This tutorial will walk you through how to use RosettaAntibodyDesign
in PyRosetta. You should also go through the parellel distribution workshop as you will most likely need to create many decoys for some of these design tasks. Note that we are using the XML interface to the code here for simplicity (and because I had a C++ workshop I am converting - truth be told). The code-level interface is as robust as the XML - but will require more knowledge use. You are welcome to play around with it - all functions have descriptions and all options are possible to change through code.
Grab a coffee, take a breath, and lets learn how to design some antibodies!
Jared Adolf-Bryfogle, Oleks Kalyuzhniy, Michael Kubitz, Brian D. Weitzner, Xiaozhen Hu, Yumiko Adachi, William R. Schief, Roland L. Dunbrack Jr.
The full RAbD manual can be found here: https://www.rosettacommons.org/docs/latest/application_documentation/antibody/RosettaAntibodyDesign
RosettaAntibodyDesign (RAbD) is a generalized framework for the design of antibodies, in which a user can easily tailor the run to their project needs. The algorithm is meant to sample the diverse sequence, structure, and binding space of an antibody-antigen complex. An app is available, and all components can be used within RosettaScripts for easy scripting of antibody design and incorporation into other Rosetta protocols.
The framework is based on rigorous bioinformatic analysis and rooted very much on our recent clustering of antibody CDR regions. It uses the North/Dunbrack CDR definition as outlined in the North/Dunbrack clustering paper. A new clustering paper will be out in the next year, and this new analysis will be incorporated into RAbD.
The supplemental methods section of the published paper has all details of the RosettaAntibodyDesign method. This manual serves to get you started running RAbD in typical use fashions.
Broadly, the RAbD protocol consists of alternating outer and inner Monte Carlo cycles. Each outer cycle consists of randomly choosing a CDR (L1, L2, etc.) from those CDRs set to design, randomly choosing a cluster and then a structure from that cluster from the database according to the input instructions, and optionally grafting that CDR's structure onto the antibody framework in place of the existing CDR (GraftDesign). The program then performs N rounds of the inner cycle, consisting of sequence design (SeqDesign) using cluster-based sequence profiles and structural constraints, energy minimization, and optional docking. Each inner cycle structurally optimizes the backbone and repacks side chains of the CDR chosen in the outer cycle as well as optional neighbors in order to optimize interactions of the CDR with the antigen and other CDRs.
Backbone dihedral angle (CircularHarmonic) constraints derived from the cluster data are applied to each CDR to limit deleterious structural perturbations. Amino acid changes are typically sampled from profiles derived for each CDR cluster in PyIgClassify. Conservative amino acid substitutions (according to the BLOSUM62 substitution matrix) may be performed when too few sequences are available to produce a profile (e.g., for H3). After each inner cycle is completed, the new sequence and structure are accepted according to the Metropolis Monte Carlo criterion. After N rounds within the inner cycle, the program returns to the outer cycle, at which point the energy of the resulting design is compared to the previous design in the outer cycle. The new design is accepted or rejected according to the Monte Carlo criterion.
If optimizing the antibody-antigen orientation during the design (dock), SiteConstraints are automatically used to keep the CDRs (paratope) facing the antigen surface. These are termed ParatopeSiteConstraints. Optionally, one can enable constraints that keep the paratope of the antibody around a target epitope (antigen binding site). These are called ParatopeEpitopeSiteConstraints as the constraints are between the paratope and the epitope. The epitope is automatically determined as the interface residues around the paratope on input into the program, however, any residue(s) can be set as the epitope to limit unwanted movement and sampling of the antibody. See the examples and options below.
More detail on the algorithm can be found in the published paper.
Antibody Design Database
This app requires the Rosetta Antibody Design Database. A database of antibodies from the original North Clustering paper is included in Rosetta and is used as the default . An updated database (which is currently updated bi-yearly) can be downloaded here: http://dunbrack2.fccc.edu/PyIgClassify/.
For C++, It should be placed in Rosetta/main/database/sampling/antibodies/
. For PyRosetta, use the cmd-line option antibody_database
and set it to the full path of the downloaded database within the init()
function as you have done in the past. It is recommended to use this up-to-date database for production runs. For this tutorial, we will use the database within Rosetta.
Starting Structure
The protocol begins with the three-dimensional structure of an antibody-antigen complex. Designs should start with an antibody bound to a target antigen (however optimizing just the antibody without the complex is also possible). Camelid antibodies are fully supported. This structure may be an experimental structure of an existing antibody in complex with its antigen, a predicted structure of an existing antibody docked computationally to its antigen, or even the best scoring result of low-resolution docking a large number of unrelated antibodies to a desired epitope on the structure of a target antigen as a prelude to de novo design.
The program CAN computationally design an antibody to anywhere on the target protein, but it is recommended to place the antibody at the target epitope. It is beyond the scope of this program to determine potential epitopes for binding, however servers and programs exist to predict these. Automatic SiteConstraints can be used to further limit the design to target regions.
Model Numbering and Light Chain identification
The input PDB file must be renumbered to the AHo Scheme and the light chain gene must be identified. This can be done through the PyIgClassify Server.
On input into the program, Rosetta assigns our CDR clusters using the same methodology as PyIgClassify. The RosettaAntibodyDesign protocol is then driven by a set of command-line options and a set of design instructions provided as an input file that controls which CDR(s) are designed and how. Details and example command lines and instruction files are provided below.
The gene of the light chain should always be set on the command-line using the option -light_chain
, these are either lamda or kappa. PyIgClassify will identify the gene of the light chain.
For this tutorial, the starting antibody is renumbered for you.
Notes for Tutorial Shortening
Always set the option, -outer_cycle_rounds
to 5 in order to run these examples quickly. The default is 25. We include this in our common options file that is read in by Rosetta at the start. We will only be outputting a single structure, but typical use of the protocol is with default settings of -outer_cycle_rounds
and an nstruct
of at least 1000, with 5000-10000 recommended for jobs that are doing a lot of grafting. For De-novo design runs, one would want to go even higher. Note that the Docking stage increases runtime significantly as well.
The total number of rounds is outer_cycle_rounds * nstruct.
General Notes
setenv PATH ${PATH}:${HOME}/rosetta_workshop/rosetta/main/source/tools
We will be using JSON output of the scorefile, as this is much easier to work with in python and pandas.
We use the option -scorefile_format json
All of our common options for the tutorial are in the common file that you will copy to your working directory.
Rosetta/PyRosetta will look for this file in your working directory or your home folder in the directory $HOME/.rosetta/flags
.
See this page for more info on using rosetta with custom config files: https://www.rosettacommons.org/docs/latest/rosetta_basics/running-rosetta-with-options#common-options-and-default-user-configuration
All tutorials have generated output in outputs/rabd
and their approximate time to finish on a single (core i7) processor.
!pip install pyrosettacolabsetup
import pyrosettacolabsetup; pyrosettacolabsetup.install_pyrosetta()
import pyrosetta; pyrosetta.init()
Make sure you are in the directory with the pdb files:
cd google_drive/MyDrive/student-notebooks/
from typing import *
import pandas
from pathlib import Path
import json
import re
#Functions we will be using. I like to collect any extra functions at the top of my notebook.
def load_json_scorefile(file_path: Path, sort_by: str="dG_separated") -> pandas.DataFrame:
"""
Read scorefile lines as a dataframe, sorted by total_score with Nan's correctly replaced.
"""
local_lines = open(file_path, 'r').readlines()
decoys=[]
for line in local_lines:
o = json.loads(line.replace("nan", "NaN"))
# print o[self.decoy_field_name]
# print repr(o)
decoys.append(o)
local_df = pandas.DataFrame.from_dict(decoys)
local_df = local_df.infer_objects()
# df.to_csv("debugging.csv", sep=",")
local_df = local_df.sort_values(sort_by, ascending=True)
return local_df
def drop_cluster_columns(local_df: pandas.DataFrame, keep_cdrs: List[str]=None) -> pandas.DataFrame:
"""
Drop cluster columns that RAbD outputs to make it easier to work with the dataframe.
"""
to_drop = []
for column in local_df.columns:
if re.search("cdr_cluster", column):
skip=False
if (keep_cdrs):
for cdr in keep_cdrs:
if re.search(cdr, column):
skip=True
break
if not skip:
to_drop.append(column)
return local_df.drop(columns=to_drop)
#Python
from pyrosetta import *
from pyrosetta.rosetta import *
from pyrosetta.teaching import *
import os
#Core Includes
from rosetta.protocols.rosetta_scripts import *
from rosetta.protocols.antibody import *
from rosetta.protocols.antibody.design import *
from rosetta.utility import *
/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/ipykernel_launcher.py:8: UserWarning: Import of 'rosetta' as a top-level module is deprecated and may be removed in 2018, import via 'pyrosetta.rosetta'.
Since we are sharing the working directory with all other notebooks, instead of using the common-configuration we spoke about in the introduction, we will be using the flags file located in the inputs directory.
init('-no_fconfig @inputs/rabd/common')
PyRosetta-4 2019 [Rosetta PyRosetta4.Release.python36.mac 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. core.init: Rosetta version: PyRosetta4.Release.python36.mac r233 2019.39+release.93456a567a8 93456a567a8125cafdf7f8cb44400bc20b570d81 http://www.pyrosetta.org 2019-09-26T14:24:44 core.init: command: PyRosetta -no_fconfig @inputs/rabd/common -database /Users/jadolfbr/Library/Python/3.6/lib/python/site-packages/pyrosetta-2019.39+release.93456a567a8-py3.6-macosx-10.6-intel.egg/pyrosetta/database basic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-443789040 seed_offset=0 real_seed=-443789040 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-443789040 RG_type=mt19937
#Import a pose
pose = pose_from_pdb("inputs/rabd/my_ab.pdb")
original_pose = pose.clone()
core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 980 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.889319 seconds. core.import_pose.import_pose: File 'inputs/rabd/my_ab.pdb' automatically determined to be of type PDB core.io.pdb.pdb_reader: Parsing 993 .pdb records with unknown format to search for Rosetta-specific comments. core.conformation.Conformation: Found disulfide between residues 771 845 core.conformation.Conformation: current variant for 771 CYS core.conformation.Conformation: current variant for 845 CYS core.conformation.Conformation: current variant for 771 CYD core.conformation.Conformation: current variant for 845 CYD core.conformation.Conformation: Found disulfide between residues 891 956 core.conformation.Conformation: current variant for 891 CYS core.conformation.Conformation: current variant for 956 CYS core.conformation.Conformation: current variant for 891 CYD core.conformation.Conformation: current variant for 956 CYD
In many of these examples, we will use the xml interface to PyRosetta for simplicity with the AntibodyDesignMover - which is the actual C++ application as a mover. https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/Movers/movers_pages/antibodies/AntibodyDesignMover
Lets copy the files we need first:
cp ../inputs/rabd/color_cdrs.pml .
cp ../inputs/rabd/rabd.xml .
You are starting design on a new antibody that is not bound to the antigen in the crystal. This is difficult and risky, but we review how one could go about this anyway. We start by selecting a framework. Here, we use the trastuzumab framework as it expresses well, is thermodynamically stable with a Tm of 69.5 degrees, and has been shown repeatedly that it can tolerate CDRs of different sequence and structure. Note that the energy of the complex is high as we are starting from a manual placement of the antibody to antigen. If we relax the structure too much, we will fall into an energy well that is hard to escape without significant sampling.
We are using an arbitrary protein at an arbitrary site for design. The PDB of our target is 1qaw. 1qaw is an oligomer of the TRP RNA-Binding Attenuation Protein from Bacillus Stearothermophilus. It is usually a monomer/dimer, but at its multimeric interface is a tryptophan residue by itself.
It's a beautiful protein, with a cool mechanism. We will attempt to build an antibody to bind to two subunits to stabilize the dimeric state of the complex in the absence of TRP. Note that denovo design currently takes a large amount of processing power. Each tutorial below is more complex than the one before it. The examples we have for this tutorial are short runs to show HOW it can be done, but more outer_cycle_rounds and nstruct would produce far better models than the ones you will see here - as we will need to sample the relative orientation of the antibody-antigen complex through docking, the CDR clusters and lengths, the internal backbone degrees of freedom of the CDRs, as well as the sequence of the CDRs and possibly the framework. As you can tell, just the sampling problem alone is difficult. However, this will give you a basis for using RAbD on your own.
Using the application is as simple as setting the -seq_design_cdrs
option.
This simply designs the CDRs of the heavy chain using cdr profiles if they exist for those clusters during flexible-backbone design. If the clusters do not exist (as is the case for H3 at the moment), we use conservative design by default. Note that InterfaceAnalyzer is run on each output decoy in the RAbD mover. Note that you can also set light_chain
on the command line if you are only working on a single PDB through the rosetta run.
<AntibodyDesignMover name="RAbD" seq_design_cdrs="L1,L3" light_chain="kappa"/>
This will take a about a minute (50 seconds on my laptop). Output structures and scores are in outputs/rabd
if you wish to copy them over - these include 4 more structures.
rabd = XmlObjects.static_get_mover('<AntibodyDesignMover name="RAbD" seq_design_cdrs="L1,L3" light_chain="kappa"/>')
if not os.getenv("DEBUG"):
rabd.apply(pose)
protocols.rosetta_scripts.RosettaScriptsParser: Generating XML Schema for rosetta_scripts... protocols.rosetta_scripts.RosettaScriptsParser: ...done protocols.rosetta_scripts.RosettaScriptsParser: Initializing schema validator... protocols.rosetta_scripts.RosettaScriptsParser: ...done protocols.rosetta_scripts.RosettaScriptsParser: Validating input script... protocols.rosetta_scripts.RosettaScriptsParser: ...done protocols.rosetta_scripts.RosettaScriptsParser: Parsed script: <ROSETTASCRIPTS> <MOVERS> <AntibodyDesignMover light_chain="kappa" name="RAbD" seq_design_cdrs="L1,L3"/> </MOVERS> <PROTOCOLS/> </ROSETTASCRIPTS> core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_env_log.txt basic.io.database: Database file opened: scoring/score_functions/InterchainPotential/interchain_pair_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/env_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cbeta_den.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/pair_log.txt basic.io.database: Database file opened: scoring/score_functions/EnvPairPotential/cenpack_log.txt core.scoring.ramachandran: shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "RAbD" of type AntibodyDesignMover protocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following movers and filters basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: SRWGGDGFYAMDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT <pyrosetta.rosetta.protocols.antibody.design.AntibodyDesignMover object at 0x12ee067a0>
Now, for the sake of learning how to do this - how would we do this in code instead of the XML - we just need to use setters.
pose = original_pose.clone()
rabd2 = AntibodyDesignMover()
cdrs = vector1_protocols_antibody_CDRNameEnum()
cdrs.append(l1)
cdrs.append(l3)
rabd2.set_seq_design_cdrs(cdrs)
rabd2.set_light_chain("kappa")
if not os.getenv("DEBUG"):
rabd2.apply(pose)
basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: SRWGGDGFYAMDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT
Score the input pose using the InterfaceAnalayzerMover
from rosetta.protocols.analysis import InterfaceAnalyzerMover
if not os.getenv("DEBUG"):
iam = InterfaceAnalyzerMover("LH_ABCDEFGIJKZ")
iam.set_pack_separated(True)
iam.apply(pose)
iam.apply(original_pose)
dg_term = "dG_separated"
print("dG Diff:", pose.scores[dg_term] - original_pose[dg_term])
protocols.analysis.InterfaceAnalyzerMover: Using explicit constructor protocols.analysis.InterfaceAnalyzerMover: Using interface constructor protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... protocols.analysis.InterfaceAnalyzerMover: Interface set residues total: 100 protocols.analysis.InterfaceAnalyzerMover: NULL scorefunction. Initialize from cmd line. core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat core.scoring.elec.util: Read 40 countpair representative atoms core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true. core.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated. core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/pyrosetta-2019.33+release.1e60c63beb5-py3.6-macosx-10.6-intel.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/pyrosetta-2019.33+release.1e60c63beb5-py3.6-macosx-10.6-intel.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.250793 seconds to load from binary core.conformation.Conformation: Found disulfide between residues 771 845 core.conformation.Conformation: current variant for 771 CYD core.conformation.Conformation: current variant for 845 CYD core.conformation.Conformation: current variant for 771 CYD core.conformation.Conformation: current variant for 845 CYD core.conformation.Conformation: Found disulfide between residues 891 956 core.conformation.Conformation: current variant for 891 CYD core.conformation.Conformation: current variant for 956 CYD core.conformation.Conformation: current variant for 891 CYD core.conformation.Conformation: current variant for 956 CYD protocols.analysis.InterfaceAnalyzerMover: Calculating dSASA protocols.analysis.InterfaceAnalyzerMover: Calculating per-res dSASA data protocols.analysis.InterfaceAnalyzerMover: included_nres: 975 core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 protocols.analysis.InterfaceAnalyzerMover: Found Hbond between chains: 12 and 9 protocols.analysis.InterfaceAnalyzerMover: Found Hbond between chains: 9 and 13 protocols.analysis.InterfaceAnalyzerMover: Found Hbond between chains: 12 and 9 protocols.analysis.InterfaceAnalyzerMover: Computing delta unsat polar residues... basic.io.database: Database file opened: scoring/score_functions/hbonds/sp2_elec_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/sp2_elec_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/sp2_elec_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/sc/sc_radii.lib protocols.analysis.InterfaceAnalyzerMover: Computing Shape Complementarity Score... protocols.analysis.InterfaceAnalyzerMover: Upstream chain(s) numbers: 12, 13, protocols.analysis.InterfaceAnalyzerMover: Downstream chain(s) numbers: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11,
Has the energy gone down after our sequence design? The dG_separated
is calculated by scoring the complex, separating the antigen from the antibody, repacking side-chains at the interface, and then taking the difference in score - i.e. the dG.
Lets take a look at scores from a previous run of 5 antibodies. The scorefiles are in json format, so it will be easy to turn them into pandas Dataframes and do some cool stuff. We'll do this often as the runtimes increase for our protocol - but all the scores in them can be accessed using the pose.scores attribute (which is PyRosetta-specific functionality.)
Are any of these better than our input pose?
df = load_json_scorefile("expected_outputs/rabd/tutA1_score.sc")
df = drop_cluster_columns(df, keep_cdrs=["L1", "L3"])
df
decoy | atom_pair_constraint | cdr_cluster_DIS_L1 | cdr_cluster_DIS_L3 | cdr_cluster_LEN_L1 | cdr_cluster_LEN_L3 | complex_normalized | dG_cross | dG_cross/dSASAx100 | dG_separated | ... | ref | sc_value | side1_normalized | side1_score | side2_normalized | side2_score | total_score | yhh_planarity | cdr_cluster_ID_L1 | cdr_cluster_ID_L3 | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
0 | tutA1_my_ab_0001 | 0.0 | 10.244154 | 14.169669 | 11.0 | 9.0 | 2.494409 | 0.0 | 0.0 | 1784.542480 | ... | 374.81054 | 0.491761 | 14.690318 | 837.348145 | 20.825792 | 874.683289 | 2432.049006 | 0.134353 | L1-11-1 | L3-9-cis7-1 |
3 | tutA1_my_ab_0004 | 0.0 | 9.604385 | 10.078285 | 11.0 | 9.0 | 2.459319 | 0.0 | 0.0 | 1820.213013 | ... | 374.09441 | 0.596517 | 14.805477 | 858.717651 | 20.484030 | 860.329285 | 2397.836108 | 0.420196 | L1-11-1 | L3-9-cis7-1 |
1 | tutA1_my_ab_0002 | 0.0 | 9.939879 | 14.834209 | 11.0 | 9.0 | 2.494796 | 0.0 | 0.0 | 1849.303833 | ... | 372.58994 | 0.468819 | 17.130129 | 907.896790 | 20.831068 | 874.904846 | 2432.425954 | 0.061565 | L1-11-1 | L3-9-cis7-1 |
4 | tutA1_my_ab_0005 | 0.0 | 13.124744 | 14.362237 | 11.0 | 9.0 | 2.667474 | 0.0 | 0.0 | 1934.344604 | ... | 374.83686 | 0.415013 | 17.054668 | 920.952087 | 22.980696 | 965.189209 | 2600.787151 | 0.044588 | L1-11-1 | L3-9-cis7-1 |
2 | tutA1_my_ab_0003 | 0.0 | 9.693962 | 12.150679 | 11.0 | 9.0 | 3.530113 | 0.0 | 0.0 | 2854.750488 | ... | 376.96998 | 0.464472 | 24.664927 | 1381.235962 | 33.255428 | 1396.727905 | 3441.859648 | 0.075642 | L1-11-1 | L3-9-cis7-1 |
5 rows × 48 columns
Now we will be enabling graft design AND sequence design on L1 and L3 loops. With an nstruct (n decoys) of 5, we are doing 25 design trials total - IE 25 actual grafts.
<AntibodyDesignMover name="RAbD" seq_design_cdrs="L1,L3" graft_design_cdrs="L1,L3">
This will take a about 2-3 times as long as sequence design, as grafting a non-breaking loop takes time. This was 738 seconds on my laptop to generate 5. Here, you will generate 1 at about 150 seconds Ouptut structures and scores are in ../expected_outputs/rabd.
Typically, we require a much higher -outer_cycle_rounds
and number of decoys to see anything significant. Did this improve energies in your single antibody? How about our pre-generated ones? Load and take a look at the scorefile as a pandas DataFrame as we did above (expected_outputs/rabd/tutA2_score.sc
).
### BEGIN SOLUTION
df_a2 = load_json_scorefile("expected_outputs/rabd/tutA2_score.sc")
df_a2 = drop_cluster_columns(df_a2, keep_cdrs=["L1", "L3"])
df_a2
### END SOLUTION
decoy | atom_pair_constraint | cdr_cluster_DIS_L1 | cdr_cluster_DIS_L3 | cdr_cluster_LEN_L1 | cdr_cluster_LEN_L3 | complex_normalized | dG_cross | dG_cross/dSASAx100 | dG_separated | ... | ref | sc_value | side1_normalized | side1_score | side2_normalized | side2_score | total_score | yhh_planarity | cdr_cluster_ID_L1 | cdr_cluster_ID_L3 | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
4 | tutA2_my_ab_0005 | 0.0 | 11.192533 | 31.677544 | 11.0 | 7.0 | 2.450019 | 0.0 | 0.0 | 1751.548462 | ... | 364.65868 | 0.564960 | 15.000569 | 825.031311 | 21.473850 | 837.480164 | 2383.868655 | 0.107882 | L1-11-1 | L3-7-1 |
2 | tutA2_my_ab_0003 | 0.0 | 20.217281 | 24.178181 | 15.0 | 11.0 | 2.760204 | 0.0 | 0.0 | 1843.231445 | ... | 375.17336 | 0.537087 | 13.518681 | 851.676880 | 21.286449 | 979.176697 | 2707.759790 | 0.221997 | L1-15-1 | L3-11-1 |
0 | tutA2_my_ab_0001 | 0.0 | 8.599037 | 27.562218 | 11.0 | 10.0 | 3.348572 | 0.0 | 0.0 | 2484.706299 | ... | 374.05882 | 0.486206 | 22.621260 | 1198.926758 | 29.544832 | 1270.427734 | 3268.206329 | 0.361406 | L1-11-1 | L3-10-cis7,8-1 |
1 | tutA2_my_ab_0002 | 0.0 | 29.971132 | 45.571491 | 17.0 | 9.0 | 3.352178 | 0.0 | 0.0 | 2587.653564 | ... | 373.00912 | 0.620726 | 18.605259 | 1265.157593 | 28.719591 | 1292.381592 | 3288.486156 | 0.126786 | L1-17-1 | L3-9-1 |
3 | tutA2_my_ab_0004 | 0.0 | 12.153269 | 17.002886 | 10.0 | 8.0 | 5.869139 | 0.0 | 0.0 | 5082.230469 | ... | 376.47676 | 0.571551 | 42.399551 | 2501.573486 | 62.364841 | 2494.593750 | 5710.672501 | 0.100791 | L1-10-2 | L3-8-1 |
5 rows × 48 columns
Lets merge these dataframes, sort by dG_separated, and see if any of our graft-design models did better.
df_tut_a12 = pandas.concat([df, df_a2], ignore_index=True).sort_values("dG_separated", ascending=True)
df_tut_a12
decoy | atom_pair_constraint | cdr_cluster_DIS_L1 | cdr_cluster_DIS_L3 | cdr_cluster_LEN_L1 | cdr_cluster_LEN_L3 | complex_normalized | dG_cross | dG_cross/dSASAx100 | dG_separated | ... | ref | sc_value | side1_normalized | side1_score | side2_normalized | side2_score | total_score | yhh_planarity | cdr_cluster_ID_L1 | cdr_cluster_ID_L3 | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
5 | tutA2_my_ab_0005 | 0.0 | 11.192533 | 31.677544 | 11.0 | 7.0 | 2.450019 | 0.0 | 0.0 | 1751.548462 | ... | 364.65868 | 0.564960 | 15.000569 | 825.031311 | 21.473850 | 837.480164 | 2383.868655 | 0.107882 | L1-11-1 | L3-7-1 |
0 | tutA1_my_ab_0001 | 0.0 | 10.244154 | 14.169669 | 11.0 | 9.0 | 2.494409 | 0.0 | 0.0 | 1784.542480 | ... | 374.81054 | 0.491761 | 14.690318 | 837.348145 | 20.825792 | 874.683289 | 2432.049006 | 0.134353 | L1-11-1 | L3-9-cis7-1 |
1 | tutA1_my_ab_0004 | 0.0 | 9.604385 | 10.078285 | 11.0 | 9.0 | 2.459319 | 0.0 | 0.0 | 1820.213013 | ... | 374.09441 | 0.596517 | 14.805477 | 858.717651 | 20.484030 | 860.329285 | 2397.836108 | 0.420196 | L1-11-1 | L3-9-cis7-1 |
6 | tutA2_my_ab_0003 | 0.0 | 20.217281 | 24.178181 | 15.0 | 11.0 | 2.760204 | 0.0 | 0.0 | 1843.231445 | ... | 375.17336 | 0.537087 | 13.518681 | 851.676880 | 21.286449 | 979.176697 | 2707.759790 | 0.221997 | L1-15-1 | L3-11-1 |
2 | tutA1_my_ab_0002 | 0.0 | 9.939879 | 14.834209 | 11.0 | 9.0 | 2.494796 | 0.0 | 0.0 | 1849.303833 | ... | 372.58994 | 0.468819 | 17.130129 | 907.896790 | 20.831068 | 874.904846 | 2432.425954 | 0.061565 | L1-11-1 | L3-9-cis7-1 |
3 | tutA1_my_ab_0005 | 0.0 | 13.124744 | 14.362237 | 11.0 | 9.0 | 2.667474 | 0.0 | 0.0 | 1934.344604 | ... | 374.83686 | 0.415013 | 17.054668 | 920.952087 | 22.980696 | 965.189209 | 2600.787151 | 0.044588 | L1-11-1 | L3-9-cis7-1 |
7 | tutA2_my_ab_0001 | 0.0 | 8.599037 | 27.562218 | 11.0 | 10.0 | 3.348572 | 0.0 | 0.0 | 2484.706299 | ... | 374.05882 | 0.486206 | 22.621260 | 1198.926758 | 29.544832 | 1270.427734 | 3268.206329 | 0.361406 | L1-11-1 | L3-10-cis7,8-1 |
8 | tutA2_my_ab_0002 | 0.0 | 29.971132 | 45.571491 | 17.0 | 9.0 | 3.352178 | 0.0 | 0.0 | 2587.653564 | ... | 373.00912 | 0.620726 | 18.605259 | 1265.157593 | 28.719591 | 1292.381592 | 3288.486156 | 0.126786 | L1-17-1 | L3-9-1 |
4 | tutA1_my_ab_0003 | 0.0 | 9.693962 | 12.150679 | 11.0 | 9.0 | 3.530113 | 0.0 | 0.0 | 2854.750488 | ... | 376.96998 | 0.464472 | 24.664927 | 1381.235962 | 33.255428 | 1396.727905 | 3441.859648 | 0.075642 | L1-11-1 | L3-9-cis7-1 |
9 | tutA2_my_ab_0004 | 0.0 | 12.153269 | 17.002886 | 10.0 | 8.0 | 5.869139 | 0.0 | 0.0 | 5082.230469 | ... | 376.47676 | 0.571551 | 42.399551 | 2501.573486 | 62.364841 | 2494.593750 | 5710.672501 | 0.100791 | L1-10-2 | L3-8-1 |
10 rows × 48 columns
Take a look at the lowest (dG) scoring pose in pymol - do you see any difference in L1 and L3 loops there? Do they make better contact than what we had before?
Lets take a look in pymol.
pymol inputs/rabd/my_ab.pdb inputs/rabd/tutA2_*
@color_cdrs.pml
center full_epitope
How different are the L1 and L3 loops? Have any changed length?
Lets take a look at the clusters in our dataframe. Have they changed from the native?
if not os.getenv("DEBUG"):
print("L1", original_pose.scores["cdr_cluster_ID_L1"])
print("L3", original_pose.scores["cdr_cluster_ID_L3"])
Here, we want to do a denovo-run (without docking), starting with random CDRs grafted in - instead of whatever we have in the antibody to start with (only for the CDRs that are actually undergoing graft-design). This is useful, as we start the design with very high energy and work our way down. Note that since this is an entirely new interface for our model protein, this interface is already at a very high energy - and so this is less needed, but it should be noted how to do this. (139 seconds on my laptop). Do this below as you have done in other tutorials - either through code or XML.
<AntibodyDesignMover name="RAbD" graft_design_cdrs="L1,L3" seq_design_cdrs="L1,L3"
random_start="1"/>
if not os.getenv("DEBUG"):
### BEGIN SOLUTION
pose = original_pose.clone()
rabd = XmlObjects.static_get_mover('<AntibodyDesignMover name="RAbD" graft_design_cdrs="L1,L3" seq_design_cdrs="L1,L3" random_start="1"/> light_chain="kappa"')
rabd.apply(pose)
# OR (REUSE code from above)
pose = original_pose.clone()
rabd2.set_seq_design_cdrs(cdrs)
rabd2.set_graft_design_cdrs(cdrs)
rabd2.set_random_start(True)
rabd2.set_light_chain("kappa")
rabd2.apply(pose)
### END SOLUTION
Would starting from a random CDR help anywhere? Perhaps if you want an entirely new cluster or length to break a patent or remove some off target effects? We will use it below to start de novo design with docking.
This tutorial will give you some exprience with an antibody design protocol using the RosettaAntibdyDesign
components. We will take the light chain CDRs from a malaria antibody and graft them into our antibody. In the tutorial we are interested in stabilizing the grafted CDRs in relation to the whole antibody, instead of interface design to an antigen.
We will graft the CDRs in, minimize the structure with CDR dihedral constraints (that use the CDR clusters) to not purturb the CDRs too much, and then design the framework around the CDRs while designing the CDRs and neighbors. The result should be mutations that better accomodate our new CDRs. This can be useful for humanizing potential antibodies or framework switching, where we want the binding properties of certain CDRs, but the stability or immunological profile of a different framework.
We are using an XML here for simplicity - all components are available in PyRosetta, but harder to setup.
cp ../inputs/rabd/ab_design_components.xml .
cp ../inputs/rabd/malaria_cdrs.pdb .
Take a look at the xml.
AntibodyCDRGrafter
to do the grafting of our CDRs.CDRDihderalConstraintMovers
for each CDR with use the CDR clusters determinedy by RosettaAntibody to keep from perturbing the CDRs too much.RestrictToCDRsAndNeighborsOperation
and the CDRResidueSelector
. This task operation controls what we pack and design. It first limits packing and design to only the CDRs and its neighbors. By specifying the design_framework=1
option we allow the neighbor framework residues to design, while the CDRs and antigen neighbors will only repack. If we wanted to disable antigen repacking, we would pass the DisableAntibodyRegionOperation task operation. Using this, we can specify any antibody region as antibody_region
, cdr_region
, or antigen_region
and we can disable just design or both packing and design.These task operations allow us to chisel exactly what we want to design in antibody, sans a residue-specific resfile (though we could combine these with one of them!). All of these tools are available in-code. If you've done the design workshop, you will know how to use them here. Checkout rosetta.protocols.antibody.task_operations
for a list of them.
Finally, we use the new SimpleMetric system to obtain our final sequence of the CDRs to compare to our native antibody as well as pymol selections of our CDRs - which you have been introduced to in the previous tutorial.
rosetta.protocols.antibody.task_operations
rosetta.protocols.antibody.constraints
rosetta.protocols.antibody.residue_selectors
More Documentation is available here:
https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/RosettaScripts
os.system('cp inputs/rabd/malaria_cdrs.pdb .')
0
if not os.getenv("DEBUG"):
pose = original_pose.clone()
parser = RosettaScriptsParser()
protocol = parser.generate_mover_and_apply_to_pose(pose, "inputs/rabd/ab_design_components.xml")
protocol.apply(pose)
protocols.rosetta_scripts.RosettaScriptsParser: Generating XML Schema for rosetta_scripts... protocols.rosetta_scripts.RosettaScriptsParser: ...done protocols.rosetta_scripts.RosettaScriptsParser: Initializing schema validator... protocols.rosetta_scripts.RosettaScriptsParser: ...done protocols.rosetta_scripts.RosettaScriptsParser: Validating input script... protocols.rosetta_scripts.RosettaScriptsParser: ...done protocols.rosetta_scripts.RosettaScriptsParser: Parsed script: <ROSETTASCRIPTS> <RESIDUE_SELECTORS> <CDR cdrs="L1,L2,L3" name="light_cdrs"/> <CDR cdrs="L1" name="L1"/> <CDR cdrs="L2" name="L2"/> <CDR cdrs="L3" name="L3"/> <AntibodyRegion name="antigen" region="antigen_region"/> <AntibodyRegion name="framework" region="framework_region"/> <AntibodyRegion name="cdrs" region="cdr_region"/> </RESIDUE_SELECTORS> <TASKOPERATIONS> <RestrictToCDRsAndNeighbors cdrs="L1,L2,L3" design_cdrs="1" design_framework="1" name="restrict_to_cdrs"/> <AddCDRProfilesOperation cdrs="L1,L2,L3" fallback_strategy="CONSERVATIVE" name="profiles"/> </TASKOPERATIONS> <MOVE_MAP_FACTORIES> <MoveMapFactory bb="0" chi="0" name="movemap_cdrs"> <Backbone residue_selector="light_cdrs"/> <Chi residue_selector="light_cdrs"/> </MoveMapFactory> </MOVE_MAP_FACTORIES> <SIMPLE_METRICS> <SasaMetric name="sasa" residue_selector="light_cdrs"/> <SelectedResiduesPyMOLMetric name="cdr_selection" residue_selector="light_cdrs"/> <SequenceMetric custom_type="L1" name="L1_seq" residue_selector="L1"/> <SequenceMetric custom_type="L2" name="L2_seq" residue_selector="L2"/> <SequenceMetric custom_type="L3" name="L3_seq" residue_selector="L3"/> <InteractionEnergyMetric name="cdr-int" residue_selector="light_cdrs" residue_selector2="antigen"/> </SIMPLE_METRICS> <MOVERS> <CDRDihedralConstraintMover cdr="L1" name="dih_mover_L1" use_cluster_csts="1"/> <CDRDihedralConstraintMover cdr="L2" name="dih_mover_L2" use_cluster_csts="1"/> <CDRDihedralConstraintMover cdr="L3" name="dih_mover_L3" use_cluster_csts="1"/> <AntibodyCDRGrafter cdr_definition="North" cdrs="L1,L2,L3" donor_structure_from_pdb="malaria_cdrs.pdb" input_ab_scheme="AHO_Scheme" name="grafter" optimize_cdr4_if_neighbor="1" optimize_cdrs="0" use_secondary_graft_mover="1"/> <PackRotamersMover name="packrot" task_operations="restrict_to_cdrs,profiles"/> <MinMover cartesian="1" movemap_factory="movemap_cdrs" name="minmover" tolerance=".1"/> <RunSimpleMetrics metrics="sasa,cdr_selection,L1_seq,L2_seq,L3_seq,cdr-int" name="design_metrics" prefix="design_"/> <RunSimpleMetrics metrics="sasa,cdr_selection,L1_seq,L2_seq,L3_seq,cdr-int" name="native_metrics" prefix="native_"/> </MOVERS> <PROTOCOLS> <Add mover_name="native_metrics"/> <Add mover_name="grafter"/> <Add mover_name="dih_mover_L1"/> <Add mover_name="dih_mover_L2"/> <Add mover_name="dih_mover_L3"/> <Add mover_name="packrot"/> <Add mover_name="minmover"/> <Add mover_name="packrot"/> <Add mover_name="minmover"/> <Add mover_name="design_metrics"/> </PROTOCOLS> </ROSETTASCRIPTS> core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 protocols.antibody.residue_selector.CDRResidueSelector: Setting CDRs from settings protocols.antibody.residue_selector.CDRResidueSelector: Setting CDRs from settings protocols.antibody.residue_selector.CDRResidueSelector: Setting CDRs from settings protocols.antibody.residue_selector.CDRResidueSelector: Setting CDRs from settings protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "restrict_to_cdrs" of type RestrictToCDRsAndNeighbors protocols.task_operations.ConservativeDesignOperation: Loading conservative mutational data protocols.antibody.task_operations.AddCDRProfilesOperation: Setting CDRs from settings protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "profiles" of type AddCDRProfilesOperation core.select.residue_selector.util: Found residue selector light_cdrs core.select.residue_selector.util: Found residue selector light_cdrs protocols.jd2.parser.MoveMapFactoryLoader: Defined MoveMap named "movemap_cdrs" core.select.residue_selector.util: Found residue selector light_cdrs core.select.residue_selector.util: Found residue selector light_cdrs core.select.residue_selector.util: Found residue selector L1 core.select.residue_selector.util: Found residue selector L2 core.select.residue_selector.util: Found residue selector L3 core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 core.select.residue_selector.util: Found residue selector light_cdrs core.select.residue_selector.util: Found residue selector antigen protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "dih_mover_L1" of type CDRDihedralConstraintMover protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "dih_mover_L2" of type CDRDihedralConstraintMover protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "dih_mover_L3" of type CDRDihedralConstraintMover protocols.antibody.AntibodyCDRGrafter: Setting CDRs from settings core.import_pose.import_pose: File 'malaria_cdrs.pdb' automatically determined to be of type PDB core.io.pdb.pdb_reader: Parsing 0 .pdb records with unknown format to search for Rosetta-specific comments. core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue CYS:CtermProteinFull 387 core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ASP:CtermProteinFull 601 core.conformation.Conformation: Found disulfide between residues 8 22 core.conformation.Conformation: current variant for 8 CYS core.conformation.Conformation: current variant for 22 CYS core.conformation.Conformation: current variant for 8 CYD core.conformation.Conformation: current variant for 22 CYD core.conformation.Conformation: Found disulfide between residues 24 36 core.conformation.Conformation: current variant for 24 CYS core.conformation.Conformation: current variant for 36 CYS core.conformation.Conformation: current variant for 24 CYD core.conformation.Conformation: current variant for 36 CYD core.conformation.Conformation: Found disulfide between residues 43 58 core.conformation.Conformation: current variant for 43 CYS core.conformation.Conformation: current variant for 58 CYS core.conformation.Conformation: current variant for 43 CYD core.conformation.Conformation: current variant for 58 CYD core.conformation.Conformation: Found disulfide between residues 52 70 core.conformation.Conformation: current variant for 52 CYS core.conformation.Conformation: current variant for 70 CYS core.conformation.Conformation: current variant for 52 CYD core.conformation.Conformation: current variant for 70 CYD core.conformation.Conformation: Found disulfide between residues 72 83 core.conformation.Conformation: current variant for 72 CYS core.conformation.Conformation: current variant for 83 CYS core.conformation.Conformation: current variant for 72 CYD core.conformation.Conformation: current variant for 83 CYD core.conformation.Conformation: Found disulfide between residues 88 98 core.conformation.Conformation: current variant for 88 CYS core.conformation.Conformation: current variant for 98 CYS core.conformation.Conformation: current variant for 88 CYD core.conformation.Conformation: current variant for 98 CYD core.conformation.Conformation: Found disulfide between residues 93 111 core.conformation.Conformation: current variant for 93 CYS core.conformation.Conformation: current variant for 111 CYS core.conformation.Conformation: current variant for 93 CYD core.conformation.Conformation: current variant for 111 CYD core.conformation.Conformation: Found disulfide between residues 113 127 core.conformation.Conformation: current variant for 113 CYS core.conformation.Conformation: current variant for 127 CYS core.conformation.Conformation: current variant for 113 CYD core.conformation.Conformation: current variant for 127 CYD core.conformation.Conformation: Found disulfide between residues 135 146 core.conformation.Conformation: current variant for 135 CYS core.conformation.Conformation: current variant for 146 CYS core.conformation.Conformation: current variant for 135 CYD core.conformation.Conformation: current variant for 146 CYD core.conformation.Conformation: Found disulfide between residues 139 155 core.conformation.Conformation: current variant for 139 CYS core.conformation.Conformation: current variant for 155 CYS core.conformation.Conformation: current variant for 139 CYD core.conformation.Conformation: current variant for 155 CYD core.conformation.Conformation: Found disulfide between residues 157 170 core.conformation.Conformation: current variant for 157 CYS core.conformation.Conformation: current variant for 170 CYS core.conformation.Conformation: current variant for 157 CYD core.conformation.Conformation: current variant for 170 CYD core.conformation.Conformation: Found disulfide between residues 197 261 core.conformation.Conformation: current variant for 197 CYS core.conformation.Conformation: current variant for 261 CYS core.conformation.Conformation: current variant for 197 CYD core.conformation.Conformation: current variant for 261 CYD core.conformation.Conformation: Found disulfide between residues 307 367 core.conformation.Conformation: current variant for 307 CYS core.conformation.Conformation: current variant for 367 CYS core.conformation.Conformation: current variant for 307 CYD core.conformation.Conformation: current variant for 367 CYD core.conformation.Conformation: Found disulfide between residues 407 481 core.conformation.Conformation: current variant for 407 CYS core.conformation.Conformation: current variant for 481 CYS core.conformation.Conformation: current variant for 407 CYD core.conformation.Conformation: current variant for 481 CYD core.conformation.Conformation: Found disulfide between residues 527 582 core.conformation.Conformation: current variant for 527 CYS core.conformation.Conformation: current variant for 582 CYS core.conformation.Conformation: current variant for 527 CYD core.conformation.Conformation: current variant for 582 CYD protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "grafter" of type AntibodyCDRGrafter core.pack.task.xml_util: Object packrot reading the following task_operations: Adding the following task operations restrict_to_cdrs profiles protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "packrot" of type PackRotamersMover protocols.minimization_packing.MinMover: Found set MoveMap factory. Using this to define MoveMap. core.select.movemap.util: Found MoveMapFactory movemap_cdrs protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "minmover" of type MinMover core.simple_metrics.util: Added simple metric SasaMetric. core.simple_metrics.util: Added simple metric SelectedResiduesPyMOLMetric. core.simple_metrics.util: Added simple metric SequenceMetric. core.simple_metrics.util: Added simple metric SequenceMetric. core.simple_metrics.util: Added simple metric SequenceMetric. core.simple_metrics.util: Added simple metric InteractionEnergyMetric. protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "design_metrics" of type RunSimpleMetrics core.simple_metrics.util: Added simple metric SasaMetric. core.simple_metrics.util: Added simple metric SelectedResiduesPyMOLMetric. core.simple_metrics.util: Added simple metric SequenceMetric. core.simple_metrics.util: Added simple metric SequenceMetric. core.simple_metrics.util: Added simple metric SequenceMetric. core.simple_metrics.util: Added simple metric InteractionEnergyMetric. protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "native_metrics" of type RunSimpleMetrics protocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following movers and filters protocols.rosetta_scripts.ParsedProtocol: added mover "native_metrics" with filter "true_filter" protocols.rosetta_scripts.ParsedProtocol: added mover "grafter" with filter "true_filter" protocols.rosetta_scripts.ParsedProtocol: added mover "dih_mover_L1" with filter "true_filter" protocols.rosetta_scripts.ParsedProtocol: added mover "dih_mover_L2" with filter "true_filter" protocols.rosetta_scripts.ParsedProtocol: added mover "dih_mover_L3" with filter "true_filter" protocols.rosetta_scripts.ParsedProtocol: added mover "packrot" with filter "true_filter" protocols.rosetta_scripts.ParsedProtocol: added mover "minmover" with filter "true_filter" protocols.rosetta_scripts.ParsedProtocol: added mover "packrot" with filter "true_filter" protocols.rosetta_scripts.ParsedProtocol: added mover "minmover" with filter "true_filter" protocols.rosetta_scripts.ParsedProtocol: added mover "design_metrics" with filter "true_filter" protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER RunSimpleMetrics - native_metrics======================= protocols.analysis.simple_metrics.RunSimpleMetricsMover: Running: SasaMetric - calculating sasa basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: SRWGGDGFYAMDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT protocols.analysis.simple_metrics.RunSimpleMetricsMover: Running: SelectedResiduesPyMOLMetric - calculating pymol_selection basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: SRWGGDGFYAMDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT protocols.analysis.simple_metrics.RunSimpleMetricsMover: Running: SequenceMetric - calculating L1_sequence basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: SRWGGDGFYAMDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT protocols.analysis.simple_metrics.RunSimpleMetricsMover: Running: SequenceMetric - calculating L2_sequence basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: SRWGGDGFYAMDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT protocols.analysis.simple_metrics.RunSimpleMetricsMover: Running: SequenceMetric - calculating L3_sequence basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: SRWGGDGFYAMDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT protocols.analysis.simple_metrics.RunSimpleMetricsMover: Running: InteractionEnergyMetric - calculating interaction_energy core.simple_metrics.metrics.InteractionEnergyMetric: [ WARNING ] ################ Cloning pose and Scoring! ############################## core.simple_metrics.metrics.InteractionEnergyMetric: [ WARNING ] Ensure that pose is scored core.simple_metrics.metrics.InteractionEnergyMetric: [ WARNING ] before using InteractionEnergyMetric for maximum performance! core.simple_metrics.metrics.InteractionEnergyMetric: [ WARNING ] ########################################################################## basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: SRWGGDGFYAMDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: SRWGGDGFYAMDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT core.simple_metrics.metrics.InteractionEnergyMetric: core.simple_metrics.metrics.InteractionEnergyMetric: fa_atr 1 core.simple_metrics.metrics.InteractionEnergyMetric: Unweighted: -74.0845 core.simple_metrics.metrics.InteractionEnergyMetric: Weighted: -74.0845 core.simple_metrics.metrics.InteractionEnergyMetric: core.simple_metrics.metrics.InteractionEnergyMetric: fa_rep 0.55 core.simple_metrics.metrics.InteractionEnergyMetric: Unweighted: 11946.9 core.simple_metrics.metrics.InteractionEnergyMetric: Weighted: 6570.79 core.simple_metrics.metrics.InteractionEnergyMetric: core.simple_metrics.metrics.InteractionEnergyMetric: fa_sol 1 core.simple_metrics.metrics.InteractionEnergyMetric: Unweighted: 58.1828 core.simple_metrics.metrics.InteractionEnergyMetric: Weighted: 58.1828 core.simple_metrics.metrics.InteractionEnergyMetric: core.simple_metrics.metrics.InteractionEnergyMetric: lk_ball_wtd 1 core.simple_metrics.metrics.InteractionEnergyMetric: Unweighted: 3.26267 core.simple_metrics.metrics.InteractionEnergyMetric: Weighted: 3.26267 core.simple_metrics.metrics.InteractionEnergyMetric: core.simple_metrics.metrics.InteractionEnergyMetric: fa_elec 1 core.simple_metrics.metrics.InteractionEnergyMetric: Unweighted: -12.7929 core.simple_metrics.metrics.InteractionEnergyMetric: Weighted: -12.7929 core.simple_metrics.metrics.InteractionEnergyMetric: core.simple_metrics.metrics.InteractionEnergyMetric: hbond_bb_sc 1 core.simple_metrics.metrics.InteractionEnergyMetric: Unweighted: -0.53415 core.simple_metrics.metrics.InteractionEnergyMetric: Weighted: -0.53415 protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER AntibodyCDRGrafter - grafter======================= basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: SRWGGDGFYAMDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT protocols.antibody.AntibodyCDRGrafter: Grafting CDR: L1 protocols.grafting.util: Returning 16 residues from 195 to 210 core.conformation.Conformation: Reverting out-of-date disulfide to thiol type at resid 3 protocols.grafting.CCDEndsGraftMover: Start: 891 End: 903 NterO: 3 CterO: 3 protocols.grafting.util: Superimposing overhang residues protocols.grafting.util: Deleting 11 residues from 892 to 902 core.conformation.Conformation: Found disulfide between residues 771 845 core.conformation.Conformation: current variant for 771 CYD core.conformation.Conformation: current variant for 845 CYD core.conformation.Conformation: current variant for 771 CYD core.conformation.Conformation: current variant for 845 CYD core.conformation.Conformation: Found disulfide between residues 891 945 core.conformation.Conformation: current variant for 891 CYD core.conformation.Conformation: current variant for 945 CYD core.conformation.Conformation: current variant for 891 CYD core.conformation.Conformation: current variant for 945 CYD protocols.grafting.util: insert_point 891 protocols.grafting.util: insert_start 892 protocols.grafting.util: insert_end 901 protocols.grafting.util: insert_length 10 protocols.grafting.util: FOLD_TREE EDGE 1 891 -1 EDGE 891 892 1 EDGE 892 964 -1 protocols.grafting.GraftMoverBase: Insertion complete. protocols.grafting.AnchoredGraftMover: Setting default movemap protocols.grafting.CCDEndsGraftMover: Start: 891 protocols.grafting.CCDEndsGraftMover: Original End: 903 protocols.grafting.CCDEndsGraftMover: End: 902 protocols.grafting.CCDEndsGraftMover: Insert Length: 10 basic.io.database: Database file opened: scoring/score_functions/centroid_smooth/cen_smooth_params.txt protocols.grafting.CCDEndsGraftMover: LOOP start: 890 stop: 893 cut: 891 size: 4 skip rate: 0 extended?: False protocols.grafting.CCDEndsGraftMover: protocols.grafting.CCDEndsGraftMover: LOOP start: 900 stop: 903 cut: 901 size: 4 skip rate: 0 extended?: False protocols.grafting.CCDEndsGraftMover: protocols.loops.FoldTreeFromLoopsWrapper: old foldtree FOLD_TREE EDGE 1 891 -1 EDGE 891 902 1 EDGE 902 974 -1 EDGE 891 892 -2 C N EDGE 892 893 -2 C N EDGE 893 894 -2 C N EDGE 894 895 -2 C N EDGE 895 896 -2 C N EDGE 896 897 -2 C N EDGE 897 898 -2 C N EDGE 898 899 -2 C N EDGE 899 900 -2 C N EDGE 900 901 -2 C N New foldtree FOLD_TREE EDGE 1 889 -1 EDGE 889 891 -1 EDGE 889 894 1 EDGE 894 892 -1 EDGE 894 899 -1 EDGE 899 901 -1 EDGE 899 904 2 EDGE 904 902 -1 EDGE 904 974 -1 protocols.grafting.util: Loop: 1 protocols.grafting.util: Add variant to: 891 protocols.grafting.util: Loop: 2 protocols.grafting.util: Add variant to: 901 protocols.grafting.util: idealized 890 protocols.grafting.util: idealized 891 protocols.grafting.util: ideal 892 protocols.grafting.util: idealized 892 protocols.grafting.util: idealized 893 protocols.grafting.util: idealized 900 protocols.grafting.util: idealized 901 protocols.grafting.util: ideal 901 protocols.grafting.util: idealized 902 protocols.grafting.util: idealized 903 core.chemical.GlobalResidueTypeSet: Finished initializing centroid residue type set. Created 62 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.027801 seconds. basic.io.database: Database file opened: scoring/score_functions/disulfides/centroid_distance_score basic.io.database: Database file opened: scoring/score_functions/disulfides/centroid_CaCbCb_angle_score basic.io.database: Database file opened: scoring/score_functions/disulfides/centroid_CaCbCbCa_dihedral_score basic.io.database: Database file opened: scoring/score_functions/disulfides/centroid_backbone_dihedral_score protocols.grafting.CCDEndsGraftMover: start 1661.69 protocols.grafting.CCDEndsGraftMover: round 1 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.60113 max: 1.5 protocols.grafting.CCDEndsGraftMover: 1 1344.14 protocols.grafting.CCDEndsGraftMover: round 2 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.62071 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 3 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.61218 max: 1.5 protocols.grafting.CCDEndsGraftMover: 3 1338.91 protocols.grafting.CCDEndsGraftMover: round 4 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.68362 max: 1.5 protocols.grafting.CCDEndsGraftMover: 4 1320.84 protocols.grafting.CCDEndsGraftMover: round 5 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.76509 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 6 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.65825 max: 1.5 protocols.grafting.CCDEndsGraftMover: 6 1313.39 protocols.grafting.CCDEndsGraftMover: round 7 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.60819 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 8 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.62875 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 9 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.6266 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 10 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.60916 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 11 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.61684 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 12 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.61848 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 13 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.61645 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 14 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.61543 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 15 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.62401 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 16 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.63562 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 17 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.64733 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 18 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.60473 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 19 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.60487 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 20 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.6193 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 21 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.60541 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 22 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.60568 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 23 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.62672 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 24 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.5793 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 25 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.5867 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 26 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.59485 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 27 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.64499 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 28 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.61149 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 29 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.63725 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 30 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.61434 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 31 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.6164 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 32 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.6038 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 33 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.61122 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 34 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.59831 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 35 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.59755 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 36 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.60123 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 37 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.59705 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 38 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.61627 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 39 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.61896 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 40 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.60807 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 41 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.60502 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 42 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.62934 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 43 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.62077 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 44 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.61599 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 45 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.6229 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 46 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.61137 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 47 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.57139 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 48 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.5991 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 49 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.6038 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 50 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.60968 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 51 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.58477 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 52 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.56761 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 53 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.63019 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 54 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.59919 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 55 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.62732 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 56 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.64698 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 57 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.61982 max: 1.5 protocols.grafting.CCDEndsGraftMover: 57 1312.52 protocols.grafting.CCDEndsGraftMover: round 58 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.60883 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 59 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.59947 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 60 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.63073 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 61 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.60254 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 62 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.61244 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 63 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.61427 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 64 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.62712 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 65 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.61469 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 66 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.60174 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 67 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.61892 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 68 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.62348 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 69 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.62007 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 70 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.62511 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 71 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.5895 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 72 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.60284 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 73 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.59508 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 74 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.58678 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 75 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.63562 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 76 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.59452 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 77 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.62141 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 78 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.6158 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 79 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.60115 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 80 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.61093 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 81 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.61939 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 82 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.60062 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 83 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.60587 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 84 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.59995 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 85 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.61391 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 86 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.60314 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 87 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.61951 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 88 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.61404 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 89 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.61096 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 90 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.59714 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 91 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.61394 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 92 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.61956 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 93 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.59923 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 94 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.61766 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 95 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.59173 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 96 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.6177 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 97 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.6377 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 98 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.61976 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 99 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.61219 max: 1.5 protocols.grafting.CCDEndsGraftMover: round 100 protocols.loops.util: PepBondGeom: 42 L C-N -- 1.58123 max: 1.5 protocols.grafting.CCDEndsGraftMover: finish 1312.52 core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 151 rotamers at 19 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph protocols.loops.util: PepBondGeom: 42 L C-N -- 1.61982 max: 1.5 protocols.grafting.CCDEndsGraftMover: Graft meets ideal geometry false protocols.grafting.CCDEndsGraftMover: Complete protocols.antibody.AntibodyCDRGrafter: Checking Geometry protocols.loops.util: PepBondGeom: 42 L C-N -- 1.61982 max: 1.5 protocols.antibody.AntibodyCDRGrafter: Graft not fully closed. Using secondary graft mover protocols.grafting.util: Deleting 11 residues from 892 to 902 core.conformation.Conformation: Found disulfide between residues 771 845 core.conformation.Conformation: current variant for 771 CYD core.conformation.Conformation: current variant for 845 CYD core.conformation.Conformation: current variant for 771 CYD core.conformation.Conformation: current variant for 845 CYD core.conformation.Conformation: Found disulfide between residues 891 945 core.conformation.Conformation: current variant for 891 CYD core.conformation.Conformation: current variant for 945 CYD core.conformation.Conformation: current variant for 891 CYD core.conformation.Conformation: current variant for 945 CYD protocols.grafting.util: insert_point 891 protocols.grafting.util: insert_start 892 protocols.grafting.util: insert_end 901 protocols.grafting.util: insert_length 10 protocols.grafting.util: FOLD_TREE EDGE 1 891 -1 EDGE 891 892 1 EDGE 892 964 -1 protocols.grafting.GraftMoverBase: Insertion complete. protocols.grafting.AnchoredGraftMover: Setting default movemap protocols.grafting.util: FOLD_TREE EDGE 1 889 -1 EDGE 889 902 -1 EDGE 889 904 1 EDGE 904 903 -1 EDGE 904 974 -1 protocols.grafting.AnchoredGraftMover: Loops: LOOP begin end cut skip_rate extended protocols.grafting.AnchoredGraftMover: LOOP start: 890 stop: 903 cut: 902 size: 14 skip rate: 0 extended?: False protocols.grafting.AnchoredGraftMover: protocols.grafting.AnchoredGraftMover: protocols.grafting.util: Loop: 1 protocols.grafting.util: Add variant to: 902 protocols.grafting.util: idealized 890 protocols.grafting.util: idealized 891 protocols.grafting.util: ideal 892 protocols.grafting.util: idealized 892 protocols.grafting.util: idealized 893 protocols.grafting.util: idealized 900 protocols.grafting.util: idealized 901 protocols.grafting.util: ideal 901 protocols.grafting.util: idealized 902 protocols.grafting.util: idealized 903 protocols.grafting.AnchoredGraftMover: start 3382.37 protocols.grafting.AnchoredGraftMover: round 1 core.optimization.LineMinimizer: [ ERROR ] Inaccurate G! step= 1.90735e-06 Deriv= -12.3575 Finite Diff= 4.77606 protocols.loops.util: PepBondGeom: 902 - 43 L Ca-C-N -- 99.5 (min): 139.257 : 134.5 (max) protocols.grafting.AnchoredGraftMover: 1 1395.71 protocols.grafting.AnchoredGraftMover: round 2 protocols.grafting.AnchoredGraftMover: Graft Closed early - returning protocols.grafting.AnchoredGraftMover: 2 1299.88 protocols.grafting.AnchoredGraftMover: finish 1299.88 core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 151 rotamers at 19 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph protocols.grafting.AnchoredGraftMover: Graft meets ideal geometry true protocols.grafting.AnchoredGraftMover: Complete protocols.antibody.AntibodyCDRGrafter: Checking Geometry antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT protocols.antibody.AntibodyCDRGrafter: Grafting CDR: L2 protocols.grafting.util: Returning 14 residues from 219 to 232 protocols.grafting.CCDEndsGraftMover: Start: 915 End: 924 NterO: 3 CterO: 3 protocols.grafting.util: Superimposing overhang residues protocols.grafting.util: Deleting 8 residues from 916 to 923 core.conformation.Conformation: Found disulfide between residues 771 845 core.conformation.Conformation: current variant for 771 CYD core.conformation.Conformation: current variant for 845 CYD core.conformation.Conformation: current variant for 771 CYD core.conformation.Conformation: current variant for 845 CYD core.conformation.Conformation: Reverting out-of-date disulfide to thiol type at resid 891 core.conformation.Conformation: Reverting out-of-date disulfide to thiol type at resid 947 protocols.grafting.util: insert_point 915 protocols.grafting.util: insert_start 916 protocols.grafting.util: insert_end 923 protocols.grafting.util: insert_length 8 protocols.grafting.util: FOLD_TREE EDGE 1 915 -1 EDGE 915 916 1 EDGE 916 966 -1 protocols.grafting.GraftMoverBase: Insertion complete. protocols.grafting.AnchoredGraftMover: Setting default movemap protocols.grafting.CCDEndsGraftMover: Start: 915 protocols.grafting.CCDEndsGraftMover: Original End: 924 protocols.grafting.CCDEndsGraftMover: End: 924 protocols.grafting.CCDEndsGraftMover: Insert Length: 8 protocols.grafting.CCDEndsGraftMover: LOOP start: 914 stop: 917 cut: 915 size: 4 skip rate: 0 extended?: False protocols.grafting.CCDEndsGraftMover: protocols.grafting.CCDEndsGraftMover: LOOP start: 922 stop: 925 cut: 923 size: 4 skip rate: 0 extended?: False protocols.grafting.CCDEndsGraftMover: protocols.loops.FoldTreeFromLoopsWrapper: old foldtree FOLD_TREE EDGE 1 915 -1 EDGE 915 924 1 EDGE 924 974 -1 EDGE 915 916 -2 C N EDGE 916 917 -2 C N EDGE 917 918 -2 C N EDGE 918 919 -2 C N EDGE 919 920 -2 C N EDGE 920 921 -2 C N EDGE 921 922 -2 C N EDGE 922 923 -2 C N New foldtree FOLD_TREE EDGE 1 913 -1 EDGE 913 915 -1 EDGE 913 918 1 EDGE 918 916 -1 EDGE 918 921 -1 EDGE 921 923 -1 EDGE 921 926 2 EDGE 926 924 -1 EDGE 926 974 -1 protocols.grafting.util: Loop: 1 protocols.grafting.util: Add variant to: 915 protocols.grafting.util: Loop: 2 protocols.grafting.util: Add variant to: 923 protocols.grafting.util: idealized 914 protocols.grafting.util: idealized 915 protocols.grafting.util: ideal 916 protocols.grafting.util: idealized 916 protocols.grafting.util: idealized 917 protocols.grafting.util: idealized 922 protocols.grafting.util: idealized 923 protocols.grafting.util: ideal 923 protocols.grafting.util: idealized 924 protocols.grafting.util: idealized 925 protocols.grafting.CCDEndsGraftMover: start 1712.66 protocols.grafting.CCDEndsGraftMover: round 1 protocols.loops.util: PepBondGeom: 923 - 72 L Ca-C-N -- 99.5 (min): 147.941 : 134.5 (max) protocols.grafting.CCDEndsGraftMover: 1 1351.45 protocols.grafting.CCDEndsGraftMover: round 2 protocols.grafting.CCDEndsGraftMover: Graft Closed early - returning protocols.grafting.CCDEndsGraftMover: 2 1256.39 protocols.grafting.CCDEndsGraftMover: finish 1256.39 core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 148 rotamers at 14 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph protocols.grafting.CCDEndsGraftMover: Graft meets ideal geometry true protocols.grafting.CCDEndsGraftMover: Complete protocols.antibody.AntibodyCDRGrafter: Checking Geometry protocols.antibody.AntibodyCDRGrafter: Success. Graft closed. antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT protocols.antibody.AntibodyCDRGrafter: Grafting CDR: L3 protocols.grafting.util: Returning 15 residues from 259 to 273 core.conformation.Conformation: Reverting out-of-date disulfide to thiol type at resid 3 protocols.grafting.CCDEndsGraftMover: Start: 955 End: 965 NterO: 3 CterO: 3 protocols.grafting.util: Superimposing overhang residues protocols.grafting.util: Deleting 9 residues from 956 to 964 core.conformation.Conformation: Found disulfide between residues 771 845 core.conformation.Conformation: current variant for 771 CYD core.conformation.Conformation: current variant for 845 CYD core.conformation.Conformation: current variant for 771 CYD core.conformation.Conformation: current variant for 845 CYD protocols.grafting.util: insert_point 955 protocols.grafting.util: insert_start 956 protocols.grafting.util: insert_end 964 protocols.grafting.util: insert_length 9 protocols.grafting.util: FOLD_TREE EDGE 1 955 -1 EDGE 955 956 1 EDGE 956 965 -1 protocols.grafting.GraftMoverBase: Insertion complete. protocols.grafting.AnchoredGraftMover: Setting default movemap protocols.grafting.CCDEndsGraftMover: Start: 955 protocols.grafting.CCDEndsGraftMover: Original End: 965 protocols.grafting.CCDEndsGraftMover: End: 965 protocols.grafting.CCDEndsGraftMover: Insert Length: 9 protocols.grafting.CCDEndsGraftMover: LOOP start: 954 stop: 957 cut: 955 size: 4 skip rate: 0 extended?: False protocols.grafting.CCDEndsGraftMover: protocols.grafting.CCDEndsGraftMover: LOOP start: 963 stop: 966 cut: 964 size: 4 skip rate: 0 extended?: False protocols.grafting.CCDEndsGraftMover: protocols.loops.FoldTreeFromLoopsWrapper: old foldtree FOLD_TREE EDGE 1 955 -1 EDGE 955 965 1 EDGE 965 974 -1 EDGE 955 956 -2 C N EDGE 956 957 -2 C N EDGE 957 958 -2 C N EDGE 958 959 -2 C N EDGE 959 960 -2 C N EDGE 960 961 -2 C N EDGE 961 962 -2 C N EDGE 962 963 -2 C N EDGE 963 964 -2 C N New foldtree FOLD_TREE EDGE 1 953 -1 EDGE 953 955 -1 EDGE 953 958 1 EDGE 958 956 -1 EDGE 958 962 -1 EDGE 962 964 -1 EDGE 962 967 2 EDGE 967 965 -1 EDGE 967 974 -1 protocols.grafting.util: Loop: 1 protocols.grafting.util: Add variant to: 955 protocols.grafting.util: Loop: 2 protocols.grafting.util: Add variant to: 964 protocols.grafting.util: idealized 954 protocols.grafting.util: idealized 955 protocols.grafting.util: ideal 956 protocols.grafting.util: idealized 956 protocols.grafting.util: idealized 957 protocols.grafting.util: idealized 963 protocols.grafting.util: idealized 964 protocols.grafting.util: ideal 964 protocols.grafting.util: idealized 965 protocols.grafting.util: idealized 966 protocols.grafting.CCDEndsGraftMover: start 1638.41 protocols.grafting.CCDEndsGraftMover: round 1 protocols.grafting.CCDEndsGraftMover: Graft Closed early - returning protocols.grafting.CCDEndsGraftMover: 1 1265.74 protocols.grafting.CCDEndsGraftMover: finish 1265.74 core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 146 rotamers at 19 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph protocols.grafting.CCDEndsGraftMover: Graft meets ideal geometry true protocols.grafting.CCDEndsGraftMover: Complete protocols.antibody.AntibodyCDRGrafter: Checking Geometry protocols.antibody.AntibodyCDRGrafter: Success. Graft closed. antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER CDRDihedralConstraintMover - dih_mover_L1======================= basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: SRWGGDGFYAMDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT protocols.antibody.constraints.CDRDihedralConstraintMover: L1-10-1 data: 42 cutoff: 10 core.scoring.constraints.ConstraintsIO: read constraints from /Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/pyrosetta-2019.33+release.1e60c63beb5-py3.6-macosx-10.6-intel.egg/pyrosetta/database/sampling/antibodies/cluster_based_constraints/CircularHarmonic/outliers_false_liberal_use_means/L1-10-1.txt core.scoring.constraints.ConstraintsIO: Read in 20 constraints protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER CDRDihedralConstraintMover - dih_mover_L2======================= basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: SRWGGDGFYAMDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT protocols.antibody.constraints.CDRDihedralConstraintMover: L2-8-1 data: 632 cutoff: 10 core.scoring.constraints.ConstraintsIO: read constraints from /Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/pyrosetta-2019.33+release.1e60c63beb5-py3.6-macosx-10.6-intel.egg/pyrosetta/database/sampling/antibodies/cluster_based_constraints/CircularHarmonic/outliers_false_liberal_use_means/L2-8-1.txt core.scoring.constraints.ConstraintsIO: Read in 16 constraints protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER CDRDihedralConstraintMover - dih_mover_L3======================= basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: SRWGGDGFYAMDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT protocols.antibody.constraints.CDRDihedralConstraintMover: L3-9-cis7-1 data: 419 cutoff: 10 core.scoring.constraints.ConstraintsIO: read constraints from /Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/pyrosetta-2019.33+release.1e60c63beb5-py3.6-macosx-10.6-intel.egg/pyrosetta/database/sampling/antibodies/cluster_based_constraints/CircularHarmonic/outliers_false_liberal_use_means/L3-9-cis7-1.txt core.scoring.constraints.ConstraintsIO: Read in 18 constraints protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER PackRotamersMover - packrot======================= basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: SRWGGDGFYAMDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: SRWGGDGFYAMDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT basic.io.database: [ WARNING ] Unable to locate database file /sampling/antibodies/antibody_database_rosetta_design.db antibody.database.AntibodyDatabaseManager: Reading from: /Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/pyrosetta-2019.33+release.1e60c63beb5-py3.6-macosx-10.6-intel.egg/pyrosetta/database//sampling/antibodies/antibody_database_rosetta_design_north_paper.db antibody.database.AntibodyDatabaseManager: Loaded L1-10-1 with 15 datapoints. antibody.database.AntibodyDatabaseManager: Loaded L2-8-1 with 153 datapoints. antibody.database.AntibodyDatabaseManager: Loaded L3-9-cis7-1 with 179 datapoints. protocols.antibody.task_operations.AddCDRProfilesOperation: applying prob task op core.pack.pack_rotamers: built 5062 rotamers at 61 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER MinMover - minmover======================= basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: SRWGGDGFGGMDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 protocols.rosetta_scripts.ParsedProtocol: [ ERROR ] Exception while processing procotol: File: /Volumes/MacintoshHD3/benchmark/W.fujii.release/rosetta.Fujii.release/_commits_/main/source/src/core/optimization/CartesianMinimizer.cc:66 [ ERROR ] UtilityExitException ERROR: Scorefunction not set up for nonideal/Cartesian scoring
--------------------------------------------------------------------------- RuntimeError Traceback (most recent call last) <ipython-input-39-59f74abbd00f> in <module>() 2 parser = RosettaScriptsParser() 3 protocol = parser.generate_mover_and_apply_to_pose(pose, "inputs/rabd/ab_design_components.xml") ----> 4 protocol.apply(pose) RuntimeError: File: /Volumes/MacintoshHD3/benchmark/W.fujii.release/rosetta.Fujii.release/_commits_/main/source/src/core/optimization/CartesianMinimizer.cc:66 [ ERROR ] UtilityExitException ERROR: Scorefunction not set up for nonideal/Cartesian scoring
If you want a challenge - try to set these up in-code without RosettaScripts. It can be tricky - which is why I made PyRosetta finally work optionally with RosettaScripts. Its good to know how to use both.
### BEGIN SOLUTION
from rosetta.protocols.antibody.residue_selector import *
from rosetta.protocols.antibody.task_operations import *
from rosetta.protocols.antibody.constraints import *
from rosetta.protocols.antibody import *
from rosetta.core.simple_metrics.metrics import *
from rosetta.core.simple_metrics.per_residue_metrics import *
from rosetta.core.select.movemap import *
from rosetta.protocols.analysis.simple_metrics import RunSimpleMetricsMover
from rosetta.core.pack.task import *
####################
## Clone our pose ##
####################
pose = original_pose.clone()
ab_info = AntibodyInfo(pose)
#########################################################
## Setup Scorefunction since we are not using cmd-line ##
#########################################################
cart = create_score_function("ref2015_cart")
#############################
## Setup Residue Selectors ##
#############################
#1 <CDR name="light_cdrs" cdrs="L1,L2,L3" />
#2 <CDR name="L1" cdrs="L1"/>
#3 <CDR name="L2" cdrs="L2"/>
#4 <CDR name="L3" cdrs="L3"/>
#5 <AntibodyRegion name="antigen" region="antigen_region" />
#6 <AntibodyRegion name="framework" region="framework_region" />
#7 <AntibodyRegion name="cdrs" region="cdr_region" />
#1 <CDR name="light_cdrs"
light_sele = CDRResidueSelector()
light_list = vector1_protocols_antibody_CDRNameEnum()
[light_list.append(x) for x in [l1, l2, l3]]
light_sele.set_cdrs(light_list)
#2 <CDR name="L1"
l1_sele = CDRResidueSelector()
l1_sele.set_cdr(l1)
#3 <CDR name="L2"
l2_sele = CDRResidueSelector()
l2_sele.set_cdr(l2)
#4 <CDR name="L3"
l3_sele = CDRResidueSelector()
l3_sele.set_cdr(l3)
#5 <AntibodyRegion name="antigen"
antigen_sele = AntibodyRegionSelector()
antigen_sele.set_region(antigen_region)
#6 <AntibodyRegion name="framework"
framework_sele = AntibodyRegionSelector()
framework_sele.set_region(framework_region)
#7 <AntibodyRegion name="cdrs"
cdrs_sele = AntibodyRegionSelector()
cdrs_sele.set_region(cdr_region)
##########################
## Setup Simple Metrics ##
##########################
#1 <SasaMetric name="sasa" residue_selector="light_cdrs" />
#2 <SelectedResiduesPyMOLMetric name="cdr_selection" residue_selector="light_cdrs" />
#3 <SequenceMetric name="L1_seq" residue_selector="L1" custom_type="L1"/>
#4 <SequenceMetric name="L2_seq" residue_selector="L2" custom_type="L2"/>
#4 <SequenceMetric name="L3_seq" residue_selector="L3" custom_type="L3"/>
#5 <InteractionEnergyMetric name="cdr-int" residue_selector="light_cdrs" residue_selector2="antigen" />
#1 <SasaMetric name="sasa"
sasa = SasaMetric(light_sele)
#2 <SelectedResiduesPyMOLMetric name="cdr_selection"
cdr_selection = SelectedResiduesPyMOLMetric(light_sele)
L1_seq = SequenceMetric(l1_sele)
L1_seq.set_custom_type("L1")
#3 <SequenceMetric name="L1_seq"
L2_seq = SequenceMetric(l2_sele)
L2_seq.set_custom_type("L2")
#4 <SequenceMetric name="L2_seq"
L3_seq = SequenceMetric(l3_sele)
L3_seq.set_custom_type("L3")
#5 <InteractionEnergyMetric name="cdr-int"
cdr_int = InteractionEnergyMetric(light_sele, antigen_sele)
cdr_int.set_scorefunction(cart)
##########################
## Setup TaskOperations ##
##########################
#1 <RestrictToCDRsAndNeighbors name="restrict_to_cdrs" cdrs="L1,L2,L3" design_framework="1" design_cdrs="1"/>
#2 <AddCDRProfilesOperation name="profiles" cdrs="L1,L2,L3" fallback_strategy="CONSERVATIVE" />
light_vec_bool = vector1_bool(6)
light_vec_bool[l1] = True
light_vec_bool[l2] = True
light_vec_bool[l3] = True
#1 <RestrictToCDRsAndNeighbors name="restrict_to_cdrs"
restrict_to_cdrs = RestrictToCDRsAndNeighbors()
restrict_to_cdrs.set_cdrs(light_vec_bool)
restrict_to_cdrs.set_allow_design_neighbor_framework(True)
restrict_to_cdrs.set_allow_design_cdr(True)
#2 <AddCDRProfilesOperation name="profiles"
profiles = AddCDRProfilesOperation()
profiles.set_cdrs(light_vec_bool)
profiles.set_fallback_strategy(design.seq_design_conservative)
##########################
## Setup MovemapFactory ##
##########################
#1 <MoveMapFactory name="movemap_cdrs" bb="0" chi="0">
#1 <Backbone residue_selector="light_cdrs" />
#1 <Chi residue_selector="light_cdrs" />
#1 </MoveMapFactory>
#1
mmf = MoveMapFactory()
mmf.all_bb(False) #First, disable everything, then enable from actions.
mmf.all_chi(False)
mmf.add_bb_action(mm_enable, light_sele)
mmf.add_chi_action(mm_enable, light_sele)
mmf.set_cartesian(True)
##################
## Setup Movers ##
##################
#1 <CDRDihedralConstraintMover name="dih_mover_L1" cdr="L1" use_cluster_csts="1" />
#2 <CDRDihedralConstraintMover name="dih_mover_L2" cdr="L2" use_cluster_csts="1" />
#3 <CDRDihedralConstraintMover name="dih_mover_L3" cdr="L3" use_cluster_csts="1" />
#4 <AntibodyCDRGrafter name="grafter" cdrs="L1,L2,L3" input_ab_scheme="AHO_Scheme" cdr_definition="North" donor_structure_from_pdb="malaria_cdrs.pdb" use_secondary_graft_mover="1" optimize_cdrs="0" optimize_cdr4_if_neighbor="1" />
#5 <PackRotamersMover name="packrot" task_operations="restrict_to_cdrs,profiles" />
# Minimize Light chain CDRs using the MoveMapFactory. We do it in cartesian to prevent lever-arm effects
#6 <MinMover name="minmover" cartesian="1" movemap_factory="movemap_cdrs" tolerance=".1"/>
# Run our metrics
#7 <RunSimpleMetrics name="design_metrics" metrics="sasa,cdr_selection,L1_seq,L2_seq,L3_seq,cdr-int" prefix="design_" />
#8 <RunSimpleMetrics name="native_metrics" metrics="sasa,cdr_selection,L1_seq,L2_seq,L3_seq,cdr-int" prefix="native_" />
#1 <CDRDihedralConstraintMover name="dih_mover_L1"
dih_csts_l1 = CDRDihedralConstraintMover()
dih_csts_l1.set_cdr(l1)
#2 <CDRDihedralConstraintMover name="dih_mover_L2"
dih_csts_l2 = CDRDihedralConstraintMover()
dih_csts_l2.set_cdr(l2)
#3 <CDRDihedralConstraintMover name="dih_mover_L3"
dih_csts_l3 = CDRDihedralConstraintMover()
dih_csts_l3.set_cdr(l3)
#4 <AntibodyCDRGrafter name="grafter"
new_pose = pose_from_pdb("malaria_cdrs.pdb")
grafter = AntibodyCDRGrafter(ab_info)
grafter.set_donor_structure(new_pose)
grafter.set_cdrs(light_vec_bool)
grafter.set_use_secondary_graft_mover_if_needed(True)
grafter.set_optimize_cdrs(False)
grafter.set_include_cdr4_in_optimization(True)
#5 <PackRotamersMover name="packrot"
tf = TaskFactory()
tf.push_back(restrict_to_cdrs)
tf.push_back(profiles)
packer = PackRotamersMover()
packer.task_factory(tf)
packer.score_function(cart)
#6 <MinMover name="minmover"
minmover = MinMover()
minmover.cartesian(True)
minmover.movemap_factory(mmf)
minmover.tolerance(.1)
minmover.score_function(cart)
#7 <RunSimpleMetrics name="design_metrics" metrics="sasa,cdr_selection,L1_seq,L2_seq,L3_seq,cdr-int"
metrics = [sasa, cdr_selection, L1_seq, L2_seq, L3_seq, cdr_int]
design_metrics = RunSimpleMetricsMover()
design_metrics.set_prefix("design_")
[design_metrics.add_simple_metric(metric) for metric in metrics] #Save a few lines as the vector1 for metrics is not yet bound to PyRosetta.
#8 <RunSimpleMetrics name="native_metrics" metrics="sasa,cdr_selection,L1_seq,L2_seq,L3_seq,cdr-int"
native_metrics = RunSimpleMetricsMover()
native_metrics.set_prefix("native_")
[native_metrics.add_simple_metric(metric) for metric in metrics]
######################
## Run The Protocol ##
######################
#You also use a MoverContainer from previous tutorials here if you wanted to.
#1 Run Metrics on the native antibody
# <Add mover_name="native_metrics" />
#2 Graft Light chain CDRs from our donor into our current antibody.
# <Add mover_name="grafter" />
#3 Add Constraints to the CDRs so that min doesn't change them too much
# <Add mover_name="dih_mover_L1" />
# <Add mover_name="dih_mover_L2" />
# <Add mover_name="dih_mover_L3" />
#4 Design framework around light chain to accomodate the grafted CDRs. Pack/Min/Pack
# <Add mover_name="packrot" />
# <Add mover_name="minmover" />
# <Add mover_name="packrot" />
# <Add mover_name="minmover" />
#5 Run Simple Metrics on the result
# <Add mover_name="design_metrics" />
if not os.getenv("DEBUG"):
#1 Run Metrics on the native antibody
native_metrics.apply(pose)
#2 Graft Light chain CDRs from our donor into our current antibody.
grafter.apply(pose)
#3 Add Constraints to the CDRs so that min doesn't change them too much
dih_csts_l1.apply(pose)
dih_csts_l2.apply(pose)
dih_csts_l3.apply(pose)
#4 Design framework around light chain to accomodate the grafted CDRs. Pack/Min/Pack
packer.apply(pose)
minmover.apply(pose)
packer.apply(pose)
minmover.apply(pose)
#5 Run Simple Metrics on the result
design_metrics.apply(pose)
### END SOLUTION
basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: SRWGGDGFYAMDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT core.scoring.etable: Starting energy table calculation core.scoring.etable: smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: Finished calculating energy tables. basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop core.scoring.CartesianBondedEnergy: Initializing IdealParametersDatabase with default Ks=300 , 80 , 20 , 10 , 40 basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-lengths.txt core.scoring.CartesianBondedEnergy: Read 757 bb-independent lengths. basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-angles.txt core.scoring.CartesianBondedEnergy: Read 1456 bb-independent angles. basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-torsions.txt core.scoring.CartesianBondedEnergy: Read 1 bb-independent torsions. basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-improper.txt core.scoring.CartesianBondedEnergy: Read 2216 bb-independent improper tors. core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 protocols.task_operations.ConservativeDesignOperation: Loading conservative mutational data core.import_pose.import_pose: File 'malaria_cdrs.pdb' automatically determined to be of type PDB core.io.pdb.pdb_reader: Parsing 0 .pdb records with unknown format to search for Rosetta-specific comments. core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue CYS:CtermProteinFull 387 core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ASP:CtermProteinFull 601 core.conformation.Conformation: Found disulfide between residues 8 22 core.conformation.Conformation: current variant for 8 CYS core.conformation.Conformation: current variant for 22 CYS core.conformation.Conformation: current variant for 8 CYD core.conformation.Conformation: current variant for 22 CYD core.conformation.Conformation: Found disulfide between residues 24 36 core.conformation.Conformation: current variant for 24 CYS core.conformation.Conformation: current variant for 36 CYS core.conformation.Conformation: current variant for 24 CYD core.conformation.Conformation: current variant for 36 CYD core.conformation.Conformation: Found disulfide between residues 43 58 core.conformation.Conformation: current variant for 43 CYS core.conformation.Conformation: current variant for 58 CYS core.conformation.Conformation: current variant for 43 CYD core.conformation.Conformation: current variant for 58 CYD core.conformation.Conformation: Found disulfide between residues 52 70 core.conformation.Conformation: current variant for 52 CYS core.conformation.Conformation: current variant for 70 CYS core.conformation.Conformation: current variant for 52 CYD core.conformation.Conformation: current variant for 70 CYD core.conformation.Conformation: Found disulfide between residues 72 83 core.conformation.Conformation: current variant for 72 CYS core.conformation.Conformation: current variant for 83 CYS core.conformation.Conformation: current variant for 72 CYD core.conformation.Conformation: current variant for 83 CYD core.conformation.Conformation: Found disulfide between residues 88 98 core.conformation.Conformation: current variant for 88 CYS core.conformation.Conformation: current variant for 98 CYS core.conformation.Conformation: current variant for 88 CYD core.conformation.Conformation: current variant for 98 CYD core.conformation.Conformation: Found disulfide between residues 93 111 core.conformation.Conformation: current variant for 93 CYS core.conformation.Conformation: current variant for 111 CYS core.conformation.Conformation: current variant for 93 CYD core.conformation.Conformation: current variant for 111 CYD core.conformation.Conformation: Found disulfide between residues 113 127 core.conformation.Conformation: current variant for 113 CYS core.conformation.Conformation: current variant for 127 CYS core.conformation.Conformation: current variant for 113 CYD core.conformation.Conformation: current variant for 127 CYD core.conformation.Conformation: Found disulfide between residues 135 146 core.conformation.Conformation: current variant for 135 CYS core.conformation.Conformation: current variant for 146 CYS core.conformation.Conformation: current variant for 135 CYD core.conformation.Conformation: current variant for 146 CYD core.conformation.Conformation: Found disulfide between residues 139 155 core.conformation.Conformation: current variant for 139 CYS core.conformation.Conformation: current variant for 155 CYS core.conformation.Conformation: current variant for 139 CYD core.conformation.Conformation: current variant for 155 CYD core.conformation.Conformation: Found disulfide between residues 157 170 core.conformation.Conformation: current variant for 157 CYS core.conformation.Conformation: current variant for 170 CYS core.conformation.Conformation: current variant for 157 CYD core.conformation.Conformation: current variant for 170 CYD core.conformation.Conformation: Found disulfide between residues 197 261 core.conformation.Conformation: current variant for 197 CYS core.conformation.Conformation: current variant for 261 CYS core.conformation.Conformation: current variant for 197 CYD core.conformation.Conformation: current variant for 261 CYD core.conformation.Conformation: Found disulfide between residues 307 367 core.conformation.Conformation: current variant for 307 CYS core.conformation.Conformation: current variant for 367 CYS core.conformation.Conformation: current variant for 307 CYD core.conformation.Conformation: current variant for 367 CYD core.conformation.Conformation: Found disulfide between residues 407 481 core.conformation.Conformation: current variant for 407 CYS core.conformation.Conformation: current variant for 481 CYS core.conformation.Conformation: current variant for 407 CYD core.conformation.Conformation: current variant for 481 CYD core.conformation.Conformation: Found disulfide between residues 527 582 core.conformation.Conformation: current variant for 527 CYS core.conformation.Conformation: current variant for 582 CYS core.conformation.Conformation: current variant for 527 CYD core.conformation.Conformation: current variant for 582 CYD protocols.analysis.simple_metrics.RunSimpleMetricsMover: Running: SasaMetric - calculating sasa basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: SRWGGDGFYAMDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT protocols.analysis.simple_metrics.RunSimpleMetricsMover: Running: SelectedResiduesPyMOLMetric - calculating pymol_selection basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: SRWGGDGFYAMDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT protocols.analysis.simple_metrics.RunSimpleMetricsMover: Running: SequenceMetric - calculating L1_sequence basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: SRWGGDGFYAMDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT protocols.analysis.simple_metrics.RunSimpleMetricsMover: Running: SequenceMetric - calculating L2_sequence basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: SRWGGDGFYAMDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT protocols.analysis.simple_metrics.RunSimpleMetricsMover: Running: SequenceMetric - calculating L3_sequence basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: SRWGGDGFYAMDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT protocols.analysis.simple_metrics.RunSimpleMetricsMover: Running: InteractionEnergyMetric - calculating interaction_energy core.scoring.CartesianBondedEnergy: Creating new peptide-bonded energy container (975) basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat core.scoring.elec.util: Read 40 countpair representative atoms core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true. core.pack.dunbrack.RotamerLibrary: shapovalov_lib::shap_dun10_smooth_level of 1( aka lowest_smooth ) got activated. core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /Users/jadolfbr/Library/Python/3.6/lib/python/site-packages/pyrosetta-2019.39+release.93456a567a8-py3.6-macosx-10.6-intel.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/Users/jadolfbr/Library/Python/3.6/lib/python/site-packages/pyrosetta-2019.39+release.93456a567a8-py3.6-macosx-10.6-intel.egg/pyrosetta/database/rotamer/shapovalov/StpDwn_0-0-0/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.252145 seconds to load from binary core.simple_metrics.metrics.InteractionEnergyMetric: [ WARNING ] ################ Cloning pose and Scoring! ############################## core.simple_metrics.metrics.InteractionEnergyMetric: [ WARNING ] Ensure that pose is scored core.simple_metrics.metrics.InteractionEnergyMetric: [ WARNING ] before using InteractionEnergyMetric for maximum performance! core.simple_metrics.metrics.InteractionEnergyMetric: [ WARNING ] ########################################################################## basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: SRWGGDGFYAMDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: SRWGGDGFYAMDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 11 Omega: TTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT core.simple_metrics.metrics.InteractionEnergyMetric: core.simple_metrics.metrics.InteractionEnergyMetric: fa_atr 1 core.simple_metrics.metrics.InteractionEnergyMetric: Unweighted: -35.7698 core.simple_metrics.metrics.InteractionEnergyMetric: Weighted: -35.7698 core.simple_metrics.metrics.InteractionEnergyMetric: core.simple_metrics.metrics.InteractionEnergyMetric: fa_rep 0.55 core.simple_metrics.metrics.InteractionEnergyMetric: Unweighted: 5415.79 core.simple_metrics.metrics.InteractionEnergyMetric: Weighted: 2978.68 core.simple_metrics.metrics.InteractionEnergyMetric: core.simple_metrics.metrics.InteractionEnergyMetric: fa_sol 1 core.simple_metrics.metrics.InteractionEnergyMetric: Unweighted: 34.2565 core.simple_metrics.metrics.InteractionEnergyMetric: Weighted: 34.2565 core.simple_metrics.metrics.InteractionEnergyMetric: core.simple_metrics.metrics.InteractionEnergyMetric: lk_ball_wtd 1 core.simple_metrics.metrics.InteractionEnergyMetric: Unweighted: 2.8777 core.simple_metrics.metrics.InteractionEnergyMetric: Weighted: 2.8777 core.simple_metrics.metrics.InteractionEnergyMetric: core.simple_metrics.metrics.InteractionEnergyMetric: fa_elec 1 core.simple_metrics.metrics.InteractionEnergyMetric: Unweighted: -8.73098 core.simple_metrics.metrics.InteractionEnergyMetric: Weighted: -8.73098 core.scoring.ScoreFunctionFactory: SCOREFUNCTION: ref2015 protocols.antibody.AntibodyCDRGrafter: Grafting CDR: L1 protocols.grafting.util: Returning 16 residues from 195 to 210 core.conformation.Conformation: Reverting out-of-date disulfide to thiol type at resid 3 protocols.grafting.CCDEndsGraftMover: Start: 891 End: 903 NterO: 3 CterO: 3 protocols.grafting.util: Superimposing overhang residues protocols.grafting.util: Deleting 11 residues from 892 to 902 core.conformation.Conformation: Found disulfide between residues 771 845 core.conformation.Conformation: current variant for 771 CYD core.conformation.Conformation: current variant for 845 CYD core.conformation.Conformation: current variant for 771 CYD core.conformation.Conformation: current variant for 845 CYD core.conformation.Conformation: Found disulfide between residues 891 945 core.conformation.Conformation: current variant for 891 CYD core.conformation.Conformation: current variant for 945 CYD core.conformation.Conformation: current variant for 891 CYD core.conformation.Conformation: current variant for 945 CYD protocols.grafting.util: insert_point 891 protocols.grafting.util: insert_start 892 protocols.grafting.util: insert_end 901 protocols.grafting.util: insert_length 10 protocols.grafting.util: FOLD_TREE EDGE 1 891 -1 EDGE 891 892 1 EDGE 892 964 -1 protocols.grafting.GraftMoverBase: Insertion complete. protocols.grafting.AnchoredGraftMover: Setting default movemap protocols.grafting.CCDEndsGraftMover: Start: 891 protocols.grafting.CCDEndsGraftMover: Original End: 903 protocols.grafting.CCDEndsGraftMover: End: 902 protocols.grafting.CCDEndsGraftMover: Insert Length: 10 basic.io.database: Database file opened: scoring/score_functions/centroid_smooth/cen_smooth_params.txt core.scoring.ramachandran: shapovalov_lib::shap_rama_smooth_level of 4( aka highest_smooth ) got activated. basic.io.database: Database file opened: scoring/score_functions/rama/shapovalov/kappa25/all.ramaProb protocols.grafting.CCDEndsGraftMover: LOOP start: 890 stop: 893 cut: 891 size: 4 skip rate: 0 extended?: False protocols.grafting.CCDEndsGraftMover: protocols.grafting.CCDEndsGraftMover: LOOP start: 900 stop: 903 cut: 901 size: 4 skip rate: 0 extended?: False protocols.grafting.CCDEndsGraftMover: protocols.loops.FoldTreeFromLoopsWrapper: old foldtree FOLD_TREE EDGE 1 891 -1 EDGE 891 902 1 EDGE 902 974 -1 EDGE 891 892 -2 C N EDGE 892 893 -2 C N EDGE 893 894 -2 C N EDGE 894 895 -2 C N EDGE 895 896 -2 C N EDGE 896 897 -2 C N EDGE 897 898 -2 C N EDGE 898 899 -2 C N EDGE 899 900 -2 C N EDGE 900 901 -2 C N New foldtree FOLD_TREE EDGE 1 889 -1 EDGE 889 891 -1 EDGE 889 894 1 EDGE 894 892 -1 EDGE 894 899 -1 EDGE 899 901 -1 EDGE 899 904 2 EDGE 904 902 -1 EDGE 904 974 -1 protocols.grafting.util: Loop: 1 protocols.grafting.util: Add variant to: 891 protocols.grafting.util: Loop: 2 protocols.grafting.util: Add variant to: 901 protocols.grafting.util: idealized 890 protocols.grafting.util: idealized 891 protocols.grafting.util: ideal 892 protocols.grafting.util: idealized 892 protocols.grafting.util: idealized 893 protocols.grafting.util: idealized 900 protocols.grafting.util: idealized 901 protocols.grafting.util: ideal 901 protocols.grafting.util: idealized 902 protocols.grafting.util: idealized 903 core.chemical.GlobalResidueTypeSet: Finished initializing centroid residue type set. Created 62 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.025629 seconds. basic.io.database: Database file opened: scoring/score_functions/disulfides/centroid_distance_score basic.io.database: Database file opened: scoring/score_functions/disulfides/centroid_CaCbCb_angle_score basic.io.database: Database file opened: scoring/score_functions/disulfides/centroid_CaCbCbCa_dihedral_score basic.io.database: Database file opened: scoring/score_functions/disulfides/centroid_backbone_dihedral_score protocols.grafting.CCDEndsGraftMover: start 1661.69 protocols.grafting.CCDEndsGraftMover: round 1 protocols.grafting.CCDEndsGraftMover: Graft Closed early - returning protocols.grafting.CCDEndsGraftMover: 1 1267.29 protocols.grafting.CCDEndsGraftMover: finish 1267.29 core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 151 rotamers at 19 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph protocols.grafting.CCDEndsGraftMover: Graft meets ideal geometry true protocols.grafting.CCDEndsGraftMover: Complete protocols.antibody.AntibodyCDRGrafter: Checking Geometry protocols.antibody.AntibodyCDRGrafter: Success. Graft closed. antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT protocols.antibody.AntibodyCDRGrafter: Grafting CDR: L2 protocols.grafting.util: Returning 14 residues from 219 to 232 protocols.grafting.CCDEndsGraftMover: Start: 915 End: 924 NterO: 3 CterO: 3 protocols.grafting.util: Superimposing overhang residues protocols.grafting.util: Deleting 8 residues from 916 to 923 core.conformation.Conformation: Found disulfide between residues 771 845 core.conformation.Conformation: current variant for 771 CYD core.conformation.Conformation: current variant for 845 CYD core.conformation.Conformation: current variant for 771 CYD core.conformation.Conformation: current variant for 845 CYD core.conformation.Conformation: Found disulfide between residues 891 947 core.conformation.Conformation: current variant for 891 CYD core.conformation.Conformation: current variant for 947 CYD core.conformation.Conformation: current variant for 891 CYD core.conformation.Conformation: current variant for 947 CYD protocols.grafting.util: insert_point 915 protocols.grafting.util: insert_start 916 protocols.grafting.util: insert_end 923 protocols.grafting.util: insert_length 8 protocols.grafting.util: FOLD_TREE EDGE 1 915 -1 EDGE 915 916 1 EDGE 916 966 -1 protocols.grafting.GraftMoverBase: Insertion complete. protocols.grafting.AnchoredGraftMover: Setting default movemap protocols.grafting.CCDEndsGraftMover: Start: 915 protocols.grafting.CCDEndsGraftMover: Original End: 924 protocols.grafting.CCDEndsGraftMover: End: 924 protocols.grafting.CCDEndsGraftMover: Insert Length: 8 protocols.grafting.CCDEndsGraftMover: LOOP start: 914 stop: 917 cut: 915 size: 4 skip rate: 0 extended?: False protocols.grafting.CCDEndsGraftMover: protocols.grafting.CCDEndsGraftMover: LOOP start: 922 stop: 925 cut: 923 size: 4 skip rate: 0 extended?: False protocols.grafting.CCDEndsGraftMover: protocols.loops.FoldTreeFromLoopsWrapper: old foldtree FOLD_TREE EDGE 1 915 -1 EDGE 915 924 1 EDGE 924 974 -1 EDGE 915 916 -2 C N EDGE 916 917 -2 C N EDGE 917 918 -2 C N EDGE 918 919 -2 C N EDGE 919 920 -2 C N EDGE 920 921 -2 C N EDGE 921 922 -2 C N EDGE 922 923 -2 C N New foldtree FOLD_TREE EDGE 1 913 -1 EDGE 913 915 -1 EDGE 913 918 1 EDGE 918 916 -1 EDGE 918 921 -1 EDGE 921 923 -1 EDGE 921 926 2 EDGE 926 924 -1 EDGE 926 974 -1 protocols.grafting.util: Loop: 1 protocols.grafting.util: Add variant to: 915 protocols.grafting.util: Loop: 2 protocols.grafting.util: Add variant to: 923 protocols.grafting.util: idealized 914 protocols.grafting.util: idealized 915 protocols.grafting.util: ideal 916 protocols.grafting.util: idealized 916 protocols.grafting.util: idealized 917 protocols.grafting.util: idealized 922 protocols.grafting.util: idealized 923 protocols.grafting.util: ideal 923 protocols.grafting.util: idealized 924 protocols.grafting.util: idealized 925 protocols.grafting.CCDEndsGraftMover: start 1669.58 protocols.grafting.CCDEndsGraftMover: round 1 protocols.loops.util: PepBondGeom: 923 - 72 L Ca-C-N -- 99.5 (min): 142.34 : 134.5 (max) protocols.grafting.CCDEndsGraftMover: 1 1306.25 protocols.grafting.CCDEndsGraftMover: round 2 protocols.grafting.CCDEndsGraftMover: Graft Closed early - returning protocols.grafting.CCDEndsGraftMover: 2 1219.92 protocols.grafting.CCDEndsGraftMover: finish 1219.92 core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 149 rotamers at 14 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph protocols.grafting.CCDEndsGraftMover: Graft meets ideal geometry true protocols.grafting.CCDEndsGraftMover: Complete protocols.antibody.AntibodyCDRGrafter: Checking Geometry protocols.antibody.AntibodyCDRGrafter: Success. Graft closed. antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT protocols.antibody.AntibodyCDRGrafter: Grafting CDR: L3 protocols.grafting.util: Returning 15 residues from 259 to 273 core.conformation.Conformation: Reverting out-of-date disulfide to thiol type at resid 3 protocols.grafting.CCDEndsGraftMover: Start: 955 End: 965 NterO: 3 CterO: 3 protocols.grafting.util: Superimposing overhang residues protocols.grafting.util: Deleting 9 residues from 956 to 964 core.conformation.Conformation: Found disulfide between residues 771 845 core.conformation.Conformation: current variant for 771 CYD core.conformation.Conformation: current variant for 845 CYD core.conformation.Conformation: current variant for 771 CYD core.conformation.Conformation: current variant for 845 CYD core.conformation.Conformation: Found disulfide between residues 891 955 core.conformation.Conformation: current variant for 891 CYD core.conformation.Conformation: current variant for 955 CYD core.conformation.Conformation: current variant for 891 CYD core.conformation.Conformation: current variant for 955 CYD protocols.grafting.util: insert_point 955 protocols.grafting.util: insert_start 956 protocols.grafting.util: insert_end 964 protocols.grafting.util: insert_length 9 protocols.grafting.util: FOLD_TREE EDGE 1 955 -1 EDGE 955 956 1 EDGE 956 965 -1 protocols.grafting.GraftMoverBase: Insertion complete. protocols.grafting.AnchoredGraftMover: Setting default movemap protocols.grafting.CCDEndsGraftMover: Start: 955 protocols.grafting.CCDEndsGraftMover: Original End: 965 protocols.grafting.CCDEndsGraftMover: End: 965 protocols.grafting.CCDEndsGraftMover: Insert Length: 9 protocols.grafting.CCDEndsGraftMover: LOOP start: 954 stop: 957 cut: 955 size: 4 skip rate: 0 extended?: False protocols.grafting.CCDEndsGraftMover: protocols.grafting.CCDEndsGraftMover: LOOP start: 963 stop: 966 cut: 964 size: 4 skip rate: 0 extended?: False protocols.grafting.CCDEndsGraftMover: protocols.loops.FoldTreeFromLoopsWrapper: old foldtree FOLD_TREE EDGE 1 955 -1 EDGE 955 965 1 EDGE 965 974 -1 EDGE 955 956 -2 C N EDGE 956 957 -2 C N EDGE 957 958 -2 C N EDGE 958 959 -2 C N EDGE 959 960 -2 C N EDGE 960 961 -2 C N EDGE 961 962 -2 C N EDGE 962 963 -2 C N EDGE 963 964 -2 C N New foldtree FOLD_TREE EDGE 1 953 -1 EDGE 953 955 -1 EDGE 953 958 1 EDGE 958 956 -1 EDGE 958 962 -1 EDGE 962 964 -1 EDGE 962 967 2 EDGE 967 965 -1 EDGE 967 974 -1 protocols.grafting.util: Loop: 1 protocols.grafting.util: Add variant to: 955 protocols.grafting.util: Loop: 2 protocols.grafting.util: Add variant to: 964 protocols.grafting.util: idealized 954 protocols.grafting.util: idealized 955 protocols.grafting.util: ideal 956 protocols.grafting.util: idealized 956 protocols.grafting.util: idealized 957 protocols.grafting.util: idealized 963 protocols.grafting.util: idealized 964 protocols.grafting.util: ideal 964 protocols.grafting.util: idealized 965 protocols.grafting.util: idealized 966 protocols.grafting.CCDEndsGraftMover: start 1612.44 protocols.grafting.CCDEndsGraftMover: round 1 protocols.grafting.CCDEndsGraftMover: Graft Closed early - returning protocols.grafting.CCDEndsGraftMover: 1 1219.16 protocols.grafting.CCDEndsGraftMover: finish 1219.16 core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 118 rotamers at 17 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph protocols.grafting.CCDEndsGraftMover: Graft meets ideal geometry true protocols.grafting.CCDEndsGraftMover: Complete protocols.antibody.AntibodyCDRGrafter: Checking Geometry protocols.antibody.AntibodyCDRGrafter: Success. Graft closed. antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: SRWGGDGFYAMDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT protocols.antibody.constraints.CDRDihedralConstraintMover: L1-10-1 data: 42 cutoff: 10 core.scoring.constraints.ConstraintsIO: read constraints from /Users/jadolfbr/Library/Python/3.6/lib/python/site-packages/pyrosetta-2019.39+release.93456a567a8-py3.6-macosx-10.6-intel.egg/pyrosetta/database/sampling/antibodies/cluster_based_constraints/CircularHarmonic/outliers_false_liberal_use_means/L1-10-1.txt core.scoring.constraints.ConstraintsIO: Read in 20 constraints basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: SRWGGDGFYAMDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT protocols.antibody.constraints.CDRDihedralConstraintMover: L2-8-1 data: 632 cutoff: 10 core.scoring.constraints.ConstraintsIO: read constraints from /Users/jadolfbr/Library/Python/3.6/lib/python/site-packages/pyrosetta-2019.39+release.93456a567a8-py3.6-macosx-10.6-intel.egg/pyrosetta/database/sampling/antibodies/cluster_based_constraints/CircularHarmonic/outliers_false_liberal_use_means/L2-8-1.txt core.scoring.constraints.ConstraintsIO: Read in 16 constraints basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: SRWGGDGFYAMDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT protocols.antibody.constraints.CDRDihedralConstraintMover: L3-9-cis7-1 data: 419 cutoff: 10 core.scoring.constraints.ConstraintsIO: read constraints from /Users/jadolfbr/Library/Python/3.6/lib/python/site-packages/pyrosetta-2019.39+release.93456a567a8-py3.6-macosx-10.6-intel.egg/pyrosetta/database/sampling/antibodies/cluster_based_constraints/CircularHarmonic/outliers_false_liberal_use_means/L3-9-cis7-1.txt core.scoring.constraints.ConstraintsIO: Read in 18 constraints basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: SRWGGDGFYAMDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: SRWGGDGFYAMDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT basic.io.database: [ WARNING ] Unable to locate database file /sampling/antibodies/antibody_database_rosetta_design.db antibody.database.AntibodyDatabaseManager: Reading from: /Users/jadolfbr/Library/Python/3.6/lib/python/site-packages/pyrosetta-2019.39+release.93456a567a8-py3.6-macosx-10.6-intel.egg/pyrosetta/database//sampling/antibodies/antibody_database_rosetta_design_north_paper.db antibody.database.AntibodyDatabaseManager: Loaded L1-10-1 with 15 datapoints. antibody.database.AntibodyDatabaseManager: Loaded L2-8-1 with 153 datapoints. antibody.database.AntibodyDatabaseManager: Loaded L3-9-cis7-1 with 179 datapoints. protocols.antibody.task_operations.AddCDRProfilesOperation: applying prob task op core.scoring.CartesianBondedEnergy: Creating new peptide-bonded energy container (974) core.pack.pack_rotamers: built 0 rotamers at 0 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: SRWGGDGFYAMDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 771 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 845 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 891 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 955 BRANCH 1 basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: SRWGGDGFYAMDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: SRWGGDGFYAMDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT basic.io.database: [ WARNING ] Unable to locate database file /sampling/antibodies/antibody_database_rosetta_design.db antibody.database.AntibodyDatabaseManager: Reading from: /Users/jadolfbr/Library/Python/3.6/lib/python/site-packages/pyrosetta-2019.39+release.93456a567a8-py3.6-macosx-10.6-intel.egg/pyrosetta/database//sampling/antibodies/antibody_database_rosetta_design_north_paper.db antibody.database.AntibodyDatabaseManager: Loaded L1-10-1 with 15 datapoints. antibody.database.AntibodyDatabaseManager: Loaded L2-8-1 with 153 datapoints. antibody.database.AntibodyDatabaseManager: Loaded L3-9-cis7-1 with 179 datapoints. protocols.antibody.task_operations.AddCDRProfilesOperation: applying prob task op core.pack.pack_rotamers: built 0 rotamers at 0 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: SRWGGDGFYAMDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 771 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 845 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 891 BRANCH 1 core.pose.util: [ WARNING ] Unable to find atom_tree atom for this Rosetta branch connection angle: residue 955 BRANCH 1 protocols.analysis.simple_metrics.RunSimpleMetricsMover: Running: SasaMetric - calculating sasa basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: SRWGGDGFYAMDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT protocols.analysis.simple_metrics.RunSimpleMetricsMover: Running: SelectedResiduesPyMOLMetric - calculating pymol_selection basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: SRWGGDGFYAMDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT protocols.analysis.simple_metrics.RunSimpleMetricsMover: Running: SequenceMetric - calculating L1_sequence basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: SRWGGDGFYAMDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT protocols.analysis.simple_metrics.RunSimpleMetricsMover: Running: SequenceMetric - calculating L2_sequence basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: SRWGGDGFYAMDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT protocols.analysis.simple_metrics.RunSimpleMetricsMover: Running: SequenceMetric - calculating L3_sequence basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: SRWGGDGFYAMDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT protocols.analysis.simple_metrics.RunSimpleMetricsMover: Running: InteractionEnergyMetric - calculating interaction_energy basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: SRWGGDGFYAMDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT basic.io.database: Database file opened: sampling/antibodies/cluster_center_dihedrals.txt protocols.antibody.AntibodyNumberingParser: Antibody numbering scheme definitions read successfully protocols.antibody.AntibodyNumberingParser: Antibody CDR definition read successfully antibody.AntibodyInfo: Successfully finished the CDR definition antibody.AntibodyInfo: AC Detecting Regular CDR H3 Stem Type antibody.AntibodyInfo: SRWGGDGFYAMDYW antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: KINKED antibody.AntibodyInfo: AC Finished Detecting Regular CDR H3 Stem Type: Kink: 1 Extended: 0 antibody.AntibodyInfo: Setting up CDR Cluster for H1 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H2 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for H3 protocols.antibody.cluster.CDRClusterMatcher: Length: 13 Omega: TTTTTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L1 protocols.antibody.cluster.CDRClusterMatcher: Length: 10 Omega: TTTTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L2 protocols.antibody.cluster.CDRClusterMatcher: Length: 8 Omega: TTTTTTTT antibody.AntibodyInfo: Setting up CDR Cluster for L3 protocols.antibody.cluster.CDRClusterMatcher: Length: 9 Omega: TTTTTTCTT core.simple_metrics.metrics.InteractionEnergyMetric: core.simple_metrics.metrics.InteractionEnergyMetric: fa_atr 1 core.simple_metrics.metrics.InteractionEnergyMetric: Unweighted: -21.8976 core.simple_metrics.metrics.InteractionEnergyMetric: Weighted: -21.8976 core.simple_metrics.metrics.InteractionEnergyMetric: core.simple_metrics.metrics.InteractionEnergyMetric: fa_rep 0.55 core.simple_metrics.metrics.InteractionEnergyMetric: Unweighted: 227.209 core.simple_metrics.metrics.InteractionEnergyMetric: Weighted: 124.965 core.simple_metrics.metrics.InteractionEnergyMetric: core.simple_metrics.metrics.InteractionEnergyMetric: fa_sol 1 core.simple_metrics.metrics.InteractionEnergyMetric: Unweighted: 20.1315 core.simple_metrics.metrics.InteractionEnergyMetric: Weighted: 20.1315 core.simple_metrics.metrics.InteractionEnergyMetric: core.simple_metrics.metrics.InteractionEnergyMetric: lk_ball_wtd 1 core.simple_metrics.metrics.InteractionEnergyMetric: Unweighted: 1.54267 core.simple_metrics.metrics.InteractionEnergyMetric: Weighted: 1.54267 core.simple_metrics.metrics.InteractionEnergyMetric: core.simple_metrics.metrics.InteractionEnergyMetric: fa_elec 1 core.simple_metrics.metrics.InteractionEnergyMetric: Unweighted: -0.883278 core.simple_metrics.metrics.InteractionEnergyMetric: Weighted: -0.883278
Here, we want to set the protocol to optimize the interface energy during Monte Carlo instead of total energy. The interface energy is calculated by the InterfaceAnalyzerMover through a specialized MonteCarlo object called MonteCarloInterface
. This is useful to improve binding energy and generally results in better interface energies . Resulting models should still be pruned for high total energy. This was benchmarked in the paper, and has been used for real-life designs to the HIV epitope (165 seconds for 1 decoy).
Use the provided XML or set this up through code.
<AntibodyDesignMover name="RAbD" seq_design_cdrs="L1,L3" graft_design_cdrs="L1,L3" mc_optimize_dG="1" />
if not os.getenv("DEBUG"):
### BEGIN SOLUTION
pose = original_pose.clone()
rabd = XmlObjects.static_get_mover('<AntibodyDesignMover name="RAbD" graft_design_cdrs="L1,L3" seq_design_cdrs="L1,L3" mc_optimize_dG="1" light_chain="kappa"/>')
rabd.apply(pose)
### END SOLUTION
Load the scorefile with nstruct=5 from expected_outputs/rabd/tutB1_score.sc
Compare this data to tutorial A2. Are the interface energies better? Has the Shape Complementarity improved (sc score) improved?
Here, we want to set the protocol to optimize the interface energy during Monte Carlo, but we want to add some total energy to the weight. Because the overall numbers of total energy will dominate the overall numbers, we only add a small weight for total energy. This has not been fully benchmarked, but if your models have very bad total energy when using opt-dG - consider using it. (178 sec for 1 nstruct)
<AntibodyDesignMover name="RAbD" seq_design_cdrs="L1,L3" graft_design_cdrs="L1,L3" mc_optimize_dG="1" mc_total_weight=".01 mc_interface_weight=".99 light_chain="kappa"/>
if not os.getenv("DEBUG"):
### BEGIN SOLUTION
pose = original_pose.clone()
rabd = XmlObjects.static_get_mover('<AntibodyDesignMover name="RAbD" seq_design_cdrs="L1,L3" graft_design_cdrs="L1,L3" mc_optimize_dG="1" mc_total_weight=".01 mc_interface_weight=".99 light_chain="kappa"/>')
rabd.apply(pose)
### END SOLUTION
Use the scorefile from an nstruct=5 run to compare total energies (total_score
) of this run vs the one right before it located at expected_outputs/rabd/tutB2_score.sc
. Are the total scores better?
This tutorial takes a long time to run as docking is fairly slow - even with the optimizations that are part of RAbD. PLEASE USE THE PREGENERATED OUTPUT. The top 10 designs from each tutorial and associated scorefiles of a 1000 nstruct cluster run are in the output directory. Note that we are starting these tutorials with a pre-relaxed structure in order to get more reliable rosetta energies. Since we are running a large nstruct, we will escape the local energy well that this leads us into.
In this example, we use integrated RosettaDock (with sequence design during the high-res step) to sample the antibody-antigen orientation, but we don't care where the antibody binds to the antigen. Just that it binds. IE - No Constraints. The RAbD protocol always has at least Paratope SiteConstraints enabled to make sure any docking is contained to the paratope (like most good docking programs).
This takes too long to run, so PLEASE USE THE OUTPUT GENERATED FOR YOU. We will use opt-dG here and for these tutorials, we will be sequence-designing all cdrs to begin to create a better interface. Note that sequence design happens whereever packing occurs - Including during high-resolution docking.
<AntibodyDesignMover name="RAbD" mc_optimize_dG="1" do_dock="1" seq_design_cdrs="L1,L2,L3,H1,H2,H3" graft_design_cdrs="L1,L2,L3,H1,H2" light_chain="kappa"/>
Use pymol to load the files, and load tutC1_score from the expected_outputs directory as a pandas dataframe.
pymol my_ab.pdb expected_outputs/rabd/top10_C1/*
@color_cdrs.pml
center full_epitope
Where is the antibody in the resulting designs? Are the interfaces restricted to the Paratope? Has the epitope moved relative to the starting interface?
Allow Dock-Design, incorporating auto-generated SiteConstraints to keep the antibody around the starting interface residues. These residues are determined by being within 6A to the CDR residues (This interface distance can be customized). Again, these results are provided for you.
<AntibodyDesignMover name="RAbD" mc_optimize_dG="1" do_dock="1" use_epitope_csts="1"
seq_design_cdrs="L1,L2,L3,H1,H2,H3" graft_design_cdrs="L1,L2,L3,H1,H2" light_chain="kappa"/>
Use pymol to load the files and checkout the scores in expected_outputs/rabd/tutC2_score.sc
as before.
pymol my_ab.pdb expected_outputs/rabd/top10_C2/*
@color_cdrs.pml
center full_epitope
How do these compare with with the previous tutorial? Are the antibodies closer to the starting interface? Are the scores better?
Allow Dock-Design, as above, but specify the Epitope Residues and Paratope CDRs to guide the dock/design to have these interact.
For now, we are more focused on the light chain. We could do this as a two-stage process, where we first optimize positioning and CDRs of the light chain and then the heavy chain or simply add heavy chain CDRs to the paratope CDRs option.
<AntibodyDesignMover name="RAbD" mc_optimize_dG="1" do_dock="1" use_epitope_csts="1"
epitope_residues="38J,52J,34K,37K" paratope_cdrs="L1,L3"
seq_design_cdrs="L1,L2,L3,H1,H2,H3" graft_design_cdrs="L1,L2,L3,H1,H2" light_chain="kappa"/>
Again, load these into Pymol and take a look at the scorefile in a dataframe.
pymol my_ab.pdb expected_outputs/rabd/top10_C3/*
@color_cdrs.pml
center full_epitope
Now that we have specified where we want the interface to be and are additionally designing more CDRS, how do the enegies compare? Are we starting to get a decent interface with the lowest energy structure?
How do these compare with the previous runs?
Once again, all output files are in expected_outputs
. Please use these if you want - as many of these take around 10 minutes to run.
More complicated design runs can be created by using the Antibody Design Instruction file. This file allows complete customization of the design run. See below for a review of the syntax of the file and possible customization. An instruction file is provided where we use conservative design on L1 and graft in L1, H2, and H1 CDRs at a longer length to attempt to create a larger interface area. More info on instruction file syntax can be found at the end of this tutorial. (150 seconds on my laptop for nstruc 1)
cp ../inputs/my_instruction_file.txt .
cp ../inputs/default_cdr_instructions.txt .
Take a look at the default CDR instructions. These are loaded by default into Rosetta. There is syntax examples at the end of the file. Run the XML or attempt to use it in-code.
<AntibodyDesignMover name="RAbD" instruction_file="my_instruction_file.txt"
seq_design_cdrs="L1,L3,H1,H2,H3" graft_design_cdrs="L1,H2,H1" random_start="1" light_chain="kappa"/>
if not os.getenv("DEBUG"):
### BEGIN SOLUTION
pose = original_pose.clone()
rabd = XmlObjects.static_get_mover('<AntibodyDesignMover name="RAbD" instruction_file="my_instruction_file.txt" seq_design_cdrs="L1,L3,H1,H2,H3" graft_design_cdrs="L1,H2,H1" random_start="1" light_chain="kappa"/>')
rabd.apply(pose)
### END SOLUTION
Here, we will disallow ANY sequence design into Proline residues and Cysteine residues, while giving a resfile to further LIMIT design and packing as specific positions. These can be given as 3 or 1 letter codes and mixed codes such as PRO and C are accepted. Note that the resfile does NOT turn any residues ON, it is simply used to optionally LIMIT design residue types and design and packing positions.
Resfile syntax can be found here: [https://www.rosettacommons.org/docs/wiki/rosetta_basics/file_types/resfiles] Note that specifying a resfile and dissalowing aa are only currently available as cmd-line options that are read by RAbD.
Runtime is less than a minute for nstruct 1.
cp ../inputs/rabd/my_resfile.resfile .
Take a look at the resfile. Can you describe what it is we are doing with it?
Unfortunately, at the moment, resfile setting is only available as a cmd-line option that needs to be set in the init()
function as -resfile my_resfile.resfile
<AntibodyDesignMover name="RAbD" seq_design_cdrs="L1,L3,H1,H2,H3" light_chain="kappa"/>
Here, we will change the mintype to relax. This mintype enables Flexible-Backbone design as we have seen in previous workshops. Our default is to use min/pack cycles, but relax typically works better. However, it also takes considerably more time! This tutorial takes about 339 seconds for one struct!
<AntibodyDesignMover name="RAbD" seq_design_cdrs="L1,L3,H1,H3" mintype="relax light_chain="kappa"/>
if not os.getenv("DEBUG"):
### BEGIN SOLUTION
pose = original_pose.clone()
rabd = XmlObjects.static_get_mover('<AntibodyDesignMover name="RAbD" seq_design_cdrs="L1,L3,H1,H3" mintype="relax" light_chain="kappa"/>')
rabd.apply(pose)
### END SOLUTION
Finally, we want to allow the framework residues AROUND the CDRs we will be designing and any interacting antigen residues to design as well here. In addition, we will disable conservative framework design as we want something funky (this is not typically recommended and is used here to indicate what you CAN do. Note that we will also design the interface of the antigen using the -design_antigen
option. This can be useful for vaccine design. Note that these design options are cmd-line ony options currently (but will be available in a later version of Rosetta). Approx 900 second runtime.
antibody_designer.linuxgccrelease -s my_ab.pdb -seq_design_cdrs L1 L3 H1 H3 \
-light_chain kappa -resfile my_resfile.resfile -disallow_aa PRO CYS \
-mintype relax -design_antigen -design_framework \
-conservative_framework_design false -nstruct 1 -out:prefix tutD4_
<AntibodyDesignMover name="RAbD" seq_design_cdrs="L1,L3,H1,H3" mintype="relax" light_chain="kappa"/>
Finally, we want increased variability for our sequence designs. So, we will increase number of sampling rounds for our lovely cluster profiles using the -seq_design_profile_samples
option, increase kT, and allow H3 stem design.
We will enable H3 Stem design here, which can cause a flipping of the H3 stem type from bulged to non-bulged and vice-versa. Typically, if you do this, you may want to run loop modeling on the top designs to confirm the H3 structure remains in-tact. Note that once again, these sequence-design specific options must be set on the cmd-line.
Description of the seq_design_profile_samples
option (default 1): "If designing using profiles, this is the number of times the profile is sampled each time packing done. Increase this number to increase variability of designs - especially if not using relax as the mintype."
This tutorial takes approx 450 seconds.
antibody_designer.linuxgccrelease -s my_ab.pdb -seq_design_cdrs L1 L2 H3 \
-graft_design_cdrs L1 L2 -light_chain kappa -design_H3_stem -inner_kt 2.0 \
-outer_kt 2.0 -seq_design_profile_samples 5 -nstruct 5 -out:prefix tutD5_
<AntibodyDesignMover name="RAbD" seq_design_cdrs="L1,L3,H1,H3" mintype="relax"
inner_kt="2.0" outer_kt="2.0"/>
How different is the sequence of L1,L2, and H3 from our starting antibody?
You should now be ready to explore and use RosettaAntibodyDesign on your own. Congrats! Thanks for going through this tutorial!
The full reference manual can be found here: https://www.rosettacommons.org/docs/latest/application_documentation/antibody/RosettaAntibodyDesign#antibody-design-cdr-instruction-file