core.init: Rosetta version unknown:3bdcad6272fdb86400b86da9e5673f3fa62656ec 2017-02-18 05:03:14 -0500 from /home/benchmark/release/rosetta/git/release/rosetta.binary.linux.release.git core.init: command: rosetta_scripts.static.linuxgccrelease @inputs/rosetta.flags core.init: 'RNG device' seed mode, using '/dev/urandom', seed=-325818827 seed_offset=0 real_seed=-325818827 core.init.random: RandomGenerator:init: Normal mode, seed=-325818827 RG_type=mt19937 core.init: found database environment variable ROSETTA3_DB: /tools/bioinfo/app/Rosetta/3.8-foss-2016b/database protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs protocols.jd2.PDBJobInputter: pushed inputs/run3-16_S_0001.pdb nstruct index 1 protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... protocols.jd2.JobDistributor: Parser is present. Input mover will be overwritten with whatever the parser creates. protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: filling pose from PDB inputs/run3-16_S_0001.pdb core.chemical.GlobalResidueTypeSet: Finished initializing fa_standard residue type set. Created 544 residue types core.chemical.GlobalResidueTypeSet: Total time to initialize 1.29 seconds. core.import_pose.import_pose: File 'inputs/run3-16_S_0001.pdb' automatically determined to be of type PDB core.scoring.ScoreFunctionFactory: SCOREFUNCTION: talaris2014 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/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/rama/Rama_smooth_dyn.dat_ss_6.4 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 basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_pp core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/ghurj/.rosetta/database/rotamer/ExtendedOpt1-5/Dunbrack10.lib.bin'. core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.34 seconds to load from binary core.pack.task: Packer task: initialize from command line() core.pack.pack_rotamers: built 3987 rotamers at 940 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating DensePDInteractionGraph core.pack.interaction_graph.interaction_graph_factory: IG: 3918760 bytes core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 2.873 chino= 2 position: 2 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 39.938 chino= 2 position: 11 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 14.899 chino= 2 position: 16 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 166.367 chino= 3 position: 22 TYR TYR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 39.511 chino= 2 position: 27 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 0.641 chino= 3 position: 28 TYR TYR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 7.289 chino= 2 position: 31 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 11.784 chino= 2 position: 46 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 16.236 chino= 2 position: 53 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 1.904 chino= 2 position: 54 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 19.790 chino= 2 position: 62 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 1.022 chino= 2 position: 68 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 12.533 chino= 2 position: 72 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 0.857 chino= 2 position: 74 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 0.293 chino= 3 position: 80 TYR TYR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 0.319 chino= 2 position: 82 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 2.886 chino= 2 position: 89 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 2.997 chino= 2 position: 92 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 68.187 chino= 2 position: 93 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 5.676 chino= 2 position: 99 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 0.682 chino= 2 position: 101 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 82.687 chino= 2 position: 112 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 0.689 chino= 3 position: 114 TYR TYR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 30.468 chino= 2 position: 117 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 0.350 chino= 3 position: 120 TYR TYR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 46.802 chino= 2 position: 121 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 144.531 chino= 2 position: 127 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 59.395 chino= 2 position: 133 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 179.923 chino= 3 position: 140 TYR TYR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 6.024 chino= 3 position: 146 TYR TYR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 3.462 chino= 3 position: 149 TYR TYR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 50.385 chino= 3 position: 154 TYR TYR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 6.795 chino= 2 position: 156 CYS CYS core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 0.644 chino= 3 position: 166 TYR TYR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 2.315 chino= 2 position: 167 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 5.361 chino= 2 position: 173 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 35.935 chino= 2 position: 175 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 19.186 chino= 2 position: 184 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 21.424 chino= 2 position: 187 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 7.494 chino= 2 position: 196 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 18.583 chino= 2 position: 199 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 178.806 chino= 3 position: 202 TYR TYR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 1.167 chino= 2 position: 204 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 0.973 chino= 3 position: 211 TYR TYR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 8.422 chino= 3 position: 214 TYR TYR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 57.505 chino= 2 position: 216 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 0.131 chino= 3 position: 220 TYR TYR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 20.841 chino= 2 position: 224 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 22.362 chino= 3 position: 230 TYR TYR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 2.501 chino= 2 position: 236 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 2.261 chino= 2 position: 249 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 102.540 chino= 2 position: 250 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 54.514 chino= 2 position: 251 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 151.589 chino= 2 position: 254 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 175.409 chino= 2 position: 257 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 14.095 chino= 2 position: 259 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 4.655 chino= 2 position: 260 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 40.301 chino= 2 position: 265 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 34.979 chino= 2 position: 276 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 18.723 chino= 2 position: 278 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 15.110 chino= 3 position: 280 TYR TYR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 16.305 chino= 2 position: 286 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 18.689 chino= 2 position: 290 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 1.051 chino= 2 position: 296 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 2.493 chino= 2 position: 297 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 18.352 chino= 2 position: 300 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 17.252 chino= 2 position: 312 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] heavyatom chi angle change: chidev= 180.000 chino= 3 position: 314 GLN GLN core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 5.848 chino= 2 position: 315 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 12.174 chino= 2 position: 319 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 3.226 chino= 2 position: 322 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 11.318 chino= 2 position: 324 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 93.473 chino= 2 position: 325 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 0.837 chino= 2 position: 334 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 9.271 chino= 3 position: 338 TYR TYR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 37.488 chino= 2 position: 348 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 0.207 chino= 2 position: 349 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 4.277 chino= 2 position: 357 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 2.862 chino= 2 position: 365 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 3.915 chino= 2 position: 368 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 18.777 chino= 2 position: 370 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 2.095 chino= 2 position: 372 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 14.954 chino= 2 position: 373 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 78.074 chino= 2 position: 374 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 1.257 chino= 2 position: 375 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 1.232 chino= 2 position: 376 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 1.582 chino= 2 position: 381 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 17.330 chino= 2 position: 385 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 2.452 chino= 2 position: 386 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 10.135 chino= 2 position: 387 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 14.333 chino= 2 position: 394 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 4.986 chino= 2 position: 402 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 12.871 chino= 2 position: 410 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 34.590 chino= 2 position: 413 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 30.308 chino= 2 position: 417 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 40.144 chino= 2 position: 418 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 1.096 chino= 3 position: 422 TYR TYR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 15.274 chino= 2 position: 430 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 34.007 chino= 2 position: 432 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 27.959 chino= 2 position: 433 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 1.465 chino= 3 position: 440 TYR TYR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 1.026 chino= 2 position: 449 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 56.108 chino= 2 position: 455 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 1.617 chino= 2 position: 458 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 35.882 chino= 2 position: 465 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 5.254 chino= 2 position: 467 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 176.733 chino= 3 position: 469 TYR TYR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 25.751 chino= 3 position: 471 TYR TYR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 12.334 chino= 2 position: 473 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 37.407 chino= 2 position: 477 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 23.611 chino= 2 position: 494 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 57.363 chino= 2 position: 501 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 19.195 chino= 3 position: 502 TYR TYR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 15.445 chino= 2 position: 504 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 28.912 chino= 2 position: 510 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 36.744 chino= 2 position: 519 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 38.932 chino= 2 position: 532 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 12.194 chino= 2 position: 538 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 1.881 chino= 3 position: 553 TYR TYR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 8.680 chino= 3 position: 557 TYR TYR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 15.501 chino= 2 position: 560 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 11.432 chino= 2 position: 561 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 15.537 chino= 2 position: 566 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 14.876 chino= 2 position: 567 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 170.657 chino= 3 position: 575 TYR TYR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 6.982 chino= 3 position: 580 TYR TYR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 14.754 chino= 2 position: 583 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 17.459 chino= 2 position: 584 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 3.485 chino= 2 position: 587 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 25.727 chino= 2 position: 599 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 179.709 chino= 3 position: 600 TYR TYR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 34.594 chino= 2 position: 602 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 4.873 chino= 2 position: 606 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 1.573 chino= 3 position: 609 TYR TYR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 11.291 chino= 2 position: 611 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 12.550 chino= 2 position: 612 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 0.533 chino= 2 position: 614 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 89.778 chino= 2 position: 615 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 20.892 chino= 2 position: 623 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 150.702 chino= 2 position: 631 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 10.408 chino= 3 position: 634 TYR TYR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 16.035 chino= 2 position: 636 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 2.385 chino= 3 position: 645 TYR TYR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 8.685 chino= 2 position: 647 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 0.308 chino= 2 position: 653 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 2.057 chino= 3 position: 654 TYR TYR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 0.894 chino= 3 position: 657 TYR TYR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 5.622 chino= 2 position: 660 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 9.437 chino= 2 position: 677 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 38.041 chino= 2 position: 678 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 4.520 chino= 2 position: 680 CYS CYS core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 179.091 chino= 3 position: 682 TYR TYR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 14.303 chino= 2 position: 687 CYS CYS core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 1.367 chino= 3 position: 695 TYR TYR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 14.032 chino= 2 position: 697 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 13.204 chino= 2 position: 708 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 2.120 chino= 3 position: 715 TYR TYR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 13.192 chino= 2 position: 716 CYS CYS core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 22.526 chino= 2 position: 723 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 6.221 chino= 2 position: 725 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 16.943 chino= 2 position: 734 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 18.704 chino= 2 position: 735 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 178.443 chino= 3 position: 736 TYR TYR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 13.321 chino= 2 position: 738 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 13.184 chino= 2 position: 739 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 37.485 chino= 2 position: 741 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 19.424 chino= 2 position: 742 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 2.834 chino= 3 position: 743 TYR TYR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 2.730 chino= 2 position: 747 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 1.129 chino= 3 position: 750 TYR TYR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 1.199 chino= 3 position: 751 TYR TYR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 15.724 chino= 2 position: 753 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 3.669 chino= 2 position: 754 CYS CYS core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 6.603 chino= 2 position: 755 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 4.085 chino= 3 position: 759 TYR TYR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 33.420 chino= 2 position: 761 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 55.319 chino= 2 position: 762 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 37.205 chino= 2 position: 767 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 4.203 chino= 2 position: 775 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 18.418 chino= 2 position: 776 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 177.245 chino= 3 position: 778 TYR TYR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 0.375 chino= 2 position: 795 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 111.320 chino= 3 position: 800 TYR TYR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 1.336 chino= 3 position: 806 TYR TYR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 4.741 chino= 3 position: 811 TYR TYR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 6.748 chino= 3 position: 812 TYR TYR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 15.187 chino= 2 position: 816 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 0.373 chino= 3 position: 829 TYR TYR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 10.080 chino= 2 position: 832 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 32.433 chino= 2 position: 835 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 10.912 chino= 2 position: 836 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 6.761 chino= 2 position: 841 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 25.770 chino= 2 position: 847 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 13.964 chino= 2 position: 852 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 7.295 chino= 2 position: 853 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 6.537 chino= 2 position: 854 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 5.759 chino= 2 position: 856 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 10.384 chino= 2 position: 866 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 14.852 chino= 2 position: 869 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 5.355 chino= 3 position: 878 TYR TYR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 49.787 chino= 3 position: 882 TYR TYR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 1.491 chino= 3 position: 886 TYR TYR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 159.491 chino= 2 position: 891 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 5.481 chino= 2 position: 893 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 1.392 chino= 2 position: 894 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 14.354 chino= 2 position: 900 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 18.229 chino= 2 position: 903 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 8.350 chino= 2 position: 905 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 0.716 chino= 2 position: 906 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 14.158 chino= 2 position: 908 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 38.350 chino= 2 position: 909 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 55.108 chino= 2 position: 911 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 10.056 chino= 2 position: 912 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 36.983 chino= 2 position: 913 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 3.881 chino= 2 position: 916 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 17.487 chino= 2 position: 918 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 17.960 chino= 2 position: 919 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 5.540 chino= 2 position: 921 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 0.550 chino= 3 position: 925 TYR TYR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 15.068 chino= 2 position: 927 THR THR core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 3.632 chino= 2 position: 932 SER SER core.io.pdb.file_data: [ OPT-H WARNING ] proton chi angle change: chidev= 2.883 chino= 3 position: 938 TYR TYR protocols.rosetta_scripts.RosettaScriptsParser: dock_design_filename=rosetta.xml 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: core.scoring.ScoreFunctionFactory: SCOREFUNCTION: talaris2014 basic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine core.scoring.etable: Using alternate parameters: LJ_RADIUS_SOFT in Etable construction. 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/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 protocols.jd2.parser.ScoreFunctionLoader: defined score function "hpatch" with weights "design_hpatch" core.select.residue_selector.LayerSelector: Setting LayerSelector to use sidechain neighbors to determine burial. core.select.residue_selector.LayerSelector: Set cutoffs for core and surface to 5.2 and 2, respectively, in LayerSelector. core.select.residue_selector.LayerSelector: Setting core=false boundary=false surface=true in LayerSelector. core.select.residue_selector.LayerSelector: Setting LayerSelector to use sidechain neighbors to determine burial. core.select.residue_selector.LayerSelector: Set cutoffs for core and surface to 5.2 and 2, respectively, in LayerSelector. protocols.jd2.parser.TaskOperationLoader: Defined TaskOperation named "protein_surface" of type OperateOnResidueSubset protocols.protein_interface_design.movers.FavorNativeResiduePreCycle: Setting res_type_constraint weight in scorefxn commandline to 1.5 Setting res_type_constraint weight in scorefxn hpatch to 1.5 Setting res_type_constraint weight in scorefxn score12 to 1.5 Setting res_type_constraint weight in scorefxn score4L to 1.5 Setting res_type_constraint weight in scorefxn score_docking to 1.5 Setting res_type_constraint weight in scorefxn score_docking_low to 1.5 Setting res_type_constraint weight in scorefxn soft_rep to 1.5 Setting res_type_constraint weight in scorefxn talaris2013 to 1.5 Setting res_type_constraint weight in scorefxn talaris2014 to 1.5 applying favor native residue to pose with weight: 1.5 protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "native" of type FavorNativeResidue protocols.RosettaScripts.util: Object design reading the following task_operations: Adding the following task operations protein_surface protocols.rosetta_scripts.RosettaScriptsParser: Defined mover named "design" of type PackRotamersMover protocols.rosetta_scripts.ParsedProtocol: ParsedProtocol mover with the following movers and filters protocols.rosetta_scripts.ParsedProtocol: added mover "native" with filter "true_filter" protocols.rosetta_scripts.ParsedProtocol: added mover "design" with filter "true_filter" protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: filling pose from saved copy inputs/run3-16_S_0001.pdb protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER FavorNativeResidue - native======================= protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN FILTER ======================= protocols.rosetta_scripts.ParsedProtocol: =======================END FILTER ======================= protocols.rosetta_scripts.ParsedProtocol: =======================BEGIN MOVER PackRotamersMover - design======================= basic.io.database: Database file opened: scoring/score_functions/SurfacePotential/average_hASA_by_res_and_neighbor.txt basic.io.database: Database file opened: scoring/score_functions/SurfacePotential/surface_score.txt basic.io.database: Database file opened: scoring/score_functions/SurfacePotential/hpatch_score.txt core.pack.interaction_graph.RotamerDots.RotamerDotsRadiusData: RotamerDotsRadiusData::RotamerDotsRadiusData(): reading in sasa radii database file core.pack.interaction_graph.RotamerDots.RotamerDotsRadiusData: ROSETTA_SASA_radii_: [ 1.89, 1.89, 2.1285, 2.0115, 1.9485, 1.665, 1.44, 1.44, 1.44, 1.44, 1.44, 1.44, 1.44, 1.44, 1.44, 1.44, 1.44, 1.44, 1.701, 1.44, 2.1285, 1.89, 1.44, 2.0425, 2.0425, 0.54, 1.08, 1.08, 0.54, 1.44, 1.6293, 1.71, 2.07, 2.22, 2.36, 1.09, 1.568, 1.0978, 0.78, 0.65, 1.185, 1.2986, 2.0425, 1.615, 1.6815, 0.2133, 1.615, 1.52, 2.0401, 1.6625, 1.52, 0.76, 1.3638, 1.7638, 1.181, 1.2255, 1.3725, 1.6215, 2.2495, 1.934, 1.6475, 1.5875, 1.572, 1.5115, 1.4805, 1.417, 2.1915, 2.14, 2.115, 2.1025, 2.0705, 2.057, 1.8205, 1.6725, 1.562, 1.5825, 1.526, 1.499, 1.4815, 1.4645, 1.4495, 1.574, 1.424, 2.2315, 2.196, 2.21, 2.235, 2.202, 2.2585, 1.8515, 1.761, 1.778, 1.803, 1.7875, 1.7735, 1.76, 1.7465, 1.684, 1.7255, 1.714, 1.7045, 1.6955, 1.687, 1.6775, 1.82, 1.5705, 1.585, 1.5345, 1.477, 1.56, 1.42, 1.377, 1.6465, 1.3525, 2.1735, 2.1485, 2.185, 2.3545, 2.375, 2.3825, 2.45, 1.8385, 1.739, 1.698, 1.712, 1.6975, 1.712, 1.712, 1.6905, 1.663, 1.6695, 1.6565, 1.6495, 1.643, 1.637, 1.624, 1.618, 0, 0, 0, 0, 0, 0, 0, 0, 0, ] core.pack.interaction_graph.RotamerDots.RotamerDotsRadiusData: RotamerDotsRadiusData::RotamerDotsRadiusData(): reading in sasa radii database file core.pack.interaction_graph.RotamerDots.RotamerDotsRadiusData: NACCESS_SASA_radii_: [ 1.76, 1.76, 1.87, 1.87, 1.87, 1.76, 1.65, 1.65, 1.65, 1.5, 1.65, 1.65, 1.4, 1.4, 1.4, 1.4, 1.4, 1.4, 1.85, 1.65, 1.87, 1.76, 1.4, 2.0425, 2.0425, 1, 1, 1, 1, 1.4, 1.8669, 1.71, 2.07, 2.22, 2.36, 1.09, 1.568, 1.0978, 0.78, 0.65, 1.185, 1.2986, 2.0425, 1.615, 1.6815, 0.2133, 1.615, 1.52, 2.0401, 1.6625, 1.52, 0.76, 1.3638, 1.7638, 1.181, 1.2255, 1.3725, 1.6215, 2.2495, 1.934, 1.6475, 1.5875, 1.572, 1.5115, 1.4805, 1.417, 2.1915, 2.14, 2.115, 2.1025, 2.0705, 2.057, 1.8205, 1.6725, 1.562, 1.5825, 1.526, 1.499, 1.4815, 1.4645, 1.4495, 1.574, 1.424, 2.2315, 2.196, 2.21, 2.235, 2.202, 2.2585, 1.8515, 1.761, 1.778, 1.803, 1.7875, 1.7735, 1.76, 1.7465, 1.684, 1.7255, 1.714, 1.7045, 1.6955, 1.687, 1.6775, 1.82, 1.5705, 1.585, 1.5345, 1.477, 1.56, 1.42, 1.377, 1.6465, 1.3525, 2.1735, 2.1485, 2.185, 2.3545, 2.375, 2.3825, 2.45, 1.8385, 1.739, 1.698, 1.712, 1.6975, 1.712, 1.712, 1.6905, 1.663, 1.6695, 1.6565, 1.6495, 1.643, 1.637, 1.624, 1.618, 0, 0, 0, 0, 0, 0, 0, 0, 0, ] core.pack.interaction_graph.RotamerDots.RotamerDotsRadiusData: get_NACCESS_SASA_radii_with_expanded_polars(): reading in sasa radii database file core.pack.interaction_graph.RotamerDots.RotamerDotsRadiusData: NACCESS_SASA_radii_with_expanded_polars_: [ 1.76, 1.76, 1.87, 1.87, 1.87, 1.76, 2.65, 2.65, 2.65, 2.5, 2.65, 2.65, 2.4, 2.4, 2.4, 2.4, 2.4, 2.4, 1.85, 2.65, 1.87, 1.76, 2.4, 2.0425, 2.0425, 1, 1, 1, 1, 2.4, 1.8669, 1.71, 2.07, 2.22, 2.36, 1.09, 1.568, 1.0978, 0.78, 0.65, 1.185, 1.2986, 2.0425, 2.615, 2.6815, 0.2133, 1.615, 2.52, 2.0401, 2.6625, 2.52, 0.76, 1.3638, 1.7638, 1.181, 1.2255, 1.3725, 1.6215, 2.2495, 1.934, 1.6475, 1.5875, 1.572, 1.5115, 1.4805, 1.417, 2.1915, 2.14, 2.115, 2.1025, 2.0705, 2.057, 1.8205, 1.6725, 1.562, 1.5825, 1.526, 1.499, 1.4815, 1.4645, 1.4495, 1.574, 1.424, 2.2315, 2.196, 2.21, 2.235, 2.202, 2.2585, 1.8515, 1.761, 1.778, 1.803, 1.7875, 1.7735, 1.76, 1.7465, 1.684, 1.7255, 1.714, 1.7045, 1.6955, 1.687, 1.6775, 1.82, 1.5705, 1.585, 1.5345, 1.477, 1.56, 1.42, 1.377, 1.6465, 1.3525, 2.1735, 2.1485, 2.185, 2.3545, 2.375, 2.3825, 2.45, 1.8385, 1.739, 1.698, 1.712, 1.6975, 1.712, 1.712, 1.6905, 1.663, 1.6695, 1.6565, 1.6495, 1.643, 1.637, 1.624, 1.618, 0, 0, 0, 0, 0, 0, 0, 0, 0, ] core.pack.interaction_graph.SurfacePotential: calculated total hpatch score: 382.56, individual patch scores: [ 100, 100, 4, 0, 0, 0.16, 1.44, 100, 0, 0.16, 0.16, 2.56, 0.16, 0, 0.16, 12.96, 0.64, 4, 0, 1.44, 12.96, 0, 2.56, 0, 0.64, 0, 0.16, 0.64, 0.16, 1.44, 0.64, 0, 2.56, 2.56, 0.64, 10.24, 0, 0.16, 0.16, 2.56, 0.64, 16, ] core.pack.interaction_graph.SurfacePotential: large patch, hpatch_score: 100, PyMOL expression: select p7, A/1/CG + A/1/SD + A/1/CE + A/2/CB + A/3/CB + A/3/CD2 + A/3/CE3 + A/3/CZ2 + A/3/CZ3 + A/3/CH2 + A/4/CG + A/4/CD1 + A/4/CD2 + A/5/CB + A/5/CD1 + A/5/CD2 + A/6/CB + A/6/CD1 + A/6/CD2 + A/8/CG1 + A/8/CG2 + A/9/CB + A/9/CD1 + A/10/CA + A/10/CB + A/11/CG2 + A/12/CG1 + A/12/CG2 + A/12/CD1 + A/14/CG + A/14/CD1 + A/14/CD2 + A/16/CB + A/16/CG2 + A/17/CA + A/17/CB + A/19/CG1 + A/19/CG2 + A/22/CD1 + A/22/CE1 + A/25/CB + A/25/CG + A/53/CG2 + A/57/CD1 + A/58/CB + A/58/CG + A/58/CD + A/59/CE1 + A/59/CZ + A/66/CD2 + A/160/CB + A/162/CB + A/162/CG + A/162/CD1 + A/162/CD2 + A/329/CE + A/380/CB + A/382/CB + A/383/CB + A/383/CD1 + A/383/CD2 + A/385/CG2 + A/422/CB + A/431/CG2 + A/434/CB + A/436/CE1 + A/439/CB + A/439/CG + A/439/CD1 + A/439/CD2 + A/439/CE1 + A/439/CE2 + A/439/CZ + A/440/CD2 + A/440/CE2 + A/443/CB + A/443/CG + A/443/CD2 + A/443/CE1 + A/443/CE2 + A/443/CZ + A/446/CG + A/446/SD + A/446/CE + A/458/CB + core.pack.interaction_graph.SurfacePotential: large patch, hpatch_score: 100, PyMOL expression: select p211, A/28/CB + A/28/CG + A/28/CD1 + A/28/CD2 + A/28/CE1 + A/28/CE2 + A/30/CB + A/30/CD1 + A/30/CD2 + A/32/CB + A/32/CG + A/32/CD1 + A/32/CD2 + A/32/CE1 + A/32/CE2 + A/32/CZ + A/34/CB + A/34/CG1 + A/34/CG2 + A/36/CD1 + A/36/CD2 + A/38/CG2 + A/38/CD1 + A/39/CA + A/39/CB + A/39/CG + A/39/CD + A/43/CB + A/43/CG + A/43/CD1 + A/43/CD2 + A/43/CE1 + A/43/CE2 + A/43/CZ + A/49/CG2 + A/49/CD1 + A/51/CB + A/51/CD1 + A/51/CD2 + A/51/CE1 + A/51/CE2 + A/51/CZ + A/71/CD1 + A/71/CD2 + A/75/CB + A/75/CG + A/75/CD + A/75/CE + A/76/CB + A/76/CG1 + A/76/CG2 + A/78/CB + A/78/CG + A/78/CD1 + A/78/CD2 + A/78/CE1 + A/78/CE2 + A/78/CZ + A/80/CD1 + A/80/CE1 + A/80/CE2 + A/87/CB + A/87/CG + A/87/CD + A/89/CB + A/89/CG2 + A/114/CB + A/114/CG + A/114/CD1 + A/114/CD2 + A/114/CE1 + A/114/CE2 + A/114/CZ + A/116/CB + A/116/SD + A/116/CE + A/118/CG2 + A/118/CD1 + A/120/CB + A/120/CG + A/120/CD1 + A/120/CD2 + A/120/CE1 + A/120/CE2 + A/122/CA + A/124/CB + A/124/CG + A/124/CD1 + A/124/CD2 + A/140/CE1 + A/153/CD1 + A/166/CB + A/166/CD2 + A/166/CE2 + A/168/CG1 + A/168/CG2 + A/170/CD1 + A/170/CD2 + A/190/CB + A/192/CB + A/196/CA + A/196/CB + A/196/CG2 + A/197/CB + A/197/CG + A/197/CD1 + A/197/CD2 + A/198/CB + A/198/CG + A/198/CD1 + A/198/CD2 + A/200/CG1 + A/200/CG2 + A/202/CB + A/202/CD1 + A/202/CE1 + A/205/CB + A/205/CG + A/205/CD + A/207/CA + A/220/CB + A/220/CG + A/220/CD1 + A/220/CD2 + A/220/CE1 + A/220/CE2 + A/220/CZ + core.pack.interaction_graph.SurfacePotential: large patch, hpatch_score: 4, PyMOL expression: select p479, A/60/CB + A/61/CG1 + A/61/CG2 + A/64/CG2 + A/64/CD1 + A/91/CG1 + A/91/CG2 + A/91/CD1 + A/93/CG2 + A/95/CB + A/95/CG + A/95/CD + A/95/CE + A/104/CG1 + A/104/CG2 + A/108/CD1 + core.pack.interaction_graph.SurfacePotential: large patch, hpatch_score: 100, PyMOL expression: select p1443, A/178/CD + A/178/CE + A/180/CA + A/180/CB + A/183/CB + A/183/CG1 + A/183/CG2 + A/188/CB + A/188/CD1 + A/188/CD2 + A/191/CB + A/191/CD + A/222/CB + A/222/CG + A/222/CD + A/222/CE + A/223/CB + A/223/CG + A/223/CD + A/226/CB + A/226/CG + A/227/CA + A/227/CB + A/227/CG + A/227/CD1 + A/227/CD2 + A/227/CE1 + A/227/CE2 + A/227/CZ + A/228/CG + A/228/CD + A/229/CB + A/229/CG1 + A/229/CG2 + A/231/CG2 + A/234/CA + A/252/CB + A/252/CG1 + A/252/CG2 + A/253/CG2 + A/256/CB + A/256/CD1 + A/256/CD2 + A/260/CB + A/264/CB + A/264/CD1 + A/264/CD2 + A/266/CD1 + A/317/CE1 + A/317/CZ + A/318/CA + A/318/CB + A/335/CD1 + A/336/CB + A/336/CG + A/339/CG2 + A/339/CD1 + A/340/CB + A/343/CB + A/347/CD1 + A/347/CD2 + A/351/CZ2 + A/351/CZ3 + A/351/CH2 + A/353/CD2 + A/355/CB + A/355/CG + A/406/CA + A/407/CA + A/407/CB + A/407/CG + A/407/SD + A/407/CE + A/410/CG2 + A/411/CB + A/411/CG + A/411/CD1 + A/411/CD2 + A/414/CB + A/415/CB + A/415/CG + A/415/CD + A/417/CG2 + A/418/CB + A/419/CE1 + A/419/CZ + A/420/CB + A/420/CG1 + A/420/CG2 + A/423/CB + A/423/CG1 + A/423/CG2 + A/437/CD1 + A/437/CD2 + A/500/CD2 + A/502/CB + A/502/CD2 + A/502/CE2 + A/515/CA + A/518/CA + A/518/CB + A/518/CG + A/518/CD + A/518/CE + A/519/CA + A/519/CB + A/519/CG2 + A/521/CG1 + A/521/CG2 + A/523/CD1 + A/552/CD + A/580/CD2 + A/580/CE1 + A/580/CE2 + A/580/CZ + A/581/CB + A/581/CD1 + A/581/CD2 + A/666/CB + A/666/CG + A/668/CB + A/668/CD + core.pack.interaction_graph.SurfacePotential: large patch, hpatch_score: 12.96, PyMOL expression: select p2967, A/361/CA + A/361/CB + A/362/CG + A/362/CD1 + A/362/CD2 + A/366/CB + A/377/CB + A/377/CG + A/377/CD + A/381/CB + A/389/CG1 + A/389/CG2 + A/392/CD2 + A/392/CE1 + A/392/CE2 + A/392/CZ + A/393/CG2 + A/395/CA + A/395/CB + A/396/CB + A/396/CG + A/396/CD + A/398/CG1 + A/398/CD1 + A/625/CA + A/626/CE1 + A/626/CZ + A/629/CG + A/629/CD1 + A/629/CD2 + A/632/CB + A/632/CD1 + A/632/CD2 + A/788/CB + A/788/CG1 + A/788/CG2 + A/796/CG + A/796/CE + A/826/CB + A/826/CD1 + A/826/CD2 + A/829/CG + A/829/CD1 + A/829/CD2 + A/829/CE1 + A/829/CE2 + A/830/CD1 + A/830/CD2 + A/833/CG + A/833/CD1 + A/833/CD2 + A/834/CA + A/858/CG + A/858/CD + A/858/CE + A/859/CB + A/860/CG2 + A/863/CB + A/867/CG2 + core.pack.interaction_graph.SurfacePotential: large patch, hpatch_score: 4, PyMOL expression: select p3571, A/442/CE + A/455/CG2 + A/456/CD1 + A/456/CD2 + A/459/CG1 + A/459/CD1 + A/462/CG + A/463/CE3 + A/463/CZ2 + A/463/CZ3 + A/463/CH2 + A/467/CB + A/496/CD2 + A/496/CE3 + A/496/CZ2 + A/496/CZ3 + A/496/CH2 + A/498/CD1 + A/526/CD + A/526/CE + A/527/CB + A/527/CG1 + core.pack.interaction_graph.SurfacePotential: large patch, hpatch_score: 12.96, PyMOL expression: select p4001, A/506/CE1 + A/506/CE2 + A/506/CZ + A/510/CB + A/510/CG2 + A/511/CB + A/511/CG + A/511/CD + A/511/CE + A/513/CB + A/513/CD1 + A/514/CB + A/514/CD1 + A/514/CD2 + A/540/CB + A/542/CB + A/542/CD1 + A/542/CD2 + A/561/CA + A/561/CB + A/564/CD2 + A/565/CG + A/565/CD1 + A/565/CD2 + A/569/CD2 + A/572/CB + A/573/CG1 + A/573/CG2 + A/575/CB + A/575/CG + A/575/CD1 + A/575/CD2 + A/575/CE1 + A/575/CE2 + A/575/CZ + A/576/CD1 + A/576/CD2 + A/577/CA + A/577/CB + A/577/CG + A/577/CD + A/577/CE + A/580/CB + A/616/CD1 + A/616/CD2 + A/903/CG2 + core.pack.interaction_graph.SurfacePotential: large patch, hpatch_score: 10.24, PyMOL expression: select p6395, A/636/CB + A/765/CD1 + A/802/CG + A/803/CA + A/803/CB + A/805/CA + A/806/CB + A/806/CG + A/806/CD1 + A/806/CD2 + A/806/CE1 + A/806/CE2 + A/807/CE1 + A/807/CZ + A/810/CA + A/810/CG + A/810/CE + A/839/CB + A/839/CD2 + A/840/CD1 + A/840/CD2 + A/842/CG1 + A/842/CG2 + A/842/CD1 + A/843/CB + A/843/CG + A/843/CD1 + A/843/CD2 + A/843/CE1 + A/843/CE2 + A/843/CZ + A/846/CB + A/846/CG + A/846/CD1 + A/846/CD2 + A/846/CE1 + A/846/CE2 + A/846/CZ + core.pack.interaction_graph.SurfacePotential: large patch, hpatch_score: 16, PyMOL expression: select p7329, A/639/CD + A/641/CG + A/642/CD2 + A/645/CD1 + A/645/CE1 + A/920/CD2 + A/922/CB + A/923/CB + A/923/CG1 + A/923/CG2 + A/924/CG1 + A/924/CG2 + A/924/CD1 + A/925/CD1 + A/925/CE1 + A/925/CE2 + A/925/CZ + A/926/CB + A/927/CB + A/927/CG2 + A/928/CD1 + A/928/CD2 + A/930/CG1 + A/930/CG2 + A/930/CD1 + A/931/CG + A/931/SD + A/931/CE + A/935/CG2 + A/935/CD1 + A/936/CD2 + A/937/CB + A/937/CG + A/937/CD + A/938/CB + A/938/CD1 + A/938/CE1 + core.pack.pack_rotamers: built 223730 rotamers at 940 positions. core.pack.interaction_graph.interaction_graph_factory: Instantiating PDHPatchInteractionGraph core.pack.interaction_graph.interaction_graph_factory: IG: 2753055960 bytes Segmentation fault