# command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 1600 examples # computed average trans backbone unit before proline from 52 examples # trans (non-proline) backbone unit: # CA= -2.2097 1.0151 -0.0046 # O= -0.1488 2.2425 0.0020 # C= -0.6903 1.1357 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4580 -0.0000 -0.0000 # cis backbone unit: # CA= -0.1462 2.4515 0.0018 # O= -2.0272 0.9713 0.0022 # C= -0.8006 1.0755 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4659 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2063 1.0654 0.0002 # O= -0.1193 2.2442 0.0054 # C= -0.6842 1.1479 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4661 -0.0000 0.0000 # After reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz have 408 chains in training database # Count of chains,residues,atoms: 408,82795,639989 # 81291 residues have no bad marker # 565 residues lack atoms needed to compute omega # 313 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 1 # HAS_OXT 265 # TOO_MANY_ATOMS 0 # TOO_FEW_ATOMS 378 # HAS_UNKNOWN_ATOMS 0 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 139 # NON_PLANAR_PEPTIDE 424 # BAD_PEPTIDE 803 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-40pc-3157.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 # command:# Making conformation for sequence T0328 numbered 1 through 311 Created new target T0328 from T0328.a2m # command:CPU_time= 6.394 sec, elapsed time= 6.438 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gvkA/T0328-2gvkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 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/T0328-2gvkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gvkA read from 2gvkA/T0328-2gvkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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 # choosing archetypes in rotamer library 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=8 Will force an alignment to be made, even if fragment is small Number of alignments=1 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gvkA/T0328-2gvkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0328 read from 2gvkA/T0328-2gvkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gvkA read from 2gvkA/T0328-2gvkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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 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=16 Will force an alignment to be made, even if fragment is small Number of alignments=2 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gvkA/T0328-2gvkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0328 read from 2gvkA/T0328-2gvkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gvkA read from 2gvkA/T0328-2gvkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=23 Will force an alignment to be made, even if fragment is small Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t0tV/T0328-1t0tV-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1t0tV expands to /projects/compbio/data/pdb/1t0t.pdb.gz 1t0tV:# T0328 read from 1t0tV/T0328-1t0tV-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t0tV read from 1t0tV/T0328-1t0tV-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1t0tV to template set # found chain 1t0tV in template 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=40 Will force an alignment to be made, even if fragment is small Number of alignments=4 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t0tV/T0328-1t0tV-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0328 read from 1t0tV/T0328-1t0tV-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t0tV read from 1t0tV/T0328-1t0tV-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1t0tV in template 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=57 Will force an alignment to be made, even if fragment is small Number of alignments=5 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t0tV/T0328-1t0tV-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0328 read from 1t0tV/T0328-1t0tV-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t0tV read from 1t0tV/T0328-1t0tV-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1t0tV in template 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=74 Will force an alignment to be made, even if fragment is small Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r8gA/T0328-1r8gA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 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/T0328-1r8gA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1r8gA read from 1r8gA/T0328-1r8gA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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 :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=82 Will force an alignment to be made, even if fragment is small Number of alignments=7 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r8gA/T0328-1r8gA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0328 read from 1r8gA/T0328-1r8gA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1r8gA read from 1r8gA/T0328-1r8gA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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 :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=96 Will force an alignment to be made, even if fragment is small Number of alignments=8 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r8gA/T0328-1r8gA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0328 read from 1r8gA/T0328-1r8gA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1r8gA read from 1r8gA/T0328-1r8gA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=109 Will force an alignment to be made, even if fragment is small Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cb2A/T0328-2cb2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 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/T0328-2cb2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cb2A read from 2cb2A/T0328-2cb2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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)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=125 Will force an alignment to be made, even if fragment is small Number of alignments=10 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cb2A/T0328-2cb2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0328 read from 2cb2A/T0328-2cb2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cb2A read from 2cb2A/T0328-2cb2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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)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=142 Will force an alignment to be made, even if fragment is small Number of alignments=11 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cb2A/T0328-2cb2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0328 read from 2cb2A/T0328-2cb2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cb2A read from 2cb2A/T0328-2cb2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=160 Will force an alignment to be made, even if fragment is small Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1aoeA/T0328-1aoeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1aoeA expands to /projects/compbio/data/pdb/1aoe.pdb.gz 1aoeA:Skipped atom 225, because occupancy 0.500 <= existing 0.500 in 1aoeA Skipped atom 227, because occupancy 0.500 <= existing 0.500 in 1aoeA Skipped atom 229, because occupancy 0.500 <= existing 0.500 in 1aoeA Skipped atom 231, because occupancy 0.500 <= existing 0.500 in 1aoeA Skipped atom 258, because occupancy 0.500 <= existing 0.500 in 1aoeA Skipped atom 329, because occupancy 0.500 <= existing 0.500 in 1aoeA Skipped atom 331, because occupancy 0.500 <= existing 0.500 in 1aoeA Skipped atom 333, because occupancy 0.500 <= existing 0.500 in 1aoeA Skipped atom 340, because occupancy 0.500 <= existing 0.500 in 1aoeA Skipped atom 342, because occupancy 0.500 <= existing 0.500 in 1aoeA Skipped atom 344, because occupancy 0.500 <= existing 0.500 in 1aoeA Skipped atom 346, because occupancy 0.500 <= existing 0.500 in 1aoeA Skipped atom 348, because occupancy 0.500 <= existing 0.500 in 1aoeA Skipped atom 350, because occupancy 0.500 <= existing 0.500 in 1aoeA Skipped atom 428, because occupancy 0.500 <= existing 0.500 in 1aoeA Skipped atom 430, because occupancy 0.500 <= existing 0.500 in 1aoeA Skipped atom 432, because occupancy 0.500 <= existing 0.500 in 1aoeA Skipped atom 434, because occupancy 0.500 <= existing 0.500 in 1aoeA Skipped atom 652, because occupancy 0.500 <= existing 0.500 in 1aoeA Skipped atom 654, because occupancy 0.500 <= existing 0.500 in 1aoeA Skipped atom 656, because occupancy 0.500 <= existing 0.500 in 1aoeA Skipped atom 658, because occupancy 0.500 <= existing 0.500 in 1aoeA Skipped atom 660, because occupancy 0.500 <= existing 0.500 in 1aoeA Skipped atom 667, because occupancy 0.500 <= existing 0.500 in 1aoeA Skipped atom 703, because occupancy 0.500 <= existing 0.500 in 1aoeA Skipped atom 705, because occupancy 0.500 <= existing 0.500 in 1aoeA Skipped atom 707, because occupancy 0.500 <= existing 0.500 in 1aoeA Skipped atom 709, because occupancy 0.500 <= existing 0.500 in 1aoeA Skipped atom 896, because occupancy 0.500 <= existing 0.500 in 1aoeA Skipped atom 898, because occupancy 0.500 <= existing 0.500 in 1aoeA Skipped atom 900, because occupancy 0.500 <= existing 0.500 in 1aoeA Skipped atom 993, because occupancy 0.500 <= existing 0.500 in 1aoeA Skipped atom 995, because occupancy 0.500 <= existing 0.500 in 1aoeA Skipped atom 997, because occupancy 0.500 <= existing 0.500 in 1aoeA Skipped atom 1073, because occupancy 0.500 <= existing 0.500 in 1aoeA Skipped atom 1075, because occupancy 0.500 <= existing 0.500 in 1aoeA Skipped atom 1077, because occupancy 0.500 <= existing 0.500 in 1aoeA Skipped atom 1116, because occupancy 0.500 <= existing 0.500 in 1aoeA Skipped atom 1118, because occupancy 0.500 <= existing 0.500 in 1aoeA Skipped atom 1120, because occupancy 0.500 <= existing 0.500 in 1aoeA Skipped atom 1122, because occupancy 0.500 <= existing 0.500 in 1aoeA # T0328 read from 1aoeA/T0328-1aoeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1aoeA read from 1aoeA/T0328-1aoeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1aoeA to template set # found chain 1aoeA in template 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=169 Will force an alignment to be made, even if fragment is small Number of alignments=13 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1aoeA/T0328-1aoeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0328 read from 1aoeA/T0328-1aoeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1aoeA read from 1aoeA/T0328-1aoeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1aoeA in template 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 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=179 Will force an alignment to be made, even if fragment is small Number of alignments=14 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1aoeA/T0328-1aoeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0328 read from 1aoeA/T0328-1aoeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1aoeA read from 1aoeA/T0328-1aoeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1aoeA in template 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=192 Will force an alignment to be made, even if fragment is small Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1omzA/T0328-1omzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1omzA expands to /projects/compbio/data/pdb/1omz.pdb.gz 1omzA:# T0328 read from 1omzA/T0328-1omzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1omzA read from 1omzA/T0328-1omzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1omzA to template set # 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=208 Will force an alignment to be made, even if fragment is small Number of alignments=16 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1omzA/T0328-1omzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0328 read from 1omzA/T0328-1omzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1omzA read from 1omzA/T0328-1omzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 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=223 Will force an alignment to be made, even if fragment is small Number of alignments=17 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1omzA/T0328-1omzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0328 read from 1omzA/T0328-1omzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1omzA read from 1omzA/T0328-1omzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=236 Will force an alignment to be made, even if fragment is small Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fj2A/T0328-1fj2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1fj2A expands to /projects/compbio/data/pdb/1fj2.pdb.gz 1fj2A:# T0328 read from 1fj2A/T0328-1fj2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fj2A read from 1fj2A/T0328-1fj2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1fj2A to template set # found chain 1fj2A in template 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=243 Will force an alignment to be made, even if fragment is small Number of alignments=19 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fj2A/T0328-1fj2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0328 read from 1fj2A/T0328-1fj2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fj2A read from 1fj2A/T0328-1fj2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fj2A in template 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=253 Will force an alignment to be made, even if fragment is small Number of alignments=20 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fj2A/T0328-1fj2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0328 read from 1fj2A/T0328-1fj2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fj2A read from 1fj2A/T0328-1fj2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fj2A in template 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=262 Will force an alignment to be made, even if fragment is small Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1iq4A/T0328-1iq4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1iq4A expands to /projects/compbio/data/pdb/1iq4.pdb.gz 1iq4A:# T0328 read from 1iq4A/T0328-1iq4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1iq4A read from 1iq4A/T0328-1iq4A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1iq4A to template set # found chain 1iq4A in template 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=270 Will force an alignment to be made, even if fragment is small Number of alignments=22 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1iq4A/T0328-1iq4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0328 read from 1iq4A/T0328-1iq4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1iq4A read from 1iq4A/T0328-1iq4A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1iq4A in template 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=281 Will force an alignment to be made, even if fragment is small Number of alignments=23 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1iq4A/T0328-1iq4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0328 read from 1iq4A/T0328-1iq4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1iq4A read from 1iq4A/T0328-1iq4A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1iq4A in template 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=288 Will force an alignment to be made, even if fragment is small Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1uc2A/T0328-1uc2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1uc2A expands to /projects/compbio/data/pdb/1uc2.pdb.gz 1uc2A:# T0328 read from 1uc2A/T0328-1uc2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1uc2A read from 1uc2A/T0328-1uc2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1uc2A to template set # 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=304 Will force an alignment to be made, even if fragment is small Number of alignments=25 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1uc2A/T0328-1uc2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0328 read from 1uc2A/T0328-1uc2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1uc2A read from 1uc2A/T0328-1uc2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 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=323 Will force an alignment to be made, even if fragment is small Number of alignments=26 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1uc2A/T0328-1uc2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0328 read from 1uc2A/T0328-1uc2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1uc2A read from 1uc2A/T0328-1uc2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=338 Will force an alignment to be made, even if fragment is small Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nriA/T0328-1nriA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 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/T0328-1nriA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nriA read from 1nriA/T0328-1nriA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1nriA to template set # 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=352 Will force an alignment to be made, even if fragment is small Number of alignments=28 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nriA/T0328-1nriA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0328 read from 1nriA/T0328-1nriA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nriA read from 1nriA/T0328-1nriA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 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=363 Will force an alignment to be made, even if fragment is small Number of alignments=29 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nriA/T0328-1nriA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0328 read from 1nriA/T0328-1nriA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nriA read from 1nriA/T0328-1nriA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.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=369 Will force an alignment to be made, even if fragment is small Number of alignments=30 # command:CPU_time= 15.561 sec, elapsed time= 16.391 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 30 Adding 48205 constraints to all_contacts Done adding distance constraints # command:CPU_time= 15.668 sec, elapsed time= 16.514 sec. # command:Reading probabilities from T0328.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 4.417 Optimizing... Probability sum: -540.974, CN propb: -540.974 weights: 0.454 constraints: 733 # command:CPU_time= 86.779 sec, elapsed time= 87.708 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 733 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 733 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 2272 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 2272 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 42748 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 42748 # command:CPU_time= 87.587 sec, elapsed time= 89.080 sec. # command: