# 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: 408,82794,639987 # 79931 residues have no bad marker # 573 residues lack atoms needed to compute omega # 313 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 0 # HAS_OXT 264 # TOO_MANY_ATOMS 0 # TOO_FEW_ATOMS 378 # HAS_UNKNOWN_ATOMS 0 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 148 # NON_PLANAR_PEPTIDE 17 # BAD_PEPTIDE 812 # HIGH_B_FACTOR 1566 # 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 T0590 numbered 1 through 137 Created new target T0590 from T0590.a2m # command:CPU_time= 5.958 sec, elapsed time= 6.346 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 2c4xA/T0590-2c4xA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2c4xA expands to /projects/compbio/data/pdb/2c4x.pdb.gz 2c4xA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0590 read from 2c4xA/T0590-2c4xA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2c4xA read from 2c4xA/T0590-2c4xA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2c4xA to template set # found chain 2c4xA in template set Warning: unaligning (T0590)S57 because first residue in template chain is (2c4xA)P2 T0590 58 :SPVLPTARFTSDITEGFAPLSVRF 2c4xA 3 :ENQAPKAIFTFSPEDPVTDENVVF # choosing archetypes in rotamer library T0590 82 :KDFSENATSRLWMFGDGNT 2c4xA 32 :IDEDGTIAYYVWDFGDGYE T0590 101 :SDSPSPLHTFFNEGEYIVSLIVSNEND 2c4xA 53 :STTPTITYKYKNPGTYKVKLIVTDNQG T0590 128 :SDSASVTIRA 2c4xA 81 :SSSFTATIKV Number of specific fragments extracted= 4 number of extra gaps= 0 total=4 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 2c4xA/T0590-2c4xA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0590 read from 2c4xA/T0590-2c4xA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2c4xA read from 2c4xA/T0590-2c4xA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2c4xA in template set Warning: unaligning (T0590)S57 because first residue in template chain is (2c4xA)P2 T0590 58 :SPVLPTARFTSDITEGFAPLSVRF 2c4xA 3 :ENQAPKAIFTFSPEDPVTDENVVF T0590 82 :KDFSENATSRLWMFGDGN 2c4xA 32 :IDEDGTIAYYVWDFGDGY T0590 100 :TSDSPSPLHTFFNEGEYIVSLIVSNEND 2c4xA 52 :TSTTPTITYKYKNPGTYKVKLIVTDNQG T0590 128 :SDSASVTI 2c4xA 81 :SSSFTATI Number of specific fragments extracted= 4 number of extra gaps= 0 total=8 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 2c4xA/T0590-2c4xA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0590 read from 2c4xA/T0590-2c4xA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2c4xA read from 2c4xA/T0590-2c4xA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2c4xA in template set Warning: unaligning (T0590)S123 because of BadResidue code BAD_PEPTIDE in next template residue (2c4xA)G153 Warning: unaligning (T0590)N124 because of BadResidue code BAD_PEPTIDE at template residue (2c4xA)G153 Warning: unaligning (T0590)E125 because of BadResidue code BAD_PEPTIDE at template residue (2c4xA)G154 T0590 2 :NARDNKFNTWNDSRG 2c4xA 34 :EDGTIAYYVWDFGDG T0590 17 :NYWSDYEGSDENGDGIGDSAYAVNPEAGSMDYMPLMEYLHSS 2c4xA 52 :TSTTPTITYKYKNPGTYKVKLIVTDNQGASSSFTATIKVTSA T0590 62 :PTARFTSDITEGFAPLSVRFKDFS 2c4xA 94 :TGDNSKFNFEDGTLGGFTTSGTNA T0590 86 :ENATSRLWMFGDG 2c4xA 119 :GVVVNTTEKAFKG T0590 103 :SPSPLHTFFNEGEYIVSLIV 2c4xA 132 :ERGLKWTVTSEGEGTAELKL T0590 126 :NDSDSA 2c4xA 155 :TIVVPG T0590 132 :SVTIR 2c4xA 162 :TMTFR Number of specific fragments extracted= 7 number of extra gaps= 1 total=15 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 1l0qA/T0590-1l0qA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1l0qA expands to /projects/compbio/data/pdb/1l0q.pdb.gz 1l0qA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: OZ1 for alphabet: pdb_atoms Bad short name: NZ2 for alphabet: pdb_atoms Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0590 read from 1l0qA/T0590-1l0qA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1l0qA read from 1l0qA/T0590-1l0qA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1l0qA to template set # found chain 1l0qA in template set T0590 2 :NARDNKFNTWNDSRGN 1l0qA 220 :DKYFNTVSMIDTGTNK T0590 18 :YWSDYEGSDENGDGIGD 1l0qA 242 :VGPDPAGIAVTPDGKKV T0590 35 :SAYAVNPEAGSMDYMPL 1l0qA 267 :TVSVIDTATNTITATMA T0590 52 :MEYLHSSPVLPTARFTSDITEGFA 1l0qA 295 :IGSIPVQPVYPSADFKSNITSGYI T0590 76 :PLSVRFKDFSENATSRLWMFGDGNTSDSPSPLHTFFNEGEYIVSLIVSNENDSDSASVTIRA 1l0qA 321 :SEPVQFTDLSKDATEWKWDFGDGSSSKKQNPTHTYSETGIYTVRLTVSNSNGTDSQISTVNV Number of specific fragments extracted= 5 number of extra gaps= 0 total=20 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 1l0qA/T0590-1l0qA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0590 read from 1l0qA/T0590-1l0qA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1l0qA read from 1l0qA/T0590-1l0qA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1l0qA in template set T0590 2 :NARDNKFNTWNDSRGNYWSDYE 1l0qA 230 :DTGTNKITARIPVGPDPAGIAV T0590 27 :ENGDGIGDS 1l0qA 252 :TPDGKKVYV T0590 36 :AYAVNPEAG 1l0qA 267 :TVSVIDTAT T0590 45 :SMDYMP 1l0qA 278 :ITATMA T0590 51 :LMEYLHSSPVLPTARFTSDITEGFA 1l0qA 294 :FIGSIPVQPVYPSADFKSNITSGYI T0590 76 :PLSVRFKDFSENATSRLWMFGDGNTSDSPSPLHTFFNEGEYIVSLIVSNENDSDSASVT 1l0qA 321 :SEPVQFTDLSKDATEWKWDFGDGSSSKKQNPTHTYSETGIYTVRLTVSNSNGTDSQIST Number of specific fragments extracted= 6 number of extra gaps= 0 total=26 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 1l0qA/T0590-1l0qA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0590 read from 1l0qA/T0590-1l0qA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1l0qA read from 1l0qA/T0590-1l0qA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1l0qA in template set T0590 2 :NARDNKFNTWNDSRG 1l0qA 220 :DKYFNTVSMIDTGTN T0590 17 :NYWSDYEGSDENGDGIGDS 1l0qA 241 :PVGPDPAGIAVTPDGKKVY T0590 36 :A 1l0qA 267 :T T0590 37 :YAVNPEAGSMDYMP 1l0qA 269 :SVIDTATNTITATM T0590 52 :MEYLHSSPVLPTARFTSDITEGFAP 1l0qA 295 :IGSIPVQPVYPSADFKSNITSGYIF T0590 77 :LSVRFKDFSENATSRLWMFGDGNTSDSPSPLHTFFNEGEYIVSLIVSNENDSDSASVTIRA 1l0qA 322 :EPVQFTDLSKDATEWKWDFGDGSSSKKQNPTHTYSETGIYTVRLTVSNSNGTDSQISTVNV Number of specific fragments extracted= 6 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 1b4rA/T0590-1b4rA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1b4rA expands to /projects/compbio/data/pdb/1b4r.pdb.gz 1b4rA:# T0590 read from 1b4rA/T0590-1b4rA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1b4rA read from 1b4rA/T0590-1b4rA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1b4rA to template set # found chain 1b4rA in template set T0590 65 :RFTSDITEGFAPLSVRF 1b4rA 9 :TLVGPHGPLASGQLAAF T0590 82 :KDFSENATSRLWMFGDGNT 1b4rA 27 :IAAPLPVTATRWDFGDGSA T0590 101 :SDSPSPLHTFFNEGEYIVSLIVSNENDSDSASVTIRA 1b4rA 49 :AAGPAASHRYVLPGRYHVTAVLALGAGSALLGTDVQV 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 1b4rA/T0590-1b4rA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0590 read from 1b4rA/T0590-1b4rA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1b4rA read from 1b4rA/T0590-1b4rA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1b4rA in template set T0590 65 :RFTSDITEGFAPLSVRF 1b4rA 9 :TLVGPHGPLASGQLAAF T0590 82 :KDFSENATSRLWMFGDGN 1b4rA 27 :IAAPLPVTATRWDFGDGS T0590 100 :TSDSPSPLHTFFNEGEYIVSLIVSNEND 1b4rA 48 :DAAGPAASHRYVLPGRYHVTAVLALGAG T0590 128 :SDSASVTI 1b4rA 78 :LLGTDVQV Number of specific fragments extracted= 4 number of extra gaps= 0 total=39 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 1b4rA/T0590-1b4rA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0590 read from 1b4rA/T0590-1b4rA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1b4rA read from 1b4rA/T0590-1b4rA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1b4rA in template set Warning: unaligning (T0590)A64 because first residue in template chain is (1b4rA)A8 T0590 65 :RFTSDITEGFAPLSVRFKDFS 1b4rA 9 :TLVGPHGPLASGQLAAFHIAA T0590 86 :ENATSRLWMFGDGNT 1b4rA 31 :LPVTATRWDFGDGSA T0590 101 :SDSPSPLHTFFNEGEYIVSLIVSNENDSDSASVTIRA 1b4rA 49 :AAGPAASHRYVLPGRYHVTAVLALGAGSALLGTDVQV Number of specific fragments extracted= 3 number of extra gaps= 0 total=42 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 2e7mA/T0590-2e7mA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2e7mA expands to /projects/compbio/data/pdb/2e7m.pdb.gz 2e7mA:# T0590 read from 2e7mA/T0590-2e7mA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2e7mA read from 2e7mA/T0590-2e7mA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2e7mA to template set # found chain 2e7mA in template set T0590 55 :LHSSPVLPTARFTSDITEGFAPLSVRF 2e7mA 7 :GPRTVKELTVSAGDNLIITLPDNEVEL T0590 82 :KDFS 2e7mA 39 :PAPP T0590 86 :ENATSRLWMF 2e7mA 44 :ETTYNYEWNL T0590 96 :GDGNT 2e7mA 57 :PTDYQ T0590 101 :SDSPSPLHTFFN 2e7mA 65 :KQGHKQTLNLSQ T0590 113 :EGEYIVSLIVSNEND 2e7mA 79 :VGLYVFKVTVSSENA T0590 128 :SDSASVTIR 2e7mA 96 :EGFVNVTVK Number of specific fragments extracted= 7 number of extra gaps= 0 total=49 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 2e7mA/T0590-2e7mA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0590 read from 2e7mA/T0590-2e7mA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2e7mA read from 2e7mA/T0590-2e7mA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2e7mA in template set T0590 56 :HSSPVLPTARFTSDITEGFAPLSVRF 2e7mA 8 :PRTVKELTVSAGDNLIITLPDNEVEL T0590 82 :KDFS 2e7mA 39 :PAPP T0590 86 :ENATSRLWMF 2e7mA 44 :ETTYNYEWNL T0590 98 :GN 2e7mA 56 :HP T0590 100 :TSDSP 2e7mA 61 :QGEIK T0590 105 :SPLHTFFN 2e7mA 69 :KQTLNLSQ T0590 113 :EGEYIVSLIVSNEND 2e7mA 79 :VGLYVFKVTVSSENA T0590 128 :SDSASVTI 2e7mA 96 :EGFVNVTV T0590 136 :RA 2e7mA 105 :PA Number of specific fragments extracted= 9 number of extra gaps= 0 total=58 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 2e7mA/T0590-2e7mA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0590 read from 2e7mA/T0590-2e7mA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2e7mA read from 2e7mA/T0590-2e7mA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2e7mA in template set T0590 56 :HSSPVLPTARFT 2e7mA 8 :PRTVKELTVSAG T0590 68 :SDITEGFAPLSVRFKDFSENATSRLWMF 2e7mA 24 :ITLPDNEVELKAFVAPAPPVETTYNYEW T0590 96 :GDGNT 2e7mA 58 :TDYQG T0590 101 :SDSPSPLHTFFN 2e7mA 65 :KQGHKQTLNLSQ T0590 113 :EGEYIVSLIVSNENDSDSASVTIRA 2e7mA 79 :VGLYVFKVTVSSENAFGEGFVNVTV Number of specific fragments extracted= 5 number of extra gaps= 0 total=63 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 2yrlA/T0590-2yrlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2yrlA expands to /projects/compbio/data/pdb/2yrl.pdb.gz 2yrlA:# T0590 read from 2yrlA/T0590-2yrlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2yrlA read from 2yrlA/T0590-2yrlA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2yrlA to template set # found chain 2yrlA in template set Warning: unaligning (T0590)H56 because first residue in template chain is (2yrlA)G1 T0590 57 :SSPVLPTARFTSDITEGFAPLSVRF 2yrlA 2 :SSGSSGQADAGPDKELTLPVDSTTL T0590 82 :KDFSENATSRLWMFGDGNT 2yrlA 31 :SSDDQKIISYLWEKTQGPD T0590 101 :SDSPSPLHTFFNEGEYIVSLIVSNEND 2yrlA 56 :ANSSVATVTGLQVGTYVFTLTVKDERN T0590 128 :SDSASVTIRA 2yrlA 84 :QSQSSVNVIV Number of specific fragments extracted= 4 number of extra gaps= 0 total=67 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 2yrlA/T0590-2yrlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0590 read from 2yrlA/T0590-2yrlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2yrlA read from 2yrlA/T0590-2yrlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2yrlA in template set T0590 57 :SSPVLPTARFTSDITEGFAPLSVRF 2yrlA 2 :SSGSSGQADAGPDKELTLPVDSTTL T0590 82 :KD 2yrlA 32 :SD T0590 85 :SENATSRLWMFGDGN 2yrlA 34 :DQKIISYLWEKTQGP T0590 100 :TSDSPSPLHTFFN 2yrlA 53 :LENANSSVATVTG T0590 113 :EGEYIVSLIVSNEND 2yrlA 68 :VGTYVFTLTVKDERN T0590 128 :SDSASVTI 2yrlA 84 :QSQSSVNV Number of specific fragments extracted= 6 number of extra gaps= 0 total=73 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 2yrlA/T0590-2yrlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0590 read from 2yrlA/T0590-2yrlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2yrlA read from 2yrlA/T0590-2yrlA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2yrlA in template set Warning: unaligning (T0590)H56 because first residue in template chain is (2yrlA)G1 T0590 57 :SSPVLPTARFTSD 2yrlA 2 :SSGSSGQADAGPD T0590 70 :ITEGFAPLSVRFK 2yrlA 17 :LTLPVDSTTLDGS T0590 83 :DFSENATSRLWMFGDGNT 2yrlA 32 :SDDQKIISYLWEKTQGPD T0590 101 :SDSPSPLHTFFNEGEYIVSLIVSNENDSDSA 2yrlA 56 :ANSSVATVTGLQVGTYVFTLTVKDERNLQSQ T0590 132 :SVTIRA 2yrlA 88 :SVNVIV Number of specific fragments extracted= 5 number of extra gaps= 0 total=78 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 1wgoA/T0590-1wgoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1wgoA expands to /projects/compbio/data/pdb/1wgo.pdb.gz 1wgoA:# T0590 read from 1wgoA/T0590-1wgoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wgoA read from 1wgoA/T0590-1wgoA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1wgoA to template set # found chain 1wgoA in template set T0590 18 :YWSDYEGSDENGDG 1wgoA 7 :GCEGGVDMQQSQVQ T0590 42 :EAGSMDYMPLMEYLHSS 1wgoA 21 :LQCPLTPPRGLQVSIQG T0590 69 :DITEGFAPLSVRF 1wgoA 38 :EAVAVRPGEDVLF T0590 82 :KDFSEN 1wgoA 53 :RQEQGD T0590 88 :ATSRLWMFGDGNT 1wgoA 61 :TTKYQVDLGDGFK T0590 101 :SDSPSPLHTFFNEGEYIVSLIVSNENDSDSASVTIRA 1wgoA 81 :LTGEPIRHRYESPGIYRVSVRAENTAGHDEAVLFVQV Number of specific fragments extracted= 6 number of extra gaps= 0 total=84 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 1wgoA/T0590-1wgoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0590 read from 1wgoA/T0590-1wgoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wgoA read from 1wgoA/T0590-1wgoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wgoA in template set T0590 20 :SDYEGSDENGDGI 1wgoA 4 :GSSGCEGGVDMQQ T0590 41 :PEAGS 1wgoA 17 :SQVQL T0590 56 :HSSPVLP 1wgoA 22 :QCPLTPP T0590 63 :TARFTSDITEGFAPLSVRF 1wgoA 32 :QVSIQGEAVAVRPGEDVLF T0590 82 :KDFSEN 1wgoA 53 :RQEQGD T0590 88 :ATSRLWMFGDGN 1wgoA 61 :TTKYQVDLGDGF T0590 100 :TSDSPSPLHTFFNEGEYIVSLIVSNENDSDSASVTI 1wgoA 80 :TLTGEPIRHRYESPGIYRVSVRAENTAGHDEAVLFV Number of specific fragments extracted= 7 number of extra gaps= 0 total=91 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 1wgoA/T0590-1wgoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0590 read from 1wgoA/T0590-1wgoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1wgoA read from 1wgoA/T0590-1wgoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1wgoA in template set T0590 14 :SRGNYWSDYEGS 1wgoA 9 :EGGVDMQQSQVQ T0590 42 :EAGSMDYMPLMEYLHSSPVLPT 1wgoA 21 :LQCPLTPPRGLQVSIQGEAVAV T0590 70 :ITEGFAPLSVRFKDFSENATSRLWMFGDGNT 1wgoA 43 :RPGEDVLFVVRQEQGDVLTTKYQVDLGDGFK T0590 101 :SDSPSPLHTFFNEGEYIVSLIVSNENDSDSASVTIR 1wgoA 81 :LTGEPIRHRYESPGIYRVSVRAENTAGHDEAVLFVQ Number of specific fragments extracted= 4 number of extra gaps= 0 total=95 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 1oflA/T0590-1oflA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1oflA expands to /projects/compbio/data/pdb/1ofl.pdb.gz 1oflA:Bad short name: OE for alphabet: pdb_atoms Skipped atom 657, because occupancy 0.5 <= existing 0.500 in 1oflA Skipped atom 658, because occupancy 0.500 <= existing 0.500 in 1oflA Skipped atom 659, because occupancy 0.500 <= existing 0.500 in 1oflA Skipped atom 660, because occupancy 0.500 <= existing 0.500 in 1oflA Skipped atom 661, because occupancy 0.500 <= existing 0.500 in 1oflA # T0590 read from 1oflA/T0590-1oflA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1oflA read from 1oflA/T0590-1oflA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1oflA to template set # found chain 1oflA in template set Warning: unaligning (T0590)Y22 because of BadResidue code BAD_PEPTIDE in next template residue (1oflA)K187 Warning: unaligning (T0590)E23 because of BadResidue code BAD_PEPTIDE at template residue (1oflA)K187 T0590 15 :R 1oflA 174 :D T0590 18 :YWSD 1oflA 182 :TARA T0590 24 :GSDENGDGIGDSA 1oflA 188 :DGSVGGPAMYHRV T0590 37 :YAVN 1oflA 204 :FFSN T0590 62 :PTARFTSDITEGFAPLSVRFKDFS 1oflA 397 :PFFKDDYFIAGKNSWTGNVALGVE T0590 86 :ENAT 1oflA 422 :GIPV T0590 94 :MFGDGNT 1oflA 428 :SANRSAY T0590 101 :SDS 1oflA 440 :KDI Number of specific fragments extracted= 8 number of extra gaps= 1 total=103 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 1oflA/T0590-1oflA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0590 read from 1oflA/T0590-1oflA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1oflA read from 1oflA/T0590-1oflA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1oflA in template set T0590 70 :ITEGFAPLSVRFKDFS 1oflA 372 :RLKFETPHQLMLKGNL T0590 86 :ENATSRLWMFGDGNTSDSPSPLHTF 1oflA 389 :FKDKPYVYPFFKDDYFIAGKNSWTG Number of specific fragments extracted= 2 number of extra gaps= 0 total=105 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 1oflA/T0590-1oflA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0590 read from 1oflA/T0590-1oflA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1oflA read from 1oflA/T0590-1oflA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1oflA in template set T0590 63 :TARFTSDITEGF 1oflA 58 :QLIVSNSGKSGL T0590 76 :PLSVRFKDFS 1oflA 70 :PITIKALNPG Number of specific fragments extracted= 2 number of extra gaps= 0 total=107 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 2o26U/T0590-2o26U-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2o26U expands to /projects/compbio/data/pdb/2o26.pdb.gz 2o26U:# T0590 read from 2o26U/T0590-2o26U-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2o26U read from 2o26U/T0590-2o26U-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2o26U to template set # found chain 2o26U in template set Warning: unaligning (T0590)G31 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2o26U)R182 T0590 4 :RDNKFNTWNDSRGN 2o26U 142 :PQVSQYSLIECDGK T0590 18 :YWSDYEGSDENGD 2o26U 166 :NPKAGITIKNVKR T0590 32 :IGDSAYAVNPEAGSMDYMPLMEYLHSSPVLPTARFTSDITEGFAPLSVRF 2o26U 183 :LCVRCAAQRDGTWLHSDKFTLKVREAIKAIPVVSVPETSHLLKKGDTFTV T0590 82 :KDFS 2o26U 237 :KDVS T0590 87 :NATSRLWMFGDGNT 2o26U 241 :TSVNSMWLKMNPQP T0590 101 :SDSPSPLHTFFNEGEYIVSLIVSNEND 2o26U 257 :IAQVKHNSWHRGDFNYERQETLTISSA T0590 128 :SDSASVTIRA 2o26U 286 :DDSGVFMCYA Number of specific fragments extracted= 7 number of extra gaps= 1 total=114 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 2o26U/T0590-2o26U-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0590 read from 2o26U/T0590-2o26U-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2o26U read from 2o26U/T0590-2o26U-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2o26U in template set Warning: unaligning (T0590)G31 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2o26U)R182 Warning: unaligning (T0590)I32 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2o26U)R182 T0590 2 :NARDNKFNTWNDSRGNYWSDYEGSD 2o26U 138 :PLTDPQVSQYSLIECDGKSLPTDLT T0590 27 :ENGD 2o26U 177 :KRAY T0590 33 :GDSAYAVNPEAGSMDYMPLMEYLHSS 2o26U 183 :LCVRCAAQRDGTWLHSDKFTLKVREA T0590 59 :PVLPTARFTSDITEGFAPLSVRF 2o26U 210 :KAIPVVSVPETSHLLKKGDTFTV T0590 82 :KDFS 2o26U 237 :KDVS T0590 87 :NATSRLWMFGDGN 2o26U 241 :TSVNSMWLKMNPQ T0590 100 :TSDSPSPLHTFFNEGEYIV 2o26U 256 :HIAQVKHNSWHRGDFNYER T0590 119 :SLIVSNENDSDSASVTIR 2o26U 292 :MCYANNTFGSANVTTTLK Number of specific fragments extracted= 8 number of extra gaps= 1 total=122 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 2o26U/T0590-2o26U-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0590 read from 2o26U/T0590-2o26U-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2o26U read from 2o26U/T0590-2o26U-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2o26U in template set T0590 5 :DNKFNTWNDSRGNYWSDYEGSDENGDGIGDS 2o26U 143 :QVSQYSLIECDGKSLPTDLTFVPNPKAGITI T0590 36 :AYAVNPEAGSMDYMPLMEYLH 2o26U 186 :RCAAQRDGTWLHSDKFTLKVR T0590 57 :S 2o26U 208 :A T0590 60 :VLPTARFTSDIT 2o26U 209 :IKAIPVVSVPET T0590 72 :EGFAPLSVRFKD 2o26U 227 :GDTFTVVCTIKD T0590 85 :SENATSRLWMFGDGNT 2o26U 239 :VSTSVNSMWLKMNPQP T0590 101 :SDSPSPLHTFFNEGE 2o26U 257 :IAQVKHNSWHRGDFN T0590 117 :IVSLIVSNENDSDSASVTIRA 2o26U 290 :VFMCYANNTFGSANVTTTLKV Number of specific fragments extracted= 8 number of extra gaps= 0 total=130 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 3ejjX/T0590-3ejjX-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3ejjX expands to /projects/compbio/data/pdb/3ejj.pdb.gz 3ejjX:# T0590 read from 3ejjX/T0590-3ejjX-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ejjX read from 3ejjX/T0590-3ejjX-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3ejjX to template set # found chain 3ejjX in template set T0590 3 :ARDNKFNTWNDSRGN 3ejjX 119 :EGQEAVLPCLITDPA T0590 18 :YWSDYEGSDENGDGI 3ejjX 157 :SPWRGFIIRKAKVLD T0590 33 :GDSAYAVNPEAGSMDYMPLMEYLHSSPVLPTARFTSDITEGFAPLSVRF 3ejjX 174 :TYVCKTMVNGRESTSTGIWLKVNRVHPEPPQIKLEPSKLVRIRGEAAQI T0590 82 :KDFSENATSRLWMFGDGNT 3ejjX 226 :ATNAEVGFNVILKRGDTKL T0590 101 :SDSPSPLHTFFNE 3ejjX 254 :DNYYKKVRALSLN T0590 114 :GEYIV 3ejjX 274 :GIYSC T0590 121 :IVSNENDSDSASVTIRA 3ejjX 279 :VASNDVGTRTATMNFQV Number of specific fragments extracted= 7 number of extra gaps= 0 total=137 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 3ejjX/T0590-3ejjX-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0590 read from 3ejjX/T0590-3ejjX-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ejjX read from 3ejjX/T0590-3ejjX-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3ejjX in template set T0590 27 :ENGDGIGDSAYAVNPEAGSMDYMPLMEYLHSS 3ejjX 167 :AKVLDSNTYVCKTMVNGRESTSTGIWLKVNRV T0590 59 :PVLPTARFTSDITEGFAPLSVRF 3ejjX 200 :PEPPQIKLEPSKLVRIRGEAAQI T0590 82 :KDFSE 3ejjX 227 :TNAEV T0590 88 :ATSRLWMF 3ejjX 232 :GFNVILKR T0590 97 :DGN 3ejjX 240 :GDT T0590 105 :SPLHTFFN 3ejjX 258 :KKVRALSL T0590 113 :EGEYIV 3ejjX 273 :AGIYSC T0590 121 :IVSNENDSDSASVTI 3ejjX 279 :VASNDVGTRTATMNF Number of specific fragments extracted= 8 number of extra gaps= 0 total=145 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 3ejjX/T0590-3ejjX-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0590 read from 3ejjX/T0590-3ejjX-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ejjX read from 3ejjX/T0590-3ejjX-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3ejjX in template set T0590 26 :DENGDGIGDSAYAVNPEAGSMDYMPLMEYLH 3ejjX 166 :KAKVLDSNTYVCKTMVNGRESTSTGIWLKVN T0590 57 :SSPVLPTARFT 3ejjX 198 :VHPEPPQIKLE T0590 68 :SDITEGFAPLSVRFK 3ejjX 213 :VRIRGEAAQIVCSAT T0590 83 :DFSENATSRLW 3ejjX 229 :AEVGFNVILKR T0590 97 :DGNT 3ejjX 240 :GDTK T0590 101 :SDSPSPLHTFFNE 3ejjX 254 :DNYYKKVRALSLN T0590 114 :GEYIV 3ejjX 274 :GIYSC T0590 121 :IVSNENDSDSASVTIRA 3ejjX 279 :VASNDVGTRTATMNFQV Number of specific fragments extracted= 8 number of extra gaps= 0 total=153 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 3l5jA/T0590-3l5jA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3l5jA expands to /projects/compbio/data/pdb/3l5j.pdb.gz 3l5jA:# T0590 read from 3l5jA/T0590-3l5jA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3l5jA read from 3l5jA/T0590-3l5jA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3l5jA to template set # found chain 3l5jA in template set T0590 3 :ARDNK 3l5jA 425 :RESVK T0590 8 :FNTWNDSRGN 3l5jA 432 :ILEWCVLSDK T0590 18 :YWSDYEGSDENGDGI 3l5jA 454 :TVHRTYLRGNLAESK T0590 33 :GDSAYAVN 3l5jA 471 :LITVTPVY T0590 42 :EAG 3l5jA 479 :ADG T0590 45 :SMDYMPLMEYLHSSPVLPT 3l5jA 483 :GSPESIKAYLKQAPPSKGP T0590 67 :TSDITEG 3l5jA 502 :TVRTKKV T0590 75 :APLSVRFKDF 3l5jA 509 :GKNEAVLEWD T0590 85 :SENATSRLWMF 3l5jA 526 :NGFIRNYTIFY T0590 96 :GDGNT 3l5jA 539 :IIGNE T0590 101 :SDSPSPLHTFF 3l5jA 548 :VDSSHTEYTLS T0590 112 :NEG 3l5jA 561 :TSD T0590 115 :EYIVSLIVSNEND 3l5jA 565 :LYMVRMAAYTDEG T0590 128 :SDSASVTIR 3l5jA 579 :KDGPEFTFT Number of specific fragments extracted= 14 number of extra gaps= 0 total=167 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 3l5jA/T0590-3l5jA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0590 read from 3l5jA/T0590-3l5jA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3l5jA read from 3l5jA/T0590-3l5jA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3l5jA in template set T0590 4 :RDNKFNTWNDSRGN 3l5jA 351 :WKSHLQNYTVNATK T0590 27 :ENGDGIGDSAYAVNPEAGSMDYMPLMEYLHSS 3l5jA 368 :NLTNDRYLATLTVRNLVGKSDAAVLTIPACDF T0590 59 :PVLPT 3l5jA 402 :THPVM T0590 69 :DITEGFAPLSVRF 3l5jA 407 :DLKAFPKDNMLWV T0590 82 :KDFSENATSRL 3l5jA 422 :TTPRESVKKYI T0590 93 :WMFGDGN 3l5jA 435 :WCVLSDK T0590 100 :TSDSPSPLHTFFN 3l5jA 450 :QEDGTVHRTYLRG T0590 113 :EGEYIVSLIVSNEND 3l5jA 467 :SKCYLITVTPVYADG T0590 128 :SDSASVTI 3l5jA 483 :GSPESIKA Number of specific fragments extracted= 9 number of extra gaps= 0 total=176 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 3l5jA/T0590-3l5jA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0590 read from 3l5jA/T0590-3l5jA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3l5jA read from 3l5jA/T0590-3l5jA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3l5jA in template set T0590 4 :RDNKFNTWNDSRG 3l5jA 339 :GKILDYEVTLTRW T0590 17 :NYWSDYEGSDENGDG 3l5jA 357 :NYTVNATKLTVNLTN T0590 32 :IGDSAYAVNPEAGSMDYMPLMEYLH 3l5jA 373 :RYLATLTVRNLVGKSDAAVLTIPAC T0590 57 :SSPVLPTARFTSDITEG 3l5jA 399 :FQATHPVMDLKAFPKDN T0590 76 :PLSVRFKDFSENATSRLWMFGDGNTSDSPSPLHTFFNEG 3l5jA 416 :MLWVEWTTPRESVKKYILEWCVLSDKAPCITDWQQEDGT T0590 115 :EYIVSLIVSNENDS 3l5jA 469 :CYLITVTPVYADGP T0590 129 :DSASVTI 3l5jA 484 :SPESIKA Number of specific fragments extracted= 7 number of extra gaps= 0 total=183 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 2kpnA/T0590-2kpnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2kpnA expands to /projects/compbio/data/pdb/2kpn.pdb.gz 2kpnA:# T0590 read from 2kpnA/T0590-2kpnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2kpnA read from 2kpnA/T0590-2kpnA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2kpnA to template set # found chain 2kpnA in template set T0590 56 :HSSPVLPTA 2kpnA 5 :ETSDLEPKL T0590 65 :RFTSDITEGFA 2kpnA 18 :GATIHVGDSFV T0590 79 :VRFKDFS 2kpnA 33 :VLAIDKE T0590 86 :ENAT 2kpnA 41 :GDLT T0590 94 :MF 2kpnA 48 :KV T0590 97 :DGNTSDSP 2kpnA 50 :DGEVDTTK T0590 113 :EGEYIVSLIVSNEND 2kpnA 58 :AGTYVLTYTVTDSKG T0590 128 :SDSASVTIRA 2kpnA 74 :EVTAKQTVTV Number of specific fragments extracted= 8 number of extra gaps= 0 total=191 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 2kpnA/T0590-2kpnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0590 read from 2kpnA/T0590-2kpnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2kpnA read from 2kpnA/T0590-2kpnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2kpnA in template set T0590 10 :TWNDSR 2kpnA 34 :LAIDKE T0590 16 :GNYW 2kpnA 41 :GDLT T0590 20 :SDYEG 2kpnA 47 :IKVDG T0590 27 :ENGDGIGDSAYAVNPEAGSMDYMPLMEYLHSSPVL 2kpnA 55 :TTKAGTYVLTYTVTDSKGHEVTAKQTVTVKVREEV Number of specific fragments extracted= 4 number of extra gaps= 0 total=195 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 2kpnA/T0590-2kpnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0590 read from 2kpnA/T0590-2kpnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2kpnA read from 2kpnA/T0590-2kpnA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2kpnA in template set T0590 13 :DSRG 2kpnA 38 :KEDG T0590 17 :NYWSDYEGSDENGDGIGDSAYAVNPEAGSMDYMPLMEYLHSSPVLP 2kpnA 45 :SKIKVDGEVDTTKAGTYVLTYTVTDSKGHEVTAKQTVTVKVREEVK Number of specific fragments extracted= 2 number of extra gaps= 0 total=197 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 3l5iA/T0590-3l5iA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3l5iA expands to /projects/compbio/data/pdb/3l5i.pdb.gz 3l5iA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0590 read from 3l5iA/T0590-3l5iA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3l5iA read from 3l5iA/T0590-3l5iA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3l5iA to template set # found chain 3l5iA in template set T0590 9 :NTWNDSRGN 3l5iA 346 :VTLTRWKSH T0590 18 :YWSDYEGSDENGDGI 3l5iA 358 :YTVNATKLTVNLTND T0590 33 :GDSAYAVN 3l5iA 375 :LATLTVRN T0590 42 :EAGSMDYMPLMEYL 3l5iA 383 :LVGKSDAAVLTIPA T0590 56 :HSSPVLPT 3l5iA 399 :FQATHPVM T0590 69 :DITEGFAPLSVRF 3l5iA 407 :DLKAFPKDNMLWV T0590 82 :KDFSENATSRLWMFGDGNTSDSPSPLHTFFNEG 3l5iA 422 :TTPRESVKKYILEWCVLSDKAPCITDWQQEDGT T0590 116 :YIVSLIVSNEND 3l5iA 470 :YLITVTPVYADG T0590 128 :SDSASVTI 3l5iA 483 :GSPESIKA Number of specific fragments extracted= 9 number of extra gaps= 0 total=206 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 3l5iA/T0590-3l5iA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0590 read from 3l5iA/T0590-3l5iA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3l5iA read from 3l5iA/T0590-3l5iA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3l5iA in template set T0590 6 :NKFNTWND 3l5iA 339 :GKILDYEV T0590 14 :SR 3l5iA 351 :WK T0590 16 :GNYWSDYEGSD 3l5iA 354 :HLQNYTVNATK T0590 27 :ENGDGIGDSAYAVNPEAGSMDYMPLMEYLHSS 3l5iA 368 :NLTNDRYLATLTVRNLVGKSDAAVLTIPACDF T0590 59 :PVLPT 3l5iA 402 :THPVM T0590 69 :DITEGFAPLSVRF 3l5iA 407 :DLKAFPKDNMLWV T0590 82 :KDFSENATSRLWMF 3l5iA 422 :TTPRESVKKYILEW T0590 96 :GDGNTSDSP 3l5iA 437 :VLSDKAPCI T0590 105 :SPLHTFFN 3l5iA 455 :VHRTYLRG T0590 113 :EGEYIVSLIVSNEND 3l5iA 467 :SKCYLITVTPVYADG T0590 128 :SDSASVTI 3l5iA 483 :GSPESIKA Number of specific fragments extracted= 11 number of extra gaps= 0 total=217 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 3l5iA/T0590-3l5iA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0590 read from 3l5iA/T0590-3l5iA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3l5iA read from 3l5iA/T0590-3l5iA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3l5iA in template set T0590 4 :RDNKFNTWNDSRG 3l5iA 339 :GKILDYEVTLTRW T0590 17 :NYWSDYEGSDENGDGIGDSAYAVNPEAGSMDYMPLMEYLH 3l5iA 358 :YTVNATKLTVNLTNDRYLATLTVRNLVGKSDAAVLTIPAC T0590 57 :SSPVLPTARFTSDITEGF 3l5iA 399 :FQATHPVMDLKAFPKDNM T0590 77 :LSVRFKDFSENATSRLWMFGDGNTSDSPSPLHTFFNEG 3l5iA 417 :LWVEWTTPRESVKKYILEWCVLSDKAPCITDWQQEDGT T0590 116 :YIVSLIVSNENDS 3l5iA 470 :YLITVTPVYADGP T0590 129 :DSASVTI 3l5iA 484 :SPESIKA Number of specific fragments extracted= 6 number of extra gaps= 0 total=223 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 1hnfA/T0590-1hnfA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1hnfA expands to /projects/compbio/data/pdb/1hnf.pdb.gz 1hnfA:# T0590 read from 1hnfA/T0590-1hnfA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hnfA read from 1hnfA/T0590-1hnfA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1hnfA to template set # found chain 1hnfA in template set T0590 3 :ARDNKFNTWNDSRGN 1hnfA 27 :SDDIDDIKWEKTSDK T0590 18 :YWSDYEGSDENGDGI 1hnfA 63 :FKNGTLKIKHLKTDD T0590 33 :GDSAYAVN 1hnfA 80 :IYKVSIYD T0590 42 :EAGSMDYMPLMEYL 1hnfA 88 :TKGKNVLEKIFDLK T0590 56 :HSSPVLPTARFTS 1hnfA 103 :QERVSKPKISWTC T0590 71 :T 1hnfA 116 :I T0590 76 :PLSVRFKDFSENATSRLWMFGDGN 1hnfA 117 :NTTLTCEVMNGTDPELNLYQDGKH T0590 101 :SDSPSPLHTFFNEGEYIVSLIVSNENDSDSASVTIRA 1hnfA 143 :LSQRVITHKWTTSLSAKFKCTAGNKVSKESSVEPVSC Number of specific fragments extracted= 8 number of extra gaps= 0 total=231 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 1hnfA/T0590-1hnfA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0590 read from 1hnfA/T0590-1hnfA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hnfA read from 1hnfA/T0590-1hnfA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1hnfA in template set T0590 3 :ARDNKFNTWNDSR 1hnfA 38 :TSDKKKIAQFRKE T0590 17 :NYWSDYEGSD 1hnfA 55 :KEKDTYKLFK T0590 27 :ENGDGIGDSAYAVNPEAG 1hnfA 73 :LKTDDQDIYKVSIYDTKG T0590 45 :SMDYMPLMEYLHSSPVLPTARFTSD 1hnfA 92 :NVLEKIFDLKIQERVSKPKISWTCI T0590 76 :PLSVRFKDFSENATSRLWMF 1hnfA 117 :NTTLTCEVMNGTDPELNLYQ T0590 97 :DGN 1hnfA 137 :DGK T0590 100 :TSDSPSPLHTFFNEGEYIVSLIVSNENDSDSASVT 1hnfA 142 :KLSQRVITHKWTTSLSAKFKCTAGNKVSKESSVEP T0590 135 :IR 1hnfA 179 :CP Number of specific fragments extracted= 8 number of extra gaps= 0 total=239 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 1hnfA/T0590-1hnfA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0590 read from 1hnfA/T0590-1hnfA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1hnfA read from 1hnfA/T0590-1hnfA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1hnfA in template set T0590 1 :MNARDNKFNTWNDSRG 1hnfA 25 :QMSDDIDDIKWEKTSD T0590 17 :NYWSDYEGSDENGDGIG 1hnfA 52 :ETFKEKDTYKLFKNGTL T0590 34 :DSAYAVNPEAGSMDYMPLMEYLHS 1hnfA 80 :IYKVSIYDTKGKNVLEKIFDLKIQ T0590 59 :PVLPTARFTSDITEG 1hnfA 104 :ERVSKPKISWTCINT T0590 78 :SVRFKDFSENATSRLWMFGDGNT 1hnfA 119 :TLTCEVMNGTDPELNLYQDGKHL T0590 101 :SDSPSPLHTFFNEGEYIVSLIVSNENDSDSASVTIRA 1hnfA 143 :LSQRVITHKWTTSLSAKFKCTAGNKVSKESSVEPVSC Number of specific fragments extracted= 6 number of extra gaps= 0 total=245 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 2v5mA/T0590-2v5mA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2v5mA expands to /projects/compbio/data/pdb/2v5m.pdb.gz 2v5mA:Skipped atom 107, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 108, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 109, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 110, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 111, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 112, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 185, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 186, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 187, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 188, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 189, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 434, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 435, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 436, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 437, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 438, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 439, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 446, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 447, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 448, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 449, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 450, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 451, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 460, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 461, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 462, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 463, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 464, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 465, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 466, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 467, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 472, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 473, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 474, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 475, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 485, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 486, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 563, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 564, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 565, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 566, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 567, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 964, because occupancy 0.400 <= existing 0.600 in 2v5mA Skipped atom 965, because occupancy 0.400 <= existing 0.600 in 2v5mA Skipped atom 966, because occupancy 0.400 <= existing 0.600 in 2v5mA Skipped atom 967, because occupancy 0.400 <= existing 0.600 in 2v5mA Skipped atom 968, because occupancy 0.400 <= existing 0.600 in 2v5mA Skipped atom 969, because occupancy 0.400 <= existing 0.600 in 2v5mA Skipped atom 970, because occupancy 0.400 <= existing 0.600 in 2v5mA Skipped atom 1111, because occupancy 0.400 <= existing 0.600 in 2v5mA Skipped atom 1112, because occupancy 0.400 <= existing 0.600 in 2v5mA Skipped atom 1113, because occupancy 0.400 <= existing 0.600 in 2v5mA Skipped atom 1114, because occupancy 0.400 <= existing 0.600 in 2v5mA Skipped atom 1115, because occupancy 0.400 <= existing 0.600 in 2v5mA Skipped atom 1116, because occupancy 0.400 <= existing 0.600 in 2v5mA Skipped atom 1176, because occupancy 0.400 <= existing 0.600 in 2v5mA Skipped atom 1177, because occupancy 0.400 <= existing 0.600 in 2v5mA Skipped atom 1178, because occupancy 0.400 <= existing 0.600 in 2v5mA Skipped atom 1179, because occupancy 0.400 <= existing 0.600 in 2v5mA Skipped atom 1189, because occupancy 0.400 <= existing 0.600 in 2v5mA Skipped atom 1190, because occupancy 0.400 <= existing 0.600 in 2v5mA Skipped atom 1191, because occupancy 0.400 <= existing 0.600 in 2v5mA Skipped atom 1192, because occupancy 0.400 <= existing 0.600 in 2v5mA Skipped atom 1193, because occupancy 0.400 <= existing 0.600 in 2v5mA Skipped atom 1203, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 1204, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 1205, because occupancy 0.400 <= existing 0.600 in 2v5mA Skipped atom 1206, because occupancy 0.400 <= existing 0.600 in 2v5mA Skipped atom 1207, because occupancy 0.400 <= existing 0.600 in 2v5mA Skipped atom 1208, because occupancy 0.400 <= existing 0.600 in 2v5mA Skipped atom 1209, because occupancy 0.400 <= existing 0.600 in 2v5mA Skipped atom 1219, because occupancy 0.400 <= existing 0.600 in 2v5mA Skipped atom 1220, because occupancy 0.400 <= existing 0.600 in 2v5mA Skipped atom 1221, because occupancy 0.400 <= existing 0.600 in 2v5mA Skipped atom 1222, because occupancy 0.400 <= existing 0.600 in 2v5mA Skipped atom 1223, because occupancy 0.400 <= existing 0.600 in 2v5mA Skipped atom 1411, because occupancy 0.200 <= existing 0.800 in 2v5mA Skipped atom 1412, because occupancy 0.200 <= existing 0.800 in 2v5mA Skipped atom 1413, because occupancy 0.200 <= existing 0.800 in 2v5mA Skipped atom 1414, because occupancy 0.200 <= existing 0.800 in 2v5mA Skipped atom 1415, because occupancy 0.200 <= existing 0.800 in 2v5mA Skipped atom 1416, because occupancy 0.200 <= existing 0.800 in 2v5mA Skipped atom 1417, because occupancy 0.200 <= existing 0.800 in 2v5mA Skipped atom 1418, because occupancy 0.200 <= existing 0.800 in 2v5mA Skipped atom 1428, because occupancy 0.200 <= existing 0.800 in 2v5mA Skipped atom 1429, because occupancy 0.200 <= existing 0.800 in 2v5mA Skipped atom 1430, because occupancy 0.200 <= existing 0.800 in 2v5mA Skipped atom 1431, because occupancy 0.200 <= existing 0.800 in 2v5mA Skipped atom 1432, because occupancy 0.200 <= existing 0.800 in 2v5mA Skipped atom 1493, because occupancy 0.400 <= existing 0.600 in 2v5mA Skipped atom 1494, because occupancy 0.400 <= existing 0.600 in 2v5mA Skipped atom 1495, because occupancy 0.400 <= existing 0.600 in 2v5mA Skipped atom 1496, because occupancy 0.400 <= existing 0.600 in 2v5mA Skipped atom 1497, because occupancy 0.400 <= existing 0.600 in 2v5mA Skipped atom 1714, because occupancy 0.400 <= existing 0.600 in 2v5mA Skipped atom 1715, because occupancy 0.400 <= existing 0.600 in 2v5mA Skipped atom 1716, because occupancy 0.400 <= existing 0.600 in 2v5mA Skipped atom 1717, because occupancy 0.400 <= existing 0.600 in 2v5mA Skipped atom 1866, because occupancy 0.300 <= existing 0.700 in 2v5mA Skipped atom 1867, because occupancy 0.300 <= existing 0.700 in 2v5mA Skipped atom 1868, because occupancy 0.300 <= existing 0.700 in 2v5mA Skipped atom 1869, because occupancy 0.300 <= existing 0.700 in 2v5mA Skipped atom 1907, because occupancy 0.300 <= existing 0.700 in 2v5mA Skipped atom 1908, because occupancy 0.300 <= existing 0.700 in 2v5mA Skipped atom 1909, because occupancy 0.300 <= existing 0.700 in 2v5mA Skipped atom 2021, because occupancy 0.300 <= existing 0.700 in 2v5mA Skipped atom 2022, because occupancy 0.300 <= existing 0.700 in 2v5mA Skipped atom 2023, because occupancy 0.300 <= existing 0.700 in 2v5mA Skipped atom 2024, because occupancy 0.300 <= existing 0.700 in 2v5mA Skipped atom 2025, because occupancy 0.300 <= existing 0.700 in 2v5mA Skipped atom 2026, because occupancy 0.300 <= existing 0.700 in 2v5mA Skipped atom 2027, because occupancy 0.300 <= existing 0.700 in 2v5mA Skipped atom 2181, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 2182, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 2183, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 2184, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 2185, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 2186, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 2383, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 2384, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 2385, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 2523, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 2524, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 2903, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 2904, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 2905, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 2906, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 2907, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 2908, because occupancy 0.500 <= existing 0.500 in 2v5mA Skipped atom 2909, because occupancy 0.500 <= existing 0.500 in 2v5mA # T0590 read from 2v5mA/T0590-2v5mA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2v5mA read from 2v5mA/T0590-2v5mA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2v5mA to template set # found chain 2v5mA in template set Warning: unaligning (T0590)N12 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2v5mA)R40 Warning: unaligning (T0590)D13 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2v5mA)R40 Warning: unaligning (T0590)D30 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2v5mA)G59 Warning: unaligning (T0590)G31 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2v5mA)G59 Warning: unaligning (T0590)I135 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2v5mA)T303 Warning: unaligning (T0590)R136 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2v5mA)T303 T0590 6 :NKFNTW 2v5mA 33 :MPEIIW T0590 14 :SRGN 2v5mA 41 :SDGT T0590 18 :YWSDYEGSDENG 2v5mA 46 :VGDVPGLRQISS T0590 32 :I 2v5mA 77 :A T0590 33 :GDSAYAVN 2v5mA 79 :VYACLARN T0590 42 :EAG 2v5mA 87 :QFG T0590 45 :SMDYMPLMEYLHSSPVL 2v5mA 91 :IISRDVHVRAVVAQYYE T0590 62 :PTARFTSDITEGFA 2v5mA 199 :GRLVITEPISSSAP T0590 76 :PLSVRF 2v5mA 227 :AHTISL T0590 83 :DFSENATSRLWMF 2v5mA 236 :AQGFPAPSFRWYK T0590 96 :GDGNT 2v5mA 250 :IEGTT T0590 101 :SDSPS 2v5mA 257 :QAVVL T0590 106 :PL 2v5mA 265 :VK T0590 108 :HTFFNE 2v5mA 271 :TLIIKD T0590 114 :GEYIV 2v5mA 283 :GKYLC T0590 121 :IVSNENDSDSASVT 2v5mA 288 :VVNNSVGGESVETV T0590 137 :A 2v5mA 304 :V Number of specific fragments extracted= 17 number of extra gaps= 3 total=262 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 2v5mA/T0590-2v5mA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0590 read from 2v5mA/T0590-2v5mA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2v5mA read from 2v5mA/T0590-2v5mA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2v5mA in template set Warning: unaligning (T0590)E53 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2v5mA)T303 Warning: unaligning (T0590)Y54 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2v5mA)T303 Warning: unaligning (T0590)S123 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2v5mA)N374 Warning: unaligning (T0590)N124 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2v5mA)N374 T0590 6 :NKFNTWNDSRGNY 2v5mA 242 :PSFRWYKFIEGTT T0590 19 :WSDYEGSD 2v5mA 256 :KQAVVLND T0590 27 :ENGDGIGDSAYAVNPEAGS 2v5mA 277 :AVVEDSGKYLCVVNNSVGG T0590 47 :DYMPLM 2v5mA 296 :ESVETV T0590 55 :LHSS 2v5mA 304 :VTAP T0590 62 :PTARFTSDITEGFAPLSVRF 2v5mA 308 :LSAKIDPPTQTVDFGRPAVF T0590 82 :KDFS 2v5mA 329 :CQYT T0590 86 :ENATSRLWMFG 2v5mA 334 :NPIKTVSWMKD T0590 98 :GNTSDSPSPLHTFFN 2v5mA 345 :GKAIGHSESVLRIES T0590 113 :EGEYIV 2v5mA 365 :KGMYQC T0590 121 :IV 2v5mA 371 :FV T0590 125 :ENDSDSASV 2v5mA 375 :DRESAEASA Number of specific fragments extracted= 12 number of extra gaps= 2 total=274 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 2v5mA/T0590-2v5mA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0590 read from 2v5mA/T0590-2v5mA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2v5mA read from 2v5mA/T0590-2v5mA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2v5mA in template set Warning: unaligning (T0590)M52 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2v5mA)T303 Warning: unaligning (T0590)E53 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2v5mA)T303 Warning: unaligning (T0590)S123 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2v5mA)N374 Warning: unaligning (T0590)N124 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2v5mA)N374 Warning: unaligning (T0590)R136 because of BadResidue code CHAIN_BREAK_BEFORE+HIGH_B_FACTOR in next template residue (2v5mA)L387 Warning: unaligning (T0590)A137 because of BadResidue code CHAIN_BREAK_BEFORE+HIGH_B_FACTOR at template residue (2v5mA)L387 T0590 5 :DNKFNTWNDSRG 2v5mA 243 :SFRWYKFIEGTT T0590 17 :NYWSDYEGSDENGDGI 2v5mA 257 :QAVVLNDRVKQVSGTL T0590 33 :GDSAYAVNPEAGSMDYMPL 2v5mA 283 :GKYLCVVNNSVGGESVETV T0590 54 :YLHSSPVLPTARFTSDITEGFAPLSVRFK 2v5mA 304 :VTAPLSAKIDPPTQTVDFGRPAVFTCQYT T0590 83 :DFSENATSRL 2v5mA 334 :NPIKTVSWMK T0590 97 :DGNTSDSPSPLHTFFN 2v5mA 344 :DGKAIGHSESVLRIES T0590 113 :EGEYI 2v5mA 365 :KGMYQ T0590 120 :LIV 2v5mA 370 :CFV T0590 125 :ENDSDSASVTI 2v5mA 375 :DRESAEASAEL Number of specific fragments extracted= 9 number of extra gaps= 3 total=283 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 1cwvA/T0590-1cwvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1cwvA expands to /projects/compbio/data/pdb/1cwv.pdb.gz 1cwvA:# T0590 read from 1cwvA/T0590-1cwvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cwvA read from 1cwvA/T0590-1cwvA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1cwvA to template set # found chain 1cwvA in template set T0590 13 :DSRGN 1cwvA 530 :DFEGK T0590 18 :YWSDYEGSDENGDGI 1cwvA 559 :DANGVARIALTNTTD T0590 33 :GDSAYAVN 1cwvA 575 :VTVVTAEV T0590 44 :GSMDYMPLMEYLHSSPVLPTARFTSDIT 1cwvA 583 :EGQRQSVDTHFVKGTIAADKSTLAAVPT T0590 72 :EGFAPLSVRF 1cwvA 615 :DGLMASTITL T0590 82 :KDFSENAT 1cwvA 627 :KDTYGDPQ T0590 90 :SRLWMFGDGNT 1cwvA 638 :NVAFDTTLGNM T0590 101 :SDSPSPLHTFF 1cwvA 654 :HNDGTYSAPLT T0590 112 :NEGEYIVSLIVSNEND 1cwvA 667 :TLGVATVTVKVDGAAF T0590 128 :SDSASVTIRA 1cwvA 684 :VPSVTVNFTA Number of specific fragments extracted= 10 number of extra gaps= 0 total=293 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 1cwvA/T0590-1cwvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0590 read from 1cwvA/T0590-1cwvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cwvA read from 1cwvA/T0590-1cwvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cwvA in template set T0590 4 :RDNKF 1cwvA 531 :FEGKP T0590 9 :NTWNDSRG 1cwvA 541 :VVITTNNG T0590 17 :NYWSDYEGSD 1cwvA 553 :KITEKTDANG T0590 27 :ENGDGIGDSAYAV 1cwvA 570 :NTTDGVTVVTAEV T0590 43 :AG 1cwvA 583 :EG T0590 47 :DYMPLMEYLHSSPVLP 1cwvA 585 :QRQSVDTHFVKGTIAA T0590 63 :TARFTSDIT 1cwvA 602 :KSTLAAVPT T0590 72 :EGFAPLSVRF 1cwvA 615 :DGLMASTITL T0590 82 :KDFSENATS 1cwvA 627 :KDTYGDPQA T0590 91 :RLWMFGDGN 1cwvA 639 :VAFDTTLGN T0590 100 :TSDS 1cwvA 653 :DHND T0590 105 :SPLHTFFNEGEYIVSLIVSNEND 1cwvA 660 :SAPLTSTTLGVATVTVKVDGAAF T0590 128 :SDSASVT 1cwvA 684 :VPSVTVN Number of specific fragments extracted= 13 number of extra gaps= 0 total=306 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 1cwvA/T0590-1cwvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0590 read from 1cwvA/T0590-1cwvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cwvA read from 1cwvA/T0590-1cwvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cwvA in template set T0590 17 :NYWSDYEGSDENGDGIGDSAYAV 1cwvA 560 :ANGVARIALTNTTDGVTVVTAEV T0590 43 :AGSMDYMPL 1cwvA 583 :EGQRQSVDT T0590 53 :EYLHSSPVLPTARFTSDIT 1cwvA 592 :HFVKGTIAADKSTLAAVPT T0590 72 :EGFAPLSVRFK 1cwvA 615 :DGLMASTITLE T0590 83 :D 1cwvA 631 :G T0590 86 :ENATSRLWMFGDGNT 1cwvA 634 :QAGANVAFDTTLGNM T0590 101 :SDSPSPLHTFF 1cwvA 654 :HNDGTYSAPLT T0590 112 :NEGEYIVSLIV 1cwvA 667 :TLGVATVTVKV T0590 124 :NENDSDSASVTIR 1cwvA 678 :DGAAFSVPSVTVN Number of specific fragments extracted= 9 number of extra gaps= 0 total=315 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 2w1nA/T0590-2w1nA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2w1nA expands to /projects/compbio/data/pdb/2w1n.pdb.gz 2w1nA:Skipped atom 668, because occupancy 0.500 <= existing 0.500 in 2w1nA Skipped atom 669, because occupancy 0.500 <= existing 0.500 in 2w1nA Skipped atom 670, because occupancy 0.500 <= existing 0.500 in 2w1nA Skipped atom 671, because occupancy 0.500 <= existing 0.500 in 2w1nA Skipped atom 672, because occupancy 0.500 <= existing 0.500 in 2w1nA Skipped atom 673, because occupancy 0.500 <= existing 0.500 in 2w1nA # T0590 read from 2w1nA/T0590-2w1nA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2w1nA read from 2w1nA/T0590-2w1nA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2w1nA to template set # found chain 2w1nA in template set Warning: unaligning (T0590)E27 because of BadResidue code BAD_PEPTIDE in next template residue (2w1nA)K872 Warning: unaligning (T0590)N28 because of BadResidue code BAD_PEPTIDE at template residue (2w1nA)K872 Warning: unaligning (T0590)H56 because of BadResidue code BAD_PEPTIDE at template residue (2w1nA)T908 T0590 4 :RDNKFNTWNDSRGN 2w1nA 829 :DDGVFVNAKKIEDG T0590 18 :YWSDYEGS 2w1nA 854 :EPLPAKEV T0590 26 :D 2w1nA 870 :E T0590 29 :GDGIGD 2w1nA 873 :TEGSNL T0590 35 :SAYAVNPEAG 2w1nA 882 :NSSVGDGEGL T0590 45 :SMDYMPLMEYL 2w1nA 895 :IAGTEKTVNII T0590 57 :SSPVL 2w1nA 909 :SPEIV T0590 62 :PTARFTSD 2w1nA 916 :PVRDFKAS T0590 73 :GFAPLSVRF 2w1nA 924 :EINKKNVTV T0590 82 :KDFS 2w1nA 935 :TEPE T0590 86 :ENATSRLWMFGDGNT 2w1nA 941 :EGLEGYILYKDGKKV T0590 101 :SDSPSPLHTFF 2w1nA 958 :IGKDETSYTFK T0590 112 :NEG 2w1nA 971 :NRH T0590 115 :EYIVSLIVSNEND 2w1nA 975 :IYNFKIAAKYSNG T0590 128 :SDSASVTIR 2w1nA 990 :SSKESLTLR Number of specific fragments extracted= 15 number of extra gaps= 2 total=330 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 2w1nA/T0590-2w1nA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0590 read from 2w1nA/T0590-2w1nA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2w1nA read from 2w1nA/T0590-2w1nA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2w1nA in template set Warning: unaligning (T0590)N28 because of BadResidue code BAD_PEPTIDE in next template residue (2w1nA)K872 Warning: unaligning (T0590)G29 because of BadResidue code BAD_PEPTIDE at template residue (2w1nA)K872 T0590 2 :NARDNKF 2w1nA 838 :KIEDGKV T0590 9 :NTWNDSRGNYWSDYEGSD 2w1nA 846 :VLVSSLTGEPLPAKEVLA T0590 27 :E 2w1nA 870 :E T0590 30 :DGIGDSAY 2w1nA 873 :TEGSNLSV T0590 38 :AVNPEAG 2w1nA 884 :SVGDGEG T0590 45 :SMDYMPLMEYLHS 2w1nA 894 :EIAGTEKTVNIIE T0590 58 :SPVLP 2w1nA 913 :VVNPV T0590 63 :TARFT 2w1nA 919 :DFKAS T0590 69 :D 2w1nA 924 :E T0590 74 :FAPLSVRF 2w1nA 925 :INKKNVTV T0590 83 :DFS 2w1nA 936 :EPE T0590 86 :ENATSRLWMFGDGN 2w1nA 941 :EGLEGYILYKDGKK T0590 100 :TSDSPSPLHTFFN 2w1nA 957 :EIGKDETSYTFKK T0590 113 :EG 2w1nA 972 :RH T0590 115 :EYIVSLIVSNEND 2w1nA 975 :IYNFKIAAKYSNG T0590 128 :SDSASVTI 2w1nA 990 :SSKESLTL Number of specific fragments extracted= 16 number of extra gaps= 1 total=346 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 2w1nA/T0590-2w1nA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0590 read from 2w1nA/T0590-2w1nA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2w1nA read from 2w1nA/T0590-2w1nA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2w1nA in template set Warning: unaligning (T0590)D26 because of BadResidue code BAD_PEPTIDE in next template residue (2w1nA)K872 Warning: unaligning (T0590)E27 because of BadResidue code BAD_PEPTIDE at template residue (2w1nA)K872 T0590 3 :ARDNKFNTWNDSRG 2w1nA 841 :DGKVRVLVSSLTGE T0590 17 :NYWSDYEG 2w1nA 857 :PAKEVLAK T0590 25 :S 2w1nA 870 :E T0590 28 :NGDGIGDSA 2w1nA 873 :TEGSNLSVT T0590 37 :YAVNPEAGSM 2w1nA 883 :SSVGDGEGLV T0590 47 :DYMPLMEYLH 2w1nA 896 :AGTEKTVNII T0590 57 :SSPVLPTARFTSD 2w1nA 911 :EIVVNPVRDFKAS T0590 71 :TEGFAPLSVRFKDFS 2w1nA 924 :EINKKNVTVTWTEPE T0590 86 :ENATSRLWMFGDGNT 2w1nA 941 :EGLEGYILYKDGKKV T0590 101 :SDSPSPLHTF 2w1nA 958 :IGKDETSYTF T0590 113 :EG 2w1nA 968 :KK T0590 115 :EYIVSLIVSNENDSDSASVTIRA 2w1nA 975 :IYNFKIAAKYSNGEVSSKESLTL Number of specific fragments extracted= 12 number of extra gaps= 1 total=358 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 1f6fB/T0590-1f6fB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1f6fB expands to /projects/compbio/data/pdb/1f6f.pdb.gz 1f6fB:# T0590 read from 1f6fB/T0590-1f6fB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f6fB read from 1f6fB/T0590-1f6fB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1f6fB to template set # found chain 1f6fB in template set Warning: unaligning (T0590)D69 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1f6fB)K119 Warning: unaligning (T0590)A75 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1f6fB)K119 T0590 2 :NARDNKFNTWND 1f6fB 29 :DGGLPTNYSLTY T0590 14 :SRG 1f6fB 44 :GEK T0590 18 :YWSDYEGSDE 1f6fB 57 :SGPNSCFFSK T0590 28 :NGDGI 1f6fB 69 :TSIWK T0590 33 :GDSAYAVN 1f6fB 76 :IITVNATN T0590 42 :EAG 1f6fB 84 :QMG T0590 45 :SMDYMPLMEYL 1f6fB 88 :SSSDPLYVDVT T0590 56 :HSSPVLPTARFTS 1f6fB 101 :VEPEPPRNLTLEV T0590 76 :PLSVRF 1f6fB 120 :KTYLWV T0590 82 :KDFSEN 1f6fB 133 :TDVKTG T0590 88 :ATSRLWMF 1f6fB 141 :TMEYEIRL T0590 96 :GDGNT 1f6fB 152 :EAEEW T0590 101 :SDSPSPLHTFFNEG 1f6fB 162 :GHQTQFKVFDLYPG T0590 115 :EYIVSLIVSNEND 1f6fB 177 :KYLVQTRCKPDHG T0590 128 :SD 1f6fB 191 :WS T0590 130 :SASVTIR 1f6fB 195 :SQESSVE Number of specific fragments extracted= 16 number of extra gaps= 0 total=374 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 1f6fB/T0590-1f6fB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0590 read from 1f6fB/T0590-1f6fB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f6fB read from 1f6fB/T0590-1f6fB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1f6fB in template set Warning: unaligning (T0590)I70 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1f6fB)K119 Warning: unaligning (T0590)A75 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1f6fB)K119 T0590 11 :WNDSRGNYWSDYEGSD 1f6fB 40 :YSKEGEKTTYECPDYK T0590 27 :ENGDGIGDSAYAVNPEAGSMDYMPLMEYLHS 1f6fB 69 :TSIWKIYIITVNATNQMGSSSSDPLYVDVTY T0590 58 :SPVLP 1f6fB 102 :EPEPP T0590 63 :TARFT 1f6fB 108 :NLTLE T0590 69 :D 1f6fB 113 :V T0590 76 :PLSVRF 1f6fB 120 :KTYLWV T0590 82 :KDFS 1f6fB 133 :TDVK T0590 86 :EN 1f6fB 138 :GW T0590 88 :ATSRLWMF 1f6fB 141 :TMEYEIRL T0590 96 :GDGN 1f6fB 152 :EAEE T0590 100 :TSDSPSPLHTFFN 1f6fB 159 :HFTGHQTQFKVFD T0590 113 :EG 1f6fB 174 :PG T0590 115 :EYIVSLIVSNEND 1f6fB 177 :KYLVQTRCKPDHG T0590 128 :SDSASVT 1f6fB 195 :SQESSVE Number of specific fragments extracted= 14 number of extra gaps= 0 total=388 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 1f6fB/T0590-1f6fB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0590 read from 1f6fB/T0590-1f6fB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f6fB read from 1f6fB/T0590-1f6fB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1f6fB in template set Warning: unaligning (T0590)D69 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (1f6fB)K119 Warning: unaligning (T0590)G73 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (1f6fB)K119 T0590 1 :MNARDNKFNTWN 1f6fB 28 :TDGGLPTNYSLT T0590 13 :DSRG 1f6fB 42 :KEGE T0590 17 :NYWSDYEGSDENGDG 1f6fB 54 :YKTSGPNSCFFSKQY T0590 33 :GDSAYAVNPEAGSMDYMPLMEYLH 1f6fB 75 :YIITVNATNQMGSSSSDPLYVDVT T0590 57 :SSPVLPTARFTS 1f6fB 102 :EPEPPRNLTLEV T0590 74 :FAPLSVRFK 1f6fB 120 :KTYLWVKWS T0590 83 :DFS 1f6fB 134 :DVK T0590 86 :ENATSRLWMFGDGNT 1f6fB 139 :WFTMEYEIRLKPEEA T0590 101 :SDSPSPLHTFFNEG 1f6fB 162 :GHQTQFKVFDLYPG T0590 115 :EYIVSLIVSNENDSDS 1f6fB 177 :KYLVQTRCKPDHGYWS Number of specific fragments extracted= 10 number of extra gaps= 0 total=398 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 1cfb/T0590-1cfb-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1cfb expands to /projects/compbio/data/pdb/1cfb.pdb.gz 1cfb:Warning: there is no chain 1cfb will retry with 1cfbA # T0590 read from 1cfb/T0590-1cfb-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cfb read from 1cfb/T0590-1cfb-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1cfb to template set # found chain 1cfb in template set T0590 2 :N 1cfb 638 :G T0590 3 :ARDNKFNTWND 1cfb 641 :RSPILHYTIQF T0590 14 :SRGN 1cfb 656 :TPAS T0590 18 :YWSDYEGSDENGDGI 1cfb 668 :PNTDSSFVVQMSPWA T0590 33 :GDSAYAVN 1cfb 685 :TFRVIAFN T0590 42 :EAG 1cfb 693 :KIG T0590 45 :SMDYMPLMEYLHS 1cfb 699 :PSAHSDSCTTQPD T0590 58 :SPVLPTARFTSDI 1cfb 714 :FKNPDNVVGQGTE T0590 76 :PLSVRF 1cfb 727 :PNNLVI T0590 82 :KDFSENATSRLWMF 1cfb 740 :IEHNAPNFHYYVSW T0590 96 :GDGNT 1cfb 758 :PAAAW T0590 101 :SDSPSPLHTFF 1cfb 768 :FDWRQNNIVIA T0590 112 :NEG 1cfb 781 :PTF T0590 115 :EYIVSLIVSNEND 1cfb 785 :KYLIKVVAINDRG T0590 128 :SDSASVTIRA 1cfb 799 :SNVAAEEVVG Number of specific fragments extracted= 15 number of extra gaps= 0 total=413 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 1cfb/T0590-1cfb-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0590 read from 1cfb/T0590-1cfb-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cfb read from 1cfb/T0590-1cfb-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cfb in template set T0590 2 :NARDNKFNTWND 1cfb 638 :GDNRSPILHYTI T0590 14 :SR 1cfb 654 :SF T0590 16 :GNY 1cfb 658 :ASW T0590 19 :WSDYEGSD 1cfb 666 :KVPNTDSS T0590 27 :ENGDGI 1cfb 677 :QMSPWA T0590 33 :GDSAYAVNPEAGSMDYMPLMEYLHSSPVLP 1cfb 684 :YTFRVIAFNKIGASPPSAHSDSCTTQPDVP T0590 63 :TARFTS 1cfb 719 :NVVGQG T0590 70 :IT 1cfb 725 :TE T0590 76 :PLSVRF 1cfb 727 :PNNLVI T0590 82 :KDFSENATSRLWMF 1cfb 740 :IEHNAPNFHYYVSW T0590 96 :GDGN 1cfb 758 :PAAA T0590 100 :TSDSPSPLHTFFN 1cfb 767 :IFDWRQNNIVIAD T0590 113 :EG 1cfb 782 :TF T0590 115 :EYIVSLIVSNEND 1cfb 785 :KYLIKVVAINDRG T0590 128 :SDSASVTI 1cfb 801 :VAAEEVVG Number of specific fragments extracted= 15 number of extra gaps= 0 total=428 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 1cfb/T0590-1cfb-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0590 read from 1cfb/T0590-1cfb-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cfb read from 1cfb/T0590-1cfb-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1cfb in template set T0590 3 :ARDNKFNTWNDSRG 1cfb 641 :RSPILHYTIQFNTS T0590 17 :NYWSDYEGSDENGDGI 1cfb 667 :VPNTDSSFVVQMSPWA T0590 33 :GDSAYAVNPEAG 1cfb 684 :YTFRVIAFNKIG T0590 45 :SMDYMPLMEYLHSSPVLPTARFTSDITEGF 1cfb 699 :PSAHSDSCTTQPDVPFKNPDNVVGQGTEPN T0590 76 :PLSVRFK 1cfb 729 :NLVISWT T0590 83 :DFSENATSRLWMFGDGNT 1cfb 741 :EHNAPNFHYYVSWKRDIP T0590 101 :SDSPSPLHTFFN 1cfb 768 :FDWRQNNIVIAD T0590 113 :EG 1cfb 782 :TF T0590 115 :EYIVSLIVSNENDS 1cfb 785 :KYLIKVVAINDRGE Number of specific fragments extracted= 9 number of extra gaps= 0 total=437 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 2wg4B/T0590-2wg4B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2wg4B expands to /projects/compbio/data/pdb/2wg4.pdb.gz 2wg4B:# T0590 read from 2wg4B/T0590-2wg4B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2wg4B read from 2wg4B/T0590-2wg4B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2wg4B to template set # found chain 2wg4B in template set Warning: unaligning (T0590)E42 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2wg4B)R460 Warning: unaligning (T0590)M46 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2wg4B)R460 Warning: unaligning (T0590)E86 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2wg4B)H575 T0590 3 :ARDNK 2wg4B 418 :TNQPP T0590 9 :NTWNDSRGNYWSDYEGSDENGDGIGDSAYAVNP 2wg4B 423 :EVFAHGLHDPGRCAVDRHPTDININLTILCSDS T0590 47 :DYMPLMEYLHSSPVL 2wg4B 461 :SSARILQIIKGKDYE T0590 62 :PTARF 2wg4B 552 :LGFGE T0590 69 :DIT 2wg4B 557 :DEL T0590 76 :PLSVRF 2wg4B 560 :GEVYIL T0590 87 :NATSRLWMFGDGNT 2wg4B 576 :NGKLYKIVDPKRPL Number of specific fragments extracted= 7 number of extra gaps= 0 total=444 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 2wg4B/T0590-2wg4B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0590 read from 2wg4B/T0590-2wg4B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2wg4B read from 2wg4B/T0590-2wg4B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2wg4B in template set Warning: unaligning (T0590)G31 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2wg4B)H315 Warning: unaligning (T0590)K82 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2wg4B)R460 Warning: unaligning (T0590)E86 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2wg4B)R460 T0590 18 :YWSDYEGSD 2wg4B 250 :YVKILTPEG T0590 32 :IGDSAYAVN 2wg4B 316 :DHILRVVEY T0590 41 :PEAG 2wg4B 328 :RKNP T0590 45 :SMDYMPLMEYLHS 2wg4B 335 :DLRTARVFLEVAE T0590 58 :SPVLPTARFTSDITEGFAPLSVRF 2wg4B 429 :LHDPGRCAVDRHPTDININLTILC T0590 87 :NATSRLW 2wg4B 461 :SSARILQ T0590 95 :FGDGNTSDSP 2wg4B 468 :IIKGKDYESE T0590 105 :SPLHTFFNEGEYIV 2wg4B 507 :GSYVFGDRNGNFLT T0590 122 :VSN 2wg4B 521 :LQQ T0590 125 :ENDSDSASVTI 2wg4B 525 :PVTKQWQEKPL Number of specific fragments extracted= 10 number of extra gaps= 0 total=454 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 2wg4B/T0590-2wg4B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0590 read from 2wg4B/T0590-2wg4B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2wg4B read from 2wg4B/T0590-2wg4B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2wg4B in template set Warning: unaligning (T0590)F84 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2wg4B)R460 Warning: unaligning (T0590)A88 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2wg4B)R460 T0590 6 :NKFNTWNDSRG 2wg4B 389 :TGSVLRLDVDT T0590 17 :NYWSDYEGS 2wg4B 401 :MCNVPYSIP T0590 27 :ENG 2wg4B 410 :RSN T0590 41 :PEAGSMDYMPLMEYLH 2wg4B 413 :PHFNSTNQPPEVFAHG T0590 58 :SPVLPTARFTSDITEGFAPLSVRFK 2wg4B 429 :LHDPGRCAVDRHPTDININLTILCS T0590 83 :D 2wg4B 455 :S T0590 89 :TSRLWMFGDGNT 2wg4B 461 :SSARILQIIKGK T0590 101 :SDSPSPLHT 2wg4B 475 :ESEPSLLEF Number of specific fragments extracted= 8 number of extra gaps= 0 total=462 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 3jz7A/T0590-3jz7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3jz7A expands to /projects/compbio/data/pdb/3jz7.pdb.gz 3jz7A:Skipped atom 18, because occupancy 0.500 <= existing 0.500 in 3jz7A Skipped atom 20, because occupancy 0.500 <= existing 0.500 in 3jz7A Skipped atom 22, because occupancy 0.500 <= existing 0.500 in 3jz7A Skipped atom 24, because occupancy 0.500 <= existing 0.500 in 3jz7A Skipped atom 26, because occupancy 0.500 <= existing 0.500 in 3jz7A Skipped atom 28, because occupancy 0.500 <= existing 0.500 in 3jz7A Skipped atom 30, because occupancy 0.500 <= existing 0.500 in 3jz7A Skipped atom 32, because occupancy 0.500 <= existing 0.500 in 3jz7A Skipped atom 34, because occupancy 0.500 <= existing 0.500 in 3jz7A Skipped atom 194, because occupancy 0.500 <= existing 0.500 in 3jz7A Skipped atom 198, because occupancy 0.500 <= existing 0.500 in 3jz7A Skipped atom 200, because occupancy 0.500 <= existing 0.500 in 3jz7A Skipped atom 202, because occupancy 0.500 <= existing 0.500 in 3jz7A Skipped atom 204, because occupancy 0.500 <= existing 0.500 in 3jz7A Skipped atom 206, because occupancy 0.500 <= existing 0.500 in 3jz7A Skipped atom 685, because occupancy 0.500 <= existing 0.500 in 3jz7A Skipped atom 689, because occupancy 0.500 <= existing 0.500 in 3jz7A Skipped atom 691, because occupancy 0.500 <= existing 0.500 in 3jz7A Skipped atom 693, because occupancy 0.500 <= existing 0.500 in 3jz7A Skipped atom 695, because occupancy 0.500 <= existing 0.500 in 3jz7A # T0590 read from 3jz7A/T0590-3jz7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3jz7A read from 3jz7A/T0590-3jz7A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3jz7A to template set # found chain 3jz7A in template set T0590 4 :RDNKFNTWNDSRGN 3jz7A 52 :PLDIEWLISPSDNQ T0590 18 :YWSDYEGSDENGDGI 3jz7A 101 :GDASINVTNLQLSDI T0590 33 :GDSAYAVN 3jz7A 117 :TYQCKVKK T0590 42 :EAGSMDYMPLMEYLHSSPV 3jz7A 125 :APGVANKKFLLTVLVKPSG T0590 62 :PTARFTSDITEGF 3jz7A 144 :TRCFVDGSEEIGN T0590 76 :PLSVRFKDFS 3jz7A 157 :DFKLKCEPKE T0590 86 :ENATSRLWMF 3jz7A 168 :SLPLQFEWQK T0590 96 :GDGNT 3jz7A 179 :SDSQT T0590 101 :SDSPSPLHTFFN 3jz7A 190 :AEMTSPVISVKN T0590 113 :EGEYIV 3jz7A 207 :SGTYSC T0590 121 :IVSNENDSDSASVTIRA 3jz7A 213 :TVQNRVGSDQCMLRLDV Number of specific fragments extracted= 11 number of extra gaps= 0 total=473 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 3jz7A/T0590-3jz7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0590 read from 3jz7A/T0590-3jz7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3jz7A read from 3jz7A/T0590-3jz7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3jz7A in template set T0590 27 :ENGDGIGDSAYAVNPEAG 3jz7A 110 :LQLSDIGTYQCKVKKAPG T0590 46 :MDYMPLMEYLHSSPVLPTARFTSDI 3jz7A 128 :VANKKFLLTVLVKPSGTRCFVDGSE T0590 74 :FAPLSVRF 3jz7A 153 :EIGNDFKL T0590 84 :FS 3jz7A 165 :KE T0590 86 :ENAT 3jz7A 169 :LPLQ T0590 91 :RLWMF 3jz7A 173 :FEWQK T0590 96 :GDGN 3jz7A 179 :SDSQ T0590 100 :TSDSPSPLHTFFN 3jz7A 189 :LAEMTSPVISVKN T0590 113 :EGEYIV 3jz7A 207 :SGTYSC T0590 121 :IVSNENDSDSASVTI 3jz7A 213 :TVQNRVGSDQCMLRL T0590 136 :R 3jz7A 231 :P Number of specific fragments extracted= 11 number of extra gaps= 0 total=484 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 3jz7A/T0590-3jz7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0590 read from 3jz7A/T0590-3jz7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3jz7A read from 3jz7A/T0590-3jz7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3jz7A in template set T0590 4 :RDNKFNTWNDSRG 3jz7A 67 :VDQVIILYSGDKI T0590 17 :NYWSDYEGSDENGDGI 3jz7A 82 :NYYPDLKGRVHFTSND T0590 33 :GDSAYAVNPEAGSMDYMPLMEYLHS 3jz7A 116 :GTYQCKVKKAPGVANKKFLLTVLVK T0590 59 :PVLPTARFTSDITEGF 3jz7A 141 :PSGTRCFVDGSEEIGN T0590 75 :APLSVRFKDFSENATSRLWMFGDGNT 3jz7A 158 :FKLKCEPKEGSLPLQFEWQKLSDSQT T0590 101 :SDSPSPLHTFFN 3jz7A 190 :AEMTSPVISVKN T0590 113 :EGEYIV 3jz7A 207 :SGTYSC T0590 121 :IVSNENDSDSASVTIRA 3jz7A 213 :TVQNRVGSDQCMLRLDV Number of specific fragments extracted= 8 number of extra gaps= 0 total=492 Will force an alignment to be made, even if fragment is small Number of alignments=60 # command:CPU_time= 16.453 sec, elapsed time= 19.526 sec. # command:DEBUG: alignment library has 60 conformations DEBUG: current conformations has 0 conformations # in ExtractAlignmentsContacts extracting from alignment library using radius 8.000 separation >= 9 style evalue NUMB_ALIGNS: 60 # Adding 1795 constraints to all_contacts Done adding distance constraints # command:CPU_time= 16.493 sec, elapsed time= 19.568 sec. # command:Reading probabilities from T0590.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 29.112 Optimizing... Probability sum: -280.615, CN propb: -280.615 weights: 0.289 constraints: 419 # command:CPU_time= 87.892 sec, elapsed time= 90.997 sec. # command:Found ConstraintSet # PrintContacts align.constraints Number of constraints in align 419 # command:Found ConstraintSet # PrintContacts align_bonus.constraints Number of constraints in align.bonus 419 # command:Found ConstraintSet # PrintContacts rejected.constraints Number of constraints in rejected 1376 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints Number of constraints in rejected.bonus 1376 # command:Found ConstraintSet # PrintContacts noncontact.constraints Number of constraints in noncontact 0 # command:Found ConstraintSet # PrintContacts noncontact_bonus.constraints Number of constraints in noncontact.bonus 0 # command:CPU_time= 87.920 sec, elapsed time= 91.754 sec. # command: