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/T0367/ # command:# Making conformation for sequence T0367 numbered 1 through 125 Created new target T0367 from T0367.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0367/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0367//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0367/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0367//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0367/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0367/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0367/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1oshA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0367 read from 1oshA/merged-good-all-a2m # 1oshA read from 1oshA/merged-good-all-a2m # found chain 1oshA in training set Warning: unaligning (T0367)D2 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1oshA)E286 T0367 3 :ELELRIRKAEKLVQDAKKEFE 1oshA 287 :NFLILTEMATNHVQVLVEFTK # choosing archetypes in rotamer library T0367 24 :MGLYERCCSTAYYAMFHAAKAMLLGYGRDSKTHR 1oshA 317 :HEDQIALLKGSAVEAMFLRSAEIFNKKLPSGHSD T0367 62 :LIWECREELGLSDDDCSKLSRAFDL 1oshA 351 :LLEERIRNSGISDEYITPMFSFYKS T0367 90 :SDYGIYK 1oshA 397 :PDRQYIK T0367 99 :SKDLAIKILKDAEIFVQKAKNAVNK 1oshA 404 :DREAVEKLQEPLLDVLQKLCKIHQP Number of specific fragments extracted= 5 number of extra gaps= 0 total=5 Number of alignments=1 # 1oshA read from 1oshA/merged-good-all-a2m # found chain 1oshA in training set Warning: unaligning (T0367)D2 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1oshA)E286 T0367 3 :ELELRIRKAEKLVQDAKKEFE 1oshA 287 :NFLILTEMATNHVQVLVEFTK T0367 24 :MGLYERCCSTAYYAMFHAAKAMLLGYGRDSKTHR 1oshA 317 :HEDQIALLKGSAVEAMFLRSAEIFNKKLPSGHSD T0367 62 :LIWECREELGLSDDDCSKLSRAFDLREESDYG 1oshA 351 :LLEERIRNSGISDEYITPMFSFYKSIGELKMT T0367 94 :IYKE 1oshA 395 :LSPD T0367 99 :SKDLAIKILKDAEIFVQKAKNAVNK 1oshA 404 :DREAVEKLQEPLLDVLQKLCKIHQP Number of specific fragments extracted= 5 number of extra gaps= 0 total=10 Number of alignments=2 # 1oshA read from 1oshA/merged-good-all-a2m # found chain 1oshA in training set Warning: unaligning (T0367)D2 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1oshA)E286 T0367 3 :ELELRIRKAEKLVQDAKKEFE 1oshA 287 :NFLILTEMATNHVQVLVEFTK T0367 24 :MGLYERCCSTAYYAMFHAAKAMLLGYGRDS 1oshA 317 :HEDQIALLKGSAVEAMFLRSAEIFNKKLPS T0367 58 :GTIYLIWECREELGLSDDDCSKLS 1oshA 347 :GHSDLLEERIRNSGISDEYITPMF T0367 82 :RAFDLREES 1oshA 372 :FYKSIGELK T0367 91 :DYGIYKEVSKDLAIKILKDAEIFVQKAKNAV 1oshA 396 :SPDRQYIKDREAVEKLQEPLLDVLQKLCKIH Number of specific fragments extracted= 5 number of extra gaps= 0 total=15 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wtyA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wtyA expands to /projects/compbio/data/pdb/1wty.pdb.gz 1wtyA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0367 read from 1wtyA/merged-good-all-a2m # 1wtyA read from 1wtyA/merged-good-all-a2m # adding 1wtyA to template set # found chain 1wtyA in template set Warning: unaligning (T0367)K123 because last residue in template chain is (1wtyA)E117 T0367 12 :EKLVQDAKKEFEMG 1wtyA 5 :ARAVERLKAALERP T0367 26 :LYERCCSTAYYAMFH 1wtyA 23 :IRDSAIQRFEFTFEL T0367 41 :AAKAMLLGYGRDSKTHRGTIYLIWE 1wtyA 41 :TLKTFLELQGLEARSPRAAIRGAFQ T0367 70 :LGLSD 1wtyA 66 :VGLLP T0367 75 :DDCSKLSRAFDLREESD 1wtyA 73 :PFWLEMLELRNLTNHTY T0367 99 :SKDLAIKI 1wtyA 90 :DEALAERI T0367 107 :LKDAEIFVQKAKNAVN 1wtyA 101 :LPKALERFQELLRRLE Number of specific fragments extracted= 7 number of extra gaps= 0 total=22 Number of alignments=4 # 1wtyA read from 1wtyA/merged-good-all-a2m # found chain 1wtyA in template set Warning: unaligning (T0367)K123 because last residue in template chain is (1wtyA)E117 T0367 12 :EKLVQDAKKEFEMG 1wtyA 5 :ARAVERLKAALERP T0367 26 :LYERCCSTAYYAMFHA 1wtyA 23 :IRDSAIQRFEFTFELA T0367 42 :AKAMLLGYGRDSKTHRGTIYLIWE 1wtyA 42 :LKTFLELQGLEARSPRAAIRGAFQ T0367 70 :LGLSD 1wtyA 66 :VGLLP T0367 75 :DDCSKLSRAFDLREESD 1wtyA 73 :PFWLEMLELRNLTNHTY T0367 99 :SKDLAIKI 1wtyA 90 :DEALAERI T0367 107 :LKDAEIFVQKAKNAVN 1wtyA 101 :LPKALERFQELLRRLE Number of specific fragments extracted= 7 number of extra gaps= 0 total=29 Number of alignments=5 # 1wtyA read from 1wtyA/merged-good-all-a2m # found chain 1wtyA in template set Warning: unaligning (T0367)K123 because last residue in template chain is (1wtyA)E117 T0367 12 :EKLVQDAKKEFEMG 1wtyA 5 :ARAVERLKAALERP T0367 26 :LYERCCSTAYYAMFHAAKAM 1wtyA 23 :IRDSAIQRFEFTFELAWKTL T0367 46 :LLGYGRDSKTHRGTIYLI 1wtyA 46 :LELQGLEARSPRAAIRGA T0367 68 :EELGLSD 1wtyA 64 :FQVGLLP T0367 75 :DDCSKLSRAFDLREESD 1wtyA 73 :PFWLEMLELRNLTNHTY T0367 99 :SKDLAIKI 1wtyA 90 :DEALAERI T0367 107 :LKDAEIFVQKAKNAVN 1wtyA 101 :LPKALERFQELLRRLE Number of specific fragments extracted= 7 number of extra gaps= 0 total=36 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cfuA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2cfuA expands to /projects/compbio/data/pdb/2cfu.pdb.gz 2cfuA:Skipped atom 87, because occupancy 0.5 <= existing 0.500 in 2cfuA Skipped atom 89, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 91, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 93, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 95, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 97, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 99, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 101, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 103, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 120, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 124, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 126, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 128, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 130, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 132, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 134, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 136, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 139, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 143, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 145, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 147, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 149, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 151, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 153, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 155, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 261, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 263, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 265, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 267, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 269, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 271, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 273, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 275, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 277, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 408, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 412, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 414, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 416, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 418, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 420, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 422, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 424, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 569, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 571, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 573, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 575, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 577, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 579, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 581, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 583, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 585, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 691, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 695, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 697, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 699, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 701, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 930, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 932, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 934, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 936, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 938, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 940, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 942, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 944, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 946, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 948, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 950, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1072, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1076, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1078, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1080, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1082, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1084, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1086, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1088, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1183, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1185, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1187, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1189, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1191, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1193, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1195, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1197, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1199, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1201, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1203, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1461, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1465, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1467, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1469, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1471, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1585, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1587, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1589, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1591, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1593, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1595, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1597, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1599, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1704, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1708, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1710, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1712, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1714, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1716, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1817, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1819, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1821, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1823, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1825, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1827, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1829, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1831, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1833, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1835, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1837, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1899, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1901, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1903, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1905, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1907, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1909, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1911, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1913, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1915, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1917, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1919, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1950, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1952, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1954, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1956, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1958, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1960, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1962, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1964, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1966, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1972, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1974, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1976, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1978, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1980, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1982, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1984, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1986, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 1988, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 2227, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 2229, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 2231, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 2233, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 2235, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 2237, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 2239, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 2241, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 2243, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 2368, because occupancy 0.300 <= existing 0.700 in 2cfuA Skipped atom 2372, because occupancy 0.300 <= existing 0.700 in 2cfuA Skipped atom 2374, because occupancy 0.300 <= existing 0.700 in 2cfuA Skipped atom 2376, because occupancy 0.300 <= existing 0.700 in 2cfuA Skipped atom 2406, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 2408, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 2410, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 2412, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 2414, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 2416, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 2418, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 2420, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 2422, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 2525, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 2529, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 2531, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 2533, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 2535, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 2537, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 2562, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 2564, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 2566, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 2568, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 2570, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 2572, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 2574, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 2576, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 2578, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 2580, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 2582, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 2624, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 2626, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 2628, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 2630, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 2632, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 2634, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 2636, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 2638, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 2640, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 2719, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 2721, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 2723, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 2725, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 2727, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 2729, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 2731, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 2733, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 2735, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 2737, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 2739, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 3508, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 3510, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 3512, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 3514, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 3516, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 3518, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 3520, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 3522, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 3524, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 3619, because occupancy 0.300 <= existing 0.700 in 2cfuA Skipped atom 3623, because occupancy 0.300 <= existing 0.700 in 2cfuA Skipped atom 3625, because occupancy 0.300 <= existing 0.700 in 2cfuA Skipped atom 3627, because occupancy 0.300 <= existing 0.700 in 2cfuA Skipped atom 3629, because occupancy 0.300 <= existing 0.700 in 2cfuA Skipped atom 3631, because occupancy 0.300 <= existing 0.700 in 2cfuA Skipped atom 3633, because occupancy 0.300 <= existing 0.700 in 2cfuA Skipped atom 3635, because occupancy 0.300 <= existing 0.700 in 2cfuA Skipped atom 3829, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 3831, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 3833, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 3835, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 3837, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 3839, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 3841, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 3843, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 3854, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 3858, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 3860, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 3862, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 3864, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 3866, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 3868, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 3870, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 3893, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 3895, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 3897, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 3899, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 3901, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 3903, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 3905, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 3907, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 3909, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 4180, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 4184, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 4186, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 4188, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 4190, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 4192, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 4194, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 4196, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 4305, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 4309, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 4311, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 4313, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 4315, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 4317, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 4319, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 4321, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 4382, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 4386, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 4388, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 4390, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 4392, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 4843, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 4845, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 4847, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 4849, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 4851, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 4853, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 4855, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 4857, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 4859, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 4886, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 4888, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 4890, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 4892, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 4894, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 4896, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 4898, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 4900, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 4902, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 4904, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 4906, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 5085, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 5089, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 5091, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 5093, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 5095, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 5108, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 5110, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 5112, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 5114, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 5116, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 5118, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 5120, because occupancy 0.500 <= existing 0.500 in 2cfuA Skipped atom 5122, because occupancy 0.500 <= existing 0.500 in 2cfuA # T0367 read from 2cfuA/merged-good-all-a2m # 2cfuA read from 2cfuA/merged-good-all-a2m # adding 2cfuA to template set # found chain 2cfuA in template set T0367 3 :ELELRIRK 2cfuA 438 :SAGRYVEY T0367 11 :AEKLVQDAKKEFEMGLYERCCSTAYYAMFH 2cfuA 449 :AERLLEQARASYARGEYRWVVEVVNRLVFA T0367 41 :AAKAMLLG 2cfuA 489 :QADALEQL T0367 57 :RGTIYLIWECRE 2cfuA 504 :GWRNSYLSAAYE T0367 69 :ELGLSDD 2cfuA 517 :RHGVPRD Number of specific fragments extracted= 5 number of extra gaps= 0 total=41 Number of alignments=7 # 2cfuA read from 2cfuA/merged-good-all-a2m # found chain 2cfuA in template set Warning: unaligning (T0367)I94 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2cfuA)G530 T0367 3 :ELELRIRK 2cfuA 438 :SAGRYVEY T0367 11 :AEKLVQDAKKEFEMGLYERCCSTAYYAMFH 2cfuA 449 :AERLLEQARASYARGEYRWVVEVVNRLVFA T0367 53 :SKTHRGTIYLIWECREEL 2cfuA 479 :EPDNRAARELQADALEQL T0367 79 :KLSRAFDLREESDYG 2cfuA 509 :YLSAAYELRHGVPRD Number of specific fragments extracted= 4 number of extra gaps= 0 total=45 Number of alignments=8 # 2cfuA read from 2cfuA/merged-good-all-a2m # found chain 2cfuA in template set T0367 98 :VSKDLAIKILKDAEIFV 2cfuA 349 :WGNAEIVEVLEKQRDLY T0367 115 :QKAKNAVNKNR 2cfuA 370 :DQTLHLANQGV Number of specific fragments extracted= 2 number of extra gaps= 0 total=47 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1khoA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1khoA expands to /projects/compbio/data/pdb/1kho.pdb.gz 1khoA:# T0367 read from 1khoA/merged-good-all-a2m # 1khoA read from 1khoA/merged-good-all-a2m # adding 1khoA to template set # found chain 1khoA in template set T0367 21 :EFEMGLYERCCSTAYYAMFHAAKA 1khoA 108 :EWKRGNYKQATFYLGEAMHYFGDA T0367 45 :MLLGYGRDS 1khoA 134 :PYHAANVTA T0367 54 :KTHRGTIYLI 1khoA 146 :PGHVKFETFA T0367 78 :SKLSRAFDLREESD 1khoA 195 :SFAKTAKDLYYSHA T0367 95 :YKEVSKDLAIKILKDA 1khoA 209 :NMSCSWDEWDYAAKVA Number of specific fragments extracted= 5 number of extra gaps= 0 total=52 Number of alignments=10 # 1khoA read from 1khoA/merged-good-all-a2m # found chain 1khoA in template set T0367 21 :EFEMGLYERCCSTAYYAMFHAAKA 1khoA 108 :EWKRGNYKQATFYLGEAMHYFGDA T0367 45 :MLLGYGRDS 1khoA 134 :PYHAANVTA T0367 54 :KTHRGTIYLIWEC 1khoA 146 :PGHVKFETFAEDR T0367 73 :SDDDCS 1khoA 172 :NDAFYS T0367 79 :KLSRAFDLREES 1khoA 196 :FAKTAKDLYYSH T0367 94 :IYKEVSKDLAIKILKDA 1khoA 208 :ANMSCSWDEWDYAAKVA Number of specific fragments extracted= 6 number of extra gaps= 0 total=58 Number of alignments=11 # 1khoA read from 1khoA/merged-good-all-a2m # found chain 1khoA in template set T0367 21 :EFEMGLYERCCSTAYYAMFHAAKA 1khoA 108 :EWKRGNYKQATFYLGEAMHYFGDA T0367 45 :MLLGYGRDSKTHRGTIYLIWECREELGLSDDDCSKLS 1khoA 134 :PYHAANVTAVDSPGHVKFETFAEDRKDQYKINTTGSK T0367 82 :RAFDLREESDYG 1khoA 175 :FYSNILTNEDFN T0367 101 :DLAIKI 1khoA 187 :SWSKEF T0367 110 :AEIFVQKAKNAVN 1khoA 193 :ARSFAKTAKDLYY Number of specific fragments extracted= 5 number of extra gaps= 0 total=63 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 16vpA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 16vpA expands to /projects/compbio/data/pdb/16vp.pdb.gz 16vpA:# T0367 read from 16vpA/merged-good-all-a2m # 16vpA read from 16vpA/merged-good-all-a2m # adding 16vpA to template set # found chain 16vpA in template set T0367 4 :LELRIRKAEKLVQ 16vpA 180 :YRYLRASVRQLHR T0367 20 :KEFEMG 16vpA 193 :QAHMRG T0367 26 :LYERCCSTAYYAMFHAAKAMLLGY 16vpA 207 :LRATIADRYYRETARLARVLFLHL T0367 57 :RGTIYLIWECREELGLSDDDCSKL 16vpA 233 :FLTREILWAAYAEQMMRPDLFDCL T0367 81 :SRAFDLREESDY 16vpA 264 :RQLAGLFQPFMF T0367 94 :IYKEVSKDLAIKIL 16vpA 283 :RGVPIEARRLRELN Number of specific fragments extracted= 6 number of extra gaps= 0 total=69 Number of alignments=13 # 16vpA read from 16vpA/merged-good-all-a2m # found chain 16vpA in template set T0367 4 :LELRIRKAEKLVQDAKK 16vpA 180 :YRYLRASVRQLHRQAHM T0367 24 :MG 16vpA 197 :RG T0367 26 :LYERCCSTAYYAMFHAAKAMLLGY 16vpA 207 :LRATIADRYYRETARLARVLFLHL T0367 58 :GTIYLIWECREELGLSDDDCS 16vpA 234 :LTREILWAAYAEQMMRPDLFD T0367 81 :SRAFDLREESDY 16vpA 264 :RQLAGLFQPFMF T0367 94 :IYKEVSKDLAIKIL 16vpA 283 :RGVPIEARRLRELN Number of specific fragments extracted= 6 number of extra gaps= 0 total=75 Number of alignments=14 # 16vpA read from 16vpA/merged-good-all-a2m # found chain 16vpA in template set T0367 4 :LELRIRKAEKLVQDAKKE 16vpA 180 :YRYLRASVRQLHRQAHMR T0367 24 :MGLY 16vpA 203 :LGEM T0367 28 :ERCCSTAYYAMFHAAKAMLLG 16vpA 209 :ATIADRYYRETARLARVLFLH Number of specific fragments extracted= 3 number of extra gaps= 0 total=78 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ftzA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2ftzA expands to /projects/compbio/data/pdb/2ftz.pdb.gz 2ftzA:Bad short name: CH1 for alphabet: pdb_atoms Skipped atom 122, because occupancy 0.500 <= existing 0.500 in 2ftzA Skipped atom 124, because occupancy 0.500 <= existing 0.500 in 2ftzA Skipped atom 126, because occupancy 0.500 <= existing 0.500 in 2ftzA Skipped atom 128, because occupancy 0.500 <= existing 0.500 in 2ftzA Skipped atom 130, because occupancy 0.500 <= existing 0.500 in 2ftzA Skipped atom 132, because occupancy 0.500 <= existing 0.500 in 2ftzA Skipped atom 138, because occupancy 0.500 <= existing 0.500 in 2ftzA Skipped atom 140, because occupancy 0.500 <= existing 0.500 in 2ftzA Skipped atom 142, because occupancy 0.500 <= existing 0.500 in 2ftzA Skipped atom 144, because occupancy 0.500 <= existing 0.500 in 2ftzA Skipped atom 146, because occupancy 0.500 <= existing 0.500 in 2ftzA Skipped atom 457, because occupancy 0.500 <= existing 0.500 in 2ftzA Skipped atom 459, because occupancy 0.500 <= existing 0.500 in 2ftzA Skipped atom 461, because occupancy 0.500 <= existing 0.500 in 2ftzA Skipped atom 463, because occupancy 0.500 <= existing 0.500 in 2ftzA Skipped atom 465, because occupancy 0.500 <= existing 0.500 in 2ftzA Skipped atom 534, because occupancy 0.500 <= existing 0.500 in 2ftzA Skipped atom 536, because occupancy 0.500 <= existing 0.500 in 2ftzA Skipped atom 538, because occupancy 0.500 <= existing 0.500 in 2ftzA Skipped atom 626, because occupancy 0.500 <= existing 0.500 in 2ftzA Skipped atom 628, because occupancy 0.500 <= existing 0.500 in 2ftzA Skipped atom 630, because occupancy 0.500 <= existing 0.500 in 2ftzA Skipped atom 632, because occupancy 0.500 <= existing 0.500 in 2ftzA Bad short name: CH1 for alphabet: pdb_atoms Skipped atom 931, because occupancy 0.500 <= existing 0.500 in 2ftzA Skipped atom 933, because occupancy 0.500 <= existing 0.500 in 2ftzA Skipped atom 939, because occupancy 0.500 <= existing 0.500 in 2ftzA Skipped atom 941, because occupancy 0.500 <= existing 0.500 in 2ftzA Skipped atom 943, because occupancy 0.500 <= existing 0.500 in 2ftzA Skipped atom 945, because occupancy 0.500 <= existing 0.500 in 2ftzA Skipped atom 947, because occupancy 0.500 <= existing 0.500 in 2ftzA Bad short name: CH1 for alphabet: pdb_atoms Skipped atom 1107, because occupancy 0.500 <= existing 0.500 in 2ftzA Skipped atom 1109, because occupancy 0.500 <= existing 0.500 in 2ftzA Skipped atom 1111, because occupancy 0.500 <= existing 0.500 in 2ftzA Skipped atom 1113, because occupancy 0.500 <= existing 0.500 in 2ftzA Bad short name: CH1 for alphabet: pdb_atoms Bad short name: CH1 for alphabet: pdb_atoms Bad short name: CH1 for alphabet: pdb_atoms Bad short name: CH1 for alphabet: pdb_atoms Bad short name: CH1 for alphabet: pdb_atoms Bad short name: CH1 for alphabet: pdb_atoms Skipped atom 1840, because occupancy 0.500 <= existing 0.500 in 2ftzA Skipped atom 1842, because occupancy 0.500 <= existing 0.500 in 2ftzA Skipped atom 1844, because occupancy 0.500 <= existing 0.500 in 2ftzA Skipped atom 1846, because occupancy 0.500 <= existing 0.500 in 2ftzA Skipped atom 1848, because occupancy 0.500 <= existing 0.500 in 2ftzA Skipped atom 1850, because occupancy 0.500 <= existing 0.500 in 2ftzA Skipped atom 1852, because occupancy 0.500 <= existing 0.500 in 2ftzA Skipped atom 1858, because occupancy 0.500 <= existing 0.500 in 2ftzA Skipped atom 1860, because occupancy 0.500 <= existing 0.500 in 2ftzA Skipped atom 1862, because occupancy 0.500 <= existing 0.500 in 2ftzA Skipped atom 1864, because occupancy 0.500 <= existing 0.500 in 2ftzA Skipped atom 1866, because occupancy 0.500 <= existing 0.500 in 2ftzA Skipped atom 1932, because occupancy 0.500 <= existing 0.500 in 2ftzA Skipped atom 1934, because occupancy 0.500 <= existing 0.500 in 2ftzA Skipped atom 1936, because occupancy 0.500 <= existing 0.500 in 2ftzA Skipped atom 1938, because occupancy 0.500 <= existing 0.500 in 2ftzA Skipped atom 1940, because occupancy 0.500 <= existing 0.500 in 2ftzA Skipped atom 2031, because occupancy 0.500 <= existing 0.500 in 2ftzA Skipped atom 2033, because occupancy 0.500 <= existing 0.500 in 2ftzA Skipped atom 2035, because occupancy 0.500 <= existing 0.500 in 2ftzA Skipped atom 2037, because occupancy 0.500 <= existing 0.500 in 2ftzA Skipped atom 2039, because occupancy 0.500 <= existing 0.500 in 2ftzA Bad short name: CH1 for alphabet: pdb_atoms Bad short name: CH1 for alphabet: pdb_atoms # T0367 read from 2ftzA/merged-good-all-a2m # 2ftzA read from 2ftzA/merged-good-all-a2m # adding 2ftzA to template set # found chain 2ftzA in template set Warning: unaligning (T0367)D2 because first residue in template chain is (2ftzA)H-3 Warning: unaligning (T0367)R7 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2ftzA)E4 Warning: unaligning (T0367)R9 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ftzA)E4 Warning: unaligning (T0367)A11 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ftzA)V6 Warning: unaligning (T0367)K54 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2ftzA)L56 Warning: unaligning (T0367)H56 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ftzA)L56 Warning: unaligning (T0367)Y95 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2ftzA)P89 Warning: unaligning (T0367)E97 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ftzA)P89 Warning: unaligning (T0367)N122 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2ftzA)I118 T0367 3 :ELEL 2ftzA -2 :HHHM T0367 12 :EKLVQ 2ftzA 7 :EERIR T0367 20 :KEFEMG 2ftzA 12 :EILRPG T0367 26 :LYERCCSTAYY 2ftzA 21 :LTEEAMLYSAT T0367 38 :MFHAAKAMLLGYGRDS 2ftzA 38 :RPLLVLTLGEDLGVEE T0367 57 :RGTIYLIWECRE 2ftzA 57 :LDVAVAVELFHT T0367 77 :CSKLSRAFDLREESDYGI 2ftzA 69 :ASLIHDDLPPIDNADFRR T0367 98 :VSKDLAIKILKD 2ftzA 95 :YGEDIALLAGDG T0367 113 :FVQKAKNAV 2ftzA 107 :LFFLAFSQI T0367 125 :R 2ftzA 119 :G Number of specific fragments extracted= 10 number of extra gaps= 0 total=88 Number of alignments=16 # 2ftzA read from 2ftzA/merged-good-all-a2m # found chain 2ftzA in template set Warning: unaligning (T0367)D2 because first residue in template chain is (2ftzA)H-3 Warning: unaligning (T0367)R7 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2ftzA)E4 Warning: unaligning (T0367)R9 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ftzA)E4 Warning: unaligning (T0367)A11 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ftzA)V6 Warning: unaligning (T0367)K54 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2ftzA)L56 Warning: unaligning (T0367)H56 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ftzA)L56 Warning: unaligning (T0367)Y95 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2ftzA)P89 Warning: unaligning (T0367)E97 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ftzA)P89 Warning: unaligning (T0367)N122 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2ftzA)I118 T0367 3 :ELEL 2ftzA -2 :HHHM T0367 12 :EKLVQ 2ftzA 7 :EERIR T0367 20 :KEFEMG 2ftzA 12 :EILRPG T0367 26 :LYERCCSTAYY 2ftzA 21 :LTEEAMLYSAT T0367 37 :AMFHAAKAMLLGYGRDS 2ftzA 37 :IRPLLVLTLGEDLGVEE T0367 57 :RGTIYLIWECRE 2ftzA 57 :LDVAVAVELFHT T0367 77 :CSKLSRAFDLREESDYGI 2ftzA 69 :ASLIHDDLPPIDNADFRR T0367 98 :VSKDLAIKILKD 2ftzA 95 :YGEDIALLAGDG T0367 113 :FVQKAKNAV 2ftzA 107 :LFFLAFSQI T0367 125 :R 2ftzA 119 :G Number of specific fragments extracted= 10 number of extra gaps= 0 total=98 Number of alignments=17 # 2ftzA read from 2ftzA/merged-good-all-a2m # found chain 2ftzA in template set Warning: unaligning (T0367)L4 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ftzA)I123 Warning: unaligning (T0367)K13 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2ftzA)L134 Warning: unaligning (T0367)V15 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ftzA)L134 Warning: unaligning (T0367)T33 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2ftzA)T164 Warning: unaligning (T0367)G48 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2ftzA)G180 Warning: unaligning (T0367)G50 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ftzA)G180 Warning: unaligning (T0367)D52 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ftzA)D182 Warning: unaligning (T0367)K54 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2ftzA)M186 Warning: unaligning (T0367)H56 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ftzA)M186 Warning: unaligning (T0367)G58 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ftzA)L188 Warning: unaligning (T0367)Y61 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2ftzA)F193 Warning: unaligning (T0367)I63 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ftzA)F193 Warning: unaligning (T0367)D75 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ftzA)D205 Warning: unaligning (T0367)L80 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2ftzA)E222 Warning: unaligning (T0367)S81 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ftzA)E222 Warning: unaligning (T0367)Y92 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ftzA)V224 Warning: unaligning (T0367)Y95 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2ftzA)V230 Warning: unaligning (T0367)V98 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ftzA)V230 Warning: unaligning (T0367)D101 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2ftzA)A235 Warning: unaligning (T0367)A103 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ftzA)A235 Warning: unaligning (T0367)K108 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2ftzA)Y242 Warning: unaligning (T0367)F113 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ftzA)Y242 Warning: unaligning (T0367)K118 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2ftzA)G249 Warning: unaligning (T0367)A120 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2ftzA)G249 T0367 5 :ELRIRKAE 2ftzA 124 :FEEFSETA T0367 16 :QDAKKEF 2ftzA 135 :LLGEAMD T0367 23 :EMGLYERCCS 2ftzA 152 :SQEMVERMYA T0367 35 :YYAMFHAAKAMLL 2ftzA 165 :GALFAFCFSAPFI T0367 53 :S 2ftzA 183 :H T0367 59 :TI 2ftzA 189 :LG T0367 64 :W 2ftzA 194 :G T0367 76 :DCSK 2ftzA 206 :ILGS T0367 93 :GI 2ftzA 225 :TL T0367 99 :SK 2ftzA 231 :GI T0367 104 :IKIL 2ftzA 236 :REMA T0367 114 :VQKA 2ftzA 243 :YEEV T0367 121 :VNK 2ftzA 250 :IES Number of specific fragments extracted= 13 number of extra gaps= 1 total=111 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v3wA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0367 read from 1v3wA/merged-good-all-a2m # 1v3wA read from 1v3wA/merged-good-all-a2m # found chain 1v3wA in training set T0367 96 :KEVSKDLAIKILKDAEIFVQKAKNAVNKNR 1v3wA 142 :RQLTEEEIEWTKKNAEIYVELAEKHIKGRK Number of specific fragments extracted= 1 number of extra gaps= 0 total=112 Number of alignments=19 # 1v3wA read from 1v3wA/merged-good-all-a2m # found chain 1v3wA in training set T0367 95 :YKEVSKDLAIKILKDAEIFVQKAKNAVNKNR 1v3wA 141 :VRQLTEEEIEWTKKNAEIYVELAEKHIKGRK Number of specific fragments extracted= 1 number of extra gaps= 0 total=113 Number of alignments=20 # 1v3wA read from 1v3wA/merged-good-all-a2m # found chain 1v3wA in training set T0367 98 :VSKDLAIKILKDAEIFVQKAKNAVNKNR 1v3wA 144 :LTEEEIEWTKKNAEIYVELAEKHIKGRK Number of specific fragments extracted= 1 number of extra gaps= 0 total=114 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1a17/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1a17 expands to /projects/compbio/data/pdb/1a17.pdb.gz 1a17:Warning: there is no chain 1a17 will retry with 1a17A # T0367 read from 1a17/merged-good-all-a2m # 1a17 read from 1a17/merged-good-all-a2m # adding 1a17 to template set # found chain 1a17 in template set T0367 7 :RIRKAEKLVQDAKKEFEMGLYERCCSTAYYAMFH 1a17 24 :ALKRAEELKTQANDYFKAKDYENAIKFYSQAIEL T0367 41 :AAKAMLLGYG 1a17 66 :GNRSLAYLRT T0367 54 :KTHRGTIYLIWECREE 1a17 76 :ECYGYALGDATRAIEL T0367 74 :DDDCSKLSRAF 1a17 92 :DKKYIKGYYRR T0367 85 :DL 1a17 104 :AS T0367 89 :ESDYG 1a17 106 :NMALG T0367 99 :SKDLAIKILKD 1a17 111 :KFRAALRDYET T0367 110 :AEIFVQKAKNAVNK 1a17 132 :AKMKYQECNKIVKQ Number of specific fragments extracted= 8 number of extra gaps= 0 total=122 Number of alignments=22 # 1a17 read from 1a17/merged-good-all-a2m # found chain 1a17 in template set T0367 7 :RIRKAEKLVQDAKKEFEMGLYERCCSTAYYAM 1a17 24 :ALKRAEELKTQANDYFKAKDYENAIKFYSQAI T0367 39 :FHAAKAMLLGYG 1a17 64 :YYGNRSLAYLRT T0367 54 :KTHRGTIYLIWECREELGLS 1a17 76 :ECYGYALGDATRAIELDKKY T0367 81 :SRAFDLREES 1a17 96 :IKGYYRRAAS T0367 91 :DYG 1a17 108 :ALG T0367 99 :SKDLAIKILKD 1a17 111 :KFRAALRDYET T0367 110 :AEIFVQKAKNAVNK 1a17 132 :AKMKYQECNKIVKQ Number of specific fragments extracted= 7 number of extra gaps= 0 total=129 Number of alignments=23 # 1a17 read from 1a17/merged-good-all-a2m # found chain 1a17 in template set T0367 8 :IRKAEKLVQDAKKEFEMGLYERCCSTAYYAMF 1a17 25 :LKRAEELKTQANDYFKAKDYENAIKFYSQAIE T0367 40 :HAAKAMLLGYG 1a17 65 :YGNRSLAYLRT T0367 54 :KTHRGTIYLIWECRE 1a17 76 :ECYGYALGDATRAIE T0367 73 :SDDDCSKLSRAFDLR 1a17 91 :LDKKYIKGYYRRAAS T0367 94 :IYKEVSKDLAIKILKDAEI 1a17 106 :NMALGKFRAALRDYETVVK T0367 113 :FVQKAKNAVNK 1a17 135 :KYQECNKIVKQ Number of specific fragments extracted= 6 number of extra gaps= 0 total=135 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wwpA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wwpA expands to /projects/compbio/data/pdb/1wwp.pdb.gz 1wwpA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0367 read from 1wwpA/merged-good-all-a2m # 1wwpA read from 1wwpA/merged-good-all-a2m # adding 1wwpA to template set # found chain 1wwpA in template set T0367 11 :AEKLVQDAKKEF 1wwpA 2 :AEKALATLKELA T0367 23 :EMGLYERCCSTAYYAMFHAAKAMLLGY 1wwpA 19 :SPVERDAAIQRFEYTFEAFWKALQAYL T0367 50 :GRDSKTHRGTIYLIWEC 1wwpA 50 :GLEGASPKGVIRLAREV T0367 71 :G 1wwpA 67 :G T0367 72 :LSDDDCSKLSRAFDLREESDYGI 1wwpA 69 :LRDEEARLALGMVDDRSLTVHTY T0367 99 :SKDLAIKILKDAEIFVQKAKNAVNKN 1wwpA 92 :NEPLARAIFRRLPDYARLMEQVLGRL Number of specific fragments extracted= 6 number of extra gaps= 0 total=141 Number of alignments=25 # 1wwpA read from 1wwpA/merged-good-all-a2m # found chain 1wwpA in template set T0367 11 :AEKLVQDAKKEFEMG 1wwpA 2 :AEKALATLKELAFLE T0367 26 :LYERCCSTAY 1wwpA 22 :ERDAAIQRFE T0367 36 :YAMFHAAKAMLLGY 1wwpA 35 :EAFWKALQAYLREK T0367 50 :GRDSKTHRGTIYLIWE 1wwpA 50 :GLEGASPKGVIRLARE T0367 70 :LG 1wwpA 66 :VG T0367 72 :LSDDDCSKLSRAFDLREESDYGI 1wwpA 69 :LRDEEARLALGMVDDRSLTVHTY T0367 99 :SKDLAIKILKDAEIFVQKAKNAVNKNR 1wwpA 92 :NEPLARAIFRRLPDYARLMEQVLGRLR Number of specific fragments extracted= 7 number of extra gaps= 0 total=148 Number of alignments=26 # 1wwpA read from 1wwpA/merged-good-all-a2m # found chain 1wwpA in template set T0367 11 :AEKLVQDAKKEF 1wwpA 2 :AEKALATLKELA T0367 23 :EMGLYERCCSTAYYAMFHAAKAM 1wwpA 19 :SPVERDAAIQRFEYTFEAFWKAL T0367 46 :LL 1wwpA 45 :LR T0367 48 :GYGRDSKTHRGTIYLIWE 1wwpA 48 :KEGLEGASPKGVIRLARE T0367 70 :LGLSDDDCSKLS 1wwpA 66 :VGLLRDEEARLA T0367 82 :RAFDLREE 1wwpA 79 :GMVDDRSL T0367 94 :IYKEVSKDLAIKILKDAEIFVQKAKNAVNK 1wwpA 87 :TVHTYNEPLARAIFRRLPDYARLMEQVLGR Number of specific fragments extracted= 7 number of extra gaps= 0 total=155 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1khyA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1khyA expands to /projects/compbio/data/pdb/1khy.pdb.gz 1khyA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0367 read from 1khyA/merged-good-all-a2m # 1khyA read from 1khyA/merged-good-all-a2m # adding 1khyA to template set # found chain 1khyA in template set Warning: unaligning (T0367)E89 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1khyA)Q82 Warning: unaligning (T0367)E97 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1khyA)Q82 T0367 2 :DELELRIRKAEKLVQ 1khyA 8 :NKFQLALADAQSLAL T0367 21 :EFEMGLY 1khyA 23 :GHDNQFI T0367 38 :MFHAAKAML 1khyA 31 :PLHLMSALL T0367 64 :WECREELGLSDDDC 1khyA 47 :SPLLTSAGINAGQL T0367 78 :SKLSRAF 1khyA 62 :TDINQAL T0367 85 :DLRE 1khyA 70 :RLPQ T0367 98 :VS 1khyA 83 :PS T0367 101 :DLAIKILKDAEIFVQK 1khyA 85 :QDLVRVLNLCDKLAQK Number of specific fragments extracted= 8 number of extra gaps= 0 total=163 Number of alignments=28 # 1khyA read from 1khyA/merged-good-all-a2m # found chain 1khyA in template set Warning: unaligning (T0367)S90 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1khyA)Q82 Warning: unaligning (T0367)E97 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1khyA)Q82 T0367 3 :ELELRIRKAEKL 1khyA 9 :KFQLALADAQSL T0367 19 :KKEFEMGLY 1khyA 21 :ALGHDNQFI T0367 38 :M 1khyA 31 :P T0367 40 :HAAKAMLLGYGRD 1khyA 32 :LHLMSALLNQEGG T0367 58 :GTIYLIWE 1khyA 45 :SVSPLLTS T0367 70 :LGLSD 1khyA 53 :AGINA T0367 75 :DDCSKLSRAFDLREE 1khyA 59 :QLRTDINQALNRLPQ T0367 98 :VS 1khyA 83 :PS T0367 101 :DLAIKILKDAEIFVQK 1khyA 85 :QDLVRVLNLCDKLAQK Number of specific fragments extracted= 9 number of extra gaps= 0 total=172 Number of alignments=29 # 1khyA read from 1khyA/merged-good-all-a2m # found chain 1khyA in template set Warning: unaligning (T0367)G93 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1khyA)Q82 Warning: unaligning (T0367)V98 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1khyA)Q82 T0367 2 :DELELRIRKAEKL 1khyA 8 :NKFQLALADAQSL T0367 19 :KKEFEMGLY 1khyA 21 :ALGHDNQFI T0367 38 :MFHAAKAMLLGYGRD 1khyA 31 :PLHLMSALLNQEGGS T0367 63 :IWECREELGLSDDDCSK 1khyA 46 :VSPLLTSAGINAGQLRT T0367 82 :RAFDLREESDY 1khyA 63 :DINQALNRLPQ T0367 99 :SKDLAIKILKDAEIFVQKA 1khyA 83 :PSQDLVRVLNLCDKLAQKR Number of specific fragments extracted= 6 number of extra gaps= 0 total=178 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ylmA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ylmA expands to /projects/compbio/data/pdb/1ylm.pdb.gz 1ylmA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0367 read from 1ylmA/merged-good-all-a2m # 1ylmA read from 1ylmA/merged-good-all-a2m # adding 1ylmA to template set # found chain 1ylmA in template set Warning: unaligning (T0367)E5 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ylmA)K11 Warning: unaligning (T0367)L6 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ylmA)K11 T0367 2 :DEL 1ylmA 7 :SKI T0367 7 :RIRKAEKLVQDA 1ylmA 12 :TLGFFEHQLALF T0367 19 :KKEFEM 1ylmA 35 :ELALQR T0367 26 :LYERCCSTAYYAMFHAAK 1ylmA 41 :IGHLLIECILDTGNDMID T0367 47 :LGYGRDSKTHRGTIYLI 1ylmA 59 :GFIMRDPGSYDDIMDIL T0367 68 :EELG 1ylmA 76 :VDEK T0367 72 :LSDDDCSKLSRAFDLREESD 1ylmA 81 :VTEKEGDELKKLIAYRKTLV T0367 93 :GIYKEVSKDLAIKILK 1ylmA 101 :QQYLLADSGELYRLIK T0367 109 :DAEIFVQKAKNAVNK 1ylmA 121 :ALQDFPKRIRSYLET Number of specific fragments extracted= 9 number of extra gaps= 1 total=187 Number of alignments=31 # 1ylmA read from 1ylmA/merged-good-all-a2m # found chain 1ylmA in template set Warning: unaligning (T0367)E5 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ylmA)K11 Warning: unaligning (T0367)L6 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ylmA)K11 T0367 2 :DEL 1ylmA 7 :SKI T0367 7 :RIRKAEKLVQDA 1ylmA 12 :TLGFFEHQLALF T0367 19 :KK 1ylmA 35 :EL T0367 26 :LYERCCSTAYYAMFHAAKAMLLGYG 1ylmA 37 :ALQRIGHLLIECILDTGNDMIDGFI T0367 51 :RDSKTHRGTIYLIW 1ylmA 63 :RDPGSYDDIMDILV T0367 69 :ELG 1ylmA 77 :DEK T0367 72 :LSDDDCSKLSRAFDLREES 1ylmA 81 :VTEKEGDELKKLIAYRKTL T0367 93 :GIYKEVSKDLAIKILK 1ylmA 101 :QQYLLADSGELYRLIK T0367 109 :DAEIFVQKAKNAVNK 1ylmA 121 :ALQDFPKRIRSYLET Number of specific fragments extracted= 9 number of extra gaps= 1 total=196 Number of alignments=32 # 1ylmA read from 1ylmA/merged-good-all-a2m # found chain 1ylmA in template set Warning: unaligning (T0367)E5 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ylmA)K11 Warning: unaligning (T0367)L6 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ylmA)K11 T0367 2 :DEL 1ylmA 7 :SKI T0367 7 :RIRKAEKLVQDA 1ylmA 12 :TLGFFEHQLALF T0367 19 :KKEF 1ylmA 35 :ELAL T0367 28 :ERCCSTAYYAMFHAAKAMLLGYGRDSKT 1ylmA 39 :QRIGHLLIECILDTGNDMIDGFIMRDPG T0367 56 :H 1ylmA 68 :Y T0367 65 :ECREELGLSDDDCSKLS 1ylmA 73 :DILVDEKVVTEKEGDEL T0367 82 :RAFDLREES 1ylmA 91 :KLIAYRKTL T0367 92 :YGIYKEVSKDLAIKILKD 1ylmA 100 :VQQYLLADSGELYRLIKA T0367 110 :AEIFVQKAKNAVN 1ylmA 122 :LQDFPKRIRSYLE Number of specific fragments extracted= 9 number of extra gaps= 1 total=205 Number of alignments=33 # 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 # T0367 read from 1gs5A/merged-good-all-a2m # 1gs5A read from 1gs5A/merged-good-all-a2m # found chain 1gs5A in training set T0367 17 :DAKKEFEMG 1gs5A 132 :LINSLLENG T0367 38 :MFHAAKAMLLGYGR 1gs5A 161 :ADQAATALAATLGA T0367 84 :FDLREESDYGIYKEVSKDLAIKILK 1gs5A 182 :VSGILDGKGQRIAEMTAAKAEQLIE Number of specific fragments extracted= 3 number of extra gaps= 0 total=208 Number of alignments=34 # 1gs5A read from 1gs5A/merged-good-all-a2m # found chain 1gs5A in training set T0367 17 :DAKKEFEMG 1gs5A 132 :LINSLLENG Number of specific fragments extracted= 1 number of extra gaps= 0 total=209 # 1gs5A read from 1gs5A/merged-good-all-a2m # found chain 1gs5A in training set T0367 17 :DAKKEFEMGLYERCCSTAYYAMFHAAKAM 1gs5A 200 :KAEQLIEQGIITDGMIVKVNAALDAARTL Number of specific fragments extracted= 1 number of extra gaps= 0 total=210 Number of alignments=35 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wolA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wolA expands to /projects/compbio/data/pdb/1wol.pdb.gz 1wolA:# T0367 read from 1wolA/merged-good-all-a2m # 1wolA read from 1wolA/merged-good-all-a2m # adding 1wolA to template set # found chain 1wolA in template set Warning: unaligning (T0367)F84 because of BadResidue code BAD_PEPTIDE in next template residue (1wolA)T81 Warning: unaligning (T0367)D85 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1wolA)P82 Warning: unaligning (T0367)V121 because of BadResidue code HAS_OXT+BAD_PEPTIDE in next template residue (1wolA)K122 T0367 1 :MDELELRIRKAEKLVQDAKKEFEMGLYERCCSTAYYAMFHAAKAMLLGYGRDSKTHR 1wolA 1 :MKRVEDWIKQAERDLEEARYAKSGGYYELACFLSQQCAEKAVKGLLQFQGIEKRGHS T0367 59 :TIYLI 1wolA 58 :ISHLL T0367 71 :GLSDD 1wolA 64 :NPPAD T0367 76 :DCSKLSRA 1wolA 72 :CATFLDKQ T0367 86 :LREESDYGIYKE 1wolA 83 :SRYPDVYYEGAP T0367 98 :VSKDLAIKILKDAEIFVQKAKNA 1wolA 98 :YTERDADECINCAIRILNWVKGQ Number of specific fragments extracted= 6 number of extra gaps= 3 total=216 Number of alignments=36 # 1wolA read from 1wolA/merged-good-all-a2m # found chain 1wolA in template set Warning: unaligning (T0367)R87 because of BadResidue code BAD_PEPTIDE in next template residue (1wolA)T81 Warning: unaligning (T0367)E88 because of BadResidue code BAD_PEPTIDE at template residue (1wolA)T81 Warning: unaligning (T0367)E89 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1wolA)P82 Warning: unaligning (T0367)V121 because of BadResidue code HAS_OXT+BAD_PEPTIDE in next template residue (1wolA)K122 T0367 1 :MDELELRIRKAEKLVQDAKKEFEMGLYERCCSTAYYAMFHAAKAMLLGYGRDSKTHR 1wolA 1 :MKRVEDWIKQAERDLEEARYAKSGGYYELACFLSQQCAEKAVKGLLQFQGIEKRGHS T0367 59 :TIYLI 1wolA 58 :ISHLL T0367 71 :GLSDDDCSKLSRAFDL 1wolA 64 :NPPADILQCATFLDKQ T0367 90 :SDYGIYKE 1wolA 83 :SRYPDVYY T0367 98 :VSKDLAIKILKDAEIFVQKAKNA 1wolA 98 :YTERDADECINCAIRILNWVKGQ Number of specific fragments extracted= 5 number of extra gaps= 2 total=221 Number of alignments=37 # 1wolA read from 1wolA/merged-good-all-a2m # found chain 1wolA in template set Warning: unaligning (T0367)C77 because of BadResidue code BAD_PEPTIDE in next template residue (1wolA)T81 Warning: unaligning (T0367)S78 because of BadResidue code BAD_PEPTIDE at template residue (1wolA)T81 Warning: unaligning (T0367)K79 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1wolA)P82 T0367 3 :ELELRIRKAEKLVQDAKKEFEMGLYERCCSTAYYAMFHAAKAMLLGYGRDSKTHRGTIYL 1wolA 3 :RVEDWIKQAERDLEEARYAKSGGYYELACFLSQQCAEKAVKGLLQFQGIEKRGHSISHLL T0367 65 :ECREELGLSDDD 1wolA 68 :DILQCATFLDKQ T0367 80 :LSRAFDLREESDYGIY 1wolA 83 :SRYPDVYYEGAPYEYY T0367 99 :SKDLAIKILKDAEIFVQKAKNA 1wolA 99 :TERDADECINCAIRILNWVKGQ Number of specific fragments extracted= 4 number of extra gaps= 1 total=225 Number of alignments=38 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sauA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0367 read from 1sauA/merged-good-all-a2m # 1sauA read from 1sauA/merged-good-all-a2m # found chain 1sauA in training set T0367 53 :SKTHRGTIYLIWECREELG 1sauA 47 :TEEHWKIIRYLRDYFIKYG T0367 72 :LSD 1sauA 67 :APP T0367 77 :CSKLSRAF 1sauA 70 :VRMLVKHC T0367 94 :IYKE 1sauA 80 :EVRP T0367 98 :VSKDLAIKI 1sauA 85 :CNLQYIYKL Number of specific fragments extracted= 5 number of extra gaps= 0 total=230 Number of alignments=39 # 1sauA read from 1sauA/merged-good-all-a2m # found chain 1sauA in training set T0367 54 :KTHRGTIYLIWECREELGLSD 1sauA 48 :EEHWKIIRYLRDYFIKYGVAP T0367 77 :CSKLSRAF 1sauA 70 :VRMLVKHC T0367 86 :L 1sauA 79 :K T0367 93 :GIYKEVSKDLAIKI 1sauA 80 :EVRPDCNLQYIYKL Number of specific fragments extracted= 4 number of extra gaps= 0 total=234 Number of alignments=40 # 1sauA read from 1sauA/merged-good-all-a2m # found chain 1sauA in training set T0367 101 :DLAIKILKDAEIFV 1sauA 48 :EEHWKIIRYLRDYF T0367 116 :KAKNAVNK 1sauA 72 :MLVKHCKK Number of specific fragments extracted= 2 number of extra gaps= 0 total=236 Number of alignments=41 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qhdA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1qhdA expands to /projects/compbio/data/pdb/1qhd.pdb.gz 1qhdA:Skipped atom 1767, because occupancy 0.500 <= existing 0.500 in 1qhdA Skipped atom 1769, because occupancy 0.500 <= existing 0.500 in 1qhdA Skipped atom 1771, because occupancy 0.500 <= existing 0.500 in 1qhdA Skipped atom 2271, because occupancy 0.500 <= existing 0.500 in 1qhdA Skipped atom 2273, because occupancy 0.500 <= existing 0.500 in 1qhdA Skipped atom 2275, because occupancy 0.500 <= existing 0.500 in 1qhdA Skipped atom 2277, because occupancy 0.500 <= existing 0.500 in 1qhdA Skipped atom 2279, because occupancy 0.500 <= existing 0.500 in 1qhdA Skipped atom 2281, because occupancy 0.500 <= existing 0.500 in 1qhdA Skipped atom 2283, because occupancy 0.500 <= existing 0.500 in 1qhdA Skipped atom 3111, because occupancy 0.500 <= existing 0.500 in 1qhdA Skipped atom 3113, because occupancy 0.500 <= existing 0.500 in 1qhdA Skipped atom 3138, because occupancy 0.500 <= existing 0.500 in 1qhdA Skipped atom 3140, because occupancy 0.500 <= existing 0.500 in 1qhdA # T0367 read from 1qhdA/merged-good-all-a2m # 1qhdA read from 1qhdA/merged-good-all-a2m # adding 1qhdA to template set # found chain 1qhdA in template set T0367 34 :AYYAMFHAAKAMLLG 1qhdA 3 :VLYSLSKTLKDARDK T0367 49 :YGRDSKTHRGTIYLIWECREELG 1qhdA 20 :EGTLYSNVSDLIQQFNQMIITMN T0367 72 :LS 1qhdA 54 :LP T0367 86 :LR 1qhdA 56 :IR T0367 88 :EESDYGIYKE 1qhdA 59 :WNFDFGLLGT T0367 98 :VSKDLAIKILKDAEIFVQKAKNAV 1qhdA 73 :LDANYVETARNTIDYFVDFVDNVC Number of specific fragments extracted= 6 number of extra gaps= 0 total=242 Number of alignments=42 # 1qhdA read from 1qhdA/merged-good-all-a2m # found chain 1qhdA in template set T0367 37 :AMFHAAKAM 1qhdA 3 :VLYSLSKTL T0367 46 :LLGY 1qhdA 14 :ARDK T0367 50 :GRDSKTHRGTIYLIWECREEL 1qhdA 21 :GTLYSNVSDLIQQFNQMIITM T0367 71 :G 1qhdA 43 :G T0367 86 :LREESDYGIYKE 1qhdA 57 :RNWNFDFGLLGT T0367 98 :VSKDLAIKILKDAEIFVQKAKNA 1qhdA 73 :LDANYVETARNTIDYFVDFVDNV Number of specific fragments extracted= 6 number of extra gaps= 0 total=248 Number of alignments=43 # 1qhdA read from 1qhdA/merged-good-all-a2m # found chain 1qhdA in template set T0367 15 :VQDAKKEF 1qhdA 11 :LKDARDKI T0367 48 :GYGRDSKTHRGTIYLIWECREELGLSDDDCSKLSRAFDLREESDYGI 1qhdA 19 :VEGTLYSNVSDLIQQFNQMIITMNGNEFQTGGIGNLPIRNWNFDFGL T0367 95 :YKEVS 1qhdA 70 :LLNLD T0367 100 :KDLAIKILKDAEIFVQKAK 1qhdA 78 :VETARNTIDYFVDFVDNVC Number of specific fragments extracted= 4 number of extra gaps= 0 total=252 Number of alignments=44 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gzsB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1gzsB expands to /projects/compbio/data/pdb/1gzs.pdb.gz 1gzsB:# T0367 read from 1gzsB/merged-good-all-a2m # 1gzsB read from 1gzsB/merged-good-all-a2m # adding 1gzsB to template set # found chain 1gzsB in template set T0367 2 :DELELRIRKAEKLV 1gzsB 81 :KVVKDFMLQTLNDI T0367 16 :QDAKK 1gzsB 98 :GSASK T0367 21 :EFEM 1gzsB 106 :YASQ T0367 27 :YERCCSTAYYAMFH 1gzsB 110 :TREAILSAVYSKNK T0367 41 :AAKAMLLGYGRDSK 1gzsB 125 :QCCNLLISKGINIA T0367 58 :GTIYLIWECREELGLS 1gzsB 139 :PFLQEIGEAAKNAGLP T0367 75 :D 1gzsB 160 :D T0367 76 :DCSKLSRAFDLREESDYG 1gzsB 172 :FITPLISSANSKYPRMFI T0367 99 :SKDLAIKILKDAEIFV 1gzsB 190 :NQHQQASFKIYAEKII T0367 115 :QKA 1gzsB 207 :TEV Number of specific fragments extracted= 10 number of extra gaps= 0 total=262 Number of alignments=45 # 1gzsB read from 1gzsB/merged-good-all-a2m # found chain 1gzsB in template set T0367 2 :DELELRI 1gzsB 81 :KVVKDFM T0367 12 :EKLVQD 1gzsB 88 :LQTLND T0367 18 :AKKEFEMG 1gzsB 96 :IRGSASKD T0367 26 :LYERCCSTAYYAMFHAAKA 1gzsB 106 :YASQTREAILSAVYSKNKD T0367 45 :MLLGYGRDS 1gzsB 129 :LLISKGINI T0367 57 :RGTIYLIWECREELGL 1gzsB 138 :APFLQEIGEAAKNAGL T0367 74 :D 1gzsB 169 :A T0367 75 :DDCSKLSRAFDLREESDYG 1gzsB 171 :PFITPLISSANSKYPRMFI T0367 99 :SKDLAIKILKDAEIFV 1gzsB 190 :NQHQQASFKIYAEKII T0367 115 :QKA 1gzsB 207 :TEV Number of specific fragments extracted= 10 number of extra gaps= 0 total=272 Number of alignments=46 # 1gzsB read from 1gzsB/merged-good-all-a2m # found chain 1gzsB in template set T0367 2 :DELELRIRKAEKLV 1gzsB 81 :KVVKDFMLQTLNDI T0367 16 :QDAKK 1gzsB 98 :GSASK T0367 21 :EFEMGLYERCCSTAYYAMFHAAKAMLLGYGRDS 1gzsB 105 :AYASQTREAILSAVYSKNKDQCCNLLISKGINI T0367 57 :RGTIYLIWECREELGLS 1gzsB 138 :APFLQEIGEAAKNAGLP T0367 74 :DDDCSKLS 1gzsB 158 :KNDVFTPS T0367 82 :RAFDLREESDYGIYKEVSKDLAIKILKDAE 1gzsB 176 :LISSANSKYPRMFINQHQQASFKIYAEKII Number of specific fragments extracted= 6 number of extra gaps= 0 total=278 Number of alignments=47 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vdrA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vdrA expands to /projects/compbio/data/pdb/1vdr.pdb.gz 1vdrA:# T0367 read from 1vdrA/merged-good-all-a2m # 1vdrA read from 1vdrA/merged-good-all-a2m # adding 1vdrA to template set # found chain 1vdrA in template set Warning: unaligning (T0367)G93 because of BadResidue code BAD_PEPTIDE in next template residue (1vdrA)V73 Warning: unaligning (T0367)I94 because of BadResidue code BAD_PEPTIDE at template residue (1vdrA)V73 T0367 87 :REESDY 1vdrA 66 :RSERSF T0367 95 :YKE 1vdrA 74 :DTA T0367 98 :VSKDLAIKILK 1vdrA 80 :ASVEEAVDIAA Number of specific fragments extracted= 3 number of extra gaps= 1 total=281 Number of alignments=48 # 1vdrA read from 1vdrA/merged-good-all-a2m # found chain 1vdrA in template set Warning: unaligning (T0367)G93 because of BadResidue code BAD_PEPTIDE in next template residue (1vdrA)V73 Warning: unaligning (T0367)I94 because of BadResidue code BAD_PEPTIDE at template residue (1vdrA)V73 T0367 87 :REESDY 1vdrA 66 :RSERSF T0367 95 :YKE 1vdrA 74 :DTA T0367 98 :VSKDLAIKILK 1vdrA 80 :ASVEEAVDIAA Number of specific fragments extracted= 3 number of extra gaps= 1 total=284 Number of alignments=49 # 1vdrA read from 1vdrA/merged-good-all-a2m # found chain 1vdrA in template set T0367 98 :VSKDLAIKILKD 1vdrA 80 :ASVEEAVDIAAS Number of specific fragments extracted= 1 number of extra gaps= 0 total=285 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kzhA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1kzhA expands to /projects/compbio/data/pdb/1kzh.pdb.gz 1kzhA:# T0367 read from 1kzhA/merged-good-all-a2m # 1kzhA read from 1kzhA/merged-good-all-a2m # adding 1kzhA to template set # found chain 1kzhA in template set Number of specific fragments extracted= 0 number of extra gaps= 0 total=285 # 1kzhA read from 1kzhA/merged-good-all-a2m # found chain 1kzhA in template set Warning: unaligning (T0367)Y92 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1kzhA)D140 Warning: unaligning (T0367)G93 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1kzhA)D140 T0367 32 :STAYYAMFHAAKAM 1kzhA 88 :HNVISGVFDAIKKF T0367 57 :RGTIYLIWE 1kzhA 111 :KGGPLGLLE T0367 70 :LG 1kzhA 120 :ND T0367 72 :LSDDDCS 1kzhA 125 :LTESLIN T0367 85 :DLREESD 1kzhA 132 :SYRNTGG T0367 94 :IYKE 1kzhA 141 :IVSS T0367 98 :VSKDLAIKILKDAEI 1kzhA 150 :ETEEHYNKALFVAKE Number of specific fragments extracted= 7 number of extra gaps= 1 total=292 Number of alignments=50 # 1kzhA read from 1kzhA/merged-good-all-a2m # found chain 1kzhA in template set T0367 106 :ILKDAEIFVQKAKN 1kzhA 227 :YSELIGNLCRDAMS Number of specific fragments extracted= 1 number of extra gaps= 0 total=293 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1na3A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0367 read from 1na3A/merged-good-all-a2m # 1na3A read from 1na3A/merged-good-all-a2m # found chain 1na3A in training set T0367 11 :AEKLVQDAKKEFEMGLYERCCSTAYYAMFH 1na3A 4 :AEAWYNLGNAYYKQGDYDEAIEYYQKALEL T0367 54 :KTHRGTIYLIWECREELG 1na3A 35 :PNNAEAWYNLGNAYYKQG T0367 99 :SKDLAIKILKDAEIF 1na3A 53 :DYDEAIEYYQKALEL T0367 117 :AKNAVNK 1na3A 74 :AKQDLGN Number of specific fragments extracted= 4 number of extra gaps= 0 total=297 Number of alignments=51 # 1na3A read from 1na3A/merged-good-all-a2m # found chain 1na3A in training set T0367 11 :AEKLVQDAKKEFEMGLYERCCSTAYYAMFH 1na3A 4 :AEAWYNLGNAYYKQGDYDEAIEYYQKALEL T0367 53 :SKTHRGTIYLIWECREELGLSDDDCSKLSRAFDLREES 1na3A 34 :DPNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPNN T0367 101 :DLAIKILKDAEI 1na3A 72 :AEAKQDLGNAKQ Number of specific fragments extracted= 3 number of extra gaps= 0 total=300 Number of alignments=52 # 1na3A read from 1na3A/merged-good-all-a2m # found chain 1na3A in training set T0367 11 :AEKLVQDAKKEFEMGLYERCCSTAYYAMFH 1na3A 4 :AEAWYNLGNAYYKQGDYDEAIEYYQKALEL T0367 53 :SKTHRGTIYLIWECREELG 1na3A 34 :DPNNAEAWYNLGNAYYKQG T0367 99 :SKDLAIKILKDAEIF 1na3A 53 :DYDEAIEYYQKALEL T0367 117 :AKNAVNK 1na3A 74 :AKQDLGN Number of specific fragments extracted= 4 number of extra gaps= 0 total=304 Number of alignments=53 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t0qA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1t0qA expands to /projects/compbio/data/pdb/1t0q.pdb.gz 1t0qA:# T0367 read from 1t0qA/merged-good-all-a2m # 1t0qA read from 1t0qA/merged-good-all-a2m # adding 1t0qA to template set # found chain 1t0qA in template set Warning: unaligning (T0367)D74 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1t0qA)P314 Warning: unaligning (T0367)R87 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1t0qA)P340 Warning: unaligning (T0367)E88 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1t0qA)P340 T0367 21 :EFEMGLYERCCSTAYYAMFHAAKAMLLGY 1t0qA 245 :LVENGKKDEAQQMVDVAIWRSWKLFSVLT T0367 50 :GRDSKT 1t0qA 280 :YTPLES T0367 57 :RGTIYLIWECREELGLS 1t0qA 296 :EWIVAQFERQLLDLGLD T0367 75 :DDCSK 1t0qA 318 :DQFMQ T0367 80 :LSRAF 1t0qA 324 :LDETH T0367 89 :ESDYGIYKEVSKDLAIKI 1t0qA 341 :TVWWDPAAGVSPEEREWL T0367 107 :LKDAEIFVQKAKNAVNKNR 1t0qA 366 :NDTWGQCWDVITDNLVNGK Number of specific fragments extracted= 7 number of extra gaps= 2 total=311 Number of alignments=54 # 1t0qA read from 1t0qA/merged-good-all-a2m # found chain 1t0qA in template set Warning: unaligning (T0367)D74 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1t0qA)P314 Warning: unaligning (T0367)R87 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1t0qA)P340 Warning: unaligning (T0367)E88 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1t0qA)P340 T0367 21 :EFEMGLYERCCSTAYYAMFHAAKAMLL 1t0qA 245 :LVENGKKDEAQQMVDVAIWRSWKLFSV T0367 48 :GYGRDSKTHR 1t0qA 278 :DYYTPLESRN T0367 58 :GTIYLIWECREELGLS 1t0qA 297 :WIVAQFERQLLDLGLD T0367 75 :DDCSKLSRAFDL 1t0qA 315 :WYWDQFMQDLDE T0367 89 :ESDYGIYKEVSKDLAIKI 1t0qA 341 :TVWWDPAAGVSPEEREWL T0367 107 :LKDAEIFVQKAKNAVNKNR 1t0qA 366 :NDTWGQCWDVITDNLVNGK Number of specific fragments extracted= 6 number of extra gaps= 2 total=317 Number of alignments=55 # 1t0qA read from 1t0qA/merged-good-all-a2m # found chain 1t0qA in template set Warning: unaligning (T0367)D74 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1t0qA)P314 Warning: unaligning (T0367)D75 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1t0qA)P314 Warning: unaligning (T0367)R87 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1t0qA)P340 Warning: unaligning (T0367)E88 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1t0qA)P340 T0367 22 :FEMGLYERCCSTAYYAMFHAAKAMLLGY 1t0qA 246 :VENGKKDEAQQMVDVAIWRSWKLFSVLT T0367 50 :GRDSKTHRGTIYL 1t0qA 282 :PLESRNQSFKEFM T0367 63 :IWECREELGLS 1t0qA 302 :FERQLLDLGLD T0367 76 :DCSKLS 1t0qA 315 :WYWDQF T0367 82 :R 1t0qA 323 :D T0367 83 :AFDL 1t0qA 335 :VWYW T0367 89 :ESDYGIYKEVSKDLAIK 1t0qA 344 :WDPAAGVSPEEREWLEE T0367 106 :ILKDAEIFVQKAKNAVNKNR 1t0qA 365 :WNDTWGQCWDVITDNLVNGK Number of specific fragments extracted= 8 number of extra gaps= 2 total=325 Number of alignments=56 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ufbA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ufbA expands to /projects/compbio/data/pdb/1ufb.pdb.gz 1ufbA:# T0367 read from 1ufbA/merged-good-all-a2m # 1ufbA read from 1ufbA/merged-good-all-a2m # adding 1ufbA to template set # found chain 1ufbA in template set T0367 3 :ELELRIRKAEKLVQDAKKEFEMGLYERCCSTAYYAMFHAAKAMLLGYGRDSKTHR 1ufbA 3 :RARDWLEQARHNLRHAQGSLGLGDYAWACFAAQQAAEAALKGLHLARGQVAWGHS T0367 59 :TIYLIWECREELGLSDDDC 1ufbA 58 :ILDLLADLPEDVDVPEDLV T0367 78 :SKLSRAF 1ufbA 80 :KVLDKYY T0367 85 :DLREESDYGIYKE 1ufbA 88 :PTRYPDAHPAGPA T0367 98 :VSKDLAIKILKDAEIFVQKAKNA 1ufbA 104 :YTRLEAEEALDLAQKILAFVEEK Number of specific fragments extracted= 5 number of extra gaps= 0 total=330 Number of alignments=57 # 1ufbA read from 1ufbA/merged-good-all-a2m # found chain 1ufbA in template set T0367 3 :ELELRIRKAEKLVQDAKKEFEMGLYERCCSTAYYAMFHAAKAMLLGYGRDSKTHR 1ufbA 3 :RARDWLEQARHNLRHAQGSLGLGDYAWACFAAQQAAEAALKGLHLARGQVAWGHS T0367 59 :TIYLIWECREELGLSDDD 1ufbA 58 :ILDLLADLPEDVDVPEDL T0367 77 :CSKLSRAF 1ufbA 79 :AKVLDKYY T0367 85 :DLREESDYGIYKE 1ufbA 88 :PTRYPDAHPAGPA T0367 98 :VSKDLAIKILKDAEIFVQKAKNA 1ufbA 104 :YTRLEAEEALDLAQKILAFVEEK Number of specific fragments extracted= 5 number of extra gaps= 0 total=335 Number of alignments=58 # 1ufbA read from 1ufbA/merged-good-all-a2m # found chain 1ufbA in template set T0367 3 :ELELRIRKAEKLVQDAKKEFEMGLYERCCSTAYYAMFHAAKAMLLGYGRDSKTHRGTIYLIW 1ufbA 3 :RARDWLEQARHNLRHAQGSLGLGDYAWACFAAQQAAEAALKGLHLARGQVAWGHSILDLLAD T0367 65 :ECREELGLSDDDCSKLSRAFDLREE 1ufbA 74 :DLVEAAKVLDKYYIPTRYPDAHPAG T0367 91 :DYG 1ufbA 99 :PAA T0367 96 :KEVSKDLAIKILKDAEIFVQKAKNA 1ufbA 102 :RHYTRLEAEEALDLAQKILAFVEEK Number of specific fragments extracted= 4 number of extra gaps= 0 total=339 Number of alignments=59 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xx1A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0367 read from 1xx1A/merged-good-all-a2m # 1xx1A read from 1xx1A/merged-good-all-a2m # found chain 1xx1A in training set T0367 34 :AYYAMFHAAKAMLLGY 1xx1A 102 :VRPAGENVAKELLQNY T0367 52 :DSKT 1xx1A 120 :NGNN T0367 56 :HRGTIYLIWECREELGL 1xx1A 138 :HYEFVRGFKEVLKKEGH T0367 74 :DDDCSK 1xx1A 155 :EDLLEK T0367 93 :GIYKE 1xx1A 167 :GPYLP T0367 98 :VSKDLAIKILKDA 1xx1A 174 :PTLDATHEAYKKA T0367 111 :EIFVQKAKNAVNK 1xx1A 207 :MARLKEAIKSRDS Number of specific fragments extracted= 7 number of extra gaps= 0 total=346 Number of alignments=60 # 1xx1A read from 1xx1A/merged-good-all-a2m # found chain 1xx1A in training set T0367 26 :LYE 1xx1A 101 :QVR T0367 36 :YAMFHAAKAMLLGY 1xx1A 104 :PAGENVAKELLQNY T0367 52 :DSKTHRGTIYLIWECREELGLS 1xx1A 134 :PDIGHYEFVRGFKEVLKKEGHE T0367 75 :DDCS 1xx1A 156 :DLLE T0367 92 :Y 1xx1A 165 :F T0367 93 :GIYKE 1xx1A 167 :GPYLP T0367 98 :VSKDLAIKILKDA 1xx1A 174 :PTLDATHEAYKKA T0367 111 :EIFVQKAKNAVNK 1xx1A 207 :MARLKEAIKSRDS Number of specific fragments extracted= 8 number of extra gaps= 0 total=354 Number of alignments=61 # 1xx1A read from 1xx1A/merged-good-all-a2m # found chain 1xx1A in training set T0367 35 :YYAMFHAAKAMLLGY 1xx1A 103 :RPAGENVAKELLQNY T0367 52 :DSKTHRGTIYLIWECREELGLSD 1xx1A 134 :PDIGHYEFVRGFKEVLKKEGHED T0367 76 :DCSKLS 1xx1A 159 :EKVGYD T0367 90 :SDYGIYKEVSKDLAIKILKDA 1xx1A 166 :SGPYLPSLPTLDATHEAYKKA T0367 111 :EIFVQKAKNAVNKN 1xx1A 207 :MARLKEAIKSRDSA Number of specific fragments extracted= 5 number of extra gaps= 0 total=359 Number of alignments=62 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o3uA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0367 read from 1o3uA/merged-good-all-a2m # 1o3uA read from 1o3uA/merged-good-all-a2m # found chain 1o3uA in training set Warning: unaligning (T0367)R87 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1o3uA)D86 Warning: unaligning (T0367)I94 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1o3uA)D86 Warning: unaligning (T0367)N124 because last residue in template chain is (1o3uA)I123 T0367 7 :RIRKAEKLVQDAKKEFEMGLYERCCSTAYYAMFHAAKAMLLGYGRDSKTHR 1o3uA 0 :HMDAAKDDLEHAKHDLEHGFYNWACFSSQQAAEKAVKAVFQRMGAQAWGYS T0367 59 :TIYLIWECREELGLSDDDCSKLSRAFDL 1o3uA 51 :VPDFLGELSSRFEIPEELMDHALELDKA T0367 95 :YKE 1o3uA 87 :ALP T0367 98 :VSKDLAIKILKDAEIFVQKAKNAVNK 1o3uA 97 :YSRIEAERLVNYAEKIIRFCEDLLSR Number of specific fragments extracted= 4 number of extra gaps= 0 total=363 Number of alignments=63 # 1o3uA read from 1o3uA/merged-good-all-a2m # found chain 1o3uA in training set Warning: unaligning (T0367)R87 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1o3uA)D86 Warning: unaligning (T0367)I94 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1o3uA)D86 T0367 7 :RIRKAEKLVQDAKKEFEMGLYERCCSTAYYAMFHAAKAMLLGYGRDSKTHR 1o3uA 0 :HMDAAKDDLEHAKHDLEHGFYNWACFSSQQAAEKAVKAVFQRMGAQAWGYS T0367 59 :TIYLIWECREELGLSDDDCSKLSRAFDL 1o3uA 51 :VPDFLGELSSRFEIPEELMDHALELDKA T0367 95 :YKE 1o3uA 87 :ALP T0367 98 :VSKDLAIKILKDAEIFVQKAKNAVNK 1o3uA 97 :YSRIEAERLVNYAEKIIRFCEDLLSR Number of specific fragments extracted= 4 number of extra gaps= 0 total=367 Number of alignments=64 # 1o3uA read from 1o3uA/merged-good-all-a2m # found chain 1o3uA in training set Warning: unaligning (T0367)E88 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1o3uA)D86 Warning: unaligning (T0367)N124 because last residue in template chain is (1o3uA)I123 T0367 7 :RIRKAEKLVQDAKKEFEMGLYERCCSTAYYAMFHAAKAMLLGYGRDSKTHRG 1o3uA 0 :HMDAAKDDLEHAKHDLEHGFYNWACFSSQQAAEKAVKAVFQRMGAQAWGYSV T0367 60 :IYLIWECREELGLSDDDCSKLS 1o3uA 52 :PDFLGELSSRFEIPEELMDHAL T0367 89 :ESDYGI 1o3uA 87 :ALPSGS T0367 95 :YKEVSKDLAIKILKDAEIFVQKAKNAVNK 1o3uA 94 :RNRYSRIEAERLVNYAEKIIRFCEDLLSR Number of specific fragments extracted= 4 number of extra gaps= 0 total=371 Number of alignments=65 # command:# PrintAlignmentsContacts allconstraints.under Using radius: 8.0000 NUMB_ALIGNS: 65 Done printing distance constraints # command: