core.init: (0) {0} Checking for fconfig files in pwd and ./rosetta/flags core.init: (1) {0} Checking for fconfig files in pwd and ./rosetta/flags core.init: (2) {0} Checking for fconfig files in pwd and ./rosetta/flags core.init: (0) {0} Rosetta version: rosetta.source.release-243 r243 2020.03+release.f1c7e97 f1c7e97dda7fb7396c009a0e507f12e970b1a21d https://www.rosettacommons.org 2020-01-18T06:21:11.685482 core.init: (1) {0} Rosetta version: rosetta.source.release-243 r243 2020.03+release.f1c7e97 f1c7e97dda7fb7396c009a0e507f12e970b1a21d https://www.rosettacommons.org 2020-01-18T06:21:11.685482 core.init: (0) {0} command: /data/rosetta_2020.03/main/source/bin/simple_cycpep_predict.cxx11threadmpiopencl.linuxgccrelease -cyclic_peptide:rand_checkpoint_file debug.gz -cyclic_peptide:checkpoint_file debug.txt -out:file:silent debug.silent -cyclic_peptide:sequence_file debug.seq -beta_nov16 -cyclic_peptide:cyclization_type terminal_disulfide -cyclic_peptide:checkpoint_job_identifier check -nstruct 100 -in:file:native debug.pdb -cyclic_peptide:cyclic_permutations false -cyclic_peptide:MPI_processes_by_level 1 2 -cyclic_peptide:MPI_batchsize_by_level 25 core.init: (1) {0} command: /data/rosetta_2020.03/main/source/bin/simple_cycpep_predict.cxx11threadmpiopencl.linuxgccrelease -cyclic_peptide:rand_checkpoint_file debug.gz -cyclic_peptide:checkpoint_file debug.txt -out:file:silent debug.silent -cyclic_peptide:sequence_file debug.seq -beta_nov16 -cyclic_peptide:cyclization_type terminal_disulfide -cyclic_peptide:checkpoint_job_identifier check -nstruct 100 -in:file:native debug.pdb -cyclic_peptide:cyclic_permutations false -cyclic_peptide:MPI_processes_by_level 1 2 -cyclic_peptide:MPI_batchsize_by_level 25 core.init: (2) {0} Rosetta version: rosetta.source.release-243 r243 2020.03+release.f1c7e97 f1c7e97dda7fb7396c009a0e507f12e970b1a21d https://www.rosettacommons.org 2020-01-18T06:21:11.685482 core.init: (2) {0} command: /data/rosetta_2020.03/main/source/bin/simple_cycpep_predict.cxx11threadmpiopencl.linuxgccrelease -cyclic_peptide:rand_checkpoint_file debug.gz -cyclic_peptide:checkpoint_file debug.txt -out:file:silent debug.silent -cyclic_peptide:sequence_file debug.seq -beta_nov16 -cyclic_peptide:cyclization_type terminal_disulfide -cyclic_peptide:checkpoint_job_identifier check -nstruct 100 -in:file:native debug.pdb -cyclic_peptide:cyclic_permutations false -cyclic_peptide:MPI_processes_by_level 1 2 -cyclic_peptide:MPI_batchsize_by_level 25 basic.random.init_random_generator: (1) {0} 'RNG device' seed mode, using '/dev/urandom', seed=1249718772 seed_offset=0 real_seed=1761634251 thread_index=0 basic.random.init_random_generator: (1) {0} RandomGenerator:init: Normal mode, seed=1761634251 RG_type=mt19937 basic.random.init_random_generator: (0) {0} 'RNG device' seed mode, using '/dev/urandom', seed=1761634250 seed_offset=0 real_seed=1761634250 thread_index=0 basic.random.init_random_generator: (0) {0} RandomGenerator:init: Normal mode, seed=1761634250 RG_type=mt19937 basic.random.init_random_generator: (2) {0} 'RNG device' seed mode, using '/dev/urandom', seed=450275684 seed_offset=0 real_seed=1761634252 thread_index=0 basic.random.init_random_generator: (2) {0} RandomGenerator:init: Normal mode, seed=1761634252 RG_type=mt19937 core.init: (0) {0} Resolved executable path: /data/rosetta_2020.03/main/source/build/src/release/linux/5.0/64/x86/gcc/7/cxx11thread-mpi-opencl/simple_cycpep_predict.cxx11threadmpiopencl.linuxgccrelease core.init: (1) {0} Resolved executable path: /data/rosetta_2020.03/main/source/build/src/release/linux/5.0/64/x86/gcc/7/cxx11thread-mpi-opencl/simple_cycpep_predict.cxx11threadmpiopencl.linuxgccrelease core.init: (1) {0} Looking for database based on location of executable: /data/rosetta_2020.03/main/database/ core.init: (2) {0} Resolved executable path: /data/rosetta_2020.03/main/source/build/src/release/linux/5.0/64/x86/gcc/7/cxx11thread-mpi-opencl/simple_cycpep_predict.cxx11threadmpiopencl.linuxgccrelease core.init: (0) {0} Looking for database based on location of executable: /data/rosetta_2020.03/main/database/ core.init: (2) {0} Looking for database based on location of executable: /data/rosetta_2020.03/main/database/ apps.public.cyclic_peptide.simple_cycpep_predict: (0) {0} Starting simple_cycpep_predict.cc, MPI version. apps.public.cyclic_peptide.simple_cycpep_predict: (0) {0} Application created 16 September 2015 by Vikram K. Mulligan, Ph.D., Baker laboratory. apps.public.cyclic_peptide.simple_cycpep_predict: (0) {0} For questions, contact vmullig@uw.edu. apps.public.cyclic_peptide.simple_cycpep_predict: (0) {0} core.scoring.ScoreFunctionFactory: (1) {0} SCOREFUNCTION: beta_nov16.wts apps.public.cyclic_peptide.simple_cycpep_predict: (0) {0} Launching 3 parallel processes with 2 levels of communication. apps.public.cyclic_peptide.simple_cycpep_predict: (0) {0} Batch size is 25 (level 1 to 2). core.scoring.ScoreFunctionFactory: (2) {0} SCOREFUNCTION: beta_nov16.wts core.scoring.ScoreFunctionFactory: (0) {0} SCOREFUNCTION: beta_nov16.wts core.scoring.etable: (2) {0} Starting energy table calculation core.scoring.etable: (1) {0} Starting energy table calculation core.scoring.etable: (1) {0} smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: (1) {0} smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: (2) {0} smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: (2) {0} smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: (1) {0} smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: (2) {0} smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: (0) {0} Starting energy table calculation core.scoring.etable: (0) {0} smooth_etable: changing atr/rep split to bottom of energy well core.scoring.etable: (0) {0} smooth_etable: spline smoothing lj etables (maxdis = 6) core.scoring.etable: (0) {0} smooth_etable: spline smoothing solvation etables (max_dis = 6) core.scoring.etable: (1) {0} Finished calculating energy tables. core.scoring.etable: (2) {0} Finished calculating energy tables. core.scoring.etable: (0) {0} Finished calculating energy tables. basic.io.database: (1) {0} Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: (2) {0} Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: (0) {0} Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv basic.io.database: (1) {0} Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: (0) {0} Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: (0) {0} Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: (1) {0} Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: (2) {0} Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv basic.io.database: (0) {0} Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: (2) {0} Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv basic.io.database: (0) {0} Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv basic.io.database: (1) {0} Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: (2) {0} Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv basic.io.database: (1) {0} Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv basic.io.database: (2) {0} Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv core.chemical.GlobalResidueTypeSet: (2) {0} Finished initializing fa_standard residue type set. Created 980 residue types core.chemical.GlobalResidueTypeSet: (2) {0} Total time to initialize 1.00406 seconds. core.chemical.GlobalResidueTypeSet: (0) {0} Finished initializing fa_standard residue type set. Created 980 residue types core.chemical.GlobalResidueTypeSet: (0) {0} Total time to initialize 1.00654 seconds. basic.io.database: (2) {0} Database file opened: scoring/score_functions/rama/fd_beta_nov2016/all.ramaProb basic.io.database: (0) {0} Database file opened: scoring/score_functions/rama/fd_beta_nov2016/all.ramaProb core.chemical.GlobalResidueTypeSet: (1) {0} Finished initializing fa_standard residue type set. Created 980 residue types core.chemical.GlobalResidueTypeSet: (1) {0} Total time to initialize 1.00594 seconds. basic.io.database: (1) {0} Database file opened: scoring/score_functions/rama/fd_beta_nov2016/all.ramaProb basic.io.database: (0) {0} Database file opened: scoring/score_functions/rama/fd_beta_nov2016/prepro.ramaProb basic.io.database: (2) {0} Database file opened: scoring/score_functions/rama/fd_beta_nov2016/prepro.ramaProb basic.io.database: (1) {0} Database file opened: scoring/score_functions/rama/fd_beta_nov2016/prepro.ramaProb basic.io.database: (0) {0} Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: (0) {0} Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: (0) {0} Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: (1) {0} Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: (1) {0} Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: (2) {0} Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt basic.io.database: (1) {0} Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: (1) {0} Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: (2) {0} Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt basic.io.database: (0) {0} Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: (2) {0} Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt basic.io.database: (2) {0} Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt basic.io.database: (1) {0} Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: (1) {0} Database file opened: scoring/score_functions/P_AA_pp/P_AA_n basic.io.database: (0) {0} Database file opened: scoring/score_functions/P_AA_pp/P_AA basic.io.database: (2) {0} Database file opened: scoring/score_functions/P_AA_pp/P_AA core.scoring.P_AA: (1) {0} shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: (1) {0} Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop basic.io.database: (0) {0} Database file opened: scoring/score_functions/P_AA_pp/P_AA_n basic.io.database: (2) {0} Database file opened: scoring/score_functions/P_AA_pp/P_AA_n core.scoring.P_AA: (2) {0} shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: (2) {0} Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop core.scoring.P_AA: (0) {0} shapovalov_lib::shap_p_aa_pp_smooth_level of 1( aka low_smooth ) got activated. basic.io.database: (0) {0} Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop basic.io.database: (2) {0} Database file opened: scoring/score_functions/bondlength_bondangle/hydroxyl_torsion_preference.txt basic.io.database: (0) {0} Database file opened: scoring/score_functions/bondlength_bondangle/hydroxyl_torsion_preference.txt basic.io.database: (1) {0} Database file opened: scoring/score_functions/bondlength_bondangle/hydroxyl_torsion_preference.txt protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI: (0) {0} Emperor read sequence from disk and and sent "CYS LYS GLY LEU ALA PHE ALA ALA GLY GLU SER CYS" to all other nodes. protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI: (0) {0} Emperor reading native pose debug.pdb from disk. core.import_pose.import_pose: (0) {0} File 'debug.pdb' automatically determined to be of type PDB core.io.pose_from_sfr.PoseFromSFRBuilder: (0) {0} [ WARNING ] discarding 1 atoms at position 11 in file debug.pdb. Best match rsd_type: SER core.io.pose_from_sfr.PoseFromSFRBuilder: (0) {0} [ WARNING ] can't find pose atom for file-residue 11 atom SG (trying to store temperature in PDBInfo) protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI: (0) {0} Read 12-residue pose from disk and broadcasted it to all other nodes. core.io.silent.SilentFileData: (1) {0} Reading all structures from suppress_bitflip core.io.silent.SilentFileData: (2) {0} Reading all structures from suppress_bitflip core.io.silent.SilentFileData: (1) {0} Finished reading 1 structures from suppress_bitflip core.io.silent.SilentFileData: (2) {0} Finished reading 1 structures from suppress_bitflip ERROR: Assertion `seqpos != 0` failed. ERROR:: Exit from: src/core/pose/variant_util.cc line: 167 ERROR: Assertion `seqpos != 0` failed. ERROR:: Exit from: src/core/pose/variant_util.cc line: 167 protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI: (1) {0} [ ERROR ] Exception in SimpleCycpepPredictApplication caught: protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI: (1) {0} [ ERROR ] File: src/core/pose/variant_util.cc:167 [ ERROR ] UtilityExitException ERROR: Assertion `seqpos != 0` failed. protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI: (1) {0} [ ERROR ] Recovering from error and continuing to next job. ERROR: Assertion `seqpos != 0` failed. ERROR:: Exit from: src/core/pose/variant_util.cc line: 167 protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI: (1) {0} [ ERROR ] Exception in SimpleCycpepPredictApplication caught: protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI: (1) {0} [ ERROR ] File: src/core/pose/variant_util.cc:167 [ ERROR ] UtilityExitException ERROR: Assertion `seqpos != 0` failed. protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI: (1) {0} [ ERROR ] Recovering from error and continuing to next job. ERROR: Assertion `seqpos != 0` failed. ERROR:: Exit from: src/core/pose/variant_util.cc line: 167 protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI: (1) {0} [ ERROR ] Exception in SimpleCycpepPredictApplication caught: protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI: (1) {0} [ ERROR ] File: src/core/pose/variant_util.cc:167 [ ERROR ] UtilityExitException ERROR: Assertion `seqpos != 0` failed. protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI: (1) {0} [ ERROR ] Recovering from error and continuing to next job. protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI: (2) {0} [ ERROR ] Exception in SimpleCycpepPredictApplication caught: protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI: (2) {0} [ ERROR ] File: src/core/pose/variant_util.cc:167 [ ERROR ] UtilityExitException ERROR: Assertion `seqpos != 0` failed. protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI: (2) {0} [ ERROR ] Recovering from error and continuing to next job. Summary for 0 job(s) returning results: MPI_slave_node Jobindex_on_node RMSD Energy Hbonds CisPepBonds Node_path_to_emperor protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI: (0) {0} Emperor is writing final structures to disk. protocols.cyclic_peptide_predict.SimpleCycpepPredictApplication_MPI_summary: (0) {0} The simple_cycpep_predict application completed 100 of 100 jobs in 0.10125 seconds. 0 jobs returned structures, the top 0 of which were written to disk. apps.public.cyclic_peptide.simple_cycpep_predict: (1) {0} Finished simple_cycpep_predict.cc. Exiting. apps.public.cyclic_peptide.simple_cycpep_predict: (0) {0} Finished simple_cycpep_predict.cc. Exiting. apps.public.cyclic_peptide.simple_cycpep_predict: (2) {0} Finished simple_cycpep_predict.cc. Exiting.