parameters: 0.6 1.3 0.5 200 50 # 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:# PrintAlignmentsContacts allconstraints.under Using radius: 8.0000 NUMB_ALIGNS: 59 Done printing distance constraints # command: