle: {0} /// Scorefunction: /// INFO:rosetta:protocols.docking.DockMCMCycle: {0} ScoreFunction::show(): weights: (fa_atr 0.8) (fa_rep 0.4) (fa_sol 0.6) (fa_elec 0.25) (pro_close 1) (fa_pair 0.8) (hbond_sr_bb 2) (hbond_lr_bb 2) (hbond_bb_sc 2) (hbond_sc 2) (dslf_ss_dst 0.5) (dslf_cs_ang 2) (dslf_ss_dih 5) (dslf_ca_dih 5) (atom_pair_constraint 1) (coordinate_constraint 1) (angle_constraint 1) (dihedral_constraint 1) (omega 0.5) (fa_dun 0.4) (p_aa_pp 0.5) (ref 1) (chainbreak 1) energy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: mhc_epitope_setup_files: INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: netcharge_setup_files: INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: aspartimide_penalty_value: 25 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT analytic_etable_evaluation: 1 EnergyMethodOptions::show: method_weights: ref 0.05 0.09 -0.65 -0.27 1.88 -0.55 1.17 -0.73 -0.42 -0.66 -0.29 -0.76 -0.33 -0.29 -0.77 0 -0.57 -0.57 2.88 0.81 EnergyMethodOptions::show: method_weights: free_res EnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: covalent_labeling_input: INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: covalent_labeling_fa_input: INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: exclude_monomer_fa_elec: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: elec_max_dis: 5.5 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: elec_min_dis: 1.6 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: elec_die: 10 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: elec_no_dis_dep_die: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: elec_sigmoidal_die: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: elec_sigmoidal_D: 80 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: elec_sigmoidal_D0: 6 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: elec_sigmoidal_S: 0.4 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: smooth_fa_elec: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: grpelec_fade_type: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: grpelec_fade_param1: 1 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: grpelec_fade_param2: 1 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: grpelec_fade_hbond: 0 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: grp_cpfxn: 1 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: grpelec_context_dependent: 0 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: use_polarization: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: use_gen_kirkwood: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: protein_dielectric: 1 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: water_dielectric: 78.3 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: exclude_DNA_DNA: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: exclude_intra_res_protein: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: count_pair_hybrid: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: count_pair_full: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: put_intra_into_total: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: eval_intrares_elec_ST_only: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: envsmooth_zero_negatives: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: pb_bound_tag: bound INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: pb_unbound_tag: unbound INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: ordered_wat_penalty: 1.221 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_ref_seq_length_: 9 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_term_length_: 3 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_scorecut_: 0 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_aa_matrix_: INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_list_defined_: 0 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_list_: INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_defined_: 0 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_: INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_rank_list_: INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_rank_defined_: 0 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_rank_: INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: hbnet_bonus_ramping_function_: "quadratic" INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: hbnet_max_network_size_: 0 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: bond_angle_central_atoms_to_score: INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: bond_angle_residue_type_param_set: none INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: exclude_DNA_DNA: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: exclude_intra_res_protein_: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: exclude_intra_res_RNA_: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: put_intra_into_total_: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: exclude_self_hbonds: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: use_hb_env_dep: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: use_hb_env_dep_DNA: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: smooth_hb_env_dep: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: bb_donor_acceptor_check: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: decompose_bb_hb_into_pair_energies: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: params_database_tag_: ref2015_params INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: use_sp2_chi_penalty_: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: sp2_BAH180_rise_: 0.75 INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: sp2_outer_width_: 0.357 INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: fade_energy_: 1 INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: exclude_ether_oxygens_: 0 INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: Mbhbond: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} HbondOptions::show: mphbond: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: hbond_energy_shift: 0 INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: water_hybrid_sf: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0 INFO:rosetta:protocols.docking.DockMCMCycle: {0} RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011 INFO:rosetta:protocols.docking.DockMCMCycle: {0} RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson INFO:rosetta:protocols.docking.DockMCMCycle: {0} RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat INFO:rosetta:protocols.docking.DockMCMCycle: {0} FreeDOF_Options::show: free_suite_bonus: -1 INFO:rosetta:protocols.docking.DockMCMCycle: {0} FreeDOF_Options::show: free_2HOprime_bonus: -0.5 INFO:rosetta:protocols.docking.DockMCMCycle: {0} FreeDOF_Options::show: free_sugar_bonus: -1 INFO:rosetta:protocols.docking.DockMCMCycle: {0} FreeDOF_Options::show: pack_phosphate_penalty: 0.25 INFO:rosetta:protocols.docking.DockMCMCycle: {0} FreeDOF_Options::show: free_side_chain_bonus: -0.5 INFO:rosetta:protocols.docking.DockMCMCycle: {0} INFO:rosetta:protocols.docking.DockMCMCycle: {0} INFO:rosetta:protocols.docking.DockMCMCycle: {0} /// Packing scorefunction: /// INFO:rosetta:protocols.docking.DockMCMCycle: {0} ScoreFunction::show(): weights: (fa_atr 1) (fa_rep 0.55) (fa_sol 1) (fa_intra_rep 0.005) (fa_intra_sol_xover4 1) (lk_ball_wtd 1) (fa_elec 1) (pro_close 1.25) (hbond_sr_bb 1) (hbond_lr_bb 1) (hbond_bb_sc 1) (hbond_sc 1) (dslf_fa13 1.25) (omega 0.4) (fa_dun 0.7) (p_aa_pp 0.6) (yhh_planarity 0.625) (ref 1) (rama_prepro 0.45) energy_method_options: EnergyMethodOptions::show: aa_composition_setup_files: INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: mhc_epitope_setup_files: INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: netcharge_setup_files: INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: aspartimide_penalty_value: 25 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: etable_type: FA_STANDARD_DEFAULT analytic_etable_evaluation: 1 EnergyMethodOptions::show: method_weights: ref 1.32468 3.25479 -2.14574 -2.72453 1.21829 0.79816 -0.30065 2.30374 -0.71458 1.66147 1.65735 -1.34026 -1.64321 -1.45095 -0.09474 -0.28969 1.15175 2.64269 2.26099 0.58223 EnergyMethodOptions::show: method_weights: free_res EnergyMethodOptions::show: unfolded_energies_type: UNFOLDED_SCORE12 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: split_unfolded_label_type: SPLIT_UNFOLDED_MM INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: split_unfolded_value_type: SPLIT_UNFOLDED_BOLTZ INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: atom_vdw_atom_type_set_name: centroid INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: covalent_labeling_input: INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: covalent_labeling_fa_input: INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: exclude_protein_protein_fa_elec: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: exclude_RNA_RNA_fa_elec: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: exclude_RNA_protein_fa_elec: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: exclude_monomer_fa_elec: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: elec_max_dis: 5.5 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: elec_min_dis: 1.6 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: elec_die: 10 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: elec_no_dis_dep_die: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: elec_sigmoidal_die: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: elec_sigmoidal_D: 80 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: elec_sigmoidal_D0: 6 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: elec_sigmoidal_S: 0.4 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: smooth_fa_elec: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: grpelec_fade_type: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: grpelec_fade_param1: 1 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: grpelec_fade_param2: 1 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: grpelec_fade_hbond: 0 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: grp_cpfxn: 1 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: elec_group_file: /scoring/score_functions/elec_group_def.dat INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: grpelec_context_dependent: 0 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: use_polarization: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: use_gen_kirkwood: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: protein_dielectric: 1 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: water_dielectric: 78.3 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: exclude_DNA_DNA: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: exclude_intra_res_protein: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: count_pair_hybrid: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: count_pair_full: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: put_intra_into_total: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: geom_sol_interres_path_distance_cutoff: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: geom_sol_intrares_path_distance_cutoff: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: eval_intrares_elec_ST_only: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: envsmooth_zero_negatives: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: cst_max_seq_sep: 18446744073709551615 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: pb_bound_tag: bound INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: pb_unbound_tag: unbound INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: ordered_wat_penalty: 1.221 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: ordered_pt_wat_penalty: 2.709 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_ref_seq_length_: 9 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_term_length_: 3 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_pssm_feat_: 1 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_scorecut_defined_: 0 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_scorecut_: 0 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_avg_rank_as_energy_: 0 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_aa_matrix_defined_: 0 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_aa_matrix_: INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_list_defined_: 0 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_list_: INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_defined_: 0 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_: INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_rank_list_defined_: 0 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_rank_list_: INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_rank_defined_: 0 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: nmer_svm_rank_: INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: voids_penalty_energy_containing_cones_cutoff_:6 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: voids_penalty_energy_cone_distance_cutoff_: 8 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: voids_penalty_energy_cone_dotproduct_cutoff_: 0.1 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: voids_penalty_energy_voxel_grid_padding_: 1 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: voids_penalty_energy_voxel_size_: 0.5 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: voids_penalty_energy_disabled_except_during_packing_: TRUE INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: hbnet_bonus_ramping_function_: "quadratic" INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: hbnet_max_network_size_: 0 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: approximate_buried_unsat_penalty_hbond_energy_threshold_: -0.25 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_atomic_depth_: 4.5 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_probe_radius_: 2.3 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: approximate_buried_unsat_penalty_burial_resolution_: 0.5 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: approximate_buried_unsat_penalty_oversat_penalty_: 1 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: approximate_buried_unsat_penalty_assume_const_backbone_:1 INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: bond_angle_central_atoms_to_score: INFO:rosetta:protocols.docking.DockMCMCycle: {0} EnergyMethodOptions::show: bond_angle_residue_type_param_set: none INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: exclude_DNA_DNA: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: exclude_intra_res_protein_: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: exclude_intra_res_RNA_: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: put_intra_into_total_: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: exclude_self_hbonds: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: use_hb_env_dep: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: use_hb_env_dep_DNA: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: smooth_hb_env_dep: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: bb_donor_acceptor_check: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: decompose_bb_hb_into_pair_energies: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: params_database_tag_: ref2015_params INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: use_sp2_chi_penalty_: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: sp2_BAH180_rise_: 0.75 INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: sp2_outer_width_: 0.357 INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: measure_sp3acc_BAH_from_hvy_: true INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: fade_energy_: 1 INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: exclude_ether_oxygens_: 0 INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: Mbhbond: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} HbondOptions::show: mphbond: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: hbond_energy_shift: 0 INFO:rosetta:protocols.docking.DockMCMCycle: {0} HBondOptions::show: water_hybrid_sf: false INFO:rosetta:protocols.docking.DockMCMCycle: {0} RNA_EnergyMethodOptions::show: syn_G_potential_bonus: 0 INFO:rosetta:protocols.docking.DockMCMCycle: {0} RNA_EnergyMethodOptions::show: torsion_potential: ps_04282011 INFO:rosetta:protocols.docking.DockMCMCycle: {0} RNA_EnergyMethodOptions::show: suiteness_bonus: Richardson INFO:rosetta:protocols.docking.DockMCMCycle: {0} RNA_EnergyMethodOptions::show: rna_base_pair_xy_filename: scoring/rna/rna_base_pair_xy.dat INFO:rosetta:protocols.docking.DockMCMCycle: {0} FreeDOF_Options::show: free_suite_bonus: -1 INFO:rosetta:protocols.docking.DockMCMCycle: {0} FreeDOF_Options::show: free_2HOprime_bonus: -0.5 INFO:rosetta:protocols.docking.DockMCMCycle: {0} FreeDOF_Options::show: free_sugar_bonus: -1 INFO:rosetta:protocols.docking.DockMCMCycle: {0} FreeDOF_Options::show: pack_phosphate_penalty: 0.25 INFO:rosetta:protocols.docking.DockMCMCycle: {0} FreeDOF_Options::show: free_side_chain_bonus: -0.5 INFO:rosetta:protocols.docking.DockMCMCycle: {0} INFO:rosetta:protocols.docking.DockMCMCycle: {0} INFO:rosetta:protocols.docking.DockMCMCycle: {0} //////////////////////////////////////////////////////////////////////////////// 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 964 rotamers at 39 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.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.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.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.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 985 rotamers at 39 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.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.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 985 rotamers at 39 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.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.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 985 rotamers at 39 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.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.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 985 rotamers at 39 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.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.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 986 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: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
Additional challenge:
All of the default variables and parameters used above are specific to
the example with inputs/test_lig.pdb
and inputs/TPA.gasteiger.fa.params
, which is supposed to be simple,
straightforward, and speedy. Here is a more practical example:
Kemp elimination has been a targeted reaction for enzyme design using Rosetta. Suppose you want to better understand the active site of these enzymes and decide to investigate using PyRosetta.
Download a copy of RCSB PDB file 3NZ1 (remove waters and any other HETATM)
Extract the 5-Nitro-Benzotriazole substrate (preferably as a .mol2 file) (Note: using PyMOL, you can save the molecule using the .mol2 extension)
Edit the PDB file removing waters, sulfate, and tartaric acid
Produce the .params
file for 5-Nitro-Benzotriazole (listed as chain X resdidue 3NY in the PDB file), lets assume the substrate is saved as a .mol2
file named 3NY.mol2
python molfile_to_params.py 3NY.mol2 -n 3NY
3NZ1.clean.pdb
hereligand_interface.py
wouldn't be here)Run the script from the commandline with appropriate arguments:
python ligand_refinement_from_command_line.py --pdb_filename 3NZ1.clean.pdb --partners A_X --ligand_params 3NY.params --jobs 400 --job_output 3NZ1_docking_output
.params
file should be supplied using the temporary method (Method 1) described above since this script is setup to do this, the file 3NY.params
should have been successfully produced in step 4., if you permanently add 3NY.params
to the chemical database, you do not need to supply anything for the --ligand_params
option.A_X
is PDB specific, if you chose to retain different chains (in step 3.) or otherwise change the chain IDs
in 3NZ1, make sure this string matches the desired chain interactionmatplotlib
module
Chapter contributors: