Branch: rosetta:main 「revision: №62162」
Test: ubuntu.gcc.integration.addsan
SubTest: cycpep_rdkit_metric
SubTest files: 「file-system-view」
Daemon: hojo-3    
State: cycpep_rdkit_metric

LogFile log1 ******** (C) Copyright Rosetta Commons Member Institutions. *************** * Use of Rosetta for commercial purposes may require purchase of a license. * ******** See LICENSE.md or email license@uw.edu for more details. ********** core.init: Rosetta extras: [] core.init: command: ROSETTA/source/bin/rosetta_scripts.default.linuxgccaddsan -in:path:database_cache_dir ROSETTA/.database-binaries/ubuntugccaddsan @inputs/rosetta.flags -database ROSETTA/database -testing:INTEGRATION_TEST basic.random.init_random_generator: Constant seed mode, seed=1111111 seed_offset=0 real_seed=1111111 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=1111111 RG_type=mt19937 protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs protocols.jd2.PDBJobInputter: pushed inputs/test.pdb nstruct index 1 protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: filling pose from PDB inputs/test.pdb core.import_pose.import_pose: File 'inputs/test.pdb' automatically determined to be of type PDB from contents. core.conformation.Conformation: [ WARNING ] missing heavyatom: OXT on residue ALA:CtermProteinFull 7 protocols.rosetta_scripts.RosettaScriptsParser: dock_design_filename=inputs/test.xml protocols.rosetta_scripts.RosettaScriptsParser: Variable substitution will occur with the following values: '%%Nres%%'='7'; protocols.rosetta_scripts.RosettaScriptsParser: Substituted script: <ROSETTASCRIPTS> # The SCOREFXNS section defines scoring functions that will be used later in the script: <SCOREFXNS> # The current Rosetta default scorefunction: <ScoreFunction name="ref" weights="ref2015" /> # The default scorefunction with increased hydrogen bond weights, and with the aa_composition, # aspartimide_penalty, and constraint score terms activated. <ScoreFunction name="ref_highhbond" weights="ref2015" > <Reweight scoretype="hbond_lr_bb" weight="5.0" /> <Reweight scoretype="hbond_sr_bb" weight="5.0" /> <Reweight scoretype="atom_pair_constraint" weight="1.0" /> <Reweight scoretype="dihedral_constraint" weight="1.0" /> <Reweight scoretype="angle_constraint" weight="1.0" /> <Reweight scoretype="aa_composition" weight="1.0" /> <Reweight scoretype="aspartimide_penalty" weight="1.0" /> </ScoreFunction> </SCOREFXNS> # The PACKER_PALETTES section defines the total set of residues with which we're designing. <PACKER_PALETTES> <CustomBaseTypePackerPalette name="palette" additional_residue_types="DALA,DGLU,DASP,DPHE,DHIS,DILE,DLYS,DLEU,DMET,DASN,DPRO,DGLN,DARG,DSER,DTHR,DVAL,DTRP,DTYR,HYP,DHYP" /> </PACKER_PALETTES> # The RESIDUE_SELECTORS section allows users to configure tools to select residues, # which are used when setting up other Rosetta modules. <RESIDUE_SELECTORS> # Select residues with mainchain phi torsion values greater than zero. These positions # will be restricted to becoming D-amino acids during design: <Phi name="posPhi" select_positive_phi="true" /> # Select residues with mainchain phi torsion values less than zero. These positions # will be restricted to becoming L-amino acids during design: <Phi name="negPhi" select_positive_phi="false" /> <Chain name="chainA" chains="A" /> </RESIDUE_SELECTORS> # The SIMPLE_METRICS section allows users to configure metrics used to measure properties of a structure. <SIMPLE_METRICS> # Metric to measure backbone hydrogen bonds: <PeptideInternalHbondsMetric name="internal_hbonds" /> <RDKitMetric name="clogp" residue_selector="chainA" metric_name="MolLogP" /> <RDKitMetric name="nhoh" residue_selector="chainA" metric_name="NHOHCount" /> <RDKitMetric name="tpsa" residue_selector="chainA" metric_name="TPSA" /> <RDKitMetric name="molwt" residue_selector="chainA" metric_name="MolWt" /> </SIMPLE_METRICS> # The FILTERS section allows users to configure filters. These measure properties of a # structure and make decisions, based on the measured properties, about whether to discard # the current structure. <FILTERS> # Filter to avoid score function artifact of having more than two hydrogen bonds to carbonyls: <OversaturatedHbondAcceptorFilter name="oversat" scorefxn="ref" max_allowed_oversaturated="0" consider_mainchain_only="false"/> # Filter to ensure a minimum number of hbonds: <PeptideInternalHbondsFilter name="min_internal_hbonds" hbond_cutoff="1" /> </FILTERS> # The TASKOPERATIONS section allows users to configure task operations, which are Rosetta modules that control the # behavior of Rosetta's "Packer" module. The Packer, in turn, is used for side-chain identity and rotamer optimization. # (As such, it is the primary tool used for sequence design.): <TASKOPERATIONS> # Task operation to read a resfile defining the D-amino acids, which will be used for design at positions with # mainchain phi torsion values greater than zero: <ReadResfile name="d_res" filename="inputs/d_res.txt" selector="posPhi"/> # Task operation to read a resfile defining the L-amino acids, which will be used for design at positions with # mainchain phi torsion values less than zero: <ReadResfile name="l_res" filename="inputs/l_res.txt" selector="negPhi"/> </TASKOPERATIONS> # The MOVERS section allows users to define movers, which are Rosetta modules that modify a structure in some way: <MOVERS> # A mover to declare a bond connecting the termini (i.e. to cyclize the peptide). In the context of Rosetta, declaring # a bond tells Rosetta that two atoms should not have Van der Waals interactions computed, but does not constrain the # bond geometry in any way. Note that the variable 7, specified on the command line, is used to specify the index # of the C-terminal residue: <DeclareBond name="peptide_bond1" res1="1" atom1="N" atom2="C" res2="7" add_termini="true" /> # The following three movers are used to set up torsion, angle, and length constraints for the terminal peptide bond, ensuring that # good bond geometry is preserved during relaxation. Again, the command-line variable 7 is used to specify the index of the # C-terminal residue: <CreateTorsionConstraint name="peptide_torsion_constraint"> <Add res1="7" res2="7" res3="1" res4="1" atom1="CA" atom2="C" atom3="N" atom4="CA" cst_func="CIRCULARHARMONIC 3.141592654 0.005" /> </CreateTorsionConstraint> <CreateAngleConstraint name="peptide_angle_constraints"> <Add res1="7" atom1="CA" res_center="7" atom_center="C" res2="1" atom2="N" cst_func="CIRCULARHARMONIC 2.02807247 0.005" /> <Add res1="7" atom1="C" res_center="1" atom_center="N" res2="1" atom2="CA" cst_func="CIRCULARHARMONIC 2.12406565 0.005" /> </CreateAngleConstraint> <CreateDistanceConstraint name="N_To_C_dist_cst"> <Add res1="7" res2="1" atom1="C" atom2="N" cst_func="HARMONIC 1.32865 0.01" /> </CreateDistanceConstraint> # Composition constraints are used with the aa_composition score term in order to add a nonlinearly-ramping penality for # deviation from a desired amino acid composition. In this case, we use them to require at least two proline residues (L- or D-), # at least one L-aspartate or L-glutamate, and at least one positively-charged residue. <AddCompositionConstraintMover name="addcompcsts" filename="inputs/desired_makeup.comp" /> # The FastDesign mover performs alternating rounds of sequence design and torsion-space energy minimization, while ramping the # repulsive term in the scorefunction (fa_rep). We use it here with a modified scorefunction with constraints and aa_composition # energy terms activated: <FastDesign name="fdes" scorefxn="ref_highhbond" packer_palette="palette" repeats="1" task_operations="d_res,l_res" ramp_down_constraints="false" > # A MoveMap is used to specify which degrees of freedom can move and which are fixed during energy minimization. Here, # we indicate that all mainchain torsions (bb)