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

RosettaAntibodyDesign

Notes

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!

Citation

Rosetta Antibody Design (RAbD): A General Framework for Computational Antibody Design, PLOS Computational Biology, 4/27/2018

Jared Adolf-Bryfogle, Oleks Kalyuzhniy, Michael Kubitz, Brian D. Weitzner, Xiaozhen Hu, Yumiko Adachi, William R. Schief, Roland L. Dunbrack Jr.

Manual

The full RAbD manual can be found here: https://www.rosettacommons.org/docs/latest/application_documentation/antibody/RosettaAntibodyDesign

Overview

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.

Algorithm

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.

General Setup and Inputs

  1. 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.

  1. 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.

  1. 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.

  2. 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.

  1. 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.

In [1]:
# Notebook setup
import sys
if 'google.colab' in sys.modules:
    !pip install pyrosettacolabsetup
    import pyrosettacolabsetup
    pyrosettacolabsetup.mount_pyrosetta_install()
    print ("Notebook is set for PyRosetta use in Colab.  Have fun!")

Make sure you are in the directory with the pdb files:

cd google_drive/My\ Drive/student-notebooks/

In [2]:
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)

Imports

In [3]:
#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'.
  

Intitlialization

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.

In [4]:
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
In [5]:
#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

Tutorial

Tutorial A: General Design

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.

Tut A1. Sequence Design

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.

In [5]:
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.

In [8]:
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

In [12]:
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?

In [30]:
df = load_json_scorefile("expected_outputs/rabd/tutA1_score.sc")
df = drop_cluster_columns(df, keep_cdrs=["L1", "L3"])
df
Out[30]:
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

Tut A2. Graft Design

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).

In [32]:
### 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
Out[32]:
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.

In [33]:
df_tut_a12 = pandas.concat([df, df_a2], ignore_index=True).sort_values("dG_separated", ascending=True)
df_tut_a12
Out[33]:
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?

In [ ]:
if not os.getenv("DEBUG"):
    print("L1", original_pose.scores["cdr_cluster_ID_L1"])
    print("L3", original_pose.scores["cdr_cluster_ID_L3"])

Tut A3. Basic De-novo run

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"/>  
In [ ]:
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.

Tut A4. RAbD Framework Components

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.

1. Copy the Files

    cp ../inputs/rabd/ab_design_components.xml .
    cp ../inputs/rabd/malaria_cdrs.pdb .


Take a look at the xml.

  • We are using the AntibodyCDRGrafter to do the grafting of our CDRs.
  • We then add constraints using CDRDihderalConstraintMovers for each CDR with use the CDR clusters determinedy by RosettaAntibody to keep from perturbing the CDRs too much.
  • Finally, we do a round of pack/min/pack using the 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.

PyRosetta Locations

rosetta.protocols.antibody.task_operations

rosetta.protocols.antibody.constraints

rosetta.protocols.antibody.residue_selectors

Documentation

2. Run the protocol or copy the output (357 seconds).

3. Look at the score file as you have before. Are the sequences different between what we started with? How about the interaction energies?

In [4]:
os.system('cp inputs/rabd/malaria_cdrs.pdb .')
Out[4]:
0
In [39]:
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

Challenge: Custom Design Protocol in code

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.

In [6]:
### 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

Tutorial B: Optimizing Interface Energy (opt-dG)

Tut B1. Optimizing dG

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" />
In [ ]:
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?

Tut B2. Optimizing Interface Energy and Total Score (opt-dG and opt-E)

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"/>
In [ ]:
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?

Tutorial C: Towards DeNovo Design: Integrated Dock/Design

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.

Tut C1. RosettaDocking

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?

Tut C2. Auto Epitope Constraints

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?

Tut C3. Specific Residue Epitope Constraints

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?

Tutorial D: Advanced Settings and CDR Instruction File Customization

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.

Tut D1. CDR Instruction File

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"/>
In [ ]:
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

Tut D2. Dissallow AAs and the Resfile

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"/>

Tut D3. Mintype

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"/>
In [ ]:
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

Tut D4. Framework Design

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"/>

Tut D5. H3 Stem, kT, and Sequence variablility.

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

In [ ]: