core.init: Checking for fconfig files in pwd and ./rosetta/flags core.init: Rosetta version: rosetta.source.release-274 r274 2020.50+release.1295438 1295438cd4bd2be39c9dbbfab8db669ab62415ab https://www.rosettacommons.org 2020-12-13T21:33:15.479874 core.init: command: /home/progs/rosetta_src_2020.50.61505_bundle/main/source//bin/cluster.linuxgccrelease @flags basic.random.init_random_generator: 'RNG device' seed mode, using '/dev/urandom', seed=-1795935972 seed_offset=0 real_seed=-1795935972 basic.random.init_random_generator: RandomGenerator:init: Normal mode, seed=-1795935972 RG_type=mt19937 Rosetta Tool: cluster - clustering tool for PDBs and or silent files Usage: PDB input: -in:file:s *.pdb or -in:file:l list_of_pdbs -no_optH Dont change positions of Hydrogen atoms! Silent input: -in:file:silent silent.out silent input filesname -in:file:s specify specific tags to be extracted, if left out all will be taken -in:file:fullatom for full atom structures -in:file:silent_struct_type specify the input silent-file format Native: -in:file:native native PDB if CaRMS is required Scorefunction: -score:weights weights weight set or weights file -score:patch patch patch set -rescore:verbose display score breakdown -rescore:output_only don't rescore Output: -nooutput don't print PDB structures -out:prefix myprefix prefix the output structures with a string Clustering: -cluster:radius Cluster radius in A (for RMS clustering) or in inverse GDT_TS for GDT clustering. Use "-1" to trigger automatic radius detection -cluster:gdtmm Cluster by gdtmm instead of rms -cluster:input_score_filter Ignore structures above certain energy -cluster:exclude_res [ ..] Exclude residue numbers -cluster:radius Cluster radius -cluster:limit_cluster_size Maximal cluster size -cluster:limit_cluster_size_percent Maximal cluster size by percentage -cluster:random_limit_cluster_size_percent Maximal cluster size by percentage, cut randomly -cluster:limit_clusters Maximal number of clusters -cluster:limit_total_structures Maximal number of structures in total -cluster:sort_groups_by_energy Sort clusters by energy. -cluster:remove_highest_energy_member Remove highest energy member of each cluster -symmetry:symmetric_rmsd For symmetric systems find the lowest rms by testing all chain combinations. Works only with silent file input that contain symmetry info and with all CA rmsd Examples: cluster -database ~/minirosetta_database -in:file:silent silent.out -in::file::binary_silentfile -in::file::fullatom -native 1a19.pdb clustered Poses are given output names in the form of: c.i.j, which denotes the jth member of the ith cluster. 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 core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 985 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 1.19534 seconds. 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.chemical.GlobalResidueTypeSet: Finished initializing centroid residue type set. Created 69 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 0.030431 seconds. core.import_pose.import_pose: File 'model_83.pdb' automatically determined to be of type PDB basic.io.database: [ WARNING ] Unable to locate database file chemical/pdb_components/components.l.cif basic.io.database: [ WARNING ] Unable to locate database file chemical/pdb_components/components.l.cif.gz core.chemical.GlobalResidueTypeSet: [ WARNING ] Could not find: 'lig' in pdb components files! Skipping residue...