# 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 T0302 numbered 1 through 132 Created new target T0302 from T0302.a2m # command:CPU_time= 6.317 sec, elapsed time= 6.357 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fqiA/T0302-1fqiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1fqiA expands to /projects/compbio/data/pdb/1fqi.pdb.gz 1fqiA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0302 read from 1fqiA/T0302-1fqiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fqiA read from 1fqiA/T0302-1fqiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1fqiA to template set # found chain 1fqiA in template set T0302 1 :SMVSPEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFK 1fqiA 286 :DIPTKMRVERWAFNFSELIRDPKGRQSFQHFLRKEFSGENLGFWEACEDLK # choosing archetypes in rotamer library T0302 53 :SKGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDLMEG 1fqiA 337 :YGDQSKVKEKAEEIYKLFLAPGARRWINIDGKTMDITVKGLKHPHRYVLDAAQTHIYMLMKKDSYARYLKSPIYKEMLAK Number of specific fragments extracted= 2 number of extra gaps= 0 total=2 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 1fqiA/T0302-1fqiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0302 read from 1fqiA/T0302-1fqiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fqiA read from 1fqiA/T0302-1fqiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fqiA in template set T0302 1 :SMVSPEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFK 1fqiA 286 :DIPTKMRVERWAFNFSELIRDPKGRQSFQHFLRKEFSGENLGFWEACEDLK T0302 53 :SKGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDLMEG 1fqiA 337 :YGDQSKVKEKAEEIYKLFLAPGARRWINIDGKTMDITVKGLKHPHRYVLDAAQTHIYMLMKKDSYARYLKSPIYKEMLAK Number of specific fragments extracted= 2 number of extra gaps= 0 total=4 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 1fqiA/T0302-1fqiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0302 read from 1fqiA/T0302-1fqiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1fqiA read from 1fqiA/T0302-1fqiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1fqiA in template set T0302 1 :SMVSPEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKK 1fqiA 286 :DIPTKMRVERWAFNFSELIRDPKGRQSFQHFLRKEFSGENLGFWEACEDLKY T0302 54 :KGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDLMEG 1fqiA 338 :GDQSKVKEKAEEIYKLFLAPGARRWINIDGKTMDITVKGLKHPHRYVLDAAQTHIYMLMKKDSYARYLKSPIYKEMLAK Number of specific fragments extracted= 2 number of extra gaps= 0 total=6 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 1dk8A/T0302-1dk8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1dk8A expands to /projects/compbio/data/pdb/1dk8.pdb.gz 1dk8A:Skipped atom 68, because occupancy 0.5 <= existing 0.500 in 1dk8A Skipped atom 70, because occupancy 0.500 <= existing 0.500 in 1dk8A Skipped atom 72, because occupancy 0.500 <= existing 0.500 in 1dk8A Skipped atom 130, because occupancy 0.500 <= existing 0.500 in 1dk8A Skipped atom 132, because occupancy 0.500 <= existing 0.500 in 1dk8A Skipped atom 134, because occupancy 0.500 <= existing 0.500 in 1dk8A Skipped atom 136, because occupancy 0.500 <= existing 0.500 in 1dk8A Skipped atom 138, because occupancy 0.500 <= existing 0.500 in 1dk8A Skipped atom 167, because occupancy 0.500 <= existing 0.500 in 1dk8A Skipped atom 169, because occupancy 0.500 <= existing 0.500 in 1dk8A Skipped atom 171, because occupancy 0.500 <= existing 0.500 in 1dk8A Skipped atom 398, because occupancy 0.500 <= existing 0.500 in 1dk8A Skipped atom 400, because occupancy 0.500 <= existing 0.500 in 1dk8A Skipped atom 422, because occupancy 0.500 <= existing 0.500 in 1dk8A Skipped atom 424, because occupancy 0.500 <= existing 0.500 in 1dk8A Skipped atom 426, because occupancy 0.500 <= existing 0.500 in 1dk8A Skipped atom 428, because occupancy 0.500 <= existing 0.500 in 1dk8A Skipped atom 430, because occupancy 0.500 <= existing 0.500 in 1dk8A Skipped atom 432, because occupancy 0.500 <= existing 0.500 in 1dk8A Skipped atom 456, because occupancy 0.500 <= existing 0.500 in 1dk8A Skipped atom 458, because occupancy 0.500 <= existing 0.500 in 1dk8A Skipped atom 460, because occupancy 0.500 <= existing 0.500 in 1dk8A Skipped atom 462, because occupancy 0.500 <= existing 0.500 in 1dk8A Skipped atom 572, because occupancy 0.500 <= existing 0.500 in 1dk8A Skipped atom 574, because occupancy 0.500 <= existing 0.500 in 1dk8A Skipped atom 576, because occupancy 0.500 <= existing 0.500 in 1dk8A Skipped atom 578, because occupancy 0.500 <= existing 0.500 in 1dk8A Skipped atom 580, because occupancy 0.500 <= existing 0.500 in 1dk8A Skipped atom 582, because occupancy 0.500 <= existing 0.500 in 1dk8A Skipped atom 627, because occupancy 0.500 <= existing 0.500 in 1dk8A Skipped atom 629, because occupancy 0.500 <= existing 0.500 in 1dk8A Skipped atom 707, because occupancy 0.500 <= existing 0.500 in 1dk8A Skipped atom 803, because occupancy 0.500 <= existing 0.500 in 1dk8A Skipped atom 805, because occupancy 0.500 <= existing 0.500 in 1dk8A Skipped atom 807, because occupancy 0.500 <= existing 0.500 in 1dk8A Skipped atom 809, because occupancy 0.500 <= existing 0.500 in 1dk8A Skipped atom 834, because occupancy 0.500 <= existing 0.500 in 1dk8A Skipped atom 836, because occupancy 0.500 <= existing 0.500 in 1dk8A Skipped atom 838, because occupancy 0.500 <= existing 0.500 in 1dk8A Skipped atom 987, because occupancy 0.500 <= existing 0.500 in 1dk8A Skipped atom 989, because occupancy 0.500 <= existing 0.500 in 1dk8A Skipped atom 1056, because occupancy 0.500 <= existing 0.500 in 1dk8A # T0302 read from 1dk8A/T0302-1dk8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dk8A read from 1dk8A/T0302-1dk8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1dk8A to template set # found chain 1dk8A in template set T0302 1 :SMVSPEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKKSK 1dk8A 112 :SASPTPPYLKWAESLHSLLDDQDGISLFRTFLKQEGCADLLDFWFACTGFRKLE T0302 55 :GPQQIHLKAKAIYEKFIQTDA 1dk8A 170 :NEEKRLKLARAIYRKYILDNN T0302 81 :LDFHTKEVITNSI 1dk8A 197 :TKPATKSFIKGCI T0302 94 :TQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDLME 1dk8A 212 :QLIDPAMFDQAQTEIQATMEENTYPSFLKSDIYLEYTR Number of specific fragments extracted= 4 number of extra gaps= 0 total=10 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 1dk8A/T0302-1dk8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0302 read from 1dk8A/T0302-1dk8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dk8A read from 1dk8A/T0302-1dk8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1dk8A in template set T0302 1 :SMVSPEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKKS 1dk8A 112 :SASPTPPYLKWAESLHSLLDDQDGISLFRTFLKQEGCADLLDFWFACTGFRKL T0302 54 :KGPQQIHLKAKAIYEKFIQTDA 1dk8A 169 :SNEEKRLKLARAIYRKYILDNN T0302 81 :LDFHTKEVITNSI 1dk8A 197 :TKPATKSFIKGCI T0302 94 :TQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDLMEG 1dk8A 212 :QLIDPAMFDQAQTEIQATMEENTYPSFLKSDIYLEYTRT Number of specific fragments extracted= 4 number of extra gaps= 0 total=14 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 1dk8A/T0302-1dk8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0302 read from 1dk8A/T0302-1dk8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1dk8A read from 1dk8A/T0302-1dk8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1dk8A in template set T0302 2 :MVSPEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKKS 1dk8A 113 :ASPTPPYLKWAESLHSLLDDQDGISLFRTFLKQEGCADLLDFWFACTGFRKL T0302 54 :KGPQQIHLKAKAIYEKFIQTDA 1dk8A 169 :SNEEKRLKLARAIYRKYILDNN T0302 81 :LDFHTKEVITNSITQ 1dk8A 197 :TKPATKSFIKGCIMK T0302 96 :PTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYL 1dk8A 214 :IDPAMFDQAQTEIQATMEENTYPSFLKSDIYL Number of specific fragments extracted= 4 number of extra gaps= 0 total=18 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 2bt2A/T0302-2bt2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2bt2A expands to /projects/compbio/data/pdb/2bt2.pdb.gz 2bt2A:Skipped atom 45, because occupancy 0.300 <= existing 0.700 in 2bt2A Skipped atom 49, because occupancy 0.300 <= existing 0.700 in 2bt2A Skipped atom 51, because occupancy 0.300 <= existing 0.700 in 2bt2A Skipped atom 477, because occupancy 0.500 <= existing 0.500 in 2bt2A Skipped atom 481, because occupancy 0.500 <= existing 0.500 in 2bt2A Skipped atom 483, because occupancy 0.500 <= existing 0.500 in 2bt2A Skipped atom 485, because occupancy 0.500 <= existing 0.500 in 2bt2A Skipped atom 487, because occupancy 0.500 <= existing 0.500 in 2bt2A Skipped atom 489, because occupancy 0.500 <= existing 0.500 in 2bt2A Skipped atom 491, because occupancy 0.500 <= existing 0.500 in 2bt2A Skipped atom 493, because occupancy 0.500 <= existing 0.500 in 2bt2A Skipped atom 542, because occupancy 0.400 <= existing 0.600 in 2bt2A Skipped atom 546, because occupancy 0.400 <= existing 0.600 in 2bt2A Skipped atom 548, because occupancy 0.400 <= existing 0.600 in 2bt2A Skipped atom 550, because occupancy 0.400 <= existing 0.600 in 2bt2A Skipped atom 552, because occupancy 0.400 <= existing 0.600 in 2bt2A Skipped atom 554, because occupancy 0.400 <= existing 0.600 in 2bt2A Skipped atom 556, because occupancy 0.400 <= existing 0.600 in 2bt2A Skipped atom 558, because occupancy 0.400 <= existing 0.600 in 2bt2A Skipped atom 641, because occupancy 0.400 <= existing 0.600 in 2bt2A Skipped atom 645, because occupancy 0.400 <= existing 0.600 in 2bt2A Skipped atom 647, because occupancy 0.400 <= existing 0.600 in 2bt2A # T0302 read from 2bt2A/T0302-2bt2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bt2A read from 2bt2A/T0302-2bt2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2bt2A to template set # found chain 2bt2A in template set T0302 5 :PEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKKSKGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDLMEG 2bt2A 56 :SEDVLGWRESFDLLLSSKNGVAAFHAFLKTEFSEENLEFWLACEEFKKIRSATKLASRAHQIFEEFICSEAPKEVNIDHETRELTRMNLQTATATCFDAAQGKTRTLMEKDSYPRFLKSPAYRDLAAQ Number of specific fragments extracted= 1 number of extra gaps= 0 total=19 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 2bt2A/T0302-2bt2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0302 read from 2bt2A/T0302-2bt2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bt2A read from 2bt2A/T0302-2bt2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2bt2A in template set T0302 5 :PEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKKSKGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDLMEG 2bt2A 56 :SEDVLGWRESFDLLLSSKNGVAAFHAFLKTEFSEENLEFWLACEEFKKIRSATKLASRAHQIFEEFICSEAPKEVNIDHETRELTRMNLQTATATCFDAAQGKTRTLMEKDSYPRFLKSPAYRDLAAQ Number of specific fragments extracted= 1 number of extra gaps= 0 total=20 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 2bt2A/T0302-2bt2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0302 read from 2bt2A/T0302-2bt2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bt2A read from 2bt2A/T0302-2bt2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2bt2A in template set T0302 5 :PEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKKSKGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDLMEG 2bt2A 56 :SEDVLGWRESFDLLLSSKNGVAAFHAFLKTEFSEENLEFWLACEEFKKIRSATKLASRAHQIFEEFICSEAPKEVNIDHETRELTRMNLQTATATCFDAAQGKTRTLMEKDSYPRFLKSPAYRDLAAQ Number of specific fragments extracted= 1 number of extra gaps= 0 total=21 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 2a72A/T0302-2a72A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2a72A expands to /projects/compbio/data/pdb/2a72.pdb.gz 2a72A:# T0302 read from 2a72A/T0302-2a72A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2a72A read from 2a72A/T0302-2a72A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2a72A to template set # found chain 2a72A in template set T0302 1 :SMVSPEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKK 2a72A 320 :KEPSQQRVKRWGFGMDEALKDPVGREQFLKFLESEFSSENLRFWLAVEDLKK T0302 54 :KGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDLMEG 2a72A 372 :RPIKEVPSRVQEIWQEFLAPGAPSAINLDSKSYDKTTHNVKEPGRYTFEDAQEHIYKLMKSDSYPRFIRSSAYQELLQA Number of specific fragments extracted= 2 number of extra gaps= 0 total=23 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 2a72A/T0302-2a72A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0302 read from 2a72A/T0302-2a72A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2a72A read from 2a72A/T0302-2a72A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2a72A in template set T0302 1 :SMVSPEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKK 2a72A 320 :KEPSQQRVKRWGFGMDEALKDPVGREQFLKFLESEFSSENLRFWLAVEDLKK T0302 54 :KGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDLMEG 2a72A 372 :RPIKEVPSRVQEIWQEFLAPGAPSAINLDSKSYDKTTHNVKEPGRYTFEDAQEHIYKLMKSDSYPRFIRSSAYQELLQA Number of specific fragments extracted= 2 number of extra gaps= 0 total=25 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 2a72A/T0302-2a72A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0302 read from 2a72A/T0302-2a72A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2a72A read from 2a72A/T0302-2a72A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2a72A in template set T0302 1 :SMVSPEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKK 2a72A 320 :KEPSQQRVKRWGFGMDEALKDPVGREQFLKFLESEFSSENLRFWLAVEDLKK T0302 54 :KGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDLMEG 2a72A 372 :RPIKEVPSRVQEIWQEFLAPGAPSAINLDSKSYDKTTHNVKEPGRYTFEDAQEHIYKLMKSDSYPRFIRSSAYQELLQA Number of specific fragments extracted= 2 number of extra gaps= 0 total=27 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 1agrE/T0302-1agrE-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1agrE expands to /projects/compbio/data/pdb/1agr.pdb.gz 1agrE:# T0302 read from 1agrE/T0302-1agrE-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1agrE read from 1agrE/T0302-1agrE-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1agrE to template set # found chain 1agrE in template set Warning: unaligning (T0302)V3 because first residue in template chain is (1agrE)V51 T0302 4 :SPEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKKSKGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLD 1agrE 52 :SQEEVKKWAESLENLINHECGLAAFKAFLKSEYSEENIDFWISCEEYKKIKSPSKLSPKAKKIYNEFISVQATKEVNLDSCTREETSRNMLEPTITCFDEAQKKIFNLMEKDSYRRFLKSRFYLD Number of specific fragments extracted= 1 number of extra gaps= 0 total=28 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 1agrE/T0302-1agrE-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0302 read from 1agrE/T0302-1agrE-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1agrE read from 1agrE/T0302-1agrE-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1agrE in template set Warning: unaligning (T0302)V3 because first residue in template chain is (1agrE)V51 T0302 4 :SPEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKKSKGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLD 1agrE 52 :SQEEVKKWAESLENLINHECGLAAFKAFLKSEYSEENIDFWISCEEYKKIKSPSKLSPKAKKIYNEFISVQATKEVNLDSCTREETSRNMLEPTITCFDEAQKKIFNLMEKDSYRRFLKSRFYLD Number of specific fragments extracted= 1 number of extra gaps= 0 total=29 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 1agrE/T0302-1agrE-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0302 read from 1agrE/T0302-1agrE-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1agrE read from 1agrE/T0302-1agrE-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1agrE in template set Warning: unaligning (T0302)V3 because first residue in template chain is (1agrE)V51 T0302 4 :SPEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKKSKGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLD 1agrE 52 :SQEEVKKWAESLENLINHECGLAAFKAFLKSEYSEENIDFWISCEEYKKIKSPSKLSPKAKKIYNEFISVQATKEVNLDSCTREETSRNMLEPTITCFDEAQKKIFNLMEKDSYRRFLKSRFYLD Number of specific fragments extracted= 1 number of extra gaps= 0 total=30 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 1eztA/T0302-1eztA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1eztA expands to /projects/compbio/data/pdb/1ezt.pdb.gz 1eztA:# T0302 read from 1eztA/T0302-1eztA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1eztA read from 1eztA/T0302-1eztA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1eztA to template set # found chain 1eztA in template set Warning: unaligning (T0302)V3 because first residue in template chain is (1eztA)V5 Warning: unaligning (T0302)E131 because last residue in template chain is (1eztA)N133 T0302 4 :SPEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKKSKGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDLM 1eztA 6 :SQEEVKKWAESLENLINHECGLAAFKAFLKSEYSEENIDFWISCEEYKKIKSPSKLSPKAKKIYNEFISVQATKEVNLDSCTREETSRNMLEPTITCFDEAQKKIFNLMEKDSYRRFLKSRFYLDLT Number of specific fragments extracted= 1 number of extra gaps= 0 total=31 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 1eztA/T0302-1eztA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0302 read from 1eztA/T0302-1eztA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1eztA read from 1eztA/T0302-1eztA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1eztA in template set Warning: unaligning (T0302)V3 because first residue in template chain is (1eztA)V5 Warning: unaligning (T0302)E131 because last residue in template chain is (1eztA)N133 T0302 4 :SPEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKKSKGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDLM 1eztA 6 :SQEEVKKWAESLENLINHECGLAAFKAFLKSEYSEENIDFWISCEEYKKIKSPSKLSPKAKKIYNEFISVQATKEVNLDSCTREETSRNMLEPTITCFDEAQKKIFNLMEKDSYRRFLKSRFYLDLT Number of specific fragments extracted= 1 number of extra gaps= 0 total=32 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 1eztA/T0302-1eztA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0302 read from 1eztA/T0302-1eztA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1eztA read from 1eztA/T0302-1eztA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1eztA in template set Warning: unaligning (T0302)V3 because first residue in template chain is (1eztA)V5 T0302 4 :SPEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKKSKGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDL 1eztA 6 :SQEEVKKWAESLENLINHECGLAAFKAFLKSEYSEENIDFWISCEEYKKIKSPSKLSPKAKKIYNEFISVQATKEVNLDSCTREETSRNMLEPTITCFDEAQKKIFNLMEKDSYRRFLKSRFYLDL Number of specific fragments extracted= 1 number of extra gaps= 0 total=33 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 1agrH/T0302-1agrH-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1agrH expands to /projects/compbio/data/pdb/1agr.pdb.gz 1agrH:# T0302 read from 1agrH/T0302-1agrH-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1agrH read from 1agrH/T0302-1agrH-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1agrH to template set # found chain 1agrH in template set Warning: unaligning (T0302)G12 because first residue in template chain is (1agrH)A60 T0302 13 :ESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKKSKGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKS 1agrH 61 :ESLENLINHECGLAAFKAFLKSEYSEENIDFWISCEEYKKIKSPSKLSPKAKKIYNEFISVQATKEVNLDSCTREETSRNMLEPTITCFDEAQKKIFNLMEKDSYRRFLKS Number of specific fragments extracted= 1 number of extra gaps= 0 total=34 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 1agrH/T0302-1agrH-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0302 read from 1agrH/T0302-1agrH-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1agrH read from 1agrH/T0302-1agrH-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1agrH in template set Warning: unaligning (T0302)G12 because first residue in template chain is (1agrH)A60 T0302 13 :ESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKKSKGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKS 1agrH 61 :ESLENLINHECGLAAFKAFLKSEYSEENIDFWISCEEYKKIKSPSKLSPKAKKIYNEFISVQATKEVNLDSCTREETSRNMLEPTITCFDEAQKKIFNLMEKDSYRRFLKS Number of specific fragments extracted= 1 number of extra gaps= 0 total=35 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 1agrH/T0302-1agrH-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0302 read from 1agrH/T0302-1agrH-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1agrH read from 1agrH/T0302-1agrH-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1agrH in template set Warning: unaligning (T0302)G12 because first residue in template chain is (1agrH)A60 T0302 13 :ESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKKSKGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKS 1agrH 61 :ESLENLINHECGLAAFKAFLKSEYSEENIDFWISCEEYKKIKSPSKLSPKAKKIYNEFISVQATKEVNLDSCTREETSRNMLEPTITCFDEAQKKIFNLMEKDSYRRFLKS Number of specific fragments extracted= 1 number of extra gaps= 0 total=36 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 1omwA/T0302-1omwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1omwA expands to /projects/compbio/data/pdb/1omw.pdb.gz 1omwA:# T0302 read from 1omwA/T0302-1omwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1omwA read from 1omwA/T0302-1omwA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1omwA to template set # found chain 1omwA in template set Warning: unaligning (T0302)L81 because of BadResidue code BAD_PEPTIDE in next template residue (1omwA)S125 Warning: unaligning (T0302)D82 because of BadResidue code BAD_PEPTIDE at template residue (1omwA)S125 T0302 9 :VKWGESFDKLLSHRDGLEAFTRFLKT 1omwA 49 :DRGEVTFEKIFSQKLGYLLFRDFCLK T0302 35 :EFSEENIEFWIACEDFKKSKGPQQIHLKAKAIYEKFIQTDA 1omwA 77 :EEAKPLVEFYEEIKKYEKLETEEERLVCSREIFDTYIMKEL T0302 76 :PKEVN 1omwA 119 :ACSHP T0302 83 :FHTKEVITNSI 1omwA 126 :KSAIEHVQGHL T0302 94 :TQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDLM 1omwA 139 :KQVPPDLFQPYIEEICQNLRGDVFQKFIESDKFTRFC Number of specific fragments extracted= 5 number of extra gaps= 1 total=41 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 1omwA/T0302-1omwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0302 read from 1omwA/T0302-1omwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1omwA read from 1omwA/T0302-1omwA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1omwA in template set Warning: unaligning (T0302)L81 because of BadResidue code BAD_PEPTIDE in next template residue (1omwA)S125 Warning: unaligning (T0302)D82 because of BadResidue code BAD_PEPTIDE at template residue (1omwA)S125 T0302 9 :VKWGESFDKLLSHRDGLEAFTRFLKT 1omwA 49 :DRGEVTFEKIFSQKLGYLLFRDFCLK T0302 35 :EFSEENIEFWIACEDFKKSKGPQQIHLKAKAIYEKFIQ 1omwA 77 :EEAKPLVEFYEEIKKYEKLETEEERLVCSREIFDTYIM T0302 76 :PKEVN 1omwA 119 :ACSHP T0302 83 :FHTKEVITNSI 1omwA 126 :KSAIEHVQGHL T0302 94 :TQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDLM 1omwA 139 :KQVPPDLFQPYIEEICQNLRGDVFQKFIESDKFTRFC Number of specific fragments extracted= 5 number of extra gaps= 1 total=46 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 1omwA/T0302-1omwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0302 read from 1omwA/T0302-1omwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1omwA read from 1omwA/T0302-1omwA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1omwA in template set Warning: unaligning (T0302)L81 because of BadResidue code BAD_PEPTIDE in next template residue (1omwA)S125 Warning: unaligning (T0302)D82 because of BadResidue code BAD_PEPTIDE at template residue (1omwA)S125 T0302 10 :KWGESFDKLLSHRDGLEAFTRFLKTEFS 1omwA 50 :RGEVTFEKIFSQKLGYLLFRDFCLKHLE T0302 38 :EENIEFWIACEDFKKSKGPQQIHLKAKAIYEKFIQT 1omwA 80 :KPLVEFYEEIKKYEKLETEEERLVCSREIFDTYIMK T0302 76 :PKEVN 1omwA 119 :ACSHP T0302 83 :FHTKEVITNSITQ 1omwA 126 :KSAIEHVQGHLVK T0302 96 :PTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDLM 1omwA 141 :VPPDLFQPYIEEICQNLRGDVFQKFIESDKFTRFC Number of specific fragments extracted= 5 number of extra gaps= 1 total=51 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 1htjF/T0302-1htjF-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1htjF expands to /projects/compbio/data/pdb/1htj.pdb.gz 1htjF:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0302 read from 1htjF/T0302-1htjF-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1htjF read from 1htjF/T0302-1htjF-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1htjF to template set # found chain 1htjF in template set T0302 8 :AVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKKS 1htjF 307 :SDIIFQDLEKLKSRPAHLGVFLRYIFSQADPSPLLFYLCAEVYQQA T0302 55 :GPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSI 1htjF 353 :SPKDSRSLGKDIWNIFLEKNAPLRVKIPEMLQAEIDSRL T0302 94 :TQPTLHSFDAAQSRVYQLMEQDS 1htjF 394 :SEDARGVLCEAQEAAMPEIQEQI T0302 124 :DIYLDLME 1htjF 417 :HDYRTKRT Number of specific fragments extracted= 4 number of extra gaps= 0 total=55 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 1htjF/T0302-1htjF-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0302 read from 1htjF/T0302-1htjF-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1htjF read from 1htjF/T0302-1htjF-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1htjF in template set T0302 11 :WGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKK 1htjF 310 :IFQDLEKLKSRPAHLGVFLRYIFSQADPSPLLFYLCAEVYQQ T0302 54 :KGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSI 1htjF 352 :ASPKDSRSLGKDIWNIFLEKNAPLRVKIPEMLQAEIDSRL T0302 94 :TQPTLHSFDAAQSRVYQLMEQDS 1htjF 394 :SEDARGVLCEAQEAAMPEIQEQI T0302 124 :DIYLDLMEG 1htjF 417 :HDYRTKRTL Number of specific fragments extracted= 4 number of extra gaps= 0 total=59 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 1htjF/T0302-1htjF-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0302 read from 1htjF/T0302-1htjF-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1htjF read from 1htjF/T0302-1htjF-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1htjF in template set T0302 11 :WGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKK 1htjF 310 :IFQDLEKLKSRPAHLGVFLRYIFSQADPSPLLFYLCAEVYQQ T0302 54 :KGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQ 1htjF 352 :ASPKDSRSLGKDIWNIFLEKNAPLRVKIPEMLQAEIDSRLRN T0302 96 :PTLHSFDAAQSRVYQLMEQDSY 1htjF 396 :DARGVLCEAQEAAMPEIQEQIH T0302 125 :IYLDLME 1htjF 418 :DYRTKRT Number of specific fragments extracted= 4 number of extra gaps= 0 total=63 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 2af0A/T0302-2af0A-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2af0A expands to /projects/compbio/data/pdb/2af0.pdb.gz 2af0A:Skipped atom 386, because occupancy 0.350 <= existing 0.650 in 2af0A Skipped atom 388, because occupancy 0.350 <= existing 0.650 in 2af0A Skipped atom 390, because occupancy 0.350 <= existing 0.650 in 2af0A Skipped atom 392, because occupancy 0.350 <= existing 0.650 in 2af0A Skipped atom 394, because occupancy 0.350 <= existing 0.650 in 2af0A # T0302 read from 2af0A/T0302-2af0A-t06-local-adpstyle5.a2m # 2af0A read from 2af0A/T0302-2af0A-t06-local-adpstyle5.a2m # adding 2af0A to template set # found chain 2af0A in template set T0302 3 :VSPEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKKSKGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDLME 2af0A 72 :PSPEEAQLWSEAFDELLASKYGLAAFRAFLKSEFCEENIEFWLACEDFKKTKSPQKLSSKARKIYTDFIEKEAPKEINIDFQTKTLIAQNIQEATSGCFTTAQKRVYSLMENNSYPRFLESEFYQDLCK Number of specific fragments extracted= 1 number of extra gaps= 0 total=64 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 2crpA/T0302-2crpA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2crpA expands to /projects/compbio/data/pdb/2crp.pdb.gz 2crpA:# T0302 read from 2crpA/T0302-2crpA-t06-local-adpstyle5.a2m # 2crpA read from 2crpA/T0302-2crpA-t06-local-adpstyle5.a2m # adding 2crpA to template set # found chain 2crpA in template set T0302 4 :SPEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKKSKGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDLMEG 2crpA 18 :SLDEALQWRDSLDKLLQNNYGLASFKSFLKSEFSEENLEFWIACEDYKKIKSPAKMAEKAKQIYEEFIQTEAPKEVNIDHFTKDITMKNLVEPSLSSFDMAQKRIHALMEKDSLPRFVRSEFYQELISG Number of specific fragments extracted= 1 number of extra gaps= 0 total=65 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 2bv1A/T0302-2bv1A-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2bv1A expands to /projects/compbio/data/pdb/2bv1.pdb.gz 2bv1A:Skipped atom 173, because occupancy 0.500 <= existing 0.500 in 2bv1A Skipped atom 175, because occupancy 0.500 <= existing 0.500 in 2bv1A Skipped atom 177, because occupancy 0.500 <= existing 0.500 in 2bv1A Skipped atom 179, because occupancy 0.500 <= existing 0.500 in 2bv1A Skipped atom 181, because occupancy 0.500 <= existing 0.500 in 2bv1A # T0302 read from 2bv1A/T0302-2bv1A-t06-local-adpstyle5.a2m # 2bv1A read from 2bv1A/T0302-2bv1A-t06-local-adpstyle5.a2m # adding 2bv1A to template set # found chain 2bv1A in template set Warning: unaligning (T0302)K77 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bv1A)Q135 Warning: unaligning (T0302)E78 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bv1A)Q135 T0302 2 :MVSPEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKKSKGP 2bv1A 60 :VLSAAEVMQWSQSLEKLLANQTGQNVFGSFLKSEFSEENIEFWLACEDYKKTESD T0302 58 :QIHLKAKAIYEKFIQTDAP 2bv1A 115 :LLPCKAEEIYKAFVHSDAA T0302 79 :VNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDLMEG 2bv1A 136 :INIDFRTRESTAKKIKAPTPTCFDEAQKVIYTLMEKDSYPRFLKSDIYLNLLND Number of specific fragments extracted= 3 number of extra gaps= 1 total=68 Will force an alignment to be made, even if fragment is small Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1iapA/T0302-1iapA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1iapA expands to /projects/compbio/data/pdb/1iap.pdb.gz 1iapA:# T0302 read from 1iapA/T0302-1iapA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1iapA read from 1iapA/T0302-1iapA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1iapA to template set # found chain 1iapA in template set T0302 13 :ESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKK 1iapA 47 :QSLEQVKRRPAHLMALLQHVALQFEPGPLLCCLHADMLGS T0302 54 :KGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSI 1iapA 87 :LGPKEAKKAFLDFYHSFLEKTAVLRVPVPPNVAFELDRTR T0302 94 :TQPTLHSFDAAQSRVYQLME 1iapA 128 :DLISEDVQRRFVQEVVQSQQ T0302 114 :QDSYTRFLK 1iapA 151 :GRQLEDFRS Number of specific fragments extracted= 4 number of extra gaps= 0 total=72 Will force an alignment to be made, even if fragment is small Number of alignments=31 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1iapA/T0302-1iapA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0302 read from 1iapA/T0302-1iapA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1iapA read from 1iapA/T0302-1iapA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1iapA in template set T0302 13 :ESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKK 1iapA 47 :QSLEQVKRRPAHLMALLQHVALQFEPGPLLCCLHADMLGS T0302 54 :KGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQ 1iapA 87 :LGPKEAKKAFLDFYHSFLEKTAVLRVPVPPNVAFELDRTRAD T0302 96 :PTLHSFDAAQSRVYQLME 1iapA 130 :ISEDVQRRFVQEVVQSQQ T0302 114 :QDSYTRFLK 1iapA 151 :GRQLEDFRS Number of specific fragments extracted= 4 number of extra gaps= 0 total=76 Will force an alignment to be made, even if fragment is small Number of alignments=32 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1iapA/T0302-1iapA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0302 read from 1iapA/T0302-1iapA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1iapA read from 1iapA/T0302-1iapA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1iapA in template set T0302 13 :ESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKK 1iapA 47 :QSLEQVKRRPAHLMALLQHVALQFEPGPLLCCLHADMLGS T0302 54 :KGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQ 1iapA 87 :LGPKEAKKAFLDFYHSFLEKTAVLRVPVPPNVAFELDRTRAD T0302 96 :PTLHSFDAAQSRVYQLME 1iapA 130 :ISEDVQRRFVQEVVQSQQ Number of specific fragments extracted= 3 number of extra gaps= 0 total=79 Will force an alignment to be made, even if fragment is small Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cmzA/T0302-1cmzA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1cmzA expands to /projects/compbio/data/pdb/1cmz.pdb.gz 1cmzA:# T0302 read from 1cmzA/T0302-1cmzA-t06-local-adpstyle5.a2m # 1cmzA read from 1cmzA/T0302-1cmzA-t06-local-adpstyle5.a2m # adding 1cmzA to template set # found chain 1cmzA in template set Warning: unaligning (T0302)V3 because first residue in template chain is (1cmzA)P79 Warning: unaligning (T0302)M130 because last residue in template chain is (1cmzA)L206 T0302 4 :SPEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKKSKGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDL 1cmzA 80 :SPEEVQSWAQSFDKLMHSPAGRSVFRAFLRTEYSEENMLFWLACEELKAEANQHVVDEKARLIYEDYVSILSPKEVSLDSRVREGINKKMQEPSAHTFDDAQLQIYTLMHRDSYPRFLSSPTYRAL Number of specific fragments extracted= 1 number of extra gaps= 0 total=80 Will force an alignment to be made, even if fragment is small Number of alignments=34 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zv4X/T0302-1zv4X-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1zv4X expands to /projects/compbio/data/pdb/1zv4.pdb.gz 1zv4X:# T0302 read from 1zv4X/T0302-1zv4X-t06-local-adpstyle5.a2m # 1zv4X read from 1zv4X/T0302-1zv4X-t06-local-adpstyle5.a2m # adding 1zv4X to template set # found chain 1zv4X in template set Warning: unaligning (T0302)D74 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1zv4X)P146 Warning: unaligning (T0302)P76 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1zv4X)P146 Warning: unaligning (T0302)K77 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1zv4X)K147 T0302 3 :VSPEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKKSKGPQQIHLKAKAIYEKFIQT 1zv4X 73 :PTAEEVLSWSQNFDKMMKAPAGRNLFREFLRTEYSEENLLFWLACEDLKKEQNKKVIEEKARMIYEDYISI T0302 78 :EVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDLMEG 1zv4X 148 :EVSLDSRVREVINRNLLDPNPHMYEDAQLQIYTLMHRDSFPRFLNSQIYKSFVES Number of specific fragments extracted= 2 number of extra gaps= 0 total=82 Will force an alignment to be made, even if fragment is small Number of alignments=35 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2es0A/T0302-2es0A-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2es0A expands to /projects/compbio/data/pdb/2es0.pdb.gz 2es0A:Skipped atom 198, because occupancy 0.500 <= existing 0.500 in 2es0A Skipped atom 202, because occupancy 0.500 <= existing 0.500 in 2es0A Skipped atom 204, because occupancy 0.500 <= existing 0.500 in 2es0A Skipped atom 206, because occupancy 0.500 <= existing 0.500 in 2es0A Skipped atom 208, because occupancy 0.500 <= existing 0.500 in 2es0A Skipped atom 338, because occupancy 0.500 <= existing 0.500 in 2es0A Skipped atom 342, because occupancy 0.500 <= existing 0.500 in 2es0A Skipped atom 344, because occupancy 0.500 <= existing 0.500 in 2es0A Skipped atom 346, because occupancy 0.500 <= existing 0.500 in 2es0A Skipped atom 348, because occupancy 0.500 <= existing 0.500 in 2es0A Skipped atom 350, because occupancy 0.500 <= existing 0.500 in 2es0A Skipped atom 352, because occupancy 0.500 <= existing 0.500 in 2es0A Skipped atom 354, because occupancy 0.500 <= existing 0.500 in 2es0A # T0302 read from 2es0A/T0302-2es0A-t06-local-adpstyle5.a2m # 2es0A read from 2es0A/T0302-2es0A-t06-local-adpstyle5.a2m # adding 2es0A to template set # found chain 2es0A in template set Warning: unaligning (T0302)M2 because first residue in template chain is (2es0A)M324 Warning: unaligning (T0302)M130 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2es0A)L452 T0302 3 :VSPEEAVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKK 2es0A 325 :PSQQRVKRWGFSFDEILKDQVGRDQFLRFLESEFSSENLRFWLAVQDLKK T0302 54 :KGPQQIHLKAKAIYEKFIQTDAPKEVNLDFHTKEVITNSITQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDL 2es0A 375 :QPLQDVAKRVEEIWQEFLAPGAPSAINLDSHSYEITSQNVKDGGRYTFEDAQEHIYKLMKSDSYARFLRSNAYQDL Number of specific fragments extracted= 2 number of extra gaps= 1 total=84 Will force an alignment to be made, even if fragment is small Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1emuA/T0302-1emuA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1emuA expands to /projects/compbio/data/pdb/1emu.pdb.gz 1emuA:Skipped atom 78, because occupancy 0.500 <= existing 0.500 in 1emuA Skipped atom 433, because occupancy 0.500 <= existing 0.500 in 1emuA Skipped atom 587, because occupancy 0.500 <= existing 0.500 in 1emuA Skipped atom 589, because occupancy 0.500 <= existing 0.500 in 1emuA Skipped atom 591, because occupancy 0.500 <= existing 0.500 in 1emuA Skipped atom 593, because occupancy 0.500 <= existing 0.500 in 1emuA Skipped atom 595, because occupancy 0.500 <= existing 0.500 in 1emuA Skipped atom 597, because occupancy 0.500 <= existing 0.500 in 1emuA Skipped atom 599, because occupancy 0.500 <= existing 0.500 in 1emuA Skipped atom 601, because occupancy 0.500 <= existing 0.500 in 1emuA Skipped atom 603, because occupancy 0.500 <= existing 0.500 in 1emuA Skipped atom 605, because occupancy 0.500 <= existing 0.500 in 1emuA Skipped atom 607, because occupancy 0.500 <= existing 0.500 in 1emuA Skipped atom 609, because occupancy 0.500 <= existing 0.500 in 1emuA Skipped atom 611, because occupancy 0.500 <= existing 0.500 in 1emuA Skipped atom 613, because occupancy 0.500 <= existing 0.500 in 1emuA Skipped atom 615, because occupancy 0.500 <= existing 0.500 in 1emuA Skipped atom 617, because occupancy 0.500 <= existing 0.500 in 1emuA Skipped atom 619, because occupancy 0.500 <= existing 0.500 in 1emuA Skipped atom 621, because occupancy 0.500 <= existing 0.500 in 1emuA Skipped atom 623, because occupancy 0.500 <= existing 0.500 in 1emuA Skipped atom 625, because occupancy 0.500 <= existing 0.500 in 1emuA Skipped atom 627, because occupancy 0.500 <= existing 0.500 in 1emuA Skipped atom 629, because occupancy 0.500 <= existing 0.500 in 1emuA Skipped atom 631, because occupancy 0.500 <= existing 0.500 in 1emuA Skipped atom 633, because occupancy 0.500 <= existing 0.500 in 1emuA Skipped atom 635, because occupancy 0.500 <= existing 0.500 in 1emuA Skipped atom 637, because occupancy 0.500 <= existing 0.500 in 1emuA Skipped atom 639, because occupancy 0.500 <= existing 0.500 in 1emuA Skipped atom 641, because occupancy 0.500 <= existing 0.500 in 1emuA Skipped atom 643, because occupancy 0.500 <= existing 0.500 in 1emuA Skipped atom 645, because occupancy 0.500 <= existing 0.500 in 1emuA Skipped atom 647, because occupancy 0.500 <= existing 0.500 in 1emuA Skipped atom 649, because occupancy 0.500 <= existing 0.500 in 1emuA Skipped atom 701, because occupancy 0.500 <= existing 0.500 in 1emuA Skipped atom 703, because occupancy 0.500 <= existing 0.500 in 1emuA Skipped atom 747, because occupancy 0.500 <= existing 0.500 in 1emuA # T0302 read from 1emuA/T0302-1emuA-t06-local-adpstyle5.a2m # 1emuA read from 1emuA/T0302-1emuA-t06-local-adpstyle5.a2m # adding 1emuA to template set # found chain 1emuA in template set T0302 8 :AVKWGESFDKLLSHRDGLEAFTRFLKTEFSEENIEFWIACEDFKKSK 1emuA 119 :YLKWAESLHSLLDDQDGISLFRTFLKQEGCADLLDFWFACTGFRKLE T0302 55 :GPQQIHLKAKAIYEKFIQTDA 1emuA 170 :NEEKRLKLARAIYRKYILDNN T0302 76 :PKEVNLDFHTKEVITNSI 1emuA 192 :IVSRQTKPATKSFIKGCI T0302 94 :TQPTLHSFDAAQSRVYQLMEQDSYTRFLKSDIYLDL 1emuA 212 :QLIDPAMFDQAQTEIQATMEENTYPSFLKSDIYLEY Number of specific fragments extracted= 4 number of extra gaps= 0 total=88 Will force an alignment to be made, even if fragment is small Number of alignments=37 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1eca/T0302-1eca-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1eca expands to /projects/compbio/data/pdb/1eca.pdb.gz 1eca:Warning: there is no chain 1eca will retry with 1ecaA Skipped atom 813, because occupancy 0.500 <= existing 0.500 in 1eca Skipped atom 1001, because occupancy 0.500 <= existing 0.500 in 1eca Skipped atom 1003, because occupancy 0.500 <= existing 0.500 in 1eca Skipped atom 1005, because occupancy 0.500 <= existing 0.500 in 1eca Skipped atom 1031, because occupancy 0.500 <= existing 0.500 in 1eca # T0302 read from 1eca/T0302-1eca-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1eca read from 1eca/T0302-1eca-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1eca to template set # found chain 1eca in template set Warning: unaligning (T0302)Y117 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1eca)A115 Warning: unaligning (T0302)T118 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1eca)A115 T0302 4 :S 1eca 2 :S T0302 22 :RDGLEAFTRFLKT 1eca 3 :ADQISTVQASFDK T0302 36 :FSEENIEFWIAC 1eca 16 :VKGDPVGILYAV T0302 50 :FK 1eca 28 :FK T0302 52 :KSKGPQQIHLKAKAIYEKF 1eca 48 :SIKGTAPFETHANRIVGFF T0302 71 :IQTDAP 1eca 69 :IIGELP T0302 80 :NLDFHTKEVITNSI 1eca 75 :NIEADVNTFVASHK T0302 94 :TQPTLHSFDAAQSRVYQLMEQD 1eca 90 :RGVTHDQLNNFRAGFVSYMKAH T0302 116 :S 1eca 113 :D T0302 119 :RFL 1eca 116 :GAE T0302 124 :DIYLDLME 1eca 119 :AAWGATLD Number of specific fragments extracted= 11 number of extra gaps= 1 total=99 Will force an alignment to be made, even if fragment is small Number of alignments=38 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1eca/T0302-1eca-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0302 read from 1eca/T0302-1eca-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1eca read from 1eca/T0302-1eca-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1eca in template set Warning: unaligning (T0302)Y117 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1eca)A115 Warning: unaligning (T0302)T118 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1eca)A115 T0302 21 :HRDGLEAFTRFLKT 1eca 2 :SADQISTVQASFDK T0302 36 :FSEENIEFWIACEDF 1eca 16 :VKGDPVGILYAVFKA T0302 51 :KKSKGPQQIHLKAKAIYEKF 1eca 47 :ESIKGTAPFETHANRIVGFF T0302 71 :IQTDAP 1eca 69 :IIGELP T0302 80 :NLDFHTKEVITNSI 1eca 75 :NIEADVNTFVASHK T0302 94 :TQPTLHSFDAAQSRVYQLMEQD 1eca 90 :RGVTHDQLNNFRAGFVSYMKAH T0302 116 :S 1eca 113 :D T0302 119 :RFL 1eca 116 :GAE T0302 124 :DIYLDLME 1eca 119 :AAWGATLD Number of specific fragments extracted= 9 number of extra gaps= 1 total=108 Will force an alignment to be made, even if fragment is small Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1eca/T0302-1eca-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0302 read from 1eca/T0302-1eca-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1eca read from 1eca/T0302-1eca-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1eca in template set Warning: unaligning (T0302)V3 because first residue in template chain is (1eca)L1 T0302 4 :SPEEAVKWGESFDKLLSHRDGLEA 1eca 2 :SADQISTVQASFDKVKGDPVGILY T0302 46 :AC 1eca 26 :AV T0302 50 :FK 1eca 28 :FK T0302 54 :KGPQ 1eca 30 :ADPS T0302 58 :QIHLKAKAIYEKFIQ 1eca 54 :PFETHANRIVGFFSK T0302 73 :TDAP 1eca 71 :GELP T0302 80 :NL 1eca 75 :NI T0302 83 :FHTKEVITNSITQ 1eca 77 :EADVNTFVASHKP T0302 96 :PTLHSFDAAQSRVYQLMEQDSY 1eca 92 :VTHDQLNNFRAGFVSYMKAHTD Number of specific fragments extracted= 9 number of extra gaps= 0 total=117 Will force an alignment to be made, even if fragment is small Number of alignments=40 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ngnA/T0302-1ngnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ngnA expands to /projects/compbio/data/pdb/1ngn.pdb.gz 1ngnA:Skipped atom 495, because occupancy 0.500 <= existing 0.500 in 1ngnA Skipped atom 497, because occupancy 0.500 <= existing 0.500 in 1ngnA Skipped atom 499, because occupancy 0.500 <= existing 0.500 in 1ngnA Skipped atom 501, because occupancy 0.500 <= existing 0.500 in 1ngnA # T0302 read from 1ngnA/T0302-1ngnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ngnA read from 1ngnA/T0302-1ngnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ngnA to template set # found chain 1ngnA in template set T0302 22 :RDGLEAFTRFLKTEFSEENIE 1ngnA 446 :KMAIPVLWEFLEKYPSAEVAR T0302 44 :WIACEDF 1ngnA 470 :WRDVSEL T0302 51 :KKSKGPQQIHLKAKAIYEKFIQTDAPKEVN 1ngnA 478 :KPLGLYDLRAKTIIKFSDEYLTKQWRYPIE T0302 81 :LDFHTKEVITNS 1ngnA 511 :IGKYGNDSYRIF T0302 95 :QPTLHSFDAAQSRVYQL 1ngnA 531 :HPEDHKLNKYHDWLWEN Number of specific fragments extracted= 5 number of extra gaps= 0 total=122 Will force an alignment to be made, even if fragment is small Number of alignments=41 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ngnA/T0302-1ngnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0302 read from 1ngnA/T0302-1ngnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ngnA read from 1ngnA/T0302-1ngnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ngnA in template set T0302 22 :RDGLEAFTRFLKTEFSEENI 1ngnA 446 :KMAIPVLWEFLEKYPSAEVA T0302 44 :WIACEDFKKS 1ngnA 470 :WRDVSELLKP T0302 54 :KGPQQIHLKAKAIYEKFIQTDAPKEVN 1ngnA 481 :GLYDLRAKTIIKFSDEYLTKQWRYPIE T0302 81 :LDFHTKEVITNSIT 1ngnA 511 :IGKYGNDSYRIFCV T0302 95 :QPTLHSFDAAQSRVYQL 1ngnA 531 :HPEDHKLNKYHDWLWEN Number of specific fragments extracted= 5 number of extra gaps= 0 total=127 Will force an alignment to be made, even if fragment is small Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ngnA/T0302-1ngnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0302 read from 1ngnA/T0302-1ngnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ngnA read from 1ngnA/T0302-1ngnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ngnA in template set T0302 21 :HRDGLEAFTRFLKTEFSEEN 1ngnA 445 :GKMAIPVLWEFLEKYPSAEV T0302 44 :WIACEDFKKS 1ngnA 470 :WRDVSELLKP T0302 54 :KGPQQIHLKAKAIYEKFIQTDAPKEVN 1ngnA 481 :GLYDLRAKTIIKFSDEYLTKQWRYPIE T0302 81 :LDFHTKEVITNSITQ 1ngnA 511 :IGKYGNDSYRIFCVN T0302 96 :PTLHSFDAAQSRVYQLMEQ 1ngnA 532 :PEDHKLNKYHDWLWENHEK Number of specific fragments extracted= 5 number of extra gaps= 0 total=132 Will force an alignment to be made, even if fragment is small Number of alignments=43 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r89A/T0302-1r89A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1r89A expands to /projects/compbio/data/pdb/1r89.pdb.gz 1r89A:# T0302 read from 1r89A/T0302-1r89A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1r89A read from 1r89A/T0302-1r89A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1r89A to template set # found chain 1r89A in template set T0302 5 :PEEA 1r89A 3 :VEEI T0302 12 :GESFDKLLSH 1r89A 7 :LEKALELVIP T0302 22 :RDGLEAFTRFLKT 1r89A 18 :EEEVRKGREAEEE T0302 43 :FWIACEDFK 1r89A 31 :LRRRLDELG T0302 56 :PQQIHLKAKAIYEKFIQ 1r89A 231 :SLDNLARFVHLCREFME T0302 73 :T 1r89A 256 :P T0302 76 :PKEVNLD 1r89A 257 :KHPLEIE T0302 83 :FHTKEVITNS 1r89A 265 :ERLRKIVEER T0302 94 :T 1r89A 275 :G T0302 95 :QPT 1r89A 287 :DIV T0302 98 :LHSFDAAQSRVYQLMEQDSY 1r89A 294 :YPQLERASRKIFEFLERENF Number of specific fragments extracted= 11 number of extra gaps= 0 total=143 Will force an alignment to be made, even if fragment is small Number of alignments=44 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r89A/T0302-1r89A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0302 read from 1r89A/T0302-1r89A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1r89A read from 1r89A/T0302-1r89A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1r89A in template set T0302 4 :SPEEAVK 1r89A 2 :KVEEILE T0302 14 :SFDKLLSH 1r89A 9 :KALELVIP T0302 22 :RDGLEAFTRFLKT 1r89A 18 :EEEVRKGREAEEE T0302 43 :FWIACEDF 1r89A 31 :LRRRLDEL T0302 57 :QQIHLKAKAIYEKFIQ 1r89A 232 :LDNLARFVHLCREFME T0302 73 :TDAPKEVN 1r89A 256 :PKHPLEIE T0302 82 :DFHTKEVITNSI 1r89A 264 :PERLRKIVEERG T0302 95 :QPTLH 1r89A 287 :DIVDD T0302 100 :SFDAAQSRVYQLMEQDSY 1r89A 296 :QLERASRKIFEFLERENF Number of specific fragments extracted= 9 number of extra gaps= 0 total=152 Will force an alignment to be made, even if fragment is small Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r89A/T0302-1r89A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0302 read from 1r89A/T0302-1r89A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1r89A read from 1r89A/T0302-1r89A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1r89A in template set T0302 5 :PEEAV 1r89A 3 :VEEIL T0302 13 :ESFDKLLS 1r89A 8 :EKALELVI T0302 21 :HRDGLEAFTR 1r89A 17 :DEEEVRKGRE T0302 46 :ACEDFKKSKGPQ 1r89A 27 :AEEELRRRLDEL T0302 58 :QIHLKAKAIYEKFIQT 1r89A 233 :DNLARFVHLCREFMEA T0302 74 :DAPKEVNLDFHTKEVITNSITQ 1r89A 255 :KPKHPLEIEPERLRKIVEERGT T0302 96 :PTLHSFDAAQSRVYQLMEQDSY 1r89A 292 :NLYPQLERASRKIFEFLERENF Number of specific fragments extracted= 7 number of extra gaps= 0 total=159 Will force an alignment to be made, even if fragment is small Number of alignments=46 # command:CPU_time= 14.451 sec, elapsed time= 15.635 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 46 Adding 8646 constraints to all_contacts Done adding distance constraints # command:CPU_time= 14.485 sec, elapsed time= 15.673 sec. # command:Reading probabilities from T0302.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 18.972 Optimizing... Probability sum: -197.922, CN propb: -197.922 weights: 0.543 constraints: 154 # command:CPU_time= 15.358 sec, elapsed time= 16.562 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 154 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 154 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 382 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 382 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 7090 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 7090 # command:CPU_time= 15.496 sec, elapsed time= 16.821 sec. # command: