core.init: Rosetta version exported from http://www.rosettacommons.org core.init: command: /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/source/bin/remodel.linuxgccrelease -database /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database -s /home/lanselibai/Cheng/20150117_Homology_disulfide/4KMT_FullAtom_missding_residue_in_HC.pdb -remodel:blueprint /home/lanselibai/Cheng/20150117_Homology_disulfide/blueprint.4KMT_350-353_437-442 -remodel:quick_and_dirty -run:chain H -remodel:num_trajectory 1 -overwrite core.init: 'RNG device' seed mode, using '/dev/urandom', seed=945475124 seed_offset=0 real_seed=945475124 core.init.random: RandomGenerator:init: Normal mode, seed=945475124 RG_type=mt19937 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 core.scoring.ScoreFunctionFactory: SCOREFUNCTION: talaris2013 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/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 protocols.jd2.PDBJobInputter: Instantiate PDBJobInputter protocols.jd2.PDBJobInputter: PDBJobInputter::fill_jobs protocols.jd2.PDBJobInputter: pushed /home/lanselibai/Cheng/20150117_Homology_disulfide/4KMT_FullAtom_missding_residue_in_HC.pdb nstruct index 1 protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ... protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job protocols.jd2.PDBJobInputter: filling pose from PDB /home/lanselibai/Cheng/20150117_Homology_disulfide/4KMT_FullAtom_missding_residue_in_HC.pdb core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 737 residue types core.conformation.Conformation: Found disulfide between residues 23 88 core.conformation.Conformation: current variant for 23 CYS core.conformation.Conformation: current variant for 88 CYS core.conformation.Conformation: current variant for 23 CYD core.conformation.Conformation: current variant for 88 CYD core.conformation.Conformation: Found disulfide between residues 134 194 core.conformation.Conformation: current variant for 134 CYS core.conformation.Conformation: current variant for 194 CYS core.conformation.Conformation: current variant for 134 CYD core.conformation.Conformation: current variant for 194 CYD core.conformation.Conformation: Found disulfide between residues 214 432 core.conformation.Conformation: current variant for 214 CYS core.conformation.Conformation: current variant for 432 CYS core.conformation.Conformation: current variant for 214 CYD core.conformation.Conformation: current variant for 432 CYD core.conformation.Conformation: Found disulfide between residues 236 310 core.conformation.Conformation: current variant for 236 CYS core.conformation.Conformation: current variant for 310 CYS core.conformation.Conformation: current variant for 236 CYD core.conformation.Conformation: current variant for 310 CYD core.conformation.Conformation: Found disulfide between residues 356 412 core.conformation.Conformation: current variant for 356 CYS core.conformation.Conformation: current variant for 412 CYS core.conformation.Conformation: current variant for 356 CYD core.conformation.Conformation: current variant for 412 CYD core.pack.task: Packer task: initialize from command line() protocols.forge.remodel.RemodelMover: apply(): entered RemodelMover apply(). pose.total_residue(): 432 protocols.forge.remodel.RemodelMover: 432 protocols.forge.remodel.RemodelMover: apply(): input PDB dssp assignment: (based on start structure) protocols.forge.remodel.RemodelMover: LLLEEEELLEEEELLLLLEEEEEEELLLLLLLEEEEEELLLLLLEEEEELLLEELLLLLLLEEEEEELLEEEEEELLLLHHHLEEEEEEELLLLLLEELLLEEEEELLLLELLEEEEELLLHHHHHHLEEEEEEEEEEEELLLLEEEEEELLEELLLLEEEEELLLLLLLLLEEEEEEEEEEHHHHHHLLEEEEEEELLLLLLLEEEEEELLLLLLEEEELLLEEELLLLLEEEEEEEELLLHHHLEEEEEEELLLLLEEEEEEEELLLLEEEELLLLLLLLEEEEEHHHLEEEEEELLLLHHHLEEEEEEEEELLLLEEEEELLLEEEEELLLLLELLEEEEELLLLLLEEEEEEEEEEEELLLLEEEEHHHLELLLEEELLLEELLLLLEEEEEEEEEEHHHLLLLLLEEEEEEHHHLEEEEEELLLLLL protocols.forge.remodel.RemodelMover: apply(): reading blueprint file protocols.forge.remodel.RemodelData: Found token 349 on blueprint line '349' protocols.forge.remodel.RemodelData: Found token K on blueprint line '349' protocols.forge.remodel.RemodelData: Found token D on blueprint line '349' protocols.forge.remodel.RemodelData: Found token PIKAA on blueprint line '349' protocols.forge.remodel.RemodelData: Found token K on blueprint line '349' protocols.forge.remodel.RemodelData: design position 349 to K LYS protocols.forge.remodel.RemodelData: Found token 0 on blueprint line '350' protocols.forge.remodel.RemodelData: Found token x on blueprint line '350' protocols.forge.remodel.RemodelData: Found token D on blueprint line '350' protocols.forge.remodel.RemodelData: Found token PIKAA on blueprint line '350' protocols.forge.remodel.RemodelData: Found token S on blueprint line '350' protocols.forge.remodel.RemodelData: design position 350 to S SER protocols.forge.remodel.RemodelData: Found token 0 on blueprint line '351' protocols.forge.remodel.RemodelData: Found token x on blueprint line '351' protocols.forge.remodel.RemodelData: Found token D on blueprint line '351' protocols.forge.remodel.RemodelData: Found token PIKAA on blueprint line '351' protocols.forge.remodel.RemodelData: Found token T on blueprint line '351' protocols.forge.remodel.RemodelData: design position 351 to T THR protocols.forge.remodel.RemodelData: Found token 0 on blueprint line '352' protocols.forge.remodel.RemodelData: Found token x on blueprint line '352' protocols.forge.remodel.RemodelData: Found token D on blueprint line '352' protocols.forge.remodel.RemodelData: Found token PIKAA on blueprint line '352' protocols.forge.remodel.RemodelData: Found token S on blueprint line '352' protocols.forge.remodel.RemodelData: design position 352 to S SER protocols.forge.remodel.RemodelData: Found token 0 on blueprint line '353' protocols.forge.remodel.RemodelData: Found token x on blueprint line '353' protocols.forge.remodel.RemodelData: Found token D on blueprint line '353' protocols.forge.remodel.RemodelData: Found token PIKAA on blueprint line '353' protocols.forge.remodel.RemodelData: Found token G on blueprint line '353' protocols.forge.remodel.RemodelData: design position 353 to G GLY protocols.forge.remodel.RemodelData: Found token 350 on blueprint line '354' protocols.forge.remodel.RemodelData: Found token G on blueprint line '354' protocols.forge.remodel.RemodelData: Found token D on blueprint line '354' protocols.forge.remodel.RemodelData: Found token PIKAA on blueprint line '354' protocols.forge.remodel.RemodelData: Found token G on blueprint line '354' protocols.forge.remodel.RemodelData: design position 354 to G GLY protocols.forge.remodel.RemodelData: Found token 432 on blueprint line '436' protocols.forge.remodel.RemodelData: Found token C on blueprint line '436' protocols.forge.remodel.RemodelData: Found token D on blueprint line '436' protocols.forge.remodel.RemodelData: Found token PIKAA on blueprint line '436' protocols.forge.remodel.RemodelData: Found token C on blueprint line '436' protocols.forge.remodel.RemodelData: design position 436 to C CYS protocols.forge.remodel.RemodelData: Found token 0 on blueprint line '437' protocols.forge.remodel.RemodelData: Found token x on blueprint line '437' protocols.forge.remodel.RemodelData: Found token D on blueprint line '437' protocols.forge.remodel.RemodelData: Found token PIKAA on blueprint line '437' protocols.forge.remodel.RemodelData: Found token T on blueprint line '437' protocols.forge.remodel.RemodelData: design position 437 to T THR protocols.forge.remodel.RemodelData: Found token 0 on blueprint line '438' protocols.forge.remodel.RemodelData: Found token x on blueprint line '438' protocols.forge.remodel.RemodelData: Found token D on blueprint line '438' protocols.forge.remodel.RemodelData: Found token PIKAA on blueprint line '438' protocols.forge.remodel.RemodelData: Found token H on blueprint line '438' protocols.forge.remodel.RemodelData: design position 438 to H HIS protocols.forge.remodel.RemodelData: Found token 0 on blueprint line '439' protocols.forge.remodel.RemodelData: Found token x on blueprint line '439' protocols.forge.remodel.RemodelData: Found token D on blueprint line '439' protocols.forge.remodel.RemodelData: Found token PIKAA on blueprint line '439' protocols.forge.remodel.RemodelData: Found token T on blueprint line '439' protocols.forge.remodel.RemodelData: design position 439 to T THR protocols.forge.remodel.RemodelData: Found token 0 on blueprint line '440' protocols.forge.remodel.RemodelData: Found token x on blueprint line '440' protocols.forge.remodel.RemodelData: Found token D on blueprint line '440' protocols.forge.remodel.RemodelData: Found token PIKAA on blueprint line '440' protocols.forge.remodel.RemodelData: Found token S on blueprint line '440' protocols.forge.remodel.RemodelData: design position 440 to S SER protocols.forge.remodel.RemodelData: Found token 0 on blueprint line '441' protocols.forge.remodel.RemodelData: Found token x on blueprint line '441' protocols.forge.remodel.RemodelData: Found token D on blueprint line '441' protocols.forge.remodel.RemodelData: Found token PIKAA on blueprint line '441' protocols.forge.remodel.RemodelData: Found token A on blueprint line '441' protocols.forge.remodel.RemodelData: design position 441 to A ALA protocols.forge.remodel.RemodelData: Found token 0 on blueprint line '442' protocols.forge.remodel.RemodelData: Found token x on blueprint line '442' protocols.forge.remodel.RemodelData: Found token D on blueprint line '442' protocols.forge.remodel.RemodelData: Found token PIKAA on blueprint line '442' protocols.forge.remodel.RemodelData: Found token A on blueprint line '442' protocols.forge.remodel.RemodelData: design position 442 to A ALA protocols.forge.remodel.RemodelData: Resfile to be used for design: NATRO start 349 H PIKAA K 350 H PIKAA S 351 H PIKAA T 352 H PIKAA S 353 H PIKAA G 354 H PIKAA G 436 H PIKAA C 437 H PIKAA T 438 H PIKAA H 439 H PIKAA T 440 H PIKAA S 441 H PIKAA A 442 H PIKAA A protocols.forge.remodel.RemodelData: SS based assignment found protocols.forge.remodel.RemodelData: sequence (based on blueprint): protocols.forge.remodel.RemodelData: DIQMTQSPSSLSASVGDRVTITCRASQSISSYLNWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYSTPLTFGQGTKVEVKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGECEVQLVQSGAEVKKPGESLKISCKGSGYSFTSYWIGWVRQMPGKGLEWMGIIYPGDSDTRYSPSFQGQVTISADKSISTAYLQWSSLKASDTAMYYCARYDGIYGELDFWGQGTLVTVSSASTKGPSVFPLAPSSKxxxxGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCxxxxxx protocols.forge.remodel.RemodelData: ss (based on blueprint): protocols.forge.remodel.RemodelData: ............................................................................................................................................................................................................................................................................................................................................................DDDDDD.................................................................................DDDDDDD protocols.forge.remodel.RemodelData: ABEGOtype: protocols.forge.remodel.RemodelData: protocols.forge.remodel.RemodelData: dssp_updated_ss: lengths = 442 protocols.forge.remodel.RemodelData: LLLEEEELLEEEELLLLLEEEEEEELLLLLLLEEEEEELLLLLLEEEEELLLEELLLLLLLEEEEEELLEEEEEELLLLHHHLEEEEEEELLLLLLEELLLEEEEELLLLELLEEEEELLLHHHHHHLEEEEEEEEEEEELLLLEEEEEELLEELLLLEEEEELLLLLLLLLEEEEEEEEEEHHHHHHLLEEEEEEELLLLLLLEEEEEELLLLLLEEEELLLEEELLLLLEEEEEEEELLLHHHLEEEEEEELLLLLEEEEEEEELLLLEEEELLLLLLLLEEEEEHHHLEEEEEELLLLHHHLEEEEEEEEELLLLEEEEELLLEEEEELLLLLELLEEEEELLLLDDDDDDEEEEEEEEEEEELLLLEEEEHHHLELLLEEELLLEELLLLLEEEEEEEEEEHHHLLLLLLEEEEEEHHHLEEEEEELLLLLDDDDDDD core.scoring.ScoreFunctionFactory: SCOREFUNCTION: talaris2013 core.pack.dunbrack: Dunbrack 2010 library took 0.195418 seconds to load from binary protocols.forge.remodel.RemodelWorkingSet: workingSetGen(): C-terminal is extended protocols.forge.remodel.RemodelWorkingSet: workingSetGen(): length change found. last blueprint line index: 442, last blueprint line original_index: 0 protocols.forge.remodel.RemodelWorkingSet: Adding lines to temp_for_truncation vector. protocols.forge.remodel.RemodelWorkingSet: temp_for_truncation.size():432 protocols.forge.remodel.RemodelWorkingSet: Setting up translate_index. protocols.forge.remodel.RemodelWorkingSet: temp_for_copy (lines_residues_to_remodel): [ 1-1, 2-2, 3-3, 4-4, 5-5, 6-6, 7-7, 8-8, 9-9, 10-10, 11-11, 12-12, 13-13, 14-14, 15-15, 16-16, 17-17, 18-18, 19-19, 20-20, 21-21, 22-22, 23-23, 24-24, 25-25, 26-26, 27-27, 28-28, 29-29, 30-30, 31-31, 32-32, 33-33, 34-34, 35-35, 36-36, 37-37, 38-38, 39-39, 40-40, 41-41, 42-42, 43-43, 44-44, 45-45, 46-46, 47-47, 48-48, 49-49, 50-50, 51-51, 52-52, 53-53, 54-54, 55-55, 56-56, 57-57, 58-58, 59-59, 60-60, 61-61, 62-62, 63-63, 64-64, 65-65, 66-66, 67-67, 68-68, 69-69, 70-70, 71-71, 72-72, 73-73, 74-74, 75-75, 76-76, 77-77, 78-78, 79-79, 80-80, 81-81, 82-82, 83-83, 84-84, 85-85, 86-86, 87-87, 88-88, 89-89, 90-90, 91-91, 92-92, 93-93, 94-94, 95-95, 96-96, 97-97, 98-98, 99-99, 100-100, 101-101, 102-102, 103-103, 104-104, 105-105, 106-106, 107-107, 108-108, 109-109, 110-110, 111-111, 112-112, 113-113, 114-114, 115-115, 116-116, 117-117, 118-118, 119-119, 120-120, 121-121, 122-122, 123-123, 124-124, 125-125, 126-126, 127-127, 128-128, 129-129, 130-130, 131-131, 132-132, 133-133, 134-134, 135-135, 136-136, 137-137, 138-138, 139-139, 140-140, 141-141, 142-142, 143-143, 144-144, 145-145, 146-146, 147-147, 148-148, 149-149, 150-150, 151-151, 152-152, 153-153, 154-154, 155-155, 156-156, 157-157, 158-158, 159-159, 160-160, 161-161, 162-162, 163-163, 164-164, 165-165, 166-166, 167-167, 168-168, 169-169, 170-170, 171-171, 172-172, 173-173, 174-174, 175-175, 176-176, 177-177, 178-178, 179-179, 180-180, 181-181, 182-182, 183-183, 184-184, 185-185, 186-186, 187-187, 188-188, 189-189, 190-190, 191-191, 192-192, 193-193, 194-194, 195-195, 196-196, 197-197, 198-198, 199-199, 200-200, 201-201, 202-202, 203-203, 204-204, 205-205, 206-206, 207-207, 208-208, 209-209, 210-210, 211-211, 212-212, 213-213, 214-214, 215-215, 216-216, 217-217, 218-218, 219-219, 220-220, 221-221, 222-222, 223-223, 224-224, 225-225, 226-226, 227-227, 228-228, 229-229, 230-230, 231-231, 232-232, 233-233, 234-234, 235-235, 236-236, 237-237, 238-238, 239-239, 240-240, 241-241, 242-242, 243-243, 244-244, 245-245, 246-246, 247-247, 248-248, 249-249, 250-250, 251-251, 252-252, 253-253, 254-254, 255-255, 256-256, 257-257, 258-258, 259-259, 260-260, 261-261, 262-262, 263-263, 264-264, 265-265, 266-266, 267-267, 268-268, 269-269, 270-270, 271-271, 272-272, 273-273, 274-274, 275-275, 276-276, 277-277, 278-278, 279-279, 280-280, 281-281, 282-282, 283-283, 284-284, 285-285, 286-286, 287-287, 288-288, 289-289, 290-290, 291-291, 292-292, 293-293, 294-294, 295-295, 296-296, 297-297, 298-298, 299-299, 300-300, 301-301, 302-302, 303-303, 304-304, 305-305, 306-306, 307-307, 308-308, 309-309, 310-310, 311-311, 312-312, 313-313, 314-314, 315-315, 316-316, 317-317, 318-318, 319-319, 320-320, 321-321, 322-322, 323-323, 324-324, 325-325, 326-326, 327-327, 328-328, 329-329, 330-330, 331-331, 332-332, 333-333, 334-334, 335-335, 336-336, 337-337, 338-338, 339-339, 340-340, 341-341, 342-342, 343-343, 344-344, 345-345, 346-346, 347-347, 348-348, 351-355, 352-356, 353-357, 354-358, 355-359, 356-360, 357-361, 358-362, 359-363, 360-364, 361-365, 362-366, 363-367, 364-368, 365-369, 366-370, 367-371, 368-372, 369-373, 370-374, 371-375, 372-376, 373-377, 374-378, 375-379, 376-380, 377-381, 378-382, 379-383, 380-384, 381-385, 382-386, 383-387, 384-388, 385-389, 386-390, 387-391, 388-392, 389-393, 390-394, 391-395, 392-396, 393-397, 394-398, 395-399, 396-400, 397-401, 398-402, 399-403, 400-404, 401-405, 402-406, 403-407, 404-408, 405-409, 406-410, 407-411, 408-412, 409-413, 410-414, 411-415, 412-416, 413-417, 414-418, 415-419, 416-420, 417-421, 418-422, 419-423, 420-424, 421-425, 422-426, 423-427, 424-428, 425-429, 426-430, 427-431, 428-432, 429-433, 430-434, 431-435, ] protocols.forge.remodel.RemodelWorkingSet: segmentStorageVector: [ segment 0: [ 349, 350, 351, 352, 353, 354, ], segment 1: [ 436, 437, 438, 439, 440, 441, 442, ], ] protocols.forge.remodel.RemodelWorkingSet: data.dssp_updated_ss: LLLEEEELLEEEELLLLLEEEEEEELLLLLLLEEEEEELLLLLLEEEEELLLEELLLLLLLEEEEEELLEEEEEELLLLHHHLEEEEEEELLLLLLEELLLEEEEELLLLELLEEEEELLLHHHHHHLEEEEEEEEEEEELLLLEEEEEELLEELLLLEEEEELLLLLLLLLEEEEEEEEEEHHHHHHLLEEEEEEELLLLLLLEEEEEELLLLLLEEEELLLEEELLLLLEEEEEEEELLLHHHLEEEEEEELLLLLEEEEEEEELLLLEEEELLLLLLLLEEEEEHHHLEEEEEELLLLHHHLEEEEEEEEELLLLEEEEELLLEEEEELLLLLELLEEEEELLLLDDDDDDEEEEEEEEEEEELLLLEEEEHHHLELLLEEELLLEELLLLLEEEEEEEEEEHHHLLLLLLEEEEEEHHHLEEEEEELLLLLDDDDDDD AA for build: VVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVV protocols.forge.remodel.RemodelWorkingSet: head 349:349, tail 350:354, gap: 6, dssp_updated_ss.size(): 442, insert_ss: DDDDDD protocols.forge.remodel.RemodelWorkingSet: normal rebuild protocols.forge.remodel.RemodelWorkingSet: head 432:436, tail 0:442, gap: 7, dssp_updated_ss.size(): 442, insert_ss: DDDDDDD protocols.forge.remodel.RemodelWorkingSet: C-terminal extension found protocols.forge.build.BuildManager: FOLD_TREE EDGE 1 214 -1 EDGE 1 215 1 EDGE 215 348 -1 EDGE 348 353 -1 JEDGE 348 355 2 N C END EDGE 355 436 -1 EDGE 355 354 -1 protocols.forge.build.BuildManager: protocols.forge.build.BuildManager: FOLD_TREE EDGE 1 214 -1 EDGE 1 215 1 EDGE 215 348 -1 EDGE 348 353 -1 JEDGE 348 355 2 N C END EDGE 355 442 -1 EDGE 355 354 -1 protocols.forge.build.BuildManager: protocols.forge.remodel.RemodelDesignMover: Creating NeighborhoodByDistanceCalculator using und_pos: [ 349 350 351 352 353 354 436 437 438 439 440 441 442 ] protocols.forge.remodel.RemodelMover: protocols.forge.remodel.RemodelMover: apply(): BUILD CYCLE REMAINING 1 protocols.forge.remodel.RemodelMover: ORIGINAL TREE: FOLD_TREE EDGE 1 214 -1 EDGE 1 215 1 EDGE 215 348 -1 EDGE 348 353 -1 JEDGE 348 355 2 N C END EDGE 355 442 -1 EDGE 355 354 -1 protocols.forge.remodel.RemodelMover: protocols.forge.remodel.RemodelMover: centroid_build(): calling VariableLengthBuild apply. core.chemical.ResidueTypeSet: Finished initializing centroid residue type set. Created 1010 residue types protocols.forge.components.VarLengthBuild: VLB count_cutpoints 1 interval.left 349 interval.right 354 protocols.forge.components.VarLengthBuild: picking 200 6-mers for position 349 core.fragment.picking_old.vall.vall_io: Reading Vall library from /home/lanselibai/Cheng/rosetta_2014.30.57114_bundle/main/database//sampling/filtered.vall.dat.2006-05-05 ... core.fragment.picking_old.vall.vall_io: 100000 core.fragment.picking_old.vall.vall_io: 200000 core.fragment.picking_old.vall.vall_io: 300000 core.fragment.picking_old.vall.vall_io: 400000 core.fragment.picking_old.vall.vall_io: 500000 core.fragment.picking_old.vall.vall_io: 600000 core.fragment.picking_old.vall.vall_io: 700000 core.fragment.picking_old.vall.vall_io: 800000 core.fragment.picking_old.vall.vall_io: 900000 core.fragment.picking_old.vall.vall_io: 1000000 core.fragment.picking_old.vall.vall_io: 1100000 core.fragment.picking_old.vall.vall_io: 1200000 core.fragment.picking_old.vall.vall_io: 1300000 core.fragment.picking_old.vall.vall_io: 1400000 core.fragment.picking_old.vall.vall_io: ... done. Read 1400124 lines. Time elapsed: 15 seconds. core.fragment.picking_old.vall.vall_io: Prior library contained 0 sections totaling 0 residues. core.fragment.picking_old.vall.vall_io: Added 62471 sections to library totaling 1400124 residues. core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDDDD | aa = ...... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 4.02265e-10 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 1.69011e-07 protocols.forge.components.VarLengthBuild: picking 200 6-mers for position 350 core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDDDE | aa = ...... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 1.10781e-09 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 9.19765e-07 protocols.forge.components.VarLengthBuild: picking 200 6-mers for position 351 core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDDEE | aa = ...... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 4.0826e-09 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 1.17325e-06 protocols.forge.components.VarLengthBuild: picking 200 6-mers for position 352 core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDEEE | aa = ...... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 9.59071e-09 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 1.35525e-06 protocols.forge.components.VarLengthBuild: picking 200 6-mers for position 353 core.fragment.picking_old.vall.eval.IdentityEval: ss = DDEEEE | aa = ...... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 4.06217e-10 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 1.92684e-06 protocols.forge.components.VarLengthBuild: picking 200 6-mers for position 354 core.fragment.picking_old.vall.eval.IdentityEval: ss = DEEEEE | aa = ...... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 1.53232e-08 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 2.97943e-06 protocols.forge.components.VarLengthBuild: picking 200 9-mers for position 349 core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDDDDEEE | aa = ......... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 1.42766e-08 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 1.55187e-06 protocols.forge.components.VarLengthBuild: picking 200 9-mers for position 350 core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDDDEEEE | aa = ......... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 2.01518e-08 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 2.06419e-06 protocols.forge.components.VarLengthBuild: picking 200 9-mers for position 351 core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDDEEEEE | aa = ......... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 3.81907e-09 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 3.00737e-06 protocols.forge.components.VarLengthBuild: picking 200 9-mers for position 352 core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDEEEEEE | aa = ......... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 1.2944e-08 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 4.60185e-06 protocols.forge.components.VarLengthBuild: picking 200 9-mers for position 353 core.fragment.picking_old.vall.eval.IdentityEval: ss = DDEEEEEEE | aa = ......... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 1.63809e-08 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 6.48203e-06 protocols.forge.components.VarLengthBuild: picking 200 9-mers for position 354 core.fragment.picking_old.vall.eval.IdentityEval: ss = DEEEEEEEE | aa = ......... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 3.04354e-09 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 1.02336e-05 protocols.forge.components.VarLengthBuild: picking 200 3-mers for position 349 core.fragment.picking_old.vall.eval.IdentityEval: ss = DDD | aa = ... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 8.2021e-10 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 1.49435e-07 protocols.forge.components.VarLengthBuild: picking 200 3-mers for position 350 core.fragment.picking_old.vall.eval.IdentityEval: ss = DDD | aa = ... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 8.68287e-10 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 1.61024e-07 protocols.forge.components.VarLengthBuild: picking 200 3-mers for position 351 core.fragment.picking_old.vall.eval.IdentityEval: ss = DDD | aa = ... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 4.11717e-11 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 1.47716e-07 protocols.forge.components.VarLengthBuild: picking 200 3-mers for position 352 core.fragment.picking_old.vall.eval.IdentityEval: ss = DDD | aa = ... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 2.6324e-10 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 1.40691e-07 protocols.forge.components.VarLengthBuild: picking 200 3-mers for position 353 core.fragment.picking_old.vall.eval.IdentityEval: ss = DDE | aa = ... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 3.00785e-09 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 7.29433e-07 protocols.forge.components.VarLengthBuild: picking 200 3-mers for position 354 core.fragment.picking_old.vall.eval.IdentityEval: ss = DEE | aa = ... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 1.01837e-09 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 8.44783e-07 protocols.forge.components.VarLengthBuild: VLB count_cutpoints 0 interval.left 436 interval.right 442 protocols.forge.components.VarLengthBuild: picking 200 7-mers for position 436 core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDDDDD | aa = ....... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 2.32257e-09 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 1.98662e-07 protocols.forge.components.VarLengthBuild: picking 200 7-mers for position 437 core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDDDDD | aa = ....... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 2.70602e-09 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 1.79599e-07 protocols.forge.components.VarLengthBuild: picking 200 7-mers for position 438 core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDDDDD | aa = ....... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 6.87564e-10 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 1.78014e-07 protocols.forge.components.VarLengthBuild: picking 200 7-mers for position 439 core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDDDDD | aa = ....... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 1.33478e-09 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 2.1344e-07 protocols.forge.components.VarLengthBuild: picking 200 7-mers for position 440 core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDDDDD | aa = ....... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 1.75653e-09 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 1.73034e-07 protocols.forge.components.VarLengthBuild: picking 200 7-mers for position 441 core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDDDDD | aa = ....... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 7.35937e-10 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 1.79219e-07 protocols.forge.components.VarLengthBuild: picking 200 7-mers for position 442 core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDDDDD | aa = ....... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 9.54689e-11 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 1.67986e-07 protocols.forge.components.VarLengthBuild: picking 200 9-mers for position 436 core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDDDDDDD | aa = ......... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 8.07295e-10 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 1.75148e-07 protocols.forge.components.VarLengthBuild: picking 200 9-mers for position 437 core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDDDDDDD | aa = ......... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 9.33294e-11 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 1.74844e-07 protocols.forge.components.VarLengthBuild: picking 200 9-mers for position 438 core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDDDDDDD | aa = ......... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 1.15225e-09 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 2.05937e-07 protocols.forge.components.VarLengthBuild: picking 200 9-mers for position 439 core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDDDDDDD | aa = ......... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 1.234e-10 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 1.78008e-07 protocols.forge.components.VarLengthBuild: picking 200 9-mers for position 440 core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDDDDDDD | aa = ......... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 8.86554e-11 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 1.94352e-07 protocols.forge.components.VarLengthBuild: picking 200 9-mers for position 441 core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDDDDDDD | aa = ......... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 7.78224e-10 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 1.97431e-07 protocols.forge.components.VarLengthBuild: picking 200 9-mers for position 442 core.fragment.picking_old.vall.eval.IdentityEval: ss = DDDDDDDDD | aa = ......... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 1.84629e-09 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 2.08433e-07 protocols.forge.components.VarLengthBuild: picking 200 3-mers for position 436 core.fragment.picking_old.vall.eval.IdentityEval: ss = DDD | aa = ... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 1.54848e-10 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 1.46335e-07 protocols.forge.components.VarLengthBuild: picking 200 3-mers for position 437 core.fragment.picking_old.vall.eval.IdentityEval: ss = DDD | aa = ... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 1.32303e-09 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 1.52589e-07 protocols.forge.components.VarLengthBuild: picking 200 3-mers for position 438 core.fragment.picking_old.vall.eval.IdentityEval: ss = DDD | aa = ... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 7.07589e-12 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 1.39566e-07 protocols.forge.components.VarLengthBuild: picking 200 3-mers for position 439 core.fragment.picking_old.vall.eval.IdentityEval: ss = DDD | aa = ... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 1.13902e-11 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 1.54474e-07 protocols.forge.components.VarLengthBuild: picking 200 3-mers for position 440 core.fragment.picking_old.vall.eval.IdentityEval: ss = DDD | aa = ... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 4.84499e-10 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 1.60223e-07 protocols.forge.components.VarLengthBuild: picking 200 3-mers for position 441 core.fragment.picking_old.vall.eval.IdentityEval: ss = DDD | aa = ... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 1.11998e-09 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 1.38771e-07 protocols.forge.components.VarLengthBuild: picking 200 3-mers for position 442 core.fragment.picking_old.vall.eval.IdentityEval: ss = DDD | aa = ... core.fragment.picking_old.vall.VallLibrarian: best fragment: score = 2.22625e-11 core.fragment.picking_old.vall.VallLibrarian: worst fragment: score = 1.36333e-07 protocols.forge.components.VarLengthBuild: total full-mer fragments: 2600 protocols.forge.components.VarLengthBuild: total 9-mer fragments: 2600 protocols.forge.components.VarLengthBuild: total 3-mer fragments: 2600 protocols.forge.components.VarLengthBuild: total 1-mer fragments: 2600 protocols.forge.remodel.RemodelLoopMover: ** randomize_stage protocols.forge.remodel.RemodelLoopMover: start stop cut cbreak protocols.forge.remodel.RemodelLoopMover: 349 354 353 13.9695 protocols.forge.remodel.RemodelLoopMover: 436 442 0 0 protocols.forge.remodel.RemodelLoopMover: * closure_attempt 1 protocols.forge.remodel.RemodelLoopMover: ** simultaneous_stage protocols.forge.remodel.RemodelLoopMover: n_loops = 2 protocols.loops.loops_main: Residue 214 is not compatible with cutpoints; variant type not changed. protocols.loops.loops_main: Residue 215 is not compatible with cutpoints; variant type not changed. protocols.loops.loops_main: Added cutpoint variant to residue 353 protocols.loops.loops_main: Added cutpoint variant to residue 354 protocols.forge.remodel.RemodelLoopMover: ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ vdw 1.000 5.279 5.279 hbond_sr_bb 1.000 -27.343 -27.343 hbond_lr_bb 1.000 -132.045 -132.045 rama 0.100 -146.206 -14.621 rg 1.000 25.218 25.218 linear_chainbreak 0.556 5.917 3.287 --------------------------------------------------- Total weighted score: -140.224 protocols.moves.MonteCarlo: MC: 2 -128.345 -140.224 -128.345 -140.224 0 0 0 rejected protocols.moves.TrialCounter: ccd_move trials= 23; accepts= 0.6087; energy_drop/trial= -0.67882 protocols.moves.TrialCounter: simul_frag trials= 1896; accepts= 0.6809; energy_drop/trial= 0.01110 protocols.forge.remodel.RemodelLoopMover: start stop cut cbreak protocols.forge.remodel.RemodelLoopMover: 349 354 353 5.91671 protocols.forge.remodel.RemodelLoopMover: 436 442 0 0 protocols.forge.remodel.RemodelLoopMover: ** independent_stage protocols.forge.remodel.RemodelLoopMover: n_loops = 2 protocols.loops.loops_main: Residue 214 is not compatible with cutpoints; variant type not changed. protocols.loops.loops_main: Residue 215 is not compatible with cutpoints; variant type not changed. protocols.forge.remodel.RemodelLoopMover: ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ vdw 1.000 5.293 5.293 hbond_sr_bb 1.000 -27.511 -27.511 hbond_lr_bb 1.000 -132.045 -132.045 rama 0.100 -131.748 -13.175 rg 1.000 25.208 25.208 linear_chainbreak 2.778 0.000 0.000 --------------------------------------------------- Total weighted score: -142.229 protocols.moves.MonteCarlo: MC: 2 -141.294 -142.229 -141.294 -142.229 0 0 0 accepted score beat last protocols.moves.TrialCounter: frag trials= 2240; accepts= 0.7513; energy_drop/trial= 0.00030 protocols.loops.loops_main: Residue 214 is not compatible with cutpoints; variant type not changed. protocols.loops.loops_main: Residue 215 is not compatible with cutpoints; variant type not changed. protocols.loops.loops_main: Added cutpoint variant to residue 353 protocols.loops.loops_main: Added cutpoint variant to residue 354 protocols.forge.remodel.RemodelLoopMover: ------------------------------------------------------------ Scores Weight Raw Score Wghtd.Score ------------------------------------------------------------ vdw 1.000 5.285 5.285 hbond_sr_bb 1.000 -26.854 -26.854 hbond_lr_bb 1.000 -132.146 -132.146 rama 0.100 -143.370 -14.337 rg 1.000 25.181 25.181 linear_chainbreak 5.000 0.008 0.040 --------------------------------------------------- Total weighted score: -142.830 protocols.moves.MonteCarlo: MC: 2 -142.83 -142.83 -142.83 -142.83 0 0 0 accepted score beat low protocols.moves.TrialCounter: ccd_move trials= 163; accepts= 0.9939; energy_drop/trial= -0.51750 protocols.moves.TrialCounter: frag trials= 1268; accepts= 0.1222; energy_drop/trial= 0.05155 protocols.forge.remodel.RemodelLoopMover: start stop cut cbreak protocols.forge.remodel.RemodelLoopMover: 349 354 353 0.016006 protocols.forge.remodel.RemodelLoopMover: 436 442 0 0 protocols.forge.remodel.RemodelLoopMover: ** boost_closure_stage core.kinematics.FoldTree: FoldTree::delete_unordered_edge(...) edge not in tree: 0 1 -1 core.kinematics.FoldTree: FOLD_TREE EDGE 1 214 -1 EDGE 1 415 1 EDGE 415 215 -1 EDGE 415 442 -1 EDGE 0 1 2 ERROR:: Exit from: src/core/kinematics/FoldTree.cc line: 876 protocols.jd2.JobDistributor: [ERROR] Exception caught by JobDistributor for job 4KMT_FullAtom_missding_residue_in_HC_0001 [ERROR] EXCN_utility_exit has been thrown from: src/core/kinematics/FoldTree.cc line: 876 protocols.jd2.JobDistributor: 4KMT_FullAtom_missding_residue_in_HC_0001 reported failure and will NOT retry protocols.jd2.JobDistributor: no more batches to process... protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 196 seconds