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/T0343/ # command:# Making conformation for sequence T0343 numbered 1 through 104 Created new target T0343 from T0343.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0343/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0343//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0343/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0343//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0343/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0343/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0343/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ygsA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2ygsA expands to /projects/compbio/data/pdb/2ygs.pdb.gz 2ygsA:# T0343 read from 2ygsA/merged-good-all-a2m # 2ygsA read from 2ygsA/merged-good-all-a2m # adding 2ygsA to template set # found chain 2ygsA in template set T0343 54 :NVQNYREAVEW 2ygsA 45 :NEPTQQQRAAM # choosing archetypes in rotamer library T0343 68 :VLERIRD 2ygsA 56 :LIKMILK T0343 87 :APPKVMKRLSLALQK 2ygsA 63 :KDNDSYVSFYNALLH Number of specific fragments extracted= 3 number of extra gaps= 0 total=3 Number of alignments=1 # 2ygsA read from 2ygsA/merged-good-all-a2m # found chain 2ygsA in template set T0343 5 :EILRKEGFLDLGE 2ygsA 27 :DHMISDGFLTISE T0343 54 :NVQNYREAVEWA 2ygsA 45 :NEPTQQQRAAML T0343 69 :LERIRD 2ygsA 57 :IKMILK T0343 87 :APPKVMKRLSLALQK 2ygsA 63 :KDNDSYVSFYNALLH Number of specific fragments extracted= 4 number of extra gaps= 0 total=7 Number of alignments=2 # 2ygsA read from 2ygsA/merged-good-all-a2m # found chain 2ygsA in template set T0343 5 :EILRKEGFLDLG 2ygsA 27 :DHMISDGFLTIS T0343 48 :KVE 2ygsA 42 :KVR T0343 54 :NVQNYREAVE 2ygsA 45 :NEPTQQQRAA T0343 67 :EVLERIRDGE 2ygsA 55 :MLIKMILKKD T0343 89 :PKVMKRLSLALQK 2ygsA 65 :NDSYVSFYNALLH Number of specific fragments extracted= 5 number of extra gaps= 0 total=12 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2eu9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2eu9A expands to /projects/compbio/data/pdb/2eu9.pdb.gz 2eu9A:Skipped atom 900, because occupancy 0.5 <= existing 0.500 in 2eu9A Skipped atom 902, because occupancy 0.500 <= existing 0.500 in 2eu9A Skipped atom 904, because occupancy 0.500 <= existing 0.500 in 2eu9A Skipped atom 939, because occupancy 0.500 <= existing 0.500 in 2eu9A Skipped atom 941, because occupancy 0.500 <= existing 0.500 in 2eu9A Skipped atom 943, because occupancy 0.500 <= existing 0.500 in 2eu9A Skipped atom 1288, because occupancy 0.500 <= existing 0.500 in 2eu9A Skipped atom 1292, because occupancy 0.500 <= existing 0.500 in 2eu9A Skipped atom 1294, because occupancy 0.500 <= existing 0.500 in 2eu9A Skipped atom 1296, because occupancy 0.500 <= existing 0.500 in 2eu9A Skipped atom 1298, because occupancy 0.500 <= existing 0.500 in 2eu9A Skipped atom 1300, because occupancy 0.500 <= existing 0.500 in 2eu9A Skipped atom 1947, because occupancy 0.500 <= existing 0.500 in 2eu9A Skipped atom 1951, because occupancy 0.500 <= existing 0.500 in 2eu9A Skipped atom 1953, because occupancy 0.500 <= existing 0.500 in 2eu9A Skipped atom 1955, because occupancy 0.500 <= existing 0.500 in 2eu9A Skipped atom 1957, because occupancy 0.500 <= existing 0.500 in 2eu9A Skipped atom 1959, because occupancy 0.500 <= existing 0.500 in 2eu9A Skipped atom 2057, because occupancy 0.500 <= existing 0.500 in 2eu9A Skipped atom 2061, because occupancy 0.500 <= existing 0.500 in 2eu9A Skipped atom 2063, because occupancy 0.500 <= existing 0.500 in 2eu9A Skipped atom 2065, because occupancy 0.500 <= existing 0.500 in 2eu9A Skipped atom 2067, because occupancy 0.500 <= existing 0.500 in 2eu9A Skipped atom 2069, because occupancy 0.500 <= existing 0.500 in 2eu9A Skipped atom 2171, because occupancy 0.500 <= existing 0.500 in 2eu9A Skipped atom 2173, because occupancy 0.500 <= existing 0.500 in 2eu9A Skipped atom 2175, because occupancy 0.500 <= existing 0.500 in 2eu9A Skipped atom 2177, because occupancy 0.500 <= existing 0.500 in 2eu9A Skipped atom 2323, because occupancy 0.500 <= existing 0.500 in 2eu9A Skipped atom 2327, because occupancy 0.500 <= existing 0.500 in 2eu9A Skipped atom 2329, because occupancy 0.500 <= existing 0.500 in 2eu9A Skipped atom 2331, because occupancy 0.500 <= existing 0.500 in 2eu9A Skipped atom 2333, because occupancy 0.500 <= existing 0.500 in 2eu9A Skipped atom 2504, because occupancy 0.500 <= existing 0.500 in 2eu9A Skipped atom 2508, because occupancy 0.500 <= existing 0.500 in 2eu9A Skipped atom 2510, because occupancy 0.500 <= existing 0.500 in 2eu9A Skipped atom 2512, because occupancy 0.500 <= existing 0.500 in 2eu9A Skipped atom 2514, because occupancy 0.500 <= existing 0.500 in 2eu9A Skipped atom 2516, because occupancy 0.500 <= existing 0.500 in 2eu9A Skipped atom 2586, because occupancy 0.500 <= existing 0.500 in 2eu9A Skipped atom 2605, because occupancy 0.500 <= existing 0.500 in 2eu9A Skipped atom 2607, because occupancy 0.500 <= existing 0.500 in 2eu9A Skipped atom 2609, because occupancy 0.500 <= existing 0.500 in 2eu9A Skipped atom 2611, because occupancy 0.500 <= existing 0.500 in 2eu9A Skipped atom 2613, because occupancy 0.500 <= existing 0.500 in 2eu9A # T0343 read from 2eu9A/merged-good-all-a2m # 2eu9A read from 2eu9A/merged-good-all-a2m # adding 2eu9A to template set # found chain 2eu9A in template set T0343 15 :LGEFIVE 2eu9A 153 :QERYEIV T0343 22 :LVY 2eu9A 168 :GKV T0343 36 :LAIYD 2eu9A 171 :VECLD T0343 41 :KKGDEWYKVEEAPNVQNYREAVEWAIEVLERIRD 2eu9A 177 :ARGKSQVALKIIRNVGKYREAARLEINVLKKIKE Number of specific fragments extracted= 4 number of extra gaps= 0 total=16 Number of alignments=4 # 2eu9A read from 2eu9A/merged-good-all-a2m # found chain 2eu9A in template set T0343 16 :GEFIVE 2eu9A 154 :ERYEIV T0343 22 :LVY 2eu9A 168 :GKV T0343 36 :LAIYD 2eu9A 171 :VECLD T0343 41 :KKGDEWYKVEEAPNVQNYREAVEWAIEVLERIRD 2eu9A 177 :ARGKSQVALKIIRNVGKYREAARLEINVLKKIKE Number of specific fragments extracted= 4 number of extra gaps= 0 total=20 Number of alignments=5 # 2eu9A read from 2eu9A/merged-good-all-a2m # found chain 2eu9A in template set T0343 16 :GEFIVELVYIDCPC 2eu9A 154 :ERYEIVGNLGEGTF T0343 33 :PPTLAIYD 2eu9A 168 :GKVVECLD T0343 41 :KKGDEWYKVEEAPNVQNYREAVEWAIEVLERIRD 2eu9A 177 :ARGKSQVALKIIRNVGKYREAARLEINVLKKIKE Number of specific fragments extracted= 3 number of extra gaps= 0 total=23 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zxfA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zxfA expands to /projects/compbio/data/pdb/1zxf.pdb.gz 1zxfA:# T0343 read from 1zxfA/merged-good-all-a2m # 1zxfA read from 1zxfA/merged-good-all-a2m # adding 1zxfA to template set # found chain 1zxfA in template set T0343 19 :IVELVYIDCPCEPIP 1zxfA 76 :TLVIGWRLNGFGRID T0343 34 :P 1zxfA 95 :S T0343 35 :TLAIYDKKGDEW 1zxfA 98 :TVTFVADGQKKT T0343 47 :YKVEEAPNVQNYREAV 1zxfA 111 :VDVEHTHFDRMGTKHA T0343 66 :IEVLERIRDG 1zxfA 127 :KRVRNGMDKG T0343 89 :PKVMKRLSLALQK 1zxfA 138 :PTILQSFQDKIDE Number of specific fragments extracted= 6 number of extra gaps= 0 total=29 Number of alignments=7 # 1zxfA read from 1zxfA/merged-good-all-a2m # found chain 1zxfA in template set T0343 19 :IVELVYIDCPCEPIP 1zxfA 76 :TLVIGWRLNGFGRID T0343 34 :PTLAIY 1zxfA 95 :SEFTVT T0343 40 :DKKGDEW 1zxfA 103 :ADGQKKT T0343 47 :YKVEEAPNVQNYRE 1zxfA 111 :VDVEHTHFDRMGTK T0343 64 :WAIEVLERIRDG 1zxfA 125 :HAKRVRNGMDKG T0343 88 :PPKVMKRLSLALQKL 1zxfA 137 :WPTILQSFQDKIDEE Number of specific fragments extracted= 6 number of extra gaps= 0 total=35 Number of alignments=8 # 1zxfA read from 1zxfA/merged-good-all-a2m # found chain 1zxfA in template set T0343 15 :LGEFIVELVYIDCPCE 1zxfA 74 :PDTLVIGWRLNGFGRI T0343 31 :PIPPTLAIYDKKGDEW 1zxfA 94 :SSEFTVTFVADGQKKT T0343 47 :YKVEEAPNV 1zxfA 113 :VEHTHFDRM T0343 58 :YREA 1zxfA 122 :GTKH T0343 65 :AIEVLERIRDG 1zxfA 126 :AKRVRNGMDKG T0343 88 :PPKVMKRLSLALQK 1zxfA 137 :WPTILQSFQDKIDE Number of specific fragments extracted= 6 number of extra gaps= 0 total=41 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wbpA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wbpA expands to /projects/compbio/data/pdb/1wbp.pdb.gz 1wbpA:# T0343 read from 1wbpA/merged-good-all-a2m # 1wbpA read from 1wbpA/merged-good-all-a2m # adding 1wbpA to template set # found chain 1wbpA in template set T0343 9 :KEGFLDLGEFIVE 1wbpA 71 :KIGDLFNGRYHVI T0343 25 :IDCPCEPIPPTLAIYDKKGDEWYKVEEAPNVQNYREAVEWAIEVLERIRDGE 1wbpA 84 :RKLGWGHFSTVWLSWDIQGKKFVAMKVVKSAEHYTETALDEIRLLKSVRNSD Number of specific fragments extracted= 2 number of extra gaps= 0 total=43 Number of alignments=10 # 1wbpA read from 1wbpA/merged-good-all-a2m # found chain 1wbpA in template set T0343 9 :KEGFLDLGEFIVE 1wbpA 71 :KIGDLFNGRYHVI T0343 25 :IDCPCEPIPPTLAIYDKKGDEWYKVEEAPNVQNYREAVEWAIEVLERIRDGE 1wbpA 84 :RKLGWGHFSTVWLSWDIQGKKFVAMKVVKSAEHYTETALDEIRLLKSVRNSD Number of specific fragments extracted= 2 number of extra gaps= 0 total=45 Number of alignments=11 # 1wbpA read from 1wbpA/merged-good-all-a2m # found chain 1wbpA in template set T0343 9 :KEGFLDLGEFIV 1wbpA 71 :KIGDLFNGRYHV T0343 24 :YIDCPCEPIPPTLAIYDKKGDEWYKVEEAPNVQNYREAVEWAIEVLERIRDGE 1wbpA 83 :IRKLGWGHFSTVWLSWDIQGKKFVAMKVVKSAEHYTETALDEIRLLKSVRNSD Number of specific fragments extracted= 2 number of extra gaps= 0 total=47 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dc1A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0343 read from 1dc1A/merged-good-all-a2m # 1dc1A read from 1dc1A/merged-good-all-a2m # found chain 1dc1A in training set Warning: unaligning (T0343)C29 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1dc1A)Q230 T0343 17 :EFIVELVYIDCP 1dc1A 208 :KKNVDICLFNCE T0343 36 :LAIYD 1dc1A 236 :LLLGE T0343 51 :EAPNVQNYREAVEWAIEVLERIRD 1dc1A 243 :GGIDPAGADEHWKTANTALTRIRN T0343 75 :GENVKLVSLDGPAPPKVMKRLSLALQK 1dc1A 272 :GLSPKTIFIGAAIEHSMAEEIWDQLQS Number of specific fragments extracted= 4 number of extra gaps= 0 total=51 Number of alignments=13 # 1dc1A read from 1dc1A/merged-good-all-a2m # found chain 1dc1A in training set Warning: unaligning (T0343)C29 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1dc1A)Q230 T0343 17 :EFIVELVYIDCP 1dc1A 208 :KKNVDICLFNCE T0343 36 :LAIYD 1dc1A 236 :LLLGE T0343 51 :EAPNVQNYREAVEWAIEVLERIR 1dc1A 243 :GGIDPAGADEHWKTANTALTRIR T0343 74 :DGENVKLVSLDGPAPPKVMKRLSLALQK 1dc1A 271 :KGLSPKTIFIGAAIEHSMAEEIWDQLQS Number of specific fragments extracted= 4 number of extra gaps= 0 total=55 Number of alignments=14 # 1dc1A read from 1dc1A/merged-good-all-a2m # found chain 1dc1A in training set Warning: unaligning (T0343)G43 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1dc1A)Q230 T0343 17 :EFIVELVYI 1dc1A 193 :GKHRTLMYN T0343 26 :DCPCEPIPPTLAIYDKK 1dc1A 203 :TVSLVKKNVDICLFNCE T0343 52 :APNVQNYREAVEWAIEVLERIRD 1dc1A 244 :GIDPAGADEHWKTANTALTRIRN T0343 75 :GENVKLVSLDGPAPPKVMKRLSLALQK 1dc1A 272 :GLSPKTIFIGAAIEHSMAEEIWDQLQS Number of specific fragments extracted= 4 number of extra gaps= 0 total=59 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ap1A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2ap1A expands to /projects/compbio/data/pdb/2ap1.pdb.gz 2ap1A:Skipped atom 67, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 69, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 71, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 319, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 655, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 728, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 730, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 732, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 734, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 736, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 738, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 740, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 742, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 744, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 746, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 748, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 759, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 763, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 765, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 767, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 769, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 833, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 837, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 839, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 841, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 843, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1053, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1055, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1376, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1380, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1382, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1384, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1386, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1388, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1390, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1392, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1718, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1722, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1724, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1726, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1728, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1730, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1869, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1873, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1875, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1877, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1983, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1987, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1989, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1991, because occupancy 0.500 <= existing 0.500 in 2ap1A # T0343 read from 2ap1A/merged-good-all-a2m # 2ap1A read from 2ap1A/merged-good-all-a2m # adding 2ap1A to template set # found chain 2ap1A in template set Warning: unaligning (T0343)G16 because first residue in template chain is (2ap1A)N-1 T0343 17 :EFIVELV 2ap1A 0 :AMYYGFD T0343 25 :IDCP 2ap1A 7 :IGGT T0343 34 :PTLAIYDKK 2ap1A 12 :IALGVFDST T0343 43 :GDEWYKVEEAP 2ap1A 22 :RLQWEKRVPTP T0343 55 :VQNYREAVEWAIEVLERIRD 2ap1A 33 :HTSYSAFLDAVCELVEEADQ T0343 75 :GENVKL 2ap1A 55 :GVKGSV T0343 81 :VSLDG 2ap1A 62 :IGIPG Number of specific fragments extracted= 7 number of extra gaps= 0 total=66 Number of alignments=16 # 2ap1A read from 2ap1A/merged-good-all-a2m # found chain 2ap1A in template set Warning: unaligning (T0343)G16 because first residue in template chain is (2ap1A)N-1 T0343 17 :EFIVELV 2ap1A 0 :AMYYGFD T0343 25 :IDCP 2ap1A 7 :IGGT T0343 33 :PPTLAIYDKK 2ap1A 11 :KIALGVFDST T0343 43 :GDEWYKVEEAP 2ap1A 22 :RLQWEKRVPTP T0343 55 :VQNYREAVEWAIEVLERIRD 2ap1A 33 :HTSYSAFLDAVCELVEEADQ T0343 75 :GENVK 2ap1A 55 :GVKGS Number of specific fragments extracted= 6 number of extra gaps= 0 total=72 Number of alignments=17 # 2ap1A read from 2ap1A/merged-good-all-a2m # found chain 2ap1A in template set Warning: unaligning (T0343)G16 because first residue in template chain is (2ap1A)N-1 T0343 17 :EFIVELVYIDCP 2ap1A 0 :AMYYGFDIGGTK T0343 34 :PTLAIYDKK 2ap1A 12 :IALGVFDST T0343 43 :GDEWYKVEEAP 2ap1A 22 :RLQWEKRVPTP T0343 55 :VQNYREAVEWAIEVLERIRD 2ap1A 33 :HTSYSAFLDAVCELVEEADQ T0343 75 :GENVKL 2ap1A 55 :GVKGSV T0343 81 :VSLDGPAPPK 2ap1A 62 :IGIPGMPETE T0343 91 :VMKRLSLAL 2ap1A 88 :LRADLSARL Number of specific fragments extracted= 7 number of extra gaps= 0 total=79 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jx4A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0343 read from 1jx4A/merged-good-all-a2m # 1jx4A read from 1jx4A/merged-good-all-a2m # found chain 1jx4A in training set Number of specific fragments extracted= 0 number of extra gaps= 0 total=79 # 1jx4A read from 1jx4A/merged-good-all-a2m # found chain 1jx4A in training set T0343 22 :LV 1jx4A 283 :AI T0343 35 :TLAIYDKKGDEWYKVEEAPNVQNYREAVEWAIEVLERIRDGENVKL 1jx4A 285 :HVVAVTEDLDIVSRGRTFPHGISKETAYSESVKLLQKILEEDERKI Number of specific fragments extracted= 2 number of extra gaps= 0 total=81 Number of alignments=19 # 1jx4A read from 1jx4A/merged-good-all-a2m # found chain 1jx4A in training set T0343 30 :EPIPP 1jx4A 277 :DKRIP T0343 35 :TLAIYDKKGDEWYKVEEAPNVQNYREAVEWAIEVLERIRD 1jx4A 285 :HVVAVTEDLDIVSRGRTFPHGISKETAYSESVKLLQKILE Number of specific fragments extracted= 2 number of extra gaps= 0 total=83 Number of alignments=20 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wnaA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0343 read from 1wnaA/merged-good-all-a2m # 1wnaA read from 1wnaA/merged-good-all-a2m # found chain 1wnaA in training set T0343 4 :REILRKE 1wnaA 14 :LEALKAA T0343 11 :GFLDLGEFIVELV 1wnaA 22 :GGLKLSEAKVYLI T0343 25 :IDCPCEPIPPTLAIYDKKGDEWYKVEEA 1wnaA 35 :TDWQDKRDQARYALLLHTGKKDLLVPDA T0343 53 :PNVQNYREAVEWAIEVLER 1wnaA 65 :PAFPGGEEALSELVGLLLA T0343 73 :RDGENVKLVSLDGP 1wnaA 84 :QGARRFYEAVVSPG T0343 87 :APPKVMKRLSL 1wnaA 106 :PPEELLKRVMA Number of specific fragments extracted= 6 number of extra gaps= 0 total=89 Number of alignments=21 # 1wnaA read from 1wnaA/merged-good-all-a2m # found chain 1wnaA in training set T0343 5 :EILRKE 1wnaA 15 :EALKAA T0343 11 :GFLDLGEFIVELV 1wnaA 22 :GGLKLSEAKVYLI T0343 25 :IDCPCEPIPPTLAIYDKKGDEWYKVEEA 1wnaA 35 :TDWQDKRDQARYALLLHTGKKDLLVPDA T0343 53 :PNVQNYREAVEWAIEVLER 1wnaA 65 :PAFPGGEEALSELVGLLLA T0343 73 :RDGENVKLVSLDGP 1wnaA 84 :QGARRFYEAVVSPG T0343 87 :APPKVMKRLSL 1wnaA 106 :PPEELLKRVMA Number of specific fragments extracted= 6 number of extra gaps= 0 total=95 Number of alignments=22 # 1wnaA read from 1wnaA/merged-good-all-a2m # found chain 1wnaA in training set T0343 4 :REILRKE 1wnaA 14 :LEALKAA T0343 11 :GFLDLGEFIVELVYIDCPCE 1wnaA 22 :GGLKLSEAKVYLITDWQDKR T0343 31 :PIPPTLAIYDKKGDEWYKVEEAPNVQNYREAVEWAIEVLER 1wnaA 43 :QARYALLLHTGKKDLLVPDAFGPAFPGGEEALSELVGLLLA T0343 73 :RDGENVKLVSLDGP 1wnaA 84 :QGARRFYEAVVSPG T0343 87 :APPKVMKRLSL 1wnaA 106 :PPEELLKRVMA Number of specific fragments extracted= 5 number of extra gaps= 0 total=100 Number of alignments=23 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hq0A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1hq0A expands to /projects/compbio/data/pdb/1hq0.pdb.gz 1hq0A:Skipped atom 1151, because occupancy 0.500 <= existing 0.500 in 1hq0A # T0343 read from 1hq0A/merged-good-all-a2m # 1hq0A read from 1hq0A/merged-good-all-a2m # adding 1hq0A to template set # found chain 1hq0A in template set T0343 21 :ELVYID 1hq0A 856 :VIITSG T0343 31 :PIPPTLAIYDKKGDEWYKV 1hq0A 862 :NLSGCTTIVARKEGYIYKV T0343 52 :APNVQNY 1hq0A 885 :TKSLAGF T0343 59 :REAVEWAIEVLERIRDGENVK 1hq0A 894 :TTGVKKAVEVLELLTKEPIPR T0343 83 :LDGPAPPKV 1hq0A 915 :VEGIMSNDF T0343 92 :MKRLSLA 1hq0A 925 :VDYLSEN Number of specific fragments extracted= 6 number of extra gaps= 0 total=106 Number of alignments=24 # 1hq0A read from 1hq0A/merged-good-all-a2m # found chain 1hq0A in template set T0343 21 :ELVYIDC 1hq0A 856 :VIITSGN T0343 32 :IPPTLAIYDKKGDEWYKV 1hq0A 863 :LSGCTTIVARKEGYIYKV T0343 51 :EAPNVQNY 1hq0A 884 :TTKSLAGF T0343 59 :REAVEWAIEVLERIRDGENVK 1hq0A 894 :TTGVKKAVEVLELLTKEPIPR T0343 83 :LDGPAPPKV 1hq0A 915 :VEGIMSNDF T0343 92 :MKRLSLA 1hq0A 925 :VDYLSEN Number of specific fragments extracted= 6 number of extra gaps= 0 total=112 Number of alignments=25 # 1hq0A read from 1hq0A/merged-good-all-a2m # found chain 1hq0A in template set T0343 19 :IVEL 1hq0A 856 :VIIT T0343 24 :Y 1hq0A 860 :S T0343 30 :EPIPPTLAIYDKKGDEWYKV 1hq0A 861 :GNLSGCTTIVARKEGYIYKV T0343 50 :EEAPNV 1hq0A 886 :KSLAGF T0343 57 :NYREAVEWAIEVLERIRDGENVK 1hq0A 892 :TSTTGVKKAVEVLELLTKEPIPR T0343 83 :LDGPAP 1hq0A 915 :VEGIMS T0343 89 :PKVMKRLSLA 1hq0A 922 :DFLVDYLSEN Number of specific fragments extracted= 7 number of extra gaps= 0 total=119 Number of alignments=26 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r6wA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0343 read from 1r6wA/merged-good-all-a2m # 1r6wA read from 1r6wA/merged-good-all-a2m # found chain 1r6wA in training set T0343 17 :EFIVEL 1r6wA 26 :TRDGLY T0343 36 :LAIYDKKGDEWYKVEEAPNV 1r6wA 32 :VCLREGEREGWGEISPLPGF T0343 56 :QNYREAVEWAIEVLERIRDGENV 1r6wA 54 :ETWEEAQSVLLAWVNNWLAGDCE Number of specific fragments extracted= 3 number of extra gaps= 0 total=122 Number of alignments=27 # 1r6wA read from 1r6wA/merged-good-all-a2m # found chain 1r6wA in training set T0343 17 :EFIVE 1r6wA 26 :TRDGL T0343 35 :TLAIYDKKGDEWYKVEEAPNV 1r6wA 31 :YVCLREGEREGWGEISPLPGF T0343 57 :NYREAVEWAIEVLERIRDGENV 1r6wA 55 :TWEEAQSVLLAWVNNWLAGDCE Number of specific fragments extracted= 3 number of extra gaps= 0 total=125 Number of alignments=28 # 1r6wA read from 1r6wA/merged-good-all-a2m # found chain 1r6wA in training set T0343 21 :ELVYIDCPCE 1r6wA 5 :QVYRWQIPMD T0343 31 :PI 1r6wA 23 :RL T0343 36 :LAIYDKKGDEWYKVEEAPNV 1r6wA 32 :VCLREGEREGWGEISPLPGF T0343 56 :QNYREAVEWAIEVLERIRDGE 1r6wA 54 :ETWEEAQSVLLAWVNNWLAGD T0343 77 :NVKLVSLDGPAPPKVMKRLSL 1r6wA 103 :NYRAAPLCNGDPDDLILKLAD Number of specific fragments extracted= 5 number of extra gaps= 0 total=130 Number of alignments=29 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bkqA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2bkqA expands to /projects/compbio/data/pdb/2bkq.pdb.gz 2bkqA:# T0343 read from 2bkqA/merged-good-all-a2m # 2bkqA read from 2bkqA/merged-good-all-a2m # adding 2bkqA to template set # found chain 2bkqA in template set Warning: unaligning (T0343)I32 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2bkqA)G100 Warning: unaligning (T0343)P33 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2bkqA)G100 Warning: unaligning (T0343)P86 because of BadResidue code BAD_PEPTIDE in next template residue (2bkqA)A154 Warning: unaligning (T0343)A87 because of BadResidue code BAD_PEPTIDE at template residue (2bkqA)A154 T0343 13 :LDLGEF 2bkqA 78 :LDLPNK T0343 19 :IVELVYIDCPCEP 2bkqA 85 :VVFLAINDNSNQA T0343 34 :PTLAIYDKKGDEWYKVEEAPNV 2bkqA 103 :WSLLVYLQDKNSFFHYDSHSRS T0343 58 :YREAVEWAIEVLERIRDGENVKLVSLDG 2bkqA 125 :NSVHAKQVAEKLEAFLGRKGDKLAFVEE T0343 88 :P 2bkqA 155 :P Number of specific fragments extracted= 5 number of extra gaps= 2 total=135 Number of alignments=30 # 2bkqA read from 2bkqA/merged-good-all-a2m # found chain 2bkqA in template set Warning: unaligning (T0343)R8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bkqA)M73 Warning: unaligning (T0343)K9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bkqA)M73 Warning: unaligning (T0343)P33 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2bkqA)G100 Warning: unaligning (T0343)P86 because of BadResidue code BAD_PEPTIDE in next template residue (2bkqA)A154 Warning: unaligning (T0343)A87 because of BadResidue code BAD_PEPTIDE at template residue (2bkqA)A154 T0343 3 :WREIL 2bkqA 67 :NPAEI T0343 10 :EG 2bkqA 74 :FL T0343 13 :LDLGEFIVELVYIDCPCEPI 2bkqA 78 :LDLPNKRVVFLAINDNSNQA T0343 34 :PTLAIYDKKGDEWYKVEEAPNV 2bkqA 103 :WSLLVYLQDKNSFFHYDSHSRS T0343 58 :YREAVEWAIEVLERIRDGENVKLVSLDG 2bkqA 125 :NSVHAKQVAEKLEAFLGRKGDKLAFVEE T0343 88 :P 2bkqA 155 :P Number of specific fragments extracted= 6 number of extra gaps= 3 total=141 Number of alignments=31 # 2bkqA read from 2bkqA/merged-good-all-a2m # found chain 2bkqA in template set Warning: unaligning (T0343)R8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bkqA)M73 Warning: unaligning (T0343)K9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bkqA)M73 Warning: unaligning (T0343)C29 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2bkqA)G100 Warning: unaligning (T0343)E30 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2bkqA)G100 Warning: unaligning (T0343)D84 because of BadResidue code BAD_PEPTIDE in next template residue (2bkqA)A154 Warning: unaligning (T0343)G85 because of BadResidue code BAD_PEPTIDE at template residue (2bkqA)A154 T0343 4 :REIL 2bkqA 68 :PAEI T0343 10 :EGF 2bkqA 74 :FLE T0343 13 :LDLGEF 2bkqA 78 :LDLPNK T0343 19 :IVELVYID 2bkqA 85 :VVFLAIND T0343 27 :CP 2bkqA 96 :QA T0343 32 :IPPTLAIYDKKGDEWYKVEEAPNV 2bkqA 101 :SHWSLLVYLQDKNSFFHYDSHSRS T0343 58 :YREAVEWAIEVLERIRD 2bkqA 125 :NSVHAKQVAEKLEAFLG T0343 75 :GENVKLVSL 2bkqA 144 :GDKLAFVEE T0343 86 :PAP 2bkqA 155 :PAQ Number of specific fragments extracted= 9 number of extra gaps= 3 total=150 Number of alignments=32 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ofuX/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ofuX expands to /projects/compbio/data/pdb/1ofu.pdb.gz 1ofuX:# T0343 read from 1ofuX/merged-good-all-a2m # 1ofuX read from 1ofuX/merged-good-all-a2m # adding 1ofuX to template set # found chain 1ofuX in template set T0343 4 :REILRKEG 1ofuX 89 :HEWLRRAG T0343 13 :LDLGEFIVE 1ofuX 97 :LNRERILLL T0343 54 :NVQNYREAVEWAIEVLE 1ofuX 106 :QAKDNAAALALSCEALR T0343 74 :DGENVKLVSLDGPAPPKVMKRLSLALQK 1ofuX 123 :LGRSHTVVSWLEPLSRAARKQLSRAAQL Number of specific fragments extracted= 4 number of extra gaps= 0 total=154 Number of alignments=33 # 1ofuX read from 1ofuX/merged-good-all-a2m # found chain 1ofuX in template set T0343 4 :REILRKEG 1ofuX 89 :HEWLRRAG T0343 13 :LDLGEFIVE 1ofuX 97 :LNRERILLL T0343 54 :NVQNYREAVEWAIEVLE 1ofuX 106 :QAKDNAAALALSCEALR T0343 74 :DGENVKLVSLDGPAPPKVMKRLSLALQKL 1ofuX 123 :LGRSHTVVSWLEPLSRAARKQLSRAAQLG Number of specific fragments extracted= 4 number of extra gaps= 0 total=158 Number of alignments=34 # 1ofuX read from 1ofuX/merged-good-all-a2m # found chain 1ofuX in template set T0343 4 :REILRKEG 1ofuX 89 :HEWLRRAG T0343 13 :LDLGEFIVE 1ofuX 97 :LNRERILLL T0343 54 :NVQNYREAVEWAIEVLE 1ofuX 106 :QAKDNAAALALSCEALR T0343 74 :DGENVKLVSLDGPAPPKVMKRLSLALQK 1ofuX 123 :LGRSHTVVSWLEPLSRAARKQLSRAAQL Number of specific fragments extracted= 4 number of extra gaps= 0 total=162 Number of alignments=35 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1p90A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0343 read from 1p90A/merged-good-all-a2m # 1p90A read from 1p90A/merged-good-all-a2m # found chain 1p90A in training set T0343 17 :E 1p90A 105 :S T0343 20 :VELVYIDCPCEPIP 1p90A 106 :IRVAIASNNGEQLD T0343 34 :PTLAIY 1p90A 126 :LRFLVY T0343 40 :DKKGDEWYKVEEAPNVQNYREAVEWAIE 1p90A 134 :SAKDASLVDIRSTLDVALAEDKNAWRVE T0343 85 :GPAPPKVMKRLSL 1p90A 172 :VSIGGPAAAKVVR Number of specific fragments extracted= 5 number of extra gaps= 0 total=167 Number of alignments=36 # 1p90A read from 1p90A/merged-good-all-a2m # found chain 1p90A in training set T0343 11 :G 1p90A 104 :G T0343 19 :IVELVYIDCPCEPIP 1p90A 105 :SIRVAIASNNGEQLD T0343 34 :PTLAIYD 1p90A 126 :LRFLVYQ T0343 41 :KKGDEWYKVEEAPNVQNYREAVEWAIE 1p90A 135 :AKDASLVDIRSTLDVALAEDKNAWRVE T0343 68 :VLERIRDGENVKLVSLDGPAPPKVMKRLSLAL 1p90A 178 :AAAKVVRAGIHPLKKPKGCAAQEAIAELQTVM Number of specific fragments extracted= 5 number of extra gaps= 0 total=172 Number of alignments=37 # 1p90A read from 1p90A/merged-good-all-a2m # found chain 1p90A in training set T0343 16 :GEFIVELVYID 1p90A 104 :GSIRVAIASNN T0343 27 :CPCEPIP 1p90A 120 :GHFGSCL T0343 35 :TLAIY 1p90A 127 :RFLVY T0343 40 :DKKGDEWYKVEEAPNVQNYREAVEWAIE 1p90A 134 :SAKDASLVDIRSTLDVALAEDKNAWRVE T0343 71 :RIRDGENVKLV 1p90A 162 :QIQDCQVLYVV T0343 86 :PAPPKVMKRLSLA 1p90A 173 :SIGGPAAAKVVRA Number of specific fragments extracted= 6 number of extra gaps= 0 total=178 Number of alignments=38 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yw5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1yw5A expands to /projects/compbio/data/pdb/1yw5.pdb.gz 1yw5A:# T0343 read from 1yw5A/merged-good-all-a2m # 1yw5A read from 1yw5A/merged-good-all-a2m # adding 1yw5A to template set # found chain 1yw5A in template set T0343 3 :WREILRKEGFLDL 1yw5A 49 :YIAKFKNNGYKPL T0343 16 :GEFIVELVYIDCPCEPIP 1yw5A 66 :GQVRVSHLLIKNNQSRKP T0343 41 :KKGDE 1yw5A 87 :KSPDG T0343 55 :VQNYREAVEWAIEVLERIRDGEN 1yw5A 93 :SRTRDESIQILKKHLERILSGEV T0343 78 :VKLVS 1yw5A 136 :LGFFS T0343 84 :DGPAPPKVMKRLS 1yw5A 141 :KGQMQPPFEEAAF Number of specific fragments extracted= 6 number of extra gaps= 0 total=184 Number of alignments=39 # 1yw5A read from 1yw5A/merged-good-all-a2m # found chain 1yw5A in template set T0343 3 :WREILRKEGFLDL 1yw5A 49 :YIAKFKNNGYKPL T0343 16 :GEFIVELVYIDCPCEPIP 1yw5A 66 :GQVRVSHLLIKNNQSRKP T0343 41 :KKGDEW 1yw5A 87 :KSPDGI T0343 55 :VQNYREAVEWAIEVLERIRDGENV 1yw5A 93 :SRTRDESIQILKKHLERILSGEVK Number of specific fragments extracted= 4 number of extra gaps= 0 total=188 Number of alignments=40 # 1yw5A read from 1yw5A/merged-good-all-a2m # found chain 1yw5A in template set T0343 2 :TWREILRKEGFLDL 1yw5A 48 :AYIAKFKNNGYKPL T0343 16 :GEFIVELVYIDCPCEPIPP 1yw5A 66 :GQVRVSHLLIKNNQSRKPK T0343 49 :VEEAPNV 1yw5A 85 :SWKSPDG T0343 56 :QNYREAVEWAIEVLERIRDGEN 1yw5A 94 :RTRDESIQILKKHLERILSGEV Number of specific fragments extracted= 4 number of extra gaps= 0 total=192 Number of alignments=41 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kjkA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1kjkA expands to /projects/compbio/data/pdb/1kjk.pdb.gz 1kjkA:# T0343 read from 1kjkA/merged-good-all-a2m # 1kjkA read from 1kjkA/merged-good-all-a2m # adding 1kjkA to template set # found chain 1kjkA in template set Warning: unaligning (T0343)E76 because last residue in template chain is (1kjkA)H59 T0343 34 :PTLAIYDKKGDEWYKVEE 1kjkA 22 :GYYCYRDPRTGKEFGLGR T0343 57 :NYREAVEWAIEVLERIRDG 1kjkA 40 :DRRIAITEAIQANIELFSG Number of specific fragments extracted= 2 number of extra gaps= 0 total=194 Number of alignments=42 # 1kjkA read from 1kjkA/merged-good-all-a2m # found chain 1kjkA in template set Warning: unaligning (T0343)E76 because last residue in template chain is (1kjkA)H59 T0343 34 :PTLAIYDKKGDEWYKVEE 1kjkA 22 :GYYCYRDPRTGKEFGLGR T0343 57 :NYREAVEWAIEVLERIRDG 1kjkA 40 :DRRIAITEAIQANIELFSG Number of specific fragments extracted= 2 number of extra gaps= 0 total=196 Number of alignments=43 # 1kjkA read from 1kjkA/merged-good-all-a2m # found chain 1kjkA in template set Warning: unaligning (T0343)E76 because last residue in template chain is (1kjkA)H59 T0343 34 :PTLAIYDKKGDEWYKVEE 1kjkA 22 :GYYCYRDPRTGKEFGLGR T0343 57 :NYREAVEWAIEVLERIRDG 1kjkA 40 :DRRIAITEAIQANIELFSG Number of specific fragments extracted= 2 number of extra gaps= 0 total=198 Number of alignments=44 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1eh2/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1eh2 expands to /projects/compbio/data/pdb/1eh2.pdb.gz 1eh2:Warning: there is no chain 1eh2 will retry with 1eh2A # T0343 read from 1eh2/merged-good-all-a2m # 1eh2 read from 1eh2/merged-good-all-a2m # adding 1eh2 to template set # found chain 1eh2 in template set T0343 59 :REAVEWAIEVLERIRDGENVK 1eh2 67 :RDEFAVAMFLVYCALEKEPVP T0343 85 :GPAP 1eh2 88 :MSLP Number of specific fragments extracted= 2 number of extra gaps= 0 total=200 Number of alignments=45 # 1eh2 read from 1eh2/merged-good-all-a2m # found chain 1eh2 in template set T0343 59 :REAVEWAIEVLERIRDGENVK 1eh2 67 :RDEFAVAMFLVYCALEKEPVP T0343 85 :GPAP 1eh2 88 :MSLP Number of specific fragments extracted= 2 number of extra gaps= 0 total=202 Number of alignments=46 # 1eh2 read from 1eh2/merged-good-all-a2m # found chain 1eh2 in template set T0343 59 :REAVEWAIEVLERIRDGE 1eh2 67 :RDEFAVAMFLVYCALEKE T0343 82 :SLDGPAPP 1eh2 85 :PVPMSLPP Number of specific fragments extracted= 2 number of extra gaps= 0 total=204 Number of alignments=47 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cwwA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1cwwA expands to /projects/compbio/data/pdb/1cww.pdb.gz 1cwwA:# T0343 read from 1cwwA/merged-good-all-a2m # 1cwwA read from 1cwwA/merged-good-all-a2m # adding 1cwwA to template set # found chain 1cwwA in template set T0343 58 :YREAVEWAIE 1cwwA 22 :TSYIMDHMIS T0343 68 :VLERIR 1cwwA 39 :EEEKVR T0343 84 :DGPAPPKVMKRLSLALQ 1cwwA 45 :NEPTQQQRAAMLIKMIL Number of specific fragments extracted= 3 number of extra gaps= 0 total=207 Number of alignments=48 # 1cwwA read from 1cwwA/merged-good-all-a2m # found chain 1cwwA in template set T0343 59 :REAVEWAIE 1cwwA 23 :SYIMDHMIS T0343 68 :VLERIRD 1cwwA 39 :EEEKVRN T0343 85 :GPAPPKVMKRLSLALQ 1cwwA 46 :EPTQQQRAAMLIKMIL Number of specific fragments extracted= 3 number of extra gaps= 0 total=210 Number of alignments=49 # 1cwwA read from 1cwwA/merged-good-all-a2m # found chain 1cwwA in template set T0343 5 :EILRKEGFLDLG 1cwwA 27 :DHMISDGFLTIS T0343 48 :KVE 1cwwA 42 :KVR T0343 54 :NVQNYREAVEWAIEV 1cwwA 45 :NEPTQQQRAAMLIKM T0343 72 :IR 1cwwA 60 :IL Number of specific fragments extracted= 4 number of extra gaps= 0 total=214 Number of alignments=50 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b49A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2b49A expands to /projects/compbio/data/pdb/2b49.pdb.gz 2b49A:Skipped atom 672, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 676, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 678, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 680, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 682, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 684, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 749, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 753, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 755, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1027, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1031, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1033, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1035, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1037, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1158, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1162, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1164, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1166, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1168, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1171, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1175, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1177, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1179, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1181, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1213, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1217, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1219, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1221, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1223, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1225, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1267, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1271, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1273, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1275, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1416, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1420, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1422, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1425, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1429, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1431, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1488, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1492, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1494, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1496, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1498, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1562, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1564, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1566, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1568, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1570, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1572, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1574, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1576, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1578, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1580, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1582, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1584, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1586, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1588, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1614, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1618, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1620, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1622, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1624, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1731, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1735, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1737, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1739, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1741, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1975, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1979, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1981, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1983, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 1985, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 2011, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 2015, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 2017, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 2020, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 2024, because occupancy 0.500 <= existing 0.500 in 2b49A Skipped atom 2026, because occupancy 0.500 <= existing 0.500 in 2b49A # T0343 read from 2b49A/merged-good-all-a2m # 2b49A read from 2b49A/merged-good-all-a2m # adding 2b49A to template set # found chain 2b49A in template set T0343 11 :GFLDLGEFIVELVYIDCPCE 2b49A 763 :DVMNHGGFHIQCQSEDCTIA T0343 35 :TLAIYDKKGDEWYKVE 2b49A 787 :EMLVTNTQTGEEHTVT T0343 51 :EAPNVQNYREAVEWAIEVLERIRDGENV 2b49A 811 :DHGVPDDSSDFLEFVNYVRSLRVDSEPV Number of specific fragments extracted= 3 number of extra gaps= 0 total=217 Number of alignments=51 # 2b49A read from 2b49A/merged-good-all-a2m # found chain 2b49A in template set T0343 11 :GFLDLGEFIVELVYIDCPCEPIPPTLAIYDKKGDEWYKVE 2b49A 763 :DVMNHGGFHIQCQSEDCTIAYVSREMLVTNTQTGEEHTVT T0343 52 :APNVQNYREAVEWAIEV 2b49A 815 :PDDSSDFLEFVNYVRSL T0343 72 :IRDGE 2b49A 832 :RVDSE Number of specific fragments extracted= 3 number of extra gaps= 0 total=220 Number of alignments=52 # 2b49A read from 2b49A/merged-good-all-a2m # found chain 2b49A in template set T0343 12 :FLDLGEFIVELVYIDCPCE 2b49A 764 :VMNHGGFHIQCQSEDCTIA T0343 32 :IPPTLAIYDKKGDEWYKV 2b49A 784 :VSREMLVTNTQTGEEHTV T0343 50 :EEAPNVQNYREAVEWAIEVLERIRDGENV 2b49A 810 :PDHGVPDDSSDFLEFVNYVRSLRVDSEPV T0343 80 :LVSLDG 2b49A 839 :LVHCSA Number of specific fragments extracted= 4 number of extra gaps= 0 total=224 Number of alignments=53 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3cla/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0343 read from 3cla/merged-good-all-a2m # 3cla read from 3cla/merged-good-all-a2m # found chain 3cla in training set T0343 21 :ELVYI 3cla 82 :ELIVW T0343 30 :EPIPPTLAIYDKKGDEWYKVE 3cla 87 :DSVDPQFTVFHQETETFSALS T0343 52 :APNVQNYREAVEWAIEVLERI 3cla 108 :CPYSSDIDQFMVNYLSVMERY T0343 74 :DGENVKL 3cla 129 :KSDTKLF T0343 83 :LDGPAP 3cla 136 :PQGVTP Number of specific fragments extracted= 5 number of extra gaps= 0 total=229 Number of alignments=54 # 3cla read from 3cla/merged-good-all-a2m # found chain 3cla in training set T0343 21 :ELVYI 3cla 82 :ELIVW T0343 30 :EPIPPTLAIYDKKGDEWYKVE 3cla 87 :DSVDPQFTVFHQETETFSALS T0343 52 :APNVQNYREAVEWAIEVLERIRD 3cla 108 :CPYSSDIDQFMVNYLSVMERYKS T0343 76 :ENVK 3cla 131 :DTKL T0343 82 :SLDGPAP 3cla 135 :FPQGVTP Number of specific fragments extracted= 5 number of extra gaps= 0 total=234 Number of alignments=55 # 3cla read from 3cla/merged-good-all-a2m # found chain 3cla in training set T0343 16 :GEFIV 3cla 81 :DELIV T0343 25 :I 3cla 86 :W T0343 30 :EPIPPTLAIYDKKGDEWYKV 3cla 87 :DSVDPQFTVFHQETETFSAL T0343 51 :EAPNVQNYREAVEWAIEVLERIRDGEN 3cla 107 :SCPYSSDIDQFMVNYLSVMERYKSDTK T0343 78 :VKLVSLDGPAPP 3cla 145 :LNISALPWVNFD Number of specific fragments extracted= 5 number of extra gaps= 0 total=239 Number of alignments=56 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1y74A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1y74A expands to /projects/compbio/data/pdb/1y74.pdb.gz 1y74A:# T0343 read from 1y74A/merged-good-all-a2m # 1y74A read from 1y74A/merged-good-all-a2m # adding 1y74A to template set # found chain 1y74A in template set T0343 57 :NYREAVEWAIEVLERIRD 1y74A 18 :GLERDVSRAVELLERLQR T0343 84 :DGPAPPKVMKRLSLALQ 1y74A 36 :SGELPPQKLQALQRVLQ Number of specific fragments extracted= 2 number of extra gaps= 0 total=241 Number of alignments=57 # 1y74A read from 1y74A/merged-good-all-a2m # found chain 1y74A in template set T0343 57 :NYREAVEWAIEVLERIRD 1y74A 18 :GLERDVSRAVELLERLQR T0343 84 :DGPAPPKVMKRLSLALQ 1y74A 36 :SGELPPQKLQALQRVLQ Number of specific fragments extracted= 2 number of extra gaps= 0 total=243 Number of alignments=58 # 1y74A read from 1y74A/merged-good-all-a2m # found chain 1y74A in template set T0343 57 :NYREAVEWAIEVLERIRDGE 1y74A 18 :GLERDVSRAVELLERLQRSG T0343 86 :PAPPKVMKRLSLALQ 1y74A 38 :ELPPQKLQALQRVLQ Number of specific fragments extracted= 2 number of extra gaps= 0 total=245 Number of alignments=59 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1q8yA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1q8yA expands to /projects/compbio/data/pdb/1q8y.pdb.gz 1q8yA:# T0343 read from 1q8yA/merged-good-all-a2m # 1q8yA read from 1q8yA/merged-good-all-a2m # adding 1q8yA to template set # found chain 1q8yA in template set T0343 9 :KEGFLDLGEFIVELVYIDCPC 1q8yA 149 :KGEPYKDARYILVRKLGWGHF T0343 35 :TLAIYDKKGDEWYKVEEAPNVQNYREAVEWAIEVLERIRDGENV 1q8yA 172 :VWLAKDMVNNTHVAMKIVRGDKVYTEAAEDEIKLLQRVNDADNT Number of specific fragments extracted= 2 number of extra gaps= 0 total=247 Number of alignments=60 # 1q8yA read from 1q8yA/merged-good-all-a2m # found chain 1q8yA in template set T0343 16 :GEFIVELVYIDCPC 1q8yA 156 :ARYILVRKLGWGHF T0343 35 :TLAIYDKKGDEWYKVEEAPNVQNYREAVEWAIEVLERIRDGENV 1q8yA 172 :VWLAKDMVNNTHVAMKIVRGDKVYTEAAEDEIKLLQRVNDADNT Number of specific fragments extracted= 2 number of extra gaps= 0 total=249 Number of alignments=61 # 1q8yA read from 1q8yA/merged-good-all-a2m # found chain 1q8yA in template set T0343 22 :LVYIDCPCEPIPPTL 1q8yA 158 :YILVRKLGWGHFSTV T0343 37 :AIYDKKGDEWYKV 1q8yA 174 :LAKDMVNNTHVAM T0343 52 :APNVQNYREAVEWAIEVLERIRDGE 1q8yA 189 :VRGDKVYTEAAEDEIKLLQRVNDAD T0343 88 :PPKVMKRLS 1q8yA 214 :NTKEDSMGA Number of specific fragments extracted= 4 number of extra gaps= 0 total=253 Number of alignments=62 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1euvA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0343 read from 1euvA/merged-good-all-a2m # 1euvA read from 1euvA/merged-good-all-a2m # found chain 1euvA in training set T0343 14 :DLGEFIVELVYIDCPCEP 1euvA 497 :QIDKLDKIFTPINLNQSH T0343 34 :PTLAIYDKKGDEWYKVEEAPNVQN 1euvA 515 :WALGIIDLKKKTIGYVDSLSNGPN T0343 58 :YREAVEWAIEVLERIRDGEN 1euvA 541 :SFAILTDLQKYVMEESKHTI T0343 78 :VKLVSLDGP 1euvA 564 :FDLIHLDCP Number of specific fragments extracted= 4 number of extra gaps= 0 total=257 Number of alignments=63 # 1euvA read from 1euvA/merged-good-all-a2m # found chain 1euvA in training set T0343 14 :DLGEFIVELVYIDCPCEP 1euvA 497 :QIDKLDKIFTPINLNQSH T0343 34 :PTLAIYDKKGDEWYKVEEA 1euvA 515 :WALGIIDLKKKTIGYVDSL T0343 53 :PNVQNYREAVEWAIEVLERIRD 1euvA 536 :GPNAMSFAILTDLQKYVMEESK T0343 75 :GENVKLVSLDGP 1euvA 561 :GEDFDLIHLDCP Number of specific fragments extracted= 4 number of extra gaps= 0 total=261 Number of alignments=64 # 1euvA read from 1euvA/merged-good-all-a2m # found chain 1euvA in training set T0343 14 :DLGEFIVELVYIDCPCE 1euvA 497 :QIDKLDKIFTPINLNQS T0343 33 :PPTLAIYDKKGDEWYKVEEAPNVQN 1euvA 514 :HWALGIIDLKKKTIGYVDSLSNGPN T0343 58 :YREAVEWAIEVLERIRD 1euvA 541 :SFAILTDLQKYVMEESK T0343 75 :GENVKLVSLDGPAPP 1euvA 561 :GEDFDLIHLDCPQQP Number of specific fragments extracted= 4 number of extra gaps= 0 total=265 Number of alignments=65 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bkrA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2bkrA expands to /projects/compbio/data/pdb/2bkr.pdb.gz 2bkrA:# T0343 read from 2bkrA/merged-good-all-a2m # 2bkrA read from 2bkrA/merged-good-all-a2m # adding 2bkrA to template set # found chain 2bkrA in template set T0343 14 :DLGEF 2bkrA 79 :DLPNK T0343 19 :IVELVYIDCPCEPIP 2bkrA 85 :VVFLAINDNSNQAAG T0343 34 :PTLAIYDKKGDEWYKVEEAPNV 2bkrA 103 :WSLLVYLQDKNSFFHYDSHSRS T0343 58 :YREAVEWAIEVLERIR 2bkrA 125 :NSVHAKQVAEKLEAFL T0343 74 :DGENVKLVSLD 2bkrA 143 :KGDKLAFVEEK T0343 87 :AP 2bkrA 154 :AP Number of specific fragments extracted= 6 number of extra gaps= 0 total=271 Number of alignments=66 # 2bkrA read from 2bkrA/merged-good-all-a2m # found chain 2bkrA in template set T0343 13 :LDLGEF 2bkrA 78 :LDLPNK T0343 19 :IVELVYIDCPCEPIP 2bkrA 85 :VVFLAINDNSNQAAG T0343 34 :PTLAIYDKKGDEWYKVEEAPN 2bkrA 103 :WSLLVYLQDKNSFFHYDSHSR T0343 57 :NYREAVEWAIEVLERIR 2bkrA 124 :SNSVHAKQVAEKLEAFL T0343 74 :DGENVKLVSL 2bkrA 143 :KGDKLAFVEE T0343 86 :PAP 2bkrA 153 :KAP Number of specific fragments extracted= 6 number of extra gaps= 0 total=277 Number of alignments=67 # 2bkrA read from 2bkrA/merged-good-all-a2m # found chain 2bkrA in template set T0343 3 :WREILRK 2bkrA 71 :IAMFLEP T0343 13 :LDLGEF 2bkrA 78 :LDLPNK T0343 19 :IVELVYIDCPCE 2bkrA 85 :VVFLAINDNSNQ T0343 31 :PIPPTLAIYDKKGDEWYKVEEA 2bkrA 100 :GSHWSLLVYLQDKNSFFHYDSH T0343 55 :VQNYREAVEWAIEVLERIR 2bkrA 122 :SRSNSVHAKQVAEKLEAFL T0343 74 :DGENVKLVSLDGPAPP 2bkrA 143 :KGDKLAFVEEKAPAQQ Number of specific fragments extracted= 6 number of extra gaps= 0 total=283 Number of alignments=68 # command:# PrintAlignmentsContacts allconstraints.under Using radius: 8.0000 NUMB_ALIGNS: 68 Done printing distance constraints # command: