# command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading dunbrack-2191.atoms # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 53157 examples # computed average trans backbone unit before proline from 2010 examples # computed average cis backbone unit from 97 examples # trans (non-proline) backbone unit: # CA= -2.2087 1.0126 -0.0030 # O= -0.1499 2.2440 0.0016 # C= -0.6889 1.1368 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4581 -0.0000 0.0000 # cis backbone unit: # CA= -0.1436 2.4534 -0.0002 # O= -2.0284 0.9742 0.0015 # C= -0.8018 1.0771 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4668 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2100 1.0631 -0.0014 # O= -0.1236 2.2458 0.0075 # C= -0.6872 1.1517 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4660 0.0000 0.0000 # After reading dunbrack-2191.atoms have 2191 chains in training database # Count of chains,residues,atoms: 2191,500310,3902258 # 493341 residues have no bad marker # 3226 residues lack atoms needed to compute omega # 1453 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 4 # HAS_OXT 1167 # TOO_MANY_ATOMS 1 # TOO_FEW_ATOMS 3052 # HAS_UNKNOWN_ATOMS 9 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 979 # NON_PLANAR_PEPTIDE 888 # BAD_PEPTIDE 2680 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-2191.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0358/ # command:# Making conformation for sequence T0358 numbered 1 through 87 Created new target T0358 from T0358.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0358/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0358//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0358/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0358//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0358/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0358/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0358/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1iscA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1iscA expands to /projects/compbio/data/pdb/1isc.pdb.gz 1iscA:# T0358 read from 1iscA/merged-good-all-a2m # 1iscA read from 1iscA/merged-good-all-a2m # adding 1iscA to template set # found chain 1iscA in template set T0358 10 :GPFTRRQAQAVTTTYSN 1iscA 86 :GEPTGKVAEAIAASFGS # choosing archetypes in rotamer library T0358 32 :DQGSHFRLVVRDTEGRMVWRAW 1iscA 117 :NFGSGWTWLVKNSDGKLAIVST Number of specific fragments extracted= 2 number of extra gaps= 0 total=2 Number of alignments=1 # 1iscA read from 1iscA/merged-good-all-a2m # found chain 1iscA in template set T0358 10 :GPFTRRQAQAVTTTYSN 1iscA 86 :GEPTGKVAEAIAASFGS T0358 32 :DQGSHFRLVVRDTEGRMVWRAW 1iscA 117 :NFGSGWTWLVKNSDGKLAIVST Number of specific fragments extracted= 2 number of extra gaps= 0 total=4 Number of alignments=2 # 1iscA read from 1iscA/merged-good-all-a2m # found chain 1iscA in template set T0358 6 :LLPP 1iscA 80 :LAPN T0358 10 :GPFTRRQAQAVTTTYSN 1iscA 86 :GEPTGKVAEAIAASFGS T0358 32 :DQGSHFRLVVRDTEGRMVWRAW 1iscA 117 :NFGSGWTWLVKNSDGKLAIVST Number of specific fragments extracted= 3 number of extra gaps= 0 total=7 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2dg5B/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2dg5B expands to /projects/compbio/data/pdb/2dg5.pdb.gz 2dg5B:# T0358 read from 2dg5B/merged-good-all-a2m # 2dg5B read from 2dg5B/merged-good-all-a2m # adding 2dg5B to template set # found chain 2dg5B in template set Warning: unaligning (T0358)D32 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2dg5B)G551 Warning: unaligning (T0358)G34 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2dg5B)G551 Warning: unaligning (T0358)V40 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2dg5B)V558 Warning: unaligning (T0358)R42 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2dg5B)V558 T0358 10 :GPFTRRQAQAVTTTYSNITLED 2dg5B 527 :KGFSPDTLKLLEAKGQKVALKE T0358 36 :HFRL 2dg5B 552 :STQS T0358 43 :DTEGRMVWRAWNFEP 2dg5B 559 :GPDGELYGASDPRSV Number of specific fragments extracted= 3 number of extra gaps= 0 total=10 Number of alignments=4 # 2dg5B read from 2dg5B/merged-good-all-a2m # found chain 2dg5B in template set Warning: unaligning (T0358)D32 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2dg5B)G551 Warning: unaligning (T0358)G34 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2dg5B)G551 Warning: unaligning (T0358)V40 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2dg5B)V558 Warning: unaligning (T0358)R42 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2dg5B)V558 T0358 8 :P 2dg5B 526 :E T0358 10 :GPFTRRQAQAVTTTYSNITLED 2dg5B 527 :KGFSPDTLKLLEAKGQKVALKE T0358 36 :HFRL 2dg5B 552 :STQS T0358 43 :DTEGRMVWRAWNFEPD 2dg5B 559 :GPDGELYGASDPRSVD Number of specific fragments extracted= 4 number of extra gaps= 0 total=14 Number of alignments=5 # 2dg5B read from 2dg5B/merged-good-all-a2m # found chain 2dg5B in template set Warning: unaligning (T0358)D32 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2dg5B)G551 Warning: unaligning (T0358)G34 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2dg5B)G551 Warning: unaligning (T0358)V40 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2dg5B)V558 Warning: unaligning (T0358)R42 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2dg5B)V558 T0358 10 :GPFTRRQAQAVTTTYSNITLED 2dg5B 527 :KGFSPDTLKLLEAKGQKVALKE T0358 35 :SH 2dg5B 552 :ST T0358 38 :RL 2dg5B 554 :QS T0358 43 :DTEGRMVWRAWNFEPD 2dg5B 559 :GPDGELYGASDPRSVD Number of specific fragments extracted= 4 number of extra gaps= 0 total=18 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vq2A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vq2A expands to /projects/compbio/data/pdb/1vq2.pdb.gz 1vq2A:# T0358 read from 1vq2A/merged-good-all-a2m # 1vq2A read from 1vq2A/merged-good-all-a2m # adding 1vq2A to template set # found chain 1vq2A in template set Warning: unaligning (T0358)T76 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vq2A)R83 T0358 14 :RRQAQAVTTTYSNITLE 1vq2A 4 :STVLQIAYLVSQESKCC T0358 34 :GSHFRLVVRD 1vq2A 21 :SWKVGAVIEK T0358 45 :EGRMVWRAWNFEPDAGEGLNRYIRTSGIRTD 1vq2A 31 :NGRIISTGYNGSPAGGVNCCDYAAEQGWLLN Number of specific fragments extracted= 3 number of extra gaps= 0 total=21 Number of alignments=7 # 1vq2A read from 1vq2A/merged-good-all-a2m # found chain 1vq2A in template set Warning: unaligning (T0358)T76 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vq2A)R83 T0358 35 :SHFRLVVRD 1vq2A 22 :WKVGAVIEK T0358 45 :EGRMVWRAWNFEPDAGEGLNRYIRTSGIRTD 1vq2A 31 :NGRIISTGYNGSPAGGVNCCDYAAEQGWLLN Number of specific fragments extracted= 2 number of extra gaps= 0 total=23 Number of alignments=8 # 1vq2A read from 1vq2A/merged-good-all-a2m # found chain 1vq2A in template set T0358 14 :RRQAQAVTTTYSNITLE 1vq2A 4 :STVLQIAYLVSQESKCC T0358 34 :GSHFRLVVRD 1vq2A 21 :SWKVGAVIEK T0358 45 :EGRMVWRAWNFEPDAGEGLNRYIRTSGIR 1vq2A 31 :NGRIISTGYNGSPAGGVNCCDYAAEQGWL Number of specific fragments extracted= 3 number of extra gaps= 0 total=26 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cqyA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1cqyA expands to /projects/compbio/data/pdb/1cqy.pdb.gz 1cqyA:# T0358 read from 1cqyA/merged-good-all-a2m # 1cqyA read from 1cqyA/merged-good-all-a2m # adding 1cqyA to template set # found chain 1cqyA in template set T0358 25 :SNITLEDDQGSHFRLVVRDTEGRMV 1cqyA 469 :GNVVLPAERNIEFKAFIKSKDGTVK Number of specific fragments extracted= 1 number of extra gaps= 0 total=27 Number of alignments=10 # 1cqyA read from 1cqyA/merged-good-all-a2m # found chain 1cqyA in template set T0358 25 :SNITLEDDQGSHFRLVVRDTEGRMVW 1cqyA 469 :GNVVLPAERNIEFKAFIKSKDGTVKS T0358 51 :RAWNFE 1cqyA 500 :QSWNPV Number of specific fragments extracted= 2 number of extra gaps= 0 total=29 Number of alignments=11 # 1cqyA read from 1cqyA/merged-good-all-a2m # found chain 1cqyA in template set T0358 26 :NITLEDDQGSHFRLVVRDTEGRMV 1cqyA 470 :NVVLPAERNIEFKAFIKSKDGTVK Number of specific fragments extracted= 1 number of extra gaps= 0 total=30 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zorA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0358/1zorA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0358/1zorA/merged-good-all-a2m.gz for input Trying 1zorA/merged-good-all-a2m Error: Couldn't open file 1zorA/merged-good-all-a2m or 1zorA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1tp6A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0358 read from 1tp6A/merged-good-all-a2m # 1tp6A read from 1tp6A/merged-good-all-a2m # found chain 1tp6A in training set T0358 37 :FRLVVRDTEGRMVWRAW 1tp6A 106 :TVVLHRDDEGRLYWRHL Number of specific fragments extracted= 1 number of extra gaps= 0 total=31 # 1tp6A read from 1tp6A/merged-good-all-a2m # found chain 1tp6A in training set T0358 28 :TLEDDQGSHFRL 1tp6A 93 :IQSDAAGRSERL T0358 40 :VVRDTEGRMVWRA 1tp6A 109 :LHRDDEGRLYWRH Number of specific fragments extracted= 2 number of extra gaps= 0 total=33 Number of alignments=13 # 1tp6A read from 1tp6A/merged-good-all-a2m # found chain 1tp6A in training set T0358 36 :HFRLVVRDTEGRMVWRAW 1tp6A 105 :STVVLHRDDEGRLYWRHL Number of specific fragments extracted= 1 number of extra gaps= 0 total=34 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2a2pA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2a2pA expands to /projects/compbio/data/pdb/2a2p.pdb.gz 2a2pA:# T0358 read from 2a2pA/merged-good-all-a2m # 2a2pA read from 2a2pA/merged-good-all-a2m # adding 2a2pA to template set # found chain 2a2pA in template set T0358 8 :PP 2a2pA 51 :NR T0358 13 :TRRQAQAVT 2a2pA 53 :LKEVKAFVT T0358 22 :TTYSNITLEDDQGSHFRLVVRDTEGRMVWRAWNFEPD 2a2pA 65 :QLYHNLVMKHLPGADPELVLLSRNYQELERIPLSQMT T0358 60 :GEGLNRYIRTSGIRTDTATRL 2a2pA 102 :RDEINALVQELGFYRKSAPEA Number of specific fragments extracted= 4 number of extra gaps= 0 total=38 Number of alignments=14 # 2a2pA read from 2a2pA/merged-good-all-a2m # found chain 2a2pA in template set T0358 12 :FTRRQAQAVT 2a2pA 52 :RLKEVKAFVT T0358 22 :TTYSNITLEDDQGSHFRLVVRDTEGRMVWRAWNFEP 2a2pA 65 :QLYHNLVMKHLPGADPELVLLSRNYQELERIPLSQM T0358 59 :AGEGLNRYIRTSGIRTDTATRLE 2a2pA 101 :TRDEINALVQELGFYRKSAPEAQ Number of specific fragments extracted= 3 number of extra gaps= 0 total=41 Number of alignments=15 # 2a2pA read from 2a2pA/merged-good-all-a2m # found chain 2a2pA in template set T0358 9 :PGPFTR 2a2pA 47 :GCQLNR T0358 15 :RQAQAV 2a2pA 54 :KEVKAF T0358 21 :TTTYSNITLEDDQGSHFRLVVRDTEGRMVWRAWNFEP 2a2pA 64 :IQLYHNLVMKHLPGADPELVLLSRNYQELERIPLSQM T0358 59 :AGEGLNRYIRTSGIRTDTA 2a2pA 101 :TRDEINALVQELGFYRKSA Number of specific fragments extracted= 4 number of extra gaps= 0 total=45 Number of alignments=16 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ui0A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0358 read from 1ui0A/merged-good-all-a2m # 1ui0A read from 1ui0A/merged-good-all-a2m # found chain 1ui0A in training set T0358 54 :NFEPDAGEGLNRYIRTSGIRTDT 1ui0A 53 :PFVGKAGQLLNRILEAAGIPREE Number of specific fragments extracted= 1 number of extra gaps= 0 total=46 Number of alignments=17 # 1ui0A read from 1ui0A/merged-good-all-a2m # found chain 1ui0A in training set T0358 54 :NFEPDAGEGLNRYIRTSGIRTDT 1ui0A 53 :PFVGKAGQLLNRILEAAGIPREE Number of specific fragments extracted= 1 number of extra gaps= 0 total=47 Number of alignments=18 # 1ui0A read from 1ui0A/merged-good-all-a2m # found chain 1ui0A in training set T0358 54 :NFEPDAGEGLNRYIRTSGIRTD 1ui0A 53 :PFVGKAGQLLNRILEAAGIPRE Number of specific fragments extracted= 1 number of extra gaps= 0 total=48 Number of alignments=19 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1m93C/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1m93C expands to /projects/compbio/data/pdb/1m93.pdb.gz 1m93C:Skipped atom 2447, because occupancy 0.48 <= existing 0.520 in 1m93C Skipped atom 2449, because occupancy 0.480 <= existing 0.520 in 1m93C Skipped atom 2451, because occupancy 0.480 <= existing 0.520 in 1m93C Skipped atom 2453, because occupancy 0.480 <= existing 0.520 in 1m93C Skipped atom 2455, because occupancy 0.480 <= existing 0.520 in 1m93C Skipped atom 2557, because occupancy 0.440 <= existing 0.560 in 1m93C # T0358 read from 1m93C/merged-good-all-a2m # 1m93C read from 1m93C/merged-good-all-a2m # adding 1m93C to template set # found chain 1m93C in template set T0358 36 :HFRLVVRDTEGRMVWRAW 1m93C 317 :PFIYVIRHVDGKILFVGR Number of specific fragments extracted= 1 number of extra gaps= 0 total=49 # 1m93C read from 1m93C/merged-good-all-a2m # found chain 1m93C in template set Warning: unaligning (T0358)D58 because last residue in template chain is (1m93C)T339 T0358 30 :EDDQ 1m93C 313 :SADH T0358 36 :HFRLVVRDTEGRMVWRAWNFEP 1m93C 317 :PFIYVIRHVDGKILFVGRYSSP Number of specific fragments extracted= 2 number of extra gaps= 0 total=51 Number of alignments=20 # 1m93C read from 1m93C/merged-good-all-a2m # found chain 1m93C in template set T0358 36 :HFRLVVRDTEGRMVW 1m93C 317 :PFIYVIRHVDGKILF Number of specific fragments extracted= 1 number of extra gaps= 0 total=52 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qx4A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1qx4A expands to /projects/compbio/data/pdb/1qx4.pdb.gz 1qx4A:# T0358 read from 1qx4A/merged-good-all-a2m # 1qx4A read from 1qx4A/merged-good-all-a2m # adding 1qx4A to template set # found chain 1qx4A in template set T0358 7 :LPPGP 1qx4A 63 :LPSPQ T0358 27 :ITLEDDQGSHFRLVVRD 1qx4A 68 :HILGLPIGQHIYLSTRI T0358 45 :EGRMVWRAWNFEPD 1qx4A 85 :DGNLVIRPYTPVSS Number of specific fragments extracted= 3 number of extra gaps= 0 total=55 Number of alignments=21 # 1qx4A read from 1qx4A/merged-good-all-a2m # found chain 1qx4A in template set T0358 27 :ITLEDDQ 1qx4A 61 :FALPSPQ T0358 34 :GSHFRLVVRD 1qx4A 75 :GQHIYLSTRI T0358 45 :EGRMVWRAWNFEP 1qx4A 85 :DGNLVIRPYTPVS Number of specific fragments extracted= 3 number of extra gaps= 0 total=58 Number of alignments=22 # 1qx4A read from 1qx4A/merged-good-all-a2m # found chain 1qx4A in template set T0358 28 :TLEDDQGSHFRLVVRD 1qx4A 69 :ILGLPIGQHIYLSTRI T0358 45 :EGRMVWRAWN 1qx4A 85 :DGNLVIRPYT T0358 55 :FEPDAGEGL 1qx4A 97 :SSDDDKGFV Number of specific fragments extracted= 3 number of extra gaps= 0 total=61 Number of alignments=23 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1b7s/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1b7s expands to /projects/compbio/data/pdb/1b7s.pdb.gz 1b7s:Warning: there is no chain 1b7s will retry with 1b7sA # T0358 read from 1b7s/merged-good-all-a2m # 1b7s read from 1b7s/merged-good-all-a2m # adding 1b7s to template set # found chain 1b7s in template set T0358 61 :EGLNRYIRTSGIRT 1b7s 6 :CELARTLKRLGMDG Number of specific fragments extracted= 1 number of extra gaps= 0 total=62 # 1b7s read from 1b7s/merged-good-all-a2m # found chain 1b7s in template set T0358 61 :EGLNRYIRTSGIR 1b7s 6 :CELARTLKRLGMD Number of specific fragments extracted= 1 number of extra gaps= 0 total=63 # 1b7s read from 1b7s/merged-good-all-a2m # found chain 1b7s in template set T0358 62 :GLNRYIRTSGIR 1b7s 7 :ELARTLKRLGMD Number of specific fragments extracted= 1 number of extra gaps= 0 total=64 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yaxA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1yaxA expands to /projects/compbio/data/pdb/1yax.pdb.gz 1yaxA:# T0358 read from 1yaxA/merged-good-all-a2m # 1yaxA read from 1yaxA/merged-good-all-a2m # adding 1yaxA to template set # found chain 1yaxA in template set T0358 12 :FTRRQAQAVTTTYS 1yaxA 51 :LLRGESNLFYTLAK T0358 26 :NITLEDDQG 1yaxA 69 :KISVELPEN T0358 35 :SHFRLVVRDTEGRMVWRAWNF 1yaxA 82 :SPTMTLIYDETGKLLWTQRNI T0358 61 :EGLNRYIRTSGIRTDTATRLE 1yaxA 103 :PWLIKSIQPEWLKTNGFHEIE Number of specific fragments extracted= 4 number of extra gaps= 0 total=68 Number of alignments=24 # 1yaxA read from 1yaxA/merged-good-all-a2m # found chain 1yaxA in template set T0358 13 :TRRQAQAVTTTYS 1yaxA 52 :LRGESNLFYTLAK T0358 26 :NITLEDDQ 1yaxA 69 :KISVELPE T0358 34 :GSHFRLVVRDTEGRMVWRAWNF 1yaxA 81 :QSPTMTLIYDETGKLLWTQRNI T0358 61 :EGLNRYIRTSGIRTDTATRLE 1yaxA 103 :PWLIKSIQPEWLKTNGFHEIE Number of specific fragments extracted= 4 number of extra gaps= 0 total=72 Number of alignments=25 # 1yaxA read from 1yaxA/merged-good-all-a2m # found chain 1yaxA in template set T0358 14 :RRQAQAVTTTY 1yaxA 53 :RGESNLFYTLA T0358 25 :SNITLEDDQG 1yaxA 68 :NKISVELPEN T0358 35 :SHFRLVVRDTEGRMVWRAWNF 1yaxA 82 :SPTMTLIYDETGKLLWTQRNI T0358 61 :EGLNRYIRTSGIRTD 1yaxA 103 :PWLIKSIQPEWLKTN Number of specific fragments extracted= 4 number of extra gaps= 0 total=76 Number of alignments=26 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ffyA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ffyA expands to /projects/compbio/data/pdb/1ffy.pdb.gz 1ffyA:# T0358 read from 1ffyA/merged-good-all-a2m # 1ffyA read from 1ffyA/merged-good-all-a2m # adding 1ffyA to template set # found chain 1ffyA in template set T0358 41 :VRDTEGRMV 1ffyA 466 :FYAENGEII T0358 55 :FEPDAGEGLNRYIRTSG 1ffyA 475 :MTKETVNHVADLFAEHG Number of specific fragments extracted= 2 number of extra gaps= 0 total=78 Number of alignments=27 # 1ffyA read from 1ffyA/merged-good-all-a2m # found chain 1ffyA in template set T0358 25 :SNITLED 1ffyA 856 :SQVKVVD T0358 32 :DQ 1ffyA 866 :DQ T0358 35 :SHFRLVVRDTEGRMVWRAWNFEPDAG 1ffyA 872 :EHGDIVIEHADGEKCERCWNYSEDLG T0358 61 :EGLNRYIRT 1ffyA 907 :PRCQQVVKS Number of specific fragments extracted= 4 number of extra gaps= 0 total=82 Number of alignments=28 # 1ffyA read from 1ffyA/merged-good-all-a2m # found chain 1ffyA in template set T0358 13 :TRRQAQAVTTTYSN 1ffyA 434 :VNWGKTRIYNMVRD T0358 28 :TLEDDQGSHFRLVVRDTEGRMVW 1ffyA 453 :ISRQRVWGVPLPVFYAENGEIIM T0358 56 :EPDAGEGLNRYIRTSGI 1ffyA 476 :TKETVNHVADLFAEHGS Number of specific fragments extracted= 3 number of extra gaps= 0 total=85 Number of alignments=29 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ebdA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ebdA expands to /projects/compbio/data/pdb/1ebd.pdb.gz 1ebdA:# T0358 read from 1ebdA/merged-good-all-a2m # 1ebdA read from 1ebdA/merged-good-all-a2m # adding 1ebdA to template set # found chain 1ebdA in template set T0358 32 :DQGSHFRLVVRDTEGRMVW 1ebdA 393 :DTDGFLKLVVRKEDGVIIG T0358 52 :AWNFEPDAGE 1ebdA 412 :AQIIGPNASD T0358 62 :GLNRYIRT 1ebdA 425 :ELGLAIEA T0358 71 :GIRTDTATR 1ebdA 433 :GMTAEDIAL Number of specific fragments extracted= 4 number of extra gaps= 0 total=89 Number of alignments=30 # 1ebdA read from 1ebdA/merged-good-all-a2m # found chain 1ebdA in template set T0358 32 :DQGSHFRLVVRDTEGRMVW 1ebdA 393 :DTDGFLKLVVRKEDGVIIG T0358 52 :AWNFEPDAGE 1ebdA 412 :AQIIGPNASD T0358 62 :GLNRYIRT 1ebdA 425 :ELGLAIEA T0358 71 :GIRTDTATRLEHHH 1ebdA 433 :GMTAEDIALTIHAH Number of specific fragments extracted= 4 number of extra gaps= 0 total=93 Number of alignments=31 # 1ebdA read from 1ebdA/merged-good-all-a2m # found chain 1ebdA in template set T0358 31 :DDQGSHFRLVVRDTEGRMV 1ebdA 392 :NDTDGFLKLVVRKEDGVII T0358 51 :RAWNFEPDAGE 1ebdA 411 :GAQIIGPNASD T0358 62 :GLNRYIRTSG 1ebdA 425 :ELGLAIEAGM T0358 76 :TATRLEHHHH 1ebdA 435 :TAEDIALTIH Number of specific fragments extracted= 4 number of extra gaps= 0 total=97 Number of alignments=32 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vjfA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vjfA expands to /projects/compbio/data/pdb/1vjf.pdb.gz 1vjfA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 250, because occupancy 0.500 <= existing 0.500 in 1vjfA Skipped atom 252, because occupancy 0.500 <= existing 0.500 in 1vjfA Skipped atom 254, because occupancy 0.500 <= existing 0.500 in 1vjfA Skipped atom 256, because occupancy 0.500 <= existing 0.500 in 1vjfA Skipped atom 258, because occupancy 0.500 <= existing 0.500 in 1vjfA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 312, because occupancy 0.400 <= existing 0.600 in 1vjfA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 314, because occupancy 0.400 <= existing 0.600 in 1vjfA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 316, because occupancy 0.400 <= existing 0.600 in 1vjfA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 318, because occupancy 0.400 <= existing 0.600 in 1vjfA Skipped atom 503, because occupancy 0.330 <= existing 0.340 in 1vjfA Skipped atom 504, because occupancy 0.330 <= existing 0.340 in 1vjfA Skipped atom 506, because occupancy 0.330 <= existing 0.340 in 1vjfA Skipped atom 507, because occupancy 0.330 <= existing 0.340 in 1vjfA Skipped atom 509, because occupancy 0.330 <= existing 0.340 in 1vjfA Skipped atom 510, because occupancy 0.330 <= existing 0.340 in 1vjfA Skipped atom 512, because occupancy 0.330 <= existing 0.340 in 1vjfA Skipped atom 513, because occupancy 0.330 <= existing 0.340 in 1vjfA Skipped atom 515, because occupancy 0.330 <= existing 0.340 in 1vjfA Skipped atom 516, because occupancy 0.330 <= existing 0.340 in 1vjfA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 693, because occupancy 0.300 <= existing 0.700 in 1vjfA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 695, because occupancy 0.300 <= existing 0.700 in 1vjfA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 697, because occupancy 0.300 <= existing 0.700 in 1vjfA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 699, because occupancy 0.300 <= existing 0.700 in 1vjfA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 771, because occupancy 0.300 <= existing 0.700 in 1vjfA Skipped atom 775, because occupancy 0.300 <= existing 0.700 in 1vjfA Skipped atom 777, because occupancy 0.300 <= existing 0.700 in 1vjfA Skipped atom 825, because occupancy 0.500 <= existing 0.500 in 1vjfA Skipped atom 827, because occupancy 0.500 <= existing 0.500 in 1vjfA Skipped atom 829, because occupancy 0.500 <= existing 0.500 in 1vjfA Skipped atom 831, because occupancy 0.500 <= existing 0.500 in 1vjfA Skipped atom 878, because occupancy 0.500 <= existing 0.500 in 1vjfA Skipped atom 880, because occupancy 0.500 <= existing 0.500 in 1vjfA Skipped atom 882, because occupancy 0.500 <= existing 0.500 in 1vjfA Skipped atom 884, because occupancy 0.500 <= existing 0.500 in 1vjfA Skipped atom 886, because occupancy 0.500 <= existing 0.500 in 1vjfA Skipped atom 888, because occupancy 0.500 <= existing 0.500 in 1vjfA Skipped atom 890, because occupancy 0.500 <= existing 0.500 in 1vjfA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1289, because occupancy 0.400 <= existing 0.600 in 1vjfA Skipped atom 1291, because occupancy 0.400 <= existing 0.600 in 1vjfA Skipped atom 1293, because occupancy 0.400 <= existing 0.600 in 1vjfA Skipped atom 1295, because occupancy 0.400 <= existing 0.600 in 1vjfA Skipped atom 1297, because occupancy 0.400 <= existing 0.600 in 1vjfA # T0358 read from 1vjfA/merged-good-all-a2m # 1vjfA read from 1vjfA/merged-good-all-a2m # adding 1vjfA to template set # found chain 1vjfA in template set Warning: unaligning (T0358)T28 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vjfA)T44 Warning: unaligning (T0358)L29 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vjfA)T44 T0358 3 :QSVL 1vjfA 19 :KTLD T0358 8 :PPGPFTRRQAQAVTTTYSNI 1vjfA 23 :HPPVFRVEEGLEIKAAMPGG T0358 30 :ED 1vjfA 45 :KN T0358 39 :LVVRDTEGRMVWRAWNFEPDAG 1vjfA 47 :LFLKDAKGQLWLISALGETTID T0358 61 :EGLNRYI 1vjfA 70 :KKLHHVI Number of specific fragments extracted= 5 number of extra gaps= 1 total=102 Number of alignments=33 # 1vjfA read from 1vjfA/merged-good-all-a2m # found chain 1vjfA in template set Warning: unaligning (T0358)T28 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vjfA)T44 Warning: unaligning (T0358)L29 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vjfA)T44 T0358 3 :QSVL 1vjfA 19 :KTLD T0358 8 :PPGPFTRRQAQAVTTTYSNI 1vjfA 23 :HPPVFRVEEGLEIKAAMPGG T0358 30 :ED 1vjfA 45 :KN T0358 39 :LVVRDTEGRMVWRAWNFEPDAG 1vjfA 47 :LFLKDAKGQLWLISALGETTID T0358 61 :EGLNRYIRTSG 1vjfA 70 :KKLHHVIGSGR Number of specific fragments extracted= 5 number of extra gaps= 1 total=107 Number of alignments=34 # 1vjfA read from 1vjfA/merged-good-all-a2m # found chain 1vjfA in template set Warning: unaligning (T0358)H36 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1vjfA)T44 Warning: unaligning (T0358)F37 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vjfA)T44 T0358 8 :PPGPFTRRQAQAVTTTY 1vjfA 23 :HPPVFRVEEGLEIKAAM T0358 33 :QGS 1vjfA 40 :PGG T0358 38 :R 1vjfA 45 :K T0358 39 :LVVRDTEGRMVWRAWNFEPDAG 1vjfA 47 :LFLKDAKGQLWLISALGETTID T0358 61 :EGLNRYIRTSGIRTDTATRLEHHHH 1vjfA 70 :KKLHHVIGSGRLSFGPQEMMLETLG Number of specific fragments extracted= 5 number of extra gaps= 1 total=112 Number of alignments=35 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2eql/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0358/2eql/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0358/2eql/merged-good-all-a2m.gz for input Trying 2eql/merged-good-all-a2m Error: Couldn't open file 2eql/merged-good-all-a2m or 2eql/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ttzA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ttzA expands to /projects/compbio/data/pdb/1ttz.pdb.gz 1ttzA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0358 read from 1ttzA/merged-good-all-a2m # 1ttzA read from 1ttzA/merged-good-all-a2m # adding 1ttzA to template set # found chain 1ttzA in template set Warning: unaligning (T0358)G71 because last residue in template chain is (1ttzA)P76 T0358 4 :SVLLPPGPFTRRQAQAVTTT 1ttzA 5 :LYQRDDCHLCDQAVEALAQA T0358 24 :YSNITLEDDQ 1ttzA 29 :FFSVFIDDDA T0358 34 :GSHFR 1ttzA 45 :GLRVP T0358 40 :VVRDTEGRMVW 1ttzA 50 :VLRDPMGRELD T0358 56 :EPDAGEGLNRYIRTS 1ttzA 61 :WPFDAPRLRAWLDAA Number of specific fragments extracted= 5 number of extra gaps= 0 total=117 Number of alignments=36 # 1ttzA read from 1ttzA/merged-good-all-a2m # found chain 1ttzA in template set Warning: unaligning (T0358)G71 because last residue in template chain is (1ttzA)P76 T0358 4 :SVLLPPGPFTRRQAQAVTTT 1ttzA 5 :LYQRDDCHLCDQAVEALAQA T0358 24 :YSNITLEDDQ 1ttzA 29 :FFSVFIDDDA T0358 34 :G 1ttzA 45 :G T0358 40 :VVRDTEGRMV 1ttzA 50 :VLRDPMGREL T0358 52 :AWNFE 1ttzA 60 :DWPFD T0358 60 :GEGLNRYIRTS 1ttzA 65 :APRLRAWLDAA Number of specific fragments extracted= 6 number of extra gaps= 0 total=123 Number of alignments=37 # 1ttzA read from 1ttzA/merged-good-all-a2m # found chain 1ttzA in template set Warning: unaligning (T0358)G71 because last residue in template chain is (1ttzA)P76 T0358 7 :LPPGPFTRRQAQAVTTTYS 1ttzA 7 :QRDDCHLCDQAVEALAQAR T0358 26 :NITLEDD 1ttzA 31 :SVFIDDD T0358 40 :VVRDTEGRMVW 1ttzA 50 :VLRDPMGRELD T0358 53 :WNFE 1ttzA 61 :WPFD T0358 60 :GEGLNRYIRTS 1ttzA 65 :APRLRAWLDAA Number of specific fragments extracted= 5 number of extra gaps= 0 total=128 Number of alignments=38 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cr5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2cr5A expands to /projects/compbio/data/pdb/2cr5.pdb.gz 2cr5A:# T0358 read from 2cr5A/merged-good-all-a2m # 2cr5A read from 2cr5A/merged-good-all-a2m # adding 2cr5A to template set # found chain 2cr5A in template set T0358 2 :TQSVLLPPGPF 2cr5A 7 :GEVPDLPEEPS T0358 31 :DDQGSHFRLVVRDTEGRMVWRA 2cr5A 18 :ETAEEVVTVALRCPNGRVLRRR T0358 54 :NFEPDAGEGLNRYIRTSGIRTDTAT 2cr5A 40 :FFKSWNSQVLLDWMMKVGYHKSLYR Number of specific fragments extracted= 3 number of extra gaps= 0 total=131 Number of alignments=39 # 2cr5A read from 2cr5A/merged-good-all-a2m # found chain 2cr5A in template set T0358 2 :TQSVLLPPGPF 2cr5A 7 :GEVPDLPEEPS T0358 31 :DDQGSHFRLVVRDTEGRMVWRA 2cr5A 18 :ETAEEVVTVALRCPNGRVLRRR T0358 54 :NFEPDAGEGLNRYIRTSGIRTDTATRLEHHH 2cr5A 40 :FFKSWNSQVLLDWMMKVGYHKSLYRLSTSFP Number of specific fragments extracted= 3 number of extra gaps= 0 total=134 Number of alignments=40 # 2cr5A read from 2cr5A/merged-good-all-a2m # found chain 2cr5A in template set T0358 6 :LLPPGP 2cr5A 11 :DLPEEP T0358 30 :EDDQGSHFRLVVRDTEGRMVWRAWNFEPD 2cr5A 17 :SETAEEVVTVALRCPNGRVLRRRFFKSWN T0358 60 :GEGLNRYIRTSGIRTD 2cr5A 46 :SQVLLDWMMKVGYHKS Number of specific fragments extracted= 3 number of extra gaps= 0 total=137 Number of alignments=41 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zkdA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zkdA expands to /projects/compbio/data/pdb/1zkd.pdb.gz 1zkdA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0358 read from 1zkdA/merged-good-all-a2m # 1zkdA read from 1zkdA/merged-good-all-a2m # adding 1zkdA to template set # found chain 1zkdA in template set T0358 10 :GPFTRRQAQAVTTTYSNITLEDD 1zkdA 120 :NPVLRQKQQTLLAGIRNIHWHDS T0358 33 :QGSHFRLVVRDTEGRMVWRAWNFEP 1zkdA 172 :TGWHERVIEIGASGELVFGVAADPI T0358 70 :SGIRTDTATRLEHHHH 1zkdA 197 :PGFEALLPPLARLSPP Number of specific fragments extracted= 3 number of extra gaps= 0 total=140 Number of alignments=42 # 1zkdA read from 1zkdA/merged-good-all-a2m # found chain 1zkdA in template set T0358 27 :ITLEDDQGSHFRLVVRDTEGRMVWRAWNFEPD 1zkdA 166 :QAIKRETGWHERVIEIGASGELVFGVAADPIP T0358 71 :GIRTDTATRLEHHHH 1zkdA 198 :GFEALLPPLARLSPP Number of specific fragments extracted= 2 number of extra gaps= 0 total=142 Number of alignments=43 # 1zkdA read from 1zkdA/merged-good-all-a2m # found chain 1zkdA in template set T0358 33 :QGSHFRLVVRDTEGRMVWRAW 1zkdA 172 :TGWHERVIEIGASGELVFGVA T0358 54 :NFEPDAGEGL 1zkdA 194 :DPIPGFEALL Number of specific fragments extracted= 2 number of extra gaps= 0 total=144 Number of alignments=44 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yx1A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1yx1A expands to /projects/compbio/data/pdb/1yx1.pdb.gz 1yx1A:Skipped atom 6, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 8, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 10, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 12, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 143, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 145, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 147, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 149, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 151, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 153, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 155, because occupancy 0.500 <= existing 0.500 in 1yx1A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 232, because occupancy 0.500 <= existing 0.500 in 1yx1A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 234, because occupancy 0.500 <= existing 0.500 in 1yx1A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 236, because occupancy 0.450 <= existing 0.450 in 1yx1A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 238, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 388, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 390, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 392, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 394, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 396, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 530, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 532, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 534, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 536, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 559, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 561, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 563, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 565, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 567, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 569, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 571, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 573, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 575, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 577, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 897, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 899, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 901, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 903, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 905, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 907, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 909, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 939, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 941, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 943, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 945, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 947, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 949, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 951, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1128, because occupancy 0.400 <= existing 0.600 in 1yx1A Skipped atom 1130, because occupancy 0.400 <= existing 0.600 in 1yx1A Skipped atom 1132, because occupancy 0.400 <= existing 0.600 in 1yx1A Skipped atom 1134, because occupancy 0.400 <= existing 0.600 in 1yx1A Skipped atom 1136, because occupancy 0.400 <= existing 0.600 in 1yx1A Skipped atom 1138, because occupancy 0.400 <= existing 0.600 in 1yx1A Skipped atom 1140, because occupancy 0.400 <= existing 0.600 in 1yx1A Skipped atom 1192, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1194, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1196, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1198, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1200, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1206, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1208, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1210, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1212, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1214, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1216, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1218, because occupancy 0.500 <= existing 0.500 in 1yx1A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1401, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1403, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1405, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1407, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1463, because occupancy 0.300 <= existing 0.700 in 1yx1A Skipped atom 1465, because occupancy 0.300 <= existing 0.700 in 1yx1A Skipped atom 1467, because occupancy 0.300 <= existing 0.700 in 1yx1A Skipped atom 1469, because occupancy 0.300 <= existing 0.700 in 1yx1A Skipped atom 1471, because occupancy 0.300 <= existing 0.700 in 1yx1A Skipped atom 1473, because occupancy 0.300 <= existing 0.700 in 1yx1A Skipped atom 1475, because occupancy 0.300 <= existing 0.700 in 1yx1A Skipped atom 1692, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1694, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1696, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1698, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1700, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1741, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1743, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1745, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1747, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1749, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1751, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 1753, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 2012, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 2014, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 2016, because occupancy 0.500 <= existing 0.500 in 1yx1A Skipped atom 2018, because occupancy 0.500 <= existing 0.500 in 1yx1A # T0358 read from 1yx1A/merged-good-all-a2m # 1yx1A read from 1yx1A/merged-good-all-a2m # adding 1yx1A to template set # found chain 1yx1A in template set T0358 13 :TRRQAQAVTTTYSNITL 1yx1A 172 :ADEAALRLGRYVGYVHC T0358 38 :RLVVRDTEGRMVW 1yx1A 189 :KAVIRNRDGKLVA Number of specific fragments extracted= 2 number of extra gaps= 0 total=146 Number of alignments=45 # 1yx1A read from 1yx1A/merged-good-all-a2m # found chain 1yx1A in template set T0358 13 :TRRQAQAVTTTYSNITL 1yx1A 172 :ADEAALRLGRYVGYVHC T0358 38 :RLVVRDTEGRMVW 1yx1A 189 :KAVIRNRDGKLVA Number of specific fragments extracted= 2 number of extra gaps= 0 total=148 Number of alignments=46 # 1yx1A read from 1yx1A/merged-good-all-a2m # found chain 1yx1A in template set T0358 17 :AQAVTTTYSNITL 1yx1A 173 :DEAALRLGRYVGY T0358 36 :HFRLVVRDTEGRMVWRAW 1yx1A 187 :HCKAVIRNRDGKLVAVPP Number of specific fragments extracted= 2 number of extra gaps= 0 total=150 Number of alignments=47 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v74A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1v74A expands to /projects/compbio/data/pdb/1v74.pdb.gz 1v74A:# T0358 read from 1v74A/merged-good-all-a2m # 1v74A read from 1v74A/merged-good-all-a2m # adding 1v74A to template set # found chain 1v74A in template set T0358 3 :QSVLLPPGPFTRRQAQAVTTTY 1v74A 613 :GDFGISDTKKNRETLTKFRDAI T0358 25 :SNITLEDDQGSHFR 1v74A 645 :EKGTYRREKGSKVY T0358 39 :LVVRDTEGRMV 1v74A 666 :VVIIKSNGEFL T0358 51 :RAWNFEPDAGEG 1v74A 677 :SGWKINPDADNG T0358 65 :RYIRTSG 1v74A 689 :RIYLETG Number of specific fragments extracted= 5 number of extra gaps= 0 total=155 Number of alignments=48 # 1v74A read from 1v74A/merged-good-all-a2m # found chain 1v74A in template set T0358 6 :LLPPGPFTRRQAQAVTTTYS 1v74A 616 :GISDTKKNRETLTKFRDAIE T0358 26 :NI 1v74A 642 :DT T0358 28 :TLEDDQGSHFR 1v74A 648 :TYRREKGSKVY T0358 39 :LVVRDTEGRMV 1v74A 666 :VVIIKSNGEFL T0358 51 :RAWNFEPDAGEG 1v74A 677 :SGWKINPDADNG T0358 65 :RYIRTSG 1v74A 689 :RIYLETG Number of specific fragments extracted= 6 number of extra gaps= 0 total=161 Number of alignments=49 # 1v74A read from 1v74A/merged-good-all-a2m # found chain 1v74A in template set T0358 4 :SVLLPPGPFTRRQAQAVTTTYSNI 1v74A 614 :DFGISDTKKNRETLTKFRDAIEEH T0358 28 :TLEDDQGSHFR 1v74A 648 :TYRREKGSKVY T0358 39 :LVVRDTEGRMV 1v74A 666 :VVIIKSNGEFL T0358 51 :RAWNFEPDAGEG 1v74A 677 :SGWKINPDADNG T0358 65 :RYIRT 1v74A 689 :RIYLE Number of specific fragments extracted= 5 number of extra gaps= 0 total=166 Number of alignments=50 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2f4qA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2f4qA expands to /projects/compbio/data/pdb/2f4q.pdb.gz 2f4qA:Skipped atom 593, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 595, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 597, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 599, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 601, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 649, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 651, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 653, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 659, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 661, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 663, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 665, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 667, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 669, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 671, because occupancy 0.500 <= existing 0.500 in 2f4qA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 936, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 938, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 940, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 1215, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 1217, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 1219, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 1225, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 1227, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 1242, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 1244, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 1246, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 1248, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 1250, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 1252, because occupancy 0.500 <= existing 0.500 in 2f4qA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1821, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 1823, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 1825, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 1827, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 1829, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 2133, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 2135, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 2137, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 2139, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 2294, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 2296, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 2298, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 2300, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 2340, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 2342, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 2344, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 2346, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 2348, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 2401, because occupancy 0.500 <= existing 0.500 in 2f4qA Skipped atom 2403, because occupancy 0.500 <= existing 0.500 in 2f4qA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0358 read from 2f4qA/merged-good-all-a2m # 2f4qA read from 2f4qA/merged-good-all-a2m # adding 2f4qA to template set # found chain 2f4qA in template set T0358 22 :TTYSNITLEDDQGSHFRLVVRDTEGRMVWRAW 2f4qA 49 :PAYQDVYVSPDAENELQAFGRDAAGRLQYRYH T0358 57 :PDA 2f4qA 81 :PDF Number of specific fragments extracted= 2 number of extra gaps= 0 total=168 Number of alignments=51 # 2f4qA read from 2f4qA/merged-good-all-a2m # found chain 2f4qA in template set T0358 22 :TTYSNITLEDDQGSHFRLVVRDTEGRMVWRAW 2f4qA 49 :PAYQDVYVSPDAENELQAFGRDAAGRLQYRYH T0358 54 :NFEPDAG 2f4qA 83 :FVQAGAL Number of specific fragments extracted= 2 number of extra gaps= 0 total=170 Number of alignments=52 # 2f4qA read from 2f4qA/merged-good-all-a2m # found chain 2f4qA in template set T0358 23 :TYSNITLEDDQGSHFRLVVRDTEGRMVWRAW 2f4qA 50 :AYQDVYVSPDAENELQAFGRDAAGRLQYRYH T0358 57 :P 2f4qA 81 :P Number of specific fragments extracted= 2 number of extra gaps= 0 total=172 Number of alignments=53 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2c3vA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2c3vA expands to /projects/compbio/data/pdb/2c3v.pdb.gz 2c3vA:Bad short name: I1 for alphabet: pdb_atoms Bad short name: I2 for alphabet: pdb_atoms Bad short name: I1 for alphabet: pdb_atoms Bad short name: I1 for alphabet: pdb_atoms Skipped atom 727, because occupancy 0.500 <= existing 0.500 in 2c3vA Skipped atom 731, because occupancy 0.500 <= existing 0.500 in 2c3vA Skipped atom 733, because occupancy 0.500 <= existing 0.500 in 2c3vA # T0358 read from 2c3vA/merged-good-all-a2m # 2c3vA read from 2c3vA/merged-good-all-a2m # adding 2c3vA to template set # found chain 2c3vA in template set Warning: unaligning (T0358)T23 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2c3vA)V128 Warning: unaligning (T0358)S25 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2c3vA)V128 T0358 26 :NITLEDDQGSHFRLVVRDTEGRMV 2c3vA 129 :KVTIEAEEGSQLRAAFNNGSGQWD Number of specific fragments extracted= 1 number of extra gaps= 0 total=173 Number of alignments=54 # 2c3vA read from 2c3vA/merged-good-all-a2m # found chain 2c3vA in template set Warning: unaligning (T0358)T23 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2c3vA)V128 Warning: unaligning (T0358)S25 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2c3vA)V128 T0358 26 :NITLEDDQGSHFRLVVRDTEGRMV 2c3vA 129 :KVTIEAEEGSQLRAAFNNGSGQWD Number of specific fragments extracted= 1 number of extra gaps= 0 total=174 Number of alignments=55 # 2c3vA read from 2c3vA/merged-good-all-a2m # found chain 2c3vA in template set T0358 27 :ITLEDDQGSHFRLVVRDTEGRMV 2c3vA 130 :VTIEAEEGSQLRAAFNNGSGQWD Number of specific fragments extracted= 1 number of extra gaps= 0 total=175 Number of alignments=56 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lktA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1lktA expands to /projects/compbio/data/pdb/1lkt.pdb.gz 1lktA:# T0358 read from 1lktA/merged-good-all-a2m # 1lktA read from 1lktA/merged-good-all-a2m # adding 1lktA to template set # found chain 1lktA in template set T0358 25 :SNITLEDDQGSHFRL 1lktA 47 :IPVYIENEDGSHVQI T0358 40 :VVRDTEGRMVW 1lktA 65 :LIINAAGKIVY Number of specific fragments extracted= 2 number of extra gaps= 0 total=177 Number of alignments=57 # 1lktA read from 1lktA/merged-good-all-a2m # found chain 1lktA in template set T0358 25 :SNITLEDDQGSHFRL 1lktA 47 :IPVYIENEDGSHVQI T0358 40 :VVRDTEGRMVW 1lktA 65 :LIINAAGKIVY Number of specific fragments extracted= 2 number of extra gaps= 0 total=179 Number of alignments=58 # 1lktA read from 1lktA/merged-good-all-a2m # found chain 1lktA in template set T0358 26 :NITLEDDQGSHFRL 1lktA 48 :PVYIENEDGSHVQI T0358 40 :VVRDTEGRMVW 1lktA 65 :LIINAAGKIVY Number of specific fragments extracted= 2 number of extra gaps= 0 total=181 Number of alignments=59 # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0358//projects/compbio/experiments/protein-predict/casp7/T0358/align.constraints_v3.costfcn or /projects/compbio/experiments/protein-predict/casp7/T0358//projects/compbio/experiments/protein-predict/casp7/T0358/align.constraints_v3.costfcn.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/T0358/align.constraints_v3.costfcn # reading script from file /projects/compbio/experiments/protein-predict/casp7/T0358/align.constraints_v3.costfcn # future Constraint commands -> align # future HelixConstraint commands -> align # future StrandConstraint commands -> align # future SheetConstraint commands -> align # future Hbond commands -> align # future SSbond commands -> align # Constraint # added constraint: constraint((T0358)V40.CB, (T0358)W50.CB) [> 3.8024 = 6.3373 < 8.2385] w=1.0000 to align # Constraint # added constraint: constraint((T0358)L39.CB, (T0358)R51.CB) [> 3.4855 = 5.8092 < 7.5519] w=0.7845 to align # Constraint # added constraint: constraint((T0358)V41.CB, (T0358)W50.CB) [> 3.6070 = 6.0117 < 7.8152] w=0.7447 to align # Constraint # added constraint: constraint((T0358)R38.CB, (T0358)A52.CB) [> 3.6634 = 6.1057 < 7.9374] w=0.7437 to align # Constraint # added constraint: constraint((T0358)L39.CB, (T0358)W50.CB) [> 4.2650 = 7.1083 < 9.2408] w=0.7306 to align # Constraint # added constraint: constraint((T0358)R38.CB, (T0358)W53.CB) [> 3.6550 = 6.0917 < 7.9192] w=0.7214 to align # Constraint # added constraint: constraint((T0358)V40.CB, (T0358)R51.CB) [> 3.7380 = 6.2300 < 8.0990] w=0.7166 to align # Constraint # added constraint: constraint((T0358)V40.CB, (T0358)V49.CB) [> 4.2224 = 7.0373 < 9.1484] w=0.7030 to align # Constraint # added constraint: constraint((T0358)V41.CB, (T0358)R51.CB) [> 3.9014 = 6.5024 < 8.4531] w=0.6721 to align # Constraint # added constraint: constraint((T0358)L39.CB, (T0358)A52.CB) [> 3.4523 = 5.7539 < 7.4801] w=0.6339 to align # Constraint # added constraint: constraint((T0358)R38.CB, (T0358)R51.CB) [> 3.9530 = 6.5884 < 8.5649] w=0.6292 to align # Constraint # added constraint: constraint((T0358)F37.CB, (T0358)W53.CB) [> 3.7612 = 6.2686 < 8.1492] w=0.6090 to align # Constraint # added constraint: constraint((T0358)H36.CB, (T0358)W53.CB) [> 3.4993 = 5.8322 < 7.5818] w=0.5534 to align # Constraint # added constraint: constraint((T0358)L39.CB, (T0358)W53.CB) [> 3.8852 = 6.4754 < 8.4180] w=0.4183 to align # Constraint # added constraint: constraint((T0358)F37.CB, (T0358)A52.CB) [> 4.1383 = 6.8971 < 8.9663] w=0.4105 to align # Constraint # added constraint: constraint((T0358)H36.CB, (T0358)A52.CB) [> 3.2960 = 5.4933 < 7.1413] w=0.3812 to align # Constraint # added constraint: constraint((T0358)H36.CB, (T0358)N54.CB) [> 4.0220 = 6.7034 < 8.7144] w=0.3566 to align # Constraint # added constraint: constraint((T0358)F37.CB, (T0358)N54.CB) [> 3.3263 = 5.5439 < 7.2071] w=0.3465 to align # Constraint # added constraint: constraint((T0358)L29.CB, (T0358)R38.CB) [> 4.0696 = 6.7827 < 8.8175] w=0.3375 to align # Constraint # added constraint: constraint((T0358)H36.CB, (T0358)F55.CB) [> 3.6594 = 6.0991 < 7.9288] w=0.3252 to align # Constraint # added constraint: constraint((T0358)R38.CB, (T0358)W50.CB) [> 3.5740 = 5.9567 < 7.7437] w=0.3218 to align # Constraint # added constraint: constraint((T0358)Y24.CB, (T0358)V41.CB) [> 3.2406 = 5.4010 < 7.0213] w=0.2438 to align # Constraint # added constraint: constraint((T0358)I27.CB, (T0358)V40.CB) [> 4.1120 = 6.8533 < 8.9093] w=0.2368 to align # Constraint # added constraint: constraint((T0358)R38.CB, (T0358)F55.CB) [> 4.4238 = 7.3730 < 9.5848] w=0.2239 to align # Constraint # added constraint: constraint((T0358)I27.CB, (T0358)V41.CB) [> 2.7155 = 4.5258 < 5.8835] w=0.2223 to align # Constraint # added constraint: constraint((T0358)I27.CB, (T0358)L39.CB) [> 3.5949 = 5.9915 < 7.7890] w=0.2121 to align # Constraint # added constraint: constraint((T0358)T28.CB, (T0358)L39.CB) [> 4.2104 = 7.0173 < 9.1225] w=0.2121 to align # Constraint # added constraint: constraint((T0358)L29.CB, (T0358)L39.CB) [> 3.0450 = 5.0750 < 6.5975] w=0.2121 to align # Constraint # added constraint: constraint((T0358)I27.CB, (T0358)R38.CB) [> 3.9187 = 6.5312 < 8.4906] w=0.2105 to align # Constraint # added constraint: constraint((T0358)L29.CB, (T0358)W50.CB) [> 3.7867 = 6.3112 < 8.2046] w=0.2043 to align # Constraint # added constraint: constraint((T0358)V40.CB, (T0358)A52.CB) [> 3.9047 = 6.5078 < 8.4601] w=0.2018 to align # Constraint # added constraint: constraint((T0358)S35.CB, (T0358)N54.CB) [> 4.2441 = 7.0735 < 9.1955] w=0.1974 to align # Constraint # added constraint: constraint((T0358)T28.CB, (T0358)R38.CB) [> 3.5106 = 5.8509 < 7.6062] w=0.1946 to align # Constraint # added constraint: constraint((T0358)F37.CB, (T0358)F55.CB) [> 3.4880 = 5.8134 < 7.5574] w=0.1944 to align # Constraint # added constraint: constraint((T0358)V20.CB, (T0358)L29.CB) [> 3.8308 = 6.3847 < 8.3001] w=0.1770 to align # Constraint # added constraint: constraint((T0358)Q16.CB, (T0358)F37.CB) [> 2.9569 = 4.9281 < 6.4065] w=0.1770 to align # Constraint # added constraint: constraint((T0358)N54.CB, (T0358)L63.CB) [> 3.6019 = 6.0031 < 7.8040] w=0.1758 to align # Constraint # added constraint: constraint((T0358)V41.CB, (T0358)S70.CB) [> 4.1647 = 6.9411 < 9.0235] w=0.1732 to align # Constraint # added constraint: constraint((T0358)V20.CB, (T0358)L39.CB) [> 3.2727 = 5.4545 < 7.0908] w=0.1705 to align # Constraint # added constraint: constraint((T0358)L39.CB, (T0358)L63.CB) [> 4.2723 = 7.1206 < 9.2567] w=0.1555 to align # Constraint # added constraint: constraint((T0358)V41.CB, (T0358)A52.CB) [> 4.5395 = 7.5659 < 9.8357] w=0.1525 to align # Constraint # added constraint: constraint((T0358)T13.CB, (T0358)F37.CB) [> 4.0659 = 6.7764 < 8.8094] w=0.1521 to align # Constraint # added constraint: constraint((T0358)A19.CB, (T0358)M48.CB) [> 3.7852 = 6.3087 < 8.2014] w=0.1382 to align # Constraint # added constraint: constraint((T0358)S35.CB, (T0358)F55.CB) [> 3.1906 = 5.3176 < 6.9128] w=0.1339 to align # Constraint # added constraint: constraint((T0358)F37.CB, (T0358)R51.CB) [> 4.4932 = 7.4886 < 9.7352] w=0.1333 to align # Constraint # added constraint: constraint((T0358)G34.CA, (T0358)E56.CB) [> 3.5838 = 5.9730 < 7.7649] w=0.1327 to align # Constraint # added constraint: constraint((T0358)A52.CB, (T0358)Y66.CB) [> 4.7311 = 7.8851 < 10.2506] w=0.1302 to align # Constraint # added constraint: constraint((T0358)F55.CB, (T0358)N64.CB) [> 4.0703 = 6.7839 < 8.8191] w=0.1265 to align # Constraint # added constraint: constraint((T0358)G34.CA, (T0358)W53.CB) [> 3.7929 = 6.3216 < 8.2181] w=0.1257 to align # Constraint # added constraint: constraint((T0358)D43.CB, (T0358)S70.CB) [> 3.8890 = 6.4817 < 8.4262] w=0.1246 to align # Constraint # added constraint: constraint((T0358)R42.CB, (T0358)I72.CB) [> 3.6147 = 6.0245 < 7.8319] w=0.1191 to align # Constraint # added constraint: constraint((T0358)D31.CB, (T0358)A52.CB) [> 3.8764 = 6.4607 < 8.3989] w=0.1178 to align # Constraint # added constraint: constraint((T0358)I27.CB, (T0358)I67.CB) [> 4.1213 = 6.8688 < 8.9294] w=0.1171 to align # Constraint # added constraint: constraint((T0358)T23.CB, (T0358)D43.CB) [> 4.6775 = 7.7958 < 10.1346] w=0.1150 to align # Constraint # added constraint: constraint((T0358)Y24.CB, (T0358)D43.CB) [> 3.5041 = 5.8401 < 7.5922] w=0.1150 to align # Constraint # added constraint: constraint((T0358)Y24.CB, (T0358)V49.CB) [> 3.9167 = 6.5279 < 8.4862] w=0.1150 to align # Constraint # added constraint: constraint((T0358)S25.CB, (T0358)V41.CB) [> 3.8969 = 6.4948 < 8.4432] w=0.1150 to align # Constraint # added constraint: constraint((T0358)S25.CB, (T0358)R42.CB) [> 2.6812 = 4.4687 < 5.8094] w=0.1150 to align # Constraint # added constraint: constraint((T0358)N26.CB, (T0358)R42.CB) [> 3.1672 = 5.2786 < 6.8622] w=0.1150 to align # Constraint # added constraint: constraint((T0358)I27.CB, (T0358)R42.CB) [> 4.5035 = 7.5059 < 9.7577] w=0.1150 to align # Constraint # added constraint: constraint((T0358)T28.CB, (T0358)V40.CB) [> 3.3072 = 5.5121 < 7.1657] w=0.1150 to align # Constraint # added constraint: constraint((T0358)F37.CB, (T0358)W50.CB) [> 3.5532 = 5.9220 < 7.6986] w=0.1150 to align # Constraint # added constraint: constraint((T0358)Y24.CB, (T0358)M48.CB) [> 4.1279 = 6.8799 < 8.9439] w=0.1121 to align # Constraint # added constraint: constraint((T0358)A17.CB, (T0358)L39.CB) [> 4.3566 = 7.2611 < 9.4394] w=0.1072 to align # Constraint # added constraint: constraint((T0358)V20.CB, (T0358)V41.CB) [> 4.2097 = 7.0161 < 9.1210] w=0.1072 to align # Constraint # added constraint: constraint((T0358)Y24.CB, (T0358)W50.CB) [> 4.5456 = 7.5760 < 9.8488] w=0.1072 to align # Constraint # added constraint: constraint((T0358)N26.CB, (T0358)V49.CB) [> 4.7020 = 7.8366 < 10.1876] w=0.1072 to align # Constraint # added constraint: constraint((T0358)I27.CB, (T0358)V49.CB) [> 2.7627 = 4.6045 < 5.9858] w=0.1072 to align # Constraint # added constraint: constraint((T0358)I27.CB, (T0358)W50.CB) [> 2.9101 = 4.8502 < 6.3053] w=0.1072 to align # Constraint # added constraint: constraint((T0358)T28.CB, (T0358)W50.CB) [> 4.6031 = 7.6719 < 9.9734] w=0.1072 to align # Constraint # added constraint: constraint((T0358)V40.CB, (T0358)N64.CB) [> 4.1545 = 6.9242 < 9.0015] w=0.1072 to align # Constraint # added constraint: constraint((T0358)V40.CB, (T0358)I67.CB) [> 4.0738 = 6.7897 < 8.8266] w=0.1072 to align # Constraint # added constraint: constraint((T0358)M48.CB, (T0358)N64.CB) [> 4.0221 = 6.7035 < 8.7146] w=0.1072 to align # Constraint # added constraint: constraint((T0358)R51.CB, (T0358)N64.CB) [> 3.9996 = 6.6660 < 8.6658] w=0.1072 to align # Constraint # added constraint: constraint((T0358)T23.CB, (T0358)A77.CB) [> 4.3688 = 7.2812 < 9.4656] w=0.1047 to align # Constraint # added constraint: constraint((T0358)V20.CB, (T0358)N54.CB) [> 4.3983 = 7.3306 < 9.5297] w=0.1047 to align # Constraint # added constraint: constraint((T0358)Q16.CB, (T0358)L63.CB) [> 4.2624 = 7.1040 < 9.2351] w=0.1047 to align # Constraint # added constraint: constraint((T0358)S25.CB, (T0358)I72.CB) [> 3.9339 = 6.5564 < 8.5234] w=0.1047 to align # Constraint # added constraint: constraint((T0358)I27.CB, (T0358)I72.CB) [> 3.4607 = 5.7678 < 7.4981] w=0.1047 to align # Constraint # added constraint: constraint((T0358)L39.CB, (T0358)Y66.CB) [> 4.7027 = 7.8379 < 10.1893] w=0.1047 to align # Constraint # added constraint: constraint((T0358)P57.CB, (T0358)Y66.CB) [> 4.7125 = 7.8542 < 10.2105] w=0.1047 to align # Constraint # added constraint: constraint((T0358)I27.CB, (T0358)F37.CB) [> 3.8838 = 6.4731 < 8.4150] w=0.1011 to align # Constraint # added constraint: constraint((T0358)R51.CB, (T0358)Y66.CB) [> 4.5405 = 7.5675 < 9.8377] w=0.0939 to align # Constraint # added constraint: constraint((T0358)A19.CB, (T0358)L63.CB) [> 2.9293 = 4.8821 < 6.3467] w=0.0913 to align # Constraint # added constraint: constraint((T0358)N26.CB, (T0358)F55.CB) [> 4.5869 = 7.6449 < 9.9383] w=0.0886 to align # Constraint # added constraint: constraint((T0358)I27.CB, (T0358)N54.CB) [> 3.0583 = 5.0972 < 6.6264] w=0.0871 to align # Constraint # added constraint: constraint((T0358)Q33.CB, (T0358)F55.CB) [> 3.8791 = 6.4651 < 8.4046] w=0.0818 to align # Constraint # added constraint: constraint((T0358)F12.CB, (T0358)F37.CB) [> 3.9124 = 6.5207 < 8.4769] w=0.0814 to align # Constraint # added constraint: constraint((T0358)F12.CB, (T0358)H36.CB) [> 4.4348 = 7.3914 < 9.6088] w=0.0814 to align # Constraint # added constraint: constraint((T0358)Y66.CB, (T0358)L80.CB) [> 2.7439 = 4.5731 < 5.9450] w=0.0800 to align # Constraint # added constraint: constraint((T0358)V49.CB, (T0358)A59.CB) [> 3.4336 = 5.7226 < 7.4394] w=0.0761 to align # Constraint # added constraint: constraint((T0358)S25.CB, (T0358)H36.CB) [> 3.8458 = 6.4096 < 8.3325] w=0.0756 to align # Constraint # added constraint: constraint((T0358)D32.CB, (T0358)A52.CB) [> 2.6414 = 4.4023 < 5.7229] w=0.0750 to align # Constraint # added constraint: constraint((T0358)T23.CB, (T0358)V49.CB) [> 4.3483 = 7.2472 < 9.4213] w=0.0750 to align # Constraint # added constraint: constraint((T0358)T22.CB, (T0358)M48.CB) [> 4.6280 = 7.7133 < 10.0273] w=0.0750 to align # Constraint # added constraint: constraint((T0358)T22.CB, (T0358)R47.CB) [> 4.6746 = 7.7909 < 10.1282] w=0.0750 to align # Constraint # added constraint: constraint((T0358)V20.CB, (T0358)M48.CB) [> 3.9040 = 6.5067 < 8.4587] w=0.0750 to align # Constraint # added constraint: constraint((T0358)A19.CB, (T0358)R42.CB) [> 4.5911 = 7.6519 < 9.9474] w=0.0750 to align # Constraint # added constraint: constraint((T0358)L29.CB, (T0358)L63.CB) [> 2.7261 = 4.5434 < 5.9065] w=0.0738 to align # Constraint # added constraint: constraint((T0358)T13.CB, (T0358)A77.CB) [> 4.7032 = 7.8387 < 10.1903] w=0.0715 to align # Constraint # added constraint: constraint((T0358)L63.CB, (T0358)L80.CB) [> 4.4120 = 7.3534 < 9.5594] w=0.0715 to align # Constraint # added constraint: constraint((T0358)I67.CB, (T0358)L80.CB) [> 4.6564 = 7.7607 < 10.0889] w=0.0715 to align # Constraint # added constraint: constraint((T0358)T13.CB, (T0358)F55.CB) [> 3.2091 = 5.3484 < 6.9530] w=0.0698 to align # Constraint # added constraint: constraint((T0358)R15.CB, (T0358)E61.CB) [> 4.2491 = 7.0818 < 9.2063] w=0.0698 to align # Constraint # added constraint: constraint((T0358)Q16.CB, (T0358)A59.CB) [> 3.5385 = 5.8974 < 7.6667] w=0.0698 to align # Constraint # added constraint: constraint((T0358)A19.CB, (T0358)N54.CB) [> 3.9573 = 6.5954 < 8.5741] w=0.0698 to align # Constraint # added constraint: constraint((T0358)A19.CB, (T0358)N64.CB) [> 3.8413 = 6.4021 < 8.3227] w=0.0698 to align # Constraint # added constraint: constraint((T0358)T22.CB, (T0358)T78.CB) [> 3.0916 = 5.1526 < 6.6984] w=0.0698 to align # Constraint # added constraint: constraint((T0358)T23.CB, (T0358)L80.CB) [> 4.7066 = 7.8444 < 10.1977] w=0.0698 to align # Constraint # added constraint: constraint((T0358)L7.CB, (T0358)G62.CA) [> 4.7749 = 7.9581 < 10.3456] w=0.0685 to align # Constraint # added constraint: constraint((T0358)L7.CB, (T0358)R65.CB) [> 3.6215 = 6.0358 < 7.8465] w=0.0685 to align # Constraint # added constraint: constraint((T0358)L7.CB, (T0358)Y66.CB) [> 3.4684 = 5.7806 < 7.5148] w=0.0685 to align # Constraint # added constraint: constraint((T0358)G10.CA, (T0358)R51.CB) [> 4.0125 = 6.6875 < 8.6937] w=0.0685 to align # Constraint # added constraint: constraint((T0358)P11.CB, (T0358)A52.CB) [> 2.7273 = 4.5455 < 5.9091] w=0.0685 to align # Constraint # added constraint: constraint((T0358)V49.CB, (T0358)S70.CB) [> 3.9421 = 6.5702 < 8.5413] w=0.0685 to align # Constraint # added constraint: constraint((T0358)Y24.CB, (T0358)W53.CB) [> 3.2177 = 5.3629 < 6.9718] w=0.0632 to align # Constraint # added constraint: constraint((T0358)T23.CB, (T0358)W53.CB) [> 3.2067 = 5.3444 < 6.9478] w=0.0632 to align # Constraint # added constraint: constraint((T0358)T22.CB, (T0358)R38.CB) [> 4.2969 = 7.1615 < 9.3100] w=0.0632 to align # Constraint # added constraint: constraint((T0358)T21.CB, (T0358)R38.CB) [> 3.3995 = 5.6659 < 7.3657] w=0.0632 to align # Constraint # added constraint: constraint((T0358)E30.CB, (T0358)N64.CB) [> 2.9757 = 4.9595 < 6.4474] w=0.0632 to align # Constraint # added constraint: constraint((T0358)T28.CB, (T0358)N64.CB) [> 2.7945 = 4.6576 < 6.0549] w=0.0632 to align # Constraint # added constraint: constraint((T0358)T28.CB, (T0358)G62.CA) [> 2.9059 = 4.8432 < 6.2962] w=0.0632 to align # Constraint # added constraint: constraint((T0358)T28.CB, (T0358)F55.CB) [> 3.4068 = 5.6781 < 7.3815] w=0.0632 to align # Constraint # added constraint: constraint((T0358)L39.CB, (T0358)A59.CB) [> 4.2391 = 7.0651 < 9.1847] w=0.0611 to align # Constraint # added constraint: constraint((T0358)E56.CB, (T0358)I72.CB) [> 4.1402 = 6.9002 < 8.9703] w=0.0510 to align # Constraint # added constraint: constraint((T0358)E30.CB, (T0358)A52.CB) [> 4.4794 = 7.4656 < 9.7053] w=0.0466 to align # Constraint # added constraint: constraint((T0358)V5.CB, (T0358)R65.CB) [> 3.5972 = 5.9954 < 7.7940] w=0.0457 to align # Constraint # added constraint: constraint((T0358)V5.CB, (T0358)R68.CB) [> 3.8531 = 6.4218 < 8.3483] w=0.0457 to align # Constraint # added constraint: constraint((T0358)F12.CB, (T0358)D31.CB) [> 3.2704 = 5.4507 < 7.0859] w=0.0457 to align # Constraint # added constraint: constraint((T0358)F12.CB, (T0358)D32.CB) [> 2.9268 = 4.8779 < 6.3413] w=0.0457 to align # Constraint # added constraint: constraint((T0358)I67.CB, (T0358)A77.CB) [> 4.0401 = 6.7334 < 8.7535] w=0.0457 to align # Constraint # added constraint: constraint((T0358)L7.CB, (T0358)L29.CB) [> 3.7621 = 6.2702 < 8.1513] w=0.0428 to align # Constraint # added constraint: constraint((T0358)D32.CB, (T0358)D43.CB) [> 3.8527 = 6.4212 < 8.3475] w=0.0371 to align # Constraint # added constraint: constraint((T0358)L29.CB, (T0358)R51.CB) [> 4.6258 = 7.7097 < 10.0225] w=0.0371 to align # Constraint # added constraint: constraint((T0358)P9.CB, (T0358)A19.CB) [> 4.0008 = 6.6680 < 8.6683] w=0.0371 to align # Constraint # added constraint: constraint((T0358)L7.CB, (T0358)T23.CB) [> 3.4445 = 5.7409 < 7.4632] w=0.0371 to align # Constraint # added constraint: constraint((T0358)P57.CB, (T0358)R68.CB) [> 3.9564 = 6.5940 < 8.5722] w=0.0371 to align # Constraint # added constraint: constraint((T0358)P8.CB, (T0358)A17.CB) [> 4.1918 = 6.9863 < 9.0822] w=0.0349 to align # Constraint # added constraint: constraint((T0358)R15.CB, (T0358)D58.CB) [> 2.5834 = 4.3057 < 5.5974] w=0.0349 to align # Constraint # added constraint: constraint((T0358)A17.CB, (T0358)P57.CB) [> 4.3044 = 7.1740 < 9.3262] w=0.0349 to align # Constraint # added constraint: constraint((T0358)A17.CB, (T0358)A59.CB) [> 4.6289 = 7.7148 < 10.0293] w=0.0349 to align # Constraint # added constraint: constraint((T0358)A17.CB, (T0358)G60.CA) [> 3.8892 = 6.4820 < 8.4266] w=0.0349 to align # Constraint # added constraint: constraint((T0358)R51.CB, (T0358)I67.CB) [> 4.3204 = 7.2006 < 9.3608] w=0.0338 to align # Constraint # added constraint: constraint((T0358)R14.CB, (T0358)L29.CB) [> 3.4529 = 5.7548 < 7.4813] w=0.0255 to align # Constraint # added constraint: constraint((T0358)Q18.CB, (T0358)L29.CB) [> 4.4165 = 7.3608 < 9.5690] w=0.0255 to align # Constraint # added constraint: constraint((T0358)M48.CB, (T0358)I67.CB) [> 3.1976 = 5.3293 < 6.9281] w=0.0254 to align # Constraint # added constraint: constraint((T0358)S25.CB, (T0358)E56.CB) [> 4.6311 = 7.7184 < 10.0340] w=0.0254 to align # Constraint # added constraint: constraint((T0358)S25.CB, (T0358)E45.CB) [> 4.3755 = 7.2926 < 9.4803] w=0.0254 to align # Constraint # added constraint: constraint((T0358)W50.CB, (T0358)A59.CB) [> 3.6864 = 6.1439 < 7.9871] w=0.0254 to align # Constraint # added constraint: constraint((T0358)S4.CB, (T0358)W53.CB) [> 2.9630 = 4.9383 < 6.4198] w=0.0247 to align # Constraint # added constraint: constraint((T0358)S4.CB, (T0358)N54.CB) [> 2.4662 = 4.1103 < 5.3434] w=0.0247 to align # Constraint # added constraint: constraint((T0358)Q3.CB, (T0358)Y24.CB) [> 4.4516 = 7.4193 < 9.6450] w=0.0238 to align # Constraint # added constraint: constraint((T0358)E30.CB, (T0358)W53.CB) [> 3.5791 = 5.9652 < 7.7547] w=0.0238 to align # Constraint # added constraint: constraint((T0358)T44.CB, (T0358)G71.CA) [> 2.5217 = 4.2029 < 5.4637] w=0.0238 to align # Constraint # added constraint: constraint((T0358)V41.CB, (T0358)R79.CB) [> 4.6326 = 7.7210 < 10.0373] w=0.0228 to align # Constraint # added constraint: constraint((T0358)I67.CB, (T0358)R79.CB) [> 4.3740 = 7.2901 < 9.4771] w=0.0228 to align # Constraint # added constraint: constraint((T0358)V5.CB, (T0358)R42.CB) [> 4.0449 = 6.7416 < 8.7640] w=0.0215 to align # Constraint # added constraint: constraint((T0358)S4.CB, (T0358)V40.CB) [> 4.4008 = 7.3346 < 9.5350] w=0.0215 to align # Constraint # added constraint: constraint((T0358)S4.CB, (T0358)Y24.CB) [> 3.2121 = 5.3534 < 6.9595] w=0.0215 to align # Constraint # added constraint: constraint((T0358)S4.CB, (T0358)V20.CB) [> 4.1407 = 6.9011 < 8.9714] w=0.0215 to align # Constraint # added constraint: constraint((T0358)V40.CB, (T0358)W53.CB) [> 4.0964 = 6.8273 < 8.8755] w=0.0215 to align # Constraint # added constraint: constraint((T0358)T22.CB, (T0358)G60.CA) [> 3.0617 = 5.1027 < 6.6336] w=0.0215 to align # Constraint # added constraint: constraint((T0358)L6.CB, (T0358)L29.CB) [> 4.2274 = 7.0456 < 9.1593] w=0.0215 to align # Constraint # added constraint: constraint((T0358)L6.CB, (T0358)I27.CB) [> 4.6457 = 7.7429 < 10.0657] w=0.0215 to align # Constraint # added constraint: constraint((T0358)L6.CB, (T0358)N26.CB) [> 3.4699 = 5.7832 < 7.5181] w=0.0215 to align # Constraint # added constraint: constraint((T0358)V40.CB, (T0358)L80.CB) [> 3.0327 = 5.0545 < 6.5709] w=0.0119 to align # Constraint # added constraint: constraint((T0358)G62.CA, (T0358)I72.CB) [> 4.7451 = 7.9085 < 10.2811] w=0.0119 to align # Constraint # added constraint: constraint((T0358)V41.CB, (T0358)D58.CB) [> 4.4683 = 7.4471 < 9.6813] w=0.0108 to align # Constraint # added constraint: constraint((T0358)V40.CB, (T0358)E56.CB) [> 4.1008 = 6.8347 < 8.8851] w=0.0108 to align # Constraint # added constraint: constraint((T0358)Y24.CB, (T0358)G62.CA) [> 4.5122 = 7.5203 < 9.7764] w=0.0108 to align # Constraint # added constraint: constraint((T0358)T21.CB, (T0358)L63.CB) [> 4.2437 = 7.0728 < 9.1946] w=0.0108 to align # Constraint # added constraint: constraint((T0358)T21.CB, (T0358)V41.CB) [> 4.7873 = 7.9788 < 10.3724] w=0.0108 to align # SetCost created cost = # ( 1.0000 * align ) # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0358/ # command:# reading script from file servers-clean.under # Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0358/decoys/ # ReadConformPDB reading from PDB file chimera2-2.pdb.gz looking for model 1 # Found a chain break before 79 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file chimera4-24.pdb.gz looking for model 1 # Found a chain break before 73 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file chimera5-2.pdb.gz looking for model 1 # Found a chain break before 79 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file chimera5-24.pdb.gz looking for model 1 # Found a chain break before 79 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS2.pdb.gz looking for model 1 # Found a chain break before 81 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS3.pdb.gz looking for model 1 # Found a chain break before 72 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS4.pdb.gz looking for model 1 # Found a chain break before 72 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS5.pdb.gz looking for model 1 # Found a chain break before 13 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS1.pdb.gz looking for model 1 # Found a chain break before 84 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_RECOM_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS3.pdb.gz looking for model 1 # Found a chain break before 83 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_RECOM_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_RECOM_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS5.pdb.gz looking for model 1 # Found a chain break before 83 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_RECOM_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS5 # ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1 # Found a chain break before 8 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS1 # ReadConformPDB reading from PDB file servers/3Dpro_TS2.pdb.gz looking for model 1 # Found a chain break before 8 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS2 # ReadConformPDB reading from PDB file servers/3Dpro_TS3.pdb.gz looking for model 1 # Found a chain break before 86 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS3 # ReadConformPDB reading from PDB file servers/3Dpro_TS4.pdb.gz looking for model 1 # Found a chain break before 81 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS4 # ReadConformPDB reading from PDB file servers/3Dpro_TS5.pdb.gz looking for model 1 # Found a chain break before 8 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS5 # ReadConformPDB reading from PDB file servers/ABIpro_TS1.pdb.gz looking for model 1 # Found a chain break before 86 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS1 # ReadConformPDB reading from PDB file servers/ABIpro_TS2.pdb.gz looking for model 1 # Found a chain break before 81 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS2 # ReadConformPDB reading from PDB file servers/ABIpro_TS3.pdb.gz looking for model 1 # Found a chain break before 76 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS3 # ReadConformPDB reading from PDB file servers/ABIpro_TS4.pdb.gz looking for model 1 # Found a chain break before 49 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS4 # ReadConformPDB reading from PDB file servers/ABIpro_TS5.pdb.gz looking for model 1 # Found a chain break before 39 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS5 # ReadConformPDB reading from PDB file servers/BayesHH_TS1.pdb.gz looking for model 1 # Found a chain break before 76 # copying to AlignedFragments data structure # naming current conformation BayesHH_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS1.pdb.gz looking for model 1 # Found a chain break before 62 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS2.pdb.gz looking for model 1 # naming current conformation Bilab-ENABLE_TS2 # ReadConformPDB reading from PDB file servers/CIRCLE_TS1.pdb.gz looking for model 1 # Found a chain break before 76 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS1 # ReadConformPDB reading from PDB file servers/CIRCLE_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS2 # ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1 # Found a chain break before 86 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS3 # ReadConformPDB reading from PDB file servers/CIRCLE_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS4 # ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS5 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS1 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS2 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS3.pdb.gz looking for model 1 # Found a chain break before 81 # copying to AlignedFragments data structure # naming current conformation CaspIta-FOX_TS3 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS4 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS5 # ReadConformPDB reading from PDB file servers/Distill_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation Distill_TS1 # ReadConformPDB reading from PDB file servers/Distill_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation Distill_TS2 # ReadConformPDB reading from PDB file servers/Distill_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation Distill_TS3 # ReadConformPDB reading from PDB file servers/Distill_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation Distill_TS4 # ReadConformPDB reading from PDB file servers/Distill_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation Distill_TS5 # ReadConformPDB reading from PDB file servers/FAMSD_TS1.pdb.gz looking for model 1 # Found a chain break before 82 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS1 # ReadConformPDB reading from PDB file servers/FAMSD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FAMSD_TS2 # ReadConformPDB reading from PDB file servers/FAMSD_TS3.pdb.gz looking for model 1 # Found a chain break before 81 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS3 # ReadConformPDB reading from PDB file servers/FAMSD_TS4.pdb.gz looking for model 1 # Found a chain break before 77 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS4 # ReadConformPDB reading from PDB file servers/FAMSD_TS5.pdb.gz looking for model 1 # Found a chain break before 67 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS5 # ReadConformPDB reading from PDB file servers/FAMS_TS1.pdb.gz looking for model 1 # Found a chain break before 85 # copying to AlignedFragments data structure # naming current conformation FAMS_TS1 # ReadConformPDB reading from PDB file servers/FAMS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FAMS_TS2 # ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1 # Found a chain break before 86 # copying to AlignedFragments data structure # naming current conformation FAMS_TS3 # ReadConformPDB reading from PDB file servers/FAMS_TS4.pdb.gz looking for model 1 # Found a chain break before 76 # copying to AlignedFragments data structure # naming current conformation FAMS_TS4 # ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1 # Found a chain break before 74 # copying to AlignedFragments data structure # naming current conformation FAMS_TS5 # ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1 # Found a chain break before 8 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS1 # ReadConformPDB reading from PDB file servers/FOLDpro_TS2.pdb.gz looking for model 1 # naming current conformation FOLDpro_TS2 # ReadConformPDB reading from PDB file servers/FOLDpro_TS3.pdb.gz looking for model 1 # Found a chain break before 8 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS3 # ReadConformPDB reading from PDB file servers/FOLDpro_TS4.pdb.gz looking for model 1 # Found a chain break before 55 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS4 # ReadConformPDB reading from PDB file servers/FOLDpro_TS5.pdb.gz looking for model 1 # Found a chain break before 8 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS5 # ReadConformPDB reading from PDB file servers/FORTE1_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL1 # ReadConformPDB reading from PDB file servers/FORTE1_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL2 # ReadConformPDB reading from PDB file servers/FORTE1_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL3 # ReadConformPDB reading from PDB file servers/FORTE1_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation FORTE1_AL4 # ReadConformPDB reading from PDB file servers/FORTE1_AL5.pdb.gz looking for model 1 Skipped atom 190, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz Skipped atom 192, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz Skipped atom 194, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz Skipped atom 196, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation FORTE1_AL5 # ReadConformPDB reading from PDB file servers/FORTE2_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE2_AL1 # ReadConformPDB reading from PDB file servers/FORTE2_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation FORTE2_AL2 # ReadConformPDB reading from PDB file servers/FORTE2_AL3.pdb.gz looking for model 1 Skipped atom 190, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 192, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 194, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz Skipped atom 196, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL3.pdb.gz # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation FORTE2_AL3 # ReadConformPDB reading from PDB file servers/FORTE2_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation FORTE2_AL4 # ReadConformPDB reading from PDB file servers/FORTE2_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation FORTE2_AL5 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS1.pdb.gz looking for model 1 # Found a chain break before 74 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS1 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS2.pdb.gz looking for model 1 # Found a chain break before 86 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS2 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS3.pdb.gz looking for model 1 # naming current conformation FPSOLVER-SERVER_TS3 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS4.pdb.gz looking for model 1 # Found a chain break before 85 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS4 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS5.pdb.gz looking for model 1 # naming current conformation FPSOLVER-SERVER_TS5 # ReadConformPDB reading from PDB file servers/FUGMOD_TS1.pdb.gz looking for model 1 # naming current conformation FUGMOD_TS1 # ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1 # naming current conformation FUGMOD_TS2 # ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1 # naming current conformation FUGMOD_TS3 # ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1 # naming current conformation FUGMOD_TS4 # ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1 # naming current conformation FUGMOD_TS5 # ReadConformPDB reading from PDB file servers/FUGUE_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGUE_AL1 # ReadConformPDB reading from PDB file servers/FUGUE_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGUE_AL2 # ReadConformPDB reading from PDB file servers/FUGUE_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation FUGUE_AL3 # ReadConformPDB reading from PDB file servers/FUGUE_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation FUGUE_AL4 # ReadConformPDB reading from PDB file servers/FUGUE_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation FUGUE_AL5 # ReadConformPDB reading from PDB file servers/FUNCTION_TS1.pdb.gz looking for model 1 # Found a chain break before 80 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS1 # ReadConformPDB reading from PDB file servers/FUNCTION_TS2.pdb.gz looking for model 1 # Found a chain break before 74 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS2 # ReadConformPDB reading from PDB file servers/FUNCTION_TS3.pdb.gz looking for model 1 # Found a chain break before 85 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS3 # ReadConformPDB reading from PDB file servers/FUNCTION_TS4.pdb.gz looking for model 1 # Found a chain break before 73 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS4 # ReadConformPDB reading from PDB file servers/FUNCTION_TS5.pdb.gz looking for model 1 # Found a chain break before 76 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS5 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS1 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS2.pdb.gz looking for model 1 # Found a chain break before 49 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS2 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1 # Found a chain break before 42 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS3 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS4 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS5 # ReadConformPDB reading from PDB file servers/HHpred1_TS1.pdb.gz looking for model 1 # Found a chain break before 11 # copying to AlignedFragments data structure # naming current conformation HHpred1_TS1 # ReadConformPDB reading from PDB file servers/HHpred2_TS1.pdb.gz looking for model 1 # Found a chain break before 11 # copying to AlignedFragments data structure # naming current conformation HHpred2_TS1 # ReadConformPDB reading from PDB file servers/HHpred3_TS1.pdb.gz looking for model 1 # Found a chain break before 54 # copying to AlignedFragments data structure # naming current conformation HHpred3_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS2 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS3 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS4 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS5 # ReadConformPDB reading from PDB file servers/LOOPP_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation LOOPP_TS1 # ReadConformPDB reading from PDB file servers/LOOPP_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation LOOPP_TS2 # ReadConformPDB reading from PDB file servers/LOOPP_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation LOOPP_TS3 # ReadConformPDB reading from PDB file servers/LOOPP_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation LOOPP_TS4 # ReadConformPDB reading from PDB file servers/LOOPP_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation LOOPP_TS5 # ReadConformPDB reading from PDB file servers/MIG_FROST_AL1.pdb.gz looking for model 1 Error: Reading chain '' from PDB file servers/MIG_FROST_AL1.pdb.gz failed---no such chain. # naming current conformation MIG_FROST_AL1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS1.pdb.gz looking for model 1 # Found a chain break before 6 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS2.pdb.gz looking for model 1 # naming current conformation Ma-OPUS-server2_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS3.pdb.gz looking for model 1 # Found a chain break before 67 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS4.pdb.gz looking for model 1 # Found a chain break before 54 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS5.pdb.gz looking for model 1 # Found a chain break before 45 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS5 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS1.pdb.gz looking for model 1 # Found a chain break before 66 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS2.pdb.gz looking for model 1 # Found a chain break before 45 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS3.pdb.gz looking for model 1 # naming current conformation Ma-OPUS-server_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS4.pdb.gz looking for model 1 # Found a chain break before 54 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS5.pdb.gz looking for model 1 # Found a chain break before 71 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS5 # ReadConformPDB reading from PDB file servers/MetaTasser_TS1.pdb.gz looking for model 1 # Found a chain break before 86 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS1 # ReadConformPDB reading from PDB file servers/MetaTasser_TS2.pdb.gz looking for model 1 # Found a chain break before 83 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS2 # ReadConformPDB reading from PDB file servers/MetaTasser_TS3.pdb.gz looking for model 1 # Found a chain break before 85 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS3 # ReadConformPDB reading from PDB file servers/MetaTasser_TS4.pdb.gz looking for model 1 # Found a chain break before 83 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS4 # ReadConformPDB reading from PDB file servers/MetaTasser_TS5.pdb.gz looking for model 1 # Found a chain break before 83 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS5 # ReadConformPDB reading from PDB file servers/NN_PUT_lab_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation NN_PUT_lab_TS1 # ReadConformPDB reading from PDB file servers/POMYSL_TS1.pdb.gz looking for model 1 # Found a chain break before 67 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS1 # ReadConformPDB reading from PDB file servers/POMYSL_TS2.pdb.gz looking for model 1 # Found a chain break before 39 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS2 # ReadConformPDB reading from PDB file servers/POMYSL_TS3.pdb.gz looking for model 1 # Found a chain break before 59 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS3 # ReadConformPDB reading from PDB file servers/POMYSL_TS4.pdb.gz looking for model 1 # Found a chain break before 84 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS4 # ReadConformPDB reading from PDB file servers/POMYSL_TS5.pdb.gz looking for model 1 # Found a chain break before 86 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS1.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS2.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS3.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS4.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS5.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO_TS1.pdb.gz looking for model 1 # naming current conformation PROTINFO_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1 # naming current conformation PROTINFO_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1 # Found a chain break before 83 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1 # naming current conformation PROTINFO_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1 # Found a chain break before 64 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS5 # ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Pcons6_TS1 # ReadConformPDB reading from PDB file servers/Pcons6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation Pcons6_TS2 # ReadConformPDB reading from PDB file servers/Pcons6_TS3.pdb.gz looking for model 1 # naming current conformation Pcons6_TS3 # ReadConformPDB reading from PDB file servers/Pcons6_TS4.pdb.gz looking for model 1 # naming current conformation Pcons6_TS4 # ReadConformPDB reading from PDB file servers/Pcons6_TS5.pdb.gz looking for model 1 # naming current conformation Pcons6_TS5 # ReadConformPDB reading from PDB file servers/Phyre-1_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation Phyre-1_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS1.pdb.gz looking for model 1 # Found a chain break before 85 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS2.pdb.gz looking for model 1 # naming current conformation Phyre-2_TS2 # ReadConformPDB reading from PDB file servers/Phyre-2_TS3.pdb.gz looking for model 1 # Found a chain break before 85 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS3 # ReadConformPDB reading from PDB file servers/Phyre-2_TS4.pdb.gz looking for model 1 # Found a chain break before 50 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS4 # ReadConformPDB reading from PDB file servers/Phyre-2_TS5.pdb.gz looking for model 1 # Found a chain break before 34 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS5 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS1.pdb.gz looking for model 1 # naming current conformation Pmodeller6_TS1 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1 # naming current conformation Pmodeller6_TS2 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1 # Found a chain break before 58 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS3 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1 # naming current conformation Pmodeller6_TS4 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS5.pdb.gz looking for model 1 # naming current conformation Pmodeller6_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS1.pdb.gz looking for model 1 # Found a chain break before 16 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS2.pdb.gz looking for model 1 # Found a chain break before 49 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS3.pdb.gz looking for model 1 # naming current conformation RAPTOR-ACE_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS4.pdb.gz looking for model 1 # naming current conformation RAPTOR-ACE_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS5.pdb.gz looking for model 1 # Found a chain break before 59 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS5 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS1.pdb.gz looking for model 1 # Found a chain break before 84 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS1 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS2.pdb.gz looking for model 1 # Found a chain break before 83 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS2 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS3.pdb.gz looking for model 1 # Found a chain break before 56 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS3 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS4.pdb.gz looking for model 1 # Found a chain break before 63 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS4 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS5.pdb.gz looking for model 1 # Found a chain break before 64 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR_TS1.pdb.gz looking for model 1 # Found a chain break before 23 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR_TS2.pdb.gz looking for model 1 # Found a chain break before 24 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR_TS3.pdb.gz looking for model 1 # naming current conformation RAPTOR_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR_TS4.pdb.gz looking for model 1 # naming current conformation RAPTOR_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR_TS5.pdb.gz looking for model 1 # naming current conformation RAPTOR_TS5 # ReadConformPDB reading from PDB file servers/ROBETTA_TS1.pdb.gz looking for model 1 # naming current conformation ROBETTA_TS1 # ReadConformPDB reading from PDB file servers/ROBETTA_TS2.pdb.gz looking for model 1 # naming current conformation ROBETTA_TS2 # ReadConformPDB reading from PDB file servers/ROBETTA_TS3.pdb.gz looking for model 1 # naming current conformation ROBETTA_TS3 # ReadConformPDB reading from PDB file servers/ROBETTA_TS4.pdb.gz looking for model 1 # naming current conformation ROBETTA_TS4 # ReadConformPDB reading from PDB file servers/ROBETTA_TS5.pdb.gz looking for model 1 # naming current conformation ROBETTA_TS5 # ReadConformPDB reading from PDB file servers/ROKKY_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS1 # ReadConformPDB reading from PDB file servers/ROKKY_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS2 # ReadConformPDB reading from PDB file servers/ROKKY_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS3 # ReadConformPDB reading from PDB file servers/ROKKY_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS4 # ReadConformPDB reading from PDB file servers/ROKKY_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS5 # ReadConformPDB reading from PDB file servers/SAM-T02_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL1 # ReadConformPDB reading from PDB file servers/SAM-T02_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL2 # ReadConformPDB reading from PDB file servers/SAM-T02_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL3 # ReadConformPDB reading from PDB file servers/SAM-T02_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL4 # ReadConformPDB reading from PDB file servers/SAM-T02_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation SAM-T02_AL5 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS1.pdb.gz looking for model 1 # Found a chain break before 73 # copying to AlignedFragments data structure # naming current conformation SAM_T06_server_TS1 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS2 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS3 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS4 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS5 # ReadConformPDB reading from PDB file servers/SP3_TS1.pdb.gz looking for model 1 # Found a chain break before 60 # copying to AlignedFragments data structure # naming current conformation SP3_TS1 # ReadConformPDB reading from PDB file servers/SP3_TS2.pdb.gz looking for model 1 # naming current conformation SP3_TS2 # ReadConformPDB reading from PDB file servers/SP3_TS3.pdb.gz looking for model 1 # naming current conformation SP3_TS3 # ReadConformPDB reading from PDB file servers/SP3_TS4.pdb.gz looking for model 1 # Found a chain break before 62 # copying to AlignedFragments data structure # naming current conformation SP3_TS4 # ReadConformPDB reading from PDB file servers/SP3_TS5.pdb.gz looking for model 1 # naming current conformation SP3_TS5 # ReadConformPDB reading from PDB file servers/SP4_TS1.pdb.gz looking for model 1 # Found a chain break before 58 # copying to AlignedFragments data structure # naming current conformation SP4_TS1 # ReadConformPDB reading from PDB file servers/SP4_TS2.pdb.gz looking for model 1 # naming current conformation SP4_TS2 # ReadConformPDB reading from PDB file servers/SP4_TS3.pdb.gz looking for model 1 # Found a chain break before 18 # copying to AlignedFragments data structure # naming current conformation SP4_TS3 # ReadConformPDB reading from PDB file servers/SP4_TS4.pdb.gz looking for model 1 # naming current conformation SP4_TS4 # ReadConformPDB reading from PDB file servers/SP4_TS5.pdb.gz looking for model 1 # Found a chain break before 39 # copying to AlignedFragments data structure # naming current conformation SP4_TS5 # ReadConformPDB reading from PDB file servers/SPARKS2_TS1.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS1 # ReadConformPDB reading from PDB file servers/SPARKS2_TS2.pdb.gz looking for model 1 # Found a chain break before 9 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS2 # ReadConformPDB reading from PDB file servers/SPARKS2_TS3.pdb.gz looking for model 1 # Found a chain break before 55 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS3 # ReadConformPDB reading from PDB file servers/SPARKS2_TS4.pdb.gz looking for model 1 # Found a chain break before 7 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS4 # ReadConformPDB reading from PDB file servers/SPARKS2_TS5.pdb.gz looking for model 1 # Found a chain break before 34 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS2 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS3 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS4 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_expm_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation UNI-EID_expm_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL2 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL3 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL4 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL5 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS1.pdb.gz looking for model 1 # Found a chain break before 56 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS1 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS2.pdb.gz looking for model 1 # Found a chain break before 58 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS2 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS3.pdb.gz looking for model 1 # Found a chain break before 83 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS3 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS4.pdb.gz looking for model 1 # Found a chain break before 75 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS4 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS5.pdb.gz looking for model 1 # Found a chain break before 54 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS5 # ReadConformPDB reading from PDB file servers/beautshot_TS1.pdb.gz looking for model 1 # Found a chain break before 85 # copying to AlignedFragments data structure # naming current conformation beautshot_TS1 # ReadConformPDB reading from PDB file servers/beautshotbase_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation beautshotbase_TS1 # ReadConformPDB reading from PDB file servers/forecast-s_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation forecast-s_AL1 # ReadConformPDB reading from PDB file servers/forecast-s_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation forecast-s_AL2 # ReadConformPDB reading from PDB file servers/forecast-s_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation forecast-s_AL3 # ReadConformPDB reading from PDB file servers/forecast-s_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation forecast-s_AL4 # ReadConformPDB reading from PDB file servers/forecast-s_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation forecast-s_AL5 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1 # Found a chain break before 70 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS2.pdb.gz looking for model 1 # naming current conformation karypis.srv.2_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS3.pdb.gz looking for model 1 # naming current conformation karypis.srv.2_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS4.pdb.gz looking for model 1 # naming current conformation karypis.srv.2_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS5.pdb.gz looking for model 1 # naming current conformation karypis.srv.2_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS1.pdb.gz looking for model 1 # Found a chain break before 84 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS2.pdb.gz looking for model 1 # Found a chain break before 84 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS3.pdb.gz looking for model 1 WARNING: atoms too close: (T0358)L6.O and (T0358)L7.N only 0.000 apart, marking (T0358)L7.N as missing # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS4.pdb.gz looking for model 1 # Found a chain break before 84 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS5.pdb.gz looking for model 1 # Found a chain break before 84 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv_TS1.pdb.gz looking for model 1 # naming current conformation karypis.srv_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv_TS2.pdb.gz looking for model 1 # Found a chain break before 29 # copying to AlignedFragments data structure # naming current conformation karypis.srv_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS5 # ReadConformPDB reading from PDB file servers/keasar-server_TS1.pdb.gz looking for model 1 # naming current conformation keasar-server_TS1 # ReadConformPDB reading from PDB file servers/keasar-server_TS2.pdb.gz looking for model 1 # naming current conformation keasar-server_TS2 # ReadConformPDB reading from PDB file servers/keasar-server_TS3.pdb.gz looking for model 1 # Found a chain break before 38 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS3 # ReadConformPDB reading from PDB file servers/keasar-server_TS4.pdb.gz looking for model 1 # Found a chain break before 37 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS4 # ReadConformPDB reading from PDB file servers/keasar-server_TS5.pdb.gz looking for model 1 # Found a chain break before 37 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS5 # ReadConformPDB reading from PDB file servers/mGen-3D_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation mGen-3D_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation nFOLD_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation nFOLD_TS2 # ReadConformPDB reading from PDB file servers/nFOLD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation nFOLD_TS3 # ReadConformPDB reading from PDB file servers/nFOLD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation nFOLD_TS4 # ReadConformPDB reading from PDB file servers/nFOLD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation nFOLD_TS5 # ReadConformPDB reading from PDB file servers/panther2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation panther2_TS1 # ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0358 can't currently be optimized by undertaker # naming current conformation shub_TS1 # command:Using radius: 8.0000 Using models AND alignments for constraints model score 0.3925 model score 0.5031 model score 0.3932 model score 0.3794 model score 0.8526 model score 0.8065 model score 0.8099 model score 0.8105 model score 1.1284 model score 0.7871 model score 0.7807 model score 0.7910 model score 0.7822 model score 0.7911 model score 0.7661 model score 1.0864 model score 0.6736 model score 0.6387 model score 2.0024 model score 0.7360 model score 0.7402 model score 0.6662 model score 0.3258 model score 0.7588 model score 0.6662 model score 0.3258 model score 0.4893 model score 0.6743 model score 0.3416 model score 0.5663 model score 2.0977 model score 1.9859 model score 0.6846 model score 0.5286 model score 0.6569 model score 0.6739 model score 0.7594 model score 1.3397 model score 1.6669 model score 0.9905 model score 0.6422 model score 1.5803 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 0.7772 model score 0.5914 model score 0.7657 model score 0.6395 model score 0.4995 model score 0.6595 model score 0.5914 model score 0.6569 model score 0.6846 model score 0.6160 model score 0.7402 model score 1.5300 model score 0.7588 model score 0.6082 model score 0.7360 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 2.1489 model score 1.4982 model score 2.1285 model score 1.4621 model score 2.0930 model score 0.7131 model score 1.9920 model score 1.3643 model score 2.3215 model score 2.2479 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 0.8135 model score 0.6160 model score 0.7125 model score 0.7842 model score 0.5537 model score 0.5380 model score 0.6869 model score 0.9268 model score 1.4767 model score 1.4868 model score 0.6274 model score 0.6274 model score 0.5535 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 0.5839 model score 0.5947 model score 0.4613 model score 0.6537 model score 0.6928 model score 0.6840 model score 0.4147 model score 2.1647 model score 1.5055 model score 0.7008 model score 0.8880 model score 0.4191 model score 0.9149 model score 0.6354 model score 0.7008 model score 1.9950 model score 0.7913 model score 0.7795 model score 0.7768 model score 0.7737 model score 0.7717 model score 1.2771 model score 1.7018 model score 1.7953 model score 1.6067 model score 1.2575 model score 1.3555 model score 0.2749 model score 0.4860 model score 0.3424 model score 0.4595 model score 0.4305 model score 0.4566 model score 0.3531 model score 0.3634 model score 0.4685 model score 2.1850 model score 0.8365 model score 1.5797 model score 0.3486 model score 0.3370 model score 0.3815 model score 0.7032 model score 0.5077 model score 0.4339 model score 0.7028 model score 0.5745 model score 0.4240 model score 0.3486 model score 0.4906 model score 0.6592 model score 0.3815 model score 0.3370 model score 0.6884 model score 0.8788 model score 0.6812 model score 0.8576 model score 0.5757 model score 0.4317 model score 0.8566 model score 0.5371 model score 0.6860 model score 0.6582 model score 0.4173 model score 0.6771 model score 0.6225 model score 0.8673 model score 0.4944 model score 0.3486 model score 0.4906 model score 0.3236 model score 0.3815 model score 0.3370 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 0.3654 model score 0.3139 model score 0.4994 model score 0.3203 model score 1.1909 model score 0.5245 model score 0.6088 model score 1.8155 model score 0.5265 model score 0.9119 model score 0.6564 model score 0.6526 model score 0.5364 model score 0.7365 model score 0.8190 model score 1.4967 model score 1.4962 model score 2.2841 model score 2.0001 model score 1.3993 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2701 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 0.1767 model score 0.2614 model score 0.0940 model score 0.1034 model score 0.0512 model score 0.6068 model score 0.5818 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.5033 model score 1.4055 model score 1.2429 model score 2.1650 model score 2.0243 model score 2.0209 model score 2.0916 model score 2.1019 model score 1.6233 model score 1.4784 model score 0.6950 model score 1.9429 model score 0.3704 model score 2.0956 model score 0.9835 model score 1.8310 model score 1.8385 model score 2.1874 model score 1.4367 model score 1.4367 model score 0.4446 model score 0.9531 model score 1.7846 model score 1.4627 model score 1.0143 model score 0.5514 model score 2.0252 model score 1.4799 USE_META, weight: 0.8647 cost: 0.3925 min: 0.0512 max: 2.3215 USE_META, weight: 0.8209 cost: 0.5031 min: 0.0512 max: 2.3215 USE_META, weight: 0.8644 cost: 0.3932 min: 0.0512 max: 2.3215 USE_META, weight: 0.8699 cost: 0.3794 min: 0.0512 max: 2.3215 USE_META, weight: 0.6823 cost: 0.8526 min: 0.0512 max: 2.3215 USE_META, weight: 0.7006 cost: 0.8065 min: 0.0512 max: 2.3215 USE_META, weight: 0.6992 cost: 0.8099 min: 0.0512 max: 2.3215 USE_META, weight: 0.6990 cost: 0.8105 min: 0.0512 max: 2.3215 USE_META, weight: 0.5730 cost: 1.1284 min: 0.0512 max: 2.3215 USE_META, weight: 0.7083 cost: 0.7871 min: 0.0512 max: 2.3215 USE_META, weight: 0.7108 cost: 0.7807 min: 0.0512 max: 2.3215 USE_META, weight: 0.7067 cost: 0.7910 min: 0.0512 max: 2.3215 USE_META, weight: 0.7102 cost: 0.7822 min: 0.0512 max: 2.3215 USE_META, weight: 0.7067 cost: 0.7911 min: 0.0512 max: 2.3215 USE_META, weight: 0.7166 cost: 0.7661 min: 0.0512 max: 2.3215 USE_META, weight: 0.5896 cost: 1.0864 min: 0.0512 max: 2.3215 USE_META, weight: 0.7533 cost: 0.6736 min: 0.0512 max: 2.3215 USE_META, weight: 0.7671 cost: 0.6387 min: 0.0512 max: 2.3215 USE_META, weight: 0.2265 cost: 2.0024 min: 0.0512 max: 2.3215 USE_META, weight: 0.7285 cost: 0.7360 min: 0.0512 max: 2.3215 USE_META, weight: 0.7269 cost: 0.7402 min: 0.0512 max: 2.3215 USE_META, weight: 0.7562 cost: 0.6662 min: 0.0512 max: 2.3215 USE_META, weight: 0.8912 cost: 0.3258 min: 0.0512 max: 2.3215 USE_META, weight: 0.7195 cost: 0.7588 min: 0.0512 max: 2.3215 USE_META, weight: 0.7562 cost: 0.6662 min: 0.0512 max: 2.3215 USE_META, weight: 0.8912 cost: 0.3258 min: 0.0512 max: 2.3215 USE_META, weight: 0.8263 cost: 0.4893 min: 0.0512 max: 2.3215 USE_META, weight: 0.7530 cost: 0.6743 min: 0.0512 max: 2.3215 USE_META, weight: 0.8849 cost: 0.3416 min: 0.0512 max: 2.3215 USE_META, weight: 0.7958 cost: 0.5663 min: 0.0512 max: 2.3215 USE_META, weight: 0.1887 cost: 2.0977 min: 0.0512 max: 2.3215 USE_META, weight: 0.2331 cost: 1.9859 min: 0.0512 max: 2.3215 USE_META, weight: 0.7489 cost: 0.6846 min: 0.0512 max: 2.3215 USE_META, weight: 0.8107 cost: 0.5286 min: 0.0512 max: 2.3215 USE_META, weight: 0.7599 cost: 0.6569 min: 0.0512 max: 2.3215 USE_META, weight: 0.7532 cost: 0.6739 min: 0.0512 max: 2.3215 USE_META, weight: 0.7193 cost: 0.7594 min: 0.0512 max: 2.3215 USE_META, weight: 0.4892 cost: 1.3397 min: 0.0512 max: 2.3215 USE_META, weight: 0.3595 cost: 1.6669 min: 0.0512 max: 2.3215 USE_META, weight: 0.6276 cost: 0.9905 min: 0.0512 max: 2.3215 USE_META, weight: 0.7657 cost: 0.6422 min: 0.0512 max: 2.3215 USE_META, weight: 0.3938 cost: 1.5803 min: 0.0512 max: 2.3215 USE_META, weight: 0.5140 cost: 1.2771 min: 0.0512 max: 2.3215 USE_META, weight: 0.5140 cost: 1.2771 min: 0.0512 max: 2.3215 USE_META, weight: 0.5140 cost: 1.2771 min: 0.0512 max: 2.3215 USE_META, weight: 0.5140 cost: 1.2771 min: 0.0512 max: 2.3215 USE_META, weight: 0.5140 cost: 1.2771 min: 0.0512 max: 2.3215 USE_META, weight: 0.7122 cost: 0.7772 min: 0.0512 max: 2.3215 USE_META, weight: 0.7858 cost: 0.5914 min: 0.0512 max: 2.3215 USE_META, weight: 0.7168 cost: 0.7657 min: 0.0512 max: 2.3215 USE_META, weight: 0.7668 cost: 0.6395 min: 0.0512 max: 2.3215 USE_META, weight: 0.8223 cost: 0.4995 min: 0.0512 max: 2.3215 USE_META, weight: 0.7589 cost: 0.6595 min: 0.0512 max: 2.3215 USE_META, weight: 0.7858 cost: 0.5914 min: 0.0512 max: 2.3215 USE_META, weight: 0.7599 cost: 0.6569 min: 0.0512 max: 2.3215 USE_META, weight: 0.7489 cost: 0.6846 min: 0.0512 max: 2.3215 USE_META, weight: 0.7761 cost: 0.6160 min: 0.0512 max: 2.3215 USE_META, weight: 0.7269 cost: 0.7402 min: 0.0512 max: 2.3215 USE_META, weight: 0.4138 cost: 1.5300 min: 0.0512 max: 2.3215 USE_META, weight: 0.7195 cost: 0.7588 min: 0.0512 max: 2.3215 USE_META, weight: 0.7792 cost: 0.6082 min: 0.0512 max: 2.3215 USE_META, weight: 0.7285 cost: 0.7360 min: 0.0512 max: 2.3215 USE_META, weight: 0.5140 cost: 1.2771 min: 0.0512 max: 2.3215 USE_META, weight: 0.5140 cost: 1.2771 min: 0.0512 max: 2.3215 USE_META, weight: 0.5140 cost: 1.2771 min: 0.0512 max: 2.3215 USE_META, weight: 0.5140 cost: 1.2771 min: 0.0512 max: 2.3215 USE_META, weight: 0.5140 cost: 1.2771 min: 0.0512 max: 2.3215 USE_META, weight: 0.5140 cost: 1.2771 min: 0.0512 max: 2.3215 USE_META, weight: 0.5140 cost: 1.2771 min: 0.0512 max: 2.3215 USE_META, weight: 0.5140 cost: 1.2771 min: 0.0512 max: 2.3215 USE_META, weight: 0.5140 cost: 1.2771 min: 0.0512 max: 2.3215 USE_META, weight: 0.5140 cost: 1.2771 min: 0.0512 max: 2.3215 USE_META, weight: 0.1684 cost: 2.1489 min: 0.0512 max: 2.3215 USE_META, weight: 0.4264 cost: 1.4982 min: 0.0512 max: 2.3215 USE_META, weight: 0.1765 cost: 2.1285 min: 0.0512 max: 2.3215 USE_META, weight: 0.4407 cost: 1.4621 min: 0.0512 max: 2.3215 USE_META, weight: 0.1906 cost: 2.0930 min: 0.0512 max: 2.3215 USE_META, weight: 0.7376 cost: 0.7131 min: 0.0512 max: 2.3215 USE_META, weight: 0.2306 cost: 1.9920 min: 0.0512 max: 2.3215 USE_META, weight: 0.4795 cost: 1.3643 min: 0.0512 max: 2.3215 USE_META, weight: 0.1000 cost: 2.3215 min: 0.0512 max: 2.3215 USE_META, weight: 0.1292 cost: 2.2479 min: 0.0512 max: 2.3215 USE_META, weight: 0.5140 cost: 1.2771 min: 0.0512 max: 2.3215 USE_META, weight: 0.5140 cost: 1.2771 min: 0.0512 max: 2.3215 USE_META, weight: 0.5140 cost: 1.2771 min: 0.0512 max: 2.3215 USE_META, weight: 0.5140 cost: 1.2771 min: 0.0512 max: 2.3215 USE_META, weight: 0.5140 cost: 1.2771 min: 0.0512 max: 2.3215 USE_META, weight: 0.6978 cost: 0.8135 min: 0.0512 max: 2.3215 USE_META, weight: 0.7761 cost: 0.6160 min: 0.0512 max: 2.3215 USE_META, weight: 0.7379 cost: 0.7125 min: 0.0512 max: 2.3215 USE_META, weight: 0.7094 cost: 0.7842 min: 0.0512 max: 2.3215 USE_META, weight: 0.8008 cost: 0.5537 min: 0.0512 max: 2.3215 USE_META, weight: 0.8070 cost: 0.5380 min: 0.0512 max: 2.3215 USE_META, weight: 0.7480 cost: 0.6869 min: 0.0512 max: 2.3215 USE_META, weight: 0.6529 cost: 0.9268 min: 0.0512 max: 2.3215 USE_META, weight: 0.4349 cost: 1.4767 min: 0.0512 max: 2.3215 USE_META, weight: 0.4309 cost: 1.4868 min: 0.0512 max: 2.3215 USE_META, weight: 0.7716 cost: 0.6274 min: 0.0512 max: 2.3215 USE_META, weight: 0.7716 cost: 0.6274 min: 0.0512 max: 2.3215 USE_META, weight: 0.8009 cost: 0.5535 min: 0.0512 max: 2.3215 USE_META, weight: 0.5140 cost: 1.2771 min: 0.0512 max: 2.3215 USE_META, weight: 0.5140 cost: 1.2771 min: 0.0512 max: 2.3215 USE_META, weight: 0.5140 cost: 1.2771 min: 0.0512 max: 2.3215 USE_META, weight: 0.5140 cost: 1.2771 min: 0.0512 max: 2.3215 USE_META, weight: 0.7888 cost: 0.5839 min: 0.0512 max: 2.3215 USE_META, weight: 0.7845 cost: 0.5947 min: 0.0512 max: 2.3215 USE_META, weight: 0.8374 cost: 0.4613 min: 0.0512 max: 2.3215 USE_META, weight: 0.7612 cost: 0.6537 min: 0.0512 max: 2.3215 USE_META, weight: 0.7457 cost: 0.6928 min: 0.0512 max: 2.3215 USE_META, weight: 0.7491 cost: 0.6840 min: 0.0512 max: 2.3215 USE_META, weight: 0.8559 cost: 0.4147 min: 0.0512 max: 2.3215 USE_META, weight: 0.1622 cost: 2.1647 min: 0.0512 max: 2.3215 USE_META, weight: 0.4235 cost: 1.5055 min: 0.0512 max: 2.3215 USE_META, weight: 0.7425 cost: 0.7008 min: 0.0512 max: 2.3215 USE_META, weight: 0.6683 cost: 0.8880 min: 0.0512 max: 2.3215 USE_META, weight: 0.8541 cost: 0.4191 min: 0.0512 max: 2.3215 USE_META, weight: 0.6576 cost: 0.9149 min: 0.0512 max: 2.3215 USE_META, weight: 0.7684 cost: 0.6354 min: 0.0512 max: 2.3215 USE_META, weight: 0.7425 cost: 0.7008 min: 0.0512 max: 2.3215 USE_META, weight: 0.2294 cost: 1.9950 min: 0.0512 max: 2.3215 USE_META, weight: 0.7066 cost: 0.7913 min: 0.0512 max: 2.3215 USE_META, weight: 0.7113 cost: 0.7795 min: 0.0512 max: 2.3215 USE_META, weight: 0.7124 cost: 0.7768 min: 0.0512 max: 2.3215 USE_META, weight: 0.7136 cost: 0.7737 min: 0.0512 max: 2.3215 USE_META, weight: 0.7144 cost: 0.7717 min: 0.0512 max: 2.3215 USE_META, weight: 0.5140 cost: 1.2771 min: 0.0512 max: 2.3215 USE_META, weight: 0.3457 cost: 1.7018 min: 0.0512 max: 2.3215 USE_META, weight: 0.3086 cost: 1.7953 min: 0.0512 max: 2.3215 USE_META, weight: 0.3834 cost: 1.6067 min: 0.0512 max: 2.3215 USE_META, weight: 0.5218 cost: 1.2575 min: 0.0512 max: 2.3215 USE_META, weight: 0.4829 cost: 1.3555 min: 0.0512 max: 2.3215 USE_META, weight: 0.9113 cost: 0.2749 min: 0.0512 max: 2.3215 USE_META, weight: 0.8276 cost: 0.4860 min: 0.0512 max: 2.3215 USE_META, weight: 0.8846 cost: 0.3424 min: 0.0512 max: 2.3215 USE_META, weight: 0.8381 cost: 0.4595 min: 0.0512 max: 2.3215 USE_META, weight: 0.8496 cost: 0.4305 min: 0.0512 max: 2.3215 USE_META, weight: 0.8393 cost: 0.4566 min: 0.0512 max: 2.3215 USE_META, weight: 0.8803 cost: 0.3531 min: 0.0512 max: 2.3215 USE_META, weight: 0.8762 cost: 0.3634 min: 0.0512 max: 2.3215 USE_META, weight: 0.8346 cost: 0.4685 min: 0.0512 max: 2.3215 USE_META, weight: 0.1541 cost: 2.1850 min: 0.0512 max: 2.3215 USE_META, weight: 0.6887 cost: 0.8365 min: 0.0512 max: 2.3215 USE_META, weight: 0.3941 cost: 1.5797 min: 0.0512 max: 2.3215 USE_META, weight: 0.8821 cost: 0.3486 min: 0.0512 max: 2.3215 USE_META, weight: 0.8867 cost: 0.3370 min: 0.0512 max: 2.3215 USE_META, weight: 0.8691 cost: 0.3815 min: 0.0512 max: 2.3215 USE_META, weight: 0.7415 cost: 0.7032 min: 0.0512 max: 2.3215 USE_META, weight: 0.8190 cost: 0.5077 min: 0.0512 max: 2.3215 USE_META, weight: 0.8483 cost: 0.4339 min: 0.0512 max: 2.3215 USE_META, weight: 0.7417 cost: 0.7028 min: 0.0512 max: 2.3215 USE_META, weight: 0.7926 cost: 0.5745 min: 0.0512 max: 2.3215 USE_META, weight: 0.8522 cost: 0.4240 min: 0.0512 max: 2.3215 USE_META, weight: 0.8821 cost: 0.3486 min: 0.0512 max: 2.3215 USE_META, weight: 0.8258 cost: 0.4906 min: 0.0512 max: 2.3215 USE_META, weight: 0.7590 cost: 0.6592 min: 0.0512 max: 2.3215 USE_META, weight: 0.8691 cost: 0.3815 min: 0.0512 max: 2.3215 USE_META, weight: 0.8867 cost: 0.3370 min: 0.0512 max: 2.3215 USE_META, weight: 0.7474 cost: 0.6884 min: 0.0512 max: 2.3215 USE_META, weight: 0.6719 cost: 0.8788 min: 0.0512 max: 2.3215 USE_META, weight: 0.7503 cost: 0.6812 min: 0.0512 max: 2.3215 USE_META, weight: 0.6803 cost: 0.8576 min: 0.0512 max: 2.3215 USE_META, weight: 0.7921 cost: 0.5757 min: 0.0512 max: 2.3215 USE_META, weight: 0.8491 cost: 0.4317 min: 0.0512 max: 2.3215 USE_META, weight: 0.6807 cost: 0.8566 min: 0.0512 max: 2.3215 USE_META, weight: 0.8074 cost: 0.5371 min: 0.0512 max: 2.3215 USE_META, weight: 0.7483 cost: 0.6860 min: 0.0512 max: 2.3215 USE_META, weight: 0.7594 cost: 0.6582 min: 0.0512 max: 2.3215 USE_META, weight: 0.8549 cost: 0.4173 min: 0.0512 max: 2.3215 USE_META, weight: 0.7519 cost: 0.6771 min: 0.0512 max: 2.3215 USE_META, weight: 0.7735 cost: 0.6225 min: 0.0512 max: 2.3215 USE_META, weight: 0.6765 cost: 0.8673 min: 0.0512 max: 2.3215 USE_META, weight: 0.8243 cost: 0.4944 min: 0.0512 max: 2.3215 USE_META, weight: 0.8821 cost: 0.3486 min: 0.0512 max: 2.3215 USE_META, weight: 0.8258 cost: 0.4906 min: 0.0512 max: 2.3215 USE_META, weight: 0.8920 cost: 0.3236 min: 0.0512 max: 2.3215 USE_META, weight: 0.8691 cost: 0.3815 min: 0.0512 max: 2.3215 USE_META, weight: 0.8867 cost: 0.3370 min: 0.0512 max: 2.3215 USE_META, weight: 0.5140 cost: 1.2771 min: 0.0512 max: 2.3215 USE_META, weight: 0.5140 cost: 1.2771 min: 0.0512 max: 2.3215 USE_META, weight: 0.5140 cost: 1.2771 min: 0.0512 max: 2.3215 USE_META, weight: 0.5140 cost: 1.2771 min: 0.0512 max: 2.3215 USE_META, weight: 0.5140 cost: 1.2771 min: 0.0512 max: 2.3215 USE_META, weight: 0.5140 cost: 1.2771 min: 0.0512 max: 2.3215 USE_META, weight: 0.5140 cost: 1.2771 min: 0.0512 max: 2.3215 USE_META, weight: 0.5140 cost: 1.2771 min: 0.0512 max: 2.3215 USE_META, weight: 0.5140 cost: 1.2771 min: 0.0512 max: 2.3215 USE_META, weight: 0.5140 cost: 1.2771 min: 0.0512 max: 2.3215 USE_META, weight: 0.8754 cost: 0.3654 min: 0.0512 max: 2.3215 USE_META, weight: 0.8959 cost: 0.3139 min: 0.0512 max: 2.3215 USE_META, weight: 0.8223 cost: 0.4994 min: 0.0512 max: 2.3215 USE_META, weight: 0.8933 cost: 0.3203 min: 0.0512 max: 2.3215 USE_META, weight: 0.5482 cost: 1.1909 min: 0.0512 max: 2.3215 USE_META, weight: 0.8124 cost: 0.5245 min: 0.0512 max: 2.3215 USE_META, weight: 0.7790 cost: 0.6088 min: 0.0512 max: 2.3215 USE_META, weight: 0.3006 cost: 1.8155 min: 0.0512 max: 2.3215 USE_META, weight: 0.8116 cost: 0.5265 min: 0.0512 max: 2.3215 USE_META, weight: 0.6588 cost: 0.9119 min: 0.0512 max: 2.3215 USE_META, weight: 0.7601 cost: 0.6564 min: 0.0512 max: 2.3215 USE_META, weight: 0.7616 cost: 0.6526 min: 0.0512 max: 2.3215 USE_META, weight: 0.8077 cost: 0.5364 min: 0.0512 max: 2.3215 USE_META, weight: 0.7283 cost: 0.7365 min: 0.0512 max: 2.3215 USE_META, weight: 0.6956 cost: 0.8190 min: 0.0512 max: 2.3215 USE_META, weight: 0.4270 cost: 1.4967 min: 0.0512 max: 2.3215 USE_META, weight: 0.4272 cost: 1.4962 min: 0.0512 max: 2.3215 USE_META, weight: 0.1148 cost: 2.2841 min: 0.0512 max: 2.3215 USE_META, weight: 0.2274 cost: 2.0001 min: 0.0512 max: 2.3215 USE_META, weight: 0.4656 cost: 1.3993 min: 0.0512 max: 2.3215 USE_META, weight: 0.5140 cost: 1.2771 min: 0.0512 max: 2.3215 USE_META, weight: 0.5140 cost: 1.2771 min: 0.0512 max: 2.3215 USE_META, weight: 0.5140 cost: 1.2771 min: 0.0512 max: 2.3215 USE_META, weight: 0.5140 cost: 1.2771 min: 0.0512 max: 2.3215 USE_META, weight: 0.5140 cost: 1.2771 min: 0.0512 max: 2.3215 USE_META, weight: 0.5168 cost: 1.2701 min: 0.0512 max: 2.3215 USE_META, weight: 0.5140 cost: 1.2771 min: 0.0512 max: 2.3215 USE_META, weight: 0.5140 cost: 1.2771 min: 0.0512 max: 2.3215 USE_META, weight: 0.5140 cost: 1.2771 min: 0.0512 max: 2.3215 USE_META, weight: 0.5140 cost: 1.2771 min: 0.0512 max: 2.3215 USE_META, weight: 0.5140 cost: 1.2771 min: 0.0512 max: 2.3215 USE_META, weight: 0.9502 cost: 0.1767 min: 0.0512 max: 2.3215 USE_META, weight: 0.9167 cost: 0.2614 min: 0.0512 max: 2.3215 USE_META, weight: 0.9830 cost: 0.0940 min: 0.0512 max: 2.3215 USE_META, weight: 0.9793 cost: 0.1034 min: 0.0512 max: 2.3215 USE_META, weight: 1.0000 cost: 0.0512 min: 0.0512 max: 2.3215 USE_META, weight: 0.7797 cost: 0.6068 min: 0.0512 max: 2.3215 USE_META, weight: 0.7897 cost: 0.5818 min: 0.0512 max: 2.3215 USE_META, weight: 0.5140 cost: 1.2771 min: 0.0512 max: 2.3215 USE_META, weight: 0.5140 cost: 1.2771 min: 0.0512 max: 2.3215 USE_META, weight: 0.5140 cost: 1.2771 min: 0.0512 max: 2.3215 USE_META, weight: 0.5140 cost: 1.2771 min: 0.0512 max: 2.3215 USE_META, weight: 0.5140 cost: 1.2771 min: 0.0512 max: 2.3215 USE_META, weight: 0.4243 cost: 1.5033 min: 0.0512 max: 2.3215 USE_META, weight: 0.4631 cost: 1.4055 min: 0.0512 max: 2.3215 USE_META, weight: 0.5276 cost: 1.2429 min: 0.0512 max: 2.3215 USE_META, weight: 0.1621 cost: 2.1650 min: 0.0512 max: 2.3215 USE_META, weight: 0.2178 cost: 2.0243 min: 0.0512 max: 2.3215 USE_META, weight: 0.2192 cost: 2.0209 min: 0.0512 max: 2.3215 USE_META, weight: 0.1912 cost: 2.0916 min: 0.0512 max: 2.3215 USE_META, weight: 0.1871 cost: 2.1019 min: 0.0512 max: 2.3215 USE_META, weight: 0.3768 cost: 1.6233 min: 0.0512 max: 2.3215 USE_META, weight: 0.4342 cost: 1.4784 min: 0.0512 max: 2.3215 USE_META, weight: 0.7448 cost: 0.6950 min: 0.0512 max: 2.3215 USE_META, weight: 0.2501 cost: 1.9429 min: 0.0512 max: 2.3215 USE_META, weight: 0.8735 cost: 0.3704 min: 0.0512 max: 2.3215 USE_META, weight: 0.1895 cost: 2.0956 min: 0.0512 max: 2.3215 USE_META, weight: 0.6304 cost: 0.9835 min: 0.0512 max: 2.3215 USE_META, weight: 0.2945 cost: 1.8310 min: 0.0512 max: 2.3215 USE_META, weight: 0.2915 cost: 1.8385 min: 0.0512 max: 2.3215 USE_META, weight: 0.1532 cost: 2.1874 min: 0.0512 max: 2.3215 USE_META, weight: 0.4508 cost: 1.4367 min: 0.0512 max: 2.3215 USE_META, weight: 0.4508 cost: 1.4367 min: 0.0512 max: 2.3215 USE_META, weight: 0.8440 cost: 0.4446 min: 0.0512 max: 2.3215 USE_META, weight: 0.6425 cost: 0.9531 min: 0.0512 max: 2.3215 USE_META, weight: 0.3128 cost: 1.7846 min: 0.0512 max: 2.3215 USE_META, weight: 0.4405 cost: 1.4627 min: 0.0512 max: 2.3215 USE_META, weight: 0.6182 cost: 1.0143 min: 0.0512 max: 2.3215 USE_META, weight: 0.8017 cost: 0.5514 min: 0.0512 max: 2.3215 USE_META, weight: 0.2175 cost: 2.0252 min: 0.0512 max: 2.3215 USE_META, weight: 0.4336 cost: 1.4799 min: 0.0512 max: 2.3215 USE_EVALUE, weight: 0.6520 eval: 6.2066 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 0.6520 eval: 6.2066 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 0.6520 eval: 6.2066 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 0.1000 eval: 15.5510 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 0.1000 eval: 15.5510 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 0.1000 eval: 15.5510 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 0.8247 eval: 3.2843 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 0.8247 eval: 3.2843 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 0.8247 eval: 3.2843 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 0.2773 eval: 12.5500 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 0.2773 eval: 12.5500 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 0.2773 eval: 12.5500 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 0.7274 eval: 4.9312 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 0.9105 eval: 1.8323 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 0.9105 eval: 1.8323 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 0.9105 eval: 1.8323 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 0.1673 eval: 14.4120 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 0.1673 eval: 14.4120 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 0.1673 eval: 14.4120 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 0.5549 eval: 7.8507 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 0.2759 eval: 12.5740 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 0.2759 eval: 12.5740 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 0.2759 eval: 12.5740 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 0.9321 eval: 1.4655 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 0.9321 eval: 1.4655 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 0.9321 eval: 1.4655 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 0.6614 eval: 6.0479 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 0.6614 eval: 6.0479 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 0.6614 eval: 6.0479 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 0.2212 eval: 13.5000 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 0.2212 eval: 13.5000 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 0.2212 eval: 13.5000 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 0.3105 eval: 11.9880 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 0.3105 eval: 11.9880 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 0.3105 eval: 11.9880 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 0.2805 eval: 12.4950 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 0.2805 eval: 12.4950 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 0.2805 eval: 12.4950 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 0.5955 eval: 7.1641 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 0.5955 eval: 7.1641 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 0.5955 eval: 7.1641 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 0.6647 eval: 5.9927 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 0.6647 eval: 5.9927 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 0.6647 eval: 5.9927 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 0.6091 eval: 6.9328 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 0.6091 eval: 6.9328 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 0.6091 eval: 6.9328 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 0.3222 eval: 11.7900 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 0.3222 eval: 11.7900 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 0.3222 eval: 11.7900 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 1.0000 eval: 0.3169 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 1.0000 eval: 0.3169 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 1.0000 eval: 0.3169 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 0.7617 eval: 4.3511 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 0.7617 eval: 4.3511 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 0.7617 eval: 4.3511 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 0.8436 eval: 2.9635 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 0.8436 eval: 2.9635 min: 0.3169 max: 15.5510 USE_EVALUE, weight: 0.8436 eval: 2.9635 min: 0.3169 max: 15.5510 Number of contacts in models: 258 Number of contacts in alignments: 59 NUMB_ALIGNS: 59 Adding 2844 constraints to all3.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all3.constraints maxweight: 1.0000 Optimizing... Probability sum: -168.5347, CN propb: -168.5347 weights: 0.2207 constraints: 192 # command:Found ConstraintSet # PrintContacts align.constraints_meta03 Number of constraints in align3.constraints 192 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_meta03 Number of constraints in align3.constraints.bonus 192 # command:Found ConstraintSet # PrintContacts rejected.constraints_meta03 Number of constraints in rejected3.constraints 2652 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_meta03 Number of constraints in rejected3.constraints.bonus 2652 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_meta03 Number of constraints in noncontact3.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_meta03 Number of constraints in noncontact3.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_meta03 Number of constraints in all3.constraints 2844 # command: