# 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 T0322 numbered 1 through 157 Created new target T0322 from T0322.a2m # command:CPU_time= 6.296 sec, elapsed time= 6.327 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fs2A/T0322-2fs2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2fs2A expands to /projects/compbio/data/pdb/2fs2.pdb.gz 2fs2A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0322 read from 2fs2A/T0322-2fs2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fs2A read from 2fs2A/T0322-2fs2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2fs2A to template set # found chain 2fs2A in template set Warning: unaligning (T0322)F47 because of BadResidue code BAD_PEPTIDE in next template residue (2fs2A)T39 Warning: unaligning (T0322)R48 because of BadResidue code BAD_PEPTIDE at template residue (2fs2A)T39 Warning: unaligning (T0322)C92 because of BadResidue code BAD_PEPTIDE in next template residue (2fs2A)D83 Warning: unaligning (T0322)D93 because of BadResidue code BAD_PEPTIDE at template residue (2fs2A)D83 Warning: unaligning (T0322)G134 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fs2A)R126 Warning: unaligning (T0322)T135 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fs2A)R126 Warning: unaligning (T0322)K139 because of BadResidue code BAD_PEPTIDE in next template residue (2fs2A)R131 Warning: unaligning (T0322)A140 because of BadResidue code BAD_PEPTIDE at template residue (2fs2A)R131 T0322 14 :PEGFSQLN 2fs2A 16 :DACAKALG # choosing archetypes in rotamer library T0322 33 :LFEHREGPGQARLA 2fs2A 24 :IDIISMDEGFAVVT T0322 49 :VEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 2fs2A 40 :VTAQMLNGHQSCHGGQLFSLADTAFAYACNSQ T0322 82 :SYSWVTVRLM 2fs2A 72 :GLAAVASACT T0322 94 :FLSGAKLGDWVEGEGELISEEDMLFTVRGRIWA 2fs2A 84 :FLRPGFAGDTLTATAQVRHQGKQTGVYDIEIVN T0322 127 :GERTLIT 2fs2A 118 :QQKTVAL T0322 136 :GVF 2fs2A 127 :GKS Number of specific fragments extracted= 7 number of extra gaps= 4 total=7 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 2fs2A/T0322-2fs2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 2fs2A/T0322-2fs2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fs2A read from 2fs2A/T0322-2fs2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fs2A in template set Warning: unaligning (T0322)F47 because of BadResidue code BAD_PEPTIDE in next template residue (2fs2A)T39 Warning: unaligning (T0322)R48 because of BadResidue code BAD_PEPTIDE at template residue (2fs2A)T39 Warning: unaligning (T0322)C92 because of BadResidue code BAD_PEPTIDE in next template residue (2fs2A)D83 Warning: unaligning (T0322)D93 because of BadResidue code BAD_PEPTIDE at template residue (2fs2A)D83 Warning: unaligning (T0322)G134 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fs2A)R126 Warning: unaligning (T0322)T135 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fs2A)R126 Warning: unaligning (T0322)K139 because of BadResidue code BAD_PEPTIDE in next template residue (2fs2A)R131 Warning: unaligning (T0322)A140 because of BadResidue code BAD_PEPTIDE at template residue (2fs2A)R131 T0322 25 :GFGRQIG 2fs2A 17 :ACAKALG T0322 33 :LFEHREGPGQARLA 2fs2A 24 :IDIISMDEGFAVVT T0322 49 :VEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 2fs2A 40 :VTAQMLNGHQSCHGGQLFSLADTAFAYACNSQ T0322 82 :SYSWVTVRLM 2fs2A 72 :GLAAVASACT T0322 94 :FLSGAKLGDWVEGEGELISEEDMLFTVRGRIWA 2fs2A 84 :FLRPGFAGDTLTATAQVRHQGKQTGVYDIEIVN T0322 127 :GERTLIT 2fs2A 118 :QQKTVAL T0322 136 :GVF 2fs2A 127 :GKS Number of specific fragments extracted= 7 number of extra gaps= 4 total=14 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 2fs2A/T0322-2fs2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 2fs2A/T0322-2fs2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fs2A read from 2fs2A/T0322-2fs2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2fs2A in template set Warning: unaligning (T0322)T10 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fs2A)L1 Warning: unaligning (T0322)F47 because of BadResidue code BAD_PEPTIDE in next template residue (2fs2A)T39 Warning: unaligning (T0322)R48 because of BadResidue code BAD_PEPTIDE at template residue (2fs2A)T39 Warning: unaligning (T0322)C92 because of BadResidue code BAD_PEPTIDE in next template residue (2fs2A)D83 Warning: unaligning (T0322)D93 because of BadResidue code BAD_PEPTIDE at template residue (2fs2A)D83 Warning: unaligning (T0322)T135 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fs2A)R126 Warning: unaligning (T0322)G136 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fs2A)R126 Warning: unaligning (T0322)A140 because of BadResidue code BAD_PEPTIDE in next template residue (2fs2A)R131 Warning: unaligning (T0322)L141 because of BadResidue code BAD_PEPTIDE at template residue (2fs2A)R131 T0322 11 :AAIPEGFSQLNWSRGFGRQIGPLFEHREGPGQARLA 2fs2A 2 :SHKAWQNAHAMYENDACAKALGIDIISMDEGFAVVT T0322 49 :VEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 2fs2A 40 :VTAQMLNGHQSCHGGQLFSLADTAFAYACNSQ T0322 82 :SYSWVTVRLM 2fs2A 72 :GLAAVASACT T0322 94 :FLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITG 2fs2A 84 :FLRPGFAGDTLTATAQVRHQGKQTGVYDIEIVNQQQKTVAL T0322 137 :VFK 2fs2A 127 :GKS Number of specific fragments extracted= 5 number of extra gaps= 5 total=19 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 1zkiA/T0322-1zkiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1zkiA expands to /projects/compbio/data/pdb/1zki.pdb.gz 1zkiA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 33, because occupancy 0.5 <= existing 0.500 in 1zkiA Skipped atom 35, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 37, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 39, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 41, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 43, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 45, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 47, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 49, because occupancy 0.500 <= existing 0.500 in 1zkiA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 141, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 143, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 145, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 147, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 149, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 151, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 153, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 155, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 201, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 203, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 205, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 207, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 209, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 211, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 213, because occupancy 0.500 <= existing 0.500 in 1zkiA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 299, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 303, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 305, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 307, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 309, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 311, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 313, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 315, because occupancy 0.500 <= existing 0.500 in 1zkiA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 528, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 532, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 534, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 536, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 538, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 540, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 542, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 544, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 754, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 756, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 758, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 760, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 762, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 764, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 766, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 768, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 770, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 772, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 887, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 889, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 891, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 893, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 895, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 897, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 899, because occupancy 0.500 <= existing 0.500 in 1zkiA Skipped atom 901, because occupancy 0.500 <= existing 0.500 in 1zkiA # T0322 read from 1zkiA/T0322-1zkiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zkiA read from 1zkiA/T0322-1zkiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1zkiA to template set # found chain 1zkiA in template set Warning: unaligning (T0322)D4 because first residue in template chain is (1zkiA)M4 Warning: unaligning (T0322)L141 because last residue in template chain is (1zkiA)L129 T0322 5 :LTDAQTAA 1zkiA 5 :PAREQMIS T0322 15 :EGFSQLN 1zkiA 13 :AYSELVG T0322 33 :LFEHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 1zkiA 20 :LDPVSLGDGVAEVRLPMAAHLRNRGGVMHGGALFSLMDVTMGLACSSS T0322 81 :KSYSWVTVRLMCDFLSGAK 1zkiA 70 :FDRQSVTLECKINYIRAVA T0322 101 :GDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKA 1zkiA 89 :DGEVRCVARVLHAGRRSLVVEAEVRQGDKLVAKGQGTFAQ Number of specific fragments extracted= 5 number of extra gaps= 0 total=24 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 1zkiA/T0322-1zkiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 1zkiA/T0322-1zkiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zkiA read from 1zkiA/T0322-1zkiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zkiA in template set Warning: unaligning (T0322)T6 because first residue in template chain is (1zkiA)M4 Warning: unaligning (T0322)L141 because last residue in template chain is (1zkiA)L129 T0322 7 :DAQTAAIPEGF 1zkiA 5 :PAREQMISAYS T0322 28 :RQIG 1zkiA 16 :ELVG T0322 33 :LFEHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQKSY 1zkiA 20 :LDPVSLGDGVAEVRLPMAAHLRNRGGVMHGGALFSLMDVTMGLACSSSHGF T0322 84 :SWVTVRLMCDFLSGAK 1zkiA 73 :QSVTLECKINYIRAVA T0322 101 :GDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKA 1zkiA 89 :DGEVRCVARVLHAGRRSLVVEAEVRQGDKLVAKGQGTFAQ Number of specific fragments extracted= 5 number of extra gaps= 0 total=29 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 1zkiA/T0322-1zkiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 1zkiA/T0322-1zkiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zkiA read from 1zkiA/T0322-1zkiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zkiA in template set T0322 26 :FGRQIGPLFEHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQK 1zkiA 13 :AYSELVGLDPVSLGDGVAEVRLPMAAHLRNRGGVMHGGALFSLMDVTMGLACSSSH T0322 82 :SYSWVTVRLMCDFLSGAK 1zkiA 71 :DRQSVTLECKINYIRAVA T0322 101 :GDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKA 1zkiA 89 :DGEVRCVARVLHAGRRSLVVEAEVRQGDKLVAKGQGTFAQ Number of specific fragments extracted= 3 number of extra gaps= 0 total=32 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 1wluA/T0322-1wluA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1wluA expands to /projects/compbio/data/pdb/1wlu.pdb.gz 1wluA:# T0322 read from 1wluA/T0322-1wluA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wluA read from 1wluA/T0322-1wluA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1wluA to template set # found chain 1wluA in template set Warning: unaligning (T0322)L141 because last residue in template chain is (1wluA)L117 T0322 23 :SRGFGRQIG 1wluA 2 :RDPFMEALG T0322 33 :LFEHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 1wluA 11 :LKVLHLAPGEAVVAGEVRADHLNLHGTAHGGFLYALADSAFALASNTR T0322 83 :YSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKA 1wluA 59 :GPAVALSCRMDYFRPLGAGARVEARAVEVNLSRRTATYRVEVVSEGKLVALFTGTVFR Number of specific fragments extracted= 3 number of extra gaps= 0 total=35 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 1wluA/T0322-1wluA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 1wluA/T0322-1wluA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wluA read from 1wluA/T0322-1wluA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wluA in template set Warning: unaligning (T0322)L141 because last residue in template chain is (1wluA)L117 T0322 23 :SRGFGRQIG 1wluA 2 :RDPFMEALG T0322 33 :LFEHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISL 1wluA 11 :LKVLHLAPGEAVVAGEVRADHLNLHGTAHGGFLYALADSAFALASNT T0322 82 :SYSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKA 1wluA 58 :RGPAVALSCRMDYFRPLGAGARVEARAVEVNLSRRTATYRVEVVSEGKLVALFTGTVFR Number of specific fragments extracted= 3 number of extra gaps= 0 total=38 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 1wluA/T0322-1wluA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 1wluA/T0322-1wluA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wluA read from 1wluA/T0322-1wluA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wluA in template set Warning: unaligning (T0322)L141 because last residue in template chain is (1wluA)L117 T0322 24 :RGFGRQIGPLFEHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 1wluA 2 :RDPFMEALGLKVLHLAPGEAVVAGEVRADHLNLHGTAHGGFLYALADSAFALASNTR T0322 83 :YSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKA 1wluA 59 :GPAVALSCRMDYFRPLGAGARVEARAVEVNLSRRTATYRVEVVSEGKLVALFTGTVFR Number of specific fragments extracted= 2 number of extra gaps= 0 total=40 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 1o0iA/T0322-1o0iA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1o0iA expands to /projects/compbio/data/pdb/1o0i.pdb.gz 1o0iA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0322 read from 1o0iA/T0322-1o0iA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o0iA read from 1o0iA/T0322-1o0iA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1o0iA to template set # found chain 1o0iA in template set Warning: unaligning (T0322)T6 because first residue in template chain is (1o0iA)L2 Warning: unaligning (T0322)A143 because last residue in template chain is (1o0iA)L138 T0322 7 :DAQTAAIPEGFSQLN 1o0iA 3 :WKKTFTLENLNQLCS T0322 24 :RGFGRQIG 1o0iA 18 :NSAVSHLG T0322 33 :LFEHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 1o0iA 26 :IEISAFGEDWIEATMPVDHRTMQPFGVLHGGVSVALAETIGSLAGSLC T0322 81 :KSYSWVTVRLMCDFLSGAKLG 1o0iA 76 :EGKTVVGLDINANHLRPVRSG T0322 103 :WVEGEGELISEEDMLFTVRGRIWA 1o0iA 97 :KVTARATPINLGRNIQVWQIDIRT T0322 127 :GERTLITGTGVFKALS 1o0iA 122 :ENKLCCVSRLTLSVIN Number of specific fragments extracted= 6 number of extra gaps= 0 total=46 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 1o0iA/T0322-1o0iA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 1o0iA/T0322-1o0iA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o0iA read from 1o0iA/T0322-1o0iA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1o0iA in template set Warning: unaligning (T0322)A143 because last residue in template chain is (1o0iA)L138 T0322 19 :QLNW 1o0iA 14 :QLCS T0322 24 :RGFGRQIG 1o0iA 18 :NSAVSHLG T0322 33 :LFEHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQKSY 1o0iA 26 :IEISAFGEDWIEATMPVDHRTMQPFGVLHGGVSVALAETIGSLAGSLCLEE T0322 84 :SWVTVRLMCDFLSGAKLG 1o0iA 79 :TVVGLDINANHLRPVRSG T0322 103 :WVEGEGELISEEDMLFTVRGRIWA 1o0iA 97 :KVTARATPINLGRNIQVWQIDIRT T0322 127 :GERTLITGTGVFKALS 1o0iA 122 :ENKLCCVSRLTLSVIN Number of specific fragments extracted= 6 number of extra gaps= 0 total=52 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 1o0iA/T0322-1o0iA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 1o0iA/T0322-1o0iA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1o0iA read from 1o0iA/T0322-1o0iA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1o0iA in template set T0322 7 :DAQTAAIPEGF 1o0iA 6 :TFTLENLNQLC T0322 24 :RGFGRQIGPLFEHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQK 1o0iA 17 :SNSAVSHLGIEISAFGEDWIEATMPVDHRTMQPFGVLHGGVSVALAETIGSLAGSLCL T0322 82 :SYSWVTVRLMCDFLSGAK 1o0iA 77 :GKTVVGLDINANHLRPVR T0322 101 :GDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKALSA 1o0iA 95 :SGKVTARATPINLGRNIQVWQIDIRTEENKLCCVSRLTLSVIN Number of specific fragments extracted= 4 number of extra gaps= 0 total=56 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 1vh5A/T0322-1vh5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vh5A expands to /projects/compbio/data/pdb/1vh5.pdb.gz 1vh5A:Skipped atom 216, because occupancy 0.500 <= existing 0.500 in 1vh5A Skipped atom 218, because occupancy 0.500 <= existing 0.500 in 1vh5A Skipped atom 220, because occupancy 0.500 <= existing 0.500 in 1vh5A Skipped atom 222, because occupancy 0.500 <= existing 0.500 in 1vh5A Skipped atom 224, because occupancy 0.500 <= existing 0.500 in 1vh5A Skipped atom 226, because occupancy 0.500 <= existing 0.500 in 1vh5A Skipped atom 228, because occupancy 0.500 <= existing 0.500 in 1vh5A Skipped atom 521, because occupancy 0.350 <= existing 0.650 in 1vh5A Skipped atom 523, because occupancy 0.350 <= existing 0.650 in 1vh5A Skipped atom 529, because occupancy 0.350 <= existing 0.650 in 1vh5A Skipped atom 531, because occupancy 0.350 <= existing 0.650 in 1vh5A Skipped atom 533, because occupancy 0.350 <= existing 0.650 in 1vh5A Skipped atom 628, because occupancy 0.350 <= existing 0.650 in 1vh5A Skipped atom 630, because occupancy 0.350 <= existing 0.650 in 1vh5A Skipped atom 632, because occupancy 0.350 <= existing 0.650 in 1vh5A Skipped atom 1012, because occupancy 0.350 <= existing 0.650 in 1vh5A Skipped atom 1014, because occupancy 0.350 <= existing 0.650 in 1vh5A # T0322 read from 1vh5A/T0322-1vh5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vh5A read from 1vh5A/T0322-1vh5A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vh5A to template set # found chain 1vh5A in template set Warning: unaligning (T0322)S2 because first residue in template chain is (1vh5A)S0 Warning: unaligning (T0322)S142 because last residue in template chain is (1vh5A)E137 T0322 3 :DDLTD 1vh5A 1 :LIWKR T0322 10 :TAAIPEGFSQLN 1vh5A 6 :KITLEALNAMGE T0322 24 :RGFGRQIG 1vh5A 18 :GNMVGFLD T0322 33 :LFEHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 1vh5A 26 :IRFEHIGDDTLEATMPVDSRTKQPFGLLHGGASVVLAESIGSVAGYLC T0322 81 :KSYSWVTVRLMCDFLSGAKLG 1vh5A 76 :GEQKVVGLEINANHVRSAREG T0322 103 :WVEGEGELISEEDMLFTVRGRIWAG 1vh5A 97 :RVRGVCKPLHLGSRHQVWQIEIFDE T0322 128 :ERTLITGTGVFKAL 1vh5A 123 :GRLCCSSRLTTAIL Number of specific fragments extracted= 7 number of extra gaps= 0 total=63 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 1vh5A/T0322-1vh5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 1vh5A/T0322-1vh5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vh5A read from 1vh5A/T0322-1vh5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vh5A in template set Warning: unaligning (T0322)S142 because last residue in template chain is (1vh5A)E137 T0322 16 :GFSQLNW 1vh5A 11 :ALNAMGE T0322 24 :RGFGRQIG 1vh5A 18 :GNMVGFLD T0322 33 :LFEHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQKSY 1vh5A 26 :IRFEHIGDDTLEATMPVDSRTKQPFGLLHGGASVVLAESIGSVAGYLCTEG T0322 84 :SWVTVRLMCDFLSGAKLG 1vh5A 79 :KVVGLEINANHVRSAREG T0322 103 :WVEGEGELISEEDMLFTVRGRIWA 1vh5A 97 :RVRGVCKPLHLGSRHQVWQIEIFD T0322 127 :GERTLITGTGVFKAL 1vh5A 122 :KGRLCCSSRLTTAIL Number of specific fragments extracted= 6 number of extra gaps= 0 total=69 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 1vh5A/T0322-1vh5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 1vh5A/T0322-1vh5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vh5A read from 1vh5A/T0322-1vh5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vh5A in template set Warning: unaligning (T0322)A143 because last residue in template chain is (1vh5A)E137 T0322 22 :WSRGFGRQIGPLFEHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQK 1vh5A 15 :MGEGNMVGFLDIRFEHIGDDTLEATMPVDSRTKQPFGLLHGGASVVLAESIGSVAGYLCT T0322 82 :SYSWVTVRLMCDFLSGAK 1vh5A 77 :EQKVVGLEINANHVRSAR T0322 101 :GDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKALS 1vh5A 95 :EGRVRGVCKPLHLGSRHQVWQIEIFDEKGRLCCSSRLTTAIL Number of specific fragments extracted= 3 number of extra gaps= 0 total=72 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 1j1yA/T0322-1j1yA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1j1yA expands to /projects/compbio/data/pdb/1j1y.pdb.gz 1j1yA:# T0322 read from 1j1yA/T0322-1j1yA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j1yA read from 1j1yA/T0322-1j1yA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1j1yA to template set # found chain 1j1yA in template set Warning: unaligning (T0322)S23 because first residue in template chain is (1j1yA)R2 Warning: unaligning (T0322)L141 because last residue in template chain is (1j1yA)L117 T0322 24 :RGFGRQIG 1j1yA 3 :DPFMEALG T0322 33 :LFEHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 1j1yA 11 :LKVLHLAPGEAVVAGEVRADHLNLHGTAHGGFLYALADSAFALASNTR T0322 83 :YSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKA 1j1yA 59 :GPAVALSCRMDYFRPLGAGARVEARAVEVNLSRRTATYRVEVVSEGKLVALFTGTVFR Number of specific fragments extracted= 3 number of extra gaps= 0 total=75 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 1j1yA/T0322-1j1yA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 1j1yA/T0322-1j1yA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j1yA read from 1j1yA/T0322-1j1yA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1j1yA in template set Warning: unaligning (T0322)S23 because first residue in template chain is (1j1yA)R2 Warning: unaligning (T0322)L141 because last residue in template chain is (1j1yA)L117 T0322 24 :RGFGRQIG 1j1yA 3 :DPFMEALG T0322 33 :LFEHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISL 1j1yA 11 :LKVLHLAPGEAVVAGEVRADHLNLHGTAHGGFLYALADSAFALASNT T0322 82 :SYSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKA 1j1yA 58 :RGPAVALSCRMDYFRPLGAGARVEARAVEVNLSRRTATYRVEVVSEGKLVALFTGTVFR Number of specific fragments extracted= 3 number of extra gaps= 0 total=78 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 1j1yA/T0322-1j1yA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 1j1yA/T0322-1j1yA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j1yA read from 1j1yA/T0322-1j1yA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1j1yA in template set Warning: unaligning (T0322)R24 because first residue in template chain is (1j1yA)R2 Warning: unaligning (T0322)L141 because last residue in template chain is (1j1yA)L117 T0322 25 :GFGRQIGPLFEHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 1j1yA 3 :DPFMEALGLKVLHLAPGEAVVAGEVRADHLNLHGTAHGGFLYALADSAFALASNTR T0322 83 :YSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKA 1j1yA 59 :GPAVALSCRMDYFRPLGAGARVEARAVEVNLSRRTATYRVEVVSEGKLVALFTGTVFR Number of specific fragments extracted= 2 number of extra gaps= 0 total=80 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 1yliA/T0322-1yliA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1yliA expands to /projects/compbio/data/pdb/1yli.pdb.gz 1yliA:Skipped atom 122, because occupancy 0.500 <= existing 0.500 in 1yliA Skipped atom 124, because occupancy 0.500 <= existing 0.500 in 1yliA Skipped atom 588, because occupancy 0.500 <= existing 0.500 in 1yliA Skipped atom 590, because occupancy 0.500 <= existing 0.500 in 1yliA Skipped atom 592, because occupancy 0.500 <= existing 0.500 in 1yliA Skipped atom 594, because occupancy 0.500 <= existing 0.500 in 1yliA Skipped atom 596, because occupancy 0.500 <= existing 0.500 in 1yliA Skipped atom 598, because occupancy 0.500 <= existing 0.500 in 1yliA Skipped atom 600, because occupancy 0.500 <= existing 0.500 in 1yliA # T0322 read from 1yliA/T0322-1yliA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yliA read from 1yliA/T0322-1yliA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1yliA to template set # found chain 1yliA in template set Warning: unaligning (T0322)A46 because of BadResidue code BAD_PEPTIDE in next template residue (1yliA)T21 Warning: unaligning (T0322)F47 because of BadResidue code BAD_PEPTIDE at template residue (1yliA)T21 T0322 41 :GQARL 1yliA 15 :GVLLL T0322 48 :RVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQKSYSWVTVRLM 1yliA 22 :LAMPSDTNANGDIFGGWIMSQMDMGGAILAKEIAHGRVVTVAVE T0322 92 :CDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIW 1yliA 67 :MNFIKPISVGDVVCCYGQCLKVGRSSIKIKVEVW T0322 126 :AG 1yliA 106 :SE T0322 128 :E 1yliA 110 :G T0322 130 :TLITGTGVFKALSARKPR 1yliA 114 :CVTDAVFTFVAVDNNGRS T0322 149 :GELAYKE 1yliA 132 :RTIPREN Number of specific fragments extracted= 7 number of extra gaps= 1 total=87 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 1yliA/T0322-1yliA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 1yliA/T0322-1yliA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yliA read from 1yliA/T0322-1yliA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yliA in template set Warning: unaligning (T0322)A46 because of BadResidue code BAD_PEPTIDE in next template residue (1yliA)T21 Warning: unaligning (T0322)F47 because of BadResidue code BAD_PEPTIDE at template residue (1yliA)T21 T0322 40 :PGQARL 1yliA 14 :KGVLLL T0322 48 :RVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQKSYSWVTVRLM 1yliA 22 :LAMPSDTNANGDIFGGWIMSQMDMGGAILAKEIAHGRVVTVAVE T0322 92 :CDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWA 1yliA 67 :MNFIKPISVGDVVCCYGQCLKVGRSSIKIKVEVWV T0322 127 :G 1yliA 107 :E T0322 128 :ER 1yliA 110 :GE T0322 130 :TLITGTGVFKALSARKPRP 1yliA 114 :CVTDAVFTFVAVDNNGRSR T0322 149 :GELA 1yliA 140 :QELE Number of specific fragments extracted= 7 number of extra gaps= 1 total=94 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 1yliA/T0322-1yliA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 1yliA/T0322-1yliA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yliA read from 1yliA/T0322-1yliA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yliA in template set Warning: unaligning (T0322)A46 because of BadResidue code BAD_PEPTIDE in next template residue (1yliA)T21 Warning: unaligning (T0322)F47 because of BadResidue code BAD_PEPTIDE at template residue (1yliA)T21 T0322 40 :PGQARL 1yliA 14 :KGVLLL T0322 48 :RVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQKSYSWVTVRLM 1yliA 22 :LAMPSDTNANGDIFGGWIMSQMDMGGAILAKEIAHGRVVTVAVE T0322 92 :CDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWA 1yliA 67 :MNFIKPISVGDVVCCYGQCLKVGRSSIKIKVEVWV T0322 127 :GERTLITGTGVFKALSARK 1yliA 110 :GERYCVTDAVFTFVAVDNN T0322 146 :PRPGELAYKE 1yliA 135 :PRENNQELEK Number of specific fragments extracted= 5 number of extra gaps= 1 total=99 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 1vpmA/T0322-1vpmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vpmA expands to /projects/compbio/data/pdb/1vpm.pdb.gz 1vpmA:Skipped atom 82, because occupancy 0.350 <= existing 0.650 in 1vpmA Skipped atom 84, because occupancy 0.350 <= existing 0.650 in 1vpmA Skipped atom 86, because occupancy 0.350 <= existing 0.650 in 1vpmA Skipped atom 88, because occupancy 0.350 <= existing 0.650 in 1vpmA Skipped atom 90, because occupancy 0.350 <= existing 0.650 in 1vpmA Skipped atom 92, because occupancy 0.350 <= existing 0.650 in 1vpmA Skipped atom 313, because occupancy 0.350 <= existing 0.650 in 1vpmA Skipped atom 315, because occupancy 0.350 <= existing 0.650 in 1vpmA Skipped atom 317, because occupancy 0.350 <= existing 0.650 in 1vpmA Skipped atom 319, because occupancy 0.350 <= existing 0.650 in 1vpmA Skipped atom 321, because occupancy 0.350 <= existing 0.650 in 1vpmA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 405, because occupancy 0.350 <= existing 0.650 in 1vpmA Skipped atom 407, because occupancy 0.350 <= existing 0.650 in 1vpmA Skipped atom 466, because occupancy 0.350 <= existing 0.650 in 1vpmA Skipped atom 468, because occupancy 0.350 <= existing 0.650 in 1vpmA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1002, because occupancy 0.350 <= existing 0.650 in 1vpmA Skipped atom 1004, because occupancy 0.350 <= existing 0.650 in 1vpmA Skipped atom 1006, because occupancy 0.350 <= existing 0.650 in 1vpmA Skipped atom 1008, because occupancy 0.350 <= existing 0.650 in 1vpmA Skipped atom 1010, because occupancy 0.350 <= existing 0.650 in 1vpmA Skipped atom 1165, because occupancy 0.350 <= existing 0.650 in 1vpmA Skipped atom 1167, because occupancy 0.350 <= existing 0.650 in 1vpmA Skipped atom 1169, because occupancy 0.350 <= existing 0.650 in 1vpmA Skipped atom 1171, because occupancy 0.350 <= existing 0.650 in 1vpmA # T0322 read from 1vpmA/T0322-1vpmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vpmA read from 1vpmA/T0322-1vpmA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vpmA to template set # found chain 1vpmA in template set Warning: unaligning (T0322)Y83 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1vpmA)A53 Warning: unaligning (T0322)S84 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1vpmA)A53 T0322 37 :REGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQKS 1vpmA 6 :PVERSRTIQTRLVLPPDTNHLGTIFGGKVLAYIDEIAALTAMKHAN T0322 85 :WVTVRLM 1vpmA 54 :VVTASID T0322 92 :CDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWA 1vpmA 62 :VDFKSSATVGDALELEGFVTHTGRTSMEVYVRVHS T0322 127 :G 1vpmA 100 :L T0322 128 :E 1vpmA 102 :G T0322 129 :RTLITGTGVFKALSARKPR 1vpmA 105 :TLTTESFLTMVAVDESGKP T0322 148 :PGEL 1vpmA 125 :PVPQ Number of specific fragments extracted= 7 number of extra gaps= 1 total=106 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 1vpmA/T0322-1vpmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 1vpmA/T0322-1vpmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vpmA read from 1vpmA/T0322-1vpmA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vpmA in template set Warning: unaligning (T0322)Y83 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1vpmA)A53 Warning: unaligning (T0322)S84 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1vpmA)A53 T0322 35 :EHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQKS 1vpmA 4 :SYPVERSRTIQTRLVLPPDTNHLGTIFGGKVLAYIDEIAALTAMKHAN T0322 85 :WVTVRLM 1vpmA 54 :VVTASID T0322 92 :CDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWA 1vpmA 62 :VDFKSSATVGDALELEGFVTHTGRTSMEVYVRVHS T0322 127 :GE 1vpmA 101 :TG T0322 129 :RTLITGTGVFKALSARKPRP 1vpmA 105 :TLTTESFLTMVAVDESGKPK T0322 149 :GELAYK 1vpmA 134 :EEEKRL Number of specific fragments extracted= 6 number of extra gaps= 1 total=112 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 1vpmA/T0322-1vpmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 1vpmA/T0322-1vpmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vpmA read from 1vpmA/T0322-1vpmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vpmA in template set Warning: unaligning (T0322)Y83 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1vpmA)A53 Warning: unaligning (T0322)S84 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1vpmA)A53 T0322 41 :GQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQKS 1vpmA 10 :SRTIQTRLVLPPDTNHLGTIFGGKVLAYIDEIAALTAMKHAN T0322 85 :WVTVRLM 1vpmA 54 :VVTASID T0322 92 :CDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIW 1vpmA 62 :VDFKSSATVGDALELEGFVTHTGRTSMEVYVRVH T0322 126 :AGERTLITGTGVFKALSARKPR 1vpmA 101 :TGERTLTTESFLTMVAVDESGK Number of specific fragments extracted= 4 number of extra gaps= 1 total=116 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 1q4uA/T0322-1q4uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1q4uA expands to /projects/compbio/data/pdb/1q4u.pdb.gz 1q4uA:Skipped atom 148, because occupancy 0.500 <= existing 0.500 in 1q4uA Skipped atom 150, because occupancy 0.500 <= existing 0.500 in 1q4uA Skipped atom 152, because occupancy 0.500 <= existing 0.500 in 1q4uA Skipped atom 154, because occupancy 0.500 <= existing 0.500 in 1q4uA Skipped atom 622, because occupancy 0.500 <= existing 0.500 in 1q4uA Skipped atom 624, because occupancy 0.500 <= existing 0.500 in 1q4uA Skipped atom 626, because occupancy 0.500 <= existing 0.500 in 1q4uA Skipped atom 628, because occupancy 0.500 <= existing 0.500 in 1q4uA Skipped atom 630, because occupancy 0.500 <= existing 0.500 in 1q4uA Skipped atom 720, because occupancy 0.500 <= existing 0.500 in 1q4uA Skipped atom 722, because occupancy 0.500 <= existing 0.500 in 1q4uA Skipped atom 724, because occupancy 0.500 <= existing 0.500 in 1q4uA Skipped atom 726, because occupancy 0.500 <= existing 0.500 in 1q4uA Skipped atom 728, because occupancy 0.500 <= existing 0.500 in 1q4uA Skipped atom 913, because occupancy 0.500 <= existing 0.500 in 1q4uA Skipped atom 915, because occupancy 0.500 <= existing 0.500 in 1q4uA # T0322 read from 1q4uA/T0322-1q4uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1q4uA read from 1q4uA/T0322-1q4uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1q4uA to template set # found chain 1q4uA in template set Warning: unaligning (T0322)R144 because last residue in template chain is (1q4uA)R150 T0322 6 :TDAQ 1q4uA 19 :ASHY T0322 23 :SRGFGRQI 1q4uA 23 :PVAYEQTL T0322 31 :G 1q4uA 35 :G T0322 33 :LFEHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 1q4uA 36 :FVIDEMTPERATASVEVTDTLRQRWGLVHGGAYCALAEMLATEATVAV T0322 81 :KSYSWVTVRLMCDFLSGAKLG 1q4uA 87 :KGMMAVGQSNHTSFFRPVKEG T0322 103 :WVEGEGELISEEDMLFTVRGRIWAG 1q4uA 108 :HVRAEAVRIHAGSTTWFWDVSLRDD T0322 128 :ERTLITGTGVFKALSA 1q4uA 134 :GRLCAVSSMSIAVRPR Number of specific fragments extracted= 7 number of extra gaps= 0 total=123 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 1q4uA/T0322-1q4uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 1q4uA/T0322-1q4uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1q4uA read from 1q4uA/T0322-1q4uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1q4uA in template set Warning: unaligning (T0322)R144 because last residue in template chain is (1q4uA)R150 T0322 3 :DDLTDAQ 1q4uA 13 :GNLPDVA T0322 11 :AAIPEGFSQLNW 1q4uA 20 :SHYPVAYEQTLD T0322 28 :RQIG 1q4uA 32 :GTVG T0322 33 :LFEHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQKSY 1q4uA 36 :FVIDEMTPERATASVEVTDTLRQRWGLVHGGAYCALAEMLATEATVAVVHE T0322 84 :SWVTVRLMCDFLSGAKLG 1q4uA 90 :MAVGQSNHTSFFRPVKEG T0322 103 :WVEGEGELISEEDMLFTVRGRIWAG 1q4uA 108 :HVRAEAVRIHAGSTTWFWDVSLRDD T0322 128 :ERTLITGTGVFKALSA 1q4uA 134 :GRLCAVSSMSIAVRPR Number of specific fragments extracted= 7 number of extra gaps= 0 total=130 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 1q4uA/T0322-1q4uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 1q4uA/T0322-1q4uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1q4uA read from 1q4uA/T0322-1q4uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1q4uA in template set Warning: unaligning (T0322)K145 because last residue in template chain is (1q4uA)R150 T0322 7 :DAQTAAIPEG 1q4uA 23 :PVAYEQTLDG T0322 30 :IGPLFEHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQK 1q4uA 33 :TVGFVIDEMTPERATASVEVTDTLRQRWGLVHGGAYCALAEMLATEATVAVV T0322 82 :SYSWVTVRLMCDFLSGAKLG 1q4uA 88 :GMMAVGQSNHTSFFRPVKEG T0322 103 :WVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKALSAR 1q4uA 108 :HVRAEAVRIHAGSTTWFWDVSLRDDAGRLCAVSSMSIAVRPR Number of specific fragments extracted= 4 number of extra gaps= 0 total=134 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 1ixlA/T0322-1ixlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ixlA expands to /projects/compbio/data/pdb/1ixl.pdb.gz 1ixlA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0322 read from 1ixlA/T0322-1ixlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ixlA read from 1ixlA/T0322-1ixlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ixlA to template set # found chain 1ixlA in template set Warning: unaligning (T0322)R147 because last residue in template chain is (1ixlA)D130 T0322 4 :DLTDAQT 1ixlA 11 :LTSRILV T0322 33 :LFEHREGPGQARLAFRVEEHH 1ixlA 18 :GKPILIKEGYAEVELETIDEM T0322 54 :TNGLGNCHGGMLMSFADMAWGRIIS 1ixlA 40 :VDEKGLVHGGFTFGLADYAAMLAVN T0322 82 :SYSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKALSARKP 1ixlA 65 :EPTVVLGKAEVRFTKPVKVGDKLVAKAKIIEDLGKKKIVEVKVYREEEVVLEGKFYCYVLEKHVL Number of specific fragments extracted= 4 number of extra gaps= 0 total=138 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 1ixlA/T0322-1ixlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 1ixlA/T0322-1ixlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ixlA read from 1ixlA/T0322-1ixlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ixlA in template set Warning: unaligning (T0322)R147 because last residue in template chain is (1ixlA)D130 T0322 15 :EGFSQLNW 1ixlA 10 :KLTSRILV T0322 33 :LFEHREGPGQARLAFRVEEHHT 1ixlA 18 :GKPILIKEGYAEVELETIDEMK T0322 55 :NGLGNCHGGMLMSFADMAWGRIIS 1ixlA 41 :DEKGLVHGGFTFGLADYAAMLAVN T0322 82 :SYSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKALSARKP 1ixlA 65 :EPTVVLGKAEVRFTKPVKVGDKLVAKAKIIEDLGKKKIVEVKVYREEEVVLEGKFYCYVLEKHVL Number of specific fragments extracted= 4 number of extra gaps= 0 total=142 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 1ixlA/T0322-1ixlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 1ixlA/T0322-1ixlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ixlA read from 1ixlA/T0322-1ixlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ixlA in template set T0322 33 :LFEHREGPGQARLAFRVEEHHT 1ixlA 18 :GKPILIKEGYAEVELETIDEMK T0322 55 :NGLGNCHGGMLMSFADMAWGRIISLQ 1ixlA 41 :DEKGLVHGGFTFGLADYAAMLAVNEP T0322 84 :SWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKALSAR 1ixlA 67 :TVVLGKAEVRFTKPVKVGDKLVAKAKIIEDLGKKKIVEVKVYREEEVVLEGKFYCYVLEKH Number of specific fragments extracted= 3 number of extra gaps= 0 total=145 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 1psuA/T0322-1psuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1psuA expands to /projects/compbio/data/pdb/1psu.pdb.gz 1psuA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0322 read from 1psuA/T0322-1psuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1psuA read from 1psuA/T0322-1psuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1psuA to template set # found chain 1psuA in template set Warning: unaligning (T0322)A140 because last residue in template chain is (1psuA)R131 T0322 14 :PEGFSQLN 1psuA 16 :DACAKALG T0322 33 :LFEHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 1psuA 24 :IDIISMDEGFAVVTMTVTAQMLNGHQSCHGGQLFSLADTAFAYACNSQ T0322 82 :SYSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWA 1psuA 72 :GLAAVASACTIDFLRPGFAGDTLTATAQVRHQGKQTGVYDIEIVN T0322 127 :GERTLITGTGVFK 1psuA 118 :QQKTVALFRGKSH Number of specific fragments extracted= 4 number of extra gaps= 0 total=149 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 1psuA/T0322-1psuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 1psuA/T0322-1psuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1psuA read from 1psuA/T0322-1psuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1psuA in template set Warning: unaligning (T0322)A140 because last residue in template chain is (1psuA)R131 T0322 21 :NWSRGFGRQIG 1psuA 13 :YENDACAKALG T0322 33 :LFEHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 1psuA 24 :IDIISMDEGFAVVTMTVTAQMLNGHQSCHGGQLFSLADTAFAYACNSQ T0322 82 :SYSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWA 1psuA 72 :GLAAVASACTIDFLRPGFAGDTLTATAQVRHQGKQTGVYDIEIVN T0322 127 :GERTLITGTGVFK 1psuA 118 :QQKTVALFRGKSH Number of specific fragments extracted= 4 number of extra gaps= 0 total=153 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 1psuA/T0322-1psuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 1psuA/T0322-1psuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1psuA read from 1psuA/T0322-1psuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1psuA in template set Warning: unaligning (T0322)L141 because last residue in template chain is (1psuA)R131 T0322 12 :AIPEGFSQLNWSRGFGRQIGPLFEHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 1psuA 3 :HKAWQNAHAMYENDACAKALGIDIISMDEGFAVVTMTVTAQMLNGHQSCHGGQLFSLADTAFAYACNSQ T0322 82 :SYSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKA 1psuA 72 :GLAAVASACTIDFLRPGFAGDTLTATAQVRHQGKQTGVYDIEIVNQQQKTVALFRGKSH Number of specific fragments extracted= 2 number of extra gaps= 0 total=155 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 1yocA/T0322-1yocA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1yocA expands to /projects/compbio/data/pdb/1yoc.pdb.gz 1yocA:# T0322 read from 1yocA/T0322-1yocA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yocA read from 1yocA/T0322-1yocA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1yocA to template set # found chain 1yocA in template set T0322 13 :IPEGFSQLNWSRGFGRQIG 1yocA 13 :PAQFSAMIGQFAPYFASIA T0322 33 :LFEHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 1yocA 32 :PQFVELRPGYAEVTFPKRREVLNHIGTVHAIALCNAAELAAGTMTDAS T0322 81 :KSYSWVTVRLMCDFLSGAK 1yocA 82 :AGHRWIPRGMTVEYLAKAT T0322 101 :GD 1yocA 101 :GD T0322 104 :VEGEGELIS 1yocA 103 :VRAVADGSQ T0322 113 :EEDMLFTVRGRIWAGERTLITGTGVFKALS 1yocA 115 :QATGNLVVPVVAYVDDKPVFRAEITMYVSQ Number of specific fragments extracted= 6 number of extra gaps= 0 total=161 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 1yocA/T0322-1yocA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 1yocA/T0322-1yocA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yocA read from 1yocA/T0322-1yocA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yocA in template set T0322 17 :FSQLNWSRGFGRQIG 1yocA 17 :SAMIGQFAPYFASIA T0322 33 :LFEHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQKSY 1yocA 32 :PQFVELRPGYAEVTFPKRREVLNHIGTVHAIALCNAAELAAGTMTDASIPA T0322 84 :SWVTVRLMCDFLSGAK 1yocA 85 :RWIPRGMTVEYLAKAT T0322 101 :GD 1yocA 101 :GD T0322 104 :VEGEGEL 1yocA 103 :VRAVADG T0322 111 :ISEEDMLFTVRGRIWAGERTLITGTGVFKALS 1yocA 113 :DWQATGNLVVPVVAYVDDKPVFRAEITMYVSQ Number of specific fragments extracted= 6 number of extra gaps= 0 total=167 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 1yocA/T0322-1yocA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 1yocA/T0322-1yocA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yocA read from 1yocA/T0322-1yocA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1yocA in template set T0322 12 :AIPEGFSQLNWSRGFGRQIGPLFEHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQK 1yocA 11 :VGPAQFSAMIGQFAPYFASIAPQFVELRPGYAEVTFPKRREVLNHIGTVHAIALCNAAELAAGTMTDASI T0322 82 :SYSWVTVRLMCDFLSGAK 1yocA 83 :GHRWIPRGMTVEYLAKAT T0322 101 :GD 1yocA 101 :GD T0322 104 :VEGEGE 1yocA 103 :VRAVAD T0322 113 :EEDMLFTVRGRIWAGERTLITGTGVFK 1yocA 115 :QATGNLVVPVVAYVDDKPVFRAEITMY Number of specific fragments extracted= 5 number of extra gaps= 0 total=172 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 2gvhA/T0322-2gvhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2gvhA expands to /projects/compbio/data/pdb/2gvh.pdb.gz 2gvhA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0322 read from 2gvhA/T0322-2gvhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gvhA read from 2gvhA/T0322-2gvhA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2gvhA to template set # found chain 2gvhA in template set Warning: unaligning (T0322)E38 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2gvhA)A147 Warning: unaligning (T0322)Q42 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gvhA)A147 Warning: unaligning (T0322)S142 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2gvhA)R258 Warning: unaligning (T0322)P146 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gvhA)R258 T0322 5 :LTDAQTAAI 2gvhA 123 :PEGEDAASY T0322 23 :SRGFGRQIG 2gvhA 132 :VLPELLTEE T0322 34 :F 2gvhA 141 :T T0322 37 :R 2gvhA 142 :P T0322 43 :ARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQKSYSWVTVRLM 2gvhA 148 :VTMVEIVFPDQANSAGRMFGGEAIAYMTKAAFVAASRYCGKLVVLASSE T0322 92 :CDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWA 2gvhA 198 :IDFARAIEIGEIVEAQAHVERVGRSSMSIQTKLWS T0322 128 :E 2gvhA 237 :T T0322 129 :RTLITGTGVFKAL 2gvhA 241 :HITATGHFTMVAV T0322 147 :RPG 2gvhA 259 :PAT Number of specific fragments extracted= 9 number of extra gaps= 0 total=181 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 2gvhA/T0322-2gvhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 2gvhA/T0322-2gvhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gvhA read from 2gvhA/T0322-2gvhA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gvhA in template set Warning: unaligning (T0322)P40 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2gvhA)A147 Warning: unaligning (T0322)Q42 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gvhA)A147 Warning: unaligning (T0322)S142 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2gvhA)R258 Warning: unaligning (T0322)P146 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gvhA)R258 T0322 27 :GRQIGPLFEHREG 2gvhA 130 :SYVLPELLTEETP T0322 43 :ARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQKSYSWVTVRLM 2gvhA 148 :VTMVEIVFPDQANSAGRMFGGEAIAYMTKAAFVAASRYCGKLVVLASSE T0322 92 :CDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWA 2gvhA 198 :IDFARAIEIGEIVEAQAHVERVGRSSMSIQTKLWS T0322 127 :G 2gvhA 237 :T T0322 130 :TLITGTGVFKAL 2gvhA 242 :ITATGHFTMVAV T0322 147 :RP 2gvhA 259 :PA Number of specific fragments extracted= 6 number of extra gaps= 0 total=187 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 2gvhA/T0322-2gvhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 2gvhA/T0322-2gvhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gvhA read from 2gvhA/T0322-2gvhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gvhA in template set Warning: unaligning (T0322)Q42 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gvhA)A147 Warning: unaligning (T0322)A143 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2gvhA)R258 Warning: unaligning (T0322)R147 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gvhA)R258 T0322 25 :GFGRQIGPLFEHREGP 2gvhA 127 :DAASYVLPELLTEETP T0322 43 :ARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQKSYSWVTVRLM 2gvhA 148 :VTMVEIVFPDQANSAGRMFGGEAIAYMTKAAFVAASRYCGKLVVLASSE T0322 92 :CDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIW 2gvhA 198 :IDFARAIEIGEIVEAQAHVERVGRSSMSIQTKLW T0322 126 :AGERTLITGTGVFKALS 2gvhA 237 :TGERHITATGHFTMVAV Number of specific fragments extracted= 4 number of extra gaps= 0 total=191 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 2b6eA/T0322-2b6eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2b6eA expands to /projects/compbio/data/pdb/2b6e.pdb.gz 2b6eA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0322 read from 2b6eA/T0322-2b6eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b6eA read from 2b6eA/T0322-2b6eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2b6eA to template set # found chain 2b6eA in template set Warning: unaligning (T0322)S142 because last residue in template chain is (2b6eA)N137 T0322 8 :AQTAAIPEGFSQLN 2b6eA 4 :KKTFTLENLNQLCS T0322 24 :RGFGRQIG 2b6eA 18 :NSAVSHLG T0322 33 :LFEHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 2b6eA 26 :IEISAFGEDWIEATMPVDHRTMQPFGVLHGGVSVALAETIGSLAGSLC T0322 81 :KSYSWVTVRLMCDFLSGAKLG 2b6eA 76 :EGKTVVGLDINANHLRPVRSG T0322 103 :WVEGEGELISEEDMLFTVRGRIWA 2b6eA 97 :KVTARATPINLGRNIQVWQIDIRT T0322 127 :GERTLITGTGVFKAL 2b6eA 122 :ENKLCCVSRLTLSVI Number of specific fragments extracted= 6 number of extra gaps= 0 total=197 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 2b6eA/T0322-2b6eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 2b6eA/T0322-2b6eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b6eA read from 2b6eA/T0322-2b6eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2b6eA in template set Warning: unaligning (T0322)S142 because last residue in template chain is (2b6eA)N137 T0322 17 :FSQLNW 2b6eA 12 :LNQLCS T0322 24 :RGFGRQIG 2b6eA 18 :NSAVSHLG T0322 33 :LFEHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQKSY 2b6eA 26 :IEISAFGEDWIEATMPVDHRTMQPFGVLHGGVSVALAETIGSLAGSLCLEE T0322 84 :SWVTVRLMCDFLSGAKLG 2b6eA 79 :TVVGLDINANHLRPVRSG T0322 103 :WVEGEGELISEEDMLFTVRGRIWA 2b6eA 97 :KVTARATPINLGRNIQVWQIDIRT T0322 127 :GERTLITGTGVFKAL 2b6eA 122 :ENKLCCVSRLTLSVI Number of specific fragments extracted= 6 number of extra gaps= 0 total=203 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 2b6eA/T0322-2b6eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 2b6eA/T0322-2b6eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b6eA read from 2b6eA/T0322-2b6eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2b6eA in template set Warning: unaligning (T0322)A143 because last residue in template chain is (2b6eA)N137 T0322 6 :TDAQTAAIPEGF 2b6eA 5 :KTFTLENLNQLC T0322 24 :RGFGRQIGPLFEHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQK 2b6eA 17 :SNSAVSHLGIEISAFGEDWIEATMPVDHRTMQPFGVLHGGVSVALAETIGSLAGSLCL T0322 82 :SYSWVTVRLMCDFLSGAK 2b6eA 77 :GKTVVGLDINANHLRPVR T0322 101 :GDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKALS 2b6eA 95 :SGKVTARATPINLGRNIQVWQIDIRTEENKLCCVSRLTLSVI Number of specific fragments extracted= 4 number of extra gaps= 0 total=207 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 2cyeA/T0322-2cyeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2cyeA expands to /projects/compbio/data/pdb/2cye.pdb.gz 2cyeA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0322 read from 2cyeA/T0322-2cyeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cyeA read from 2cyeA/T0322-2cyeA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2cyeA to template set # found chain 2cyeA in template set Warning: unaligning (T0322)Q80 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2cyeA)D46 T0322 40 :PG 2cyeA 2 :EG T0322 42 :QARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISL 2cyeA 5 :PVRVRVDVRFRDLDPLGHVNNAVFLSYMELARIRYFQR T0322 83 :YSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKALSARKPRPGE 2cyeA 51 :GHFVVARMEVDYLRPILLGDEVFVGVRTVGLGRSSLRMEHLVTANGESAAKGLGVLVWLEGGRPAPLP Number of specific fragments extracted= 3 number of extra gaps= 0 total=210 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 2cyeA/T0322-2cyeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 2cyeA/T0322-2cyeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cyeA read from 2cyeA/T0322-2cyeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2cyeA in template set Warning: unaligning (T0322)Q80 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2cyeA)D46 Warning: unaligning (T0322)Y83 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2cyeA)D46 T0322 40 :PG 2cyeA 2 :EG T0322 42 :QARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISL 2cyeA 5 :PVRVRVDVRFRDLDPLGHVNNAVFLSYMELARIRYFQR T0322 84 :SWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKALSARKPRP 2cyeA 52 :HFVVARMEVDYLRPILLGDEVFVGVRTVGLGRSSLRMEHLVTANGESAAKGLGVLVWLEGGRPAP T0322 149 :GELAYKE 2cyeA 118 :PEAIRER Number of specific fragments extracted= 4 number of extra gaps= 0 total=214 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 2cyeA/T0322-2cyeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 2cyeA/T0322-2cyeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cyeA read from 2cyeA/T0322-2cyeA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2cyeA in template set Warning: unaligning (T0322)Q80 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2cyeA)D46 T0322 39 :GPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISL 2cyeA 2 :EGFPVRVRVDVRFRDLDPLGHVNNAVFLSYMELARIRYFQR T0322 82 :SYSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKALSARKPRPGELAYKEEA 2cyeA 50 :EGHFVVARMEVDYLRPILLGDEVFVGVRTVGLGRSSLRMEHLVTANGESAAKGLGVLVWLEGGRPAPLPEAIRERI Number of specific fragments extracted= 2 number of extra gaps= 0 total=216 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 1t82A/T0322-1t82A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1t82A expands to /projects/compbio/data/pdb/1t82.pdb.gz 1t82A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0322 read from 1t82A/T0322-1t82A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t82A read from 1t82A/T0322-1t82A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1t82A to template set # found chain 1t82A in template set Warning: unaligning (T0322)I13 because first residue in template chain is (1t82A)M1 Warning: unaligning (T0322)S142 because last residue in template chain is (1t82A)P143 T0322 14 :PEGFSQL 1t82A 2 :DELLNRL T0322 21 :NWSRGFGRQIG 1t82A 13 :HSTIPVSEFMQ T0322 33 :LFEHREGPGQARLAFRVEEH 1t82A 24 :IAPLSFTDGELSVSAPLAPN T0322 54 :TNGLGNCHGGMLMSFADMAWGRIISLQ 1t82A 44 :INLHHTMFAGSIYTIMTLTGWGMVWLQ T0322 81 :KS 1t82A 74 :LN T0322 83 :YSWVTVRLMCDFLSGAKLGD 1t82A 78 :GDIVLADAHIRYLAPVTSAP T0322 105 :EGEGELIS 1t82A 98 :EVKVRWPD T0322 113 :EEDMLFTVRGRIWAGERTLITGTGVFKAL 1t82A 114 :GRKAKVKLEVQLFCDGKLCAQFDGLYVSV Number of specific fragments extracted= 8 number of extra gaps= 0 total=224 Will force an alignment to be made, even if fragment is small Number of alignments=46 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t82A/T0322-1t82A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 1t82A/T0322-1t82A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t82A read from 1t82A/T0322-1t82A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1t82A in template set Warning: unaligning (T0322)Q9 because first residue in template chain is (1t82A)M1 Warning: unaligning (T0322)S142 because last residue in template chain is (1t82A)P143 T0322 10 :TAAIPEGFSQLNWSRGFGRQIG 1t82A 2 :DELLNRLRQTWHSTIPVSEFMQ T0322 33 :LFEHREGPGQARLAFRVEE 1t82A 24 :IAPLSFTDGELSVSAPLAP T0322 53 :HTNGLGNCHGGM 1t82A 43 :NINLHHTMFAGS T0322 65 :LMSFADMAWGRIISLQKSY 1t82A 58 :IMTLTGWGMVWLQQQLLNV T0322 84 :SWVTVRLMCDFLSGAKLGDWVEGE 1t82A 79 :DIVLADAHIRYLAPVTSAPEVKVR T0322 111 :ISEEDMLFTVRGRIWAGERTLITGTGVFKAL 1t82A 112 :QRGRKAKVKLEVQLFCDGKLCAQFDGLYVSV Number of specific fragments extracted= 6 number of extra gaps= 0 total=230 Will force an alignment to be made, even if fragment is small Number of alignments=47 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t82A/T0322-1t82A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 1t82A/T0322-1t82A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t82A read from 1t82A/T0322-1t82A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1t82A in template set Warning: unaligning (T0322)T10 because first residue in template chain is (1t82A)M1 T0322 11 :AAIPEGFSQLNWSRGFGRQIGPLFEHREGPGQARLAFRV 1t82A 2 :DELLNRLRQTWHSTIPVSEFMQIAPLSFTDGELSVSAPL T0322 51 :EHHTNGLGNCHGGM 1t82A 41 :APNINLHHTMFAGS T0322 65 :LMSFADMAWGRIISLQK 1t82A 58 :IMTLTGWGMVWLQQQLL T0322 82 :SYSWVTVRLMCDFLSGAKLGDWVEGE 1t82A 77 :DGDIVLADAHIRYLAPVTSAPEVKVR T0322 112 :SEEDMLFTVRGRIWAGERTLITGTGVFK 1t82A 113 :RGRKAKVKLEVQLFCDGKLCAQFDGLYV Number of specific fragments extracted= 5 number of extra gaps= 0 total=235 Will force an alignment to be made, even if fragment is small Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sh8A/T0322-1sh8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1sh8A expands to /projects/compbio/data/pdb/1sh8.pdb.gz 1sh8A:# T0322 read from 1sh8A/T0322-1sh8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sh8A read from 1sh8A/T0322-1sh8A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1sh8A to template set # found chain 1sh8A in template set T0322 10 :TAAIPEGFSQLNWSRGFGRQIG 1sh8A 2 :PLPTELARHLTEEKIAFVQRSG T0322 33 :LFEHREGPGQARLAFR 1sh8A 24 :LRAEVLEPGYVRLRMP T0322 50 :EEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 1sh8A 40 :GAGNENHIGSMYAGALFTLAELPGGALFLTS T0322 81 :KSYSWVTVRLMCDFLSGAK 1sh8A 74 :ARFYPIVKEMTLRFRRPAK T0322 101 :GD 1sh8A 93 :GD T0322 104 :VEGEGELIS 1sh8A 95 :IRVEARLDA T0322 113 :EEDMLFTVRGRIWA 1sh8A 116 :RGKAEYSLELQLTD T0322 127 :GERTLITGTGVFKALSARKP 1sh8A 131 :QGEVVAESAALYQLRSHARP Number of specific fragments extracted= 8 number of extra gaps= 0 total=243 Will force an alignment to be made, even if fragment is small Number of alignments=49 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sh8A/T0322-1sh8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 1sh8A/T0322-1sh8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sh8A read from 1sh8A/T0322-1sh8A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1sh8A in template set T0322 18 :SQLNWSRGFGRQIG 1sh8A 10 :HLTEEKIAFVQRSG T0322 33 :LFEHREGPGQARLAFR 1sh8A 24 :LRAEVLEPGYVRLRMP T0322 50 :EEHHTNGLGNCHGGMLMSFADMAWGRIISLQKSY 1sh8A 40 :GAGNENHIGSMYAGALFTLAELPGGALFLTSFDS T0322 84 :SWVTVRLMCDFLSGAK 1sh8A 77 :YPIVKEMTLRFRRPAK T0322 101 :GD 1sh8A 93 :GD T0322 104 :VEGEGEL 1sh8A 95 :IRVEARL T0322 114 :EDMLFTVRGRIWA 1sh8A 117 :GKAEYSLELQLTD T0322 127 :GERTLITGTGVFKALSARKPR 1sh8A 131 :QGEVVAESAALYQLRSHARPG Number of specific fragments extracted= 8 number of extra gaps= 0 total=251 Will force an alignment to be made, even if fragment is small Number of alignments=50 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sh8A/T0322-1sh8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 1sh8A/T0322-1sh8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sh8A read from 1sh8A/T0322-1sh8A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1sh8A in template set T0322 7 :DAQTAAIPEGFSQL 1sh8A 2 :PLPTELARHLTEEK T0322 25 :GFGRQIGPLFEHREGPGQARLAFR 1sh8A 16 :IAFVQRSGLRAEVLEPGYVRLRMP T0322 50 :EEHHTNGLGNCHGGMLMSFADMAWGRIISLQK 1sh8A 40 :GAGNENHIGSMYAGALFTLAELPGGALFLTSF T0322 82 :SYSWVTVRLMCDFLSGAK 1sh8A 75 :RFYPIVKEMTLRFRRPAK T0322 101 :GD 1sh8A 93 :GD T0322 104 :VEGEGE 1sh8A 95 :IRVEAR T0322 114 :EDMLFTVRGRIWAGERTLITGTGVFKALSA 1sh8A 117 :GKAEYSLELQLTDEQGEVVAESAALYQLRS T0322 145 :KPRPG 1sh8A 147 :HARPG Number of specific fragments extracted= 8 number of extra gaps= 0 total=259 Will force an alignment to be made, even if fragment is small Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z6bA/T0322-1z6bA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1z6bA expands to /projects/compbio/data/pdb/1z6b.pdb.gz 1z6bA:# T0322 read from 1z6bA/T0322-1z6bA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z6bA read from 1z6bA/T0322-1z6bA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1z6bA to template set # found chain 1z6bA in template set Warning: unaligning (T0322)A8 because first residue in template chain is (1z6bA)D84 Warning: unaligning (T0322)H53 because of BadResidue code BAD_PEPTIDE in next template residue (1z6bA)F134 Warning: unaligning (T0322)T54 because of BadResidue code BAD_PEPTIDE at template residue (1z6bA)F134 Warning: unaligning (T0322)K81 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1z6bA)N166 Warning: unaligning (T0322)E113 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1z6bA)S200 T0322 9 :QTAAIPEGFSQLNWSRGFGRQIG 1z6bA 85 :TSIDIEDIKKILPHRYPFLLVDK T0322 34 :FEHREGPGQARLAFRVEE 1z6bA 108 :VIYMQPNKTIIGLKQVST T0322 52 :H 1z6bA 132 :G T0322 55 :NGLGNCHGGMLMSFADMAWGRIISLQ 1z6bA 135 :PQKQIMPGVLQIEALAQLAGILCLKS T0322 83 :YSWVTVRLM 1z6bA 167 :NLFLFAGVD T0322 92 :CDFLSGAKLGDWVEGEGELIS 1z6bA 177 :VRWKKPVLPGDTLTMQANLIS T0322 114 :EDMLFTVRGRIWAGERTLITGT 1z6bA 201 :SLGIAKLSGVGYVNGKVVINIS T0322 136 :GVFKA 1z6bA 224 :MTFAL Number of specific fragments extracted= 8 number of extra gaps= 2 total=267 Will force an alignment to be made, even if fragment is small Number of alignments=52 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z6bA/T0322-1z6bA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 1z6bA/T0322-1z6bA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z6bA read from 1z6bA/T0322-1z6bA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1z6bA in template set Warning: unaligning (T0322)H53 because of BadResidue code BAD_PEPTIDE in next template residue (1z6bA)F134 Warning: unaligning (T0322)T54 because of BadResidue code BAD_PEPTIDE at template residue (1z6bA)F134 Warning: unaligning (T0322)K81 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1z6bA)N166 Warning: unaligning (T0322)S112 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1z6bA)S200 Warning: unaligning (T0322)E113 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1z6bA)S200 T0322 2 :SDDLTDAQ 1z6bA 86 :SIDIEDIK T0322 11 :AAIPEGFSQLNW 1z6bA 94 :KILPHRYPFLLV T0322 32 :PLFEHREGPGQARLAFRVEEH 1z6bA 106 :DKVIYMQPNKTIIGLKQVSTN T0322 55 :NGLGNCHGGMLMSFADMAWGRIISLQ 1z6bA 135 :PQKQIMPGVLQIEALAQLAGILCLKS T0322 84 :SWVTVRLM 1z6bA 168 :LFLFAGVD T0322 92 :CDFLSGAKLGDWVEGEGELI 1z6bA 177 :VRWKKPVLPGDTLTMQANLI T0322 114 :EDMLFTVRGRIWAGERTLITGT 1z6bA 201 :SLGIAKLSGVGYVNGKVVINIS T0322 136 :GVFKA 1z6bA 224 :MTFAL Number of specific fragments extracted= 8 number of extra gaps= 2 total=275 Will force an alignment to be made, even if fragment is small Number of alignments=53 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z6bA/T0322-1z6bA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 1z6bA/T0322-1z6bA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z6bA read from 1z6bA/T0322-1z6bA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1z6bA in template set Warning: unaligning (T0322)H53 because of BadResidue code BAD_PEPTIDE in next template residue (1z6bA)F134 Warning: unaligning (T0322)T54 because of BadResidue code BAD_PEPTIDE at template residue (1z6bA)F134 Warning: unaligning (T0322)K81 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1z6bA)N166 Warning: unaligning (T0322)S82 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1z6bA)N166 Warning: unaligning (T0322)S112 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1z6bA)S200 Warning: unaligning (T0322)E113 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1z6bA)S200 Warning: unaligning (T0322)S142 because last residue in template chain is (1z6bA)S229 T0322 7 :DAQTAAIP 1z6bA 86 :SIDIEDIK T0322 19 :Q 1z6bA 94 :K T0322 21 :NWSRGFGRQIGPLFEHREGPGQARLAFRVEEH 1z6bA 95 :ILPHRYPFLLVDKVIYMQPNKTIIGLKQVSTN T0322 55 :NGLGNCHGGMLMSFADMAWGRIISLQ 1z6bA 135 :PQKQIMPGVLQIEALAQLAGILCLKS T0322 83 :YSWVTVRLM 1z6bA 167 :NLFLFAGVD T0322 92 :CDFLSGAKLGDWVEGEGELI 1z6bA 177 :VRWKKPVLPGDTLTMQANLI T0322 114 :EDMLFTVRGRIWAGERTLITGTGVFKAL 1z6bA 201 :SLGIAKLSGVGYVNGKVVINISEMTFAL Number of specific fragments extracted= 7 number of extra gaps= 2 total=282 Will force an alignment to be made, even if fragment is small Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1s5uA/T0322-1s5uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1s5uA expands to /projects/compbio/data/pdb/1s5u.pdb.gz 1s5uA:# T0322 read from 1s5uA/T0322-1s5uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1s5uA read from 1s5uA/T0322-1s5uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1s5uA to template set # found chain 1s5uA in template set Warning: unaligning (T0322)G41 because first residue in template chain is (1s5uA)T4 T0322 42 :QARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 1s5uA 5 :LFRWPVRVYYEDTDAGGVVYHASYVAFYERARTEMLRHH T0322 81 :KSYSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWA 1s5uA 53 :ERVAFVVRKMTVEYYAPARLDDMLEIQTEITSMRGTSLVFTQRIVN T0322 127 :GERTLITGTGVFKALSARKPRPGELAYK 1s5uA 100 :ENTLLNEAEVLVVCVDPLKMKPRALPKS Number of specific fragments extracted= 3 number of extra gaps= 0 total=285 Will force an alignment to be made, even if fragment is small Number of alignments=55 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1s5uA/T0322-1s5uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 1s5uA/T0322-1s5uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1s5uA read from 1s5uA/T0322-1s5uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1s5uA in template set Warning: unaligning (T0322)G41 because first residue in template chain is (1s5uA)T4 T0322 42 :QARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 1s5uA 5 :LFRWPVRVYYEDTDAGGVVYHASYVAFYERARTEMLRHH T0322 82 :SY 1s5uA 44 :HF T0322 84 :SWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWA 1s5uA 56 :AFVVRKMTVEYYAPARLDDMLEIQTEITSMRGTSLVFTQRIVN T0322 127 :GERTLITGTGVFKALSARKPRP 1s5uA 100 :ENTLLNEAEVLVVCVDPLKMKP T0322 149 :GELAYK 1s5uA 125 :PKSIVA Number of specific fragments extracted= 5 number of extra gaps= 0 total=290 Will force an alignment to be made, even if fragment is small Number of alignments=56 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1s5uA/T0322-1s5uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 1s5uA/T0322-1s5uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1s5uA read from 1s5uA/T0322-1s5uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1s5uA in template set T0322 42 :QARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQK 1s5uA 5 :LFRWPVRVYYEDTDAGGVVYHASYVAFYERARTEMLRHHH T0322 82 :SYSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKALSAR 1s5uA 54 :RVAFVVRKMTVEYYAPARLDDMLEIQTEITSMRGTSLVFTQRIVNAENTLLNEAEVLVVCVDP Number of specific fragments extracted= 2 number of extra gaps= 0 total=292 Will force an alignment to be made, even if fragment is small Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z54A/T0322-1z54A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1z54A expands to /projects/compbio/data/pdb/1z54.pdb.gz 1z54A:# T0322 read from 1z54A/T0322-1z54A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z54A read from 1z54A/T0322-1z54A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1z54A to template set # found chain 1z54A in template set T0322 43 :ARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 1z54A 3 :SVTRIKVRYAETDQMGVVHHSVYAVYLEAARVDFLERA T0322 81 :KSYSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKALSARKPRPGE 1z54A 50 :RGVFFPVVELGLTFRAPARFGEVVEVRTRLAELSSRALLFRYRVEREGVLLAEGFTRHLCQVGERAARIP Number of specific fragments extracted= 2 number of extra gaps= 0 total=294 Will force an alignment to be made, even if fragment is small Number of alignments=58 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z54A/T0322-1z54A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 1z54A/T0322-1z54A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z54A read from 1z54A/T0322-1z54A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1z54A in template set T0322 43 :ARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 1z54A 3 :SVTRIKVRYAETDQMGVVHHSVYAVYLEAARVDFLERA T0322 82 :SY 1z54A 41 :GL T0322 84 :SWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKALSARKPRP 1z54A 53 :FFPVVELGLTFRAPARFGEVVEVRTRLAELSSRALLFRYRVEREGVLLAEGFTRHLCQVGERAAR T0322 149 :GELAYKE 1z54A 119 :PEDIYRA Number of specific fragments extracted= 4 number of extra gaps= 0 total=298 Will force an alignment to be made, even if fragment is small Number of alignments=59 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z54A/T0322-1z54A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 1z54A/T0322-1z54A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z54A read from 1z54A/T0322-1z54A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1z54A in template set T0322 43 :ARLAFRVEEHHTNGLGNCH 1z54A 3 :SVTRIKVRYAETDQMGVVH T0322 64 :MLMSFADMAWGRIISLQK 1z54A 24 :VYAVYLEAARVDFLERAG T0322 82 :SYSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKALSARKPRPGELAYKEE 1z54A 51 :GVFFPVVELGLTFRAPARFGEVVEVRTRLAELSSRALLFRYRVEREGVLLAEGFTRHLCQVGERAARIPEDIYRA Number of specific fragments extracted= 3 number of extra gaps= 0 total=301 Will force an alignment to be made, even if fragment is small Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1u1zA/T0322-1u1zA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1u1zA expands to /projects/compbio/data/pdb/1u1z.pdb.gz 1u1zA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0322 read from 1u1zA/T0322-1u1zA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u1zA read from 1u1zA/T0322-1u1zA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1u1zA to template set # found chain 1u1zA in template set Warning: unaligning (T0322)T10 because first residue in template chain is (1u1zA)M1 Warning: unaligning (T0322)H53 because of BadResidue code BAD_PEPTIDE in next template residue (1u1zA)F50 Warning: unaligning (T0322)T54 because of BadResidue code BAD_PEPTIDE at template residue (1u1zA)F50 Warning: unaligning (T0322)Y83 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u1zA)T85 Warning: unaligning (T0322)S142 because last residue in template chain is (1u1zA)K145 T0322 11 :AAIPEGFSQLNWSRGFGRQIG 1u1zA 2 :MDINEIREYLPHRYPFLLVDR T0322 33 :LFEHREGPGQARLAFRVE 1u1zA 23 :VVELDIEGKRIRAYKNVS T0322 51 :EH 1u1zA 47 :NG T0322 55 :NGLGNCHGGMLMSFADMAWGRIISLQKS 1u1zA 51 :PEHPIMPGVLIIEAMAQAAGILGFKMLD T0322 84 :SWVTVRLM 1u1zA 86 :LYYFVGSD T0322 92 :CDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKAL 1u1zA 95 :LRFRQPVLPGDQLQLHAKFISVKRSIWKFDCHATVDDKPVCSAEIICAER Number of specific fragments extracted= 6 number of extra gaps= 1 total=307 Will force an alignment to be made, even if fragment is small Number of alignments=61 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1u1zA/T0322-1u1zA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 1u1zA/T0322-1u1zA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u1zA read from 1u1zA/T0322-1u1zA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1u1zA in template set Warning: unaligning (T0322)S2 because first residue in template chain is (1u1zA)M1 Warning: unaligning (T0322)H53 because of BadResidue code BAD_PEPTIDE in next template residue (1u1zA)F50 Warning: unaligning (T0322)T54 because of BadResidue code BAD_PEPTIDE at template residue (1u1zA)F50 Warning: unaligning (T0322)S142 because last residue in template chain is (1u1zA)K145 T0322 3 :DDLTDAQ 1u1zA 2 :MDINEIR T0322 11 :AAIPEGFSQLNW 1u1zA 9 :EYLPHRYPFLLV T0322 33 :LFEHREG 1u1zA 21 :DRVVELD T0322 40 :PGQARLAFRVEEH 1u1zA 30 :GKRIRAYKNVSIN T0322 55 :NGLGNCHGGMLMSFADMAWGRIISLQKSY 1u1zA 51 :PEHPIMPGVLIIEAMAQAAGILGFKMLDV T0322 84 :SWVTVRLM 1u1zA 86 :LYYFVGSD T0322 92 :CDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKAL 1u1zA 95 :LRFRQPVLPGDQLQLHAKFISVKRSIWKFDCHATVDDKPVCSAEIICAER Number of specific fragments extracted= 7 number of extra gaps= 1 total=314 Will force an alignment to be made, even if fragment is small Number of alignments=62 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1u1zA/T0322-1u1zA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 1u1zA/T0322-1u1zA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1u1zA read from 1u1zA/T0322-1u1zA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1u1zA in template set Warning: unaligning (T0322)H53 because of BadResidue code BAD_PEPTIDE in next template residue (1u1zA)F50 Warning: unaligning (T0322)T54 because of BadResidue code BAD_PEPTIDE at template residue (1u1zA)F50 Warning: unaligning (T0322)Y83 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1u1zA)T85 T0322 14 :PEGFSQLNWSRGFGRQIGPLFEHREGPGQARLAFRVE 1u1zA 4 :INEIREYLPHRYPFLLVDRVVELDIEGKRIRAYKNVS T0322 51 :EH 1u1zA 47 :NG T0322 55 :NGLGNCHGGMLMSFADMAWGRIISLQK 1u1zA 51 :PEHPIMPGVLIIEAMAQAAGILGFKML T0322 84 :SWVTVRLM 1u1zA 86 :LYYFVGSD T0322 92 :CDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVF 1u1zA 95 :LRFRQPVLPGDQLQLHAKFISVKRSIWKFDCHATVDDKPVCSAEIIC Number of specific fragments extracted= 5 number of extra gaps= 1 total=319 Will force an alignment to be made, even if fragment is small Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b3nA/T0322-2b3nA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2b3nA expands to /projects/compbio/data/pdb/2b3n.pdb.gz 2b3nA:Skipped atom 125, because occupancy 0.330 <= existing 0.330 in 2b3nA Skipped atom 126, because occupancy 0.330 <= existing 0.330 in 2b3nA Skipped atom 130, because occupancy 0.330 <= existing 0.330 in 2b3nA Skipped atom 131, because occupancy 0.330 <= existing 0.330 in 2b3nA Skipped atom 133, because occupancy 0.330 <= existing 0.330 in 2b3nA Skipped atom 134, because occupancy 0.330 <= existing 0.330 in 2b3nA Skipped atom 146, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 150, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 152, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 154, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 156, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 158, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 254, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 258, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 260, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 262, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 264, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 266, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 269, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 273, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 275, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 277, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 279, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 338, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 342, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 344, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 346, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 348, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 350, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 365, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 369, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 371, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 373, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 375, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 377, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 448, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 450, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 452, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 454, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 456, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 458, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 460, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 462, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 676, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 680, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 682, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 684, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 731, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 735, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 737, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 827, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 831, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 833, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 835, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 853, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 855, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 857, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 859, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 861, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 863, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 865, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 867, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 869, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 880, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 882, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 884, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 886, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 888, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 890, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1017, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1021, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1023, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1025, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1027, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1029, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1036, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1040, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1042, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1044, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1054, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1058, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1060, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1092, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1096, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1098, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1100, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1102, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1245, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1249, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1251, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1253, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1262, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1264, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1266, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1268, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1270, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1272, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1274, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1276, because occupancy 0.500 <= existing 0.500 in 2b3nA Skipped atom 1278, because occupancy 0.500 <= existing 0.500 in 2b3nA # T0322 read from 2b3nA/T0322-2b3nA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b3nA read from 2b3nA/T0322-2b3nA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2b3nA to template set # found chain 2b3nA in template set Warning: unaligning (T0322)G27 because of BadResidue code BAD_PEPTIDE in next template residue (2b3nA)K27 Warning: unaligning (T0322)R28 because of BadResidue code BAD_PEPTIDE at template residue (2b3nA)K27 Warning: unaligning (T0322)W125 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2b3nA)T144 Warning: unaligning (T0322)A126 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2b3nA)T144 T0322 14 :PEGFSQLNWSRGF 2b3nA 13 :EEMKGIYSKKGGK T0322 29 :QIGPLFE 2b3nA 28 :PFEKFEG T0322 37 :REGPG 2b3nA 35 :ELKEG T0322 42 :QARLAFRV 2b3nA 41 :RFEYEKKL T0322 50 :EEH 2b3nA 76 :TRF T0322 56 :GLGNCHGGMLMSFAD 2b3nA 79 :GGRVVHGMLTTSLVS T0322 75 :RIISLQ 2b3nA 94 :AAVARL T0322 82 :SYSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRI 2b3nA 100 :PGTVVLLEQSFRYTSPVRIGDVVRVEGVVSGVEKNRYTIDVKC T0322 127 :GERTLITGTGVFKA 2b3nA 145 :GDKVVAEGVVKVLI Number of specific fragments extracted= 9 number of extra gaps= 2 total=328 Will force an alignment to be made, even if fragment is small Number of alignments=64 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b3nA/T0322-2b3nA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 2b3nA/T0322-2b3nA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b3nA read from 2b3nA/T0322-2b3nA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2b3nA in template set Warning: unaligning (T0322)S2 because first residue in template chain is (2b3nA)E5 Warning: unaligning (T0322)D3 because of BadResidue code BAD_PEPTIDE at template residue (2b3nA)V6 Warning: unaligning (T0322)D4 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b3nA)K7 Warning: unaligning (T0322)R24 because of BadResidue code BAD_PEPTIDE in next template residue (2b3nA)K27 Warning: unaligning (T0322)W125 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2b3nA)T144 Warning: unaligning (T0322)A126 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2b3nA)T144 T0322 5 :LTDAQTAA 2b3nA 8 :MMSLLEEM T0322 14 :PEGFSQLNWS 2b3nA 16 :KGIYSKKGGK T0322 25 :GFGRQIG 2b3nA 28 :PFEKFEG T0322 37 :REGPG 2b3nA 35 :ELKEG T0322 42 :QARLAFRV 2b3nA 41 :RFEYEKKL T0322 50 :EEH 2b3nA 76 :TRF T0322 56 :GLGNCHGGMLMSFA 2b3nA 79 :GGRVVHGMLTTSLV T0322 74 :GRIISLQ 2b3nA 93 :SAAVARL T0322 82 :SYSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRI 2b3nA 100 :PGTVVLLEQSFRYTSPVRIGDVVRVEGVVSGVEKNRYTIDVKC T0322 127 :GERTLITGTGVFKA 2b3nA 145 :GDKVVAEGVVKVLI Number of specific fragments extracted= 10 number of extra gaps= 2 total=338 Will force an alignment to be made, even if fragment is small Number of alignments=65 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b3nA/T0322-2b3nA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 2b3nA/T0322-2b3nA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2b3nA read from 2b3nA/T0322-2b3nA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2b3nA in template set Warning: unaligning (T0322)W125 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2b3nA)T144 Warning: unaligning (T0322)A126 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2b3nA)T144 T0322 56 :GLGNCHGG 2b3nA 79 :GGRVVHGM T0322 68 :FADMAWGRIISLQ 2b3nA 87 :LTTSLVSAAVARL T0322 82 :SYSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRI 2b3nA 100 :PGTVVLLEQSFRYTSPVRIGDVVRVEGVVSGVEKNRYTIDVKC T0322 127 :GERTLITGTGV 2b3nA 145 :GDKVVAEGVVK Number of specific fragments extracted= 4 number of extra gaps= 1 total=342 Will force an alignment to be made, even if fragment is small Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1njkA/T0322-1njkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1njkA expands to /projects/compbio/data/pdb/1njk.pdb.gz 1njkA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0322 read from 1njkA/T0322-1njkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1njkA read from 1njkA/T0322-1njkA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1njkA to template set # found chain 1njkA in template set Warning: unaligning (T0322)Q42 because first residue in template chain is (1njkA)H0 T0322 43 :ARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 1njkA 1 :MQTQIKVRGYHLDVYQHVNNARYLEFLEEARWDGLENS T0322 81 :KSYSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWA 1njkA 47 :HNIAFVVVNININYRRPAVLSDLLTITSQLQQLNGKSGILSQVITL T0322 128 :ERTLITGTGVFKALSARKPR 1njkA 96 :GQVVADALITFVCIDLKTQK Number of specific fragments extracted= 3 number of extra gaps= 0 total=345 Will force an alignment to be made, even if fragment is small Number of alignments=67 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1njkA/T0322-1njkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 1njkA/T0322-1njkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1njkA read from 1njkA/T0322-1njkA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1njkA in template set Warning: unaligning (T0322)Q42 because first residue in template chain is (1njkA)H0 T0322 43 :ARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIIS 1njkA 1 :MQTQIKVRGYHLDVYQHVNNARYLEFLEEARWDGLE T0322 82 :SY 1njkA 37 :NS T0322 84 :SWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWA 1njkA 50 :AFVVVNININYRRPAVLSDLLTITSQLQQLNGKSGILSQVITL T0322 127 :GERTLITGTGVFKALSARKPRP 1njkA 95 :EGQVVADALITFVCIDLKTQKA T0322 149 :GELAY 1njkA 121 :GELRE Number of specific fragments extracted= 5 number of extra gaps= 0 total=350 Will force an alignment to be made, even if fragment is small Number of alignments=68 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1njkA/T0322-1njkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 1njkA/T0322-1njkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1njkA read from 1njkA/T0322-1njkA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1njkA in template set Warning: unaligning (T0322)Q42 because first residue in template chain is (1njkA)H0 T0322 43 :ARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRII 1njkA 1 :MQTQIKVRGYHLDVYQHVNNARYLEFLEEARWDGL T0322 78 :SLQKSYSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAG 1njkA 44 :MTAHNIAFVVVNININYRRPAVLSDLLTITSQLQQLNGKSGILSQVITLE T0322 128 :ERTLITGTGVFKALS 1njkA 95 :EGQVVADALITFVCI Number of specific fragments extracted= 3 number of extra gaps= 0 total=353 Will force an alignment to be made, even if fragment is small Number of alignments=69 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gf6A/T0322-2gf6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2gf6A expands to /projects/compbio/data/pdb/2gf6.pdb.gz 2gf6A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0322 read from 2gf6A/T0322-2gf6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gf6A read from 2gf6A/T0322-2gf6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2gf6A to template set # found chain 2gf6A in template set Warning: unaligning (T0322)L141 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gf6A)N114 Warning: unaligning (T0322)S142 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gf6A)N114 T0322 44 :RLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 2gf6A 7 :VFEDVVRIYDTDAQGIAHYAAYYRFFTNTIEKFIKEK T0322 81 :KSYSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKA 2gf6A 53 :ENLWFVIAESHAIYHRPVKLGDKLTVLLNPKILSNKTIKFEFKVLKDGELTTEGYVIQIA T0322 143 :ARKPRPGELAYK 2gf6A 115 :PKIWKSTEMPKE Number of specific fragments extracted= 3 number of extra gaps= 1 total=356 Will force an alignment to be made, even if fragment is small Number of alignments=70 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gf6A/T0322-2gf6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 2gf6A/T0322-2gf6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gf6A read from 2gf6A/T0322-2gf6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gf6A in template set Warning: unaligning (T0322)L141 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gf6A)N114 Warning: unaligning (T0322)S142 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gf6A)N114 T0322 44 :RLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQKSY 2gf6A 7 :VFEDVVRIYDTDAQGIAHYAAYYRFFTNTIEKFIKEKVGI T0322 84 :SWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKA 2gf6A 56 :WFVIAESHAIYHRPVKLGDKLTVLLNPKILSNKTIKFEFKVLKDGELTTEGYVIQIA T0322 143 :ARKPRP 2gf6A 115 :PKIWKS T0322 149 :GELAYKE 2gf6A 125 :KEIMDKL Number of specific fragments extracted= 4 number of extra gaps= 1 total=360 Will force an alignment to be made, even if fragment is small Number of alignments=71 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gf6A/T0322-2gf6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 2gf6A/T0322-2gf6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gf6A read from 2gf6A/T0322-2gf6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gf6A in template set Warning: unaligning (T0322)L141 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gf6A)N114 Warning: unaligning (T0322)S142 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gf6A)N114 T0322 44 :RLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQK 2gf6A 7 :VFEDVVRIYDTDAQGIAHYAAYYRFFTNTIEKFIKEKV T0322 82 :SYSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKA 2gf6A 54 :NLWFVIAESHAIYHRPVKLGDKLTVLLNPKILSNKTIKFEFKVLKDGELTTEGYVIQIA T0322 143 :ARK 2gf6A 115 :PKI Number of specific fragments extracted= 3 number of extra gaps= 1 total=363 Will force an alignment to be made, even if fragment is small Number of alignments=72 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cwzA/T0322-2cwzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2cwzA expands to /projects/compbio/data/pdb/2cwz.pdb.gz 2cwzA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0322 read from 2cwzA/T0322-2cwzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cwzA read from 2cwzA/T0322-2cwzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2cwzA to template set # found chain 2cwzA in template set T0322 39 :GPG 2cwzA 5 :PEG T0322 42 :QARLAFRVEEHHT 2cwzA 9 :EAVFETVVTPEMT T0322 55 :NGLGNCHGGMLMSFADMAWGRIISLQ 2cwzA 29 :PVHPVYATYWMVKHMELAGRKIILPF T0322 81 :KSYSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAG 2cwzA 57 :EGEEGIGSYVEARHLASALPGMRVRVVARHEKTEGNRVYARVEAYNE T0322 128 :ERTLITGTGVFKALS 2cwzA 105 :GDLIGVGRTEQVILP Number of specific fragments extracted= 5 number of extra gaps= 0 total=368 Will force an alignment to be made, even if fragment is small Number of alignments=73 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cwzA/T0322-2cwzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 2cwzA/T0322-2cwzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cwzA read from 2cwzA/T0322-2cwzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2cwzA in template set T0322 38 :EGPG 2cwzA 4 :IPEG T0322 42 :QARLAFRVEEHHT 2cwzA 9 :EAVFETVVTPEMT T0322 55 :NGLGNCHGGMLMSFADMAWGRIISLQKSY 2cwzA 29 :PVHPVYATYWMVKHMELAGRKIILPFLEE T0322 84 :SWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAG 2cwzA 60 :EGIGSYVEARHLASALPGMRVRVVARHEKTEGNRVYARVEAYNE T0322 128 :ERTLITGTGVFKALSA 2cwzA 105 :GDLIGVGRTEQVILPK T0322 150 :ELAYKEE 2cwzA 121 :AKVEALF Number of specific fragments extracted= 6 number of extra gaps= 0 total=374 Will force an alignment to be made, even if fragment is small Number of alignments=74 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cwzA/T0322-2cwzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 2cwzA/T0322-2cwzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cwzA read from 2cwzA/T0322-2cwzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2cwzA in template set T0322 38 :EGPGQARLAFRVEEHHT 2cwzA 5 :PEGYEAVFETVVTPEMT T0322 64 :MLMSFADMAWGRIISLQK 2cwzA 38 :WMVKHMELAGRKIILPFL T0322 82 :SYSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKALSA 2cwzA 58 :GEEGIGSYVEARHLASALPGMRVRVVARHEKTEGNRVYARVEAYNELGDLIGVGRTEQVILP T0322 150 :ELAYKEE 2cwzA 120 :KAKVEAL Number of specific fragments extracted= 4 number of extra gaps= 0 total=378 Will force an alignment to be made, even if fragment is small Number of alignments=75 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2aliA/T0322-2aliA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2aliA expands to /projects/compbio/data/pdb/2ali.pdb.gz 2aliA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 157, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 161, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 163, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 165, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 167, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 169, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 171, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 197, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 201, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 203, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 205, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 718, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 722, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 724, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 726, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 728, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 730, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 732, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 734, because occupancy 0.500 <= existing 0.500 in 2aliA Skipped atom 745, because occupancy 0.400 <= existing 0.600 in 2aliA Skipped atom 749, because occupancy 0.400 <= existing 0.600 in 2aliA Skipped atom 751, because occupancy 0.400 <= existing 0.600 in 2aliA Skipped atom 753, because occupancy 0.400 <= existing 0.600 in 2aliA Skipped atom 755, because occupancy 0.400 <= existing 0.600 in 2aliA Skipped atom 757, because occupancy 0.400 <= existing 0.600 in 2aliA Skipped atom 759, because occupancy 0.400 <= existing 0.600 in 2aliA Skipped atom 860, because occupancy 0.400 <= existing 0.600 in 2aliA Skipped atom 864, because occupancy 0.400 <= existing 0.600 in 2aliA Skipped atom 866, because occupancy 0.400 <= existing 0.600 in 2aliA Skipped atom 886, because occupancy 0.400 <= existing 0.600 in 2aliA Skipped atom 890, because occupancy 0.400 <= existing 0.600 in 2aliA Skipped atom 892, because occupancy 0.400 <= existing 0.600 in 2aliA Skipped atom 894, because occupancy 0.400 <= existing 0.600 in 2aliA # T0322 read from 2aliA/T0322-2aliA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2aliA read from 2aliA/T0322-2aliA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2aliA to template set # found chain 2aliA in template set Warning: unaligning (T0322)F34 because first residue in template chain is (2aliA)Q5 T0322 35 :EH 2aliA 6 :LL T0322 43 :ARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 2aliA 8 :HTAHIPVRWGDMDSYGHVNNTLYFQYLEEARVAWFETL T0322 83 :YSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWA 2aliA 54 :EGPVVLQSLHTYLKPVVHPATVVVELYAGRLGTSSLVLEHRLHT T0322 127 :G 2aliA 99 :E T0322 128 :ERTLITGTGVFKALSARKPRPGELAYKE 2aliA 102 :QGTYGEGHCKLVWVRHAENRSTPVPDSI Number of specific fragments extracted= 5 number of extra gaps= 0 total=383 Will force an alignment to be made, even if fragment is small Number of alignments=76 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2aliA/T0322-2aliA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 2aliA/T0322-2aliA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2aliA read from 2aliA/T0322-2aliA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2aliA in template set Warning: unaligning (T0322)F34 because first residue in template chain is (2aliA)Q5 T0322 35 :EH 2aliA 6 :LL T0322 43 :ARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 2aliA 8 :HTAHIPVRWGDMDSYGHVNNTLYFQYLEEARVAWFETL T0322 82 :SY 2aliA 46 :GI T0322 84 :SWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWA 2aliA 55 :GPVVLQSLHTYLKPVVHPATVVVELYAGRLGTSSLVLEHRLHT T0322 127 :GER 2aliA 102 :QGT T0322 130 :TLITGTGVFKALSARKPRP 2aliA 106 :GEGHCKLVWVRHAENRSTP T0322 149 :GELAYKE 2aliA 126 :PDSIRAA Number of specific fragments extracted= 7 number of extra gaps= 0 total=390 Will force an alignment to be made, even if fragment is small Number of alignments=77 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2aliA/T0322-2aliA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 2aliA/T0322-2aliA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2aliA read from 2aliA/T0322-2aliA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2aliA in template set Warning: unaligning (T0322)F34 because first residue in template chain is (2aliA)Q5 T0322 35 :EHR 2aliA 6 :LLH T0322 44 :RLAFRVEEHHTNGLGNC 2aliA 9 :TAHIPVRWGDMDSYGHV T0322 64 :MLMSFADMAWGRIISLQK 2aliA 29 :LYFQYLEEARVAWFETLG T0322 82 :SYSWVTVRLM 2aliA 51 :GAAEGPVVLQ T0322 92 :CDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGER 2aliA 63 :HTYLKPVVHPATVVVELYAGRLGTSSLVLEHRLHTLED T0322 130 :TLITGTGVFKALSARKPRPGELAYKE 2aliA 106 :GEGHCKLVWVRHAENRSTPVPDSIRA Number of specific fragments extracted= 6 number of extra gaps= 0 total=396 Will force an alignment to be made, even if fragment is small Number of alignments=78 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2av9A/T0322-2av9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2av9A expands to /projects/compbio/data/pdb/2av9.pdb.gz 2av9A:Skipped atom 226, because occupancy 0.500 <= existing 0.500 in 2av9A Skipped atom 230, because occupancy 0.500 <= existing 0.500 in 2av9A Skipped atom 232, because occupancy 0.500 <= existing 0.500 in 2av9A Skipped atom 234, because occupancy 0.500 <= existing 0.500 in 2av9A Skipped atom 236, because occupancy 0.500 <= existing 0.500 in 2av9A Skipped atom 238, because occupancy 0.500 <= existing 0.500 in 2av9A Skipped atom 240, because occupancy 0.500 <= existing 0.500 in 2av9A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0322 read from 2av9A/T0322-2av9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2av9A read from 2av9A/T0322-2av9A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2av9A to template set # found chain 2av9A in template set Warning: unaligning (T0322)D3 because first residue in template chain is (2av9A)P5 Warning: unaligning (T0322)K99 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2av9A)F78 Warning: unaligning (T0322)L100 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2av9A)F78 T0322 4 :DLTDAQT 2av9A 6 :RPLREQY T0322 33 :LFEHREG 2av9A 13 :LHFQPIS T0322 49 :VEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 2av9A 20 :TRWHDNDIYGHVNNVTYYAFFDTAVNTYLIER T0322 81 :KS 2av9A 57 :QG T0322 83 :YSWVTVRLMCDFLSGA 2av9A 61 :VIGLVVSSSCDYFAPV T0322 101 :GDWVEGEGELISEEDMLFTVRGRIWAGE 2av9A 79 :PQRIEMGLRVARLGNSSVQYELALFLEG T0322 129 :RTLITGTGVFKALSARKPRPGELAYK 2av9A 109 :EACAAGRFVHVFVERRSSRPVAIPQE Number of specific fragments extracted= 7 number of extra gaps= 1 total=403 Will force an alignment to be made, even if fragment is small Number of alignments=79 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2av9A/T0322-2av9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 2av9A/T0322-2av9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2av9A read from 2av9A/T0322-2av9A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2av9A in template set Warning: unaligning (T0322)K99 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2av9A)F78 Warning: unaligning (T0322)L100 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2av9A)F78 T0322 26 :FGRQ 2av9A 9 :REQY T0322 33 :LFEH 2av9A 13 :LHFQ T0322 46 :AFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQKSY 2av9A 17 :PISTRWHDNDIYGHVNNVTYYAFFDTAVNTYLIERGGL T0322 84 :SWVTVRLMCDFLSGA 2av9A 62 :IGLVVSSSCDYFAPV T0322 101 :GDWVEGEGELISEEDMLFTVRGRIWAGE 2av9A 79 :PQRIEMGLRVARLGNSSVQYELALFLEG T0322 129 :RTLITGTGVFKALSARKPRP 2av9A 109 :EACAAGRFVHVFVERRSSRP T0322 149 :GELAY 2av9A 133 :QELRD Number of specific fragments extracted= 7 number of extra gaps= 1 total=410 Will force an alignment to be made, even if fragment is small Number of alignments=80 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2av9A/T0322-2av9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 2av9A/T0322-2av9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2av9A read from 2av9A/T0322-2av9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2av9A in template set Warning: unaligning (T0322)S23 because first residue in template chain is (2av9A)P5 Warning: unaligning (T0322)K99 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2av9A)F78 Warning: unaligning (T0322)L100 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2av9A)F78 T0322 24 :RGFGRQIGPLFEHR 2av9A 6 :RPLREQYLHFQPIS T0322 49 :VEEHHTNGLGNC 2av9A 20 :TRWHDNDIYGHV T0322 64 :MLMSFADMAWGRIISLQK 2av9A 35 :TYYAFFDTAVNTYLIERG T0322 82 :SYSWVTVRLMCDFLSGA 2av9A 60 :EVIGLVVSSSCDYFAPV T0322 101 :GDWVEGEGELISEEDMLFTVRGRIWAGERTL 2av9A 79 :PQRIEMGLRVARLGNSSVQYELALFLEGQRE T0322 132 :ITGTGVFKALSARKPRPGE 2av9A 112 :AAGRFVHVFVERRSSRPVA T0322 151 :LAYKEE 2av9A 133 :QELRDA Number of specific fragments extracted= 7 number of extra gaps= 1 total=417 Will force an alignment to be made, even if fragment is small Number of alignments=81 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lo7A/T0322-1lo7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1lo7A expands to /projects/compbio/data/pdb/1lo7.pdb.gz 1lo7A:Skipped atom 253, because occupancy 0.500 <= existing 0.500 in 1lo7A Skipped atom 255, because occupancy 0.500 <= existing 0.500 in 1lo7A Skipped atom 257, because occupancy 0.500 <= existing 0.500 in 1lo7A Skipped atom 259, because occupancy 0.500 <= existing 0.500 in 1lo7A Skipped atom 532, because occupancy 0.500 <= existing 0.500 in 1lo7A Skipped atom 534, because occupancy 0.500 <= existing 0.500 in 1lo7A Skipped atom 800, because occupancy 0.500 <= existing 0.500 in 1lo7A Skipped atom 802, because occupancy 0.500 <= existing 0.500 in 1lo7A Skipped atom 970, because occupancy 0.500 <= existing 0.500 in 1lo7A Skipped atom 972, because occupancy 0.500 <= existing 0.500 in 1lo7A Skipped atom 974, because occupancy 0.500 <= existing 0.500 in 1lo7A Skipped atom 976, because occupancy 0.500 <= existing 0.500 in 1lo7A Skipped atom 1133, because occupancy 0.500 <= existing 0.500 in 1lo7A Skipped atom 1135, because occupancy 0.500 <= existing 0.500 in 1lo7A # T0322 read from 1lo7A/T0322-1lo7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lo7A read from 1lo7A/T0322-1lo7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1lo7A to template set # found chain 1lo7A in template set T0322 42 :QARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 1lo7A 4 :SITMQQRIEFGDCDPAGIVWYPNYHRWLDAASRNYFIKC T0322 82 :S 1lo7A 43 :G T0322 83 :YSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWA 1lo7A 57 :VGTPIVSCNASFVCTASYDDVLTIETCIKEWRRKSFVQRHSVSR T0322 127 :GE 1lo7A 104 :GG T0322 129 :RTLITGTGV 1lo7A 108 :QLVMRADEI T0322 138 :FKALSARKPRPGELAYK 1lo7A 119 :FAMNDGERLRAIEVPAD Number of specific fragments extracted= 6 number of extra gaps= 0 total=423 Will force an alignment to be made, even if fragment is small Number of alignments=82 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lo7A/T0322-1lo7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 1lo7A/T0322-1lo7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lo7A read from 1lo7A/T0322-1lo7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1lo7A in template set T0322 42 :QARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 1lo7A 4 :SITMQQRIEFGDCDPAGIVWYPNYHRWLDAASRNYFIKC T0322 82 :SY 1lo7A 43 :GL T0322 84 :SWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWA 1lo7A 58 :GTPIVSCNASFVCTASYDDVLTIETCIKEWRRKSFVQRHSVSR T0322 127 :GE 1lo7A 104 :GG T0322 129 :RTLITGTGV 1lo7A 108 :QLVMRADEI T0322 138 :FKALSAR 1lo7A 119 :FAMNDGE Number of specific fragments extracted= 6 number of extra gaps= 0 total=429 Will force an alignment to be made, even if fragment is small Number of alignments=83 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lo7A/T0322-1lo7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 1lo7A/T0322-1lo7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lo7A read from 1lo7A/T0322-1lo7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1lo7A in template set T0322 42 :QARLAFRVEEHHTNGLGNC 1lo7A 4 :SITMQQRIEFGDCDPAGIV T0322 65 :LMSFADMAWGRIISLQK 1lo7A 27 :YHRWLDAASRNYFIKCG T0322 83 :YS 1lo7A 59 :TP T0322 87 :TVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWA 1lo7A 61 :IVSCNASFVCTASYDDVLTIETCIKEWRRKSFVQRHSVSR T0322 127 :GER 1lo7A 103 :PGG T0322 130 :TLITGTGVFK 1lo7A 111 :MRADEIRVFA Number of specific fragments extracted= 6 number of extra gaps= 0 total=435 Will force an alignment to be made, even if fragment is small Number of alignments=84 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1c8uA/T0322-1c8uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1c8uA expands to /projects/compbio/data/pdb/1c8u.pdb.gz 1c8uA:# T0322 read from 1c8uA/T0322-1c8uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1c8uA read from 1c8uA/T0322-1c8uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1c8uA to template set # found chain 1c8uA in template set Warning: unaligning (T0322)N55 because of BadResidue code BAD_PEPTIDE in next template residue (1c8uA)G30 Warning: unaligning (T0322)G56 because of BadResidue code BAD_PEPTIDE at template residue (1c8uA)G30 Warning: unaligning (T0322)L57 because of BadResidue code BAD_PEPTIDE at template residue (1c8uA)L31 Warning: unaligning (T0322)G58 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1c8uA)R32 T0322 13 :IPEGFSQLN 1c8uA 5 :LKNLLTLLN T0322 35 :EHREGPGQARL 1c8uA 14 :LEKIEEGLFRG T0322 48 :RVE 1c8uA 25 :QSE T0322 54 :T 1c8uA 28 :D T0322 59 :NCHGGMLMSF 1c8uA 33 :QVFGGQVVGQ T0322 72 :AWGRIISLQKS 1c8uA 43 :ALYAAKETVPE T0322 85 :WVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKALSARKPR 1c8uA 55 :RLVHSFHSYFLRPGDSKKPIIYDVETLRDGNSFSARRVAAIQNGKPIFYMTASFQAPEAGFEH T0322 148 :PGELA 1c8uA 123 :SAPAP Number of specific fragments extracted= 8 number of extra gaps= 1 total=443 Will force an alignment to be made, even if fragment is small Number of alignments=85 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1c8uA/T0322-1c8uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 1c8uA/T0322-1c8uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1c8uA read from 1c8uA/T0322-1c8uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1c8uA in template set Warning: unaligning (T0322)G56 because of BadResidue code BAD_PEPTIDE in next template residue (1c8uA)G30 Warning: unaligning (T0322)L57 because of BadResidue code BAD_PEPTIDE at template residue (1c8uA)G30 Warning: unaligning (T0322)G58 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1c8uA)R32 T0322 20 :LNWS 1c8uA 8 :LLTL T0322 33 :LFEHREGPGQARL 1c8uA 12 :LNLEKIEEGLFRG T0322 51 :E 1c8uA 25 :Q T0322 53 :HTN 1c8uA 26 :SED T0322 59 :NCHGGMLMSFA 1c8uA 33 :QVFGGQVVGQA T0322 74 :GRIISLQKSYSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKALSARKP 1c8uA 44 :LYAAKETVPEERLVHSFHSYFLRPGDSKKPIIYDVETLRDGNSFSARRVAAIQNGKPIFYMTASFQAPEAGFE T0322 149 :GELAYKEEA 1c8uA 145 :PPVLKDKFI Number of specific fragments extracted= 7 number of extra gaps= 2 total=450 Will force an alignment to be made, even if fragment is small Number of alignments=86 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1c8uA/T0322-1c8uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 1c8uA/T0322-1c8uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1c8uA read from 1c8uA/T0322-1c8uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1c8uA in template set Warning: unaligning (T0322)N55 because of BadResidue code BAD_PEPTIDE in next template residue (1c8uA)G30 Warning: unaligning (T0322)G56 because of BadResidue code BAD_PEPTIDE at template residue (1c8uA)G30 Warning: unaligning (T0322)L57 because of BadResidue code BAD_PEPTIDE at template residue (1c8uA)L31 Warning: unaligning (T0322)G58 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1c8uA)R32 T0322 36 :HREGPGQARL 1c8uA 15 :EKIEEGLFRG T0322 51 :EHHT 1c8uA 25 :QSED T0322 59 :NCHGGMLMSFA 1c8uA 33 :QVFGGQVVGQA T0322 73 :WGRIISLQK 1c8uA 44 :LYAAKETVP T0322 82 :SYSWV 1c8uA 54 :ERLVH T0322 89 :RLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKA 1c8uA 59 :SFHSYFLRPGDSKKPIIYDVETLRDGNSFSARRVAAIQNGKPIFYMTASFQA Number of specific fragments extracted= 6 number of extra gaps= 1 total=456 Will force an alignment to be made, even if fragment is small Number of alignments=87 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1iq6A/T0322-1iq6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1iq6A expands to /projects/compbio/data/pdb/1iq6.pdb.gz 1iq6A:# T0322 read from 1iq6A/T0322-1iq6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1iq6A read from 1iq6A/T0322-1iq6A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1iq6A to template set # found chain 1iq6A in template set T0322 54 :TNGLGNCHGGMLMSFADMAWG 1iq6A 46 :AFERPIVHGMLLASLFSGLLG T0322 78 :SLQKSYSWVTVRLMCDFLSGAKLGDWVEGEGELIS 1iq6A 67 :QQLPGKGSIYLGQSLSFKLPVFVGDEVTAEVEVTA T0322 113 :EEDMLFTVRGRIWA 1iq6A 104 :EDKPIATLTTRIFT T0322 127 :GERTLITGTGVFKA 1iq6A 119 :GGALAVTGEAVVKL Number of specific fragments extracted= 4 number of extra gaps= 0 total=460 Will force an alignment to be made, even if fragment is small Number of alignments=88 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1iq6A/T0322-1iq6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 1iq6A/T0322-1iq6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1iq6A read from 1iq6A/T0322-1iq6A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1iq6A in template set T0322 56 :GLGNCHGGMLMSFA 1iq6A 48 :ERPIVHGMLLASLF T0322 73 :WGRIISLQKSYSWVTVRLMCDFLSGAKLGDWVEGEGELISE 1iq6A 62 :SGLLGQQLPGKGSIYLGQSLSFKLPVFVGDEVTAEVEVTAL T0322 114 :EDMLFTVRGRIWA 1iq6A 105 :DKPIATLTTRIFT T0322 127 :GERTLITGTGVFK 1iq6A 119 :GGALAVTGEAVVK Number of specific fragments extracted= 4 number of extra gaps= 0 total=464 Will force an alignment to be made, even if fragment is small Number of alignments=89 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1iq6A/T0322-1iq6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 1iq6A/T0322-1iq6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1iq6A read from 1iq6A/T0322-1iq6A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1iq6A in template set T0322 59 :NCHGGMLMS 1iq6A 51 :IVHGMLLAS T0322 72 :AWGRIISLQK 1iq6A 60 :LFSGLLGQQL T0322 82 :SYSWV 1iq6A 73 :GSIYL T0322 89 :RLMCDFLSGAKLGDWVEGEGELIS 1iq6A 78 :GQSLSFKLPVFVGDEVTAEVEVTA T0322 113 :EEDMLFTVRGRIWAGERTLITGTGVFKA 1iq6A 104 :EDKPIATLTTRIFTQGGALAVTGEAVVK Number of specific fragments extracted= 5 number of extra gaps= 0 total=469 Will force an alignment to be made, even if fragment is small Number of alignments=90 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2essA/T0322-2essA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2essA expands to /projects/compbio/data/pdb/2ess.pdb.gz 2essA:Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 3, because occupancy 0.500 <= existing 0.500 in 2essA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 7, because occupancy 0.500 <= existing 0.500 in 2essA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 9, because occupancy 0.500 <= existing 0.500 in 2essA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 13, because occupancy 0.500 <= existing 0.500 in 2essA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 331, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 335, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 337, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 472, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 476, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 478, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 480, because occupancy 0.500 <= existing 0.500 in 2essA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1165, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1169, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1171, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1173, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1175, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1177, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1179, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1181, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1218, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1222, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1224, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1226, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1228, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1255, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1259, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1261, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1263, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1357, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1361, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1363, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1365, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1367, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1369, because occupancy 0.500 <= existing 0.500 in 2essA Skipped atom 1371, because occupancy 0.500 <= existing 0.500 in 2essA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0322 read from 2essA/T0322-2essA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2essA read from 2essA/T0322-2essA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2essA to template set # found chain 2essA in template set Warning: unaligning (T0322)K145 because of BadResidue code BAD_PEPTIDE in next template residue (2essA)R121 Warning: unaligning (T0322)P146 because of BadResidue code BAD_PEPTIDE at template residue (2essA)R121 Warning: unaligning (T0322)P148 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2essA)A124 Warning: unaligning (T0322)G149 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2essA)A124 Warning: unaligning (T0322)K154 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2essA)L129 T0322 7 :DAQTA 2essA 3 :EENKI T0322 43 :ARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 2essA 8 :GTYQFVAEPFHVDFNGRLTMGVLGNHLLNCAGFHASDR T0322 81 :KSYSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWA 2essA 55 :DNYTWVLSRLAIELDEMPYQYEKFSVQTWVENVYRLFTDRNFAVID T0322 127 :GERTLITGTGVFKALSAR 2essA 102 :DGKKIGYARSVWAMINLN T0322 147 :R 2essA 122 :K Number of specific fragments extracted= 5 number of extra gaps= 2 total=474 Will force an alignment to be made, even if fragment is small Number of alignments=91 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2essA/T0322-2essA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 2essA/T0322-2essA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2essA read from 2essA/T0322-2essA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2essA in template set Warning: unaligning (T0322)K145 because of BadResidue code BAD_PEPTIDE in next template residue (2essA)R121 Warning: unaligning (T0322)P146 because of BadResidue code BAD_PEPTIDE at template residue (2essA)R121 Warning: unaligning (T0322)P148 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2essA)A124 T0322 27 :GRQIG 2essA 4 :ENKIG T0322 44 :RLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 2essA 9 :TYQFVAEPFHVDFNGRLTMGVLGNHLLNCAGFHASDR T0322 82 :SY 2essA 46 :GF T0322 84 :SWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWA 2essA 58 :TWVLSRLAIELDEMPYQYEKFSVQTWVENVYRLFTDRNFAVID T0322 127 :GERTLITGTGVFKALSAR 2essA 102 :DGKKIGYARSVWAMINLN T0322 147 :R 2essA 122 :K Number of specific fragments extracted= 6 number of extra gaps= 2 total=480 Will force an alignment to be made, even if fragment is small Number of alignments=92 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2essA/T0322-2essA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 2essA/T0322-2essA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2essA read from 2essA/T0322-2essA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2essA in template set T0322 43 :ARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQK 2essA 8 :GTYQFVAEPFHVDFNGRLTMGVLGNHLLNCAGFHASDRG T0322 82 :SYSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFKALSAR 2essA 56 :NYTWVLSRLAIELDEMPYQYEKFSVQTWVENVYRLFTDRNFAVIDKDGKKIGYARSVWAMINL Number of specific fragments extracted= 2 number of extra gaps= 0 total=482 Will force an alignment to be made, even if fragment is small Number of alignments=93 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mkaA/T0322-1mkaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1mkaA expands to /projects/compbio/data/pdb/1mka.pdb.gz 1mkaA:# T0322 read from 1mkaA/T0322-1mkaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mkaA read from 1mkaA/T0322-1mkaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1mkaA to template set # found chain 1mkaA in template set Warning: unaligning (T0322)I30 because of BadResidue code BAD_PEPTIDE in next template residue (1mkaA)N32 Warning: unaligning (T0322)L57 because of BadResidue code BAD_PEPTIDE in next template residue (1mkaA)F71 T0322 7 :DAQTAAIPEGFS 1mkaA 3 :KRESYTKEDLLA T0322 19 :QLNWSRGFGRQ 1mkaA 20 :LFGAKGPQLPA T0322 31 :G 1mkaA 37 :D T0322 34 :FEHREGPG 1mkaA 38 :RVVKMTET T0322 42 :QARLAFRVEEHH 1mkaA 53 :YVEAELDINPDL T0322 54 :TNG 1mkaA 67 :FGC T0322 58 :GNCHGGMLMSFADMAWGRIISLQ 1mkaA 75 :PVMPGCLGLDAMWQLVGFYLGWL T0322 82 :S 1mkaA 98 :G T0322 83 :YSWVTVRLM 1mkaA 101 :GKGRALGVG T0322 92 :CDFLSGAKLGD 1mkaA 111 :VKFTGQVLPTA T0322 103 :WVEGEGELIS 1mkaA 123 :KVTYRIHFKR T0322 113 :EEDMLFTVRGRIWAGERTLITGT 1mkaA 136 :RRLIMGLADGEVLVDGRLIYTAS T0322 136 :GVFKALSARK 1mkaA 160 :LKVGLFQDTS Number of specific fragments extracted= 13 number of extra gaps= 2 total=495 Will force an alignment to be made, even if fragment is small Number of alignments=94 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mkaA/T0322-1mkaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 1mkaA/T0322-1mkaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mkaA read from 1mkaA/T0322-1mkaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mkaA in template set Warning: unaligning (T0322)S23 because of BadResidue code BAD_PEPTIDE in next template residue (1mkaA)N32 Warning: unaligning (T0322)R24 because of BadResidue code BAD_PEPTIDE at template residue (1mkaA)N32 Warning: unaligning (T0322)L57 because of BadResidue code BAD_PEPTIDE in next template residue (1mkaA)F71 T0322 10 :TAAIPEGFSQLNW 1mkaA 18 :GELFGAKGPQLPA T0322 25 :GF 1mkaA 33 :ML T0322 29 :QIG 1mkaA 35 :MMD T0322 34 :FEHREGPG 1mkaA 38 :RVVKMTET T0322 42 :QARLAFRVEEHHT 1mkaA 53 :YVEAELDINPDLW T0322 55 :NG 1mkaA 68 :GC T0322 58 :GNCHGGMLMSFADMAWGRIISLQ 1mkaA 75 :PVMPGCLGLDAMWQLVGFYLGWL T0322 82 :SY 1mkaA 98 :GG T0322 84 :SWVTVRLM 1mkaA 102 :KGRALGVG T0322 92 :CDFLSGAKLG 1mkaA 111 :VKFTGQVLPT T0322 102 :DWVEGEGEL 1mkaA 122 :KKVTYRIHF T0322 111 :ISEEDMLFTVRGRIWAGERTLITGT 1mkaA 134 :VNRRLIMGLADGEVLVDGRLIYTAS T0322 136 :GVFKALSARK 1mkaA 160 :LKVGLFQDTS Number of specific fragments extracted= 13 number of extra gaps= 2 total=508 Will force an alignment to be made, even if fragment is small Number of alignments=95 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mkaA/T0322-1mkaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 1mkaA/T0322-1mkaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mkaA read from 1mkaA/T0322-1mkaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mkaA in template set Warning: unaligning (T0322)F26 because of BadResidue code BAD_PEPTIDE in next template residue (1mkaA)N32 Warning: unaligning (T0322)G27 because of BadResidue code BAD_PEPTIDE at template residue (1mkaA)N32 T0322 3 :DDLTDAQTAAIPEGFSQLNWSRG 1mkaA 2 :DKRESYTKEDLLASGRGELFGAK T0322 28 :RQIGP 1mkaA 33 :MLMMD T0322 34 :FEHREGP 1mkaA 38 :RVVKMTE T0322 41 :GQARLAFRVEEHHT 1mkaA 52 :GYVEAELDINPDLW T0322 56 :GLGNCHGGMLMSFADMAWGRIISLQK 1mkaA 73 :GDPVMPGCLGLDAMWQLVGFYLGWLG T0322 82 :SYSWVTVRLM 1mkaA 100 :EGKGRALGVG T0322 92 :CDFLSGAKLG 1mkaA 111 :VKFTGQVLPT T0322 102 :DWVEGEGE 1mkaA 122 :KKVTYRIH T0322 110 :LISEEDMLFTVRGRIWAGERTLITGTGVFKALSARK 1mkaA 133 :IVNRRLIMGLADGEVLVDGRLIYTASDLKVGLFQDT Number of specific fragments extracted= 9 number of extra gaps= 1 total=517 Will force an alignment to be made, even if fragment is small Number of alignments=96 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1tbuA/T0322-1tbuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1tbuA expands to /projects/compbio/data/pdb/1tbu.pdb.gz 1tbuA:# T0322 read from 1tbuA/T0322-1tbuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tbuA read from 1tbuA/T0322-1tbuA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1tbuA to template set # found chain 1tbuA in template set Warning: unaligning (T0322)G31 because first residue in template chain is (1tbuA)K13 Warning: unaligning (T0322)P32 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1tbuA)I14 Warning: unaligning (T0322)L33 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1tbuA)L15 Warning: unaligning (T0322)V49 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1tbuA)T40 Warning: unaligning (T0322)C60 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1tbuA)T40 T0322 34 :FEHREGPGQARLAFR 1tbuA 16 :ELVPLSPTSFVTKYL T0322 61 :HGGMLM 1tbuA 41 :FGGTLV T0322 71 :MAWGRIISLQKSYSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFK 1tbuA 47 :SQSLLASLHTVPLNFFPTSLHSYFIKGGDPRTKITYHVQNLRNGRNFIHKQVSAYQHDKLIFTSMILFA Number of specific fragments extracted= 3 number of extra gaps= 0 total=520 Will force an alignment to be made, even if fragment is small Number of alignments=97 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1tbuA/T0322-1tbuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 1tbuA/T0322-1tbuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tbuA read from 1tbuA/T0322-1tbuA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1tbuA in template set Warning: unaligning (T0322)G31 because first residue in template chain is (1tbuA)K13 Warning: unaligning (T0322)P32 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1tbuA)I14 Warning: unaligning (T0322)L33 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1tbuA)L15 Warning: unaligning (T0322)V49 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1tbuA)T40 Warning: unaligning (T0322)C60 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1tbuA)T40 T0322 34 :FEHREGPGQARLAFR 1tbuA 16 :ELVPLSPTSFVTKYL T0322 61 :HGGMLMSFA 1tbuA 41 :FGGTLVSQS T0322 74 :GRIISLQKSYSWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFK 1tbuA 50 :LLASLHTVPLNFFPTSLHSYFIKGGDPRTKITYHVQNLRNGRNFIHKQVSAYQHDKLIFTSMILFA Number of specific fragments extracted= 3 number of extra gaps= 0 total=523 Will force an alignment to be made, even if fragment is small Number of alignments=98 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1tbuA/T0322-1tbuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 1tbuA/T0322-1tbuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1tbuA read from 1tbuA/T0322-1tbuA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1tbuA in template set Warning: unaligning (T0322)V49 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1tbuA)T40 Warning: unaligning (T0322)C60 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1tbuA)T40 Warning: unaligning (T0322)A140 because last residue in template chain is (1tbuA)V116 T0322 35 :EHREGPGQARLAFR 1tbuA 17 :LVPLSPTSFVTKYL T0322 61 :HGGMLM 1tbuA 41 :FGGTLV T0322 71 :MAWGRIISLQK 1tbuA 47 :SQSLLASLHTV T0322 82 :SYSWV 1tbuA 60 :NFFPT T0322 89 :RLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAGERTLITGTGVFK 1tbuA 65 :SLHSYFIKGGDPRTKITYHVQNLRNGRNFIHKQVSAYQHDKLIFTSMILFA Number of specific fragments extracted= 5 number of extra gaps= 0 total=528 Will force an alignment to be made, even if fragment is small Number of alignments=99 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bi0A/T0322-2bi0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2bi0A expands to /projects/compbio/data/pdb/2bi0.pdb.gz 2bi0A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0322 read from 2bi0A/T0322-2bi0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bi0A read from 2bi0A/T0322-2bi0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2bi0A to template set # found chain 2bi0A in template set T0322 8 :AQTAAIPEGFSQLNWSRGFGRQIG 2bi0A 187 :TAHWDGAVFRKRVPGPHFDAGIAG T0322 34 :FEHREGP 2bi0A 211 :AVLHSTA T0322 47 :FRV 2bi0A 218 :DLV T0322 50 :EEHHTNGL 2bi0A 239 :DWRVSGRR T0322 59 :NCHGGMLMSFA 2bi0A 247 :LVYGGHTIGLA T0322 73 :WGRIISLQ 2bi0A 258 :LAQATRLL T0322 82 :SYSWVTVRLM 2bi0A 266 :PNLATVLDWE T0322 92 :CDFLSGAKLGDWVEGEGELIS 2bi0A 277 :CDHTAPVHEGDTLYSELHIES T0322 113 :EEDMLFTVRGRIWA 2bi0A 302 :ADGGVLGLRSLVYA T0322 127 :G 2bi0A 318 :D T0322 128 :E 2bi0A 320 :A T0322 129 :RTLITGTGVFKA 2bi0A 325 :RQVLDWRFSALQ Number of specific fragments extracted= 12 number of extra gaps= 0 total=540 Will force an alignment to be made, even if fragment is small Number of alignments=100 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bi0A/T0322-2bi0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 2bi0A/T0322-2bi0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bi0A read from 2bi0A/T0322-2bi0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2bi0A in template set T0322 50 :EEHHTNGL 2bi0A 239 :DWRVSGRR T0322 59 :NCHGGMLMSFA 2bi0A 247 :LVYGGHTIGLA T0322 74 :GRIISLQKSYSWVTVRLM 2bi0A 258 :LAQATRLLPNLATVLDWE T0322 92 :CDFLSGAKLGDWVEGEGELISE 2bi0A 277 :CDHTAPVHEGDTLYSELHIESA T0322 114 :EDMLFTVRGRIWA 2bi0A 303 :DGGVLGLRSLVYA T0322 127 :G 2bi0A 318 :D T0322 129 :RTLITGTGVFKA 2bi0A 325 :RQVLDWRFSALQ Number of specific fragments extracted= 7 number of extra gaps= 0 total=547 Will force an alignment to be made, even if fragment is small Number of alignments=101 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bi0A/T0322-2bi0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 2bi0A/T0322-2bi0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2bi0A read from 2bi0A/T0322-2bi0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2bi0A in template set T0322 53 :HTNGLGNCHGGMLMSF 2bi0A 241 :RVSGRRLVYGGHTIGL T0322 72 :AWGRIISLQKSYSWVTVRLMCDFLSGAKLGDWVEGEGELISEED 2bi0A 257 :ALAQATRLLPNLATVLDWESCDHTAPVHEGDTLYSELHIESAQA T0322 116 :MLFTVRGRIWA 2bi0A 305 :GVLGLRSLVYA Number of specific fragments extracted= 3 number of extra gaps= 0 total=550 Will force an alignment to be made, even if fragment is small Number of alignments=102 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bvqA/T0322-1bvqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1bvqA expands to /projects/compbio/data/pdb/1bvq.pdb.gz 1bvqA:# T0322 read from 1bvqA/T0322-1bvqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bvqA read from 1bvqA/T0322-1bvqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1bvqA to template set # found chain 1bvqA in template set Warning: unaligning (T0322)Y153 because of BadResidue code BAD_PEPTIDE in next template residue (1bvqA)D135 Warning: unaligning (T0322)K154 because of BadResidue code BAD_PEPTIDE at template residue (1bvqA)D135 T0322 42 :QARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 1bvqA 4 :SITMQQRIEFGDCDPAGIVWYPNYHRWLDAASRNYFIKC T0322 83 :YSWV 1bvqA 54 :RGIV T0322 87 :TVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWA 1bvqA 61 :IVSCNASFVCTASYDDVLTIETCIKEWRRKSFVQRHSVSR T0322 127 :GE 1bvqA 103 :PG T0322 129 :RTLITGTGV 1bvqA 108 :QLVMRADEI T0322 138 :FKALSARKPRPGELA 1bvqA 119 :FAMNDGERLRAIEVP Number of specific fragments extracted= 6 number of extra gaps= 1 total=556 Will force an alignment to be made, even if fragment is small Number of alignments=103 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bvqA/T0322-1bvqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 1bvqA/T0322-1bvqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bvqA read from 1bvqA/T0322-1bvqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1bvqA in template set T0322 42 :QARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQ 1bvqA 4 :SITMQQRIEFGDCDPAGIVWYPNYHRWLDAASRNYFIKC T0322 82 :SY 1bvqA 43 :GL T0322 84 :SWVTVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWA 1bvqA 58 :GTPIVSCNASFVCTASYDDVLTIETCIKEWRRKSFVQRHSVSR T0322 127 :GE 1bvqA 103 :PG T0322 129 :RTLITGTGVF 1bvqA 108 :QLVMRADEIR T0322 139 :KALSAR 1bvqA 120 :AMNDGE Number of specific fragments extracted= 6 number of extra gaps= 0 total=562 Will force an alignment to be made, even if fragment is small Number of alignments=104 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bvqA/T0322-1bvqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0322 read from 1bvqA/T0322-1bvqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1bvqA read from 1bvqA/T0322-1bvqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1bvqA in template set T0322 42 :QARLAFRVEEHHTNGLGNC 1bvqA 4 :SITMQQRIEFGDCDPAGIV T0322 64 :MLMSFADMAWGRIISLQK 1bvqA 26 :NYHRWLDAASRNYFIKCG T0322 83 :YSWV 1bvqA 54 :RGIV T0322 87 :TVRLMCDFLSGAKLGDWVEGEGELISEEDMLFTVRGRI 1bvqA 61 :IVSCNASFVCTASYDDVLTIETCIKEWRRKSFVQRHSV T0322 125 :WAGER 1bvqA 101 :TTPGG T0322 130 :TLITGT 1bvqA 108 :QLVMRA Number of specific fragments extracted= 6 number of extra gaps= 0 total=568 Will force an alignment to be made, even if fragment is small Number of alignments=105 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cy9A/T0322-2cy9A-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2cy9A expands to /projects/compbio/data/pdb/2cy9.pdb.gz 2cy9A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0322 read from 2cy9A/T0322-2cy9A-t06-local-adpstyle5.a2m # 2cy9A read from 2cy9A/T0322-2cy9A-t06-local-adpstyle5.a2m # adding 2cy9A to template set # found chain 2cy9A in template set Warning: unaligning (T0322)S18 because first residue in template chain is (2cy9A)K13 Warning: unaligning (T0322)Q19 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2cy9A)V14 Warning: unaligning (T0322)L20 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2cy9A)M15 Warning: unaligning (T0322)N21 because of BadResidue code BAD_PEPTIDE at template residue (2cy9A)F16 Warning: unaligning (T0322)W22 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2cy9A)K17 Warning: unaligning (T0322)S23 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2cy9A)P19 Warning: unaligning (T0322)R24 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2cy9A)P19 Warning: unaligning (T0322)F26 because of BadResidue code BAD_PEPTIDE in next template residue (2cy9A)D22 Warning: unaligning (T0322)G27 because of BadResidue code BAD_PEPTIDE at template residue (2cy9A)D22 Warning: unaligning (T0322)Q29 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2cy9A)V24 Warning: unaligning (T0322)I30 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2cy9A)L25 Warning: unaligning (T0322)G31 because of BadResidue code BAD_PEPTIDE at template residue (2cy9A)E26 Warning: unaligning (T0322)P32 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2cy9A)K27 Warning: unaligning (T0322)L33 because of BadResidue code BAD_PEPTIDE at template residue (2cy9A)V28 Warning: unaligning (T0322)F34 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2cy9A)L30 Warning: unaligning (T0322)E35 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2cy9A)L30 Warning: unaligning (T0322)H36 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2cy9A)S32 Warning: unaligning (T0322)R37 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2cy9A)S32 Warning: unaligning (T0322)E38 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2cy9A)A33 Warning: unaligning (T0322)G39 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2cy9A)P35 Warning: unaligning (T0322)P40 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2cy9A)P35 Warning: unaligning (T0322)Q42 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2cy9A)L38 Warning: unaligning (T0322)A43 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2cy9A)L38 Warning: unaligning (T0322)L57 because of BadResidue code BAD_PEPTIDE in next template residue (2cy9A)G53 Warning: unaligning (T0322)G58 because of BadResidue code BAD_PEPTIDE at template residue (2cy9A)G53 Warning: unaligning (T0322)N59 because of BadResidue code BAD_PEPTIDE at template residue (2cy9A)T54 Warning: unaligning (T0322)C60 because of BadResidue code BAD_PEPTIDE in next template residue (2cy9A)H56 Warning: unaligning (T0322)H61 because of BadResidue code BAD_PEPTIDE at template residue (2cy9A)H56 Warning: unaligning (T0322)G62 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2cy9A)G57 Warning: unaligning (T0322)G63 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2cy9A)G58 Warning: unaligning (T0322)I76 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2cy9A)L72 Warning: unaligning (T0322)I77 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2cy9A)L72 Warning: unaligning (T0322)S78 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2cy9A)M73 Warning: unaligning (T0322)Q80 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2cy9A)P80 Warning: unaligning (T0322)S84 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2cy9A)P80 Warning: unaligning (T0322)W85 because of BadResidue code BAD_PEPTIDE at template residue (2cy9A)G81 Warning: unaligning (T0322)T87 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2cy9A)V84 Warning: unaligning (T0322)V88 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2cy9A)V84 Warning: unaligning (T0322)G97 because of BadResidue code BAD_PEPTIDE in next template residue (2cy9A)A94 Warning: unaligning (T0322)A98 because of BadResidue code BAD_PEPTIDE at template residue (2cy9A)A94 Warning: unaligning (T0322)L100 because of BadResidue code BAD_PEPTIDE in next template residue (2cy9A)G97 Warning: unaligning (T0322)G101 because of BadResidue code BAD_PEPTIDE at template residue (2cy9A)G97 Warning: unaligning (T0322)W103 because of BadResidue code BAD_PEPTIDE in next template residue (2cy9A)I100 Warning: unaligning (T0322)V104 because of BadResidue code BAD_PEPTIDE at template residue (2cy9A)I100 Warning: unaligning (T0322)E113 because of BadResidue code BAD_PEPTIDE in next template residue (2cy9A)G110 Warning: unaligning (T0322)E114 because of BadResidue code BAD_PEPTIDE at template residue (2cy9A)G110 Warning: unaligning (T0322)D115 because of BadResidue code BAD_PEPTIDE at template residue (2cy9A)K111 Warning: unaligning (T0322)M116 because of BadResidue code BAD_PEPTIDE at template residue (2cy9A)T112 Warning: unaligning (T0322)L117 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2cy9A)A114 Warning: unaligning (T0322)F118 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2cy9A)A114 Warning: unaligning (T0322)T119 because of BadResidue code BAD_PEPTIDE at template residue (2cy9A)F115 Warning: unaligning (T0322)G122 because of BadResidue code BAD_PEPTIDE in next template residue (2cy9A)D119 Warning: unaligning (T0322)R123 because of BadResidue code BAD_PEPTIDE at template residue (2cy9A)D119 Warning: unaligning (T0322)E128 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2cy9A)G126 Warning: unaligning (T0322)R129 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2cy9A)K127 Warning: unaligning (T0322)T130 because of BadResidue code BAD_PEPTIDE in next template residue (2cy9A)I129 Warning: unaligning (T0322)L131 because of BadResidue code BAD_PEPTIDE at template residue (2cy9A)I129 Warning: unaligning (T0322)G134 because of BadResidue code BAD_PEPTIDE in next template residue (2cy9A)R133 Warning: unaligning (T0322)T135 because of BadResidue code BAD_PEPTIDE at template residue (2cy9A)R133 T0322 25 :G 2cy9A 20 :G T0322 41 :G 2cy9A 36 :E T0322 44 :RLAFRVEEHHTNG 2cy9A 39 :ICEMKVEEQHTNK T0322 64 :MLMSFADMAWGR 2cy9A 59 :LTATLVDSISTM T0322 79 :L 2cy9A 74 :C T0322 86 :V 2cy9A 82 :V T0322 89 :RLMCDFLS 2cy9A 85 :DMNITYMS T0322 99 :K 2cy9A 95 :K T0322 102 :D 2cy9A 98 :E T0322 105 :EGEGELIS 2cy9A 101 :VITAHILK T0322 120 :VR 2cy9A 116 :AS T0322 124 :IWAG 2cy9A 120 :LTNK T0322 132 :IT 2cy9A 130 :AQ T0322 136 :GVF 2cy9A 134 :HTK Number of specific fragments extracted= 14 number of extra gaps= 12 total=582 Will force an alignment to be made, even if fragment is small Number of alignments=106 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1sbkA/T0322-1sbkA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1sbkA expands to /projects/compbio/data/pdb/1sbk.pdb.gz 1sbkA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0322 read from 1sbkA/T0322-1sbkA-t06-local-adpstyle5.a2m # 1sbkA read from 1sbkA/T0322-1sbkA-t06-local-adpstyle5.a2m # adding 1sbkA to template set # found chain 1sbkA in template set T0322 24 :RGFGRQIG 1sbkA 18 :GNMVGFLD T0322 33 :LFEHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQKS 1sbkA 26 :IRFEHIGDDTLEATMPVDSRTKQPFGLLHGGASVVLAESIGSVAGYLCTE T0322 83 :YSWVTVRLMCDFLSGAKLG 1sbkA 78 :QKVVGLEINANHVRSAREG T0322 103 :WVEGEGELISEEDMLFTVRGRIWAG 1sbkA 97 :RVRGVCKPLHLGSRHQVWQIEIFDE T0322 128 :ERTLITGTGVFKAL 1sbkA 123 :GRLCCSSRLTTAIL Number of specific fragments extracted= 5 number of extra gaps= 0 total=587 Will force an alignment to be made, even if fragment is small Number of alignments=107 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1y7uA/T0322-1y7uA-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1y7uA expands to /projects/compbio/data/pdb/1y7u.pdb.gz 1y7uA:Skipped atom 177, because occupancy 0.500 <= existing 0.500 in 1y7uA Skipped atom 179, because occupancy 0.500 <= existing 0.500 in 1y7uA Skipped atom 181, because occupancy 0.500 <= existing 0.500 in 1y7uA Skipped atom 183, because occupancy 0.500 <= existing 0.500 in 1y7uA Skipped atom 185, because occupancy 0.500 <= existing 0.500 in 1y7uA Skipped atom 187, because occupancy 0.500 <= existing 0.500 in 1y7uA Skipped atom 189, because occupancy 0.500 <= existing 0.500 in 1y7uA Skipped atom 191, because occupancy 0.500 <= existing 0.500 in 1y7uA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1136, because occupancy 0.500 <= existing 0.500 in 1y7uA Skipped atom 1138, because occupancy 0.500 <= existing 0.500 in 1y7uA Skipped atom 1140, because occupancy 0.500 <= existing 0.500 in 1y7uA Skipped atom 1142, because occupancy 0.500 <= existing 0.500 in 1y7uA Skipped atom 1144, because occupancy 0.500 <= existing 0.500 in 1y7uA Skipped atom 1146, because occupancy 0.500 <= existing 0.500 in 1y7uA Skipped atom 1148, because occupancy 0.500 <= existing 0.500 in 1y7uA Skipped atom 1150, because occupancy 0.500 <= existing 0.500 in 1y7uA Skipped atom 1152, because occupancy 0.500 <= existing 0.500 in 1y7uA Skipped atom 1154, because occupancy 0.500 <= existing 0.500 in 1y7uA Skipped atom 1156, because occupancy 0.500 <= existing 0.500 in 1y7uA Skipped atom 1172, because occupancy 0.500 <= existing 0.500 in 1y7uA Skipped atom 1174, because occupancy 0.500 <= existing 0.500 in 1y7uA Skipped atom 1176, because occupancy 0.500 <= existing 0.500 in 1y7uA Skipped atom 1178, because occupancy 0.500 <= existing 0.500 in 1y7uA Skipped atom 1180, because occupancy 0.500 <= existing 0.500 in 1y7uA Skipped atom 1182, because occupancy 0.500 <= existing 0.500 in 1y7uA Skipped atom 1184, because occupancy 0.500 <= existing 0.500 in 1y7uA Skipped atom 1186, because occupancy 0.500 <= existing 0.500 in 1y7uA Skipped atom 1188, because occupancy 0.500 <= existing 0.500 in 1y7uA Skipped atom 1219, because occupancy 0.500 <= existing 0.500 in 1y7uA Skipped atom 1221, because occupancy 0.500 <= existing 0.500 in 1y7uA Skipped atom 1223, because occupancy 0.500 <= existing 0.500 in 1y7uA Skipped atom 1225, because occupancy 0.500 <= existing 0.500 in 1y7uA Skipped atom 1227, because occupancy 0.500 <= existing 0.500 in 1y7uA Skipped atom 1229, because occupancy 0.500 <= existing 0.500 in 1y7uA Skipped atom 1231, because occupancy 0.500 <= existing 0.500 in 1y7uA Skipped atom 1233, because occupancy 0.500 <= existing 0.500 in 1y7uA Skipped atom 1235, because occupancy 0.500 <= existing 0.500 in 1y7uA Skipped atom 1237, because occupancy 0.500 <= existing 0.500 in 1y7uA Skipped atom 1239, because occupancy 0.500 <= existing 0.500 in 1y7uA # T0322 read from 1y7uA/T0322-1y7uA-t06-local-adpstyle5.a2m # 1y7uA read from 1y7uA/T0322-1y7uA-t06-local-adpstyle5.a2m # adding 1y7uA to template set # found chain 1y7uA in template set T0322 35 :EHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQKSYSWVTVRLM 1y7uA 9 :GKTANESRVFKTSRVFPTDLNDHNTLFGGKILSEMDMVASISASRHSRKECVTASMD T0322 92 :CDFLSGAKLGDWVEGEGELISEEDMLFTVRGRIWAG 1y7uA 67 :VDFLHPVRSSDCVSYESFVIWTGRTSMEVFVKVVSE T0322 129 :RTLITGTGVFKALSARKPR 1y7uA 110 :RIAATSFVTFVALSKENNP T0322 148 :PGELAYKE 1y7uA 131 :VPRVIPDT Number of specific fragments extracted= 4 number of extra gaps= 0 total=591 Will force an alignment to be made, even if fragment is small Number of alignments=108 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vh9A/T0322-1vh9A-t06-local-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vh9A expands to /projects/compbio/data/pdb/1vh9.pdb.gz 1vh9A:Skipped atom 819, because occupancy 0.350 <= existing 0.650 in 1vh9A Skipped atom 821, because occupancy 0.350 <= existing 0.650 in 1vh9A Skipped atom 823, because occupancy 0.350 <= existing 0.650 in 1vh9A Skipped atom 825, because occupancy 0.350 <= existing 0.650 in 1vh9A Skipped atom 827, because occupancy 0.350 <= existing 0.650 in 1vh9A Skipped atom 880, because occupancy 0.350 <= existing 0.650 in 1vh9A Skipped atom 882, because occupancy 0.350 <= existing 0.650 in 1vh9A Skipped atom 884, because occupancy 0.350 <= existing 0.650 in 1vh9A Skipped atom 886, because occupancy 0.350 <= existing 0.650 in 1vh9A Skipped atom 984, because occupancy 0.350 <= existing 0.650 in 1vh9A # T0322 read from 1vh9A/T0322-1vh9A-t06-local-adpstyle5.a2m # 1vh9A read from 1vh9A/T0322-1vh9A-t06-local-adpstyle5.a2m # adding 1vh9A to template set # found chain 1vh9A in template set Warning: unaligning (T0322)S142 because last residue in template chain is (1vh9A)G137 T0322 24 :RGFGRQIG 1vh9A 18 :NTMVAHLG T0322 33 :LFEHREGPGQARLAFRVEEHHTNGLGNCHGGMLMSFADMAWGRIISLQKS 1vh9A 26 :IVYTRLGDDVLEAEMPVDTRTHQPFGLLHGGASAALAETLGSMAGFMMTR T0322 83 :YSWVTVRLMCDFLSGAKLG 1vh9A 78 :QCVVGTELNATHHRPVSEG T0322 103 :WVEGEGELISEEDMLFTVRGRIWAG 1vh9A 97 :KVRGVCQPLHLGRQNQSWEIVVFDE T0322 128 :ERTLITGTGVFKAL 1vh9A 123 :GRRCCTCRLGTAVL Number of specific fragments extracted= 5 number of extra gaps= 0 total=596 Will force an alignment to be made, even if fragment is small Number of alignments=109 # command:CPU_time= 23.844 sec, elapsed time= 27.551 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 109 Adding 12246 constraints to all_contacts Done adding distance constraints # command:CPU_time= 23.922 sec, elapsed time= 27.638 sec. # command:Reading probabilities from T0322.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 61.813 Optimizing... Probability sum: -295.352, CN propb: -295.352 weights: 0.443 constraints: 416 # command:CPU_time= 68.269 sec, elapsed time= 72.014 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 416 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 416 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 1108 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 1108 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 9502 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 9502 # command:CPU_time= 68.468 sec, elapsed time= 72.388 sec. # command: