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/T0328/ # command:# Making conformation for sequence T0328 numbered 1 through 311 Created new target T0328 from T0328.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0328/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0328//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0328/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0328//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0328/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0328/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0328/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1aoeA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0328 read from 1aoeA/merged-good-all-a2m # 1aoeA read from 1aoeA/merged-good-all-a2m # found chain 1aoeA in training set Warning: unaligning (T0328)D142 because of BadResidue code BAD_PEPTIDE in next template residue (1aoeA)G114 Warning: unaligning (T0328)S143 because of BadResidue code BAD_PEPTIDE at template residue (1aoeA)G114 T0328 34 :SQLRPC 1aoeA 30 :RKEIRY # choosing archetypes in rotamer library T0328 47 :IYELTDQYSDSAFNGFVAIGANYWDSLYPESRP 1aoeA 36 :FKDVTTRTTKPNTRNAVIMGRKTWESIPQKFRP T0328 85 :FPAM 1aoeA 69 :LPDR T0328 90 :EGNREAPAIE 1aoeA 78 :SRSYENEIID T0328 105 :HLRCDR 1aoeA 90 :IIHASS T0328 118 :ANEISQMFEDLVELVEE 1aoeA 96 :IESSLNLVSDVERVFII T0328 157 :KGRHRQEVALV 1aoeA 123 :NNSLVSHLLIT T0328 168 :GSEDPEFK 1aoeA 136 :EHPSPESI T0328 188 :NLSKWHRLPLKKQEDIIGRTKQ 1aoeA 152 :PLESWTKQPKSELQKFVGDTVL T0328 210 :DNIEYES 1aoeA 175 :DDIKEGD Number of specific fragments extracted= 10 number of extra gaps= 1 total=10 Number of alignments=1 # 1aoeA read from 1aoeA/merged-good-all-a2m # found chain 1aoeA in training set Warning: unaligning (T0328)S143 because of BadResidue code BAD_PEPTIDE at template residue (1aoeA)G114 T0328 42 :NVAQYIYELTDQYSDSAFNGFVAIGANYWDSLYPESRP 1aoeA 31 :KEIRYFKDVTTRTTKPNTRNAVIMGRKTWESIPQKFRP T0328 85 :FPAM 1aoeA 69 :LPDR T0328 90 :EGNREAPAIEY 1aoeA 78 :SRSYENEIIDD T0328 105 :HLRCDR 1aoeA 90 :IIHASS T0328 118 :ANEISQMFEDLVELV 1aoeA 96 :IESSLNLVSDVERVF T0328 157 :KGRHRQEVALV 1aoeA 123 :NNSLVSHLLIT T0328 168 :GSEDPEFK 1aoeA 136 :EHPSPESI T0328 188 :NLSKWHRLPLKKQEDIIG 1aoeA 152 :PLESWTKQPKSELQKFVG T0328 211 :NIEYESE 1aoeA 170 :DTVLEDD Number of specific fragments extracted= 9 number of extra gaps= 1 total=19 Number of alignments=2 # 1aoeA read from 1aoeA/merged-good-all-a2m # found chain 1aoeA in training set Warning: unaligning (T0328)D142 because of BadResidue code BAD_PEPTIDE in next template residue (1aoeA)G114 Warning: unaligning (T0328)S143 because of BadResidue code BAD_PEPTIDE at template residue (1aoeA)G114 T0328 32 :VESQLRPCIANVA 1aoeA 28 :RLRKEIRYFKDVT T0328 52 :DQYSDSAFNGFVAIGANYWDSLYP 1aoeA 41 :TRTTKPNTRNAVIMGRKTWESIPQ T0328 81 :MLKPFPAMQ 1aoeA 65 :KFRPLPDRL T0328 90 :EGNREAPAIEYD 1aoeA 78 :SRSYENEIIDDN T0328 105 :HLRCDRYDILH 1aoeA 90 :IIHASSIESSL T0328 123 :QMFEDL 1aoeA 101 :NLVSDV T0328 136 :RGFRFM 1aoeA 107 :ERVFII T0328 144 :RDLTG 1aoeA 115 :AEIYN T0328 156 :PKG 1aoeA 122 :INN T0328 160 :HRQEVALV 1aoeA 125 :SLVSHLLI T0328 168 :GSEDPEFKG 1aoeA 136 :EHPSPESIE T0328 188 :NLSKWHRLPLKKQEDIIG 1aoeA 152 :PLESWTKQPKSELQKFVG T0328 211 :NIEYESEDKPLTSHIKRVNLK 1aoeA 170 :DTVLEDDIKEGDFTYNYTLWT Number of specific fragments extracted= 13 number of extra gaps= 1 total=32 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gvkA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2gvkA expands to /projects/compbio/data/pdb/2gvk.pdb.gz 2gvkA:Skipped atom 32, because occupancy 0.5 <= existing 0.500 in 2gvkA Skipped atom 36, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 38, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 40, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 42, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 61, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 65, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 67, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 69, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 71, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 108, because occupancy 0.300 <= existing 0.700 in 2gvkA Skipped atom 112, because occupancy 0.300 <= existing 0.700 in 2gvkA Skipped atom 114, because occupancy 0.300 <= existing 0.700 in 2gvkA Skipped atom 116, because occupancy 0.300 <= existing 0.700 in 2gvkA Skipped atom 118, because occupancy 0.300 <= existing 0.700 in 2gvkA Skipped atom 120, because occupancy 0.300 <= existing 0.700 in 2gvkA Skipped atom 131, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 135, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 137, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 139, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 211, because occupancy 0.300 <= existing 0.700 in 2gvkA Skipped atom 215, because occupancy 0.300 <= existing 0.700 in 2gvkA Skipped atom 217, because occupancy 0.300 <= existing 0.700 in 2gvkA Skipped atom 219, because occupancy 0.300 <= existing 0.700 in 2gvkA Skipped atom 221, because occupancy 0.300 <= existing 0.700 in 2gvkA Skipped atom 292, because occupancy 0.300 <= existing 0.700 in 2gvkA Skipped atom 296, because occupancy 0.300 <= existing 0.700 in 2gvkA Skipped atom 298, because occupancy 0.300 <= existing 0.700 in 2gvkA Skipped atom 300, because occupancy 0.300 <= existing 0.700 in 2gvkA Skipped atom 302, because occupancy 0.300 <= existing 0.700 in 2gvkA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 413, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 417, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 419, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 421, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 423, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 425, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 427, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 429, because occupancy 0.500 <= existing 0.500 in 2gvkA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 486, because occupancy 0.250 <= existing 0.250 in 2gvkA Skipped atom 491, because occupancy 0.250 <= existing 0.250 in 2gvkA Skipped atom 494, because occupancy 0.250 <= existing 0.250 in 2gvkA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 677, because occupancy 0.350 <= existing 0.350 in 2gvkA Skipped atom 678, because occupancy 0.300 <= existing 0.350 in 2gvkA Skipped atom 682, because occupancy 0.350 <= existing 0.350 in 2gvkA Skipped atom 683, because occupancy 0.300 <= existing 0.350 in 2gvkA Skipped atom 685, because occupancy 0.350 <= existing 0.350 in 2gvkA Skipped atom 686, because occupancy 0.300 <= existing 0.350 in 2gvkA Skipped atom 707, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 711, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 713, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 868, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 872, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 874, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 876, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 878, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 880, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 882, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 884, because occupancy 0.500 <= existing 0.500 in 2gvkA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 970, because occupancy 0.250 <= existing 0.500 in 2gvkA Skipped atom 971, because occupancy 0.250 <= existing 0.500 in 2gvkA Skipped atom 975, because occupancy 0.250 <= existing 0.500 in 2gvkA Skipped atom 976, because occupancy 0.250 <= existing 0.500 in 2gvkA Skipped atom 978, because occupancy 0.250 <= existing 0.500 in 2gvkA Skipped atom 979, because occupancy 0.250 <= existing 0.500 in 2gvkA Skipped atom 982, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 986, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 988, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 990, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 992, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 1060, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 1064, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 1066, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 1068, because occupancy 0.500 <= existing 0.500 in 2gvkA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1228, because occupancy 0.400 <= existing 0.600 in 2gvkA Skipped atom 1232, because occupancy 0.400 <= existing 0.600 in 2gvkA Skipped atom 1234, because occupancy 0.400 <= existing 0.600 in 2gvkA Skipped atom 1236, because occupancy 0.400 <= existing 0.600 in 2gvkA Skipped atom 1238, because occupancy 0.400 <= existing 0.600 in 2gvkA Skipped atom 1252, because occupancy 0.400 <= existing 0.600 in 2gvkA Skipped atom 1256, because occupancy 0.400 <= existing 0.600 in 2gvkA Skipped atom 1258, because occupancy 0.400 <= existing 0.600 in 2gvkA Skipped atom 1260, because occupancy 0.400 <= existing 0.600 in 2gvkA Skipped atom 1262, because occupancy 0.400 <= existing 0.600 in 2gvkA Skipped atom 1264, because occupancy 0.400 <= existing 0.600 in 2gvkA Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1545, because occupancy 0.500 <= existing 0.500 in 2gvkA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1549, because occupancy 0.500 <= existing 0.500 in 2gvkA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1551, because occupancy 0.500 <= existing 0.500 in 2gvkA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1553, because occupancy 0.350 <= existing 0.350 in 2gvkA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1555, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 1597, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 1601, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 1603, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 1605, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 1607, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 1624, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 1628, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 1630, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 1632, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 1634, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 1636, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 1639, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 1643, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 1645, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 1647, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 1649, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 1651, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 1729, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 1731, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 1733, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 1735, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 1737, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 1739, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 1741, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 1743, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 1745, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 1747, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 1749, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 1784, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 1788, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 1790, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 1792, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 1794, because occupancy 0.500 <= existing 0.500 in 2gvkA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 2015, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 2019, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 2021, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 2023, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 2025, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 2052, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 2056, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 2058, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 2060, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 2062, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 2064, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 2186, because occupancy 0.300 <= existing 0.700 in 2gvkA Skipped atom 2190, because occupancy 0.300 <= existing 0.700 in 2gvkA Skipped atom 2192, because occupancy 0.300 <= existing 0.700 in 2gvkA Skipped atom 2194, because occupancy 0.300 <= existing 0.700 in 2gvkA Skipped atom 2196, because occupancy 0.300 <= existing 0.700 in 2gvkA Skipped atom 2198, because occupancy 0.300 <= existing 0.700 in 2gvkA Skipped atom 2200, because occupancy 0.300 <= existing 0.700 in 2gvkA Skipped atom 2202, because occupancy 0.300 <= existing 0.700 in 2gvkA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 2273, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 2277, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 2279, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 2281, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 2283, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 2335, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 2339, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 2341, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 2343, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 2345, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 2347, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 2349, because occupancy 0.500 <= existing 0.500 in 2gvkA Skipped atom 2351, because occupancy 0.500 <= existing 0.500 in 2gvkA # T0328 read from 2gvkA/merged-good-all-a2m # 2gvkA read from 2gvkA/merged-good-all-a2m # adding 2gvkA to template set # found chain 2gvkA in template set Warning: unaligning (T0328)R242 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gvkA)A246 Warning: unaligning (T0328)Q243 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gvkA)A246 T0328 9 :EQLGVCAEGNLHSVYLMFNANDN 2gvkA 12 :IPQDVAGKQGENVIFIVYNLTDS T0328 32 :VESQLRPCIANVAQYIYELTDQYSDSAFNGFVAIGANYWDSLYPE 2gvkA 37 :TVDKVKDVCANFSAMIRSMRNRFPDMQFSCTMGFGADAWTRLFPD T0328 77 :SRPEMLKPFPAMQEGNREAPAIEYDLFVHLRCDRYDILHLVANEISQMFEDLVELVEEERGFRFMDSRDLTGFVDGTENPKGRH 2gvkA 83 :GKPKELSTFSEIKGEKYTAVSTPGDLLFHIRAKQMGLCFEFASILDEKLKGAVVSVDETHGFRYMDGKAIIGFVDGTENPAVDE T0328 161 :RQEVALVGSEDPEFKGGSYIHVQKYAHNLSKWHRLPLKKQEDIIGRTKQDNIEYESEDKPLTSHIKRVNLK 2gvkA 168 :PYHFAVIGEEDADFAGGSYVFVQKYIHDMVAWNALPVEQQEKVIGRHKFNDVELSDEEKPGNAHNAVTNIG T0328 234 :NG 2gvkA 239 :DD T0328 238 :IEIL 2gvkA 241 :LKIV T0328 244 :SMPY 2gvkA 247 :NMPF T0328 248 :GSLKEQGLMFISTCRTPDHFEKMLHSMVFGDGAGNHDHLMHFTSALTGSSFFAPSLDFLMQF 2gvkA 253 :TSKGEYGTYFIGYASTFSTTRRMLENMFIGSPAGNTDRLLDFSTAITGTLFFVPSYDLLGEL Number of specific fragments extracted= 8 number of extra gaps= 1 total=40 Number of alignments=4 # 2gvkA read from 2gvkA/merged-good-all-a2m # found chain 2gvkA in template set Warning: unaligning (T0328)R242 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gvkA)A246 Warning: unaligning (T0328)Q243 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gvkA)A246 T0328 9 :EQLGVCAEGNLHSVYLMFNANDN 2gvkA 12 :IPQDVAGKQGENVIFIVYNLTDS T0328 32 :VESQLRPCIANVAQYIYELTDQYSDSAFNGFVAIGANYWDSLYPE 2gvkA 37 :TVDKVKDVCANFSAMIRSMRNRFPDMQFSCTMGFGADAWTRLFPD T0328 77 :SRPEMLKPFPAMQEGNREAPAIEYDLFVHLRCDRYDILHLVANEISQMFEDLVELVEEERGFRFMDSRDLTGFVDGTENPKGRH 2gvkA 83 :GKPKELSTFSEIKGEKYTAVSTPGDLLFHIRAKQMGLCFEFASILDEKLKGAVVSVDETHGFRYMDGKAIIGFVDGTENPAVDE T0328 162 :QEVALVGSEDPEFKGGSYIHVQKYAHNLSKWHRLPLKKQEDIIGRTKQDNIEYESEDKPLTSHIKRVNLK 2gvkA 169 :YHFAVIGEEDADFAGGSYVFVQKYIHDMVAWNALPVEQQEKVIGRHKFNDVELSDEEKPGNAHNAVTNIG T0328 233 :ENG 2gvkA 239 :DDL T0328 239 :EIL 2gvkA 242 :KIV T0328 244 :SMPYGSLK 2gvkA 247 :NMPFANTS T0328 252 :EQGLMFISTCRTPDHFEKMLHSMVFGDGAGNHDHLMHFTSALTGSSFFAPSLDFLMQFDN 2gvkA 257 :EYGTYFIGYASTFSTTRRMLENMFIGSPAGNTDRLLDFSTAITGTLFFVPSYDLLGELGE Number of specific fragments extracted= 8 number of extra gaps= 1 total=48 Number of alignments=5 # 2gvkA read from 2gvkA/merged-good-all-a2m # found chain 2gvkA in template set Warning: unaligning (T0328)N5 because first residue in template chain is (2gvkA)F8 Warning: unaligning (T0328)R242 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gvkA)A246 Warning: unaligning (T0328)Q243 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gvkA)A246 T0328 6 :MPREQLGVCAEGNLHSVYLMFNANDN 2gvkA 9 :GGHIPQDVAGKQGENVIFIVYNLTDS T0328 32 :VESQLRPCIANVAQYIYELTDQYSDSAFNGFVAIGANYWDSLYPE 2gvkA 37 :TVDKVKDVCANFSAMIRSMRNRFPDMQFSCTMGFGADAWTRLFPD T0328 77 :SRPEMLKPFPAMQEGNREAPAIEYDLFVHLRCDRYDILHLVANEISQMFEDLVELVEEERGFRFMDSRDLTGFVDGTENPKGRHR 2gvkA 83 :GKPKELSTFSEIKGEKYTAVSTPGDLLFHIRAKQMGLCFEFASILDEKLKGAVVSVDETHGFRYMDGKAIIGFVDGTENPAVDEN T0328 162 :QEVALVGSEDPEFKGGSYIHVQKYAHNLSKWHRLPLKKQEDIIGRTKQDNIEYESEDKPL 2gvkA 169 :YHFAVIGEEDADFAGGSYVFVQKYIHDMVAWNALPVEQQEKVIGRHKFNDVELSDEEKPG T0328 239 :EIL 2gvkA 242 :KIV T0328 244 :SMPYGSL 2gvkA 247 :NMPFANT T0328 251 :KEQGLMFISTCRTPDHFEKMLHSMVFGDGAGNHDHLMHFTSALTGSSFFAPSLDFLMQFDN 2gvkA 256 :GEYGTYFIGYASTFSTTRRMLENMFIGSPAGNTDRLLDFSTAITGTLFFVPSYDLLGELGE Number of specific fragments extracted= 7 number of extra gaps= 1 total=55 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vdwA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0328 read from 1vdwA/merged-good-all-a2m # 1vdwA read from 1vdwA/merged-good-all-a2m # found chain 1vdwA in training set Warning: unaligning (T0328)V32 because first residue in template chain is (1vdwA)S2 Warning: unaligning (T0328)A87 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vdwA)E42 Warning: unaligning (T0328)R93 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vdwA)E42 T0328 33 :ESQLRPCIANVAQYIYE 1vdwA 3 :VKTWRKIAIDIIRDFDH T0328 68 :NYWDSL 1vdwA 20 :NIMPLF T0328 77 :SRPEMLKPFP 1vdwA 26 :GNPKASETIS T0328 94 :E 1vdwA 43 :T T0328 111 :YDILHLVANEISQMFEDL 1vdwA 44 :KVVDKVAENIIISKFKDL T0328 129 :VELVEEERGFRFMD 1vdwA 63 :VNVVSEEIGRIDQG T0328 157 :KGRHRQEVALVGSED 1vdwA 144 :ELAEKPSISFYTKGK T0328 176 :GGSYIHVQKYAHN 1vdwA 173 :GAIALELAYLARG T0328 194 :RL 1vdwA 186 :AL T0328 223 :SHIKRVNLKDENGKSI 1vdwA 209 :AREAGAIVKDLDGKDV T0328 244 :SMPYGSLKEQGLMFI 1vdwA 225 :EITFSATEKVNIIAA T0328 262 :RTPDHFEKMLH 1vdwA 240 :NNEELLETILR Number of specific fragments extracted= 12 number of extra gaps= 0 total=67 Number of alignments=7 # 1vdwA read from 1vdwA/merged-good-all-a2m # found chain 1vdwA in training set Warning: unaligning (T0328)V32 because first residue in template chain is (1vdwA)S2 Warning: unaligning (T0328)A87 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vdwA)E42 Warning: unaligning (T0328)R93 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vdwA)E42 T0328 33 :ESQLRPCIANVAQYIYE 1vdwA 3 :VKTWRKIAIDIIRDFDH T0328 68 :NYWDSL 1vdwA 20 :NIMPLF T0328 77 :SRPEMLKPFP 1vdwA 26 :GNPKASETIS T0328 94 :E 1vdwA 43 :T T0328 111 :YDILHLVANEISQMFEDL 1vdwA 44 :KVVDKVAENIIISKFKDL T0328 129 :VELVEEERGFRFMD 1vdwA 63 :VNVVSEEIGRIDQG T0328 157 :KGRHR 1vdwA 144 :ELAEK T0328 227 :RVNLKDENGKSI 1vdwA 213 :GAIVKDLDGKDV T0328 244 :SMPYGSLKEQGLMF 1vdwA 225 :EITFSATEKVNIIA T0328 261 :CRTPDHFEKMLH 1vdwA 239 :ANNEELLETILR Number of specific fragments extracted= 10 number of extra gaps= 0 total=77 Number of alignments=8 # 1vdwA read from 1vdwA/merged-good-all-a2m # found chain 1vdwA in training set Warning: unaligning (T0328)V32 because first residue in template chain is (1vdwA)S2 Warning: unaligning (T0328)A87 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vdwA)E42 Warning: unaligning (T0328)R93 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vdwA)E42 T0328 33 :ESQLRPCIANVAQYIYE 1vdwA 3 :VKTWRKIAIDIIRDFDH T0328 68 :NYWDSL 1vdwA 20 :NIMPLF T0328 77 :SRPEMLKPFP 1vdwA 26 :GNPKASETIS T0328 94 :E 1vdwA 43 :T T0328 111 :YDILHLVANEISQMFEDL 1vdwA 44 :KVVDKVAENIIISKFKDL T0328 129 :VELVEEERGFRFM 1vdwA 63 :VNVVSEEIGRIDQ T0328 158 :GRHRQEVALV 1vdwA 108 :EKDPIYAFIY T0328 176 :GGSY 1vdwA 131 :KGSY T0328 210 :DN 1vdwA 136 :NG T0328 212 :IEYESEDKPL 1vdwA 140 :IKVRELAEKP T0328 222 :TSH 1vdwA 213 :GAI T0328 230 :LKDENGKSIE 1vdwA 216 :VKDLDGKDVE T0328 245 :MPYGSLKEQGLMFI 1vdwA 226 :ITFSATEKVNIIAA T0328 262 :RTPDHFEKMLH 1vdwA 240 :NNEELLETILR Number of specific fragments extracted= 14 number of extra gaps= 0 total=91 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1uc2A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1uc2A expands to /projects/compbio/data/pdb/1uc2.pdb.gz 1uc2A:# T0328 read from 1uc2A/merged-good-all-a2m # 1uc2A read from 1uc2A/merged-good-all-a2m # adding 1uc2A to template set # found chain 1uc2A in template set T0328 10 :QLGVCAE 1uc2A 89 :PGGIGYD T0328 19 :LHSVYLMFNANDN 1uc2A 96 :INCGVRLIRTNLT T0328 32 :VESQLRPCIANVAQY 1uc2A 112 :VRPRIKQLVDTLFKN T0328 53 :QYSDS 1uc2A 128 :PSGVG T0328 68 :NYWDSL 1uc2A 164 :RDLERL T0328 74 :YPESRPEMLK 1uc2A 175 :MEGADPEAVS T0328 84 :PFPAMQEGNR 1uc2A 194 :QLGSLGSGNH T0328 97 :AIEYDLFVHLRCDRYDILHLVANEISQMFEDLVEL 1uc2A 224 :LFEGQVVVMVHTGSRGLGHQVASDYLRIMERAIRK T0328 151 :DGTENP 1uc2A 259 :YRIPWP T0328 159 :RHRQEVALVGSE 1uc2A 265 :DRELVSVPFQSE T0328 172 :PEFKGGSYIHVQKYAHNL 1uc2A 286 :KAAANFAWANRQMITHWV T0328 197 :LKKQEDIIGRTKQDNIEYE 1uc2A 304 :RESFQEVFKQDPEGDLGMD T0328 221 :LTSH 1uc2A 326 :DVAH T0328 225 :IKRVNLK 1uc2A 332 :GKVEEHE T0328 233 :ENGKSIE 1uc2A 339 :VDGKRVK T0328 256 :MFISTCR 1uc2A 346 :VIVHRKG T0328 263 :T 1uc2A 358 :P T0328 277 :GDGAGNHDHLMH 1uc2A 359 :PGHEAVPRLYRD T0328 294 :TGSSFFAPS 1uc2A 371 :VGQPVLIPG Number of specific fragments extracted= 19 number of extra gaps= 0 total=110 Number of alignments=10 # 1uc2A read from 1uc2A/merged-good-all-a2m # found chain 1uc2A in template set T0328 10 :QLGVCAE 1uc2A 89 :PGGIGYD T0328 19 :LHSVYLMFNAN 1uc2A 96 :INCGVRLIRTN T0328 30 :DNVESQLRPCIANVAQYI 1uc2A 110 :KEVRPRIKQLVDTLFKNV T0328 57 :SAF 1uc2A 163 :ERD T0328 66 :GANYW 1uc2A 166 :LERLE T0328 71 :DSLYPESRPEML 1uc2A 172 :GGRMEGADPEAV T0328 83 :KPFPAMQEGNR 1uc2A 193 :PQLGSLGSGNH T0328 96 :PAIEYDLFVHLRCDRYDILHLVANEISQMFEDLVEL 1uc2A 223 :GLFEGQVVVMVHTGSRGLGHQVASDYLRIMERAIRK T0328 151 :DGTENP 1uc2A 259 :YRIPWP T0328 160 :HRQEVALVGSE 1uc2A 266 :RELVSVPFQSE T0328 174 :FKGGSYIHVQKYAHNL 1uc2A 288 :AANFAWANRQMITHWV T0328 197 :LKKQEDIIGRTKQDNIEYE 1uc2A 304 :RESFQEVFKQDPEGDLGMD T0328 222 :TSH 1uc2A 327 :VAH T0328 225 :IKRVNLK 1uc2A 332 :GKVEEHE T0328 233 :ENGKSIE 1uc2A 339 :VDGKRVK T0328 255 :LMFISTC 1uc2A 346 :VIVHRKG Number of specific fragments extracted= 16 number of extra gaps= 0 total=126 Number of alignments=11 # 1uc2A read from 1uc2A/merged-good-all-a2m # found chain 1uc2A in template set T0328 10 :QLGVCAEGNLHSVYLMFNANDN 1uc2A 89 :PGGIGYDINCGVRLIRTNLTEK T0328 32 :VESQLRPCIANVAQY 1uc2A 112 :VRPRIKQLVDTLFKN T0328 50 :LTDQ 1uc2A 129 :SGVG T0328 54 :YSDSAF 1uc2A 161 :GWERDL T0328 67 :ANYWDSLYP 1uc2A 167 :ERLEEGGRM T0328 76 :ESRPEMLK 1uc2A 177 :GADPEAVS T0328 85 :FPAMQEGNR 1uc2A 195 :LGSLGSGNH T0328 96 :PAIEYDLFVHLRCDRYDILHLVANEISQMFEDLVEL 1uc2A 223 :GLFEGQVVVMVHTGSRGLGHQVASDYLRIMERAIRK T0328 153 :TENPKGRHRQEVALV 1uc2A 259 :YRIPWPDRELVSVPF T0328 174 :FKGGSYIHVQKYAHNL 1uc2A 288 :AANFAWANRQMITHWV T0328 197 :LKKQEDIIGRTKQDNIEYE 1uc2A 304 :RESFQEVFKQDPEGDLGMD T0328 222 :TSHIKRVN 1uc2A 329 :HNIGKVEE T0328 231 :KDENGKSIEIL 1uc2A 337 :HEVDGKRVKVI T0328 242 :RQSMPYGSL 1uc2A 354 :TRAFPPGHE T0328 251 :KEQGLMFIS 1uc2A 381 :MGTASYILA Number of specific fragments extracted= 15 number of extra gaps= 0 total=141 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zvdA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zvdA expands to /projects/compbio/data/pdb/1zvd.pdb.gz 1zvdA:Skipped atom 96, because occupancy 0.500 <= existing 0.500 in 1zvdA Skipped atom 98, because occupancy 0.500 <= existing 0.500 in 1zvdA Skipped atom 100, because occupancy 0.500 <= existing 0.500 in 1zvdA Skipped atom 102, because occupancy 0.500 <= existing 0.500 in 1zvdA Skipped atom 104, because occupancy 0.500 <= existing 0.500 in 1zvdA Skipped atom 106, because occupancy 0.500 <= existing 0.500 in 1zvdA Skipped atom 108, because occupancy 0.500 <= existing 0.500 in 1zvdA Skipped atom 110, because occupancy 0.500 <= existing 0.500 in 1zvdA Skipped atom 112, because occupancy 0.500 <= existing 0.500 in 1zvdA Skipped atom 114, because occupancy 0.500 <= existing 0.500 in 1zvdA Skipped atom 116, because occupancy 0.500 <= existing 0.500 in 1zvdA Skipped atom 344, because occupancy 0.500 <= existing 0.500 in 1zvdA Skipped atom 348, because occupancy 0.500 <= existing 0.500 in 1zvdA Skipped atom 350, because occupancy 0.500 <= existing 0.500 in 1zvdA Skipped atom 352, because occupancy 0.500 <= existing 0.500 in 1zvdA Skipped atom 354, because occupancy 0.500 <= existing 0.500 in 1zvdA Skipped atom 356, because occupancy 0.500 <= existing 0.500 in 1zvdA Skipped atom 358, because occupancy 0.500 <= existing 0.500 in 1zvdA Skipped atom 360, because occupancy 0.500 <= existing 0.500 in 1zvdA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1552, because occupancy 0.500 <= existing 0.500 in 1zvdA Skipped atom 1556, because occupancy 0.500 <= existing 0.500 in 1zvdA Skipped atom 1558, because occupancy 0.500 <= existing 0.500 in 1zvdA Skipped atom 1560, because occupancy 0.500 <= existing 0.500 in 1zvdA Skipped atom 1562, because occupancy 0.500 <= existing 0.500 in 1zvdA Skipped atom 1564, because occupancy 0.500 <= existing 0.500 in 1zvdA Skipped atom 1566, because occupancy 0.500 <= existing 0.500 in 1zvdA Skipped atom 1696, because occupancy 0.500 <= existing 0.500 in 1zvdA Skipped atom 1700, because occupancy 0.500 <= existing 0.500 in 1zvdA Skipped atom 1702, because occupancy 0.500 <= existing 0.500 in 1zvdA Skipped atom 2319, because occupancy 0.500 <= existing 0.500 in 1zvdA Skipped atom 2323, because occupancy 0.500 <= existing 0.500 in 1zvdA Skipped atom 2325, because occupancy 0.500 <= existing 0.500 in 1zvdA Skipped atom 2327, because occupancy 0.500 <= existing 0.500 in 1zvdA Skipped atom 2329, because occupancy 0.500 <= existing 0.500 in 1zvdA Skipped atom 2331, because occupancy 0.500 <= existing 0.500 in 1zvdA # T0328 read from 1zvdA/merged-good-all-a2m # 1zvdA read from 1zvdA/merged-good-all-a2m # adding 1zvdA to template set # found chain 1zvdA in template set Warning: unaligning (T0328)E94 because of BadResidue code BAD_PEPTIDE in next template residue (1zvdA)D433 Warning: unaligning (T0328)D109 because of BadResidue code BAD_PEPTIDE at template residue (1zvdA)D433 Warning: unaligning (T0328)D218 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1zvdA)K569 Warning: unaligning (T0328)K219 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1zvdA)K569 Warning: unaligning (T0328)P220 because of BadResidue code BAD_PEPTIDE at template residue (1zvdA)S570 Warning: unaligning (T0328)L221 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1zvdA)P572 Warning: unaligning (T0328)L230 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1zvdA)P572 Warning: unaligning (T0328)D232 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1zvdA)E575 Warning: unaligning (T0328)E233 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1zvdA)E575 Warning: unaligning (T0328)N234 because of BadResidue code BAD_PEPTIDE at template residue (1zvdA)E576 Warning: unaligning (T0328)G235 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1zvdA)N577 T0328 36 :LRPCIANVAQYIYE 1zvdA 372 :LVQKLKILRQELSQ T0328 53 :QYSDSAFNGFVAIGANYWDSLYP 1zvdA 386 :QQPQAGHCRIEVSREEIFEESYR T0328 76 :ESRPEMLKP 1zvdA 412 :KMRPKDLWK T0328 87 :AMQEGNR 1zvdA 425 :KFRGEEG T0328 110 :RYDILHLVANEI 1zvdA 434 :YGGVAREWLYLL T0328 122 :SQMFEDLVELVEEE 1zvdA 447 :HEMLNPYYGLFQYS T0328 158 :GRHRQEVALVGSEDPEFKGGSYIHVQKYAHNLSKWHRL 1zvdA 461 :RDDIYTLQINPDSAVNPEHLSYFHFVGRIMGMAVFHGH T0328 196 :PLKKQEDIIGRTKQ 1zvdA 505 :TLPFYKQLLGKSIT T0328 211 :NIEYESE 1zvdA 561 :QHELKPN T0328 231 :K 1zvdA 573 :V T0328 238 :IEILRQS 1zvdA 582 :VRLYVNW T0328 260 :TCRTP 1zvdA 590 :FLRGI T0328 265 :DHFEKMLHSMV 1zvdA 596 :AQFLALQKGFN T0328 300 :APSLDFLMQFD 1zvdA 608 :VIPQHLLKTFD Number of specific fragments extracted= 14 number of extra gaps= 3 total=155 Number of alignments=13 # 1zvdA read from 1zvdA/merged-good-all-a2m # found chain 1zvdA in template set Warning: unaligning (T0328)E94 because of BadResidue code BAD_PEPTIDE in next template residue (1zvdA)D433 Warning: unaligning (T0328)D109 because of BadResidue code BAD_PEPTIDE at template residue (1zvdA)D433 T0328 36 :LRPCIANVAQYIYE 1zvdA 372 :LVQKLKILRQELSQ T0328 53 :QYSDSAFNGFVAIGANYWDSLYP 1zvdA 386 :QQPQAGHCRIEVSREEIFEESYR T0328 76 :ESRPEML 1zvdA 412 :KMRPKDL T0328 87 :AMQEGNR 1zvdA 425 :KFRGEEG T0328 110 :RYDILHLVANEIS 1zvdA 434 :YGGVAREWLYLLS T0328 123 :QMFEDLVELVEEERGF 1zvdA 448 :EMLNPYYGLFQYSRDD T0328 155 :NP 1zvdA 470 :NP T0328 173 :EFKGGSYIHVQKYAHNL 1zvdA 592 :RGIEAQFLALQKGFNEV T0328 190 :SKWHRLPLKKQEDIIGRTK 1zvdA 612 :HLLKTFDEKELELIICGLG T0328 217 :ED 1zvdA 631 :KI T0328 220 :PLTSHIKRVNLK 1zvdA 710 :LPKAHTCFNRID T0328 258 :ISTCRTPDHFEKMLHSMV 1zvdA 722 :IPPYESYEKLYEKLLTAI Number of specific fragments extracted= 12 number of extra gaps= 1 total=167 Number of alignments=14 # 1zvdA read from 1zvdA/merged-good-all-a2m # found chain 1zvdA in template set Warning: unaligning (T0328)E94 because of BadResidue code BAD_PEPTIDE in next template residue (1zvdA)D433 Warning: unaligning (T0328)D109 because of BadResidue code BAD_PEPTIDE at template residue (1zvdA)D433 Warning: unaligning (T0328)G235 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1zvdA)K569 Warning: unaligning (T0328)K236 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1zvdA)K569 Warning: unaligning (T0328)S237 because of BadResidue code BAD_PEPTIDE at template residue (1zvdA)S570 Warning: unaligning (T0328)I238 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1zvdA)P572 Warning: unaligning (T0328)P246 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1zvdA)P572 Warning: unaligning (T0328)G248 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1zvdA)E575 Warning: unaligning (T0328)S249 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1zvdA)E575 Warning: unaligning (T0328)L250 because of BadResidue code BAD_PEPTIDE at template residue (1zvdA)E576 T0328 36 :LRPCIANVAQYIYEL 1zvdA 372 :LVQKLKILRQELSQQ T0328 53 :QYSDSAFNGFV 1zvdA 387 :QPQAGHCRIEV T0328 66 :GANYWDSLYP 1zvdA 399 :REEIFEESYR T0328 76 :ESRPEMLKP 1zvdA 412 :KMRPKDLWK T0328 87 :AMQEGNR 1zvdA 425 :KFRGEEG T0328 110 :RYDILHLVANEISQMFEDL 1zvdA 434 :YGGVAREWLYLLSHEMLNP T0328 134 :EERGFRFM 1zvdA 453 :YYGLFQYS T0328 159 :RHRQEVALVGSEDPEFKG 1zvdA 461 :RDDIYTLQINPDSAVNPE T0328 177 :GSYIHVQKYAHNLSKWHR 1zvdA 480 :LSYFHFVGRIMGMAVFHG T0328 195 :LPLKKQEDIIGRTKQDN 1zvdA 504 :FTLPFYKQLLGKSITLD T0328 224 :HIKR 1zvdA 558 :EIIQ T0328 229 :NLKDEN 1zvdA 562 :HELKPN T0328 247 :Y 1zvdA 573 :V T0328 265 :DHFEKMLHSMVFGDGAGNHDHLMHFTS 1zvdA 580 :EYVRLYVNWRFLRGIEAQFLALQKGFN T0328 300 :APSLDFLMQFD 1zvdA 608 :VIPQHLLKTFD Number of specific fragments extracted= 15 number of extra gaps= 3 total=182 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cb2A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2cb2A expands to /projects/compbio/data/pdb/2cb2.pdb.gz 2cb2A:Skipped atom 164, because occupancy 0.430 <= existing 0.570 in 2cb2A Skipped atom 166, because occupancy 0.430 <= existing 0.570 in 2cb2A Skipped atom 168, because occupancy 0.430 <= existing 0.570 in 2cb2A Skipped atom 170, because occupancy 0.430 <= existing 0.570 in 2cb2A Skipped atom 172, because occupancy 0.430 <= existing 0.570 in 2cb2A Skipped atom 174, because occupancy 0.430 <= existing 0.570 in 2cb2A Skipped atom 176, because occupancy 0.430 <= existing 0.570 in 2cb2A Skipped atom 178, because occupancy 0.430 <= existing 0.570 in 2cb2A Skipped atom 262, because occupancy 0.490 <= existing 0.510 in 2cb2A Skipped atom 264, because occupancy 0.490 <= existing 0.510 in 2cb2A Skipped atom 266, because occupancy 0.490 <= existing 0.510 in 2cb2A Skipped atom 369, because occupancy 0.480 <= existing 0.520 in 2cb2A Skipped atom 371, because occupancy 0.480 <= existing 0.520 in 2cb2A Skipped atom 373, because occupancy 0.480 <= existing 0.520 in 2cb2A Skipped atom 375, because occupancy 0.480 <= existing 0.520 in 2cb2A Skipped atom 542, because occupancy 0.310 <= existing 0.690 in 2cb2A Skipped atom 544, because occupancy 0.310 <= existing 0.690 in 2cb2A Skipped atom 847, because occupancy 0.490 <= existing 0.510 in 2cb2A Skipped atom 849, because occupancy 0.490 <= existing 0.510 in 2cb2A Skipped atom 851, because occupancy 0.490 <= existing 0.510 in 2cb2A Skipped atom 853, because occupancy 0.490 <= existing 0.510 in 2cb2A Skipped atom 855, because occupancy 0.490 <= existing 0.510 in 2cb2A Skipped atom 857, because occupancy 0.490 <= existing 0.510 in 2cb2A Skipped atom 859, because occupancy 0.490 <= existing 0.510 in 2cb2A Skipped atom 861, because occupancy 0.490 <= existing 0.510 in 2cb2A Skipped atom 1372, because occupancy 0.410 <= existing 0.590 in 2cb2A Skipped atom 1374, because occupancy 0.410 <= existing 0.590 in 2cb2A Skipped atom 1462, because occupancy 0.380 <= existing 0.620 in 2cb2A Skipped atom 1464, because occupancy 0.380 <= existing 0.620 in 2cb2A Skipped atom 1466, because occupancy 0.380 <= existing 0.620 in 2cb2A Skipped atom 1468, because occupancy 0.380 <= existing 0.620 in 2cb2A Skipped atom 1495, because occupancy 0.380 <= existing 0.620 in 2cb2A Skipped atom 1497, because occupancy 0.380 <= existing 0.620 in 2cb2A Skipped atom 1499, because occupancy 0.380 <= existing 0.620 in 2cb2A Skipped atom 1501, because occupancy 0.380 <= existing 0.620 in 2cb2A Skipped atom 1503, because occupancy 0.380 <= existing 0.620 in 2cb2A Skipped atom 1505, because occupancy 0.380 <= existing 0.620 in 2cb2A Skipped atom 1702, because occupancy 0.450 <= existing 0.550 in 2cb2A Skipped atom 1704, because occupancy 0.450 <= existing 0.550 in 2cb2A Skipped atom 1706, because occupancy 0.450 <= existing 0.550 in 2cb2A Skipped atom 1958, because occupancy 0.420 <= existing 0.580 in 2cb2A Skipped atom 1960, because occupancy 0.420 <= existing 0.580 in 2cb2A Skipped atom 1962, because occupancy 0.420 <= existing 0.580 in 2cb2A Skipped atom 1964, because occupancy 0.420 <= existing 0.580 in 2cb2A Skipped atom 2015, because occupancy 0.340 <= existing 0.660 in 2cb2A Skipped atom 2018, because occupancy 0.340 <= existing 0.660 in 2cb2A Skipped atom 2401, because occupancy 0.500 <= existing 0.500 in 2cb2A Skipped atom 2403, because occupancy 0.500 <= existing 0.500 in 2cb2A Skipped atom 2405, because occupancy 0.500 <= existing 0.500 in 2cb2A Skipped atom 2407, because occupancy 0.500 <= existing 0.500 in 2cb2A # T0328 read from 2cb2A/merged-good-all-a2m # 2cb2A read from 2cb2A/merged-good-all-a2m # adding 2cb2A to template set # found chain 2cb2A in template set Warning: unaligning (T0328)G17 because first residue in template chain is (2cb2A)P2 Warning: unaligning (T0328)I47 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2cb2A)M32 Warning: unaligning (T0328)E49 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2cb2A)M32 Warning: unaligning (T0328)E213 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2cb2A)P229 Warning: unaligning (T0328)Y214 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2cb2A)P229 Warning: unaligning (T0328)K251 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2cb2A)T244 T0328 18 :NLHSVYLMFNANDN 2cb2A 3 :KPYVAINMAELKNE T0328 34 :SQLRPCIANVAQY 2cb2A 17 :PKTFEMFASVGPK T0328 50 :LTDQYSDS 2cb2A 33 :VTARHPGF T0328 74 :YPE 2cb2A 54 :FGN T0328 87 :AMQEGNREA 2cb2A 57 :RYGGAKMDM T0328 96 :PAIEYDLFVHLRCDRYDILHLVANE 2cb2A 68 :ESSTVRVLQYTFWKDWKDHEEMHRQ T0328 121 :ISQMFEDL 2cb2A 97 :LFRLCYSC T0328 129 :VELVEEERGF 2cb2A 106 :SQMIWGPWEP T0328 144 :RD 2cb2A 147 :LD T0328 150 :VDGTENPKGRHRQEVALV 2cb2A 149 :IPVISQPYGKRVVAFAEH T0328 169 :SED 2cb2A 170 :PGK T0328 178 :SYIHVQKYAHNLSKWHRL 2cb2A 173 :EKQFEDAIVRTLEMLKKA T0328 196 :PLKKQEDII 2cb2A 213 :GAKGFHQVL T0328 207 :TKQDNI 2cb2A 222 :ENPGSL T0328 215 :ESEDKPLT 2cb2A 230 :DPNNVMYS T0328 248 :GSL 2cb2A 239 :PEA T0328 252 :EQGLMFISTCRTPDHFEKMLHSMVF 2cb2A 245 :PQQYIVHVEWANTDALMFGMGRVLL Number of specific fragments extracted= 17 number of extra gaps= 2 total=199 Number of alignments=16 # 2cb2A read from 2cb2A/merged-good-all-a2m # found chain 2cb2A in template set Warning: unaligning (T0328)G17 because first residue in template chain is (2cb2A)P2 Warning: unaligning (T0328)I47 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2cb2A)M32 Warning: unaligning (T0328)E49 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2cb2A)M32 Warning: unaligning (T0328)K219 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2cb2A)P229 Warning: unaligning (T0328)P220 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2cb2A)P229 T0328 18 :NLHSVYLMFNANDN 2cb2A 3 :KPYVAINMAELKNE T0328 34 :SQLRPCIANVAQY 2cb2A 17 :PKTFEMFASVGPK T0328 50 :LTDQYSD 2cb2A 33 :VTARHPG T0328 86 :PAMQEGNREA 2cb2A 56 :NRYGGAKMDM T0328 96 :PAIEYDLFVHLRCDRYDILHLVANE 2cb2A 68 :ESSTVRVLQYTFWKDWKDHEEMHRQ T0328 121 :ISQMFEDLV 2cb2A 97 :LFRLCYSCA T0328 130 :ELVEEERGF 2cb2A 107 :QMIWGPWEP T0328 143 :SRD 2cb2A 146 :PLD T0328 150 :VDGTENPKGRHRQEVALVG 2cb2A 149 :IPVISQPYGKRVVAFAEHS T0328 169 :SED 2cb2A 170 :PGK T0328 178 :SYIHVQKYAHNLSKWHRL 2cb2A 173 :EKQFEDAIVRTLEMLKKA T0328 196 :PLKKQEDIIG 2cb2A 213 :GAKGFHQVLE T0328 214 :YESED 2cb2A 223 :NPGSL T0328 229 :NLK 2cb2A 230 :DPN T0328 244 :SMPYGSLK 2cb2A 233 :NVMYSVPE T0328 252 :EQGLMFISTCRTPDHFEKMLHSMVF 2cb2A 245 :PQQYIVHVEWANTDALMFGMGRVLL Number of specific fragments extracted= 16 number of extra gaps= 1 total=215 Number of alignments=17 # 2cb2A read from 2cb2A/merged-good-all-a2m # found chain 2cb2A in template set Warning: unaligning (T0328)G17 because first residue in template chain is (2cb2A)P2 Warning: unaligning (T0328)I47 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2cb2A)M32 Warning: unaligning (T0328)E49 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2cb2A)M32 Warning: unaligning (T0328)K251 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2cb2A)T244 T0328 18 :NLHSVYLMFNANDN 2cb2A 3 :KPYVAINMAELKNE T0328 34 :SQLRPCIANVAQY 2cb2A 17 :PKTFEMFASVGPK T0328 50 :LTDQ 2cb2A 33 :VTAR T0328 54 :YSDSA 2cb2A 52 :LPFGN T0328 73 :LYPESR 2cb2A 57 :RYGGAK T0328 85 :F 2cb2A 63 :M T0328 87 :AMQE 2cb2A 64 :DMTK T0328 96 :PAIEYDLFVHLRCDRYDILHLVANE 2cb2A 68 :ESSTVRVLQYTFWKDWKDHEEMHRQ T0328 121 :ISQMFEDLV 2cb2A 97 :LFRLCYSCA T0328 130 :ELVEEERGFRFM 2cb2A 107 :QMIWGPWEPIYE T0328 142 :DSRDL 2cb2A 145 :KPLDI T0328 151 :DGTENPKGRHRQEVALV 2cb2A 150 :PVISQPYGKRVVAFAEH T0328 168 :GSEDPE 2cb2A 169 :IPGKEK T0328 180 :IHVQKYAHNLSKW 2cb2A 175 :QFEDAIVRTLEML T0328 217 :EDKPLTSHIKRVNLKD 2cb2A 188 :KKAPGFLGAMVLKEIG T0328 243 :QSMPYGSL 2cb2A 208 :GSMQFGAK T0328 252 :EQGLMFISTCRTPDHFEKMLHSMVFGDG 2cb2A 245 :PQQYIVHVEWANTDALMFGMGRVLLYPE T0328 281 :GNHDHLMH 2cb2A 275 :QVHDEVLD Number of specific fragments extracted= 18 number of extra gaps= 1 total=233 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t0tV/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0328 read from 1t0tV/merged-good-all-a2m # 1t0tV read from 1t0tV/merged-good-all-a2m # found chain 1t0tV in training set Warning: unaligning (T0328)S21 because of BadResidue code BAD_PEPTIDE in next template residue (1t0tV)L14 Warning: unaligning (T0328)V22 because of BadResidue code BAD_PEPTIDE at template residue (1t0tV)L14 Warning: unaligning (T0328)L255 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1t0tV)G198 Warning: unaligning (T0328)M256 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1t0tV)G198 T0328 19 :LH 1t0tV 11 :WY T0328 23 :YLMFNANDN 1t0tV 15 :HDFRTIDWS T0328 32 :VESQLRPCIANVAQYIYELTDQYSDSAFNGFV 1t0tV 29 :PNEEREAAISEFLALVDQWETTESEKQGSHAV T0328 94 :EAPAIEYDLFVHLRCDRYDILHLVANEISQM 1t0tV 62 :TIVGQKADILFMILRPTLDELHEIETALNKT T0328 125 :FEDLVELVEEERGF 1t0tV 94 :LADYLLPAYSYVSV T0328 139 :RFM 1t0tV 112 :NYL T0328 150 :VDGTENP 1t0tV 115 :ASGSEDP T0328 160 :HRQEVALV 1t0tV 136 :PKTNYICF T0328 168 :GSED 1t0tV 150 :RQGN T0328 192 :WHRLPLKKQE 1t0tV 156 :WYMLSMEQRR T0328 202 :DIIGRTKQDNIEY 1t0tV 172 :GMTGRKYAGKVTQ T0328 226 :KRVNLKDENG 1t0tV 185 :IITGSVGLDD T0328 253 :QG 1t0tV 195 :FE T0328 257 :FISTCRTPDHFEKMLHSMV 1t0tV 199 :VTLFSDDALQFKKLVYEMR T0328 282 :NHDHLMHF 1t0tV 218 :FDEVSARF T0328 292 :ALTGSSFFA 1t0tV 226 :GEFGSFFVG T0328 301 :PSLDFLM 1t0tV 237 :LPMENVS Number of specific fragments extracted= 17 number of extra gaps= 2 total=250 Number of alignments=19 # 1t0tV read from 1t0tV/merged-good-all-a2m # found chain 1t0tV in training set Warning: unaligning (T0328)S21 because of BadResidue code BAD_PEPTIDE in next template residue (1t0tV)L14 Warning: unaligning (T0328)V22 because of BadResidue code BAD_PEPTIDE at template residue (1t0tV)L14 Warning: unaligning (T0328)L255 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1t0tV)G198 Warning: unaligning (T0328)M256 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1t0tV)G198 T0328 19 :LH 1t0tV 11 :WY T0328 23 :YLMFNANDN 1t0tV 15 :HDFRTIDWS T0328 32 :VESQLRPCIANVAQYIYELTDQYSDSAFNGFV 1t0tV 29 :PNEEREAAISEFLALVDQWETTESEKQGSHAV T0328 93 :REAPAIEYDLFVHLRCDRYDILHLVANEISQ 1t0tV 61 :YTIVGQKADILFMILRPTLDELHEIETALNK T0328 124 :MFEDLVELVEEERGF 1t0tV 93 :KLADYLLPAYSYVSV T0328 139 :RFM 1t0tV 112 :NYL T0328 150 :VDGTENP 1t0tV 115 :ASGSEDP T0328 158 :GRHRQEVALV 1t0tV 134 :ILPKTNYICF T0328 168 :GSED 1t0tV 150 :RQGN T0328 192 :WHRLPLKKQE 1t0tV 156 :WYMLSMEQRR T0328 202 :DIIGRTKQDNIE 1t0tV 172 :GMTGRKYAGKVT T0328 225 :IKRVNLKDENG 1t0tV 184 :QIITGSVGLDD T0328 253 :QG 1t0tV 195 :FE T0328 257 :FISTCRTPDHFEKMLHSMV 1t0tV 199 :VTLFSDDALQFKKLVYEMR T0328 282 :NHDHLMHFTS 1t0tV 218 :FDEVSARFGE T0328 294 :TGSSFFA 1t0tV 228 :FGSFFVG T0328 301 :PSLDFLMQF 1t0tV 237 :LPMENVSSF Number of specific fragments extracted= 17 number of extra gaps= 2 total=267 Number of alignments=20 # 1t0tV read from 1t0tV/merged-good-all-a2m # found chain 1t0tV in training set Warning: unaligning (T0328)S21 because of BadResidue code BAD_PEPTIDE in next template residue (1t0tV)L14 Warning: unaligning (T0328)V22 because of BadResidue code BAD_PEPTIDE at template residue (1t0tV)L14 Warning: unaligning (T0328)L255 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1t0tV)G198 Warning: unaligning (T0328)M256 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1t0tV)G198 T0328 19 :LH 1t0tV 11 :WY T0328 23 :YLMFNANDN 1t0tV 15 :HDFRTIDWS T0328 32 :VESQLRPCIANVAQYIYELTDQ 1t0tV 29 :PNEEREAAISEFLALVDQWETT T0328 94 :EAPAIEYDLFVHLRCDRYDILHLVANEISQ 1t0tV 62 :TIVGQKADILFMILRPTLDELHEIETALNK T0328 124 :MFEDLVELVEEERGFRFM 1t0tV 93 :KLADYLLPAYSYVSVVEL T0328 142 :DSRD 1t0tV 120 :DPYQ T0328 159 :RH 1t0tV 124 :IP T0328 161 :RQEVALV 1t0tV 137 :KTNYICF T0328 168 :GSED 1t0tV 151 :QGND T0328 191 :KWHRLPLKKQED 1t0tV 155 :NWYMLSMEQRRE T0328 203 :IIGRTKQDN 1t0tV 173 :MTGRKYAGK T0328 223 :SHIKRVNLKD 1t0tV 182 :VTQIITGSVG T0328 247 :Y 1t0tV 192 :L T0328 251 :KEQG 1t0tV 193 :DDFE T0328 257 :FISTCRTPDHFEKMLHSMV 1t0tV 199 :VTLFSDDALQFKKLVYEMR T0328 282 :NHDHLMHFTSA 1t0tV 218 :FDEVSARFGEF T0328 295 :GSSF 1t0tV 229 :GSFF Number of specific fragments extracted= 17 number of extra gaps= 2 total=284 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1omzA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1omzA expands to /projects/compbio/data/pdb/1omz.pdb.gz 1omzA:# T0328 read from 1omzA/merged-good-all-a2m # 1omzA read from 1omzA/merged-good-all-a2m # adding 1omzA to template set # found chain 1omzA in template set Warning: unaligning (T0328)P196 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1omzA)A287 T0328 24 :LMFNA 1omzA 69 :LIMQT T0328 30 :DNVESQLRPCIANVA 1omzA 74 :YNRTDLLLRLLNHYQ T0328 55 :SDSAF 1omzA 89 :AVPSL T0328 60 :NGFVAIGA 1omzA 95 :KVIVVWNN T0328 68 :NYWDSLYP 1omzA 110 :ELWNSLGP T0328 76 :ESRPEMLKPFPAMQEG 1omzA 130 :NKMRNRLQVFPEVETN T0328 102 :LFVHLRCDR 1omzA 146 :AVLMVDDDT T0328 111 :YDILHLVANEISQMFEDL 1omzA 158 :AQDLVFAFSIWQQFPDQI T0328 129 :VELVEEERGF 1omzA 178 :FVPRKHVSTS T0328 148 :GFVDGTENPKGRH 1omzA 195 :GFELQTPGPGNGD T0328 161 :RQEVALVGSE 1omzA 213 :LIGASFFNSK T0328 181 :HVQKYAHNLSKWHRL 1omzA 223 :YLELFQKQPAAVHAL T0328 197 :LKKQE 1omzA 288 :EHFLQ T0328 202 :DII 1omzA 302 :NIY T0328 217 :EDKPLT 1omzA 305 :DGMPLK Number of specific fragments extracted= 15 number of extra gaps= 0 total=299 Number of alignments=22 # 1omzA read from 1omzA/merged-good-all-a2m # found chain 1omzA in template set T0328 23 :YLMFNAN 1omzA 68 :TLIMQTY T0328 31 :NVESQLRPCIANVAQ 1omzA 75 :NRTDLLLRLLNHYQA T0328 55 :S 1omzA 90 :V T0328 57 :SAF 1omzA 91 :PSL T0328 60 :NGFVAIGA 1omzA 95 :KVIVVWNN T0328 68 :NYWDSLYP 1omzA 110 :ELWNSLGP T0328 76 :ESRPEMLKPFPAMQEG 1omzA 130 :NKMRNRLQVFPEVETN T0328 102 :LFVHLRCD 1omzA 146 :AVLMVDDD T0328 110 :RYDILHLVANEISQMFEDL 1omzA 157 :SAQDLVFAFSIWQQFPDQI T0328 129 :VELVEEERGF 1omzA 178 :FVPRKHVSTS T0328 148 :GFVDGTENPKGRH 1omzA 195 :GFELQTPGPGNGD T0328 161 :RQEVALVGSE 1omzA 213 :LIGASFFNSK T0328 181 :HVQKYAHNLSKWHRL 1omzA 223 :YLELFQKQPAAVHAL T0328 198 :KKQE 1omzA 289 :HFLQ T0328 202 :DII 1omzA 302 :NIY T0328 210 :DNIEYESED 1omzA 305 :DGMPLKYSN Number of specific fragments extracted= 16 number of extra gaps= 0 total=315 Number of alignments=23 # 1omzA read from 1omzA/merged-good-all-a2m # found chain 1omzA in template set T0328 27 :NA 1omzA 72 :QT T0328 30 :DNVESQLRPCIANVAQ 1omzA 74 :YNRTDLLLRLLNHYQA T0328 55 :SDSAFNGFVAIGA 1omzA 90 :VPSLHKVIVVWNN T0328 68 :NYWDSLYP 1omzA 110 :ELWNSLGP T0328 77 :SRPEMLKPFPAMQEG 1omzA 131 :KMRNRLQVFPEVETN T0328 102 :LFVHLRCD 1omzA 146 :AVLMVDDD T0328 110 :RYDILHLVANEISQM 1omzA 157 :SAQDLVFAFSIWQQF T0328 126 :EDLVE 1omzA 172 :PDQII T0328 131 :LVEEERGFRFMD 1omzA 184 :VSTSSGIYSYGG T0328 149 :FVDGTENPKGRHRQEVALV 1omzA 196 :FELQTPGPGNGDQYSMVLI T0328 168 :GS 1omzA 220 :NS T0328 180 :IH 1omzA 222 :KY T0328 189 :LSKWHRLPL 1omzA 224 :LELFQKQPA Number of specific fragments extracted= 13 number of extra gaps= 0 total=328 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o08A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0328 read from 1o08A/merged-good-all-a2m # 1o08A read from 1o08A/merged-good-all-a2m # found chain 1o08A in training set T0328 29 :NDN 1o08A 1060 :ADK T0328 32 :VESQLRPCIANVAQYIYELTDQYSDS 1o08A 1065 :SAEEFKELAKRKNDNYVKMIQDVSPA T0328 58 :AFNGFVAIGANYWDSLYP 1o08A 1107 :KIKIALASASKNGPFLLE T0328 76 :ESRPEMLK 1o08A 1126 :MNLTGYFD T0328 84 :PFPAMQEGNRE 1o08A 1137 :DPAEVAASKPA T0328 95 :APAIEYDLFVHLRC 1o08A 1158 :VGVAPSESIGLEDS T0328 112 :DILHLVANEI 1o08A 1172 :QAGIQAIKDS T0328 122 :SQMFEDLVE 1o08A 1191 :PEDLGDDIV T0328 166 :LV 1o08A 1200 :IV T0328 190 :SKWHRLPLKKQEDII 1o08A 1202 :PDTSHYTLEFLKEVW Number of specific fragments extracted= 10 number of extra gaps= 0 total=338 Number of alignments=25 # 1o08A read from 1o08A/merged-good-all-a2m # found chain 1o08A in training set T0328 29 :NDN 1o08A 1060 :ADK T0328 32 :VESQLRPCIANVAQYIYELTDQYSD 1o08A 1065 :SAEEFKELAKRKNDNYVKMIQDVSP T0328 57 :SAFNGFVAIGANYWDSLYP 1o08A 1106 :NKIKIALASASKNGPFLLE T0328 77 :SRPEMLK 1o08A 1127 :NLTGYFD T0328 84 :PFPAMQEGNREA 1o08A 1137 :DPAEVAASKPAP T0328 96 :PAIEYDLFVHLRC 1o08A 1159 :GVAPSESIGLEDS T0328 112 :DILHLVANEIS 1o08A 1172 :QAGIQAIKDSG T0328 123 :QMFEDLVELVEEER 1o08A 1192 :EDLGDDIVIVPDTS Number of specific fragments extracted= 8 number of extra gaps= 0 total=346 Number of alignments=26 # 1o08A read from 1o08A/merged-good-all-a2m # found chain 1o08A in training set T0328 28 :ANDN 1o08A 1059 :LADK T0328 32 :VESQLRPCIANVAQYIYELTDQYSDSA 1o08A 1065 :SAEEFKELAKRKNDNYVKMIQDVSPAD T0328 59 :FNGFVAIGAN 1o08A 1108 :IKIALASASK T0328 69 :YWDSLYP 1o08A 1122 :LLERMNL T0328 76 :E 1o08A 1130 :G T0328 77 :SRPEMLKPF 1o08A 1136 :ADPAEVAAS T0328 87 :A 1o08A 1146 :P T0328 110 :RYDILHLVANE 1o08A 1147 :APDIFIAAAHA Number of specific fragments extracted= 8 number of extra gaps= 0 total=354 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fj2A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0328 read from 1fj2A/merged-good-all-a2m # 1fj2A read from 1fj2A/merged-good-all-a2m # found chain 1fj2A in training set Warning: unaligning (T0328)N29 because of BadResidue code BAD_PEPTIDE at template residue (1fj2A)S74 Warning: unaligning (T0328)D30 because of BadResidue code BAD_PEPTIDE in next template residue (1fj2A)D76 Warning: unaligning (T0328)N31 because of BadResidue code BAD_PEPTIDE at template residue (1fj2A)D76 Warning: unaligning (T0328)Q89 because of BadResidue code BAD_PEPTIDE in next template residue (1fj2A)Q149 Warning: unaligning (T0328)E90 because of BadResidue code BAD_PEPTIDE at template residue (1fj2A)Q149 Warning: unaligning (T0328)A95 because of BadResidue code BAD_PEPTIDE in next template residue (1fj2A)A155 Warning: unaligning (T0328)P96 because of BadResidue code BAD_PEPTIDE at template residue (1fj2A)A155 T0328 32 :VESQLRPCIANVAQYIYELTDQYSDS 1fj2A 80 :DESGIKQAAENIKALIDQEVKNGIPS T0328 58 :AFNGFVAIGANYWD 1fj2A 130 :KLAGVTALSCWLPL T0328 79 :P 1fj2A 144 :R T0328 86 :PAM 1fj2A 145 :ASF T0328 91 :GNRE 1fj2A 150 :GPIG T0328 97 :AIEYD 1fj2A 156 :NRDIS T0328 103 :FVHLRCDR 1fj2A 161 :ILQCHGDC T0328 111 :YDILHLVANEISQMF 1fj2A 174 :LMFGSLTVEKLKTLV T0328 126 :EDLVELVEE 1fj2A 190 :PANVTFKTY T0328 136 :RGFRF 1fj2A 199 :EGMMH Number of specific fragments extracted= 10 number of extra gaps= 3 total=364 Number of alignments=28 # 1fj2A read from 1fj2A/merged-good-all-a2m # found chain 1fj2A in training set Warning: unaligning (T0328)A28 because of BadResidue code BAD_PEPTIDE in next template residue (1fj2A)S74 Warning: unaligning (T0328)N29 because of BadResidue code BAD_PEPTIDE at template residue (1fj2A)S74 Warning: unaligning (T0328)D30 because of BadResidue code BAD_PEPTIDE in next template residue (1fj2A)D76 Warning: unaligning (T0328)N31 because of BadResidue code BAD_PEPTIDE at template residue (1fj2A)D76 Warning: unaligning (T0328)Y74 because of BadResidue code BAD_PEPTIDE in next template residue (1fj2A)Q128 Warning: unaligning (T0328)P75 because of BadResidue code BAD_PEPTIDE at template residue (1fj2A)Q128 Warning: unaligning (T0328)Q89 because of BadResidue code BAD_PEPTIDE in next template residue (1fj2A)Q149 Warning: unaligning (T0328)E90 because of BadResidue code BAD_PEPTIDE at template residue (1fj2A)Q149 Warning: unaligning (T0328)A95 because of BadResidue code BAD_PEPTIDE in next template residue (1fj2A)A155 Warning: unaligning (T0328)P96 because of BadResidue code BAD_PEPTIDE at template residue (1fj2A)A155 T0328 32 :VESQLRPCIANVAQYIYELTDQYSDSAFNGFVAIGANYW 1fj2A 80 :DESGIKQAAENIKALIDQEVKNGIPSNRIILGGFSQGGA T0328 71 :DSL 1fj2A 124 :ALT T0328 81 :MLKPFPAM 1fj2A 140 :WLPLRASF T0328 91 :GNRE 1fj2A 150 :GPIG T0328 97 :AIEYDLFVHLRCD 1fj2A 156 :NRDISILQCHGDC T0328 111 :YDILHLVANEISQMF 1fj2A 174 :LMFGSLTVEKLKTLV T0328 126 :EDLVELVEEERGF 1fj2A 190 :PANVTFKTYEGMM Number of specific fragments extracted= 7 number of extra gaps= 4 total=371 Number of alignments=29 # 1fj2A read from 1fj2A/merged-good-all-a2m # found chain 1fj2A in training set Warning: unaligning (T0328)A28 because of BadResidue code BAD_PEPTIDE in next template residue (1fj2A)S74 Warning: unaligning (T0328)N29 because of BadResidue code BAD_PEPTIDE at template residue (1fj2A)S74 Warning: unaligning (T0328)D30 because of BadResidue code BAD_PEPTIDE in next template residue (1fj2A)D76 Warning: unaligning (T0328)N31 because of BadResidue code BAD_PEPTIDE at template residue (1fj2A)D76 Warning: unaligning (T0328)P75 because of BadResidue code BAD_PEPTIDE in next template residue (1fj2A)Q128 Warning: unaligning (T0328)E76 because of BadResidue code BAD_PEPTIDE at template residue (1fj2A)Q128 Warning: unaligning (T0328)Q89 because of BadResidue code BAD_PEPTIDE in next template residue (1fj2A)Q149 Warning: unaligning (T0328)E90 because of BadResidue code BAD_PEPTIDE at template residue (1fj2A)Q149 Warning: unaligning (T0328)A95 because of BadResidue code BAD_PEPTIDE in next template residue (1fj2A)A155 Warning: unaligning (T0328)P96 because of BadResidue code BAD_PEPTIDE at template residue (1fj2A)A155 T0328 32 :VESQLRPCIANVAQYIYELTDQYSDSAFNGFVAIGA 1fj2A 80 :DESGIKQAAENIKALIDQEVKNGIPSNRIILGGFSQ T0328 68 :NYWDSLY 1fj2A 120 :SLYTALT T0328 79 :P 1fj2A 142 :P T0328 84 :PFPAM 1fj2A 143 :LRASF T0328 91 :GNRE 1fj2A 150 :GPIG T0328 97 :AIEYDLF 1fj2A 156 :NRDISIL T0328 105 :HLRCD 1fj2A 163 :QCHGD T0328 110 :RYDILHLVANEISQMFE 1fj2A 173 :PLMFGSLTVEKLKTLVN T0328 127 :DLVELVE 1fj2A 191 :ANVTFKT Number of specific fragments extracted= 9 number of extra gaps= 4 total=380 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fm0E/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0328 read from 1fm0E/merged-good-all-a2m # 1fm0E read from 1fm0E/merged-good-all-a2m # found chain 1fm0E in training set T0328 24 :LMFNANDN 1fm0E 50 :LTLEHYPG T0328 32 :VESQLRPCIANVA 1fm0E 59 :TEKALAEIVDEAR T0328 52 :DQYSDSAFNGFVAI 1fm0E 72 :NRWPLGRVTVIHRI T0328 86 :PAMQEG 1fm0E 86 :GELWPG T0328 99 :EYDLFVHLRCDRYDILHLVANEISQMFEDLVEL 1fm0E 92 :DEIVFVGVTSAHRSSAFEAGQFIMDYLKTRAPF Number of specific fragments extracted= 5 number of extra gaps= 0 total=385 Number of alignments=31 # 1fm0E read from 1fm0E/merged-good-all-a2m # found chain 1fm0E in training set T0328 24 :LMFNANDN 1fm0E 50 :LTLEHYPG T0328 32 :VESQLRPCIANVAQY 1fm0E 59 :TEKALAEIVDEARNR T0328 54 :YSDSAFNGFVA 1fm0E 74 :WPLGRVTVIHR T0328 85 :FPAMQEG 1fm0E 85 :IGELWPG T0328 99 :EYDLFVHLRCDRYDILHLVANEISQMFEDL 1fm0E 92 :DEIVFVGVTSAHRSSAFEAGQFIMDYLKTR T0328 129 :VELVEEERGF 1fm0E 124 :FWKREATPEG T0328 139 :R 1fm0E 135 :R Number of specific fragments extracted= 7 number of extra gaps= 0 total=392 Number of alignments=32 # 1fm0E read from 1fm0E/merged-good-all-a2m # found chain 1fm0E in training set T0328 24 :LMFNANDN 1fm0E 50 :LTLEHYPG T0328 32 :VESQLRPCIANVAQY 1fm0E 59 :TEKALAEIVDEARNR T0328 54 :YSDSAFNGFVAI 1fm0E 74 :WPLGRVTVIHRI T0328 86 :PAMQEG 1fm0E 86 :GELWPG T0328 99 :EYDLFVHLRCDRYDILHLVANEISQMFEDLVELVE 1fm0E 92 :DEIVFVGVTSAHRSSAFEAGQFIMDYLKTRAPFWK Number of specific fragments extracted= 5 number of extra gaps= 0 total=397 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1a8y/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1a8y expands to /projects/compbio/data/pdb/1a8y.pdb.gz 1a8y:Warning: there is no chain 1a8y will retry with 1a8yA # T0328 read from 1a8y/merged-good-all-a2m # 1a8y read from 1a8y/merged-good-all-a2m # adding 1a8y to template set # found chain 1a8y in template set Warning: unaligning (T0328)N18 because of BadResidue code BAD_PEPTIDE in next template residue (1a8y)N22 Warning: unaligning (T0328)L19 because of BadResidue code BAD_PEPTIDE at template residue (1a8y)N22 Warning: unaligning (T0328)A41 because of BadResidue code BAD_PEPTIDE in next template residue (1a8y)M53 Warning: unaligning (T0328)N42 because of BadResidue code BAD_PEPTIDE at template residue (1a8y)M53 Warning: unaligning (T0328)I204 because of BadResidue code BAD_PEPTIDE in next template residue (1a8y)T189 Warning: unaligning (T0328)G205 because of BadResidue code BAD_PEPTIDE at template residue (1a8y)T189 Warning: unaligning (T0328)D210 because of BadResidue code BAD_PEPTIDE at template residue (1a8y)E204 Warning: unaligning (T0328)D218 because of BadResidue code BAD_PEPTIDE in next template residue (1a8y)K211 Warning: unaligning (T0328)K219 because of BadResidue code BAD_PEPTIDE at template residue (1a8y)K211 T0328 1 :MDIQNMPREQLGVCAEG 1a8y 4 :LDFPEYDGVDRVINVNA T0328 20 :HSVYLMFNA 1a8y 30 :YEVLALLYH T0328 29 :NDNVESQ 1a8y 41 :PEDDKAS T0328 37 :RPCI 1a8y 48 :QRQF T0328 43 :VAQYIYELTDQYSDSAFNGFVAIGA 1a8y 54 :EELILELAAQVLEDKGVGFGLVDSE T0328 68 :NYWDSL 1a8y 82 :AVAKKL T0328 87 :AMQE 1a8y 88 :GLTE T0328 99 :EYDLFVH 1a8y 92 :EDSIYVF T0328 106 :LRCDR 1a8y 104 :IEYDG T0328 111 :YDILHLVANEI 1a8y 112 :ADTLVEFLLDV T0328 125 :FEDLVELV 1a8y 123 :LEDPVELI T0328 141 :MDSRDLTGFV 1a8y 131 :EGERELQAFE T0328 157 :KGRHRQEVALVGSEDP 1a8y 141 :NIEDEIKLIGYFKNKD T0328 174 :FK 1a8y 157 :SE T0328 181 :HVQKYAHNLSKWHRL 1a8y 159 :HYKAFKEAAEEFHPY T0328 197 :LKKQEDI 1a8y 181 :DSKVAKK T0328 207 :TKQ 1a8y 190 :LKL T0328 211 :NIEY 1a8y 205 :PVTI T0328 217 :E 1a8y 209 :P T0328 220 :PLT 1a8y 212 :PNS T0328 236 :KS 1a8y 216 :EE T0328 238 :IEILRQSMPY 1a8y 219 :VNFVEEHRRS T0328 249 :SLK 1a8y 244 :DDM T0328 253 :QGLMFISTCRTP 1a8y 247 :DGIHIVAFAEEA T0328 265 :DHFEKMLHSM 1a8y 260 :PDGYEFLEIL T0328 275 :VFGDGAGNHDH 1a8y 272 :VAQDNTDNPDL Number of specific fragments extracted= 26 number of extra gaps= 5 total=423 Number of alignments=34 # 1a8y read from 1a8y/merged-good-all-a2m # found chain 1a8y in template set Warning: unaligning (T0328)N18 because of BadResidue code BAD_PEPTIDE in next template residue (1a8y)N22 Warning: unaligning (T0328)L19 because of BadResidue code BAD_PEPTIDE at template residue (1a8y)N22 Warning: unaligning (T0328)A41 because of BadResidue code BAD_PEPTIDE in next template residue (1a8y)M53 Warning: unaligning (T0328)N42 because of BadResidue code BAD_PEPTIDE at template residue (1a8y)M53 Warning: unaligning (T0328)I204 because of BadResidue code BAD_PEPTIDE in next template residue (1a8y)T189 Warning: unaligning (T0328)G205 because of BadResidue code BAD_PEPTIDE at template residue (1a8y)T189 T0328 1 :MDIQNMPREQLGVCAEG 1a8y 4 :LDFPEYDGVDRVINVNA T0328 20 :HSVYLMFNA 1a8y 31 :EVLALLYHE T0328 29 :NDNVESQ 1a8y 41 :PEDDKAS T0328 37 :RPCI 1a8y 48 :QRQF T0328 43 :VAQYIYELTDQYSDSAFNGFVAIGA 1a8y 54 :EELILELAAQVLEDKGVGFGLVDSE T0328 68 :NYWDSL 1a8y 82 :AVAKKL T0328 81 :M 1a8y 88 :G T0328 88 :MQ 1a8y 89 :LT T0328 98 :IEYDLFVH 1a8y 91 :EEDSIYVF T0328 106 :LRCDR 1a8y 104 :IEYDG T0328 111 :YDILHLVANEIS 1a8y 112 :ADTLVEFLLDVL T0328 126 :EDLVELV 1a8y 124 :EDPVELI T0328 141 :MDSRDLTGFV 1a8y 131 :EGERELQAFE T0328 157 :KGRHRQEVALVGSE 1a8y 141 :NIEDEIKLIGYFKN T0328 172 :PEFK 1a8y 155 :KDSE T0328 181 :HVQKYAHNLSKWHRL 1a8y 159 :HYKAFKEAAEEFHPY T0328 196 :PLKKQED 1a8y 181 :DSKVAKK T0328 206 :RT 1a8y 190 :LK T0328 209 :QDNIEY 1a8y 192 :LNEIDF T0328 222 :TSHIKRVN 1a8y 227 :RSTLRKLK T0328 252 :EQGLMFISTCR 1a8y 246 :MDGIHIVAFAE T0328 263 :TPDHFEKMLHSMVFGDGAGN 1a8y 261 :DGYEFLEILKSVAQDNTDNP T0328 284 :D 1a8y 281 :D Number of specific fragments extracted= 23 number of extra gaps= 3 total=446 Number of alignments=35 # 1a8y read from 1a8y/merged-good-all-a2m # found chain 1a8y in template set Warning: unaligning (T0328)A41 because of BadResidue code BAD_PEPTIDE in next template residue (1a8y)M53 Warning: unaligning (T0328)N42 because of BadResidue code BAD_PEPTIDE at template residue (1a8y)M53 Warning: unaligning (T0328)I204 because of BadResidue code BAD_PEPTIDE in next template residue (1a8y)T189 Warning: unaligning (T0328)G205 because of BadResidue code BAD_PEPTIDE at template residue (1a8y)T189 Warning: unaligning (T0328)D210 because of BadResidue code BAD_PEPTIDE at template residue (1a8y)E204 Warning: unaligning (T0328)S216 because of BadResidue code BAD_PEPTIDE in next template residue (1a8y)K211 Warning: unaligning (T0328)E217 because of BadResidue code BAD_PEPTIDE at template residue (1a8y)K211 T0328 21 :SVYLMFNANDNVESQLRPCI 1a8y 32 :VLALLYHEPPEDDKASQRQF T0328 43 :VAQYIYELTDQYSDSAFNGFVAIGAN 1a8y 54 :EELILELAAQVLEDKGVGFGLVDSEK T0328 69 :YWDSLY 1a8y 83 :VAKKLG T0328 88 :MQ 1a8y 89 :LT T0328 98 :IEYDLFVH 1a8y 91 :EEDSIYVF T0328 106 :LRCD 1a8y 104 :IEYD T0328 110 :RYDILHLVANEIS 1a8y 111 :SADTLVEFLLDVL T0328 126 :EDLVELVE 1a8y 124 :EDPVELIE T0328 142 :DSRDLTGFV 1a8y 132 :GERELQAFE T0328 157 :KGRHRQEVALV 1a8y 141 :NIEDEIKLIGY T0328 168 :GSEDP 1a8y 154 :NKDSE T0328 174 :F 1a8y 159 :H T0328 179 :YIHVQKYAHNL 1a8y 160 :YKAFKEAAEEF T0328 193 :HR 1a8y 171 :HP T0328 195 :L 1a8y 180 :F T0328 197 :LKKQEDI 1a8y 181 :DSKVAKK T0328 206 :RTKQ 1a8y 190 :LKLN T0328 211 :NIEYE 1a8y 205 :PVTIP T0328 218 :DKP 1a8y 212 :PNS T0328 222 :TSHIKRVNLKDE 1a8y 225 :HRRSTLRKLKPE T0328 251 :KEQGLMFISTCR 1a8y 245 :DMDGIHIVAFAE T0328 263 :TPDHFEKMLHSMVFGDGAGN 1a8y 261 :DGYEFLEILKSVAQDNTDNP T0328 294 :TGSSFFAPS 1a8y 281 :DLSIIWIDP Number of specific fragments extracted= 23 number of extra gaps= 4 total=469 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3gcb/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 3gcb expands to /projects/compbio/data/pdb/3gcb.pdb.gz 3gcb:Warning: there is no chain 3gcb will retry with 3gcbA # T0328 read from 3gcb/merged-good-all-a2m # 3gcb read from 3gcb/merged-good-all-a2m # adding 3gcb to template set # found chain 3gcb in template set T0328 32 :VESQLRPCIANVAQYIYELTDQYSDS 3gcb 176 :WNSLLTTKLREFAETLRTALKERSAD T0328 58 :AFNGFV 3gcb 267 :TPVSLI T0328 84 :PFPAMQEGNR 3gcb 273 :NDPRHPYGKL T0328 94 :EAPAIEYDLFVHLRCDRYDILHLVANEISQM 3gcb 288 :LGNVLGGDAVIYLNVDNETLSKLVVKRLQNN T0328 139 :RFMDSRD 3gcb 341 :ELWNYPA T0328 147 :TG 3gcb 348 :IG T0328 153 :TENP 3gcb 350 :YNLP T0328 157 :KGRHRQEVALV 3gcb 380 :ETSKLPLRYRV T0328 168 :GSEDPEFKGGSYIHVQKYAHNL 3gcb 393 :SWGKDSGKDGLYVMTQKYFEEY T0328 192 :WHRLPLKKQE 3gcb 422 :INELPKELAS T0328 203 :IIGRTKQDNIEY 3gcb 432 :KFTSGKEEPIVL Number of specific fragments extracted= 11 number of extra gaps= 0 total=480 Number of alignments=37 # 3gcb read from 3gcb/merged-good-all-a2m # found chain 3gcb in template set T0328 32 :VESQLRPCIANVAQYIYELTDQYSD 3gcb 176 :WNSLLTTKLREFAETLRTALKERSA T0328 57 :SAFNGFV 3gcb 266 :STPVSLI T0328 84 :PFPAMQEGN 3gcb 273 :NDPRHPYGK T0328 93 :REAPAIEYDLFVHLRCDRYDILHLVANEIS 3gcb 287 :RLGNVLGGDAVIYLNVDNETLSKLVVKRLQ T0328 139 :RFMDSRDL 3gcb 341 :ELWNYPAI T0328 152 :GTENP 3gcb 349 :GYNLP T0328 157 :KGRHRQEVALV 3gcb 380 :ETSKLPLRYRV T0328 168 :GSEDPEFKGGSYIHVQKYAHNL 3gcb 393 :SWGKDSGKDGLYVMTQKYFEEY T0328 192 :WHRLPLKKQ 3gcb 422 :INELPKELA T0328 202 :DIIGRTKQDNIEYESED 3gcb 431 :SKFTSGKEEPIVLPIWD Number of specific fragments extracted= 10 number of extra gaps= 0 total=490 Number of alignments=38 # 3gcb read from 3gcb/merged-good-all-a2m # found chain 3gcb in template set T0328 30 :DNVESQLRPCIANVAQYIYELTDQ 3gcb 199 :SADDSIIVTLREQMQREIFRLMSL T0328 54 :YSDSAFNGFVA 3gcb 263 :LDPSTPVSLIN T0328 85 :FPAMQEGNR 3gcb 274 :DPRHPYGKL T0328 94 :EAPAIEYDLFVHLRCDRYDILHLVANEISQ 3gcb 288 :LGNVLGGDAVIYLNVDNETLSKLVVKRLQN T0328 160 :HRQEVALV 3gcb 318 :NKAVFFGS T0328 171 :DPEF 3gcb 339 :DIEL T0328 187 :HNLSKWHRLPLKKQEDIIG 3gcb 343 :WNYPAIGYNLPQQKASRIR T0328 215 :ESEDKPLTSHIKRVNLKDENGKSIEILRQSMPYGSL 3gcb 362 :YHESLMTHAMLITGCHVDETSKLPLRYRVENSWGKD T0328 251 :KEQGLMFIS 3gcb 399 :GKDGLYVMT T0328 264 :PDHFEKM 3gcb 408 :QKYFEEY Number of specific fragments extracted= 10 number of extra gaps= 0 total=500 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1iq4A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0328 read from 1iq4A/merged-good-all-a2m # 1iq4A read from 1iq4A/merged-good-all-a2m # found chain 1iq4A in training set T0328 75 :PESRPEMLKPF 1iq4A 21 :NYKSIMQVPKI T0328 100 :YDLFVHLRCDR 1iq4A 32 :EKIVINMGVGD T0328 111 :YDILHLVANEISQMFEDLVELVEEERGFRFMDSR 1iq4A 47 :PKALDSAVEELTLIAGQRPVVTRAKKSIAGFRLR T0328 157 :KGRHRQEVALV 1iq4A 81 :QGMPIGAKVTL T0328 177 :GSYIHVQKYAH 1iq4A 95 :RMYEFLDKLIS T0328 188 :NLSKWHRLP 1iq4A 107 :SLPRARDFR T0328 208 :KQDNIEYESED 1iq4A 116 :GVSKKSFDGRG T0328 226 :KRVNLKD 1iq4A 128 :YTLGIKE T0328 234 :N 1iq4A 139 :P T0328 244 :SMPY 1iq4A 140 :EIDY T0328 248 :GSLKEQGLMFISTCRTPDHFEKMLHSM 1iq4A 147 :NKVRGMDIVIVTTANTDEEARELLALL Number of specific fragments extracted= 11 number of extra gaps= 0 total=511 Number of alignments=40 # 1iq4A read from 1iq4A/merged-good-all-a2m # found chain 1iq4A in training set T0328 17 :GNLHSVYLMFNAND 1iq4A 29 :PKIEKIVINMGVGD T0328 31 :NVE 1iq4A 45 :QNP T0328 38 :PCIANVAQYIYELTDQYSD 1iq4A 48 :KALDSAVEELTLIAGQRPV T0328 70 :WDSLYP 1iq4A 108 :LPRARD T0328 76 :E 1iq4A 124 :G T0328 77 :SRPEM 1iq4A 133 :KEQLI T0328 85 :FPAMQEGNR 1iq4A 138 :FPEIDYDKV T0328 95 :APAIEYDLFVHLRCDRYDILHLVANEI 1iq4A 147 :NKVRGMDIVIVTTANTDEEARELLALL Number of specific fragments extracted= 8 number of extra gaps= 0 total=519 Number of alignments=41 # 1iq4A read from 1iq4A/merged-good-all-a2m # found chain 1iq4A in training set T0328 5 :NMPREQL 1iq4A 22 :YKSIMQV T0328 17 :GNLHSVYLMFNAND 1iq4A 29 :PKIEKIVINMGVGD T0328 31 :NVE 1iq4A 45 :QNP T0328 38 :PCIANVAQYIYELTDQ 1iq4A 48 :KALDSAVEELTLIAGQ T0328 77 :SRPEM 1iq4A 133 :KEQLI T0328 85 :FPAMQEGNR 1iq4A 138 :FPEIDYDKV T0328 95 :APAIEYDLFVHLRCDRYDILHLVANEI 1iq4A 147 :NKVRGMDIVIVTTANTDEEARELLALL Number of specific fragments extracted= 7 number of extra gaps= 0 total=526 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zdzA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zdzA expands to Error: no filename for 1zdzA 1zdzA expands to Error: no filename for 1zdzA 1zdzA expands to Error: no filename for 1zdzA # T0328 read from 1zdzA/merged-good-all-a2m # 1zdzA read from 1zdzA/merged-good-all-a2m # adding 1zdzA to template set Error: can't find template for 1zdzA or 1zdzA, so skipping it. # 1zdzA read from 1zdzA/merged-good-all-a2m # adding 1zdzA to template set Error: can't find template for 1zdzA or 1zdzA, so skipping it. # 1zdzA read from 1zdzA/merged-good-all-a2m # adding 1zdzA to template set Error: can't find template for 1zdzA or 1zdzA, so skipping it. # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r8gA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1r8gA expands to /projects/compbio/data/pdb/1r8g.pdb.gz 1r8gA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0328 read from 1r8gA/merged-good-all-a2m # 1r8gA read from 1r8gA/merged-good-all-a2m # adding 1r8gA to template set # found chain 1r8gA in template set Warning: unaligning (T0328)S77 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1r8gA)N122 T0328 16 :EGNLHSVYLMFNANDN 1r8gA 53 :DITESMLELATDVCRD T0328 33 :ESQLRPCIANVAQYIYELTDQYSDS 1r8gA 69 :INQAAGQFSAMQKVVLQAATDHHLE T0328 78 :RPEMLKP 1r8gA 123 :FGYLIQQ T0328 97 :AIEYDLFVHLRCDRYDILHLVANEISQM 1r8gA 130 :ATVFGQHVHVGCASGDDAIYLLHGLSRF T0328 130 :ELVEEERGFRFMDSRDLTG 1r8gA 169 :PYMQGTDTRFASSRPNIFS T0328 149 :FVDGTENPK 1r8gA 189 :FPDNGPMPW T0328 159 :RH 1r8gA 199 :SN T0328 182 :VQKYAHNLSKWHRL 1r8gA 201 :WQQFEALFRCLSYT T0328 207 :TKQDNI 1r8gA 215 :TMIDSI T0328 213 :EY 1r8gA 222 :DL T0328 220 :PL 1r8gA 224 :HW T0328 224 :HIKRV 1r8gA 226 :DIRPS T0328 251 :KEQGLMFISTCRTP 1r8gA 231 :PHFGTVEVRVMDTP T0328 265 :DHFEKMLHSMV 1r8gA 248 :SHAVNMAGLIQ Number of specific fragments extracted= 14 number of extra gaps= 0 total=540 Number of alignments=43 # 1r8gA read from 1r8gA/merged-good-all-a2m # found chain 1r8gA in template set Warning: unaligning (T0328)S77 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1r8gA)N122 T0328 16 :EGNLHSVYLMFNANDNV 1r8gA 53 :DITESMLELATDVCRDI T0328 34 :SQLRPCIANVAQYIYELTDQYSD 1r8gA 70 :NQAAGQFSAMQKVVLQAATDHHL T0328 78 :RPEMLKPFPAMQ 1r8gA 123 :FGYLIQQATVFG T0328 102 :LFVHLRCDRYDILHLVANEIS 1r8gA 135 :QHVHVGCASGDDAIYLLHGLS T0328 129 :VELVEEERGFRFMDSRDLT 1r8gA 168 :SPYMQGTDTRFASSRPNIF T0328 148 :GFVDGTENP 1r8gA 188 :AFPDNGPMP T0328 252 :EQGLMFISTC 1r8gA 232 :HFGTVEVRVM T0328 262 :RTPDHFEKMLHSMVF 1r8gA 245 :LTLSHAVNMAGLIQA Number of specific fragments extracted= 8 number of extra gaps= 0 total=548 Number of alignments=44 # 1r8gA read from 1r8gA/merged-good-all-a2m # found chain 1r8gA in template set Warning: unaligning (T0328)S77 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1r8gA)N122 T0328 16 :EGNLHSVYLMFNAN 1r8gA 53 :DITESMLELATDVC T0328 31 :NVESQLRPCIANVAQYIYELTDQ 1r8gA 67 :RDINQAAGQFSAMQKVVLQAATD T0328 78 :RPEMLKPFPAMQ 1r8gA 123 :FGYLIQQATVFG T0328 102 :LFVHLRCDRYDILHLVANEISQMFE 1r8gA 135 :QHVHVGCASGDDAIYLLHGLSRFVP T0328 129 :V 1r8gA 168 :S T0328 133 :EEERGFRFM 1r8gA 169 :PYMQGTDTR T0328 142 :DSRDLTG 1r8gA 181 :SRPNIFS T0328 149 :FVDGTENPKGRH 1r8gA 189 :FPDNGPMPWVSN T0328 182 :VQKYAHNLSKWHRL 1r8gA 201 :WQQFEALFRCLSYT T0328 218 :DKPL 1r8gA 215 :TMID T0328 222 :TSHIKRVNL 1r8gA 222 :DLHWDIRPS T0328 251 :KEQGLMFISTC 1r8gA 231 :PHFGTVEVRVM T0328 262 :RTPDHFEKMLHSMV 1r8gA 245 :LTLSHAVNMAGLIQ Number of specific fragments extracted= 13 number of extra gaps= 0 total=561 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ys4A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ys4A expands to /projects/compbio/data/pdb/1ys4.pdb.gz 1ys4A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0328 read from 1ys4A/merged-good-all-a2m # 1ys4A read from 1ys4A/merged-good-all-a2m # adding 1ys4A to template set # found chain 1ys4A in template set T0328 43 :VAQYIYELTDQYSDSAFNGFVA 1ys4A 20 :VGQRFVQLLADHPMFELTALAA T0328 65 :IGANYWDSL 1ys4A 46 :AGKKYKDAC T0328 74 :YPESRPEMLKPFPAMQEGNREAPAIEYDLFVH 1ys4A 58 :QDRDIPENIKDMVVIPTDPKHEEFEDVDIVFS T0328 108 :CDRYDILHLVANEISQM 1ys4A 90 :ALPSDLAKKFEPEFAKE T0328 125 :FEDLVELVEE 1ys4A 131 :NADHLELIEI T0328 143 :SRDLTGFV 1ys4A 141 :QREKRGWD T0328 157 :KGRHRQEVALV 1ys4A 242 :NRVAVIDGHTE T0328 168 :GSE 1ys4A 259 :KEG T0328 195 :LPLKKQEDIIGRTKQ 1ys4A 262 :AEPEEIKEVMDKFDP T0328 210 :DNIEYESEDKPLT 1ys4A 278 :KDLNLPTYAKPIV T0328 230 :LKDENGKSIEILRQSMPY 1ys4A 292 :REEIDRPQPRLDRNEGNG T0328 248 :GSLKEQGLMFIS 1ys4A 320 :DPIFDVKYTALE Number of specific fragments extracted= 12 number of extra gaps= 0 total=573 Number of alignments=46 # 1ys4A read from 1ys4A/merged-good-all-a2m # found chain 1ys4A in template set T0328 43 :VAQYIYELTDQYSDSAFNGFV 1ys4A 20 :VGQRFVQLLADHPMFELTALA T0328 65 :IGANYW 1ys4A 41 :ASERSA T0328 71 :DSL 1ys4A 52 :DAC T0328 74 :YPESRPEMLKPFPAMQEGNREAPAIEYDLFVH 1ys4A 58 :QDRDIPENIKDMVVIPTDPKHEEFEDVDIVFS T0328 108 :CDRYDILHLVANEISQM 1ys4A 90 :ALPSDLAKKFEPEFAKE T0328 129 :VELV 1ys4A 108 :KLIF T0328 147 :TGFVDGTENP 1ys4A 115 :SAYRMEEDVP T0328 157 :KGRHRQEVALV 1ys4A 242 :NRVAVIDGHTE T0328 168 :GSE 1ys4A 259 :KEG T0328 195 :LPLKKQEDIIG 1ys4A 262 :AEPEEIKEVMD T0328 206 :RTKQDNIEYESEDKPLT 1ys4A 274 :FDPLKDLNLPTYAKPIV T0328 229 :NLKDENGKSIEILRQ 1ys4A 291 :IREEIDRPQPRLDRN T0328 247 :YGSLK 1ys4A 306 :EGNGM T0328 252 :EQGLMFISTC 1ys4A 322 :IFDVKYTALE Number of specific fragments extracted= 14 number of extra gaps= 0 total=587 Number of alignments=47 # 1ys4A read from 1ys4A/merged-good-all-a2m # found chain 1ys4A in template set T0328 17 :GNLHSVYLMFNANDN 1ys4A 247 :IDGHTESIFVKTKEG T0328 32 :VESQLRPCIAN 1ys4A 263 :EPEEIKEVMDK T0328 54 :YSDSAFNGFVA 1ys4A 305 :NEGNGMSIVVG T0328 95 :APAIEYDLFVHLRCDR 1ys4A 318 :RKDPIFDVKYTALEHN T0328 111 :YDILHLVANEISQMF 1ys4A 339 :AGASVLNAEYFVKKY Number of specific fragments extracted= 5 number of extra gaps= 0 total=592 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ftrA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0328 read from 1ftrA/merged-good-all-a2m # 1ftrA read from 1ftrA/merged-good-all-a2m # found chain 1ftrA in training set Warning: unaligning (T0328)F103 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ftrA)F169 Warning: unaligning (T0328)V104 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ftrA)F169 T0328 15 :AEGNLHSVYLMFNAND 1ftrA 66 :TPDGRPGVTIMIGHND T0328 33 :ESQLRPCI 1ftrA 82 :EDELKEQL T0328 44 :AQYIYELTDQYSDS 1ftrA 90 :LDRIGQCVMTAPTA T0328 94 :EAPAIE 1ftrA 157 :SFGITT T0328 100 :YDL 1ftrA 165 :AGG T0328 105 :HLRCDRYDILHLVANEISQMFEDL 1ftrA 170 :YIMAESQPAGLQAAEAAVDAIKGV T0328 136 :RGF 1ftrA 194 :EGA T0328 139 :RFMDSRDL 1ftrA 198 :APFPGGIV T0328 148 :GFVDGTENPKGRHRQE 1ftrA 206 :ASASKVGSKQYDFLPA T0328 169 :SE 1ftrA 222 :ST T0328 189 :LSKWH 1ftrA 224 :NDAYC T0328 207 :TKQDNIEYESEDK 1ftrA 229 :PTVEDNELPEGVK T0328 253 :QGLMFISTCRTPDHFEKMLHSMV 1ftrA 242 :CVYEIVINGLNEEAVKEAMRVGI T0328 276 :FGDGAGNHDH 1ftrA 278 :AGNFGGKLGQ T0328 286 :LMH 1ftrA 292 :LHD Number of specific fragments extracted= 15 number of extra gaps= 1 total=607 Number of alignments=49 # 1ftrA read from 1ftrA/merged-good-all-a2m # found chain 1ftrA in training set Warning: unaligning (T0328)F103 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1ftrA)F169 Warning: unaligning (T0328)V104 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ftrA)F169 T0328 15 :AEGNLHSVYLMFNA 1ftrA 66 :TPDGRPGVTIMIGH T0328 31 :NVESQLRPCI 1ftrA 80 :NDEDELKEQL T0328 44 :AQYIYELTDQYSD 1ftrA 90 :LDRIGQCVMTAPT T0328 101 :DL 1ftrA 166 :GG T0328 105 :HLRCDRYDILHLVANEISQMFEDL 1ftrA 170 :YIMAESQPAGLQAAEAAVDAIKGV T0328 136 :RGF 1ftrA 194 :EGA T0328 139 :RFMDSRDL 1ftrA 198 :APFPGGIV T0328 148 :GFVDGTE 1ftrA 206 :ASASKVG T0328 168 :GSEDPEFKGG 1ftrA 213 :SKQYDFLPAS T0328 189 :LSKW 1ftrA 224 :NDAY T0328 206 :RT 1ftrA 229 :PT T0328 209 :QDNIEYESEDK 1ftrA 231 :VEDNELPEGVK T0328 226 :KR 1ftrA 242 :CV T0328 255 :LMFISTCRTPDHFEKMLHSMV 1ftrA 244 :YEIVINGLNEEAVKEAMRVGI T0328 276 :FGDGA 1ftrA 268 :CQQPG Number of specific fragments extracted= 15 number of extra gaps= 1 total=622 Number of alignments=50 # 1ftrA read from 1ftrA/merged-good-all-a2m # found chain 1ftrA in training set Warning: unaligning (T0328)V104 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1ftrA)F169 T0328 16 :EGNLHSVYLMF 1ftrA 69 :GRPGVTIMIGH T0328 31 :NVESQLRPCI 1ftrA 80 :NDEDELKEQL T0328 44 :AQYIYELTDQ 1ftrA 90 :LDRIGQCVMT T0328 54 :YSDSAFN 1ftrA 109 :MPEAEKE T0328 66 :GANYWDSLYP 1ftrA 121 :GYKLSFFGDG T0328 94 :EAPAIEYDLF 1ftrA 134 :EDELDGRKVW T0328 105 :HLRCDRYDILHLVANEISQMFEDL 1ftrA 170 :YIMAESQPAGLQAAEAAVDAIKGV T0328 136 :RGFRFMDSRDLTG 1ftrA 194 :EGAYAPFPGGIVA T0328 149 :FVDGTENPKGRHRQE 1ftrA 209 :SKVGSKQYDFLPAST T0328 189 :LSKWH 1ftrA 224 :NDAYC T0328 207 :TKQDNIEYESEDK 1ftrA 229 :PTVEDNELPEGVK T0328 224 :HIKRVN 1ftrA 242 :CVYEIV T0328 259 :STCRTPDHFEKMLHSMV 1ftrA 248 :INGLNEEAVKEAMRVGI T0328 284 :D 1ftrA 265 :E Number of specific fragments extracted= 14 number of extra gaps= 1 total=636 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fxlA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0328 read from 1fxlA/merged-good-all-a2m # 1fxlA read from 1fxlA/merged-good-all-a2m # found chain 1fxlA in training set T0328 22 :VYLMFNANDN 1fxlA 40 :NLIVNYLPQN T0328 32 :VESQLRPCIANV 1fxlA 51 :TQEEFRSLFGSI T0328 83 :KPFPAMQ 1fxlA 63 :GEIESCK T0328 90 :EGNREAPAIEY 1fxlA 72 :RDKITGQSLGY T0328 102 :L 1fxlA 83 :G T0328 105 :HLRCDRYDILHLVANEI 1fxlA 84 :FVNYIDPKDAEKAINTL T0328 126 :E 1fxlA 101 :N T0328 137 :GFRFMD 1fxlA 102 :GLRLQT T0328 149 :FVDGTENPKGRHRQE 1fxlA 110 :IKVSYARPSSASIRD T0328 164 :VALVGSEDPE 1fxlA 126 :NLYVSGLPKT T0328 195 :LPLKKQEDII 1fxlA 136 :MTQKELEQLF T0328 210 :DN 1fxlA 146 :SQ T0328 217 :EDKPLTS 1fxlA 148 :YGRIITS T0328 227 :RVNLKDENGKSI 1fxlA 155 :RILVDQVTGVSR T0328 254 :GLMFIST 1fxlA 167 :GVGFIRF T0328 262 :RTPDHFEKMLHSMVFGDGAGNHDHL 1fxlA 174 :DKRIEAEEAIKGLNGQKPSGATEPI Number of specific fragments extracted= 16 number of extra gaps= 0 total=652 Number of alignments=52 # 1fxlA read from 1fxlA/merged-good-all-a2m # found chain 1fxlA in training set T0328 22 :VYLMFNANDN 1fxlA 40 :NLIVNYLPQN T0328 32 :VESQLRPCIAN 1fxlA 51 :TQEEFRSLFGS T0328 82 :LKPFPAMQ 1fxlA 62 :IGEIESCK T0328 90 :EGNREAPAIEY 1fxlA 72 :RDKITGQSLGY T0328 102 :LFVHL 1fxlA 83 :GFVNY T0328 109 :DRYDI 1fxlA 88 :IDPKD T0328 118 :ANEISQMFEDL 1fxlA 93 :AEKAINTLNGL T0328 134 :EERGFR 1fxlA 104 :RLQTKT T0328 149 :FVDGTENPKGRHRQEV 1fxlA 110 :IKVSYARPSSASIRDA T0328 165 :ALVGSEDPE 1fxlA 127 :LYVSGLPKT T0328 195 :LPLKKQEDIIGRTK 1fxlA 136 :MTQKELEQLFSQYG T0328 219 :K 1fxlA 150 :R T0328 225 :IK 1fxlA 151 :II T0328 227 :RVNLKDENGKSI 1fxlA 155 :RILVDQVTGVSR T0328 254 :GLMFIS 1fxlA 167 :GVGFIR T0328 261 :CRTPDHFEKMLHSMVFGDGAGNHDHL 1fxlA 173 :FDKRIEAEEAIKGLNGQKPSGATEPI Number of specific fragments extracted= 16 number of extra gaps= 0 total=668 Number of alignments=53 # 1fxlA read from 1fxlA/merged-good-all-a2m # found chain 1fxlA in training set T0328 23 :YLMFNANDN 1fxlA 41 :LIVNYLPQN T0328 32 :VESQLRPCIANV 1fxlA 51 :TQEEFRSLFGSI T0328 83 :KPFP 1fxlA 63 :GEIE T0328 87 :AMQEGNREAPAIEY 1fxlA 69 :KLVRDKITGQSLGY T0328 104 :VHLRCDRYDI 1fxlA 83 :GFVNYIDPKD T0328 118 :ANEISQMFEDL 1fxlA 93 :AEKAINTLNGL T0328 130 :ELVEEERGFRFM 1fxlA 104 :RLQTKTIKVSYA T0328 155 :NPKGRH 1fxlA 116 :RPSSAS T0328 161 :RQEVALVGSEDP 1fxlA 123 :RDANLYVSGLPK T0328 194 :RLPLKKQEDIIG 1fxlA 135 :TMTQKELEQLFS T0328 216 :SE 1fxlA 147 :QY T0328 222 :TSHIKRVNLKDENGK 1fxlA 149 :GRIITSRILVDQVTG T0328 251 :KEQGLMFIST 1fxlA 164 :VSRGVGFIRF T0328 262 :RTPDHFEKMLHSMVFGDGAGN 1fxlA 174 :DKRIEAEEAIKGLNGQKPSGA Number of specific fragments extracted= 14 number of extra gaps= 0 total=682 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nriA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1nriA expands to /projects/compbio/data/pdb/1nri.pdb.gz 1nriA:Skipped atom 200, because occupancy 0.500 <= existing 0.500 in 1nriA Skipped atom 202, because occupancy 0.500 <= existing 0.500 in 1nriA Skipped atom 204, because occupancy 0.500 <= existing 0.500 in 1nriA Skipped atom 206, because occupancy 0.500 <= existing 0.500 in 1nriA Skipped atom 208, because occupancy 0.500 <= existing 0.500 in 1nriA Skipped atom 210, because occupancy 0.500 <= existing 0.500 in 1nriA Skipped atom 212, because occupancy 0.500 <= existing 0.500 in 1nriA Skipped atom 214, because occupancy 0.500 <= existing 0.500 in 1nriA Skipped atom 216, because occupancy 0.500 <= existing 0.500 in 1nriA Skipped atom 218, because occupancy 0.500 <= existing 0.500 in 1nriA Skipped atom 220, because occupancy 0.500 <= existing 0.500 in 1nriA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 947, because occupancy 0.500 <= existing 0.500 in 1nriA Skipped atom 949, because occupancy 0.500 <= existing 0.500 in 1nriA Skipped atom 951, because occupancy 0.500 <= existing 0.500 in 1nriA Skipped atom 953, because occupancy 0.500 <= existing 0.500 in 1nriA Skipped atom 955, because occupancy 0.500 <= existing 0.500 in 1nriA Skipped atom 957, because occupancy 0.500 <= existing 0.500 in 1nriA Skipped atom 959, because occupancy 0.500 <= existing 0.500 in 1nriA Skipped atom 961, because occupancy 0.500 <= existing 0.500 in 1nriA Skipped atom 963, because occupancy 0.500 <= existing 0.500 in 1nriA Skipped atom 965, because occupancy 0.500 <= existing 0.500 in 1nriA Skipped atom 1158, because occupancy 0.500 <= existing 0.500 in 1nriA Skipped atom 1160, because occupancy 0.500 <= existing 0.500 in 1nriA Skipped atom 1162, because occupancy 0.500 <= existing 0.500 in 1nriA Skipped atom 1164, because occupancy 0.500 <= existing 0.500 in 1nriA Skipped atom 1166, because occupancy 0.500 <= existing 0.500 in 1nriA Skipped atom 1168, because occupancy 0.500 <= existing 0.500 in 1nriA Skipped atom 1170, because occupancy 0.500 <= existing 0.500 in 1nriA Skipped atom 1172, because occupancy 0.500 <= existing 0.500 in 1nriA Skipped atom 1174, because occupancy 0.500 <= existing 0.500 in 1nriA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1574, because occupancy 0.500 <= existing 0.500 in 1nriA Skipped atom 1576, because occupancy 0.500 <= existing 0.500 in 1nriA Skipped atom 1578, because occupancy 0.500 <= existing 0.500 in 1nriA Skipped atom 1580, because occupancy 0.500 <= existing 0.500 in 1nriA Skipped atom 1582, because occupancy 0.500 <= existing 0.500 in 1nriA Skipped atom 1584, because occupancy 0.500 <= existing 0.500 in 1nriA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M WARNING: atom 1820 has residue number 249 < previous residue 306 in 1nriA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0328 read from 1nriA/merged-good-all-a2m # 1nriA read from 1nriA/merged-good-all-a2m # adding 1nriA to template set # found chain 1nriA in template set T0328 33 :ESQLRPCIANVAQYIYELTDQYSD 1nriA 47 :IESCLPQISLAVEQIVQAFQQGGR T0328 58 :AFNGFV 1nriA 100 :MVKGII T0328 76 :ESRPEMLKPFPA 1nriA 113 :RHPVEGAEDNTK T0328 94 :EAPAIEYDLFVHLRCDR 1nriA 132 :SIHFSKNDVLVGIAASG T0328 111 :YDILHLVANEISQM 1nriA 150 :TPYVIAGLQYAKSL T0328 125 :FED 1nriA 178 :MAE T0328 161 :RQEVALV 1nriA 181 :IADIAIE T0328 169 :SED 1nriA 191 :GPE T0328 172 :PEFKGGSYIHVQKYAHNL 1nriA 197 :GSSRLKSGTAQKMVLNML T0328 197 :LKKQEDIIGRTKQ 1nriA 215 :TTASMILLGKCYE T0328 210 :DNIEY 1nriA 231 :VDVQA Number of specific fragments extracted= 11 number of extra gaps= 0 total=693 Number of alignments=55 # 1nriA read from 1nriA/merged-good-all-a2m # found chain 1nriA in template set T0328 33 :ESQLRPCIANVAQYIYELTDQYSD 1nriA 47 :IESCLPQISLAVEQIVQAFQQGGR T0328 57 :SAFNGFVAIGANYWDSLYP 1nriA 99 :EMVKGIIAGGECAIRHPVE T0328 81 :MLKPFP 1nriA 118 :GAEDNT T0328 92 :N 1nriA 124 :K T0328 94 :EAPAIEYDLFVHLRCD 1nriA 132 :SIHFSKNDVLVGIAAS T0328 110 :RYDILHLVANEISQM 1nriA 149 :RTPYVIAGLQYAKSL T0328 127 :DLVELVE 1nriA 164 :GALTISI T0328 153 :TENPKGR 1nriA 171 :ASNPKSE T0328 160 :HRQEVALV 1nriA 180 :EIADIAIE T0328 169 :SED 1nriA 191 :GPE T0328 172 :PEFKGGSYIHVQKYAHNL 1nriA 197 :GSSRLKSGTAQKMVLNML T0328 197 :LKKQEDIIGRT 1nriA 215 :TTASMILLGKC T0328 209 :QDNIEYESE 1nriA 226 :YENLMVDVQ T0328 262 :RTPDHFEKMLHSMV 1nriA 235 :ASNEKLKARAVRIV Number of specific fragments extracted= 14 number of extra gaps= 0 total=707 Number of alignments=56 # 1nriA read from 1nriA/merged-good-all-a2m # found chain 1nriA in template set T0328 33 :ESQLRPCIANVAQYIYELTDQ 1nriA 47 :IESCLPQISLAVEQIVQAFQQ T0328 54 :YSDSAFNGFVA 1nriA 96 :VSTEMVKGIIA T0328 73 :LYP 1nriA 107 :GGE T0328 76 :ESRPEMLKPFPA 1nriA 113 :RHPVEGAEDNTK T0328 95 :APAIEYDLFVHLRCD 1nriA 133 :IHFSKNDVLVGIAAS T0328 110 :RYDILHLVANEISQM 1nriA 149 :RTPYVIAGLQYAKSL Number of specific fragments extracted= 6 number of extra gaps= 0 total=713 Number of alignments=57 # command:# PrintAlignmentsContacts allconstraints.under Using radius: 8.0000 NUMB_ALIGNS: 57 Done printing distance constraints # command: