# 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/T0312/ # command:# Making conformation for sequence T0312 numbered 1 through 146 Created new target T0312 from T0312.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0312/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0312//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0312/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0312//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0312/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0312/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0312/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 2al3A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2al3A expands to /projects/compbio/data/pdb/2al3.pdb.gz 2al3A:# T0312 read from 2al3A/merged-good-all-a2m # 2al3A read from 2al3A/merged-good-all-a2m # adding 2al3A to template set # found chain 2al3A in template set T0312 5 :EFEVGKGFLLRLDYGKDLVRQIEEFLEEKGIH 2al3A 15 :LAPNGRRHTVKVTPSTVLLQVLEDTCRRQDFN # choosing archetypes in rotamer library T0312 46 :VRSAVIGYYD 2al3A 47 :PSEYDLKFQR T0312 64 :KELMEPL 2al3A 57 :TVLDLSL Number of specific fragments extracted= 3 number of extra gaps= 0 total=3 Number of alignments=1 # 2al3A read from 2al3A/merged-good-all-a2m # found chain 2al3A in template set T0312 5 :EFEVGKGFLLRLDYGKDLVRQIEEFLEEKGIH 2al3A 15 :LAPNGRRHTVKVTPSTVLLQVLEDTCRRQDFN T0312 46 :VRSAVIGY 2al3A 47 :PSEYDLKF Number of specific fragments extracted= 2 number of extra gaps= 0 total=5 Number of alignments=2 # 2al3A read from 2al3A/merged-good-all-a2m # found chain 2al3A in template set T0312 6 :FEVGKGFLLRLDYGKDLVRQIEEFLEEKGIH 2al3A 16 :APNGRRHTVKVTPSTVLLQVLEDTCRRQDFN T0312 46 :VRSAVIGY 2al3A 47 :PSEYDLKF Number of specific fragments extracted= 2 number of extra gaps= 0 total=7 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f89A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1f89A expands to /projects/compbio/data/pdb/1f89.pdb.gz 1f89A:# T0312 read from 1f89A/merged-good-all-a2m # 1f89A read from 1f89A/merged-good-all-a2m # adding 1f89A to template set # found chain 1f89A in template set T0312 8 :VGKGFLLRL 1f89A 7 :LSQKIKVAL T0312 17 :DYGKDLVRQIEEFLEEK 1f89A 23 :PDKMANLQRAATFIERA T0312 34 :G 1f89A 44 :P T0312 36 :HAAHISAIGAV 1f89A 45 :DTKLVVLPECF T0312 49 :AVIGYYDQEKK 1f89A 68 :SEVINPKEPST T0312 72 :ILSLSGNVSM 1f89A 92 :IILVGGTIPE T0312 82 :KDSKPFCHIHVLLGKDGEVYGGHL 1f89A 104 :PKTDKIYNTSIIFNEDGKLIDKHR Number of specific fragments extracted= 7 number of extra gaps= 0 total=14 Number of alignments=4 # 1f89A read from 1f89A/merged-good-all-a2m # found chain 1f89A in template set T0312 8 :VGKGFLLRL 1f89A 7 :LSQKIKVAL T0312 17 :DYGKDLVRQIEEFLEEK 1f89A 23 :PDKMANLQRAATFIERA T0312 34 :GIHAAHISAIGAV 1f89A 43 :QPDTKLVVLPECF T0312 47 :RSA 1f89A 57 :SPY T0312 59 :KEYVKKELMEPLE 1f89A 65 :RKYSEVINPKEPS T0312 72 :ILSLSGNVSM 1f89A 92 :IILVGGTIPE T0312 82 :KDSKPFCHIHVLLGKDGEVYGGHL 1f89A 104 :PKTDKIYNTSIIFNEDGKLIDKHR T0312 106 :FSAEVF 1f89A 152 :EKSTTI T0312 112 :A 1f89A 159 :T T0312 113 :CEVFVL 1f89A 162 :GKFGVG Number of specific fragments extracted= 10 number of extra gaps= 0 total=24 Number of alignments=5 # 1f89A read from 1f89A/merged-good-all-a2m # found chain 1f89A in template set T0312 7 :EVGKGFLLR 1f89A 8 :SQKIKVALV T0312 17 :DYGKDLVRQIEEFLEEK 1f89A 23 :PDKMANLQRAATFIERA T0312 36 :HAAHISAIGAVR 1f89A 45 :DTKLVVLPECFN T0312 52 :GYYDQEKKE 1f89A 57 :SPYSTDQFR T0312 68 :EPLEILSLSGNVSMKDSKPFCHIHVLLGKDGEVYGGHL 1f89A 90 :FKIILVGGTIPELDPKTDKIYNTSIIFNEDGKLIDKHR Number of specific fragments extracted= 5 number of extra gaps= 0 total=29 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1c1yB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1c1yB expands to /projects/compbio/data/pdb/1c1y.pdb.gz 1c1yB:Skipped atom 1478, because occupancy 0.5 <= existing 0.500 in 1c1yB Skipped atom 1480, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1482, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1484, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1486, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1488, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1490, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1492, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1494, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1496, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1498, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1581, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1583, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1585, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1587, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1589, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1591, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1593, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1595, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1597, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1599, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1609, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1611, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1613, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1615, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1617, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1619, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1629, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1631, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1633, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1635, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1637, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1639, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1641, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1643, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1984, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1986, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1988, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1990, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1992, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1994, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1996, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 1998, because occupancy 0.500 <= existing 0.500 in 1c1yB Skipped atom 2000, because occupancy 0.500 <= existing 0.500 in 1c1yB # T0312 read from 1c1yB/merged-good-all-a2m # 1c1yB read from 1c1yB/merged-good-all-a2m # adding 1c1yB to template set # found chain 1c1yB in template set T0312 6 :FEVGKGFLLRLDYGKDLVRQIEEFLEEKGIH 1c1yB 62 :LPNKQRTVVNVRNGMSLHDCLMKALKVRGLQ T0312 47 :RSA 1c1yB 94 :ECC T0312 50 :VIGYYDQEKKEYVKKELME 1c1yB 98 :VFRLLHEHKGKKARLDWNT Number of specific fragments extracted= 3 number of extra gaps= 0 total=32 Number of alignments=7 # 1c1yB read from 1c1yB/merged-good-all-a2m # found chain 1c1yB in template set T0312 5 :EFEVGKGFLLRLDYGKDLVRQIEEFLEEKGIH 1c1yB 61 :FLPNKQRTVVNVRNGMSLHDCLMKALKVRGLQ T0312 48 :SAVIGYYDQEKKEY 1c1yB 95 :CCAVFRLLHEHKGK T0312 63 :KKELM 1c1yB 109 :KARLD Number of specific fragments extracted= 3 number of extra gaps= 0 total=35 Number of alignments=8 # 1c1yB read from 1c1yB/merged-good-all-a2m # found chain 1c1yB in template set T0312 6 :FEVGKGFLLRLDYGKDLVRQIEEFLEEKGIH 1c1yB 62 :LPNKQRTVVNVRNGMSLHDCLMKALKVRGLQ T0312 56 :QEK 1c1yB 93 :PEC T0312 113 :CEVFVLPLSGEAPERAFDEQTGLFLW 1c1yB 96 :CAVFRLLHEHKGKKARLDWNTDAASL Number of specific fragments extracted= 3 number of extra gaps= 0 total=38 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gs5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0312 read from 1gs5A/merged-good-all-a2m # 1gs5A read from 1gs5A/merged-good-all-a2m # found chain 1gs5A in training set T0312 21 :DLVRQIEEFLEEKGIH 1gs5A 83 :TANKTLLAWAKKHQIA T0312 38 :AHISAIGAVRSAVIGYYDQEKKEY 1gs5A 99 :AVGLFLGDGDSVKVTQLDEELGHV T0312 62 :VKKEL 1gs5A 124 :LAQPG T0312 67 :MEPLEILSLSG 1gs5A 139 :NGYLPVVSSIG T0312 80 :SMKDSKPFC 1gs5A 150 :VTDEGQLMN Number of specific fragments extracted= 5 number of extra gaps= 0 total=43 Number of alignments=10 # 1gs5A read from 1gs5A/merged-good-all-a2m # found chain 1gs5A in training set T0312 21 :DLVRQIEEFLEEKGIH 1gs5A 83 :TANKTLLAWAKKHQIA T0312 38 :AHISAIGAVRSAVIGYYDQEKKEYVKKEL 1gs5A 99 :AVGLFLGDGDSVKVTQLDEELGHVGLAQP T0312 67 :MEPLEILS 1gs5A 139 :NGYLPVVS T0312 77 :GNVSMKDSKPFC 1gs5A 147 :SIGVTDEGQLMN Number of specific fragments extracted= 4 number of extra gaps= 0 total=47 Number of alignments=11 # 1gs5A read from 1gs5A/merged-good-all-a2m # found chain 1gs5A in training set T0312 21 :DLVRQIEEFLEEKGIH 1gs5A 83 :TANKTLLAWAKKHQIA T0312 38 :AHISAIGAVRSAVIGYYDQEKKE 1gs5A 99 :AVGLFLGDGDSVKVTQLDEELGH T0312 77 :GNVSMK 1gs5A 123 :GLAQPG T0312 83 :DSKPFCHIHVLLGKDGEVYG 1gs5A 139 :NGYLPVVSSIGVTDEGQLMN Number of specific fragments extracted= 4 number of extra gaps= 0 total=51 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w41A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1w41A expands to /projects/compbio/data/pdb/1w41.pdb.gz 1w41A:# T0312 read from 1w41A/merged-good-all-a2m # 1w41A read from 1w41A/merged-good-all-a2m # adding 1w41A to template set # found chain 1w41A in template set T0312 10 :KGFLLRLDY 1w41A 32 :AKLIIVARN T0312 19 :GKDLVRQIEEFLEEKGIHAAHI 1w41A 42 :RPDIKEDIEYYARLSGIPVYEF Number of specific fragments extracted= 2 number of extra gaps= 0 total=53 Number of alignments=13 # 1w41A read from 1w41A/merged-good-all-a2m # found chain 1w41A in template set T0312 9 :GKGFLLRLDY 1w41A 31 :GAKLIIVARN T0312 19 :GKDLVRQIEEFLEEKGIHAAHI 1w41A 42 :RPDIKEDIEYYARLSGIPVYEF Number of specific fragments extracted= 2 number of extra gaps= 0 total=55 Number of alignments=14 # 1w41A read from 1w41A/merged-good-all-a2m # found chain 1w41A in template set T0312 9 :GKGFLLRLDY 1w41A 31 :GAKLIIVARN T0312 19 :GKDLVRQIEEFLEEKGIHAAHI 1w41A 42 :RPDIKEDIEYYARLSGIPVYEF Number of specific fragments extracted= 2 number of extra gaps= 0 total=57 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1c3mA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1c3mA expands to /projects/compbio/data/pdb/1c3m.pdb.gz 1c3mA:# T0312 read from 1c3mA/merged-good-all-a2m # 1c3mA read from 1c3mA/merged-good-all-a2m # adding 1c3mA to template set # found chain 1c3mA in template set T0312 6 :FEVGKGFLLRLDYG 1c3mA 15 :GNGGKRWLQTAHGG T0312 36 :HAAHISAIG 1c3mA 29 :KITSIIIKG T0312 45 :AVRSAVIGYYDQEK 1c3mA 40 :CIFSIQFVYKDKDN T0312 59 :KEYVKKELMEPLEILSLSGNVSMKDS 1c3mA 66 :DKAETITFAEDEDITAISGTFGAYYH T0312 86 :PFCHIHVLLGKDGEVYGGHL 1c3mA 92 :MTVVTSLTFQTNKKVYGPFG T0312 106 :FSAEVFACEVFVL 1c3mA 134 :SGDVLDSIGGVVV Number of specific fragments extracted= 6 number of extra gaps= 0 total=63 Number of alignments=16 # 1c3mA read from 1c3mA/merged-good-all-a2m # found chain 1c3mA in template set T0312 7 :EVGKGFLLRLDYG 1c3mA 16 :NGGKRWLQTAHGG T0312 36 :HAAHISAIG 1c3mA 29 :KITSIIIKG T0312 45 :AVRSAVIGYYDQEK 1c3mA 40 :CIFSIQFVYKDKDN T0312 59 :KEYVKKELMEPLEILSLSGNVSM 1c3mA 66 :DKAETITFAEDEDITAISGTFGA T0312 82 :KD 1c3mA 90 :YH T0312 86 :PFCHIHVLLGKDGEVYGGHL 1c3mA 92 :MTVVTSLTFQTNKKVYGPFG T0312 107 :SAEVFACEVF 1c3mA 124 :KGKFAGFFGN Number of specific fragments extracted= 7 number of extra gaps= 0 total=70 Number of alignments=17 # 1c3mA read from 1c3mA/merged-good-all-a2m # found chain 1c3mA in template set T0312 3 :VFEFEVGKGFLLRLDYGK 1c3mA 22 :LQTAHGGKITSIIIKGGT T0312 45 :AVRSAVIGYYDQEKKE 1c3mA 40 :CIFSIQFVYKDKDNIE T0312 61 :YVKKELMEPLEILSLSGNVSMKDSKPFCH 1c3mA 68 :AETITFAEDEDITAISGTFGAYYHMTVVT T0312 91 :HVLLGKDGEVYGGHLFSAEVF 1c3mA 97 :SLTFQTNKKVYGPFGTVASSS T0312 116 :FVLPLSGEAPE 1c3mA 118 :FSLPLTKGKFA Number of specific fragments extracted= 5 number of extra gaps= 0 total=75 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wrvA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wrvA expands to /projects/compbio/data/pdb/1wrv.pdb.gz 1wrvA:# T0312 read from 1wrvA/merged-good-all-a2m # 1wrvA read from 1wrvA/merged-good-all-a2m # adding 1wrvA to template set # found chain 1wrvA in template set T0312 19 :GKDLVRQIEEFLEEKGIHAAHI 1wrvA 75 :PEELEEAIKEVVRRNGYRSCYI T0312 49 :AVIGYYDQEKKEYV 1wrvA 98 :PLAWMGAKALGVNP T0312 67 :MEPLEILSLS 1wrvA 114 :NNPAEVMVAA Number of specific fragments extracted= 3 number of extra gaps= 0 total=78 Number of alignments=19 # 1wrvA read from 1wrvA/merged-good-all-a2m # found chain 1wrvA in template set T0312 20 :KDLVRQIEEFLEEKGIHAAHISAIGAV 1wrvA 76 :EELEEAIKEVVRRNGYRSCYIRPLAWM T0312 48 :SAVIGYY 1wrvA 116 :PAEVMVA T0312 76 :SGNVSMKDSKPFCH 1wrvA 181 :EALLLDEEGYVAEG T0312 90 :IHVLLGKDGEVYG 1wrvA 197 :ENLFFVRDGVIYA Number of specific fragments extracted= 4 number of extra gaps= 0 total=82 Number of alignments=20 # 1wrvA read from 1wrvA/merged-good-all-a2m # found chain 1wrvA in template set T0312 20 :KDLVRQIEEFLEEKGIHAAHIS 1wrvA 76 :EELEEAIKEVVRRNGYRSCYIR T0312 51 :IGYYDQEKKE 1wrvA 99 :LAWMGAKALG T0312 68 :EPLEILSLSGN 1wrvA 115 :NPAEVMVAAWE Number of specific fragments extracted= 3 number of extra gaps= 0 total=85 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gskA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0312 read from 1gskA/merged-good-all-a2m # 1gskA read from 1gskA/merged-good-all-a2m # found chain 1gskA in training set Warning: unaligning (T0312)G102 because of BadResidue code BAD_PEPTIDE in next template residue (1gskA)L265 Warning: unaligning (T0312)G103 because of BadResidue code BAD_PEPTIDE at template residue (1gskA)L265 T0312 11 :GFLLRLDYGK 1gskA 169 :VGAYIIHDPK T0312 33 :KGIHAAHISAIGAV 1gskA 187 :DEYDVPLLITDRTI T0312 47 :RSAVIGYYDQEKK 1gskA 204 :GSLFYPSAPENPS T0312 64 :KELMEPL 1gskA 217 :PSLPNPS T0312 71 :EILS 1gskA 232 :TILV T0312 76 :SGNVSM 1gskA 236 :NGKVWP T0312 84 :SKPFCHIHVLLGKDGEVY 1gskA 246 :EPRKYRFRVINASNTRTY T0312 104 :HL 1gskA 266 :SL T0312 106 :FS 1gskA 283 :LP T0312 108 :AEVF 1gskA 286 :SVKL T0312 112 :ACEV 1gskA 291 :SFSL T0312 116 :FVLPLSGEAPERAF 1gskA 302 :IIIDFTAYEGESII T0312 130 :DEQTGLFLW 1gskA 327 :NPETDANIM T0312 139 :LEHHHHHH 1gskA 339 :VTKPLAQK Number of specific fragments extracted= 14 number of extra gaps= 1 total=99 Number of alignments=22 # 1gskA read from 1gskA/merged-good-all-a2m # found chain 1gskA in training set Warning: unaligning (T0312)G102 because of BadResidue code BAD_PEPTIDE in next template residue (1gskA)L265 T0312 11 :GFLLRLDYGK 1gskA 169 :VGAYIIHDPK T0312 33 :KGIHAAHISAIGAV 1gskA 187 :DEYDVPLLITDRTI T0312 47 :RS 1gskA 204 :GS T0312 51 :IGYYDQEK 1gskA 206 :LFYPSAPE T0312 59 :KEYVKKELMEPL 1gskA 217 :PSLPNPSIVPAF T0312 72 :ILSLSGNVSM 1gskA 232 :TILVNGKVWP T0312 84 :SKPFCHIHVLLGKDGEVY 1gskA 246 :EPRKYRFRVINASNTRTY T0312 103 :GHLFSAEV 1gskA 280 :GGLLPRSV T0312 111 :F 1gskA 289 :L T0312 113 :CEV 1gskA 292 :FSL T0312 116 :FVLPLSGEAPERAF 1gskA 302 :IIIDFTAYEGESII T0312 130 :DEQTGLFLWL 1gskA 327 :NPETDANIMQ T0312 140 :EHH 1gskA 340 :TKP T0312 143 :HHH 1gskA 345 :QKD Number of specific fragments extracted= 14 number of extra gaps= 1 total=113 Number of alignments=23 # 1gskA read from 1gskA/merged-good-all-a2m # found chain 1gskA in training set Warning: unaligning (T0312)N78 because of BadResidue code BAD_PEPTIDE in next template residue (1gskA)L265 Warning: unaligning (T0312)V79 because of BadResidue code BAD_PEPTIDE at template residue (1gskA)L265 T0312 65 :ELMEPLEILSL 1gskA 244 :EVEPRKYRFRV T0312 76 :SG 1gskA 262 :TY T0312 80 :SMKDSKPFCHIHV 1gskA 266 :SLDNGGDFIQIGS T0312 102 :GGHLFSA 1gskA 279 :DGGLLPR T0312 109 :EVF 1gskA 287 :VKL T0312 112 :ACEVFVLPL 1gskA 298 :ERYDIIIDF T0312 121 :SGEA 1gskA 310 :EGES T0312 125 :PERAFDEQTGLFLWLE 1gskA 322 :CGGDVNPETDANIMQF Number of specific fragments extracted= 8 number of extra gaps= 1 total=121 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1n6aA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0312 read from 1n6aA/merged-good-all-a2m # 1n6aA read from 1n6aA/merged-good-all-a2m # found chain 1n6aA in training set Warning: unaligning (T0312)K59 because first residue in template chain is (1n6aA)H116 T0312 60 :EYVKKELMEPLE 1n6aA 117 :GVCWIYYPDGGS T0312 75 :LSGNV 1n6aA 129 :LVGEV T0312 81 :MKDSKPFC 1n6aA 134 :NEDGEMTG T0312 89 :HIHVLLGKDGEVYGGHLFSAEVF 1n6aA 143 :KIAYVYPDERTALYGKFIDGEMI T0312 112 :ACEVFVLPLSGEAPERAFDEQTGLFLW 1n6aA 167 :GKLATLMSTEEGRPHFELMPGNSVYHF T0312 140 :EHH 1n6aA 195 :KST T0312 144 :HH 1n6aA 198 :SS Number of specific fragments extracted= 7 number of extra gaps= 0 total=128 Number of alignments=25 # 1n6aA read from 1n6aA/merged-good-all-a2m # found chain 1n6aA in training set Warning: unaligning (T0312)K59 because first residue in template chain is (1n6aA)H116 T0312 60 :EYVKKELMEPLEILS 1n6aA 117 :GVCWIYYPDGGSLVG T0312 78 :N 1n6aA 132 :E T0312 80 :SMKDSKPFC 1n6aA 133 :VNEDGEMTG T0312 89 :HI 1n6aA 143 :KI T0312 92 :VLLGK 1n6aA 145 :AYVYP T0312 97 :DGEVYGGHLFSAEVF 1n6aA 151 :ERTALYGKFIDGEMI T0312 112 :ACEVFVLPLSGEAPERAFDEQTGLFLWLEHHHHH 1n6aA 167 :GKLATLMSTEEGRPHFELMPGNSVYHFDKSTSSC Number of specific fragments extracted= 7 number of extra gaps= 0 total=135 Number of alignments=26 # 1n6aA read from 1n6aA/merged-good-all-a2m # found chain 1n6aA in training set Warning: unaligning (T0312)K59 because first residue in template chain is (1n6aA)H116 T0312 60 :EYVKKELMEPL 1n6aA 117 :GVCWIYYPDGG T0312 74 :SLSGNVS 1n6aA 128 :SLVGEVN T0312 82 :KDSKPF 1n6aA 135 :EDGEMT T0312 88 :CHIHVLLGKDGEVYGGHLFSAEVF 1n6aA 142 :EKIAYVYPDERTALYGKFIDGEMI T0312 112 :ACEVFVLPLSGEAPERAFDEQTGLFLWLE 1n6aA 167 :GKLATLMSTEEGRPHFELMPGNSVYHFDK Number of specific fragments extracted= 5 number of extra gaps= 0 total=140 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i1kA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1i1kA expands to /projects/compbio/data/pdb/1i1k.pdb.gz 1i1kA:# T0312 read from 1i1kA/merged-good-all-a2m # 1i1kA read from 1i1kA/merged-good-all-a2m # adding 1i1kA to template set # found chain 1i1kA in template set T0312 20 :KDLVRQIEEFLEEKGIHAAHI 1i1kA 76 :DELMEACRDVIRKNNLTSAYI T0312 49 :AVIGYYDQEKKEYVKKEL 1i1kA 98 :PLIFVGDVGMGVNPPAGY T0312 69 :PLEILSLS 1i1kA 116 :STDVIIAA Number of specific fragments extracted= 3 number of extra gaps= 0 total=143 Number of alignments=28 # 1i1kA read from 1i1kA/merged-good-all-a2m # found chain 1i1kA in template set T0312 20 :KDLVRQIEEFLEEKGIHAAHI 1i1kA 76 :DELMEACRDVIRKNNLTSAYI T0312 49 :AVIGYYDQEKKEYVKKELM 1i1kA 98 :PLIFVGDVGMGVNPPAGYS T0312 70 :LEILSLS 1i1kA 117 :TDVIIAA Number of specific fragments extracted= 3 number of extra gaps= 0 total=146 Number of alignments=29 # 1i1kA read from 1i1kA/merged-good-all-a2m # found chain 1i1kA in template set T0312 20 :KDLVRQIEEFLEEKGIHAAHIS 1i1kA 76 :DELMEACRDVIRKNNLTSAYIR T0312 49 :AVIGYYDQEKKE 1i1kA 98 :PLIFVGDVGMGV T0312 63 :KKELMEPLEILSLSG 1i1kA 110 :NPPAGYSTDVIIAAF Number of specific fragments extracted= 3 number of extra gaps= 0 total=149 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fukA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1fukA expands to /projects/compbio/data/pdb/1fuk.pdb.gz 1fukA:# T0312 read from 1fukA/merged-good-all-a2m # 1fukA read from 1fukA/merged-good-all-a2m # adding 1fukA to template set # found chain 1fukA in template set Warning: unaligning (T0312)G9 because first residue in template chain is (1fukA)I233 T0312 10 :KGFLLRLDYGKDLVRQIEEFLEEKGIHAAHISAI 1fukA 234 :KQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCN Number of specific fragments extracted= 1 number of extra gaps= 0 total=150 Number of alignments=31 # 1fukA read from 1fukA/merged-good-all-a2m # found chain 1fukA in template set Warning: unaligning (T0312)G9 because first residue in template chain is (1fukA)I233 T0312 10 :KGFLLRLDYGKDLVRQIEEFLEEKGIHAAHISAI 1fukA 234 :KQFYVNVEEEEYKYECLTDLYDSISVTQAVIFCN Number of specific fragments extracted= 1 number of extra gaps= 0 total=151 Number of alignments=32 # 1fukA read from 1fukA/merged-good-all-a2m # found chain 1fukA in template set T0312 10 :KGFLLRLDYGKDLVRQIEEFLEEKGIHAAHISA 1fukA 234 :KQFYVNVEEEEYKYECLTDLYDSISVTQAVIFC Number of specific fragments extracted= 1 number of extra gaps= 0 total=152 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xv2A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1xv2A expands to /projects/compbio/data/pdb/1xv2.pdb.gz 1xv2A:Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 # T0312 read from 1xv2A/merged-good-all-a2m # 1xv2A read from 1xv2A/merged-good-all-a2m # adding 1xv2A to template set # found chain 1xv2A in template set T0312 9 :GKGFLLRLDYGKDLVRQIEEFLEEKG 1xv2A 82 :SKTFPLQQLSQDDVFAQIKNEMLSEN T0312 36 :HAAHISAIGAVRSAVIGYYDQEKKEY 1xv2A 108 :LFSAVKIYGTFKHMHVRMMPAQQPPY T0312 67 :MEPLE 1xv2A 142 :RQPEE T0312 72 :ILSLSGNVSMKD 1xv2A 152 :RGAIVGFFTPEL T0312 84 :SKPFCHIHVLLGKDGEVYGGHLFSAEVFACEVFVLPLS 1xv2A 166 :GVGSAGFHIHFADDERAYGGHVLDFEVDDVVVEIQNFE T0312 124 :APERAFDEQ 1xv2A 204 :TFQQHFPVN Number of specific fragments extracted= 6 number of extra gaps= 0 total=158 Number of alignments=34 # 1xv2A read from 1xv2A/merged-good-all-a2m # found chain 1xv2A in template set T0312 20 :KDLVRQIEEFLEEKGI 1xv2A 93 :DDVFAQIKNEMLSENL T0312 37 :AAHISAIGAVRSAVIGYYDQEKKEY 1xv2A 109 :FSAVKIYGTFKHMHVRMMPAQQPPY T0312 62 :VKKELME 1xv2A 144 :PEEKRQD T0312 70 :LE 1xv2A 151 :IR T0312 73 :LSLSGNVSMKD 1xv2A 153 :GAIVGFFTPEL T0312 84 :SKPFCHIHVLLGKDGEVYGGHLFSAEVFACEVFVLPLS 1xv2A 166 :GVGSAGFHIHFADDERAYGGHVLDFEVDDVVVEIQNFE Number of specific fragments extracted= 6 number of extra gaps= 0 total=164 Number of alignments=35 # 1xv2A read from 1xv2A/merged-good-all-a2m # found chain 1xv2A in template set T0312 19 :GKDLVRQIEEF 1xv2A 92 :QDDVFAQIKNE T0312 36 :HAAHISAIGAVRSAVIGYYDQEKKE 1xv2A 108 :LFSAVKIYGTFKHMHVRMMPAQQPP T0312 61 :YVKKELME 1xv2A 143 :QPEEKRQD T0312 71 :EILSLSGNVSMKD 1xv2A 151 :IRGAIVGFFTPEL T0312 84 :SKPFCHIHVLLGKDG 1xv2A 168 :GSAGFHIHFADDERA T0312 101 :YGGHLFSAEVFACEVFVLPLS 1xv2A 183 :YGGHVLDFEVDDVVVEIQNFE Number of specific fragments extracted= 6 number of extra gaps= 0 total=170 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t0bA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0312 read from 1t0bA/merged-good-all-a2m # 1t0bA read from 1t0bA/merged-good-all-a2m # found chain 1t0bA in training set Warning: unaligning (T0312)P69 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1t0bA)Y155 Warning: unaligning (T0312)L70 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1t0bA)Y155 T0312 20 :KDLVRQIEEFLEEK 1t0bA 81 :DEVVERVHRRVLEG T0312 37 :AAHISAIGAV 1t0bA 95 :MGLIVLHSGH T0312 47 :RSAVIGYYDQEKK 1t0bA 126 :EKERLWVVAPGHP T0312 60 :EYVKKELME 1t0bA 145 :PYIELEQEE T0312 71 :EILSL 1t0bA 166 :ETIFI T0312 79 :VSMKDSKPFCHIHVLLGKDGEVYG 1t0bA 171 :SWFEGGEVFRSGCTFTRGKGKIFY Number of specific fragments extracted= 6 number of extra gaps= 1 total=176 Number of alignments=37 # 1t0bA read from 1t0bA/merged-good-all-a2m # found chain 1t0bA in training set Warning: unaligning (T0312)P69 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1t0bA)Y155 Warning: unaligning (T0312)L70 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1t0bA)Y155 T0312 19 :GKDLVRQIEEFLEEK 1t0bA 80 :KDEVVERVHRRVLEG T0312 37 :AAHISAI 1t0bA 95 :MGLIVLH T0312 44 :GAV 1t0bA 103 :GHF T0312 48 :SAVIGYYDQEK 1t0bA 127 :KERLWVVAPGH T0312 59 :KEYVKKELME 1t0bA 144 :GPYIELEQEE T0312 71 :EILS 1t0bA 166 :ETIF T0312 78 :NVSMKDSKPFCHIHVLLGKDGEVYG 1t0bA 170 :ISWFEGGEVFRSGCTFTRGKGKIFY Number of specific fragments extracted= 7 number of extra gaps= 1 total=183 Number of alignments=38 # 1t0bA read from 1t0bA/merged-good-all-a2m # found chain 1t0bA in training set Warning: unaligning (T0312)V62 because of BadResidue code BAD_PEPTIDE in next template residue (1t0bA)F158 Warning: unaligning (T0312)K63 because of BadResidue code BAD_PEPTIDE at template residue (1t0bA)F158 T0312 20 :KDLVRQIEEFLEE 1t0bA 81 :DEVVERVHRRVLE T0312 36 :HAAHISAIGAVR 1t0bA 94 :GMGLIVLHSGHF T0312 48 :SAVIGYYDQEKKE 1t0bA 127 :KERLWVVAPGHPI T0312 61 :Y 1t0bA 156 :G T0312 64 :KELMEP 1t0bA 159 :FDIPEP T0312 74 :SLSGNVSMKDSKPFCHIHVLLGKDGEVYG 1t0bA 166 :ETIFISWFEGGEVFRSGCTFTRGKGKIFY Number of specific fragments extracted= 6 number of extra gaps= 1 total=189 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1m1hA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1m1hA expands to /projects/compbio/data/pdb/1m1h.pdb.gz 1m1hA:# T0312 read from 1m1hA/merged-good-all-a2m # 1m1hA read from 1m1hA/merged-good-all-a2m # adding 1m1hA to template set # found chain 1m1hA in template set Warning: unaligning (T0312)K2 because first residue in template chain is (1m1hA)Q5 T0312 3 :VFEFE 1m1hA 6 :VQELE T0312 9 :GKGFLLRLDYGK 1m1hA 11 :KKWYALQVEPGK T0312 21 :DLVRQIEEFLEEKGIH 1m1hA 25 :EAKENLLKVLELEGLK T0312 47 :RSAVIGY 1m1hA 52 :EKVVIRA T0312 57 :EKKEYVKKELMEPLEILSLSG 1m1hA 59 :QGKEKYRLSLKGNARDISVLG T0312 84 :SKPFCHIHV 1m1hA 80 :KKGVTTFRI T0312 96 :KDGE 1m1hA 89 :ENGE T0312 115 :VFVLPLSG 1m1hA 93 :VKVVESVE T0312 123 :EAP 1m1hA 108 :PPI T0312 126 :ERAFDEQTGLFLW 1m1hA 115 :QKITCKENKTEAK Number of specific fragments extracted= 10 number of extra gaps= 0 total=199 Number of alignments=40 # 1m1hA read from 1m1hA/merged-good-all-a2m # found chain 1m1hA in template set T0312 3 :VFEFE 1m1hA 6 :VQELE T0312 9 :GKGFLLRLDYGK 1m1hA 11 :KKWYALQVEPGK T0312 21 :DLVRQIEEFLEEKGIH 1m1hA 25 :EAKENLLKVLELEGLK T0312 43 :IGAVRSAVIGY 1m1hA 48 :VPAEEKVVIRA T0312 57 :EKKEYVKKELMEPLEILSLSG 1m1hA 59 :QGKEKYRLSLKGNARDISVLG T0312 84 :SKPFCHIHV 1m1hA 80 :KKGVTTFRI T0312 96 :KDGEVYG 1m1hA 89 :ENGEVKV T0312 107 :SAEVF 1m1hA 113 :PGQKI T0312 112 :A 1m1hA 119 :C T0312 113 :CEVFVLP 1m1hA 124 :TEAKIVL Number of specific fragments extracted= 10 number of extra gaps= 0 total=209 Number of alignments=41 # 1m1hA read from 1m1hA/merged-good-all-a2m # found chain 1m1hA in template set T0312 7 :EVGKGFLLRLDYGK 1m1hA 9 :LEKKWYALQVEPGK T0312 21 :DLVRQIEEFLEEKGIH 1m1hA 25 :EAKENLLKVLELEGLK T0312 46 :VRSAVIGYYD 1m1hA 49 :PAEEKVVIRA T0312 57 :EKKEYVKKELMEPLEILSL 1m1hA 59 :QGKEKYRLSLKGNARDISV T0312 76 :SGNVSMKDSKPFCH 1m1hA 83 :VTTFRIENGEVKVV T0312 94 :LGKDG 1m1hA 110 :ISKPG T0312 109 :EVF 1m1hA 115 :QKI T0312 112 :ACEVFVLPLSG 1m1hA 123 :KTEAKIVLDNK Number of specific fragments extracted= 8 number of extra gaps= 0 total=217 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1iyeA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1iyeA expands to /projects/compbio/data/pdb/1iye.pdb.gz 1iyeA:# T0312 read from 1iyeA/merged-good-all-a2m # 1iyeA read from 1iyeA/merged-good-all-a2m # adding 1iyeA to template set # found chain 1iyeA in template set T0312 20 :KDLVRQIEEFLEEKGIHAAHI 1iyeA 76 :DELMEACRDVIRKNNLTSAYI T0312 49 :AVIGYYDQEKKEYVKK 1iyeA 98 :PLIFVGDVGMGVNPPA T0312 67 :MEPLEILSLS 1iyeA 114 :GYSTDVIIAA Number of specific fragments extracted= 3 number of extra gaps= 0 total=220 Number of alignments=43 # 1iyeA read from 1iyeA/merged-good-all-a2m # found chain 1iyeA in template set T0312 20 :KDLVRQIEEFLEEKGIHAAHI 1iyeA 76 :DELMEACRDVIRKNNLTSAYI T0312 49 :AVIGYYDQEKKEYVKKEL 1iyeA 98 :PLIFVGDVGMGVNPPAGY T0312 69 :PLEILSLS 1iyeA 116 :STDVIIAA Number of specific fragments extracted= 3 number of extra gaps= 0 total=223 Number of alignments=44 # 1iyeA read from 1iyeA/merged-good-all-a2m # found chain 1iyeA in template set T0312 20 :KDLVRQIEEFLEEKGIHAAHIS 1iyeA 76 :DELMEACRDVIRKNNLTSAYIR T0312 49 :AVIGYYDQEKK 1iyeA 98 :PLIFVGDVGMG T0312 62 :VKKELMEPLEILSLS 1iyeA 109 :VNPPAGYSTDVIIAA Number of specific fragments extracted= 3 number of extra gaps= 0 total=226 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cr1A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1cr1A expands to /projects/compbio/data/pdb/1cr1.pdb.gz 1cr1A:# T0312 read from 1cr1A/merged-good-all-a2m # 1cr1A read from 1cr1A/merged-good-all-a2m # adding 1cr1A to template set # found chain 1cr1A in template set Warning: unaligning (T0312)R47 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cr1A)T484 Warning: unaligning (T0312)K64 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cr1A)T484 Warning: unaligning (T0312)M81 because of BadResidue code BAD_PEPTIDE in next template residue (1cr1A)N505 Warning: unaligning (T0312)K82 because of BadResidue code BAD_PEPTIDE at template residue (1cr1A)N505 Warning: unaligning (T0312)D83 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cr1A)L513 Warning: unaligning (T0312)F87 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cr1A)L513 Warning: unaligning (T0312)H141 because last residue in template chain is (1cr1A)Y547 T0312 20 :KDLVRQIEEFLEEKGI 1cr1A 443 :DNLMTKLKGFAKSTGV T0312 39 :HISAIGAV 1cr1A 459 :VLVVICHL T0312 65 :ELMEP 1cr1A 485 :DLRGS T0312 70 :LEILS 1cr1A 496 :SDTII T0312 78 :NVS 1cr1A 501 :ALE T0312 88 :CHIHVLLGK 1cr1A 514 :VLVRILKCR T0312 97 :DGE 1cr1A 524 :TGD T0312 108 :AEVF 1cr1A 527 :TGIA T0312 112 :AC 1cr1A 532 :YM T0312 128 :AFDEQTGLFLWLE 1cr1A 534 :EYNKETGWLEPSS Number of specific fragments extracted= 10 number of extra gaps= 1 total=236 Number of alignments=46 # 1cr1A read from 1cr1A/merged-good-all-a2m # found chain 1cr1A in template set Warning: unaligning (T0312)R47 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cr1A)T484 Warning: unaligning (T0312)K64 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cr1A)T484 Warning: unaligning (T0312)M81 because of BadResidue code BAD_PEPTIDE in next template residue (1cr1A)N505 Warning: unaligning (T0312)K82 because of BadResidue code BAD_PEPTIDE at template residue (1cr1A)N505 Warning: unaligning (T0312)D83 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cr1A)L513 Warning: unaligning (T0312)F87 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cr1A)L513 Warning: unaligning (T0312)H141 because last residue in template chain is (1cr1A)Y547 T0312 20 :KDLVRQIEEFLEEKGI 1cr1A 443 :DNLMTKLKGFAKSTGV T0312 39 :HISAIGAV 1cr1A 459 :VLVVICHL T0312 65 :ELMEP 1cr1A 485 :DLRGS T0312 70 :LEILS 1cr1A 496 :SDTII T0312 78 :NVS 1cr1A 501 :ALE T0312 88 :CHIHVLLGK 1cr1A 514 :VLVRILKCR T0312 97 :DGE 1cr1A 524 :TGD T0312 108 :AEVF 1cr1A 527 :TGIA T0312 112 :AC 1cr1A 532 :YM T0312 128 :AFDEQTGLFLWLE 1cr1A 534 :EYNKETGWLEPSS Number of specific fragments extracted= 10 number of extra gaps= 1 total=246 Number of alignments=47 # 1cr1A read from 1cr1A/merged-good-all-a2m # found chain 1cr1A in template set Warning: unaligning (T0312)R47 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cr1A)T484 Warning: unaligning (T0312)K64 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cr1A)T484 Warning: unaligning (T0312)L94 because of BadResidue code BAD_PEPTIDE in next template residue (1cr1A)N505 Warning: unaligning (T0312)G95 because of BadResidue code BAD_PEPTIDE at template residue (1cr1A)N505 Warning: unaligning (T0312)K96 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cr1A)L513 Warning: unaligning (T0312)V110 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cr1A)L513 T0312 20 :KDLVRQIEEFLEEKGI 1cr1A 443 :DNLMTKLKGFAKSTGV T0312 39 :HISAIGAV 1cr1A 459 :VLVVICHL T0312 65 :ELMEP 1cr1A 485 :DLRGS T0312 86 :PFCHIHVL 1cr1A 496 :SDTIIALE T0312 111 :FACEVFVLPLSGEA 1cr1A 514 :VLVRILKCRFTGDT T0312 125 :PERAFDEQTGLF 1cr1A 531 :GYMEYNKETGWL Number of specific fragments extracted= 6 number of extra gaps= 1 total=252 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2f69A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2f69A expands to /projects/compbio/data/pdb/2f69.pdb.gz 2f69A:Skipped atom 16, because occupancy 0.500 <= existing 0.500 in 2f69A Skipped atom 18, because occupancy 0.500 <= existing 0.500 in 2f69A Skipped atom 25, because occupancy 0.500 <= existing 0.500 in 2f69A Skipped atom 476, because occupancy 0.500 <= existing 0.500 in 2f69A Skipped atom 478, because occupancy 0.500 <= existing 0.500 in 2f69A Skipped atom 480, because occupancy 0.500 <= existing 0.500 in 2f69A Skipped atom 482, because occupancy 0.500 <= existing 0.500 in 2f69A Skipped atom 484, because occupancy 0.500 <= existing 0.500 in 2f69A Skipped atom 494, because occupancy 0.500 <= existing 0.500 in 2f69A Skipped atom 496, because occupancy 0.500 <= existing 0.500 in 2f69A Skipped atom 498, because occupancy 0.500 <= existing 0.500 in 2f69A Skipped atom 500, because occupancy 0.500 <= existing 0.500 in 2f69A Skipped atom 502, because occupancy 0.500 <= existing 0.500 in 2f69A Skipped atom 504, because occupancy 0.500 <= existing 0.500 in 2f69A Skipped atom 506, because occupancy 0.500 <= existing 0.500 in 2f69A Skipped atom 661, because occupancy 0.500 <= existing 0.500 in 2f69A Skipped atom 861, because occupancy 0.500 <= existing 0.500 in 2f69A Skipped atom 915, because occupancy 0.500 <= existing 0.500 in 2f69A Skipped atom 1125, because occupancy 0.500 <= existing 0.500 in 2f69A Skipped atom 1127, because occupancy 0.500 <= existing 0.500 in 2f69A Skipped atom 1129, because occupancy 0.500 <= existing 0.500 in 2f69A Skipped atom 1198, because occupancy 0.500 <= existing 0.500 in 2f69A Skipped atom 1276, because occupancy 0.500 <= existing 0.500 in 2f69A Skipped atom 1278, because occupancy 0.500 <= existing 0.500 in 2f69A Skipped atom 1280, because occupancy 0.500 <= existing 0.500 in 2f69A Skipped atom 1713, because occupancy 0.500 <= existing 0.500 in 2f69A Skipped atom 1715, because occupancy 0.500 <= existing 0.500 in 2f69A # T0312 read from 2f69A/merged-good-all-a2m # 2f69A read from 2f69A/merged-good-all-a2m # adding 2f69A to template set # found chain 2f69A in template set Warning: unaligning (T0312)K59 because first residue in template chain is (2f69A)H116 T0312 60 :EYVKKELMEPLEILS 2f69A 117 :GVCWIYYPDGGSLVG T0312 78 :NV 2f69A 132 :EV T0312 81 :MKDSKPFC 2f69A 134 :NEDGEMTG T0312 89 :HIHVLLGKDGEVYGGHLFSAEVF 2f69A 143 :KIAYVYPDERTALYGKFIDGEMI T0312 112 :ACEVFVLPLSGEAPERAFDEQTGLFLW 2f69A 167 :GKLATLMSTEEGRPHFELMPGNSVYHF T0312 142 :HHHH 2f69A 196 :STSS Number of specific fragments extracted= 6 number of extra gaps= 0 total=258 Number of alignments=49 # 2f69A read from 2f69A/merged-good-all-a2m # found chain 2f69A in template set Warning: unaligning (T0312)K59 because first residue in template chain is (2f69A)H116 T0312 60 :EYVKKELMEPLEILS 2f69A 117 :GVCWIYYPDGGSLVG T0312 78 :N 2f69A 132 :E T0312 80 :SMKDSKPFCHIHVLLGK 2f69A 133 :VNEDGEMTGEKIAYVYP T0312 97 :DGEVYGGHLFSAEVF 2f69A 151 :ERTALYGKFIDGEMI T0312 112 :ACEVFVLPLSGEAPERAFDEQTGLFLWLEHHHH 2f69A 167 :GKLATLMSTEEGRPHFELMPGNSVYHFDKSTSS Number of specific fragments extracted= 5 number of extra gaps= 0 total=263 Number of alignments=50 # 2f69A read from 2f69A/merged-good-all-a2m # found chain 2f69A in template set Warning: unaligning (T0312)K59 because first residue in template chain is (2f69A)H116 T0312 60 :EYVKKELMEPL 2f69A 117 :GVCWIYYPDGG T0312 74 :SLSGNVS 2f69A 128 :SLVGEVN T0312 82 :KDSKPF 2f69A 135 :EDGEMT T0312 88 :CHIHVLLGKDGEVYGGHLFSAEVF 2f69A 142 :EKIAYVYPDERTALYGKFIDGEMI T0312 112 :ACEVFVLPLSGEAPERAFDEQTGLFLWLE 2f69A 167 :GKLATLMSTEEGRPHFELMPGNSVYHFDK Number of specific fragments extracted= 5 number of extra gaps= 0 total=268 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vcoA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vcoA expands to /projects/compbio/data/pdb/1vco.pdb.gz 1vcoA:# T0312 read from 1vcoA/merged-good-all-a2m # 1vcoA read from 1vcoA/merged-good-all-a2m # adding 1vcoA to template set # found chain 1vcoA in template set T0312 20 :KDLVRQIEEFLEEKGIHAAHISAIGAVRS 1vcoA 130 :DEIKERIRKVAEEQKAEIVVVEVGGTVGD Number of specific fragments extracted= 1 number of extra gaps= 0 total=269 Number of alignments=52 # 1vcoA read from 1vcoA/merged-good-all-a2m # found chain 1vcoA in template set T0312 20 :KDLVRQIEEFLEEKGIHAAHISAIGAVRS 1vcoA 130 :DEIKERIRKVAEEQKAEIVVVEVGGTVGD Number of specific fragments extracted= 1 number of extra gaps= 0 total=270 Number of alignments=53 # 1vcoA read from 1vcoA/merged-good-all-a2m # found chain 1vcoA in template set T0312 20 :KDLVRQIEEFLEEKGIHAAHISAIGAVRS 1vcoA 130 :DEIKERIRKVAEEQKAEIVVVEVGGTVGD Number of specific fragments extracted= 1 number of extra gaps= 0 total=271 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ys7A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ys7A expands to /projects/compbio/data/pdb/1ys7.pdb.gz 1ys7A:# T0312 read from 1ys7A/merged-good-all-a2m # 1ys7A read from 1ys7A/merged-good-all-a2m # adding 1ys7A to template set # found chain 1ys7A in template set Warning: unaligning (T0312)K10 because first residue in template chain is (1ys7A)S7 T0312 11 :GFLLRLDYGKDLVRQIEEFLEEKGIHAAHI 1ys7A 8 :PRVLVVDDDSDVLASLERGLRLSGFEVATA Number of specific fragments extracted= 1 number of extra gaps= 0 total=272 Number of alignments=55 # 1ys7A read from 1ys7A/merged-good-all-a2m # found chain 1ys7A in template set Warning: unaligning (T0312)K10 because first residue in template chain is (1ys7A)S7 T0312 11 :GFLLRLDYGKDLVRQIEEFLEEKGIHAAH 1ys7A 8 :PRVLVVDDDSDVLASLERGLRLSGFEVAT Number of specific fragments extracted= 1 number of extra gaps= 0 total=273 Number of alignments=56 # 1ys7A read from 1ys7A/merged-good-all-a2m # found chain 1ys7A in template set Warning: unaligning (T0312)K10 because first residue in template chain is (1ys7A)S7 T0312 11 :GFLLRLDYGKDLVRQIEEFLEEKGIHAAH 1ys7A 8 :PRVLVVDDDSDVLASLERGLRLSGFEVAT Number of specific fragments extracted= 1 number of extra gaps= 0 total=274 Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gnxA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2gnxA expands to /projects/compbio/data/pdb/2gnx.pdb.gz 2gnxA:Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: UNK for alphabet: ExtAA Replacing UNK with X Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 # T0312 read from 2gnxA/merged-good-all-a2m # 2gnxA read from 2gnxA/merged-good-all-a2m # adding 2gnxA to template set # found chain 2gnxA in template set Warning: unaligning (T0312)K58 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gnxA)Q345 T0312 19 :GKDLVRQIEEFLEEKGIHAAHI 2gnxA 294 :NPDLFGKISSFIRKYDAANVSL T0312 59 :KEYVKKELMEPL 2gnxA 346 :YPAVVSLPSDRP T0312 72 :ILSLSG 2gnxA 381 :VVHFYD T0312 82 :KD 2gnxA 387 :DK T0312 84 :S 2gnxA 390 :Q T0312 88 :CHIHVLLGKDG 2gnxA 391 :STYFLTRPEPH T0312 112 :ACEVFVLP 2gnxA 402 :FTIVVIFE Number of specific fragments extracted= 7 number of extra gaps= 0 total=281 Number of alignments=58 # 2gnxA read from 2gnxA/merged-good-all-a2m # found chain 2gnxA in template set Warning: unaligning (T0312)Y54 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2gnxA)Q345 T0312 19 :GKDLVRQIEEFLEEKGI 2gnxA 294 :NPDLFGKISSFIRKYDA T0312 47 :RSAVIGY 2gnxA 311 :ANVSLIF T0312 77 :GNVSMKDS 2gnxA 348 :AVVSLPSD T0312 85 :KPFCH 2gnxA 379 :EKVVH T0312 90 :IHVLLGK 2gnxA 391 :STYFLTR T0312 112 :ACEVFVLP 2gnxA 402 :FTIVVIFE T0312 127 :RAFDEQ 2gnxA 410 :SKKSER Number of specific fragments extracted= 7 number of extra gaps= 0 total=288 Number of alignments=59 # 2gnxA read from 2gnxA/merged-good-all-a2m # found chain 2gnxA in template set T0312 19 :GKDLVRQIEEFLEEKGIHAAHIS 2gnxA 294 :NPDLFGKISSFIRKYDAANVSLI T0312 61 :YVKKELM 2gnxA 381 :VVHFYDD T0312 73 :LSLSGNVSMKD 2gnxA 391 :STYFLTRPEPH T0312 88 :CHIHVLLGK 2gnxA 402 :FTIVVIFES Number of specific fragments extracted= 4 number of extra gaps= 0 total=292 Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wn2A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wn2A expands to /projects/compbio/data/pdb/1wn2.pdb.gz 1wn2A:Skipped atom 169, because occupancy 0.500 <= existing 0.500 in 1wn2A Skipped atom 171, because occupancy 0.500 <= existing 0.500 in 1wn2A Skipped atom 173, because occupancy 0.500 <= existing 0.500 in 1wn2A Skipped atom 505, because occupancy 0.500 <= existing 0.500 in 1wn2A Skipped atom 507, because occupancy 0.500 <= existing 0.500 in 1wn2A Skipped atom 509, because occupancy 0.500 <= existing 0.500 in 1wn2A Skipped atom 511, because occupancy 0.500 <= existing 0.500 in 1wn2A Skipped atom 527, because occupancy 0.500 <= existing 0.500 in 1wn2A Skipped atom 529, because occupancy 0.500 <= existing 0.500 in 1wn2A Skipped atom 531, because occupancy 0.500 <= existing 0.500 in 1wn2A Skipped atom 533, because occupancy 0.500 <= existing 0.500 in 1wn2A Skipped atom 590, because occupancy 0.500 <= existing 0.500 in 1wn2A Skipped atom 592, because occupancy 0.500 <= existing 0.500 in 1wn2A Skipped atom 594, because occupancy 0.500 <= existing 0.500 in 1wn2A Skipped atom 596, because occupancy 0.500 <= existing 0.500 in 1wn2A Skipped atom 767, because occupancy 0.500 <= existing 0.500 in 1wn2A Skipped atom 769, because occupancy 0.500 <= existing 0.500 in 1wn2A Skipped atom 833, because occupancy 0.500 <= existing 0.500 in 1wn2A Skipped atom 835, because occupancy 0.500 <= existing 0.500 in 1wn2A Skipped atom 837, because occupancy 0.500 <= existing 0.500 in 1wn2A Skipped atom 839, because occupancy 0.500 <= existing 0.500 in 1wn2A # T0312 read from 1wn2A/merged-good-all-a2m # 1wn2A read from 1wn2A/merged-good-all-a2m # adding 1wn2A to template set # found chain 1wn2A in template set T0312 8 :VGKGFLLRLDYGKDLVR 1wn2A 54 :GQKKVVVKVESEEELFK T0312 26 :IEEFLEEKGIHAAHI 1wn2A 71 :LKAEAEKLGLPNALI T0312 53 :YYDQEKK 1wn2A 90 :LTEIPPG T0312 69 :PLEILS 1wn2A 97 :TVTVLA T0312 76 :SGN 1wn2A 103 :VGP Number of specific fragments extracted= 5 number of extra gaps= 0 total=297 Number of alignments=61 # 1wn2A read from 1wn2A/merged-good-all-a2m # found chain 1wn2A in template set T0312 8 :VGKGFLLRLDYGKDLVR 1wn2A 54 :GQKKVVVKVESEEELFK T0312 26 :IEEFLEEKGIHAAHI 1wn2A 71 :LKAEAEKLGLPNALI T0312 52 :GYYDQEK 1wn2A 86 :RDAGLTE T0312 61 :YV 1wn2A 93 :IP T0312 67 :MEPLEILSL 1wn2A 95 :PGTVTVLAV T0312 77 :G 1wn2A 104 :G Number of specific fragments extracted= 6 number of extra gaps= 0 total=303 Number of alignments=62 # 1wn2A read from 1wn2A/merged-good-all-a2m # found chain 1wn2A in template set T0312 8 :VGKGFLLRLDYGKDLVR 1wn2A 54 :GQKKVVVKVESEEELFK T0312 26 :IEEFLEEKGIHAAHIS 1wn2A 71 :LKAEAEKLGLPNALIR T0312 54 :YDQEK 1wn2A 88 :AGLTE T0312 81 :MKDSKPFCHIHV 1wn2A 93 :IPPGTVTVLAVG Number of specific fragments extracted= 4 number of extra gaps= 0 total=307 Number of alignments=63 # command:Using radius: 8.0000 Alignment mode NUMB_ALIGNS: 63 Adding 1909 constraints to all.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all.constraints maxweight: 1.0000 Optimizing... Probability sum: -250.7802, CN propb: -250.7802 weights: 0.1904 constraints: 706 # command:Found ConstraintSet # PrintContacts align.constraints_v3 Number of constraints in align.constraints 706 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_v3 Number of constraints in align.constraints.bonus 706 # command:Found ConstraintSet # PrintContacts rejected.constraints_v3 Number of constraints in rejected.constraints 1203 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_v3 Number of constraints in rejected.constraints.bonus 1203 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_v3 Number of constraints in noncontact.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_v3 Number of constraints in noncontact.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_v3 Number of constraints in all.constraints 1909 # command: