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/T0373/ # command:# Making conformation for sequence T0373 numbered 1 through 147 Created new target T0373 from T0373.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0373/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0373//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0373/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0373//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0373/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0373/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0373/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hw5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1hw5A expands to /projects/compbio/data/pdb/1hw5.pdb.gz 1hw5A:Skipped atom 179, because occupancy 0.5 <= existing 0.500 in 1hw5A Skipped atom 181, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 183, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 185, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 187, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 302, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 304, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 306, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 308, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 310, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 408, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 410, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 412, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 414, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 649, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 651, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 653, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 655, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 657, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 715, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 717, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 719, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 721, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 723, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 725, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 727, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1001, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1003, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1005, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1007, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1009, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1011, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1013, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1076, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1078, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1080, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1082, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1084, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1375, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1377, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1379, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1381, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1383, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1385, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1387, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1474, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1476, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1478, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1480, because occupancy 0.500 <= existing 0.500 in 1hw5A Skipped atom 1482, because occupancy 0.500 <= existing 0.500 in 1hw5A # T0373 read from 1hw5A/merged-good-all-a2m # 1hw5A read from 1hw5A/merged-good-all-a2m # adding 1hw5A to template set # found chain 1hw5A in template set Warning: unaligning (T0373)R63 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1hw5A)R180 Warning: unaligning (T0373)S64 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1hw5A)R180 T0373 8 :QLAAHLRSQVTTLTRRLRR 1hw5A 111 :DILMRLSAQMARRLQVLAE # choosing archetypes in rotamer library T0373 27 :EAQADPVQFSQLVVLGAIDRLGG 1hw5A 133 :NLAFLDVTGRIAQTLLNLAKQPD T0373 50 :D 1hw5A 160 :P T0373 51 :VTPSELAAAERM 1hw5A 167 :ITRQEIGQIVGC T0373 65 :SNLAALLRELERGGLIV 1hw5A 181 :ETVGRILKMLEDQNLIS Number of specific fragments extracted= 5 number of extra gaps= 1 total=5 Number of alignments=1 # 1hw5A read from 1hw5A/merged-good-all-a2m # found chain 1hw5A in template set Warning: unaligning (T0373)R63 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1hw5A)R180 Warning: unaligning (T0373)S64 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1hw5A)R180 T0373 4 :NQDLQLAAHLRSQVTTLTRRLRREAQADPVQFSQLVVLGAIDRLG 1hw5A 110 :PDILMRLSAQMARRLQVLAEKVGNLAFLDVTGRIAQTLLNLAKQP T0373 51 :VTPSELAAAERM 1hw5A 167 :ITRQEIGQIVGC T0373 65 :SNLAALLRELERGGLIVR 1hw5A 181 :ETVGRILKMLEDQNLISA Number of specific fragments extracted= 3 number of extra gaps= 1 total=8 Number of alignments=2 # 1hw5A read from 1hw5A/merged-good-all-a2m # found chain 1hw5A in template set Warning: unaligning (T0373)R63 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1hw5A)R180 Warning: unaligning (T0373)S64 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1hw5A)R180 T0373 4 :NQDLQLAAHLRSQVTTLTRRLRREAQADPVQFSQLVVLGAIDRLGG 1hw5A 110 :PDILMRLSAQMARRLQVLAEKVGNLAFLDVTGRIAQTLLNLAKQPD T0373 51 :VTPSELAAAERM 1hw5A 167 :ITRQEIGQIVGC T0373 65 :SNLAALLRELERGGLIVRH 1hw5A 181 :ETVGRILKMLEDQNLISAH Number of specific fragments extracted= 3 number of extra gaps= 1 total=11 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2eshA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2eshA expands to /projects/compbio/data/pdb/2esh.pdb.gz 2eshA:Skipped atom 109, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 111, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 113, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 115, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 117, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 119, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 121, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 401, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 403, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 405, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 407, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 409, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 411, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 413, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 415, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 417, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 419, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 421, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 631, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 633, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 635, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 637, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 639, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 641, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 643, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 645, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 647, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 649, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 651, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 786, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 788, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 790, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 792, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 794, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 796, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 798, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 800, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 802, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 955, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 957, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 959, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 961, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 963, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 965, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 967, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 969, because occupancy 0.500 <= existing 0.500 in 2eshA Skipped atom 971, because occupancy 0.500 <= existing 0.500 in 2eshA # T0373 read from 2eshA/merged-good-all-a2m # 2eshA read from 2eshA/merged-good-all-a2m # adding 2eshA to template set # found chain 2eshA in template set Warning: unaligning (T0373)P2 because first residue in template chain is (2eshA)R4 Warning: unaligning (T0373)Q8 because of BadResidue code BAD_PEPTIDE in next template residue (2eshA)G11 Warning: unaligning (T0373)L9 because of BadResidue code BAD_PEPTIDE at template residue (2eshA)G11 Warning: unaligning (T0373)Q34 because of BadResidue code BAD_PEPTIDE in next template residue (2eshA)I43 Warning: unaligning (T0373)L47 because of BadResidue code BAD_PEPTIDE at template residue (2eshA)I43 Warning: unaligning (T0373)T52 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2eshA)H48 Warning: unaligning (T0373)R63 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2eshA)H48 Warning: unaligning (T0373)S64 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2eshA)M49 Warning: unaligning (T0373)S65 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2eshA)G50 Warning: unaligning (T0373)N66 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2eshA)N51 Warning: unaligning (T0373)L70 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2eshA)L56 Warning: unaligning (T0373)L71 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2eshA)L56 Warning: unaligning (T0373)S97 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2eshA)P84 Warning: unaligning (T0373)S98 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2eshA)P84 T0373 3 :TNQDL 2eshA 5 :GGRGF T0373 10 :AAHLRSQVTTLTR 2eshA 12 :WWLASTILLLVAE T0373 23 :RLRREAQADPV 2eshA 31 :ELAERLAEFGI T0373 48 :GG 2eshA 44 :PG T0373 51 :V 2eshA 46 :I T0373 67 :LAA 2eshA 52 :IYR T0373 72 :RELERGGLIVRHADPQ 2eshA 57 :ADLEESGFLSTEWDTT T0373 88 :DGRRTRVSL 2eshA 74 :SPPRKIYRI T0373 99 :EGRRNLYGNRAKREE 2eshA 85 :QGKLYLREILRSLED T0373 115 :LVRAM 2eshA 100 :MKRRI T0373 129 :ALLAA 2eshA 105 :ETLEE T0373 137 :LLTR 2eshA 110 :RIKR Number of specific fragments extracted= 12 number of extra gaps= 5 total=23 Number of alignments=4 # 2eshA read from 2eshA/merged-good-all-a2m # found chain 2eshA in template set Warning: unaligning (T0373)R63 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2eshA)H48 Warning: unaligning (T0373)S64 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2eshA)H48 Warning: unaligning (T0373)S65 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2eshA)G50 Warning: unaligning (T0373)N66 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2eshA)N51 Warning: unaligning (T0373)L70 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2eshA)L56 Warning: unaligning (T0373)L71 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2eshA)L56 Warning: unaligning (T0373)S97 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2eshA)P84 Warning: unaligning (T0373)S98 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2eshA)P84 T0373 35 :FSQLVVLGAIDR 2eshA 13 :WLASTILLLVAE T0373 49 :GDVTPSELAAAE 2eshA 25 :KPSHGYELAERL T0373 61 :RM 2eshA 45 :GI T0373 67 :LAA 2eshA 52 :IYR T0373 72 :RELERGGLIVRHADPQ 2eshA 57 :ADLEESGFLSTEWDTT T0373 88 :DGRRTRVSL 2eshA 74 :SPPRKIYRI T0373 99 :EGRRNLYGNRAKREEWLVRAM 2eshA 85 :QGKLYLREILRSLEDMKRRIE T0373 130 :LLAA 2eshA 106 :TLEE T0373 137 :LLT 2eshA 110 :RIK Number of specific fragments extracted= 9 number of extra gaps= 4 total=32 Number of alignments=5 # 2eshA read from 2eshA/merged-good-all-a2m # found chain 2eshA in template set Warning: unaligning (T0373)Q8 because of BadResidue code BAD_PEPTIDE in next template residue (2eshA)G11 Warning: unaligning (T0373)L9 because of BadResidue code BAD_PEPTIDE at template residue (2eshA)G11 Warning: unaligning (T0373)Q34 because of BadResidue code BAD_PEPTIDE in next template residue (2eshA)I43 Warning: unaligning (T0373)G48 because of BadResidue code BAD_PEPTIDE at template residue (2eshA)I43 Warning: unaligning (T0373)T52 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2eshA)H48 Warning: unaligning (T0373)R63 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2eshA)H48 Warning: unaligning (T0373)S64 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2eshA)M49 Warning: unaligning (T0373)S65 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2eshA)G50 Warning: unaligning (T0373)N66 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2eshA)N51 Warning: unaligning (T0373)L70 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2eshA)L56 Warning: unaligning (T0373)L71 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2eshA)L56 Warning: unaligning (T0373)S97 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2eshA)P84 Warning: unaligning (T0373)S98 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2eshA)P84 T0373 10 :AAHLRSQVTTLT 2eshA 12 :WWLASTILLLVA T0373 22 :RRLRREAQADPV 2eshA 30 :YELAERLAEFGI T0373 49 :GDV 2eshA 44 :PGI T0373 67 :LAA 2eshA 52 :IYR T0373 72 :RELERGGLIVRHADPQ 2eshA 57 :ADLEESGFLSTEWDTT T0373 88 :DGRRTRVSL 2eshA 74 :SPPRKIYRI T0373 99 :EGRRNLYGNRAKREEWLVR 2eshA 85 :QGKLYLREILRSLEDMKRR T0373 128 :RALLAAAGPL 2eshA 104 :IETLEERIKR Number of specific fragments extracted= 8 number of extra gaps= 5 total=40 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r1tA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0373 read from 1r1tA/merged-good-all-a2m # 1r1tA read from 1r1tA/merged-good-all-a2m # found chain 1r1tA in training set T0373 18 :TTLTRRLRREAQ 1r1tA 33 :AQSLAEFFAVLA T0373 34 :QFSQLVVLGAIDR 1r1tA 45 :DPNRLRLLSLLAR T0373 48 :GG 1r1tA 58 :SE T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHAD 1r1tA 60 :LCVGDLAQAIGVSESAVSHQLRSLRNLRLVSYRKQ T0373 89 :GRRTRVSLS 1r1tA 95 :GRHVYYQLQ T0373 98 :SEGRRNLYGNRAK 1r1tA 105 :HHIVALYQNALDH Number of specific fragments extracted= 6 number of extra gaps= 0 total=46 Number of alignments=7 # 1r1tA read from 1r1tA/merged-good-all-a2m # found chain 1r1tA in training set T0373 1 :MPTNQDL 1r1tA 26 :QAIAPEV T0373 18 :TTLTRRLRREAQ 1r1tA 33 :AQSLAEFFAVLA T0373 34 :QFSQLVVLGAIDR 1r1tA 45 :DPNRLRLLSLLAR T0373 49 :GDVTPSELAAAERMRSSNLAALLRELERGGLIVRHAD 1r1tA 58 :SELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSYRKQ T0373 89 :GRRTRVSLS 1r1tA 95 :GRHVYYQLQ T0373 98 :SEGRRNLYGNRAK 1r1tA 105 :HHIVALYQNALDH Number of specific fragments extracted= 6 number of extra gaps= 0 total=52 Number of alignments=8 # 1r1tA read from 1r1tA/merged-good-all-a2m # found chain 1r1tA in training set T0373 18 :TTLTRRLRREAQ 1r1tA 33 :AQSLAEFFAVLA T0373 34 :QFSQLVVLGAIDR 1r1tA 45 :DPNRLRLLSLLAR T0373 49 :GDVTPSELAAAERMRSSNLAALLRELERGGLIVRHA 1r1tA 58 :SELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSYRK T0373 88 :DGRRTRVSLSSE 1r1tA 94 :QGRHVYYQLQDH T0373 106 :GNRAKREEWLVR 1r1tA 106 :HIVALYQNALDH Number of specific fragments extracted= 5 number of extra gaps= 0 total=57 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2a61A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2a61A expands to /projects/compbio/data/pdb/2a61.pdb.gz 2a61A:Skipped atom 654, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 656, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 658, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 660, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 662, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 664, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 666, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 668, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 670, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 672, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 674, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 920, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 922, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 924, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 926, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 928, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 930, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 932, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 934, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 1079, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 1081, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 1083, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 1085, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 1087, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 1089, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 1091, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 1093, because occupancy 0.500 <= existing 0.500 in 2a61A # T0373 read from 2a61A/merged-good-all-a2m # 2a61A read from 2a61A/merged-good-all-a2m # adding 2a61A to template set # found chain 2a61A in template set Warning: unaligning (T0373)T3 because first residue in template chain is (2a61A)K5 T0373 4 :NQDLQL 2a61A 6 :QPFERI T0373 13 :LRSQVTTLTRRLRREAQADPVQFSQLVVLGAIDRLGG 2a61A 12 :LREICFMVKVEGRKVLRDFGITPAQFDILQKIYFEGP T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREE 2a61A 49 :KRPGELSVLLGVAKSTVTGLVKRLEADGYLTRTPDPADRRAYFLVITRKGEEVIEKVIERREN T0373 115 :LVRAMHACLDESERALLAAAGPLLTRLAQ 2a61A 112 :FIEKITSDLGKEKSSKILDYLKELKGVME Number of specific fragments extracted= 4 number of extra gaps= 0 total=61 Number of alignments=10 # 2a61A read from 2a61A/merged-good-all-a2m # found chain 2a61A in template set Warning: unaligning (T0373)D6 because first residue in template chain is (2a61A)K5 T0373 7 :LQLAAHLRSQVTTLTRRLRREAQADPVQFSQLVVLGAIDR 2a61A 6 :QPFERILREICFMVKVEGRKVLRDFGITPAQFDILQKIYF T0373 48 :GGDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREEWLVRAM 2a61A 46 :EGPKRPGELSVLLGVAKSTVTGLVKRLEADGYLTRTPDPADRRAYFLVITRKGEEVIEKVIERRENFIEKIT T0373 121 :ACLDESERALLAAAGPLLTRLAQF 2a61A 118 :SDLGKEKSSKILDYLKELKGVMER Number of specific fragments extracted= 3 number of extra gaps= 0 total=64 Number of alignments=11 # 2a61A read from 2a61A/merged-good-all-a2m # found chain 2a61A in template set T0373 11 :AHLRSQVTTLTRRLRREAQADPVQFSQLVVLGAIDR 2a61A 10 :RILREICFMVKVEGRKVLRDFGITPAQFDILQKIYF T0373 48 :GGDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREEWLVR 2a61A 46 :EGPKRPGELSVLLGVAKSTVTGLVKRLEADGYLTRTPDPADRRAYFLVITRKGEEVIEKVIERRENFIEK T0373 119 :MHACLDESERALLAAAGPLLTRLAQ 2a61A 116 :ITSDLGKEKSSKILDYLKELKGVME Number of specific fragments extracted= 3 number of extra gaps= 0 total=67 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1smtA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1smtA expands to /projects/compbio/data/pdb/1smt.pdb.gz 1smtA:# T0373 read from 1smtA/merged-good-all-a2m # 1smtA read from 1smtA/merged-good-all-a2m # adding 1smtA to template set # found chain 1smtA in template set T0373 18 :TTLTRRLRREAQ 1smtA 33 :AQSLAEFFAVLA T0373 34 :QFSQLVVLGAIDR 1smtA 45 :DPNRLRLLSLLAR T0373 48 :GG 1smtA 58 :SE T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHAD 1smtA 60 :LCVGDLAQAIGVSESAVSHQLRSLRNLRLVSYRKQ T0373 89 :GRRTRVSLS 1smtA 95 :GRHVYYQLQ T0373 98 :SEGRRNLYGNRAKREE 1smtA 105 :HHIVALYQNALDHLQE Number of specific fragments extracted= 6 number of extra gaps= 0 total=73 Number of alignments=13 # 1smtA read from 1smtA/merged-good-all-a2m # found chain 1smtA in template set T0373 2 :PTNQDL 1smtA 27 :AIAPEV T0373 18 :TTLTRRLRREAQ 1smtA 33 :AQSLAEFFAVLA T0373 34 :QFSQLVVLGAID 1smtA 45 :DPNRLRLLSLLA T0373 48 :GGDVTPSELAAAERMRSSNLAALLRELERGGLIVRHAD 1smtA 57 :RSELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSYRKQ T0373 89 :GRRTRVSLS 1smtA 95 :GRHVYYQLQ T0373 98 :SEGRRNLYGNRAKREE 1smtA 105 :HHIVALYQNALDHLQE Number of specific fragments extracted= 6 number of extra gaps= 0 total=79 Number of alignments=14 # 1smtA read from 1smtA/merged-good-all-a2m # found chain 1smtA in template set T0373 18 :TTLTRRLRREAQ 1smtA 33 :AQSLAEFFAVLA T0373 34 :QFSQLVVLGAIDR 1smtA 45 :DPNRLRLLSLLAR T0373 49 :GDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADP 1smtA 58 :SELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSYRKQG T0373 90 :RRTRVSLSSE 1smtA 96 :RHVYYQLQDH T0373 106 :GNRAKREEWLVR 1smtA 106 :HIVALYQNALDH T0373 119 :MHA 1smtA 118 :LQE Number of specific fragments extracted= 6 number of extra gaps= 0 total=85 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1smtB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1smtB expands to /projects/compbio/data/pdb/1smt.pdb.gz 1smtB:# T0373 read from 1smtB/merged-good-all-a2m # 1smtB read from 1smtB/merged-good-all-a2m # adding 1smtB to template set # found chain 1smtB in template set T0373 18 :TTLTRRLRREAQ 1smtB 33 :AQSLAEFFAVLA T0373 34 :QFSQLVVLGAIDR 1smtB 45 :DPNRLRLLSLLAR T0373 48 :GG 1smtB 58 :SE T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHADP 1smtB 60 :LCVGDLAQAIGVSESAVSHQLRSLRNLRLVSYRKQG T0373 90 :RRTRVSLS 1smtB 96 :RHVYYQLQ T0373 98 :SEGRRNLYGNRAKR 1smtB 105 :HHIVALYQNALDHL Number of specific fragments extracted= 6 number of extra gaps= 0 total=91 Number of alignments=16 # 1smtB read from 1smtB/merged-good-all-a2m # found chain 1smtB in template set T0373 1 :MPTNQDL 1smtB 26 :QAIAPEV T0373 18 :TTLTRRLRREAQ 1smtB 33 :AQSLAEFFAVLA T0373 34 :QFSQLVVLGAID 1smtB 45 :DPNRLRLLSLLA T0373 48 :GGDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADP 1smtB 57 :RSELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSYRKQG T0373 90 :RRTRVSLS 1smtB 96 :RHVYYQLQ T0373 98 :SEGRRNLYGNRAKR 1smtB 105 :HHIVALYQNALDHL Number of specific fragments extracted= 6 number of extra gaps= 0 total=97 Number of alignments=17 # 1smtB read from 1smtB/merged-good-all-a2m # found chain 1smtB in template set T0373 18 :TTLTRRLRREAQ 1smtB 33 :AQSLAEFFAVLA T0373 34 :QFSQLVVLGAIDR 1smtB 45 :DPNRLRLLSLLAR T0373 49 :GDVTPSELAAAERMRSSNLAALLRELERGGLIVRHAD 1smtB 58 :SELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSYRKQ T0373 89 :GRRTRVSLSSE 1smtB 95 :GRHVYYQLQDH T0373 106 :GNRAKREEWLVR 1smtB 106 :HIVALYQNALDH Number of specific fragments extracted= 5 number of extra gaps= 0 total=102 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bi0/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1bi0 expands to /projects/compbio/data/pdb/1bi0.pdb.gz 1bi0:Warning: there is no chain 1bi0 will retry with 1bi0A # T0373 read from 1bi0/merged-good-all-a2m # 1bi0 read from 1bi0/merged-good-all-a2m # adding 1bi0 to template set # found chain 1bi0 in template set Warning: unaligning (T0373)L131 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1bi0)R103 Warning: unaligning (T0373)A133 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1bi0)R103 T0373 36 :SQLVVLGAIDRLGGDVTPSELAAAERMRSSNLAALLRELERGGLIVRH 1bi0 10 :MYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVA T0373 87 :QDGR 1bi0 58 :SDRS T0373 94 :VSLSSEGRRNLYGNRAKRE 1bi0 62 :LQMTPTGRTLATAVMRKHR T0373 115 :LVRAMHAC 1bi0 81 :LAERLLTD T0373 123 :LD 1bi0 92 :LD T0373 125 :ESERAL 1bi0 95 :NKVHDE T0373 134 :AG 1bi0 104 :WE T0373 136 :PLLTRLAQFEEP 1bi0 111 :EVERRLVKVLKD Number of specific fragments extracted= 8 number of extra gaps= 0 total=110 Number of alignments=19 # 1bi0 read from 1bi0/merged-good-all-a2m # found chain 1bi0 in template set Warning: unaligning (T0373)L131 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1bi0)R103 Warning: unaligning (T0373)A133 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1bi0)R103 T0373 35 :FSQLVVLGAIDRLGGDVTPSELAAAERMRSSNLAALLRELERGGLIVR 1bi0 9 :EMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVV T0373 85 :DPQDG 1bi0 57 :ASDRS T0373 94 :VSLSSEGRRNLYGNRAKREEWLVRAM 1bi0 62 :LQMTPTGRTLATAVMRKHRLAERLLT T0373 121 :ACLD 1bi0 88 :DIIG T0373 125 :ESERAL 1bi0 95 :NKVHDE T0373 134 :AG 1bi0 104 :WE T0373 136 :PLLTRLAQFEEP 1bi0 111 :EVERRLVKVLKD Number of specific fragments extracted= 7 number of extra gaps= 0 total=117 Number of alignments=20 # 1bi0 read from 1bi0/merged-good-all-a2m # found chain 1bi0 in template set T0373 36 :SQLVVLGAIDR 1bi0 10 :MYLRTIYELEE T0373 48 :GGD 1bi0 21 :EGV T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHADP 1bi0 25 :PLRARIAERLEQSGPTVSQTVARMERDGLVVVASDR T0373 93 :RVSLSSEGRRNLYGNRAKREEWLVRA 1bi0 61 :SLQMTPTGRTLATAVMRKHRLAERLL T0373 119 :MHACLDES 1bi0 88 :DIIGLDIN Number of specific fragments extracted= 5 number of extra gaps= 0 total=122 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xmaA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1xmaA expands to /projects/compbio/data/pdb/1xma.pdb.gz 1xmaA:Skipped atom 237, because occupancy 0.350 <= existing 0.650 in 1xmaA Skipped atom 239, because occupancy 0.350 <= existing 0.650 in 1xmaA Skipped atom 241, because occupancy 0.350 <= existing 0.650 in 1xmaA Skipped atom 243, because occupancy 0.350 <= existing 0.650 in 1xmaA Skipped atom 245, because occupancy 0.350 <= existing 0.650 in 1xmaA Skipped atom 436, because occupancy 0.350 <= existing 0.650 in 1xmaA Skipped atom 438, because occupancy 0.350 <= existing 0.650 in 1xmaA Skipped atom 440, because occupancy 0.350 <= existing 0.650 in 1xmaA Skipped atom 722, because occupancy 0.350 <= existing 0.650 in 1xmaA Skipped atom 724, because occupancy 0.350 <= existing 0.650 in 1xmaA # T0373 read from 1xmaA/merged-good-all-a2m # 1xmaA read from 1xmaA/merged-good-all-a2m # adding 1xmaA to template set # found chain 1xmaA in template set Warning: unaligning (T0373)P86 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xmaA)K72 Warning: unaligning (T0373)G89 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xmaA)K72 Warning: unaligning (T0373)D124 because last residue in template chain is (1xmaA)K106 T0373 35 :FSQLVVLGAIDR 1xmaA 10 :YVDTIILSLLIE T0373 48 :GG 1xmaA 22 :GD T0373 51 :VTPSELAAAER 1xmaA 24 :SYGYEISKNIR T0373 62 :MRSSNLAALLRELERGGLIVRHA 1xmaA 43 :IKETTLYSAFARLEKNGYIKSYY T0373 85 :D 1xmaA 68 :E T0373 90 :RRTRVSLSSEGRRNLYGNRAKREE 1xmaA 73 :RRTYYRITPEGIKYYKQKCEEWEL T0373 115 :LVRAMHACL 1xmaA 97 :TKKVINKFV Number of specific fragments extracted= 7 number of extra gaps= 0 total=129 Number of alignments=22 # 1xmaA read from 1xmaA/merged-good-all-a2m # found chain 1xmaA in template set Warning: unaligning (T0373)P86 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xmaA)K72 Warning: unaligning (T0373)G89 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xmaA)K72 Warning: unaligning (T0373)D124 because last residue in template chain is (1xmaA)K106 T0373 35 :FSQLVVLGAIDR 1xmaA 10 :YVDTIILSLLIE T0373 49 :GDVTPSELAAAER 1xmaA 22 :GDSYGYEISKNIR T0373 62 :MRSSNLAALLRELERGGLIVRHA 1xmaA 43 :IKETTLYSAFARLEKNGYIKSYY T0373 85 :D 1xmaA 68 :E T0373 90 :RRTRVSLSSEGRRNLYGNRAKREEWLVRAM 1xmaA 73 :RRTYYRITPEGIKYYKQKCEEWELTKKVIN T0373 121 :ACL 1xmaA 103 :KFV Number of specific fragments extracted= 6 number of extra gaps= 0 total=135 Number of alignments=23 # 1xmaA read from 1xmaA/merged-good-all-a2m # found chain 1xmaA in template set Warning: unaligning (T0373)P86 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1xmaA)K72 Warning: unaligning (T0373)G89 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xmaA)K72 Warning: unaligning (T0373)D124 because last residue in template chain is (1xmaA)K106 T0373 35 :FSQLVVLGAIDR 1xmaA 10 :YVDTIILSLLIE T0373 49 :GDVTPSELAAAER 1xmaA 22 :GDSYGYEISKNIR T0373 62 :MRSSNLAALLRELERGGLIVRH 1xmaA 43 :IKETTLYSAFARLEKNGYIKSY T0373 84 :AD 1xmaA 67 :EE T0373 90 :RRTRVSLSSEGRRNLYGNRAKREEWLVR 1xmaA 73 :RRTYYRITPEGIKYYKQKCEEWELTKKV T0373 119 :MHACL 1xmaA 101 :INKFV Number of specific fragments extracted= 6 number of extra gaps= 0 total=141 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1c0wA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1c0wA expands to /projects/compbio/data/pdb/1c0w.pdb.gz 1c0wA:# T0373 read from 1c0wA/merged-good-all-a2m # 1c0wA read from 1c0wA/merged-good-all-a2m # adding 1c0wA to template set # found chain 1c0wA in template set T0373 35 :FSQLVVLGAIDRLGGDVTPSELAAAERMRSSNLAALLRELERGGLIVRH 1c0wA 9 :EMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVA T0373 87 :QDGR 1c0wA 58 :SDRS T0373 94 :VSLSSEGRRNLYGNRAKR 1c0wA 62 :LQMTPTGRTLATAVMRKH T0373 112 :EE 1c0wA 95 :NK T0373 115 :LVRAMHAC 1c0wA 97 :VHDEACRW T0373 123 :LDES 1c0wA 108 :MSDE T0373 137 :LLTRLAQFEEP 1c0wA 112 :VERRLVKVLKD Number of specific fragments extracted= 7 number of extra gaps= 0 total=148 Number of alignments=25 # 1c0wA read from 1c0wA/merged-good-all-a2m # found chain 1c0wA in template set T0373 32 :PVQFSQLVVLGAIDRL 1c0wA 3 :DLVDTTEMYLRTIYEL T0373 48 :GGDVTPSELAAAERMRSSNLAALLRELERGGLIVR 1c0wA 22 :GVTPLRARIAERLEQSGPTVSQTVARMERDGLVVV T0373 85 :DPQDG 1c0wA 57 :ASDRS T0373 94 :VSLSSEGRRNLYGNRAKREEWLVRAM 1c0wA 62 :LQMTPTGRTLATAVMRKHRLAERLLT T0373 121 :ACLD 1c0wA 88 :DIIG T0373 125 :ESERALLAAAG 1c0wA 95 :NKVHDEACRWE T0373 136 :PLLTRLAQFEEP 1c0wA 111 :EVERRLVKVLKD Number of specific fragments extracted= 7 number of extra gaps= 0 total=155 Number of alignments=26 # 1c0wA read from 1c0wA/merged-good-all-a2m # found chain 1c0wA in template set T0373 35 :FSQLVVLGAIDRLGGDVTPSELAAAERMRSSNLAALLRELERGGLIVRHAD 1c0wA 9 :EMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASD T0373 89 :G 1c0wA 60 :R T0373 93 :RVSLSSEGRRNLYGNRAKREEWLVR 1c0wA 61 :SLQMTPTGRTLATAVMRKHRLAERL T0373 119 :MHACLD 1c0wA 86 :LTDIIG T0373 132 :AAAGPLLTRLA 1c0wA 95 :NKVHDEACRWE Number of specific fragments extracted= 5 number of extra gaps= 0 total=160 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1b1bA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1b1bA expands to /projects/compbio/data/pdb/1b1b.pdb.gz 1b1bA:# T0373 read from 1b1bA/merged-good-all-a2m # 1b1bA read from 1b1bA/merged-good-all-a2m # adding 1b1bA to template set # found chain 1b1bA in template set T0373 35 :FSQLVVLGAIDRLGGDVTPSELAAAERMRSSNLAALLRELERGGLIVRH 1b1bA 9 :EMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVA T0373 87 :QDGR 1b1bA 58 :GDRH T0373 94 :VSLSSEGRRNLYGNRAKRE 1b1bA 62 :LELTEKGRALAIAVMRKHR T0373 114 :WLVRAMHAC 1b1bA 81 :LAERLLVDV T0373 125 :ESERALLAAA 1b1bA 95 :EEVHAEACRW T0373 136 :PLLTRLAQFEEP 1b1bA 111 :DVERRLVKVLNN Number of specific fragments extracted= 6 number of extra gaps= 0 total=166 Number of alignments=28 # 1b1bA read from 1b1bA/merged-good-all-a2m # found chain 1b1bA in template set T0373 35 :FSQLVVLGAIDRLGGDVTPSELAAAERMRSSNLAALLRELERGGLIVRH 1b1bA 9 :EMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVA T0373 87 :QDGR 1b1bA 58 :GDRH T0373 94 :VSLSSEGRRNLYGNRAKREEWLVRAM 1b1bA 62 :LELTEKGRALAIAVMRKHRLAERLLV T0373 121 :ACLD 1b1bA 88 :DVIG T0373 125 :ESERALLAAA 1b1bA 95 :EEVHAEACRW T0373 136 :PLLTRLAQFEEP 1b1bA 111 :DVERRLVKVLNN Number of specific fragments extracted= 6 number of extra gaps= 0 total=172 Number of alignments=29 # 1b1bA read from 1b1bA/merged-good-all-a2m # found chain 1b1bA in template set T0373 37 :QLVVLGAIDR 1b1bA 8 :TEMYLRTIYD T0373 47 :LGGD 1b1bA 20 :EEGV T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRH 1b1bA 25 :PLRARIAERLDQSGPTVSQTVSRMERDGLLRVA T0373 87 :QDG 1b1bA 58 :GDR T0373 93 :RVSLSSEGRRNLYGNRAKR 1b1bA 61 :HLELTEKGRALAIAVMRKH T0373 112 :EEWLVR 1b1bA 98 :HAEACR T0373 119 :MHACLDES 1b1bA 104 :WEHVMSED T0373 130 :LLAAAGP 1b1bA 112 :VERRLVK Number of specific fragments extracted= 8 number of extra gaps= 0 total=180 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2f2eA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2f2eA expands to /projects/compbio/data/pdb/2f2e.pdb.gz 2f2eA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 955, because occupancy 0.500 <= existing 0.500 in 2f2eA Skipped atom 959, because occupancy 0.500 <= existing 0.500 in 2f2eA Skipped atom 961, because occupancy 0.500 <= existing 0.500 in 2f2eA Skipped atom 963, because occupancy 0.500 <= existing 0.500 in 2f2eA Skipped atom 965, because occupancy 0.500 <= existing 0.500 in 2f2eA # T0373 read from 2f2eA/merged-good-all-a2m # 2f2eA read from 2f2eA/merged-good-all-a2m # adding 2f2eA to template set # found chain 2f2eA in template set T0373 37 :QLVVLGAIDR 2f2eA 26 :SMLIVRDAFE T0373 48 :GG 2f2eA 36 :GL T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRT 2f2eA 38 :TRFGEFQKSLGLAKNILAARLRNLVEHGVMVAVPAESGSHQE T0373 94 :VSLSSEGR 2f2eA 80 :YRLTDKGR T0373 106 :GNRAKREEWLVRAMHACLDES 2f2eA 88 :ALFPLLVAIRQWGEDYFFAPD Number of specific fragments extracted= 5 number of extra gaps= 0 total=185 Number of alignments=31 # 2f2eA read from 2f2eA/merged-good-all-a2m # found chain 2f2eA in template set T0373 37 :QLVVLGAID 2f2eA 26 :SMLIVRDAF T0373 48 :GGDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRR 2f2eA 35 :EGLTRFGEFQKSLGLAKNILAARLRNLVEHGVMVAVPAESGSHQ T0373 93 :RVSLSSEGRRNLYGNRAKREEWLV 2f2eA 79 :EYRLTDKGRALFPLLVAIRQWGED T0373 121 :AC 2f2eA 103 :YF Number of specific fragments extracted= 4 number of extra gaps= 0 total=189 Number of alignments=32 # 2f2eA read from 2f2eA/merged-good-all-a2m # found chain 2f2eA in template set T0373 37 :QLVVLGAIDR 2f2eA 26 :SMLIVRDAFE T0373 49 :GDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRT 2f2eA 36 :GLTRFGEFQKSLGLAKNILAARLRNLVEHGVMVAVPAESGSHQE T0373 94 :VSLSSEGR 2f2eA 80 :YRLTDKGR T0373 106 :GNRAKREEWLVRAMHACLDES 2f2eA 88 :ALFPLLVAIRQWGEDYFFAPD Number of specific fragments extracted= 4 number of extra gaps= 0 total=193 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sd4A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1sd4A expands to /projects/compbio/data/pdb/1sd4.pdb.gz 1sd4A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0373 read from 1sd4A/merged-good-all-a2m # 1sd4A read from 1sd4A/merged-good-all-a2m # adding 1sd4A to template set # found chain 1sd4A in template set Warning: unaligning (T0373)A30 because first residue in template chain is (1sd4A)Q5 T0373 31 :DPVQFSQLVVLGAIDRLGG 1sd4A 6 :VEISMAEWDVMNIIWDKKS T0373 51 :VTPSELAAAER 1sd4A 25 :VSANEIVVEIQ T0373 62 :MRSSNLAALLRELERGGLIVRHADPQ 1sd4A 40 :VSDKTIRTLITRLYKKEIIKRYKSEN T0373 91 :RTRVSLS 1sd4A 66 :IYFYSSN T0373 98 :SEGRRNLYGNRAK 1sd4A 76 :DDIKMKTAKTFLN T0373 113 :E 1sd4A 89 :K T0373 114 :WLVRAMHAC 1sd4A 97 :SLVLNFAKN T0373 123 :LDESERALLAA 1sd4A 108 :LNNKEIEELRD T0373 137 :LLTR 1sd4A 119 :ILND Number of specific fragments extracted= 9 number of extra gaps= 0 total=202 Number of alignments=34 # 1sd4A read from 1sd4A/merged-good-all-a2m # found chain 1sd4A in template set Warning: unaligning (T0373)A30 because first residue in template chain is (1sd4A)Q5 T0373 31 :DPVQFSQLVVLGAIDRL 1sd4A 6 :VEISMAEWDVMNIIWDK T0373 49 :GDVTPSELAAAE 1sd4A 23 :KSVSANEIVVEI T0373 61 :RMRSSNLAALLRELERGGLIVRHADPQ 1sd4A 39 :EVSDKTIRTLITRLYKKEIIKRYKSEN T0373 91 :RTRVSLS 1sd4A 66 :IYFYSSN T0373 98 :SEGRRNLYGNR 1sd4A 76 :DDIKMKTAKTF T0373 109 :AKR 1sd4A 96 :KSL T0373 114 :WLVRAMHACLDESERALLAA 1sd4A 99 :VLNFAKNEELNNKEIEELRD T0373 137 :LLTR 1sd4A 119 :ILND Number of specific fragments extracted= 8 number of extra gaps= 0 total=210 Number of alignments=35 # 1sd4A read from 1sd4A/merged-good-all-a2m # found chain 1sd4A in template set T0373 31 :DPVQFSQLVVLGAIDR 1sd4A 6 :VEISMAEWDVMNIIWD T0373 48 :GGDVTPSELAAAER 1sd4A 22 :KKSVSANEIVVEIQ T0373 62 :MRSSNLAALLRELERGGLIVRHADPQ 1sd4A 40 :VSDKTIRTLITRLYKKEIIKRYKSEN T0373 91 :RTRVSLS 1sd4A 66 :IYFYSSN T0373 98 :SEGRRNLYGNR 1sd4A 76 :DDIKMKTAKTF T0373 109 :AKREEWLVR 1sd4A 96 :KSLVLNFAK T0373 120 :HACLDESERALLAAAGPL 1sd4A 105 :NEELNNKEIEELRDILND Number of specific fragments extracted= 7 number of extra gaps= 0 total=217 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fswA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fswA expands to /projects/compbio/data/pdb/2fsw.pdb.gz 2fswA:Skipped atom 36, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 38, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 40, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 42, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 44, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 46, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 48, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 50, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 52, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 54, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 56, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 58, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 60, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 62, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 64, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 66, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 68, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 70, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 72, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 74, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 76, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 78, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 80, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 82, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 84, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 86, because occupancy 0.500 <= existing 0.500 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 179, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 181, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 183, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 185, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 187, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 189, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 191, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 193, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 195, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 324, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 326, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 328, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 330, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 332, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 334, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 336, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 338, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 340, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 342, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 344, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 362, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 364, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 366, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 368, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 370, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 372, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 374, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 376, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 378, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 397, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 399, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 401, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 403, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 405, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 407, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 409, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 411, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 413, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 415, because occupancy 0.400 <= existing 0.600 in 2fswA Skipped atom 417, because occupancy 0.400 <= existing 0.600 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 524, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 526, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 528, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 530, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 532, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 534, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 536, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 538, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 540, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 609, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 611, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 613, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 615, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 617, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 619, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 621, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 623, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 625, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 694, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 696, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 698, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 700, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 702, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 704, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 706, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 708, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 710, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 712, because occupancy 0.500 <= existing 0.500 in 2fswA Skipped atom 714, because occupancy 0.500 <= existing 0.500 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 894, because occupancy 0.400 <= existing 0.600 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 896, because occupancy 0.400 <= existing 0.600 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 898, because occupancy 0.400 <= existing 0.600 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 900, because occupancy 0.400 <= existing 0.600 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 902, because occupancy 0.400 <= existing 0.600 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 904, because occupancy 0.400 <= existing 0.600 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 906, because occupancy 0.300 <= existing 0.340 in 2fswA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 908, because occupancy 0.400 <= existing 0.600 in 2fswA # T0373 read from 2fswA/merged-good-all-a2m # 2fswA read from 2fswA/merged-good-all-a2m # adding 2fswA to template set # found chain 2fswA in template set T0373 41 :LGAIDRLGGD 2fswA 25 :LLIIFQINRR T0373 51 :VTPSELAAAE 2fswA 36 :IRYGELKRAI T0373 61 :RMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEG 2fswA 47 :GISEKMLIDELKFLCGKGLIKKKQYPEVPPRVEYSLTPLG T0373 105 :YGNRAKREE 2fswA 87 :EKVLPIIDE T0373 115 :LVRAMHA 2fswA 96 :IAKFGME Number of specific fragments extracted= 5 number of extra gaps= 0 total=222 Number of alignments=37 # 2fswA read from 2fswA/merged-good-all-a2m # found chain 2fswA in template set T0373 30 :ADP 2fswA 20 :AGK T0373 36 :SQLVVLGAID 2fswA 23 :WTLLIIFQIN T0373 48 :GGDVTPSELAAAE 2fswA 33 :RRIIRYGELKRAI T0373 61 :RMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEG 2fswA 47 :GISEKMLIDELKFLCGKGLIKKKQYPEVPPRVEYSLTPLG T0373 105 :YGNRAKREEWLVRAM 2fswA 87 :EKVLPIIDEIAKFGM T0373 121 :A 2fswA 102 :E Number of specific fragments extracted= 6 number of extra gaps= 0 total=228 Number of alignments=38 # 2fswA read from 2fswA/merged-good-all-a2m # found chain 2fswA in template set T0373 40 :VLGAIDRLGGD 2fswA 24 :TLLIIFQINRR T0373 51 :VTPSELAAAE 2fswA 36 :IRYGELKRAI T0373 61 :RMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGR 2fswA 47 :GISEKMLIDELKFLCGKGLIKKKQYPEVPPRVEYSLTPLGE T0373 106 :GNRAKREEWLVR 2fswA 88 :KVLPIIDEIAKF T0373 119 :MHA 2fswA 100 :GME Number of specific fragments extracted= 5 number of extra gaps= 0 total=233 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z91A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1z91A expands to /projects/compbio/data/pdb/1z91.pdb.gz 1z91A:# T0373 read from 1z91A/merged-good-all-a2m # 1z91A read from 1z91A/merged-good-all-a2m # adding 1z91A to template set # found chain 1z91A in template set Warning: unaligning (T0373)T3 because first residue in template chain is (1z91A)M8 Warning: unaligning (T0373)E146 because last residue in template chain is (1z91A)H144 T0373 4 :NQDLQLAAHLRSQVTTLTRRLRREAQADPVQFSQLVVLGAIDRLGG 1z91A 9 :KLENQLSFLLYASSREMTKQYKPLLDKLNITYPQYLALLLLWEHET T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRN 1z91A 55 :LTVKKMGEQLYLDSGTLTPMLKRMEQQGLITRKRSEEDERSVLISLTEDGALL T0373 104 :LYGNRAKREE 1z91A 111 :AVDIPGTILG T0373 120 :HACLDESERALLAA 1z91A 121 :LSKQSGEDLKQLKS T0373 137 :LLTRLAQFE 1z91A 135 :ALYTLLETL Number of specific fragments extracted= 5 number of extra gaps= 0 total=238 Number of alignments=40 # 1z91A read from 1z91A/merged-good-all-a2m # found chain 1z91A in template set Warning: unaligning (T0373)T3 because first residue in template chain is (1z91A)M8 Warning: unaligning (T0373)E146 because last residue in template chain is (1z91A)H144 T0373 4 :NQDLQLAAHLRSQVTTLTRRLRREAQADPVQFSQLVVLGAIDRL 1z91A 9 :KLENQLSFLLYASSREMTKQYKPLLDKLNITYPQYLALLLLWEH T0373 49 :GDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRN 1z91A 53 :ETLTVKKMGEQLYLDSGTLTPMLKRMEQQGLITRKRSEEDERSVLISLTEDGALL T0373 104 :LYGNRAKREEW 1z91A 111 :AVDIPGTILGL T0373 121 :ACLDESERALLAA 1z91A 122 :SKQSGEDLKQLKS T0373 137 :LLTRLAQFE 1z91A 135 :ALYTLLETL Number of specific fragments extracted= 5 number of extra gaps= 0 total=243 Number of alignments=41 # 1z91A read from 1z91A/merged-good-all-a2m # found chain 1z91A in template set T0373 11 :AHLRSQVTTLTRRLRREAQADPVQFSQLVVLGAIDR 1z91A 16 :FLLYASSREMTKQYKPLLDKLNITYPQYLALLLLWE T0373 48 :GGDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRN 1z91A 52 :HETLTVKKMGEQLYLDSGTLTPMLKRMEQQGLITRKRSEEDERSVLISLTEDGALL T0373 104 :LYG 1z91A 111 :AVD T0373 111 :REEWLVR 1z91A 114 :IPGTILG T0373 120 :HACLDESERALLAAAGPLLTR 1z91A 121 :LSKQSGEDLKQLKSALYTLLE Number of specific fragments extracted= 5 number of extra gaps= 0 total=248 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zybA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zybA expands to /projects/compbio/data/pdb/1zyb.pdb.gz 1zybA:Skipped atom 11, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 13, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 15, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 17, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 80, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 82, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 84, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 86, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 88, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 90, because occupancy 0.500 <= existing 0.500 in 1zybA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 223, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 225, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 227, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 229, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 231, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 427, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 429, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 431, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 433, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 435, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 528, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 530, because occupancy 0.500 <= existing 0.500 in 1zybA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 938, because occupancy 0.300 <= existing 0.700 in 1zybA Skipped atom 940, because occupancy 0.300 <= existing 0.700 in 1zybA Skipped atom 942, because occupancy 0.300 <= existing 0.700 in 1zybA Skipped atom 972, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 974, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 1034, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 1036, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 1080, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 1082, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 1084, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 1086, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 1088, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 1090, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 1092, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 1094, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 1138, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 1140, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 1142, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 1144, because occupancy 0.500 <= existing 0.500 in 1zybA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1240, because occupancy 0.300 <= existing 0.700 in 1zybA Skipped atom 1242, because occupancy 0.300 <= existing 0.700 in 1zybA Skipped atom 1244, because occupancy 0.300 <= existing 0.700 in 1zybA Skipped atom 1246, because occupancy 0.300 <= existing 0.700 in 1zybA Skipped atom 1278, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 1280, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 1282, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 1284, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 1286, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 1288, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 1290, because occupancy 0.500 <= existing 0.500 in 1zybA Skipped atom 1382, because occupancy 0.300 <= existing 0.700 in 1zybA Skipped atom 1384, because occupancy 0.300 <= existing 0.700 in 1zybA Skipped atom 1503, because occupancy 0.300 <= existing 0.700 in 1zybA Skipped atom 1505, because occupancy 0.300 <= existing 0.700 in 1zybA Skipped atom 1507, because occupancy 0.300 <= existing 0.700 in 1zybA Skipped atom 1509, because occupancy 0.300 <= existing 0.700 in 1zybA Skipped atom 1511, because occupancy 0.300 <= existing 0.700 in 1zybA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0373 read from 1zybA/merged-good-all-a2m # 1zybA read from 1zybA/merged-good-all-a2m # adding 1zybA to template set # found chain 1zybA in template set T0373 12 :HLRSQVTTLTRRLRREAQAD 1zybA 124 :IFRLNYMNIVSNRAQNLYSR T0373 32 :PVQFSQLVVLGAIDRL 1zybA 148 :PTLDLKSKIIRFFLSH T0373 48 :GGD 1zybA 168 :QGE T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRH 1zybA 175 :VKMDDLARCLDDTRLNISKTLNELQDNGLIELH T0373 89 :GRRTRV 1zybA 208 :RKEILI Number of specific fragments extracted= 5 number of extra gaps= 0 total=253 Number of alignments=43 # 1zybA read from 1zybA/merged-good-all-a2m # found chain 1zybA in template set T0373 7 :LQLAAHLRSQVTTLTRRLRREAQADPVQFSQLVVLGAIDRL 1zybA 123 :DIFRLNYMNIVSNRAQNLYSRLWDEPTLDLKSKIIRFFLSH T0373 48 :GGD 1zybA 168 :QGE T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRH 1zybA 175 :VKMDDLARCLDDTRLNISKTLNELQDNGLIELH T0373 89 :GRRTRV 1zybA 208 :RKEILI Number of specific fragments extracted= 4 number of extra gaps= 0 total=257 Number of alignments=44 # 1zybA read from 1zybA/merged-good-all-a2m # found chain 1zybA in template set T0373 7 :LQLAAHLRSQVTTLTRRLRREAQADPVQFSQLVVLGAIDR 1zybA 123 :DIFRLNYMNIVSNRAQNLYSRLWDEPTLDLKSKIIRFFLS T0373 48 :GGD 1zybA 168 :QGE T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHA 1zybA 175 :VKMDDLARCLDDTRLNISKTLNELQDNGLIELHR T0373 90 :RRTRV 1zybA 209 :KEILI Number of specific fragments extracted= 4 number of extra gaps= 0 total=261 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fxaA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fxaA expands to /projects/compbio/data/pdb/2fxa.pdb.gz 2fxaA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 461, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 463, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 465, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 467, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 469, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 471, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 473, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 475, because occupancy 0.500 <= existing 0.500 in 2fxaA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 567, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 569, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 571, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 573, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 575, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 577, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 579, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 581, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 583, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 585, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 683, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 685, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 687, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 689, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 691, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 693, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 695, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 697, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 699, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 701, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 703, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 705, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 707, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 709, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 711, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 713, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 715, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 717, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 719, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 721, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 747, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 749, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 751, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 753, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 755, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 757, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 759, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 761, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 763, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 765, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 767, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 833, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 837, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 839, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 841, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 843, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 845, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 918, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 920, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 922, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 924, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 926, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 928, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 930, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 932, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 934, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 936, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 938, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 940, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 942, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 944, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1117, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1121, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1123, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1125, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1127, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1129, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1131, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1183, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1185, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1187, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1189, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1191, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1193, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1195, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1197, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1199, because occupancy 0.500 <= existing 0.500 in 2fxaA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1272, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1276, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1278, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1280, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1282, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1284, because occupancy 0.500 <= existing 0.500 in 2fxaA Skipped atom 1286, because occupancy 0.500 <= existing 0.500 in 2fxaA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0373 read from 2fxaA/merged-good-all-a2m # 2fxaA read from 2fxaA/merged-good-all-a2m # adding 2fxaA to template set # found chain 2fxaA in template set Warning: unaligning (T0373)T3 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fxaA)D9 Warning: unaligning (T0373)N4 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fxaA)D9 Warning: unaligning (T0373)D85 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fxaA)T102 Warning: unaligning (T0373)T92 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fxaA)T102 T0373 2 :P 2fxaA 7 :P T0373 5 :QDLQLAAHLRSQVTTLTRRLRREAQADPVQFSQLVVLGAIDRLGG 2fxaA 16 :FTQKMAQLSKALWKSIEKDWQQWLKPYDLNINEHHILWIAYQLNG T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHA 2fxaA 61 :ASISEIAKFGVMHVSTAFNFSKKLEERGYLRFSK T0373 93 :RVSLSSEGRRNLYGNRAK 2fxaA 103 :YVQLTEEGTEVFWSLLEE Number of specific fragments extracted= 4 number of extra gaps= 1 total=265 Number of alignments=46 # 2fxaA read from 2fxaA/merged-good-all-a2m # found chain 2fxaA in template set Warning: unaligning (T0373)T3 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fxaA)D9 Warning: unaligning (T0373)N4 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fxaA)D9 Warning: unaligning (T0373)D85 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fxaA)T102 Warning: unaligning (T0373)T92 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fxaA)T102 T0373 1 :MP 2fxaA 6 :PP T0373 5 :QD 2fxaA 10 :VK T0373 7 :LQLAAHLRSQVTTLTRRLRREAQADPVQFSQLVVLGAIDRLGG 2fxaA 18 :QKMAQLSKALWKSIEKDWQQWLKPYDLNINEHHILWIAYQLNG T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHA 2fxaA 61 :ASISEIAKFGVMHVSTAFNFSKKLEERGYLRFSK T0373 93 :RVSLSSEGRRNLYGNRA 2fxaA 103 :YVQLTEEGTEVFWSLLE T0373 111 :REEW 2fxaA 128 :VFKG T0373 115 :LVRAM 2fxaA 135 :LYHLF T0373 121 :ACLD 2fxaA 140 :GKFP T0373 125 :ESERALLAAAGP 2fxaA 146 :AEMMCMIRHIYG T0373 139 :TRLAQFEE 2fxaA 158 :DDFMEIFE Number of specific fragments extracted= 10 number of extra gaps= 1 total=275 Number of alignments=47 # 2fxaA read from 2fxaA/merged-good-all-a2m # found chain 2fxaA in template set Warning: unaligning (T0373)D85 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2fxaA)T102 Warning: unaligning (T0373)T92 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2fxaA)T102 T0373 10 :AAHLRSQVTTLTRRLRREAQADPVQFSQLVVLGAIDR 2fxaA 21 :AQLSKALWKSIEKDWQQWLKPYDLNINEHHILWIAYQ T0373 48 :GGDVTPSELAAAERMRSSNLAALLRELERGGLIVRHA 2fxaA 58 :LNGASISEIAKFGVMHVSTAFNFSKKLEERGYLRFSK T0373 93 :RVSLSSEGRRNLYGNRAK 2fxaA 103 :YVQLTEEGTEVFWSLLEE T0373 112 :EEWLVR 2fxaA 133 :QPLYHL T0373 120 :HACLD 2fxaA 139 :FGKFP T0373 125 :ESERALLAA 2fxaA 146 :AEMMCMIRH Number of specific fragments extracted= 6 number of extra gaps= 0 total=281 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2dtr/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2dtr expands to /projects/compbio/data/pdb/2dtr.pdb.gz 2dtr:Warning: there is no chain 2dtr will retry with 2dtrA # T0373 read from 2dtr/merged-good-all-a2m # 2dtr read from 2dtr/merged-good-all-a2m # adding 2dtr to template set # found chain 2dtr in template set T0373 36 :SQLVVLGAIDRLGGDVTPSELAAAERMRSSNLAALLRELERGGLIVRH 2dtr 10 :MYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVA T0373 87 :QDGR 2dtr 58 :SDRS T0373 94 :VSLSSEGRRNLYGNRAKRE 2dtr 62 :LQMTPTGRTLATAVMRKHR T0373 114 :WLVRAMHAC 2dtr 81 :LAERLLTDI T0373 127 :ERALLAAAG 2dtr 97 :VHDEACRWE T0373 136 :PLLTRLAQFEEP 2dtr 111 :EVERRLVKVLKD Number of specific fragments extracted= 6 number of extra gaps= 0 total=287 Number of alignments=49 # 2dtr read from 2dtr/merged-good-all-a2m # found chain 2dtr in template set T0373 35 :FSQLVVLGAIDRLGGDVTPSELAAAERMRSSNLAALLRELERGGLIVR 2dtr 9 :EMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVV T0373 85 :DPQDG 2dtr 57 :ASDRS T0373 94 :VSLSSEGRRNLYGNRAKREEWLVRAM 2dtr 62 :LQMTPTGRTLATAVMRKHRLAERLLT T0373 121 :ACLD 2dtr 88 :DIIG T0373 125 :ESERALLAAAG 2dtr 95 :NKVHDEACRWE T0373 136 :PLLTRLAQFEEP 2dtr 111 :EVERRLVKVLKD Number of specific fragments extracted= 6 number of extra gaps= 0 total=293 Number of alignments=50 # 2dtr read from 2dtr/merged-good-all-a2m # found chain 2dtr in template set T0373 36 :SQLVVLGAIDR 2dtr 10 :MYLRTIYELEE T0373 48 :GGD 2dtr 21 :EGV T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHADP 2dtr 25 :PLRARIAERLEQSGPTVSQTVARMERDGLVVVASDR T0373 93 :RVSLSSEGRRNLYGNRAKR 2dtr 61 :SLQMTPTGRTLATAVMRKH T0373 112 :EEWLVR 2dtr 98 :HDEACR T0373 119 :MHACLDES 2dtr 104 :WEHVMSDE T0373 130 :LLAAAGP 2dtr 112 :VERRLVK Number of specific fragments extracted= 7 number of extra gaps= 0 total=300 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b0lA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2b0lA expands to /projects/compbio/data/pdb/2b0l.pdb.gz 2b0lA:Skipped atom 32, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 34, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 36, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 38, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 40, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 42, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 44, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 46, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 48, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 50, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 123, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 125, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 127, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 129, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 131, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 133, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 135, because occupancy 0.200 <= existing 0.800 in 2b0lA Skipped atom 137, because occupancy 0.200 <= existing 0.800 in 2b0lA # T0373 read from 2b0lA/merged-good-all-a2m # 2b0lA read from 2b0lA/merged-good-all-a2m # adding 2b0lA to template set # found chain 2b0lA in template set Warning: unaligning (T0373)R46 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)E193 Warning: unaligning (T0373)L47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)E193 Warning: unaligning (T0373)A69 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)A220 Warning: unaligning (T0373)L70 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)A220 Warning: unaligning (T0373)I80 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)E231 Warning: unaligning (T0373)V81 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)E231 Warning: unaligning (T0373)H83 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)S234 Warning: unaligning (T0373)A84 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)S234 Warning: unaligning (T0373)D85 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)L235 Warning: unaligning (T0373)P86 because of BadResidue code BAD_PEPTIDE in next template residue (2b0lA)M237 Warning: unaligning (T0373)G89 because of BadResidue code BAD_PEPTIDE at template residue (2b0lA)M237 Warning: unaligning (T0373)G106 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)L256 T0373 7 :L 2b0lA 169 :K T0373 22 :RRLRREAQ 2b0lA 170 :AVVQMAIS T0373 32 :PVQFSQLVVLGAID 2b0lA 178 :SLSYSELEAIEHIF T0373 48 :GGD 2b0lA 195 :DGN T0373 51 :VTPSELAAAERMRSSNLA 2b0lA 201 :LVASKIADRVGITRSVIV T0373 71 :LRELERGGL 2b0lA 221 :LRKLESAGV T0373 82 :R 2b0lA 232 :S T0373 90 :RRTRVSL 2b0lA 238 :KGTYIKV T0373 97 :SSEGRRNLY 2b0lA 246 :NNKFLIELE Number of specific fragments extracted= 9 number of extra gaps= 5 total=309 Number of alignments=52 # 2b0lA read from 2b0lA/merged-good-all-a2m # found chain 2b0lA in template set Warning: unaligning (T0373)R46 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)E193 Warning: unaligning (T0373)L47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)E193 Warning: unaligning (T0373)A69 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)A220 Warning: unaligning (T0373)L70 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)A220 Warning: unaligning (T0373)I80 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)E231 Warning: unaligning (T0373)V81 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)E231 Warning: unaligning (T0373)H83 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)S234 Warning: unaligning (T0373)A84 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)S234 Warning: unaligning (T0373)D85 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)L235 Warning: unaligning (T0373)P86 because of BadResidue code BAD_PEPTIDE in next template residue (2b0lA)M237 Warning: unaligning (T0373)G89 because of BadResidue code BAD_PEPTIDE at template residue (2b0lA)M237 Warning: unaligning (T0373)G106 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)L256 T0373 4 :NQDLQL 2b0lA 166 :HMSKAV T0373 24 :LRREAQ 2b0lA 172 :VQMAIS T0373 32 :PVQFSQLVVLGAID 2b0lA 178 :SLSYSELEAIEHIF T0373 48 :GG 2b0lA 196 :GN T0373 50 :DVTPSELAAAERMRSSNLA 2b0lA 200 :LLVASKIADRVGITRSVIV T0373 71 :LRELERGGL 2b0lA 221 :LRKLESAGV T0373 82 :R 2b0lA 232 :S T0373 90 :RRTRVSLS 2b0lA 238 :KGTYIKVL T0373 98 :SEGRRNLY 2b0lA 247 :NKFLIELE Number of specific fragments extracted= 9 number of extra gaps= 5 total=318 Number of alignments=53 # 2b0lA read from 2b0lA/merged-good-all-a2m # found chain 2b0lA in template set Warning: unaligning (T0373)R46 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)E193 Warning: unaligning (T0373)A69 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)A220 Warning: unaligning (T0373)L70 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)A220 Warning: unaligning (T0373)I80 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)E231 Warning: unaligning (T0373)V81 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)E231 Warning: unaligning (T0373)H83 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)S234 Warning: unaligning (T0373)A84 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)S234 Warning: unaligning (T0373)D85 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b0lA)L235 Warning: unaligning (T0373)P86 because of BadResidue code BAD_PEPTIDE in next template residue (2b0lA)M237 Warning: unaligning (T0373)Q87 because of BadResidue code BAD_PEPTIDE at template residue (2b0lA)M237 Warning: unaligning (T0373)G106 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b0lA)L256 T0373 21 :TRRLRREAQ 2b0lA 169 :KAVVQMAIS T0373 32 :PVQFSQLVVLGAID 2b0lA 178 :SLSYSELEAIEHIF T0373 47 :LGGD 2b0lA 194 :LDGN T0373 51 :VTPSELAAAERMRSSNLA 2b0lA 201 :LVASKIADRVGITRSVIV T0373 71 :LRELERGGL 2b0lA 221 :LRKLESAGV T0373 82 :R 2b0lA 232 :S T0373 88 :DGRRTRV 2b0lA 238 :KGTYIKV T0373 96 :LSSEGRRNLY 2b0lA 245 :LNNKFLIELE Number of specific fragments extracted= 8 number of extra gaps= 5 total=326 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z1dA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1z1dA expands to /projects/compbio/data/pdb/1z1d.pdb.gz 1z1dA:# T0373 read from 1z1dA/merged-good-all-a2m # 1z1dA read from 1z1dA/merged-good-all-a2m # adding 1z1dA to template set # found chain 1z1dA in template set Warning: unaligning (T0373)A30 because first residue in template chain is (1z1dA)A202 T0373 31 :DPVQFSQLVVLGAIDRLGGD 1z1dA 203 :NGLTVAQNQVLNLIKACPRP T0373 51 :VTPSELAAAE 1z1dA 225 :LNFQDLKNQL T0373 61 :RMRSSNLAALLRELERGGLIVRHADP 1z1dA 236 :HMSVSSIKQAVDFLSNEGHIYSTVDD Number of specific fragments extracted= 3 number of extra gaps= 0 total=329 Number of alignments=55 # 1z1dA read from 1z1dA/merged-good-all-a2m # found chain 1z1dA in template set Warning: unaligning (T0373)A30 because first residue in template chain is (1z1dA)A202 T0373 31 :DPVQFSQLVVLGAIDRL 1z1dA 203 :NGLTVAQNQVLNLIKAC T0373 48 :GGDVTPSELAAAE 1z1dA 222 :PEGLNFQDLKNQL T0373 61 :RMRSSNLAALLRELERGGLIVRHADPQ 1z1dA 236 :HMSVSSIKQAVDFLSNEGHIYSTVDDD T0373 93 :RVS 1z1dA 263 :HFK Number of specific fragments extracted= 4 number of extra gaps= 0 total=333 Number of alignments=56 # 1z1dA read from 1z1dA/merged-good-all-a2m # found chain 1z1dA in template set Warning: unaligning (T0373)A30 because first residue in template chain is (1z1dA)A202 T0373 31 :DPVQFSQLVVLGAIDRLGGD 1z1dA 203 :NGLTVAQNQVLNLIKACPRP T0373 51 :VTPSELAAAE 1z1dA 225 :LNFQDLKNQL T0373 61 :RMRSSNLAALLRELERGGLIVRHADPQ 1z1dA 236 :HMSVSSIKQAVDFLSNEGHIYSTVDDD Number of specific fragments extracted= 3 number of extra gaps= 0 total=336 Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2co5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2co5A expands to /projects/compbio/data/pdb/2co5.pdb.gz 2co5A:Skipped atom 41, because occupancy 0.500 <= existing 0.500 in 2co5A Skipped atom 42, because occupancy 0.500 <= existing 0.500 in 2co5A Skipped atom 43, because occupancy 0.500 <= existing 0.500 in 2co5A Skipped atom 44, because occupancy 0.500 <= existing 0.500 in 2co5A Skipped atom 45, because occupancy 0.500 <= existing 0.500 in 2co5A Skipped atom 46, because occupancy 0.500 <= existing 0.500 in 2co5A Skipped atom 47, because occupancy 0.500 <= existing 0.500 in 2co5A Skipped atom 48, because occupancy 0.500 <= existing 0.500 in 2co5A Skipped atom 735, because occupancy 0.500 <= existing 0.500 in 2co5A Skipped atom 736, because occupancy 0.500 <= existing 0.500 in 2co5A Skipped atom 737, because occupancy 0.500 <= existing 0.500 in 2co5A Skipped atom 738, because occupancy 0.500 <= existing 0.500 in 2co5A Skipped atom 739, because occupancy 0.500 <= existing 0.500 in 2co5A Skipped atom 740, because occupancy 0.500 <= existing 0.500 in 2co5A # T0373 read from 2co5A/merged-good-all-a2m # 2co5A read from 2co5A/merged-good-all-a2m # adding 2co5A to template set # found chain 2co5A in template set Warning: unaligning (T0373)D85 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2co5A)P66 Warning: unaligning (T0373)P86 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2co5A)P66 Warning: unaligning (T0373)Q87 because of BadResidue code BAD_PEPTIDE at template residue (2co5A)D67 T0373 35 :FSQLVVLGAIDRLGGDV 2co5A 9 :INYYIILKVLVINGSRL T0373 53 :PSELAAAER 2co5A 31 :RSEILKRFD T0373 62 :MRSSNLAALLRELERGGLIVRHA 2co5A 42 :ISDGVLYPLIDSLIDDKILREEE T0373 88 :DG 2co5A 68 :GK T0373 93 :RVSLSSEGRRNLYGNRAKREE 2co5A 70 :VLFLTEKGMKEFEELHEFFKK T0373 115 :LV 2co5A 91 :IV Number of specific fragments extracted= 6 number of extra gaps= 1 total=342 Number of alignments=58 # 2co5A read from 2co5A/merged-good-all-a2m # found chain 2co5A in template set Warning: unaligning (T0373)D85 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2co5A)P66 Warning: unaligning (T0373)P86 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2co5A)P66 Warning: unaligning (T0373)Q87 because of BadResidue code BAD_PEPTIDE at template residue (2co5A)D67 T0373 35 :FSQLVVLGAIDRLGGDVT 2co5A 9 :INYYIILKVLVINGSRLE T0373 53 :PSELAAAE 2co5A 31 :RSEILKRF T0373 61 :RMRSSNLAALLRELERGGLIVRHA 2co5A 41 :DISDGVLYPLIDSLIDDKILREEE T0373 88 :DG 2co5A 68 :GK T0373 93 :RVSLSSEGRRNLYGNRAKREEWL 2co5A 70 :VLFLTEKGMKEFEELHEFFKKIV Number of specific fragments extracted= 5 number of extra gaps= 1 total=347 Number of alignments=59 # 2co5A read from 2co5A/merged-good-all-a2m # found chain 2co5A in template set Warning: unaligning (T0373)D85 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2co5A)P66 Warning: unaligning (T0373)P86 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2co5A)P66 Warning: unaligning (T0373)Q87 because of BadResidue code BAD_PEPTIDE at template residue (2co5A)D67 T0373 35 :FSQLVVLGAIDRLGGD 2co5A 9 :INYYIILKVLVINGSR T0373 53 :PSELAAAER 2co5A 31 :RSEILKRFD T0373 62 :MRSSNLAALLRELERGGLIVRHA 2co5A 42 :ISDGVLYPLIDSLIDDKILREEE T0373 88 :DG 2co5A 68 :GK T0373 93 :RVSLSSEGRRNLYGNRAKREEWL 2co5A 70 :VLFLTEKGMKEFEELHEFFKKIV Number of specific fragments extracted= 5 number of extra gaps= 1 total=352 Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xnpA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1xnpA expands to Error: no filename for 1xnpA 1xnpA expands to Error: no filename for 1xnpA 1xnpA expands to Error: no filename for 1xnpA # T0373 read from 1xnpA/merged-good-all-a2m # 1xnpA read from 1xnpA/merged-good-all-a2m # adding 1xnpA to template set Error: can't find template for 1xnpA or 1xnpA, so skipping it. # 1xnpA read from 1xnpA/merged-good-all-a2m # adding 1xnpA to template set Error: can't find template for 1xnpA or 1xnpA, so skipping it. # 1xnpA read from 1xnpA/merged-good-all-a2m # adding 1xnpA to template set Error: can't find template for 1xnpA or 1xnpA, so skipping it. # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z7uA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1z7uA expands to /projects/compbio/data/pdb/1z7u.pdb.gz 1z7uA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 60, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 62, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 64, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 66, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 68, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 70, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 72, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 74, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 76, because occupancy 0.500 <= existing 0.500 in 1z7uA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 259, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 261, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 263, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 265, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 267, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 269, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 271, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 273, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 275, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 297, because occupancy 0.400 <= existing 0.600 in 1z7uA Skipped atom 299, because occupancy 0.400 <= existing 0.600 in 1z7uA Skipped atom 301, because occupancy 0.400 <= existing 0.600 in 1z7uA Skipped atom 303, because occupancy 0.400 <= existing 0.600 in 1z7uA Skipped atom 305, because occupancy 0.400 <= existing 0.600 in 1z7uA Skipped atom 307, because occupancy 0.400 <= existing 0.600 in 1z7uA Skipped atom 309, because occupancy 0.400 <= existing 0.600 in 1z7uA Skipped atom 311, because occupancy 0.400 <= existing 0.600 in 1z7uA Skipped atom 313, because occupancy 0.400 <= existing 0.600 in 1z7uA Skipped atom 315, because occupancy 0.400 <= existing 0.600 in 1z7uA Skipped atom 317, because occupancy 0.400 <= existing 0.600 in 1z7uA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 596, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 598, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 600, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 602, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 604, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 606, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 608, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 610, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 909, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 911, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 913, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 915, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 917, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 919, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 921, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 923, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 925, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 927, because occupancy 0.500 <= existing 0.500 in 1z7uA Skipped atom 929, because occupancy 0.500 <= existing 0.500 in 1z7uA # T0373 read from 1z7uA/merged-good-all-a2m # 1z7uA read from 1z7uA/merged-good-all-a2m # adding 1z7uA to template set # found chain 1z7uA in template set T0373 36 :SQLVVLGAIDR 1z7uA 20 :WKLSLMDELFQ T0373 48 :GG 1z7uA 31 :GT T0373 51 :VTPSELAAAE 1z7uA 33 :KRNGELMRAL T0373 61 :RMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREE 1z7uA 44 :GITQRVLTDRLREMEKDGLVHRESFNELPPRVEYTLTPEGYALYDALSSLCHW T0373 115 :LVRAMHA 1z7uA 97 :GETFAQK Number of specific fragments extracted= 5 number of extra gaps= 0 total=357 Number of alignments=61 # 1z7uA read from 1z7uA/merged-good-all-a2m # found chain 1z7uA in template set T0373 6 :DLQL 1z7uA 6 :QTSI T0373 22 :RRLRREAQ 1z7uA 10 :NLALSTIN T0373 35 :FSQLVVLGAIDR 1z7uA 19 :KWKLSLMDELFQ T0373 49 :GDVTPSELAAAE 1z7uA 31 :GTKRNGELMRAL T0373 61 :RMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREEWLVRAMH 1z7uA 44 :GITQRVLTDRLREMEKDGLVHRESFNELPPRVEYTLTPEGYALYDALSSLCHWGETFAQK Number of specific fragments extracted= 5 number of extra gaps= 0 total=362 Number of alignments=62 # 1z7uA read from 1z7uA/merged-good-all-a2m # found chain 1z7uA in template set T0373 25 :RREAQADPVQFSQLVVLGAIDR 1z7uA 9 :INLALSTINGKWKLSLMDELFQ T0373 49 :GDVTPSELAAAE 1z7uA 31 :GTKRNGELMRAL T0373 61 :RMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREEWLVR 1z7uA 44 :GITQRVLTDRLREMEKDGLVHRESFNELPPRVEYTLTPEGYALYDALSSLCHWGETF T0373 119 :MHA 1z7uA 101 :AQK Number of specific fragments extracted= 4 number of extra gaps= 0 total=366 Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fbhA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fbhA expands to /projects/compbio/data/pdb/2fbh.pdb.gz 2fbhA:Skipped atom 109, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 111, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 113, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 115, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 117, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 119, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 121, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 123, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 125, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 127, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 129, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 272, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 274, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 276, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 278, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 280, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 282, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 284, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 286, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 403, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 405, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 407, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 409, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 411, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 413, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 415, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 417, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 419, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 421, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 423, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 480, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 482, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 484, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 486, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 488, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 490, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 492, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 494, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 496, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 666, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 668, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 670, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 672, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 674, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 676, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 678, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 680, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 682, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 835, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 837, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 839, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 841, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 843, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 845, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 847, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 849, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 851, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 876, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 878, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 880, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 882, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 884, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 886, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 1002, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 1004, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 1006, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 1008, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 1010, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 1012, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 1014, because occupancy 0.500 <= existing 0.500 in 2fbhA Skipped atom 1016, because occupancy 0.500 <= existing 0.500 in 2fbhA # T0373 read from 2fbhA/merged-good-all-a2m # 2fbhA read from 2fbhA/merged-good-all-a2m # adding 2fbhA to template set # found chain 2fbhA in template set Warning: unaligning (T0373)S36 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fbhA)R37 Warning: unaligning (T0373)Q37 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fbhA)R37 Warning: unaligning (T0373)E60 because of BadResidue code BAD_PEPTIDE in next template residue (2fbhA)G61 Warning: unaligning (T0373)R61 because of BadResidue code BAD_PEPTIDE at template residue (2fbhA)G61 T0373 12 :HLRSQVTTLTRRLRREAQADPVQF 2fbhA 12 :LLAQTSRAWRAELDRRLSHLGLSQ T0373 38 :LVVLGAIDRLGGDVTPSELAAA 2fbhA 38 :WLVLLHLARHRDSPTQRELAQS T0373 62 :MRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREE 2fbhA 62 :VEGPTLARLLDGLESQGLVRRLAVAEDRRAKHIVLTPKADVLIADIEAIAAS T0373 115 :LVRAMHACLDESERALLAA 2fbhA 114 :VRNDVLTGIDESEQALCQQ T0373 137 :LLTRLAQF 2fbhA 133 :VLLRILAN Number of specific fragments extracted= 5 number of extra gaps= 2 total=371 Number of alignments=64 # 2fbhA read from 2fbhA/merged-good-all-a2m # found chain 2fbhA in template set Warning: unaligning (T0373)S36 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fbhA)R37 Warning: unaligning (T0373)Q37 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fbhA)R37 Warning: unaligning (T0373)E60 because of BadResidue code BAD_PEPTIDE in next template residue (2fbhA)G61 Warning: unaligning (T0373)R61 because of BadResidue code BAD_PEPTIDE at template residue (2fbhA)G61 T0373 12 :HLRSQVTTLTRRLRREAQADPVQF 2fbhA 12 :LLAQTSRAWRAELDRRLSHLGLSQ T0373 38 :LVVLGAIDRLGGDVTPSELAAA 2fbhA 38 :WLVLLHLARHRDSPTQRELAQS T0373 62 :MRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREEWLVRAM 2fbhA 62 :VEGPTLARLLDGLESQGLVRRLAVAEDRRAKHIVLTPKADVLIADIEAIAASVRNDVL T0373 121 :ACLDESERALLAA 2fbhA 120 :TGIDESEQALCQQ T0373 137 :LLTRLAQF 2fbhA 133 :VLLRILAN Number of specific fragments extracted= 5 number of extra gaps= 2 total=376 Number of alignments=65 # 2fbhA read from 2fbhA/merged-good-all-a2m # found chain 2fbhA in template set Warning: unaligning (T0373)S36 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fbhA)R37 Warning: unaligning (T0373)Q37 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fbhA)R37 Warning: unaligning (T0373)E60 because of BadResidue code BAD_PEPTIDE in next template residue (2fbhA)G61 Warning: unaligning (T0373)R61 because of BadResidue code BAD_PEPTIDE at template residue (2fbhA)G61 T0373 13 :LRSQVTTLTRRLRREAQADPVQF 2fbhA 13 :LAQTSRAWRAELDRRLSHLGLSQ T0373 38 :LVVLGAIDRLGGDVTPSELAAA 2fbhA 38 :WLVLLHLARHRDSPTQRELAQS T0373 62 :MRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREEWLVR 2fbhA 62 :VEGPTLARLLDGLESQGLVRRLAVAEDRRAKHIVLTPKADVLIADIEAIAASVRND T0373 119 :MHACLDESERALLAAAGPLLTRLAQF 2fbhA 118 :VLTGIDESEQALCQQVLLRILANLEN Number of specific fragments extracted= 4 number of extra gaps= 2 total=380 Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bjaA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1bjaA expands to /projects/compbio/data/pdb/1bja.pdb.gz 1bjaA:# T0373 read from 1bjaA/merged-good-all-a2m # 1bjaA read from 1bjaA/merged-good-all-a2m # adding 1bjaA to template set # found chain 1bjaA in template set T0373 23 :RLRREAQAD 1bjaA 6 :YIIKASNDV T0373 33 :VQFSQLVVLGAIDRLGG 1bjaA 15 :LNEKTATILITIAKKDF T0373 51 :VTPSELAAA 1bjaA 32 :ITAAEVREV T0373 60 :ERMRSSNLAALLRELERGGLIVRH 1bjaA 42 :PDLGNAVVNSNIGVLIKKGLVEKS T0373 87 :QD 1bjaA 66 :GD T0373 93 :RVSLSSEGRRNLYGNRAKREE 1bjaA 68 :GLIITGEAQDIISNAATLYAQ Number of specific fragments extracted= 6 number of extra gaps= 0 total=386 Number of alignments=67 # 1bjaA read from 1bjaA/merged-good-all-a2m # found chain 1bjaA in template set T0373 22 :RRLRREAQAD 1bjaA 5 :TYIIKASNDV T0373 33 :VQFSQLVVLGAIDRLGG 1bjaA 15 :LNEKTATILITIAKKDF T0373 51 :VTPSELAAAE 1bjaA 32 :ITAAEVREVH T0373 61 :RMRSSNLAALLRELERGGLIVR 1bjaA 43 :DLGNAVVNSNIGVLIKKGLVEK T0373 85 :DPQ 1bjaA 65 :SGD T0373 93 :RVSLSSEGRRNLYGNRAKREE 1bjaA 68 :GLIITGEAQDIISNAATLYAQ Number of specific fragments extracted= 6 number of extra gaps= 0 total=392 Number of alignments=68 # 1bjaA read from 1bjaA/merged-good-all-a2m # found chain 1bjaA in template set T0373 32 :PVQFSQLVVLGAIDR 1bjaA 14 :VLNEKTATILITIAK T0373 48 :GGDVTPSELAAAE 1bjaA 29 :KDFITAAEVREVH T0373 61 :RMRSSNLAALLRELERGGLIVRHAD 1bjaA 43 :DLGNAVVNSNIGVLIKKGLVEKSGD T0373 93 :RVSLSSEGRRNLYGNRAKREEW 1bjaA 68 :GLIITGEAQDIISNAATLYAQE Number of specific fragments extracted= 4 number of extra gaps= 0 total=396 Number of alignments=69 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mkmA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1mkmA expands to /projects/compbio/data/pdb/1mkm.pdb.gz 1mkmA:# T0373 read from 1mkmA/merged-good-all-a2m # 1mkmA read from 1mkmA/merged-good-all-a2m # adding 1mkmA to template set # found chain 1mkmA in template set T0373 38 :LVVLGAIDRLGGDVTPSELAAAERMRSSNLAALLRELERGGLIVRH 1mkmA 8 :FEILDFIVKNPGDVSVSEIAEKFNMSVSNAYKYMVVLEEKGFVLRK T0373 87 :QDGRRTR 1mkmA 54 :KDKRYVP T0373 109 :AKREE 1mkmA 62 :YKLIE T0373 115 :LVRAMHACLD 1mkmA 67 :YGSFVLRRFN T0373 127 :ERALLAA 1mkmA 77 :IRDIAHD T0373 137 :LLTRLAQFEE 1mkmA 84 :HLVDIMKRTG Number of specific fragments extracted= 6 number of extra gaps= 0 total=402 Number of alignments=70 # 1mkmA read from 1mkmA/merged-good-all-a2m # found chain 1mkmA in template set T0373 36 :SQLVVLGAIDRLGGDVTPSELAAAERMRSSNLAALLRELERGGLIVRH 1mkmA 6 :KAFEILDFIVKNPGDVSVSEIAEKFNMSVSNAYKYMVVLEEKGFVLRK T0373 87 :QDGR 1mkmA 54 :KDKR T0373 94 :VSLSSEGRRNLYG 1mkmA 58 :YVPGYKLIEYGSF T0373 107 :NRAKREEWLVRAM 1mkmA 77 :IRDIAHDHLVDIM T0373 121 :AC 1mkmA 90 :KR Number of specific fragments extracted= 5 number of extra gaps= 0 total=407 Number of alignments=71 # 1mkmA read from 1mkmA/merged-good-all-a2m # found chain 1mkmA in template set T0373 37 :QLVVLGAIDRLGGDVTPSELAAAERMRSSNLAALLRELERGGLIVRH 1mkmA 7 :AFEILDFIVKNPGDVSVSEIAEKFNMSVSNAYKYMVVLEEKGFVLRK T0373 87 :QDGRRTR 1mkmA 54 :KDKRYVP T0373 110 :KREEWLVR 1mkmA 63 :KLIEYGSF T0373 119 :MHACLD 1mkmA 71 :VLRRFN T0373 127 :ERALLAAAGPLLTRLA 1mkmA 77 :IRDIAHDHLVDIMKRT Number of specific fragments extracted= 5 number of extra gaps= 0 total=412 Number of alignments=72 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ethA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2ethA expands to /projects/compbio/data/pdb/2eth.pdb.gz 2ethA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1046, because occupancy 0.500 <= existing 0.500 in 2ethA Skipped atom 1050, because occupancy 0.500 <= existing 0.500 in 2ethA Skipped atom 1052, because occupancy 0.500 <= existing 0.500 in 2ethA # T0373 read from 2ethA/merged-good-all-a2m # 2ethA read from 2ethA/merged-good-all-a2m # adding 2ethA to template set # found chain 2ethA in template set Warning: unaligning (T0373)P2 because first residue in template chain is (2ethA)H0 T0373 3 :TNQDLQL 2ethA 1 :MDALEIF T0373 18 :TTLTRRLRREAQADP 2ethA 8 :KTLFSLVMRFSSYLP T0373 33 :VQFSQLVVLGAIDRLGG 2ethA 30 :MKTTELYAFLYVALFGP T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREE 2ethA 47 :KKMKEIAEFLSTTKSNVTNVVDSLEKRGLVVREMDPVDRRTYRVVLTEKGKEIFGEILSNFES T0373 115 :LVRAMHACLDESERALLAA 2ethA 110 :LLKSVLEKFSEEDFKVVSE T0373 137 :LLTRLAQF 2ethA 129 :GFNRMVEA Number of specific fragments extracted= 6 number of extra gaps= 0 total=418 Number of alignments=73 # 2ethA read from 2ethA/merged-good-all-a2m # found chain 2ethA in template set Warning: unaligning (T0373)P2 because first residue in template chain is (2ethA)H0 T0373 3 :TNQDLQL 2ethA 1 :MDALEIF T0373 18 :TTLTRRLRREAQADP 2ethA 8 :KTLFSLVMRFSSYLP T0373 33 :VQFSQLVVLGAIDRL 2ethA 30 :MKTTELYAFLYVALF T0373 49 :GDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREEWLVRAM 2ethA 45 :GPKKMKEIAEFLSTTKSNVTNVVDSLEKRGLVVREMDPVDRRTYRVVLTEKGKEIFGEILSNFESLLKSVL T0373 121 :ACLDESERALLAA 2ethA 116 :EKFSEEDFKVVSE T0373 137 :LLTRLAQF 2ethA 129 :GFNRMVEA Number of specific fragments extracted= 6 number of extra gaps= 0 total=424 Number of alignments=74 # 2ethA read from 2ethA/merged-good-all-a2m # found chain 2ethA in template set Warning: unaligning (T0373)F144 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ethA)E140 Warning: unaligning (T0373)E145 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ethA)E140 T0373 19 :TLTRRLRREAQADP 2ethA 6 :IFKTLFSLVMRFSS T0373 33 :VQFSQLVVLGAIDR 2ethA 30 :MKTTELYAFLYVAL T0373 48 :GGDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREEWLVR 2ethA 44 :FGPKKMKEIAEFLSTTKSNVTNVVDSLEKRGLVVREMDPVDRRTYRVVLTEKGKEIFGEILSNFESLLKS T0373 119 :MHACLDESERALLAAAGPLLTRLAQ 2ethA 114 :VLEKFSEEDFKVVSEGFNRMVEALS Number of specific fragments extracted= 4 number of extra gaps= 1 total=428 Number of alignments=75 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lj9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1lj9A expands to /projects/compbio/data/pdb/1lj9.pdb.gz 1lj9A:# T0373 read from 1lj9A/merged-good-all-a2m # 1lj9A read from 1lj9A/merged-good-all-a2m # adding 1lj9A to template set # found chain 1lj9A in template set Warning: unaligning (T0373)T3 because first residue in template chain is (1lj9A)T2 T0373 4 :NQDLQL 1lj9A 3 :DILREI T0373 14 :RSQVTTLTRRLRREAQADPVQFSQLVVLGAIDRLGG 1lj9A 9 :GMIARALDSISNIEFKELSLTRGQYLYLVRVCENPG T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREE 1lj9A 45 :IIQEKIAELIKVDRTTAARAIKRLEEQGFIYRQEDASNKKIKRIYATEKGKNVYPIIVRENQH T0373 115 :LVRAMHACLDESERALLAA 1lj9A 108 :SNQVALQGLSEVEISQLAD T0373 137 :LLTRLAQF 1lj9A 127 :YLVRMRKN Number of specific fragments extracted= 5 number of extra gaps= 0 total=433 Number of alignments=76 # 1lj9A read from 1lj9A/merged-good-all-a2m # found chain 1lj9A in template set T0373 5 :Q 1lj9A 4 :I T0373 10 :AAHLRSQVTTLTRRLRREAQADPVQFSQLVVLGAIDRLGG 1lj9A 5 :LREIGMIARALDSISNIEFKELSLTRGQYLYLVRVCENPG T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREEWLVRAM 1lj9A 45 :IIQEKIAELIKVDRTTAARAIKRLEEQGFIYRQEDASNKKIKRIYATEKGKNVYPIIVRENQHSNQVAL T0373 121 :ACLDESERALLAA 1lj9A 114 :QGLSEVEISQLAD T0373 137 :LLTRLAQF 1lj9A 127 :YLVRMRKN Number of specific fragments extracted= 5 number of extra gaps= 0 total=438 Number of alignments=77 # 1lj9A read from 1lj9A/merged-good-all-a2m # found chain 1lj9A in template set T0373 11 :AHLRSQVTTLTRRLRREAQADPVQFSQLVVLGAIDR 1lj9A 6 :REIGMIARALDSISNIEFKELSLTRGQYLYLVRVCE T0373 48 :GGDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREEWLVR 1lj9A 42 :NPGIIQEKIAELIKVDRTTAARAIKRLEEQGFIYRQEDASNKKIKRIYATEKGKNVYPIIVRENQHSNQV T0373 119 :MHACLDESERALLAAAGPLLTRL 1lj9A 112 :ALQGLSEVEISQLADYLVRMRKN Number of specific fragments extracted= 3 number of extra gaps= 0 total=441 Number of alignments=78 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1dpuA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1dpuA expands to /projects/compbio/data/pdb/1dpu.pdb.gz 1dpuA:# T0373 read from 1dpuA/merged-good-all-a2m # 1dpuA read from 1dpuA/merged-good-all-a2m # adding 1dpuA to template set # found chain 1dpuA in template set Warning: unaligning (T0373)A30 because first residue in template chain is (1dpuA)A202 T0373 31 :DPVQFSQLVVLGAIDRLGGD 1dpuA 203 :NGLTVAQNQVLNLIKACPRP T0373 51 :VTPSELAAAE 1dpuA 225 :LNFQDLKNQL T0373 61 :RMRSSNLAALLRELERGGLIVRHADPQ 1dpuA 236 :HMSVSSIKQAVDFLSNEGHIYSTVDDD T0373 93 :RVSLSS 1dpuA 263 :HFKSTD Number of specific fragments extracted= 4 number of extra gaps= 0 total=445 Number of alignments=79 # 1dpuA read from 1dpuA/merged-good-all-a2m # found chain 1dpuA in template set Warning: unaligning (T0373)A30 because first residue in template chain is (1dpuA)A202 T0373 31 :DPVQFSQLVVLGAIDRLGGD 1dpuA 203 :NGLTVAQNQVLNLIKACPRP T0373 51 :VTPSELAAAE 1dpuA 225 :LNFQDLKNQL T0373 61 :RMRSSNLAALLRELERGGLIVRHADPQ 1dpuA 236 :HMSVSSIKQAVDFLSNEGHIYSTVDDD T0373 93 :RVSLSS 1dpuA 263 :HFKSTD Number of specific fragments extracted= 4 number of extra gaps= 0 total=449 Number of alignments=80 # 1dpuA read from 1dpuA/merged-good-all-a2m # found chain 1dpuA in template set Warning: unaligning (T0373)A30 because first residue in template chain is (1dpuA)A202 T0373 31 :DPVQFSQLVVLGAIDRLGGD 1dpuA 203 :NGLTVAQNQVLNLIKACPRP T0373 51 :VTPSELAAAE 1dpuA 225 :LNFQDLKNQL T0373 61 :RMRSSNLAALLRELERGGLIVRHADPQ 1dpuA 236 :HMSVSSIKQAVDFLSNEGHIYSTVDDD T0373 93 :RVSLS 1dpuA 263 :HFKST Number of specific fragments extracted= 4 number of extra gaps= 0 total=453 Number of alignments=81 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yg2A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1yg2A expands to /projects/compbio/data/pdb/1yg2.pdb.gz 1yg2A:# T0373 read from 1yg2A/merged-good-all-a2m # 1yg2A read from 1yg2A/merged-good-all-a2m # adding 1yg2A to template set # found chain 1yg2A in template set Warning: unaligning (T0373)D85 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yg2A)V68 Warning: unaligning (T0373)R93 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yg2A)V68 T0373 36 :SQLVVLGAIDR 1yg2A 3 :LPHVILTVLST T0373 48 :GG 1yg2A 14 :RD T0373 51 :VTPSELAAAER 1yg2A 16 :ATGYDITKEFS T0373 62 :MRSSNLAALLRELERGGLIVRHA 1yg2A 35 :ASHQQVYRELNKMGEQGLVTCVL T0373 94 :VSLSSEGRRNLYGNRA 1yg2A 69 :YSITQAGRSALGEWFD T0373 113 :E 1yg2A 95 :E T0373 115 :LVRAMHAC 1yg2A 96 :FSAKLMAC T0373 125 :ESERALLAAAGPLLTRLAQF 1yg2A 109 :EPYRLQLAELVEESRKLVAH Number of specific fragments extracted= 8 number of extra gaps= 0 total=461 Number of alignments=82 # 1yg2A read from 1yg2A/merged-good-all-a2m # found chain 1yg2A in template set Warning: unaligning (T0373)D85 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yg2A)V68 Warning: unaligning (T0373)R93 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yg2A)V68 T0373 36 :SQLVVLGAIDR 1yg2A 3 :LPHVILTVLST T0373 49 :GDVTPSELAAAER 1yg2A 14 :RDATGYDITKEFS T0373 62 :MRSSNLAALLRELERGGLIVRHA 1yg2A 35 :ASHQQVYRELNKMGEQGLVTCVL T0373 94 :VSLSSEGRRNLYGNRA 1yg2A 69 :YSITQAGRSALGEWFD T0373 110 :KREEWLVRA 1yg2A 95 :EFSAKLMAC T0373 121 :ACLD 1yg2A 104 :SVQS T0373 125 :ESERALLAAAGPLLTRLAQF 1yg2A 109 :EPYRLQLAELVEESRKLVAH Number of specific fragments extracted= 7 number of extra gaps= 0 total=468 Number of alignments=83 # 1yg2A read from 1yg2A/merged-good-all-a2m # found chain 1yg2A in template set Warning: unaligning (T0373)D85 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yg2A)V68 Warning: unaligning (T0373)R93 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yg2A)V68 T0373 37 :QLVVLGAIDR 1yg2A 4 :PHVILTVLST T0373 49 :GDVTPSELAAAER 1yg2A 14 :RDATGYDITKEFS T0373 62 :MRSSNLAALLRELERGGLIVRHA 1yg2A 35 :ASHQQVYRELNKMGEQGLVTCVL T0373 94 :VSLSSEGRRNLYGNRA 1yg2A 69 :YSITQAGRSALGEWFD T0373 110 :KREEWLVR 1yg2A 95 :EFSAKLMA T0373 119 :M 1yg2A 103 :C T0373 121 :ACLD 1yg2A 104 :SVQS T0373 125 :ESERALLAAAGPLLTRLAQ 1yg2A 109 :EPYRLQLAELVEESRKLVA Number of specific fragments extracted= 8 number of extra gaps= 0 total=476 Number of alignments=84 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1okrA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1okrA expands to /projects/compbio/data/pdb/1okr.pdb.gz 1okrA:# T0373 read from 1okrA/merged-good-all-a2m # 1okrA read from 1okrA/merged-good-all-a2m # adding 1okrA to template set # found chain 1okrA in template set Warning: unaligning (T0373)D31 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1okrA)Y6 Warning: unaligning (T0373)P86 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1okrA)K65 Warning: unaligning (T0373)Q87 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1okrA)K65 T0373 32 :PVQFSQLVVLGAIDRLGG 1okrA 7 :EISSAEWEVMNIIWMKKY T0373 51 :VTPSELAAAER 1okrA 25 :ASANNIIEEIQ T0373 62 :MRSSNLAALLRELERGGLIVRHAD 1okrA 40 :WSPKTIRTLITRLYKKGFIDRKKD T0373 91 :RTRVSLS 1okrA 66 :IFQYYSL T0373 98 :SEGRRNLYGNRAKR 1okrA 76 :SDIKYKTSKNFINK T0373 113 :EWLVRAMHAC 1okrA 96 :NSLVLNFVEK T0373 123 :LDESERALLAA 1okrA 108 :LSQDEIEELRN T0373 137 :L 1okrA 119 :I Number of specific fragments extracted= 8 number of extra gaps= 2 total=484 Number of alignments=85 # 1okrA read from 1okrA/merged-good-all-a2m # found chain 1okrA in template set Warning: unaligning (T0373)D31 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1okrA)Y6 Warning: unaligning (T0373)P86 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1okrA)K65 Warning: unaligning (T0373)Q87 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1okrA)K65 T0373 32 :PVQFSQLVVLGAIDRL 1okrA 7 :EISSAEWEVMNIIWMK T0373 49 :GDVTPSELAAAE 1okrA 23 :KYASANNIIEEI T0373 61 :RMRSSNLAALLRELERGGLIVRHAD 1okrA 39 :DWSPKTIRTLITRLYKKGFIDRKKD T0373 91 :RTRVSLS 1okrA 66 :IFQYYSL T0373 98 :SEGRRNLYGNR 1okrA 76 :SDIKYKTSKNF T0373 109 :AKREEWLVRA 1okrA 96 :NSLVLNFVEK T0373 121 :ACLDESERALLAA 1okrA 106 :EDLSQDEIEELRN Number of specific fragments extracted= 7 number of extra gaps= 2 total=491 Number of alignments=86 # 1okrA read from 1okrA/merged-good-all-a2m # found chain 1okrA in template set Warning: unaligning (T0373)P86 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1okrA)K65 Warning: unaligning (T0373)Q87 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1okrA)K65 T0373 32 :PVQFSQLVVLGAIDR 1okrA 7 :EISSAEWEVMNIIWM T0373 48 :GGDVTPSELAAAER 1okrA 22 :KKYASANNIIEEIQ T0373 62 :MRSSNLAALLRELERGGLIVRHAD 1okrA 40 :WSPKTIRTLITRLYKKGFIDRKKD T0373 91 :RTRVSLS 1okrA 66 :IFQYYSL T0373 98 :SEGRRNLYGNR 1okrA 76 :SDIKYKTSKNF T0373 109 :AKREEWLVR 1okrA 96 :NSLVLNFVE T0373 120 :HACLDESERALLAAA 1okrA 105 :KEDLSQDEIEELRNI Number of specific fragments extracted= 7 number of extra gaps= 1 total=498 Number of alignments=87 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lnwA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1lnwA expands to /projects/compbio/data/pdb/1lnw.pdb.gz 1lnwA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0373 read from 1lnwA/merged-good-all-a2m # 1lnwA read from 1lnwA/merged-good-all-a2m # adding 1lnwA to template set # found chain 1lnwA in template set T0373 2 :PTNQDLQLAAHLRSQVTTLTRRLRRE 1lnwA 6 :NPDLMPALMAVFQHVRTRIQSELDCQ T0373 30 :ADPVQFSQLVVLGAIDRLGG 1lnwA 32 :RLDLTPPDVHVLKLIDEQRG T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREE 1lnwA 52 :LNLQDLGRQMCRDKALITRKIRELEGRNLVRRERNPSDQRSFQLFLTDEGLAIHQHAEAIMSR T0373 115 :LVRAMHACLDESERALLAA 1lnwA 115 :VHDELFAPLTPVEQATLVH T0373 137 :LLTRLAQF 1lnwA 134 :LLDQCLAA Number of specific fragments extracted= 5 number of extra gaps= 0 total=503 Number of alignments=88 # 1lnwA read from 1lnwA/merged-good-all-a2m # found chain 1lnwA in template set Warning: unaligning (T0373)E145 because last residue in template chain is (1lnwA)Q142 T0373 1 :MPTNQDLQLAAHLRSQVTTLTRRLRRE 1lnwA 5 :VNPDLMPALMAVFQHVRTRIQSELDCQ T0373 30 :ADPVQFSQLVVLGAIDRLGG 1lnwA 32 :RLDLTPPDVHVLKLIDEQRG T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREEWLVRAM 1lnwA 52 :LNLQDLGRQMCRDKALITRKIRELEGRNLVRRERNPSDQRSFQLFLTDEGLAIHQHAEAIMSRVHDELF T0373 121 :ACLDESERALLAA 1lnwA 121 :APLTPVEQATLVH T0373 137 :LLTRLAQF 1lnwA 134 :LLDQCLAA Number of specific fragments extracted= 5 number of extra gaps= 0 total=508 Number of alignments=89 # 1lnwA read from 1lnwA/merged-good-all-a2m # found chain 1lnwA in template set T0373 14 :RSQVTTLTRRLRREAQADP 1lnwA 14 :MAVFQHVRTRIQSELDCQR T0373 33 :VQFSQLVVLGAIDR 1lnwA 35 :LTPPDVHVLKLIDE T0373 48 :GGDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREEWLVR 1lnwA 49 :QRGLNLQDLGRQMCRDKALITRKIRELEGRNLVRRERNPSDQRSFQLFLTDEGLAIHQHAEAIMSRVHDE T0373 119 :MHACLDESERALLAAAGPL 1lnwA 119 :LFAPLTPVEQATLVHLLDQ Number of specific fragments extracted= 4 number of extra gaps= 0 total=512 Number of alignments=90 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fu4A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fu4A expands to /projects/compbio/data/pdb/2fu4.pdb.gz 2fu4A:Skipped atom 148, because occupancy 0.500 <= existing 0.500 in 2fu4A Skipped atom 152, because occupancy 0.500 <= existing 0.500 in 2fu4A Skipped atom 154, because occupancy 0.500 <= existing 0.500 in 2fu4A Skipped atom 156, because occupancy 0.500 <= existing 0.500 in 2fu4A Skipped atom 158, because occupancy 0.500 <= existing 0.500 in 2fu4A Skipped atom 600, because occupancy 0.500 <= existing 0.500 in 2fu4A Skipped atom 602, because occupancy 0.500 <= existing 0.500 in 2fu4A Skipped atom 604, because occupancy 0.500 <= existing 0.500 in 2fu4A Skipped atom 606, because occupancy 0.500 <= existing 0.500 in 2fu4A Skipped atom 608, because occupancy 0.500 <= existing 0.500 in 2fu4A Skipped atom 610, because occupancy 0.500 <= existing 0.500 in 2fu4A Skipped atom 647, because occupancy 0.500 <= existing 0.500 in 2fu4A Skipped atom 649, because occupancy 0.500 <= existing 0.500 in 2fu4A Skipped atom 651, because occupancy 0.500 <= existing 0.500 in 2fu4A Skipped atom 653, because occupancy 0.500 <= existing 0.500 in 2fu4A Skipped atom 655, because occupancy 0.500 <= existing 0.500 in 2fu4A Skipped atom 657, because occupancy 0.500 <= existing 0.500 in 2fu4A Skipped atom 659, because occupancy 0.500 <= existing 0.500 in 2fu4A # T0373 read from 2fu4A/merged-good-all-a2m # 2fu4A read from 2fu4A/merged-good-all-a2m # adding 2fu4A to template set # found chain 2fu4A in template set T0373 27 :EAQADPV 2fu4A 7 :ALKKAGL T0373 34 :QFSQLVVLGAIDR 2fu4A 16 :TLPRLKILEVLQE T0373 48 :GG 2fu4A 29 :PD T0373 50 :DVTPSELAAAE 2fu4A 33 :HVSAEDLYKRL T0373 62 :MRSSNLAALLRELERGGLIVRHADPQDGRR 2fu4A 50 :IGLATVYRVLNQFDDAGIVTRHNFEGGKSV T0373 94 :VSL 2fu4A 80 :FEL Number of specific fragments extracted= 6 number of extra gaps= 0 total=518 Number of alignments=91 # 2fu4A read from 2fu4A/merged-good-all-a2m # found chain 2fu4A in template set Warning: unaligning (T0373)S97 because last residue in template chain is (2fu4A)T83 T0373 26 :REAQADPV 2fu4A 6 :TALKKAGL T0373 34 :QFSQLVVLGAIDR 2fu4A 16 :TLPRLKILEVLQE T0373 48 :GG 2fu4A 29 :PD T0373 50 :DVTPSELAAAE 2fu4A 33 :HVSAEDLYKRL T0373 62 :MRSSNLAALLRELERGGLIVRHADPQDGRR 2fu4A 50 :IGLATVYRVLNQFDDAGIVTRHNFEGGKSV T0373 94 :VSL 2fu4A 80 :FEL Number of specific fragments extracted= 6 number of extra gaps= 0 total=524 Number of alignments=92 # 2fu4A read from 2fu4A/merged-good-all-a2m # found chain 2fu4A in template set T0373 27 :EAQADPV 2fu4A 7 :ALKKAGL T0373 34 :QFSQLVVLGAIDR 2fu4A 16 :TLPRLKILEVLQE T0373 48 :GG 2fu4A 29 :PD T0373 51 :VTPSELAAAE 2fu4A 34 :VSAEDLYKRL T0373 62 :MRSSNLAALLRELERGGLIVRHADPQDGRRTR 2fu4A 50 :IGLATVYRVLNQFDDAGIVTRHNFEGGKSVFE Number of specific fragments extracted= 5 number of extra gaps= 0 total=529 Number of alignments=93 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jgsA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1jgsA expands to /projects/compbio/data/pdb/1jgs.pdb.gz 1jgsA:# T0373 read from 1jgsA/merged-good-all-a2m # 1jgsA read from 1jgsA/merged-good-all-a2m # adding 1jgsA to template set # found chain 1jgsA in template set T0373 2 :PTNQDLQL 1jgsA 11 :IIPLGRLI T0373 14 :RSQVTTLTRRLRREAQADPVQFSQLVVLGAIDRLGG 1jgsA 19 :HMVNQKKDRLLNEYLSPLDITAAQFKVLCSIRCAAC T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREEWLVRAMHAC 1jgsA 55 :ITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTGGAAICEQCHQLVGQDLHQELTKN T0373 126 :SERALLAA 1jgsA 133 :ATLEYLLK T0373 143 :QFE 1jgsA 141 :KVL Number of specific fragments extracted= 5 number of extra gaps= 0 total=534 Number of alignments=94 # 1jgsA read from 1jgsA/merged-good-all-a2m # found chain 1jgsA in template set Warning: unaligning (T0373)P2 because first residue in template chain is (1jgsA)L7 Warning: unaligning (T0373)E146 because last residue in template chain is (1jgsA)P144 T0373 3 :TNQDLQLAAHLRSQVTTLTRRLRREAQADPVQFSQLVVLGAIDRL 1jgsA 8 :FNEIIPLGRLIHMVNQKKDRLLNEYLSPLDITAAQFKVLCSIRCA T0373 49 :GDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREEWLVRAM 1jgsA 53 :ACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTGGAAICEQCHQLVGQDLHQEL T0373 120 :HACLDESERALLAA 1jgsA 127 :LTADEVATLEYLLK T0373 143 :QFE 1jgsA 141 :KVL Number of specific fragments extracted= 4 number of extra gaps= 0 total=538 Number of alignments=95 # 1jgsA read from 1jgsA/merged-good-all-a2m # found chain 1jgsA in template set T0373 2 :PTNQDLQ 1jgsA 11 :IIPLGRL T0373 13 :LRSQVTTLTRRLRREAQADPVQFSQLVVLGAIDR 1jgsA 18 :IHMVNQKKDRLLNEYLSPLDITAAQFKVLCSIRC T0373 48 :GGDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREEWLVRAMHACLDESERALLAAAGP 1jgsA 52 :AACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTGGAAICEQCHQLVGQDLHQELTKNLTADEVATLEYLLK Number of specific fragments extracted= 3 number of extra gaps= 0 total=541 Number of alignments=96 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ub9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ub9A expands to /projects/compbio/data/pdb/1ub9.pdb.gz 1ub9A:# T0373 read from 1ub9A/merged-good-all-a2m # 1ub9A read from 1ub9A/merged-good-all-a2m # adding 1ub9A to template set # found chain 1ub9A in template set T0373 34 :QFSQLVVLGAIDRLGG 1ub9A 15 :NPVRLGIMIFLLPRRK T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREE 1ub9A 31 :APFSQIQKVLDLTPGNLDSHIRVLERNGLVKTYKVIADRPRTVVEITDFGMEEAKRFLSSLKA T0373 115 :LVRAM 1ub9A 94 :VIDGL Number of specific fragments extracted= 3 number of extra gaps= 0 total=544 Number of alignments=97 # 1ub9A read from 1ub9A/merged-good-all-a2m # found chain 1ub9A in template set T0373 34 :QFSQLVVLGAIDRL 1ub9A 15 :NPVRLGIMIFLLPR T0373 49 :GDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREEWLVRA 1ub9A 29 :RKAPFSQIQKVLDLTPGNLDSHIRVLERNGLVKTYKVIADRPRTVVEITDFGMEEAKRFLSSLKAVIDGL Number of specific fragments extracted= 2 number of extra gaps= 0 total=546 Number of alignments=98 # 1ub9A read from 1ub9A/merged-good-all-a2m # found chain 1ub9A in template set T0373 34 :QFSQLVVLGAIDR 1ub9A 15 :NPVRLGIMIFLLP T0373 48 :GGDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREEWLVR 1ub9A 28 :RRKAPFSQIQKVLDLTPGNLDSHIRVLERNGLVKTYKVIADRPRTVVEITDFGMEEAKRFLSSLKAVIDG T0373 119 :M 1ub9A 98 :L Number of specific fragments extracted= 3 number of extra gaps= 0 total=549 Number of alignments=99 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yyvA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1yyvA expands to /projects/compbio/data/pdb/1yyv.pdb.gz 1yyvA:Skipped atom 310, because occupancy 0.490 <= existing 0.510 in 1yyvA Skipped atom 312, because occupancy 0.490 <= existing 0.510 in 1yyvA Skipped atom 314, because occupancy 0.490 <= existing 0.510 in 1yyvA Skipped atom 316, because occupancy 0.490 <= existing 0.510 in 1yyvA Skipped atom 318, because occupancy 0.490 <= existing 0.510 in 1yyvA Skipped atom 320, because occupancy 0.490 <= existing 0.510 in 1yyvA Skipped atom 322, because occupancy 0.490 <= existing 0.510 in 1yyvA Bad short name: CH1 for alphabet: pdb_atoms Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: CH1 for alphabet: pdb_atoms Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 637, because occupancy 0.460 <= existing 0.540 in 1yyvA Skipped atom 639, because occupancy 0.460 <= existing 0.540 in 1yyvA Skipped atom 641, because occupancy 0.460 <= existing 0.540 in 1yyvA Skipped atom 643, because occupancy 0.460 <= existing 0.540 in 1yyvA Skipped atom 645, because occupancy 0.460 <= existing 0.540 in 1yyvA Skipped atom 647, because occupancy 0.460 <= existing 0.540 in 1yyvA Bad short name: CH1 for alphabet: pdb_atoms # T0373 read from 1yyvA/merged-good-all-a2m # 1yyvA read from 1yyvA/merged-good-all-a2m # adding 1yyvA to template set # found chain 1yyvA in template set Warning: unaligning (T0373)A58 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yyvA)M55 Warning: unaligning (T0373)E60 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yyvA)M55 Warning: unaligning (T0373)S64 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yyvA)M62 Warning: unaligning (T0373)N66 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yyvA)M62 Warning: unaligning (T0373)I80 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yyvA)N77 Warning: unaligning (T0373)V81 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yyvA)N77 Warning: unaligning (T0373)Y105 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yyvA)V103 Warning: unaligning (T0373)N107 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yyvA)V103 T0373 26 :REAQ 1yyvA 27 :KHVT T0373 34 :QFSQLVVLGAID 1yyvA 31 :SRWGVLILVALR T0373 48 :GGDVTPSELA 1yyvA 43 :DGTHRFSDLR T0373 61 :RMR 1yyvA 57 :GVS T0373 67 :LAALLRELERGGL 1yyvA 63 :LAQSLQALEQDGF T0373 82 :RHADPQDGRRTRVSLSSEGRRNL 1yyvA 78 :RVSYPVVPPHVEYSLTPLGEQVS T0373 108 :RAKREEWLVRA 1yyvA 104 :AALADWIELNL Number of specific fragments extracted= 7 number of extra gaps= 1 total=556 Number of alignments=100 # 1yyvA read from 1yyvA/merged-good-all-a2m # found chain 1yyvA in template set Warning: unaligning (T0373)A58 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yyvA)M55 Warning: unaligning (T0373)E60 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yyvA)M55 Warning: unaligning (T0373)S64 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yyvA)M62 Warning: unaligning (T0373)N66 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yyvA)M62 Warning: unaligning (T0373)I80 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yyvA)N77 Warning: unaligning (T0373)V81 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yyvA)N77 Warning: unaligning (T0373)Y105 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yyvA)V103 Warning: unaligning (T0373)N107 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yyvA)V103 T0373 7 :L 1yyvA 23 :R T0373 19 :TLTRRLR 1yyvA 24 :EVLKHVT T0373 34 :QFSQLVVLGAID 1yyvA 31 :SRWGVLILVALR T0373 48 :GGDVTPSELA 1yyvA 43 :DGTHRFSDLR T0373 61 :RMR 1yyvA 57 :GVS T0373 67 :LAALLRELERGGL 1yyvA 63 :LAQSLQALEQDGF T0373 82 :RHADPQDGRRTRVSLSSEGRRNL 1yyvA 78 :RVSYPVVPPHVEYSLTPLGEQVS T0373 108 :RAKREEWLVRAM 1yyvA 104 :AALADWIELNLP Number of specific fragments extracted= 8 number of extra gaps= 1 total=564 Number of alignments=101 # 1yyvA read from 1yyvA/merged-good-all-a2m # found chain 1yyvA in template set Warning: unaligning (T0373)A58 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yyvA)M55 Warning: unaligning (T0373)E60 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yyvA)M55 Warning: unaligning (T0373)S64 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yyvA)M62 Warning: unaligning (T0373)N66 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yyvA)M62 Warning: unaligning (T0373)I80 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1yyvA)N77 Warning: unaligning (T0373)V81 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1yyvA)N77 Warning: unaligning (T0373)Y105 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1yyvA)V103 Warning: unaligning (T0373)N107 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1yyvA)V103 Warning: unaligning (T0373)D124 because last residue in template chain is (1yyvA)E122 T0373 23 :RLRREAQ 1yyvA 24 :EVLKHVT T0373 34 :QFSQLVVLGAIDR 1yyvA 31 :SRWGVLILVALRD T0373 49 :GDVTPSELA 1yyvA 44 :GTHRFSDLR T0373 61 :RMR 1yyvA 57 :GVS T0373 67 :LAALLRELERGGL 1yyvA 63 :LAQSLQALEQDGF T0373 82 :RHADPQDGRRTRVSLSSEGRRNL 1yyvA 78 :RVSYPVVPPHVEYSLTPLGEQVS T0373 108 :RAKREEWLVRA 1yyvA 104 :AALADWIELNL T0373 119 :MHACL 1yyvA 117 :VLAQR Number of specific fragments extracted= 8 number of extra gaps= 1 total=572 Number of alignments=102 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2g7uA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2g7uA expands to /projects/compbio/data/pdb/2g7u.pdb.gz 2g7uA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0373 read from 2g7uA/merged-good-all-a2m # 2g7uA read from 2g7uA/merged-good-all-a2m # adding 2g7uA to template set # found chain 2g7uA in template set T0373 2 :PTNQDLQLAAHLRS 2g7uA 7 :DYIQSIERGFAVLL T0373 47 :LGGD 2g7uA 22 :FDAQ T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRH 2g7uA 29 :PTLAELATEAGLSRPAVRRILLTLQKLGYVAGS T0373 86 :PQ 2g7uA 62 :GG T0373 93 :RVSLSSEGRRN 2g7uA 64 :RWSLTPRVLSI T0373 105 :YGNRAKREE 2g7uA 75 :GQHYSESHA T0373 115 :LVRAMHA 2g7uA 84 :LIEAAMP T0373 137 :LLTRLAQF 2g7uA 91 :RLLEVAEK Number of specific fragments extracted= 8 number of extra gaps= 0 total=580 Number of alignments=103 # 2g7uA read from 2g7uA/merged-good-all-a2m # found chain 2g7uA in template set T0373 1 :MPTNQDLQLAAHLRS 2g7uA 6 :RDYIQSIERGFAVLL T0373 29 :Q 2g7uA 23 :D T0373 48 :GG 2g7uA 24 :AQ T0373 50 :DVTPSELAAAERMRSSNLAALLRELERGGLIVRH 2g7uA 28 :NPTLAELATEAGLSRPAVRRILLTLQKLGYVAGS T0373 86 :PQ 2g7uA 62 :GG T0373 93 :RVSLSSEGRRN 2g7uA 64 :RWSLTPRVLSI T0373 105 :YGNRAKREEWLVRAM 2g7uA 75 :GQHYSESHALIEAAM T0373 136 :PLLTRLAQF 2g7uA 90 :PRLLEVAEK Number of specific fragments extracted= 8 number of extra gaps= 0 total=588 Number of alignments=104 # 2g7uA read from 2g7uA/merged-good-all-a2m # found chain 2g7uA in template set T0373 1 :MPTNQDLQLAAHLRSQ 2g7uA 6 :RDYIQSIERGFAVLLA T0373 47 :LGGD 2g7uA 22 :FDAQ T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHAD 2g7uA 29 :PTLAELATEAGLSRPAVRRILLTLQKLGYVAGSGG T0373 93 :RVSLSSEGRRNL 2g7uA 64 :RWSLTPRVLSIG T0373 121 :ACLD 2g7uA 76 :QHYS T0373 125 :ESERALLAAAGPLLTRLAQ 2g7uA 82 :HALIEAAMPRLLEVAEKTQ Number of specific fragments extracted= 6 number of extra gaps= 0 total=594 Number of alignments=105 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cfxA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2cfxA expands to /projects/compbio/data/pdb/2cfx.pdb.gz 2cfxA:# T0373 read from 2cfxA/merged-good-all-a2m # 2cfxA read from 2cfxA/merged-good-all-a2m # adding 2cfxA to template set # found chain 2cfxA in template set Warning: unaligning (T0373)S64 because of BadResidue code BAD_PEPTIDE in next template residue (2cfxA)P34 Warning: unaligning (T0373)S65 because of BadResidue code BAD_PEPTIDE at template residue (2cfxA)P34 Warning: unaligning (T0373)A84 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2cfxA)L54 Warning: unaligning (T0373)D85 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2cfxA)L54 T0373 32 :PVQFSQLVVLGAIDR 2cfxA 2 :KLDQIDLNIIEELKK T0373 48 :GGDVTPSELAAAERMR 2cfxA 17 :DSRLSMRELGRKIKLS T0373 66 :NLAALLRELERGGLIVRH 2cfxA 35 :SVTERVRQLESFGIIKQY T0373 86 :PQDGRRTRVSLS 2cfxA 61 :LGLPVSCIVEAT T0373 98 :SEGRRNLYGN 2cfxA 79 :ERFKSYIQTL T0373 108 :RAKREE 2cfxA 112 :LEAVED T0373 115 :LVRAMHA 2cfxA 118 :FINKTSP Number of specific fragments extracted= 7 number of extra gaps= 2 total=601 Number of alignments=106 # 2cfxA read from 2cfxA/merged-good-all-a2m # found chain 2cfxA in template set Warning: unaligning (T0373)D31 because first residue in template chain is (2cfxA)M1 Warning: unaligning (T0373)S64 because of BadResidue code BAD_PEPTIDE in next template residue (2cfxA)P34 Warning: unaligning (T0373)S65 because of BadResidue code BAD_PEPTIDE at template residue (2cfxA)P34 Warning: unaligning (T0373)V81 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2cfxA)L54 Warning: unaligning (T0373)R82 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2cfxA)L54 T0373 32 :PVQFSQLVVLGAIDR 2cfxA 2 :KLDQIDLNIIEELKK T0373 48 :GGDVTPSELAAAERMR 2cfxA 17 :DSRLSMRELGRKIKLS T0373 66 :NLAALLRELERGGLI 2cfxA 35 :SVTERVRQLESFGII T0373 83 :HAD 2cfxA 55 :EVD T0373 86 :PQDGRRTRVSLS 2cfxA 61 :LGLPVSCIVEAT T0373 98 :SEGRRNLYGN 2cfxA 79 :ERFKSYIQTL T0373 108 :RAKREEWLVRA 2cfxA 112 :LEAVEDFINKT Number of specific fragments extracted= 7 number of extra gaps= 2 total=608 Number of alignments=107 # 2cfxA read from 2cfxA/merged-good-all-a2m # found chain 2cfxA in template set Warning: unaligning (T0373)S64 because of BadResidue code BAD_PEPTIDE in next template residue (2cfxA)P34 Warning: unaligning (T0373)S65 because of BadResidue code BAD_PEPTIDE at template residue (2cfxA)P34 T0373 32 :PVQFSQLVVLGAIDR 2cfxA 2 :KLDQIDLNIIEELKK T0373 48 :GGDVTPSELAAAERMR 2cfxA 17 :DSRLSMRELGRKIKLS T0373 66 :NLAALLRELERGGLIVRH 2cfxA 35 :SVTERVRQLESFGIIKQY T0373 85 :DPQDGRRTRVSLS 2cfxA 60 :KLGLPVSCIVEAT T0373 98 :SEGRRNLYGN 2cfxA 79 :ERFKSYIQTL Number of specific fragments extracted= 5 number of extra gaps= 1 total=613 Number of alignments=108 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1tbxA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1tbxA expands to /projects/compbio/data/pdb/1tbx.pdb.gz 1tbxA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0373 read from 1tbxA/merged-good-all-a2m # 1tbxA read from 1tbxA/merged-good-all-a2m # adding 1tbxA to template set # found chain 1tbxA in template set T0373 36 :SQLVVLGAIDRLGG 1tbxA 9 :PEAIVLAYLYDNEG T0373 51 :VTPSELAAAER 1tbxA 23 :IATYDLYKKVN T0373 62 :MRSSNLAALLRELERGGLIVRHADPQ 1tbxA 38 :MSTATFYDAKKFLIQEGFVKERQERG T0373 91 :RTRVSLSSEGRRNLYGNRAKREE 1tbxA 64 :EKRLYLTEKGKLFAISLKTAIET T0373 115 :LVRAMHA 1tbxA 87 :YKQIKKR Number of specific fragments extracted= 5 number of extra gaps= 0 total=618 Number of alignments=109 # 1tbxA read from 1tbxA/merged-good-all-a2m # found chain 1tbxA in template set T0373 36 :SQLVVLGAIDRLGG 1tbxA 9 :PEAIVLAYLYDNEG T0373 51 :VTPSELAAAER 1tbxA 23 :IATYDLYKKVN T0373 62 :MRSSNLAALLRELERGGLIVRHADPQ 1tbxA 38 :MSTATFYDAKKFLIQEGFVKERQERG T0373 91 :RTRVSLSSEGRRNLYGNRAKREEWLVRAM 1tbxA 64 :EKRLYLTEKGKLFAISLKTAIETYKQIKK T0373 121 :A 1tbxA 93 :R Number of specific fragments extracted= 5 number of extra gaps= 0 total=623 Number of alignments=110 # 1tbxA read from 1tbxA/merged-good-all-a2m # found chain 1tbxA in template set T0373 36 :SQLVVLGAIDR 1tbxA 9 :PEAIVLAYLYD T0373 48 :GGDVTPSELAAAER 1tbxA 20 :NEGIATYDLYKKVN T0373 62 :MRSSNLAALLRELERGGLIVRHADPQDG 1tbxA 38 :MSTATFYDAKKFLIQEGFVKERQERGEK T0373 93 :RVSLSSEGRRNLYGNRAKREEWLVR 1tbxA 66 :RLYLTEKGKLFAISLKTAIETYKQI T0373 119 :MHACL 1tbxA 91 :KKRHH Number of specific fragments extracted= 5 number of extra gaps= 0 total=628 Number of alignments=111 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ddnA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ddnA expands to /projects/compbio/data/pdb/1ddn.pdb.gz 1ddnA:# T0373 read from 1ddnA/merged-good-all-a2m # 1ddnA read from 1ddnA/merged-good-all-a2m # adding 1ddnA to template set # found chain 1ddnA in template set T0373 35 :FSQLVVLGAIDRLGGDVTPSELAAAERMRSSNLAALLRELERGGLIVRH 1ddnA 9 :EMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVA T0373 87 :QDGR 1ddnA 58 :SDRS T0373 94 :VSLSSEGRRNLYGNRAKRE 1ddnA 62 :LQMTPTGRTLATAVMRKHR T0373 114 :WLVRAMHAC 1ddnA 81 :LAERLLTDI T0373 123 :LDESERALLAA 1ddnA 108 :MSDEVERRLVK Number of specific fragments extracted= 5 number of extra gaps= 0 total=633 Number of alignments=112 # 1ddnA read from 1ddnA/merged-good-all-a2m # found chain 1ddnA in template set Warning: unaligning (T0373)E145 because last residue in template chain is (1ddnA)L120 T0373 34 :QFSQLVVLGAIDRLGGDVTPSELAAAERMRSSNLAALLRELERGGLIVRH 1ddnA 8 :TEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVA T0373 87 :QDGR 1ddnA 58 :SDRS T0373 94 :VSLSSEGRRNLYGNRAKR 1ddnA 62 :LQMTPTGRTLATAVMRKH T0373 113 :EWLVRAMHA 1ddnA 80 :RLAERLLTD T0373 122 :CLD 1ddnA 91 :GLD T0373 125 :ESERALLAAAG 1ddnA 95 :NKVHDEADRWE T0373 136 :PLLTRLAQF 1ddnA 111 :EVERRLVKV Number of specific fragments extracted= 7 number of extra gaps= 0 total=640 Number of alignments=113 # 1ddnA read from 1ddnA/merged-good-all-a2m # found chain 1ddnA in template set T0373 35 :FSQLVVLGAIDR 1ddnA 9 :EMYLRTIYELEE T0373 48 :GGD 1ddnA 21 :EGV T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHADP 1ddnA 25 :PLRARIAERLEQSGPTVSQTVARMERDGLVVVASDR T0373 93 :RVSLSSEGRRNLYGNRAKRE 1ddnA 61 :SLQMTPTGRTLATAVMRKHR T0373 114 :WLVRAMHA 1ddnA 81 :LAERLLTD T0373 122 :CLDESERALLAA 1ddnA 107 :VMSDEVERRLVK Number of specific fragments extracted= 6 number of extra gaps= 0 total=646 Number of alignments=114 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r1uA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1r1uA expands to /projects/compbio/data/pdb/1r1u.pdb.gz 1r1uA:# T0373 read from 1r1uA/merged-good-all-a2m # 1r1uA read from 1r1uA/merged-good-all-a2m # adding 1r1uA to template set # found chain 1r1uA in template set T0373 19 :TLTRRLRREAQ 1r1uA 14 :ERVTEIFKALG T0373 34 :QFSQLVVLGAIDR 1r1uA 25 :DYNRIRIMELLSV T0373 48 :GG 1r1uA 38 :SE T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQ 1r1uA 40 :ASVGHISHQLNLSQSNVSHQLKLLKSVHLVKAKRQGQ T0373 91 :RTRVSLSS 1r1uA 77 :SMIYSLDD T0373 99 :EGRRNLYGNRAK 1r1uA 86 :HVATMLKQAIHH Number of specific fragments extracted= 6 number of extra gaps= 0 total=652 Number of alignments=115 # 1r1uA read from 1r1uA/merged-good-all-a2m # found chain 1r1uA in template set T0373 18 :TTLTRRLRREAQA 1r1uA 13 :LERVTEIFKALGD T0373 35 :FSQLVVLGAIDR 1r1uA 26 :YNRIRIMELLSV T0373 49 :GDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQ 1r1uA 38 :SEASVGHISHQLNLSQSNVSHQLKLLKSVHLVKAKRQGQ T0373 91 :RTRVSLSS 1r1uA 77 :SMIYSLDD T0373 99 :EGRRNLYGNRA 1r1uA 86 :HVATMLKQAIH T0373 117 :R 1r1uA 97 :H Number of specific fragments extracted= 6 number of extra gaps= 0 total=658 Number of alignments=116 # 1r1uA read from 1r1uA/merged-good-all-a2m # found chain 1r1uA in template set T0373 22 :RRLRREAQADPVQFSQLVVLGAIDR 1r1uA 13 :LERVTEIFKALGDYNRIRIMELLSV T0373 49 :GDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQ 1r1uA 38 :SEASVGHISHQLNLSQSNVSHQLKLLKSVHLVKAKRQGQ T0373 91 :RTRVSLSSE 1r1uA 77 :SMIYSLDDI T0373 106 :GNRAKREEWLVR 1r1uA 86 :HVATMLKQAIHH T0373 119 :M 1r1uA 98 :A Number of specific fragments extracted= 5 number of extra gaps= 0 total=663 Number of alignments=117 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1u2wA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1u2wA expands to /projects/compbio/data/pdb/1u2w.pdb.gz 1u2wA:# T0373 read from 1u2wA/merged-good-all-a2m # 1u2wA read from 1u2wA/merged-good-all-a2m # adding 1u2wA to template set # found chain 1u2wA in template set Warning: unaligning (T0373)H83 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u2wA)L94 Warning: unaligning (T0373)R91 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u2wA)L94 T0373 21 :TRRLRREAQ 1u2wA 32 :VSQILKAIA T0373 35 :FSQLVVLGAIDRLGG 1u2wA 42 :ENRAKITYALCQDEE T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVR 1u2wA 57 :LCVCDIANILGVTIANASHHLRTLYKQGVVNF T0373 92 :TRVSLS 1u2wA 95 :ALYSLG T0373 98 :SEGRRNLYGNRAK 1u2wA 102 :EHIRQIMMIALAH Number of specific fragments extracted= 5 number of extra gaps= 0 total=668 Number of alignments=118 # 1u2wA read from 1u2wA/merged-good-all-a2m # found chain 1u2wA in template set Warning: unaligning (T0373)H83 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u2wA)L94 Warning: unaligning (T0373)R91 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u2wA)L94 T0373 2 :PTNQDLQLAAHLRS 1u2wA 12 :YDEEKVNRIQGDLQ T0373 21 :TRRLRREAQA 1u2wA 32 :VSQILKAIAD T0373 35 :FSQLVVLGAIDR 1u2wA 42 :ENRAKITYALCQ T0373 48 :GGDVTPSELAAAERMRSSNLAALLRELERGGLIVR 1u2wA 54 :DEELCVCDIANILGVTIANASHHLRTLYKQGVVNF T0373 92 :TRVSLS 1u2wA 95 :ALYSLG T0373 98 :SEGRRNLYGNRAK 1u2wA 102 :EHIRQIMMIALAH Number of specific fragments extracted= 6 number of extra gaps= 0 total=674 Number of alignments=119 # 1u2wA read from 1u2wA/merged-good-all-a2m # found chain 1u2wA in template set Warning: unaligning (T0373)H83 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1u2wA)L94 Warning: unaligning (T0373)R91 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u2wA)L94 T0373 21 :TRRLRREAQ 1u2wA 32 :VSQILKAIA T0373 34 :QFSQLVVLGAIDR 1u2wA 41 :DENRAKITYALCQ T0373 48 :GGDVTPSELAAAERMRSSNLAALLRELERGGLIVR 1u2wA 54 :DEELCVCDIANILGVTIANASHHLRTLYKQGVVNF T0373 92 :TRVSLS 1u2wA 95 :ALYSLG T0373 98 :SEGRRNLYGNRAK 1u2wA 102 :EHIRQIMMIALAH Number of specific fragments extracted= 5 number of extra gaps= 0 total=679 Number of alignments=120 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1s3jA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1s3jA expands to /projects/compbio/data/pdb/1s3j.pdb.gz 1s3jA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 993, because occupancy 0.400 <= existing 0.600 in 1s3jA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 995, because occupancy 0.400 <= existing 0.600 in 1s3jA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 997, because occupancy 0.350 <= existing 0.530 in 1s3jA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 999, because occupancy 0.400 <= existing 0.600 in 1s3jA # T0373 read from 1s3jA/merged-good-all-a2m # 1s3jA read from 1s3jA/merged-good-all-a2m # adding 1s3jA to template set # found chain 1s3jA in template set T0373 4 :NQDLQLAAHLRSQVTTLTRRLRREAQADPVQFSQLVVLGAIDRLGG 1s3jA 6 :QLMSDIQLSLQALFQKIQPEMLESMEKQGVTPAQLFVLASLKKHGS T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREE 1s3jA 52 :LKVSEIAERMEVKPSAVTLMADRLEQKNLIARTHNTKDRRVIDLSLTDEGDIKFEEVLAGRKA T0373 115 :LVRAMHACLDESERALLAAAGPLLTRL 1s3jA 115 :IMARYLSFLTEEEMLQAAHITAKLAQA Number of specific fragments extracted= 3 number of extra gaps= 0 total=682 Number of alignments=121 # 1s3jA read from 1s3jA/merged-good-all-a2m # found chain 1s3jA in template set Warning: unaligning (T0373)E145 because last residue in template chain is (1s3jA)D145 T0373 3 :TNQDLQLAAHLRSQVTTLTRRLRREAQADPVQFSQLVVLGAIDRL 1s3jA 5 :DQLMSDIQLSLQALFQKIQPEMLESMEKQGVTPAQLFVLASLKKH T0373 49 :GDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREEWLVRAM 1s3jA 50 :GSLKVSEIAERMEVKPSAVTLMADRLEQKNLIARTHNTKDRRVIDLSLTDEGDIKFEEVLAGRKAIMARYL T0373 121 :ACLDESERALLAAAGPLLTRLAQF 1s3jA 121 :SFLTEEEMLQAAHITAKLAQAAET Number of specific fragments extracted= 3 number of extra gaps= 0 total=685 Number of alignments=122 # 1s3jA read from 1s3jA/merged-good-all-a2m # found chain 1s3jA in template set Warning: unaligning (T0373)E145 because last residue in template chain is (1s3jA)D145 T0373 8 :QLAAHLRSQVTTLTRRLRREAQADPVQFSQLVVLGAIDR 1s3jA 10 :DIQLSLQALFQKIQPEMLESMEKQGVTPAQLFVLASLKK T0373 48 :GGDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREEWLVR 1s3jA 49 :HGSLKVSEIAERMEVKPSAVTLMADRLEQKNLIARTHNTKDRRVIDLSLTDEGDIKFEEVLAGRKAIMAR T0373 119 :MHACLDESERALLAAAGPLLTRLAQF 1s3jA 119 :YLSFLTEEEMLQAAHITAKLAQAAET Number of specific fragments extracted= 3 number of extra gaps= 0 total=688 Number of alignments=123 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1on2A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0373 read from 1on2A/merged-good-all-a2m # 1on2A read from 1on2A/merged-good-all-a2m # found chain 1on2A in training set T0373 35 :FSQLVVLGAIDRLGG 1on2A 8 :MYIEQIYMLIEEKGY T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRH 1on2A 23 :ARVSDIAEALAVHPSSVTKMVQKLDKDEYLIYE T0373 87 :QDG 1on2A 56 :KYR T0373 93 :RVSLSSEGRRNLYGNRAKRE 1on2A 59 :GLVLTSKGKKIGKRLVYRHE T0373 114 :WLVRAM 1on2A 79 :LLEQFL T0373 120 :HACLDESER 1on2A 86 :IIGVDEEKI T0373 129 :ALLAA 1on2A 111 :DRIGD T0373 137 :LLTRL 1on2A 116 :LVQYF Number of specific fragments extracted= 8 number of extra gaps= 0 total=696 Number of alignments=124 # 1on2A read from 1on2A/merged-good-all-a2m # found chain 1on2A in training set Warning: unaligning (T0373)V33 because first residue in template chain is (1on2A)T2 T0373 34 :QFSQLVVLGAIDRL 1on2A 3 :TPSMEMYIEQIYML T0373 48 :GGDVTPSELAAAERMRSSNLAALLRELERGGLIVRH 1on2A 20 :KGYARVSDIAEALAVHPSSVTKMVQKLDKDEYLIYE T0373 86 :PQD 1on2A 56 :KYR T0373 93 :RVSLSSEGRRNLYGNRAKR 1on2A 59 :GLVLTSKGKKIGKRLVYRH T0373 113 :EWLVRAM 1on2A 78 :ELLEQFL T0373 121 :ACLDESERALLAA 1on2A 103 :HHLSWNSIDRIGD T0373 137 :LLTRLA 1on2A 116 :LVQYFE Number of specific fragments extracted= 7 number of extra gaps= 0 total=703 Number of alignments=125 # 1on2A read from 1on2A/merged-good-all-a2m # found chain 1on2A in training set T0373 35 :FSQLVVLGAIDR 1on2A 8 :MYIEQIYMLIEE T0373 48 :GGDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADP 1on2A 20 :KGYARVSDIAEALAVHPSSVTKMVQKLDKDEYLIYEKYR T0373 93 :RVSLSSEGRRNLYGNRAKREEWLVRAMHACLDESER 1on2A 59 :GLVLTSKGKKIGKRLVYRHELLEQFLRIIGVDEEKI T0373 129 :ALLAAAGPLLT 1on2A 111 :DRIGDLVQYFE Number of specific fragments extracted= 4 number of extra gaps= 0 total=707 Number of alignments=126 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sfxA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0373 read from 1sfxA/merged-good-all-a2m # 1sfxA read from 1sfxA/merged-good-all-a2m # found chain 1sfxA in training set T0373 2 :PTNQDLQL 1sfxA 1 :MSNPLGEL T0373 25 :RREAQADPVQFSQLVVLGAIDRLGG 1sfxA 9 :VKALEKLSFKPSDVRIYSLLLERGG T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSE 1sfxA 34 :MRVSEIARELDLSARFVRDRLKVLLKRGFVRREIVEKGWVGYIYSAEKP T0373 102 :RNLYGNRAKREEWLVRAMHACLD 1sfxA 83 :EKVLKEFKSSILGEIERIEKMFT Number of specific fragments extracted= 4 number of extra gaps= 0 total=711 Number of alignments=127 # 1sfxA read from 1sfxA/merged-good-all-a2m # found chain 1sfxA in training set T0373 1 :MPTNQDLQLA 1sfxA 0 :HMSNPLGELV T0373 26 :REAQADPVQFSQLVVLGAIDRLGG 1sfxA 10 :KALEKLSFKPSDVRIYSLLLERGG T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSE 1sfxA 34 :MRVSEIARELDLSARFVRDRLKVLLKRGFVRREIVEKGWVGYIYSAEKP T0373 102 :RNLYGNRAKREEWLVRAMHACLD 1sfxA 83 :EKVLKEFKSSILGEIERIEKMFT Number of specific fragments extracted= 4 number of extra gaps= 0 total=715 Number of alignments=128 # 1sfxA read from 1sfxA/merged-good-all-a2m # found chain 1sfxA in training set T0373 22 :RRLRREAQADPVQFSQLVVLGAIDR 1sfxA 6 :GELVKALEKLSFKPSDVRIYSLLLE T0373 48 :GGDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSE 1sfxA 31 :RGGMRVSEIARELDLSARFVRDRLKVLLKRGFVRREIVEKGWVGYIYSAEKP T0373 102 :RNLYGNRAKREEWLVRAMHACLDE 1sfxA 83 :EKVLKEFKSSILGEIERIEKMFTD Number of specific fragments extracted= 3 number of extra gaps= 0 total=718 Number of alignments=129 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ulyA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ulyA expands to /projects/compbio/data/pdb/1uly.pdb.gz 1ulyA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0373 read from 1ulyA/merged-good-all-a2m # 1ulyA read from 1ulyA/merged-good-all-a2m # adding 1ulyA to template set # found chain 1ulyA in template set T0373 35 :FSQLVVLGAIDR 1ulyA 20 :DTRRKILKLLRN T0373 48 :GG 1ulyA 32 :KE T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHADP 1ulyA 34 :MTISQLSEILGKTPQTIYHHIEKLKEAGLVEVKRTE T0373 87 :QDGRRTRVSLS 1ulyA 72 :GNLVEKYYGRT T0373 98 :SEGRRNLYGNRAKREE 1ulyA 95 :EELRYIARSRLKTKID T0373 115 :LVRA 1ulyA 111 :IFKR T0373 125 :ESERALLAA 1ulyA 122 :NELLNIMDR T0373 137 :LLTRLAQ 1ulyA 131 :MSQKEFD Number of specific fragments extracted= 8 number of extra gaps= 0 total=726 Number of alignments=130 # 1ulyA read from 1ulyA/merged-good-all-a2m # found chain 1ulyA in template set T0373 6 :DLQLAAHLR 1ulyA 10 :DPEVIKVML T0373 34 :QFSQLVVLGAID 1ulyA 19 :EDTRRKILKLLR T0373 48 :GGDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADP 1ulyA 31 :NKEMTISQLSEILGKTPQTIYHHIEKLKEAGLVEVKRTE T0373 87 :QDGRRTRVSLS 1ulyA 72 :GNLVEKYYGRT T0373 98 :SEGRRNLYGNRAKREEWLVRAM 1ulyA 95 :EELRYIARSRLKTKIDIFKRLG T0373 121 :ACLD 1ulyA 117 :YQFE T0373 125 :ESERALLAAAG 1ulyA 122 :NELLNIMDRMS T0373 136 :PLLTRLAQ 1ulyA 141 :RISKYIEE Number of specific fragments extracted= 8 number of extra gaps= 0 total=734 Number of alignments=131 # 1ulyA read from 1ulyA/merged-good-all-a2m # found chain 1ulyA in template set T0373 35 :FSQLVVLGAIDR 1ulyA 20 :DTRRKILKLLRN T0373 49 :GDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADP 1ulyA 32 :KEMTISQLSEILGKTPQTIYHHIEKLKEAGLVEVKRTE T0373 87 :QDGRRTRVSLS 1ulyA 72 :GNLVEKYYGRT T0373 98 :SEGRRNLYGNRAKREEWLVR 1ulyA 95 :EELRYIARSRLKTKIDIFKR T0373 121 :ACLD 1ulyA 115 :LGYQ T0373 125 :ESERALLAAAGPLLTR 1ulyA 122 :NELLNIMDRMSQKEFD Number of specific fragments extracted= 6 number of extra gaps= 0 total=740 Number of alignments=132 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1p4xA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1p4xA expands to /projects/compbio/data/pdb/1p4x.pdb.gz 1p4xA:# T0373 read from 1p4xA/merged-good-all-a2m # 1p4xA read from 1p4xA/merged-good-all-a2m # adding 1p4xA to template set # found chain 1p4xA in template set T0373 2 :PTNQDLQLAAHLR 1p4xA 5 :NHDKIRDFIIIEA T0373 20 :LTRRLRREAQ 1p4xA 18 :YMFRFKKKVK T0373 30 :ADPVQFSQLVVLGAIDRLGGD 1p4xA 29 :EVDMTIKEFILLTYLFHQQEN T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREEWLVRAMHAC 1p4xA 51 :LPFKKIVSDLCYKQSDLVQHIKVLVKHSYISKVRSKIDERNTYISISEEQREKIAERVTLFDQIIKQFNLAD T0373 128 :RALLAAAG 1p4xA 133 :SKEFLNLM T0373 136 :PLLTRLAQ 1p4xA 144 :MYFKNIIK Number of specific fragments extracted= 6 number of extra gaps= 0 total=746 Number of alignments=133 # 1p4xA read from 1p4xA/merged-good-all-a2m # found chain 1p4xA in template set T0373 2 :PTNQDLQLAAHLRSQVTTLTRRLR 1p4xA 4 :NNHDKIRDFIIIEAYMFRFKKKVK T0373 29 :QADPVQFSQLVVLGAIDRLGG 1p4xA 28 :PEVDMTIKEFILLTYLFHQQE T0373 50 :DVTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREEWLVRAMHAC 1p4xA 50 :TLPFKKIVSDLCYKQSDLVQHIKVLVKHSYISKVRSKIDERNTYISISEEQREKIAERVTLFDQIIKQFNLAD T0373 123 :LD 1p4xA 124 :SE T0373 126 :SERALLAAAGPLLTRLAQ 1p4xA 134 :KEFLNLMMYTMYFKNIIK Number of specific fragments extracted= 5 number of extra gaps= 0 total=751 Number of alignments=134 # 1p4xA read from 1p4xA/merged-good-all-a2m # found chain 1p4xA in template set T0373 2 :PTNQDLQLAAHLRSQVTTLTRRLRR 1p4xA 4 :NNHDKIRDFIIIEAYMFRFKKKVKP T0373 30 :ADPVQFSQLVVLGAIDRLGGD 1p4xA 29 :EVDMTIKEFILLTYLFHQQEN T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNRAKREEWLVRAMHAC 1p4xA 51 :LPFKKIVSDLCYKQSDLVQHIKVLVKHSYISKVRSKIDERNTYISISEEQREKIAERVTLFDQIIKQFNLAD Number of specific fragments extracted= 3 number of extra gaps= 0 total=754 Number of alignments=135 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2dbbA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2dbbA expands to /projects/compbio/data/pdb/2dbb.pdb.gz 2dbbA:# T0373 read from 2dbbA/merged-good-all-a2m # 2dbbA read from 2dbbA/merged-good-all-a2m # adding 2dbbA to template set # found chain 2dbbA in template set Warning: unaligning (T0373)P32 because first residue in template chain is (2dbbA)K6 T0373 33 :VQFSQLVVLGAIDR 2dbbA 7 :LDRVDMQLVKILSE T0373 48 :GGDVTPSELAAAERMRSSNLAALLRELERGGLI 2dbbA 21 :NSRLTYRELADILNTTRQRIARRIDKLKKLGII T0373 81 :VRHADPQDGRRTRVSLS 2dbbA 57 :TIIPDIDKLGYMYAIVL T0373 107 :NRAKREE 2dbbA 78 :VPSDADK T0373 115 :LVRAMHAC 2dbbA 85 :VISEISDI T0373 124 :DESERALLAA 2dbbA 116 :DIKDAENLIS T0373 140 :RLAQFEEP 2dbbA 126 :EFLQRIKN Number of specific fragments extracted= 7 number of extra gaps= 0 total=761 Number of alignments=136 # 2dbbA read from 2dbbA/merged-good-all-a2m # found chain 2dbbA in template set Warning: unaligning (T0373)P32 because first residue in template chain is (2dbbA)K6 T0373 33 :VQFSQLVVLGAIDRLGG 2dbbA 7 :LDRVDMQLVKILSENSR T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLI 2dbbA 24 :LTYRELADILNTTRQRIARRIDKLKKLGII T0373 81 :VRHADPQDGRRTRVSLS 2dbbA 57 :TIIPDIDKLGYMYAIVL T0373 98 :SEGRRNLYGN 2dbbA 83 :DKVISEISDI T0373 109 :AKREEWLVRAM 2dbbA 118 :KDAENLISEFL T0373 121 :ACLD 2dbbA 129 :QRIK Number of specific fragments extracted= 6 number of extra gaps= 0 total=767 Number of alignments=137 # 2dbbA read from 2dbbA/merged-good-all-a2m # found chain 2dbbA in template set Warning: unaligning (T0373)P32 because first residue in template chain is (2dbbA)K6 T0373 33 :VQFSQLVVLGAIDR 2dbbA 7 :LDRVDMQLVKILSE T0373 48 :GGDVTPSELAAAERMRSSNLAALLRELERGGLI 2dbbA 21 :NSRLTYRELADILNTTRQRIARRIDKLKKLGII T0373 81 :VRHADPQDGRRTRVSL 2dbbA 57 :TIIPDIDKLGYMYAIV T0373 98 :SEGRRNLYGN 2dbbA 83 :DKVISEISDI T0373 108 :RAKREEWLVR 2dbbA 117 :IKDAENLISE T0373 119 :MHACLDE 2dbbA 127 :FLQRIKN Number of specific fragments extracted= 6 number of extra gaps= 0 total=773 Number of alignments=138 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r7jA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0373 read from 1r7jA/merged-good-all-a2m # 1r7jA read from 1r7jA/merged-good-all-a2m # found chain 1r7jA in training set T0373 38 :LVVLGAID 1r7jA 11 :QAILEACK T0373 48 :GG 1r7jA 19 :SG T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRH 1r7jA 21 :SPKTRIMYGANLSYALTGRYIKMLMDLEIIRQE T0373 86 :PQ 1r7jA 54 :GK T0373 93 :RVSLSSEGRRNLYGNRAKREE 1r7jA 56 :QYMLTKKGEELLEDIRKFNEM T0373 115 :LVRA 1r7jA 77 :RKNM T0373 129 :ALLAA 1r7jA 81 :DQLKE T0373 140 :RLAQF 1r7jA 86 :KINSV Number of specific fragments extracted= 8 number of extra gaps= 0 total=781 Number of alignments=139 # 1r7jA read from 1r7jA/merged-good-all-a2m # found chain 1r7jA in training set Warning: unaligning (T0373)E146 because last residue in template chain is (1r7jA)S92 T0373 36 :SQLVVLGAID 1r7jA 9 :IIQAILEACK T0373 48 :GG 1r7jA 19 :SG T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRH 1r7jA 21 :SPKTRIMYGANLSYALTGRYIKMLMDLEIIRQE T0373 86 :PQ 1r7jA 54 :GK T0373 93 :RVSLSSEGRRNLYGNRAKREEWLVRAM 1r7jA 56 :QYMLTKKGEELLEDIRKFNEMRKNMDQ T0373 137 :LLTRLAQFE 1r7jA 83 :LKEKINSVL Number of specific fragments extracted= 6 number of extra gaps= 0 total=787 Number of alignments=140 # 1r7jA read from 1r7jA/merged-good-all-a2m # found chain 1r7jA in training set T0373 42 :GAIDRLGGDVTPSELAAAERMRSSNLAALLRELERGGLIVRHAD 1r7jA 12 :AILEACKSGSPKTRIMYGANLSYALTGRYIKMLMDLEIIRQEGK T0373 93 :RVSLSSEGRRNLYGNRAKREEWLVRAMHA 1r7jA 56 :QYMLTKKGEELLEDIRKFNEMRKNMDQLK T0373 133 :A 1r7jA 85 :E Number of specific fragments extracted= 3 number of extra gaps= 0 total=790 Number of alignments=141 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f5tA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1f5tA expands to /projects/compbio/data/pdb/1f5t.pdb.gz 1f5tA:# T0373 read from 1f5tA/merged-good-all-a2m # 1f5tA read from 1f5tA/merged-good-all-a2m # adding 1f5tA to template set # found chain 1f5tA in template set T0373 36 :SQLVVLGAIDRLGGDVTPSELAAAERMRSSNLAALLRELERGGLIVRH 1f5tA 1010 :MYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVA T0373 87 :QDGR 1f5tA 1058 :SDRS T0373 94 :VSLSSEGRRNLYGNRAKRE 1f5tA 1062 :LQMTPTGRTLATAVMRKHR T0373 114 :WLVRAMHAC 1f5tA 1081 :LAERLLTDI T0373 123 :LDESERALLAA 1f5tA 1108 :MSDEVERRLVK Number of specific fragments extracted= 5 number of extra gaps= 0 total=795 Number of alignments=142 # 1f5tA read from 1f5tA/merged-good-all-a2m # found chain 1f5tA in template set T0373 35 :FSQLVVLGAIDRLGGDVTPSELAAAERMRSSNLAALLRELERGGLIVR 1f5tA 1009 :EMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVV T0373 85 :DPQDG 1f5tA 1057 :ASDRS T0373 94 :VSLSSEGRRNLYGNRAKR 1f5tA 1062 :LQMTPTGRTLATAVMRKH T0373 113 :EWLVRAMHACLD 1f5tA 1080 :RLAERLLTDIIG T0373 125 :ESERALLAA 1f5tA 1098 :HDEADRWEH T0373 136 :PLLTRLAQ 1f5tA 1111 :EVERRLVK Number of specific fragments extracted= 6 number of extra gaps= 0 total=801 Number of alignments=143 # 1f5tA read from 1f5tA/merged-good-all-a2m # found chain 1f5tA in template set T0373 35 :FSQLVVLGAIDR 1f5tA 1009 :EMYLRTIYELEE T0373 48 :GGD 1f5tA 1021 :EGV T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHADP 1f5tA 1025 :PLRARIAERLEQSGPTVSQTVARMERDGLVVVASDR T0373 93 :RVSLSSEGRRNLYGNRAKR 1f5tA 1061 :SLQMTPTGRTLATAVMRKH T0373 113 :EWLVRAMHA 1f5tA 1080 :RLAERLLTD T0373 122 :CLDESERALLAA 1f5tA 1107 :VMSDEVERRLVK Number of specific fragments extracted= 6 number of extra gaps= 0 total=807 Number of alignments=144 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fbiA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fbiA expands to /projects/compbio/data/pdb/2fbi.pdb.gz 2fbiA:Skipped atom 2, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 4, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 6, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 8, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 10, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 12, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 14, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 16, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 18, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 20, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 22, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 250, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 252, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 254, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 256, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 258, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 260, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 262, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 264, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 266, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 443, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 445, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 447, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 449, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 451, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 453, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 455, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 457, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 718, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 720, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 722, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 724, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 726, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 728, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 730, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 732, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 734, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 736, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 738, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 829, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 831, because occupancy 0.400 <= existing 0.600 in 2fbiA Skipped atom 833, because occupancy 0.400 <= existing 0.600 in 2fbiA Skipped atom 835, because occupancy 0.400 <= existing 0.600 in 2fbiA Skipped atom 837, because occupancy 0.400 <= existing 0.600 in 2fbiA Skipped atom 839, because occupancy 0.400 <= existing 0.600 in 2fbiA Skipped atom 891, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 893, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 895, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 897, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 899, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 901, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 903, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 905, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1017, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1019, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1021, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1023, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1025, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1027, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1029, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1031, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1033, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1091, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1093, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1095, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1097, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1099, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1101, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1103, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1105, because occupancy 0.500 <= existing 0.500 in 2fbiA Skipped atom 1107, because occupancy 0.500 <= existing 0.500 in 2fbiA # T0373 read from 2fbiA/merged-good-all-a2m # 2fbiA read from 2fbiA/merged-good-all-a2m # adding 2fbiA to template set # found chain 2fbiA in template set Warning: unaligning (T0373)P2 because first residue in template chain is (2fbiA)R5 Warning: unaligning (T0373)P32 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fbiA)L32 Warning: unaligning (T0373)V33 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fbiA)L32 Warning: unaligning (T0373)Q87 because of BadResidue code BAD_PEPTIDE in next template residue (2fbiA)D86 Warning: unaligning (T0373)D88 because of BadResidue code BAD_PEPTIDE at template residue (2fbiA)D86 T0373 3 :TNQDLQLA 2fbiA 6 :PSLTLTLL T0373 15 :SQVTTLTRRLRREAQAD 2fbiA 14 :QAREAAMSFFRPSLNQH T0373 34 :QFSQLVVLGAIDRLGG 2fbiA 33 :TEQQWRVIRILRQQGE T0373 51 :VTPSELAAAERMRSSNLAALLRELERGGLIVRHADP 2fbiA 49 :MESYQLANQACILRPSMTGVLARLERDGIVRRWKAP T0373 89 :GRRTRVSLSSEGRRNLYGNRAKREE 2fbiA 87 :QRRVYVNLTEKGQQCFVSMSGDMEK T0373 115 :LVRAMHACLDESERALLAA 2fbiA 112 :NYQRIQERFGEEKLAQLLE T0373 137 :LLTRLAQF 2fbiA 131 :LLNELKKI Number of specific fragments extracted= 7 number of extra gaps= 2 total=814 Number of alignments=145 # 2fbiA read from 2fbiA/merged-good-all-a2m # found chain 2fbiA in template set Warning: unaligning (T0373)P2 because first residue in template chain is (2fbiA)R5 Warning: unaligning (T0373)P32 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fbiA)L32 Warning: unaligning (T0373)V33 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fbiA)L32 Warning: unaligning (T0373)Q87 because of BadResidue code BAD_PEPTIDE in next template residue (2fbiA)D86 Warning: unaligning (T0373)D88 because of BadResidue code BAD_PEPTIDE at template residue (2fbiA)D86 T0373 3 :TNQDLQL 2fbiA 6 :PSLTLTL T0373 14 :RSQVTTLTRRLRREAQAD 2fbiA 13 :LQAREAAMSFFRPSLNQH T0373 34 :QFSQLVVLGAIDRL 2fbiA 33 :TEQQWRVIRILRQQ T0373 49 :GDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADP 2fbiA 47 :GEMESYQLANQACILRPSMTGVLARLERDGIVRRWKAP T0373 89 :GRRTRVSLSSEGRRNLYGNRAKREEWLVRAM 2fbiA 87 :QRRVYVNLTEKGQQCFVSMSGDMEKNYQRIQ T0373 121 :ACLDESERALLAA 2fbiA 118 :ERFGEEKLAQLLE T0373 137 :LLTRLAQFE 2fbiA 131 :LLNELKKIK Number of specific fragments extracted= 7 number of extra gaps= 2 total=821 Number of alignments=146 # 2fbiA read from 2fbiA/merged-good-all-a2m # found chain 2fbiA in template set Warning: unaligning (T0373)P32 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fbiA)L32 Warning: unaligning (T0373)V33 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fbiA)L32 Warning: unaligning (T0373)Q87 because of BadResidue code BAD_PEPTIDE in next template residue (2fbiA)D86 Warning: unaligning (T0373)D88 because of BadResidue code BAD_PEPTIDE at template residue (2fbiA)D86 T0373 14 :RSQVTTLTRRLRREAQAD 2fbiA 13 :LQAREAAMSFFRPSLNQH T0373 34 :QFSQLVVLGAIDR 2fbiA 33 :TEQQWRVIRILRQ T0373 48 :GGDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADP 2fbiA 46 :QGEMESYQLANQACILRPSMTGVLARLERDGIVRRWKAP T0373 89 :GRRTRVSLSSEGRRNLYGNRAKREEWLVR 2fbiA 87 :QRRVYVNLTEKGQQCFVSMSGDMEKNYQR T0373 119 :MHACLDESERALLAAAGPL 2fbiA 116 :IQERFGEEKLAQLLELLNE Number of specific fragments extracted= 5 number of extra gaps= 2 total=826 Number of alignments=147 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fx7A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1fx7A expands to /projects/compbio/data/pdb/1fx7.pdb.gz 1fx7A:Skipped atom 596, because occupancy 0.500 <= existing 0.500 in 1fx7A Skipped atom 598, because occupancy 0.500 <= existing 0.500 in 1fx7A Skipped atom 600, because occupancy 0.500 <= existing 0.500 in 1fx7A Skipped atom 602, because occupancy 0.500 <= existing 0.500 in 1fx7A Skipped atom 872, because occupancy 0.500 <= existing 0.500 in 1fx7A Skipped atom 874, because occupancy 0.500 <= existing 0.500 in 1fx7A Skipped atom 876, because occupancy 0.500 <= existing 0.500 in 1fx7A Skipped atom 878, because occupancy 0.500 <= existing 0.500 in 1fx7A Skipped atom 1703, because occupancy 0.500 <= existing 0.500 in 1fx7A Skipped atom 1705, because occupancy 0.500 <= existing 0.500 in 1fx7A Skipped atom 1707, because occupancy 0.500 <= existing 0.500 in 1fx7A Skipped atom 1709, because occupancy 0.500 <= existing 0.500 in 1fx7A # T0373 read from 1fx7A/merged-good-all-a2m # 1fx7A read from 1fx7A/merged-good-all-a2m # adding 1fx7A to template set # found chain 1fx7A in template set T0373 35 :FSQLVVLGAIDRLGGDVTPSELAAAERMRSSNLAALLRELERGGLIVRH 1fx7A 9 :EMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVA T0373 87 :QDGR 1fx7A 58 :GDRH T0373 94 :VSLSSEGRRNLYGNRAKR 1fx7A 62 :LELTEKGRALAIAVMRKH T0373 112 :EE 1fx7A 95 :EE T0373 115 :LVRAMHAC 1fx7A 97 :VHAEACRW T0373 123 :LDES 1fx7A 108 :MSED T0373 137 :LLTRLAQFEEP 1fx7A 112 :VERRLVKVLNN Number of specific fragments extracted= 7 number of extra gaps= 0 total=833 Number of alignments=148 # 1fx7A read from 1fx7A/merged-good-all-a2m # found chain 1fx7A in template set T0373 35 :FSQLVVLGAIDRLGGDVTPSELAAAERMRSSNLAALLRELERGGLIVR 1fx7A 9 :EMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRV T0373 85 :DPQ 1fx7A 57 :AGD T0373 89 :GR 1fx7A 60 :RH T0373 94 :VSLSSEGRRNLYGNRAKREEWLVRAM 1fx7A 62 :LELTEKGRALAIAVMRKHRLAERLLV T0373 121 :ACLD 1fx7A 88 :DVIG T0373 125 :ESERALLAAA 1fx7A 95 :EEVHAEACRW T0373 135 :GPLLTRLAQFEE 1fx7A 110 :EDVERRLVKVLN Number of specific fragments extracted= 7 number of extra gaps= 0 total=840 Number of alignments=149 # 1fx7A read from 1fx7A/merged-good-all-a2m # found chain 1fx7A in template set T0373 35 :FSQLVVLGAIDRLGGDVTPSELAAAERMRSSNLAALLRELERGGLIVRH 1fx7A 9 :EMYLRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVA T0373 87 :QDG 1fx7A 58 :GDR T0373 93 :RVSLSSEGRRNLYGNRAKREEWLVR 1fx7A 61 :HLELTEKGRALAIAVMRKHRLAERL T0373 119 :MHACLD 1fx7A 86 :LVDVIG Number of specific fragments extracted= 4 number of extra gaps= 0 total=844 Number of alignments=150 # command:# PrintAlignmentsContacts allconstraints.under Using radius: 8.0000 NUMB_ALIGNS: 150 Done printing distance constraints # command: