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

LogFile log ******** (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.score_function_corrections: [ WARNING ] Flag -restore_talaris_behavior is set but -weights are also specified. Not changing input weights file! core.init: Rosetta extras: [] core.init: command: /home/benchmark/rosetta/source/bin/fit_helixparams.default.linuxgccaddsan -in:path:database_cache_dir /home/benchmark/rosetta/.database-binaries/ubuntugccaddsan @flags -database /home/benchmark/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 apps.pilot.vmullig.fit_helixparams: Starting fit_helixparams.cc apps.pilot.vmullig.fit_helixparams: Pilot app created 23 October 2014 by Vikram K. Mulligan, Ph.D., Baker laboratory. apps.pilot.vmullig.fit_helixparams: App updated 29 May 2015 to support multiple residues per repeating unit. apps.pilot.vmullig.fit_helixparams: For questions, contact vmullig@uw.edu. apps.pilot.vmullig.fit_helixparams: apps.pilot.vmullig.fit_helixparams: Building 75 repeat polymer (150 residues) from ALA, DALA building blocks. core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch LowerDNA as requested core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch UpperDNA as requested core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch VirtualDNAPhosphate as requested core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch ShoveBB as requested core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch VirtualBB as requested core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch N_acetylated as requested core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch C_methylamidated as requested core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch SpecialRotamer as requested core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch Cterm_amidation as requested core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch pro_hydroxylated_case1 as requested core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch pro_hydroxylated_case2 as requested core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch ser_phosphorylated as requested core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch thr_phosphorylated as requested core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch tyr_phosphorylated as requested core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch tyr_sulfated as requested core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch lys_monomethylated as requested core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch lys_dimethylated as requested core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch lys_trimethylated as requested core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch lys_acetylated as requested core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch glu_carboxylated as requested core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch cys_acetylated as requested core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch tyr_diiodinated as requested core.chemical.GlobalResidueTypeSet: While generating GlobalResidueTypeSet fa_standard: Skipping patch MethylatedProteinCterm as requested protocols.helical_bundle.FitSimpleHelix: Fitting reference atom CA in reference residue (residue 2). protocols.helical_bundle.FitSimpleHelix: Reference atom r1 = 41.4493 protocols.helical_bundle.FitSimpleHelix: Reference atom omega1 = 0.0685808 protocols.helical_bundle.FitSimpleHelix: Reference atom dz1 = -3.4015e-06 protocols.helical_bundle.FitSimpleHelix: Reference atom delta_omega1 = 0 protocols.helical_bundle.FitSimpleHelix: Reference atom delta_z1 = 0 protocols.helical_bundle.FitSimpleHelix: Aligning pose to ideal helix. protocols.helical_bundle.FitSimpleHelix: Fitting N atom. protocols.helical_bundle.FitSimpleHelix: Atom N r1 = 41.0653 protocols.helical_bundle.FitSimpleHelix: omega1 = 0.0685808 protocols.helical_bundle.FitSimpleHelix: dz1 = -3.4015e-06 protocols.helical_bundle.FitSimpleHelix: Atom N delta_omega1 = -0.0271239 protocols.helical_bundle.FitSimpleHelix: Atom N delta_z1 = 0.852134 protocols.helical_bundle.FitSimpleHelix: Fitting C atom. protocols.helical_bundle.FitSimpleHelix: Atom C r1 = 41.935 protocols.helical_bundle.FitSimpleHelix: omega1 = 0.0685808 protocols.helical_bundle.FitSimpleHelix: dz1 = -3.4015e-06 protocols.helical_bundle.FitSimpleHelix: Atom C delta_omega1 = -6.25485 protocols.helical_bundle.FitSimpleHelix: Atom C delta_z1 = 0.830492 protocols.helical_bundle.FitSimpleHelix: Fitting N atom. protocols.helical_bundle.FitSimpleHelix: Atom N r1 = 41.0653 protocols.helical_bundle.FitSimpleHelix: omega1 = 0.0685808 protocols.helical_bundle.FitSimpleHelix: dz1 = -3.4015e-06 protocols.helical_bundle.FitSimpleHelix: Atom N delta_omega1 = -0.0271238 protocols.helical_bundle.FitSimpleHelix: Atom N delta_z1 = 1.67345 protocols.helical_bundle.FitSimpleHelix: Fitting CA atom. protocols.helical_bundle.FitSimpleHelix: Atom CA r1 = 41.4495 protocols.helical_bundle.FitSimpleHelix: omega1 = 0.0685808 protocols.helical_bundle.FitSimpleHelix: dz1 = -3.4015e-06 protocols.helical_bundle.FitSimpleHelix: Atom CA delta_omega1 = -6.86362e-07 protocols.helical_bundle.FitSimpleHelix: Atom CA delta_z1 = 2.52559 protocols.helical_bundle.FitSimpleHelix: Fitting C atom. protocols.helical_bundle.FitSimpleHelix: Atom C r1 = 41.9355 protocols.helical_bundle.FitSimpleHelix: omega1 = 0.0685808 protocols.helical_bundle.FitSimpleHelix: dz1 = -3.4015e-06 protocols.helical_bundle.FitSimpleHelix: Atom C delta_omega1 = -144.485 protocols.helical_bundle.FitSimpleHelix: Atom C delta_z1 = 1.69565 protocols.helical_bundle.FitSimpleHelix: Fit complete. apps.pilot.vmullig.fit_helixparams: Writing result.pdb. apps.pilot.vmullig.fit_helixparams: Writing result.crick_params apps.pilot.vmullig.fit_helixparams: apps.pilot.vmullig.fit_helixparams: Results from the fitter: apps.pilot.vmullig.fit_helixparams: Res ID Atom r1 omega1 z1 delta_omega1 delta_z1 apps.pilot.vmullig.fit_helixparams: 1 1 N 41.065259 0.068580826 -3.401503e-06 -0.02712388 0.85213429 apps.pilot.vmullig.fit_helixparams: 1 2 CA * 41.449324 0.068580826 -3.401503e-06 0 0 apps.pilot.vmullig.fit_helixparams: 1 3 C 41.935023 0.068580826 -3.401503e-06 -6.254854 0.83049243 apps.pilot.vmullig.fit_helixparams: 2 1 N 41.065259 0.068580826 -3.401503e-06 -0.027123838 1.6734528 apps.pilot.vmullig.fit_helixparams: 2 2 CA 41.449499 0.068580826 -3.401503e-06 -6.8636187e-07 2.5255863 apps.pilot.vmullig.fit_helixparams: 2 3 C 41.935455 0.068580826 -3.401503e-06 -144.48493 1.6956542 apps.pilot.vmullig.fit_helixparams: (*Reference atom.) apps.pilot.vmullig.fit_helixparams: apps.pilot.vmullig.fit_helixparams: Finished fit_helixparams.cc. Exiting.