# 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 T0378 numbered 1 through 254 Created new target T0378 from T0378.a2m # command:CPU_time= 6.166 sec, elapsed time= 6.211 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gz0A/T0378-1gz0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1gz0A expands to /projects/compbio/data/pdb/1gz0.pdb.gz 1gz0A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0378 read from 1gz0A/T0378-1gz0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gz0A read from 1gz0A/T0378-1gz0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1gz0A to template set # found chain 1gz0A in template set Warning: unaligning (T0378)A24 because first residue in template chain is (1gz0A)S2 T0378 25 :FAVEGPKLVGEMLPFYR 1gz0A 3 :EMIYGIHAVQALLERAP # choosing archetypes in rotamer library T0378 42 :CRMLVGT 1gz0A 22 :FQEVFIL T0378 49 :AAMLR 1gz0A 37 :LPLIH T0378 55 :VSTPHDAEVVELPESF 1gz0A 42 :ALESQGVVIQLANRQY T0378 72 :FKRISTQTTPQPLMAVF 1gz0A 58 :LDEKSDGAVHQGIIARV T0378 89 :DLPAEPEPVV 1gz0A 76 :PGRQYQENDL T0378 99 :EGLTLLLDGVQDPGNVGTILRTADWFGIRHVWLGTGSADVFSPKVVQASMGALARVQPTPLKNTVDTLAYFRRQGIPVYGAFLDGQSLYEA 1gz0A 94 :QPFLLILDGVTDPHNLGACLRSADAAGVHAVIVPKDRSAQLNATAKKVACGAAESVPLIRVTNLARTMRMLQEENIWIVGTAGEADHTLYQ T0378 192 :PNFTEPAILVLGSEGRGISPEVAAEITDRLTIP 1gz0A 185 :SKMTGRLALVMGAEGEGMRRLTREHCDELISIP T0378 230 :VKGHTESLNVAIATAILCSEWRRR 1gz0A 218 :MAGSVSSLNVSVATGICLFEAVRQ Number of specific fragments extracted= 9 number of extra gaps= 0 total=9 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 1gz0A/T0378-1gz0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0378 read from 1gz0A/T0378-1gz0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gz0A read from 1gz0A/T0378-1gz0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gz0A in template set Warning: unaligning (T0378)A24 because first residue in template chain is (1gz0A)S2 T0378 25 :FAVEGPKLVGEMLPFYR 1gz0A 3 :EMIYGIHAVQALLERAP T0378 42 :CRMLVGTAAM 1gz0A 22 :FQEVFILKGR T0378 56 :STPH 1gz0A 32 :EDKR T0378 60 :DAEVVELPESF 1gz0A 47 :GVVIQLANRQY T0378 72 :FKRISTQTTPQPLMAVFD 1gz0A 58 :LDEKSDGAVHQGIIARVK T0378 91 :PAEPEPVVE 1gz0A 76 :PGRQYQEND T0378 100 :GLTLLLDGVQDPGNVGTILRTADWFGIRHVWLGTGSADVFSPKVVQASMGALARVQPTPLKNTVDTLAYFRRQGIPVYGAFLDGQSLYEA 1gz0A 95 :PFLLILDGVTDPHNLGACLRSADAAGVHAVIVPKDRSAQLNATAKKVACGAAESVPLIRVTNLARTMRMLQEENIWIVGTAGEADHTLYQ T0378 192 :PNFTEPAILVLGSEGRGISPEVAAEITDRLTIP 1gz0A 185 :SKMTGRLALVMGAEGEGMRRLTREHCDELISIP T0378 230 :VKGHTESLNVAIATAILCSEWRR 1gz0A 218 :MAGSVSSLNVSVATGICLFEAVR Number of specific fragments extracted= 9 number of extra gaps= 0 total=18 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 1gz0A/T0378-1gz0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0378 read from 1gz0A/T0378-1gz0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1gz0A read from 1gz0A/T0378-1gz0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1gz0A in template set Warning: unaligning (T0378)A24 because first residue in template chain is (1gz0A)S2 T0378 25 :FAVEGPKLVGEMLPFY 1gz0A 3 :EMIYGIHAVQALLERA T0378 41 :RCRMLVGTA 1gz0A 20 :ERFQEVFIL T0378 50 :AMLRAVSTPHDAEVVELPESFDFKRISTQTTPQPLMAVFDLPAEPEPVVE 1gz0A 36 :LLPLIHALESQGVVIQLANRQYLDEKSDGAVHQGIIARVKPGRQYQENDL T0378 100 :GLTLLLDGVQDPGNVGTILRTADWFGIRHVWLGTGSADVFSPKVVQASMGALARVQPTPLKNTVDTLAYFRRQGIPVYGAFLDGQS 1gz0A 95 :PFLLILDGVTDPHNLGACLRSADAAGVHAVIVPKDRSAQLNATAKKVACGAAESVPLIRVTNLARTMRMLQEENIWIVGTAGEADH T0378 188 :EAPLPNFTEPAILVLGSEGRGISPEVAAEITDRLTIPA 1gz0A 181 :TLYQSKMTGRLALVMGAEGEGMRRLTREHCDELISIPM T0378 231 :KGHTESLNVAIATAILCSEWRRR 1gz0A 219 :AGSVSSLNVSVATGICLFEAVRQ Number of specific fragments extracted= 6 number of extra gaps= 0 total=24 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 1x7oA/T0378-1x7oA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1x7oA expands to /projects/compbio/data/pdb/1x7o.pdb.gz 1x7oA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0378 read from 1x7oA/T0378-1x7oA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1x7oA read from 1x7oA/T0378-1x7oA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1x7oA to template set # found chain 1x7oA in template set Warning: unaligning (T0378)S3 because first residue in template chain is (1x7oA)R18 Warning: unaligning (T0378)K73 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1x7oA)E95 Warning: unaligning (T0378)R74 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1x7oA)E95 Warning: unaligning (T0378)Q78 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1x7oA)E101 Warning: unaligning (T0378)T79 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1x7oA)E101 T0378 4 :ANQIKFLRSLRER 1x7oA 19 :NARFQQWQALLGN T0378 17 :KYRLREQAFAVEGPKLVGEMLPF 1x7oA 33 :NKRTRAGEFLVMGVRPISLAVEH T0378 40 :YRCRMLVGTA 1x7oA 57 :WPVRTLLYDG T0378 50 :AMLRAVSTPHDAEVVELPESF 1x7oA 72 :KWARELLRTVRTEQIAMAPDL T0378 72 :F 1x7oA 93 :L T0378 75 :IS 1x7oA 96 :LG T0378 77 :T 1x7oA 99 :K T0378 80 :TPQPLMAVFDLPAEPEPVV 1x7oA 102 :APPEVVAVVEMPADDLDRI T0378 99 :EG 1x7oA 124 :ED T0378 101 :LTLLLDGVQDPGNVGTILRTADWFGIRHVWLGTGSADVFSPKVVQASMGALARVQPTPLKNTVDTLAYF 1x7oA 127 :LGVLFDRPTSPGNIGSIIRSADALGAHGLIVAGHAADVYDPKSVRSSTGSLFSLPAVRVPSPGEVMDWV T0378 170 :RRQG 1x7oA 199 :RAAG T0378 174 :IPVYGAFLDGQSLYEA 1x7oA 205 :IVLVGTDEHGDCDVFD T0378 192 :PNFTEPAILVLGSEGRGISPEVAAEITDRLTIP 1x7oA 221 :FDFTQPTLLLIGNETAGLSNAWRTLCDYTVSIP T0378 230 :VKGHTESLNVAIATAILCSEWRRR 1x7oA 254 :MAGSASSLNAANAATAILYEAVRQ Number of specific fragments extracted= 14 number of extra gaps= 2 total=38 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 1x7oA/T0378-1x7oA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0378 read from 1x7oA/T0378-1x7oA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1x7oA read from 1x7oA/T0378-1x7oA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1x7oA in template set Warning: unaligning (T0378)S3 because first residue in template chain is (1x7oA)R18 Warning: unaligning (T0378)K73 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1x7oA)E95 Warning: unaligning (T0378)R74 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1x7oA)E95 Warning: unaligning (T0378)Q78 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1x7oA)E101 Warning: unaligning (T0378)T79 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1x7oA)E101 Warning: unaligning (T0378)R253 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1x7oA)R282 T0378 4 :ANQIKFLRSL 1x7oA 19 :NARFQQWQAL T0378 14 :RERKYRLREQAFAVEGPKLVGEMLPFYR 1x7oA 30 :GNRNKRTRAGEFLVMGVRPISLAVEHGW T0378 42 :CRMLVGTA 1x7oA 59 :VRTLLYDG T0378 50 :AMLRAVSTPHDAEVVELPESF 1x7oA 72 :KWARELLRTVRTEQIAMAPDL T0378 72 :F 1x7oA 93 :L T0378 75 :I 1x7oA 96 :L T0378 76 :ST 1x7oA 98 :EK T0378 80 :TPQPLMAVFDLPAEPEPVVE 1x7oA 102 :APPEVVAVVEMPADDLDRIP T0378 100 :G 1x7oA 125 :D T0378 101 :LTLLLDGVQDPGNVGTILRTADWFGIRHVWLGTGSADVFSPKVVQASMGALARVQPTPLKN 1x7oA 127 :LGVLFDRPTSPGNIGSIIRSADALGAHGLIVAGHAADVYDPKSVRSSTGSLFSLPAVRVPS T0378 162 :TVDTLAYFRRQG 1x7oA 191 :VMDWVEARRAAG T0378 174 :IPVYGAFLDGQSLYEA 1x7oA 205 :IVLVGTDEHGDCDVFD T0378 192 :PNFTEPAILVLGSEGRGISPEVAAEITDRLTIP 1x7oA 221 :FDFTQPTLLLIGNETAGLSNAWRTLCDYTVSIP T0378 230 :VKGHTESLNVAIATAILCSEWRR 1x7oA 254 :MAGSASSLNAANAATAILYEAVR Number of specific fragments extracted= 14 number of extra gaps= 3 total=52 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 1x7oA/T0378-1x7oA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0378 read from 1x7oA/T0378-1x7oA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1x7oA read from 1x7oA/T0378-1x7oA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1x7oA in template set Warning: unaligning (T0378)S3 because first residue in template chain is (1x7oA)R18 Warning: unaligning (T0378)K73 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1x7oA)E95 Warning: unaligning (T0378)R74 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1x7oA)E95 Warning: unaligning (T0378)Q78 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1x7oA)E101 Warning: unaligning (T0378)T79 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1x7oA)E101 T0378 4 :ANQIKFLRS 1x7oA 19 :NARFQQWQA T0378 13 :LRERKYRLREQAFAVEGPKLVGEMLPFYRCRMLVGTA 1x7oA 29 :LGNRNKRTRAGEFLVMGVRPISLAVEHGWPVRTLLYD T0378 50 :AMLRAVSTPHDAEVVELPESFDF 1x7oA 71 :SKWARELLRTVRTEQIAMAPDLL T0378 75 :IS 1x7oA 96 :LG T0378 77 :T 1x7oA 99 :K T0378 80 :TPQPLMAVFDLPAEPEPVVE 1x7oA 102 :APPEVVAVVEMPADDLDRIP T0378 100 :GLTLLLDGVQDPGNVGTILRTADWFGIRHVWLGTGSADVFSPKVVQASMGALARVQPTPLKN 1x7oA 126 :FLGVLFDRPTSPGNIGSIIRSADALGAHGLIVAGHAADVYDPKSVRSSTGSLFSLPAVRVPS T0378 162 :TVDTLAYFRRQG 1x7oA 191 :VMDWVEARRAAG T0378 174 :IPVYGAFLDGQS 1x7oA 205 :IVLVGTDEHGDC T0378 188 :EAPLPNFTEPAILVLGSEGRGISPEVAAEITDRLTIPA 1x7oA 217 :DVFDFDFTQPTLLLIGNETAGLSNAWRTLCDYTVSIPM T0378 231 :KGHTESLNVAIATAILCSEWRRRS 1x7oA 255 :AGSASSLNAANAATAILYEAVRQR Number of specific fragments extracted= 11 number of extra gaps= 2 total=63 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 1ipaA/T0378-1ipaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ipaA expands to /projects/compbio/data/pdb/1ipa.pdb.gz 1ipaA:# T0378 read from 1ipaA/T0378-1ipaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ipaA read from 1ipaA/T0378-1ipaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ipaA to template set # found chain 1ipaA in template set Warning: unaligning (T0378)V55 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ipaA)L74 Warning: unaligning (T0378)A61 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ipaA)L74 T0378 1 :MLSANQIKFLRSLRERKYRLREQAFAVEGPKLVGEMLPF 1ipaA 5 :STANPRIKELARLLERKHRDSQRRFLIEGAREIERALQA T0378 40 :YRCRMLVGT 1ipaA 45 :IELEQALVW T0378 49 :AAMLRA 1ipaA 62 :QQVYAA T0378 62 :EVVELPESF 1ipaA 75 :ALLEVSEAV T0378 72 :FKRISTQTTPQPLMAVFDLPAEPEPVV 1ipaA 84 :LKKLSVRDNPAGLIALARMPERTLEEY T0378 99 :EGLTLLLDGVQDPGNVGTILRTADWFGIRHVWLGTG 1ipaA 115 :DALILVAVGLEKPGNLGAVLRSADAAGAEAVLVAGG T0378 136 :ADVFSPKVVQASMGALARVQPTP 1ipaA 151 :VDLYSPQVIRNSTGVVFSLRTLA T0378 160 :KNTVDTLAYFRRQGIPVYGAFLDGQSLYEA 1ipaA 174 :ASESEVLDWIKQHNLPLVATTPHAEALYWE T0378 192 :PNFTEPAILVLGSEGRGISPEVAAEITDRLTIP 1ipaA 204 :ANLRPPVAIAVGPEHEGLRAAWLEAAQTQVRIP T0378 230 :VKGHTESLNVAIATAILCSEWRRR 1ipaA 237 :MQGQADSLNVSVSAALLLYEALRQ Number of specific fragments extracted= 10 number of extra gaps= 0 total=73 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 1ipaA/T0378-1ipaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0378 read from 1ipaA/T0378-1ipaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ipaA read from 1ipaA/T0378-1ipaA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ipaA in template set Warning: unaligning (T0378)V55 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ipaA)L74 Warning: unaligning (T0378)A61 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ipaA)L74 T0378 3 :SANQIKFLRSLRERKYRLREQAFAVEGPKLVGEMLPFYR 1ipaA 7 :ANPRIKELARLLERKHRDSQRRFLIEGAREIERALQAGI T0378 42 :CRMLVGTA 1ipaA 47 :LEQALVWE T0378 50 :AMLRA 1ipaA 63 :QVYAA T0378 62 :EVVELPESF 1ipaA 75 :ALLEVSEAV T0378 72 :FKRISTQTTPQPLMAVFDLPAEPEPVVE 1ipaA 84 :LKKLSVRDNPAGLIALARMPERTLEEYR T0378 100 :GLTLLLDGVQDPGNVGTILRTADWFGIRHVWLGTG 1ipaA 116 :ALILVAVGLEKPGNLGAVLRSADAAGAEAVLVAGG T0378 136 :ADVFSPKVVQASMGALARVQPTP 1ipaA 151 :VDLYSPQVIRNSTGVVFSLRTLA T0378 160 :KNTVDTLAYFRRQGIPVYGAFLDGQSLYEA 1ipaA 174 :ASESEVLDWIKQHNLPLVATTPHAEALYWE T0378 192 :PNFTEPAILVLGSEGRGISPEVAAEITDRLTIP 1ipaA 204 :ANLRPPVAIAVGPEHEGLRAAWLEAAQTQVRIP T0378 230 :VKGHTESLNVAIATAILCSEWRR 1ipaA 237 :MQGQADSLNVSVSAALLLYEALR Number of specific fragments extracted= 10 number of extra gaps= 0 total=83 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 1ipaA/T0378-1ipaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0378 read from 1ipaA/T0378-1ipaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ipaA read from 1ipaA/T0378-1ipaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ipaA in template set Warning: unaligning (T0378)S56 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ipaA)L74 Warning: unaligning (T0378)E62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ipaA)L74 T0378 3 :SANQIKFLRSLRERKYRLREQAFAVEGPKLVGEMLPFYRCRMLVGTA 1ipaA 7 :ANPRIKELARLLERKHRDSQRRFLIEGAREIERALQAGIELEQALVW T0378 50 :AMLRAV 1ipaA 62 :QQVYAA T0378 63 :VVELPESFDFKRISTQTTPQPLMAVFDLPAEPEPVVE 1ipaA 75 :ALLEVSEAVLKKLSVRDNPAGLIALARMPERTLEEYR T0378 100 :GLTLLLDGVQDPGNVGTILRTADWFGIRHVWLGT 1ipaA 116 :ALILVAVGLEKPGNLGAVLRSADAAGAEAVLVAG T0378 135 :SADVFSPKVVQASMGALARVQPTP 1ipaA 150 :GVDLYSPQVIRNSTGVVFSLRTLA T0378 160 :KNTVDTLAYFRRQGIPVYGAFLDGQS 1ipaA 174 :ASESEVLDWIKQHNLPLVATTPHAEA T0378 188 :EAPLPNFTEPAILVLGSEGRGISPEVAAEITDRLTIPA 1ipaA 200 :LYWEANLRPPVAIAVGPEHEGLRAAWLEAAQTQVRIPM T0378 231 :KGHTESLNVAIATAILCSEWRRRS 1ipaA 238 :QGQADSLNVSVSAALLLYEALRQR Number of specific fragments extracted= 8 number of extra gaps= 0 total=91 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 1v2xA/T0378-1v2xA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1v2xA expands to /projects/compbio/data/pdb/1v2x.pdb.gz 1v2xA:# T0378 read from 1v2xA/T0378-1v2xA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v2xA read from 1v2xA/T0378-1v2xA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1v2xA to template set # found chain 1v2xA in template set T0378 4 :ANQIKFLRSLRERKYRL 1v2xA 2 :RERTEARRRRIEEVLRR T0378 97 :VVEGLTLLLDGVQDPGNVGTILRTADWFGIRHVWLGTGSADVFS 1v2xA 19 :RQPDLTVLLENVHKPHNLSAILRTCDAVGVLEAHAVNPTGGVPT T0378 146 :ASMGALARVQPTPLKNTVDTLAYFRRQGIPVYGAFLDGQSLYEAP 1v2xA 66 :TSGGSHKWVYLRVHPDLHEAFRFLKERGFTVYATALREDARDFRE T0378 192 :PNFTEPAILVLGSEGRGISPEVAAEITDRLTIP 1v2xA 111 :VDYTKPTAVLFGAEKWGVSEEALALADGAIKIP T0378 230 :VKGHTESLNVAIATAILCSEWRRR 1v2xA 144 :MLGMVQSLNVSVAAAVILFEAQRQ Number of specific fragments extracted= 5 number of extra gaps= 0 total=96 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 1v2xA/T0378-1v2xA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0378 read from 1v2xA/T0378-1v2xA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v2xA read from 1v2xA/T0378-1v2xA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1v2xA in template set T0378 4 :ANQIKFLRSLRERKYR 1v2xA 3 :ERTEARRRRIEEVLRR T0378 97 :VVEGLTLLLDGVQDPGNVGTILRTADWFGIRHVWLGTGSADVFS 1v2xA 19 :RQPDLTVLLENVHKPHNLSAILRTCDAVGVLEAHAVNPTGGVPT T0378 147 :SMGALARVQPTPLKNTVDTLAYFRRQGIPVYGAFLDGQSLYEAP 1v2xA 67 :SGGSHKWVYLRVHPDLHEAFRFLKERGFTVYATALREDARDFRE T0378 192 :PNFTEPAILVLGSEGRGISPEVAAEITDRLTIP 1v2xA 111 :VDYTKPTAVLFGAEKWGVSEEALALADGAIKIP T0378 230 :VKGHTESLNVAIATAILCSEWRR 1v2xA 144 :MLGMVQSLNVSVAAAVILFEAQR Number of specific fragments extracted= 5 number of extra gaps= 0 total=101 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 1v2xA/T0378-1v2xA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0378 read from 1v2xA/T0378-1v2xA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v2xA read from 1v2xA/T0378-1v2xA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1v2xA in template set T0378 7 :IKFLR 1v2xA 6 :EARRR T0378 71 :DFKRISTQTTP 1v2xA 11 :RIEEVLRRRQP T0378 100 :GLTLLLDGVQDPGNVGTILRTADWFGIRHVWLGTGSADVFS 1v2xA 22 :DLTVLLENVHKPHNLSAILRTCDAVGVLEAHAVNPTGGVPT T0378 146 :ASMGALARVQPTPLKNTVDTLAYFRRQGIPVYGAFLDGQS 1v2xA 66 :TSGGSHKWVYLRVHPDLHEAFRFLKERGFTVYATALREDA T0378 187 :YEAPLPNFTEPAILVLGSEGRGISPEVAAEITDRLTIPA 1v2xA 106 :RDFREVDYTKPTAVLFGAEKWGVSEEALALADGAIKIPM T0378 231 :KGHTESLNVAIATAILCSEWRRR 1v2xA 145 :LGMVQSLNVSVAAAVILFEAQRQ Number of specific fragments extracted= 6 number of extra gaps= 0 total=107 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 1zjrA/T0378-1zjrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1zjrA expands to /projects/compbio/data/pdb/1zjr.pdb.gz 1zjrA:# T0378 read from 1zjrA/T0378-1zjrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zjrA read from 1zjrA/T0378-1zjrA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1zjrA to template set # found chain 1zjrA in template set T0378 5 :NQIKFLRSLRER 1zjrA 7 :VLEKRLKRLREV T0378 37 :LPF 1zjrA 19 :LEK T0378 97 :VVEGLTLLLDGVQDPGNVGTILRTADWFGIRHVWLGTG 1zjrA 22 :RQKDLIVFADNVKNEHNFSAIVRTCDAVGVLYLYYYHA T0378 135 :SADVFSPK 1zjrA 62 :KKAKINEG T0378 146 :ASMGALARVQPTPLKNTVDTLAYFRRQGIPVYGAFLDGQSLYEAP 1zjrA 70 :ITQGSHKWVFIEKVDNPVQKLLEFKNRGFQIVATWLSKESVNFRE T0378 192 :PNFTEPAILVLGSEGRGISPEVAAEITDRLTIP 1zjrA 115 :VDYTKPTVLVVGNELQGVSPEIVEIADKKIVIP T0378 230 :VKGHTESLNVAIATAILCSEWRRR 1zjrA 148 :MYGMAQSLNVSVATGIILYEAQRQ Number of specific fragments extracted= 7 number of extra gaps= 0 total=114 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 1zjrA/T0378-1zjrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0378 read from 1zjrA/T0378-1zjrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zjrA read from 1zjrA/T0378-1zjrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zjrA in template set Warning: unaligning (T0378)A4 because first residue in template chain is (1zjrA)L6 T0378 5 :NQIKFLRSLRER 1zjrA 7 :VLEKRLKRLREV T0378 72 :FKR 1zjrA 19 :LEK T0378 97 :VVEGLTLLLDGVQDPGNVGTILRTADWFGIRHVWLGTGS 1zjrA 22 :RQKDLIVFADNVKNEHNFSAIVRTCDAVGVLYLYYYHAE T0378 136 :ADVFSP 1zjrA 63 :KAKINE T0378 145 :QASMGALARVQPTPLKNTVDTLAYFRRQGIPVYGAFLDGQSLYEAP 1zjrA 69 :GITQGSHKWVFIEKVDNPVQKLLEFKNRGFQIVATWLSKESVNFRE T0378 192 :PNFTEPAILVLGSEGRGISPEVAAEITDRLTIP 1zjrA 115 :VDYTKPTVLVVGNELQGVSPEIVEIADKKIVIP T0378 230 :VKGHTESLNVAIATAILCSEWRR 1zjrA 148 :MYGMAQSLNVSVATGIILYEAQR Number of specific fragments extracted= 7 number of extra gaps= 0 total=121 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 1zjrA/T0378-1zjrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0378 read from 1zjrA/T0378-1zjrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zjrA read from 1zjrA/T0378-1zjrA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zjrA in template set Warning: unaligning (T0378)A4 because first residue in template chain is (1zjrA)L6 T0378 5 :NQIKFLRSLRER 1zjrA 7 :VLEKRLKRLREV T0378 76 :ST 1zjrA 19 :LE T0378 98 :V 1zjrA 21 :K T0378 100 :GLTLLLDGVQDPGNVGTILRTADWFGIRHVWLGT 1zjrA 25 :DLIVFADNVKNEHNFSAIVRTCDAVGVLYLYYYH T0378 134 :GSADVFSPK 1zjrA 62 :KKAKINEGI T0378 147 :SMGALARVQPTPLKNTVDTLAYFRRQGIPVYGAFLDGQS 1zjrA 71 :TQGSHKWVFIEKVDNPVQKLLEFKNRGFQIVATWLSKES T0378 187 :YEAPLPNFTEPAILVLGSEGRGISPEVAAEITDRLTIPA 1zjrA 110 :VNFREVDYTKPTVLVVGNELQGVSPEIVEIADKKIVIPM T0378 231 :KGHTESLNVAIATAILCSEWRRR 1zjrA 149 :YGMAQSLNVSVATGIILYEAQRQ Number of specific fragments extracted= 8 number of extra gaps= 0 total=129 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 1mxiA/T0378-1mxiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1mxiA expands to /projects/compbio/data/pdb/1mxi.pdb.gz 1mxiA:# T0378 read from 1mxiA/T0378-1mxiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mxiA read from 1mxiA/T0378-1mxiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1mxiA to template set # found chain 1mxiA in template set Warning: unaligning (T0378)G100 because first residue in template chain is (1mxiA)M1 T0378 101 :LTLLLDGVQDPGNVGTILRTADWFGIR 1mxiA 2 :LDIVLYEPEIPQNTGNIIRLCANTGFR T0378 129 :VWLGTGSADVF 1mxiA 29 :LHLIEPLGFTW T0378 140 :SPKVVQASMGALARVQPTPLKNTVDTLAYF 1mxiA 41 :DKRLRRSGLDYHEFAEIKRHKTFEAFLESE T0378 175 :PVYGAFLDGQSLYEA 1mxiA 74 :RLFALTTKGCPAHSQ T0378 192 :PNFTEPAILVLGSEGRGISPEVAAEI 1mxiA 89 :VKFKLGDYLMFGPETRGIPMSILNEM T0378 218 :TDRLTIP 1mxiA 117 :EQKIRIP T0378 230 :VKGHTESLNVAIATAILCSEWRRR 1mxiA 124 :MTANSRSMNLSNSVAVTVYEAWRQ Number of specific fragments extracted= 7 number of extra gaps= 0 total=136 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 1mxiA/T0378-1mxiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0378 read from 1mxiA/T0378-1mxiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mxiA read from 1mxiA/T0378-1mxiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mxiA in template set Warning: unaligning (T0378)G100 because first residue in template chain is (1mxiA)M1 T0378 101 :LTLLLDGVQDPGNVGTILRTADWFGIR 1mxiA 2 :LDIVLYEPEIPQNTGNIIRLCANTGFR T0378 129 :VWLGTGSADVF 1mxiA 29 :LHLIEPLGFTW T0378 140 :SPKVVQASMGALARVQPTPLKNTVDTLAYF 1mxiA 41 :DKRLRRSGLDYHEFAEIKRHKTFEAFLESE T0378 175 :PVYGAFLDGQSLYEA 1mxiA 74 :RLFALTTKGCPAHSQ T0378 192 :PNFTEPAILVLGSEGRGISPEVAAEI 1mxiA 89 :VKFKLGDYLMFGPETRGIPMSILNEM T0378 218 :TDRLTIP 1mxiA 117 :EQKIRIP T0378 230 :VKGHTESLNVAIATAILCSEWRR 1mxiA 124 :MTANSRSMNLSNSVAVTVYEAWR Number of specific fragments extracted= 7 number of extra gaps= 0 total=143 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 1mxiA/T0378-1mxiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0378 read from 1mxiA/T0378-1mxiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mxiA read from 1mxiA/T0378-1mxiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1mxiA in template set T0378 101 :LTLLLDGVQDPGNVGTILRTADWFGIRHVWLGTGSADVFSPKVVQASMGALARVQPTPLKNTVDTLAYF 1mxiA 2 :LDIVLYEPEIPQNTGNIIRLCANTGFRLHLIEPLGFTWDDKRLRRSGLDYHEFAEIKRHKTFEAFLESE T0378 175 :PVYGAFLDGQS 1mxiA 74 :RLFALTTKGCP T0378 188 :EAPLPNFTEPAILVLGSEGRGISPEVAAEI 1mxiA 85 :AHSQVKFKLGDYLMFGPETRGIPMSILNEM T0378 218 :TDRLTIPA 1mxiA 117 :EQKIRIPM T0378 231 :KGHTESLNVAIATAILCSEWRRR 1mxiA 125 :TANSRSMNLSNSVAVTVYEAWRQ Number of specific fragments extracted= 5 number of extra gaps= 0 total=148 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 1z85A/T0378-1z85A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1z85A expands to /projects/compbio/data/pdb/1z85.pdb.gz 1z85A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1584, because occupancy 0.35 <= existing 0.650 in 1z85A Skipped atom 1586, because occupancy 0.350 <= existing 0.650 in 1z85A Skipped atom 1588, because occupancy 0.350 <= existing 0.650 in 1z85A # T0378 read from 1z85A/T0378-1z85A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z85A read from 1z85A/T0378-1z85A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1z85A to template set # found chain 1z85A in template set Warning: unaligning (T0378)L181 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1z85A)Q159 Warning: unaligning (T0378)S185 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1z85A)Q159 Warning: unaligning (T0378)L186 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1z85A)N160 Warning: unaligning (T0378)Y187 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1z85A)L161 Warning: unaligning (T0378)P224 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1z85A)L202 T0378 8 :KFLRSLRERKYRLREQAFAVEG 1z85A 18 :EREAHHMRVVRLKEGDVIEATD T0378 40 :YRCRMLVG 1z85A 40 :GNGFSYTC T0378 63 :VVELPESF 1z85A 49 :LKSLKKKT T0378 84 :LMAVF 1z85A 57 :AAAKI T0378 89 :DLPAEPEPVVEGLTLL 1z85A 63 :KVEEKEKEPTEKLSVV T0378 106 :DGVQDPGNVGTILRTADWFGIRHVWLGT 1z85A 79 :VPIGRWERTRFLIEKCVELGVDEIFFHK T0378 134 :GSADVFS 1z85A 109 :RSQHEIS T0378 141 :PK 1z85A 117 :DK T0378 143 :VVQAS 1z85A 123 :VREAA T0378 148 :MGALARVQPTPLKNT 1z85A 130 :CKRYLFPKVSFLEKL T0378 175 :PVYGAF 1z85A 149 :NVITLD T0378 188 :EA 1z85A 162 :LD T0378 192 :PNFTEPAILVLGSEG 1z85A 164 :ANLEGSITVVVGPEG T0378 208 :GISPEVAAEITDRLTI 1z85A 179 :GFSEKERELLRSSTTI Number of specific fragments extracted= 14 number of extra gaps= 0 total=162 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 1z85A/T0378-1z85A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0378 read from 1z85A/T0378-1z85A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z85A read from 1z85A/T0378-1z85A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1z85A in template set Warning: unaligning (T0378)L181 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1z85A)Q159 Warning: unaligning (T0378)S185 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1z85A)Q159 Warning: unaligning (T0378)L186 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1z85A)N160 Warning: unaligning (T0378)Y187 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1z85A)L161 Warning: unaligning (T0378)P224 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1z85A)L202 T0378 4 :ANQIKFLRSL 1z85A 18 :EREAHHMRVV T0378 18 :YRLREQAFAVEGPK 1z85A 28 :RLKEGDVIEATDGN T0378 43 :RMLV 1z85A 43 :FSYT T0378 63 :VVELPESF 1z85A 49 :LKSLKKKT T0378 84 :LMAVFD 1z85A 57 :AAAKIV T0378 90 :LPAEPEPVVEGLTLL 1z85A 64 :VEEKEKEPTEKLSVV T0378 106 :DGVQDPGNVGTILRTADWFGIRHVWLGT 1z85A 79 :VPIGRWERTRFLIEKCVELGVDEIFFHK T0378 134 :GSADVFS 1z85A 109 :RSQHEIS T0378 141 :PK 1z85A 117 :DK T0378 143 :VVQAS 1z85A 123 :VREAA T0378 148 :MGALARVQPTPLKNT 1z85A 130 :CKRYLFPKVSFLEKL T0378 175 :PVYGAF 1z85A 149 :NVITLD T0378 188 :EA 1z85A 162 :LD T0378 192 :PNFTEPAILVLGSEG 1z85A 164 :ANLEGSITVVVGPEG T0378 208 :GISPEVAAEITDRLTI 1z85A 179 :GFSEKERELLRSSTTI Number of specific fragments extracted= 15 number of extra gaps= 0 total=177 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 1z85A/T0378-1z85A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0378 read from 1z85A/T0378-1z85A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1z85A read from 1z85A/T0378-1z85A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1z85A in template set Warning: unaligning (T0378)L181 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1z85A)Q159 Warning: unaligning (T0378)S185 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1z85A)Q159 Warning: unaligning (T0378)E188 because of BadResidue code TOO_FEW_ATOMS+NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1z85A)N160 Warning: unaligning (T0378)A189 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1z85A)L161 T0378 24 :AFAVEGPKLVGEMLPFYRC 1z85A 12 :GEVIFDEREAHHMRVVRLK T0378 43 :RMLVGTA 1z85A 34 :VIEATDG T0378 79 :TTPQPLMAVFDLPAEPEPVVEGLTLLLD 1z85A 53 :KKKTAAAKIVKVEEKEKEPTEKLSVVVP T0378 112 :GNVGTILRTADWFGIRHVWLGT 1z85A 85 :ERTRFLIEKCVELGVDEIFFHK T0378 134 :GSADVFS 1z85A 109 :RSQHEIS T0378 141 :PKVVQAS 1z85A 121 :IVVREAA T0378 148 :MGALARVQPTPLKNT 1z85A 130 :CKRYLFPKVSFLEKL T0378 173 :GIPVYGAF 1z85A 147 :SGNVITLD T0378 190 :PLPNFTEPAILVLGSEG 1z85A 162 :LDANLEGSITVVVGPEG T0378 208 :GISPEVAAEITDRLTI 1z85A 179 :GFSEKERELLRSSTTI Number of specific fragments extracted= 10 number of extra gaps= 0 total=187 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 1v6zA/T0378-1v6zA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1v6zA expands to /projects/compbio/data/pdb/1v6z.pdb.gz 1v6zA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0378 read from 1v6zA/T0378-1v6zA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v6zA read from 1v6zA/T0378-1v6zA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1v6zA to template set # found chain 1v6zA in template set T0378 31 :KLVGEMLPFYRC 1v6zA 18 :RETRHLVEVLRA T0378 58 :PHDAEVVELPE 1v6zA 30 :RVGDRFTVFDG T0378 81 :PQPLMAVF 1v6zA 41 :EREALAEV T0378 89 :DLPAE 1v6zA 50 :DLGPP T0378 94 :PEPVV 1v6zA 64 :RPERE T0378 99 :EGLTLLLDGV 1v6zA 71 :VEVVLYVALL T0378 110 :DPGNVGTILRTADWFGIRHV 1v6zA 81 :KGDKLAEVVRAATELGATRI T0378 130 :WLGTGSADV 1v6zA 102 :PLVTRHSVP T0378 139 :FSPK 1v6zA 113 :MGEG T0378 143 :VVQASM 1v6zA 121 :LRAVAL T0378 167 :AYFRRQGI 1v6zA 127 :EAAKQSGR T0378 177 :YGAFLDGQSLYEAPLPNFTEPAILVLGSEG 1v6zA 155 :GLVAHVGATARVREVLDPEKPLALAVGPEG T0378 208 :GISPEVAAEITD 1v6zA 185 :GFAEEEVALLEA T0378 221 :LT 1v6zA 199 :FT T0378 223 :IPASGLSVK 1v6zA 202 :VSLGRRILR T0378 239 :VAIATAILCSE 1v6zA 211 :AETAALALLAL Number of specific fragments extracted= 16 number of extra gaps= 0 total=203 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 1v6zA/T0378-1v6zA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0378 read from 1v6zA/T0378-1v6zA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v6zA read from 1v6zA/T0378-1v6zA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1v6zA in template set T0378 8 :KFLRSLRERKYRLREQAFAVEGP 1v6zA 18 :RETRHLVEVLRARVGDRFTVFDG T0378 81 :PQPLMAVF 1v6zA 41 :EREALAEV T0378 89 :DLPAEPEPVVEGLTLLLDGVQD 1v6zA 61 :EERRPEREVGVEVVLYVALLKG T0378 112 :GNVGTILRTADWFGIRHVW 1v6zA 83 :DKLAEVVRAATELGATRIQ T0378 131 :LGTGSADV 1v6zA 103 :LVTRHSVP T0378 139 :FS 1v6zA 113 :MG T0378 141 :PKVVQASMGALA 1v6zA 119 :RRLRAVALEAAK T0378 153 :RVQPTPLKN 1v6zA 140 :VLPPIPLKA T0378 175 :PVYGAFLDGQSLYE 1v6zA 154 :QGLVAHVGATARVR T0378 190 :PLPNFTEPAILVLGSEG 1v6zA 168 :EVLDPEKPLALAVGPEG T0378 208 :GISPEVAAEITD 1v6zA 185 :GFAEEEVALLEA T0378 221 :LT 1v6zA 199 :FT T0378 223 :IPASGLSVK 1v6zA 202 :VSLGRRILR T0378 239 :VAIATAILC 1v6zA 211 :AETAALALL Number of specific fragments extracted= 14 number of extra gaps= 0 total=217 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 1v6zA/T0378-1v6zA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0378 read from 1v6zA/T0378-1v6zA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v6zA read from 1v6zA/T0378-1v6zA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1v6zA in template set T0378 30 :PKLVGEMLPFYRC 1v6zA 17 :LRETRHLVEVLRA T0378 43 :RMLVGTA 1v6zA 34 :RFTVFDG T0378 79 :TTPQPLMAVFDLPAEPEPVVEGLTLLLDGVQD 1v6zA 51 :LGPPLRYRVLEERRPEREVGVEVVLYVALLKG T0378 112 :GNVGTILRTADWFGIRHV 1v6zA 83 :DKLAEVVRAATELGATRI T0378 130 :WLGTGSADVFS 1v6zA 102 :PLVTRHSVPKE T0378 141 :PKVVQAS 1v6zA 119 :RRLRAVA T0378 148 :MGALARVQPTPLKN 1v6zA 132 :SGRVVVPEVLPPIP T0378 175 :PVYGAFLDGQS 1v6zA 154 :QGLVAHVGATA T0378 187 :YEAPLPNFTEPAILVLGSEG 1v6zA 165 :RVREVLDPEKPLALAVGPEG T0378 208 :GISPEVAAEI 1v6zA 185 :GFAEEEVALL T0378 219 :DRLTIPASGLSV 1v6zA 198 :GFTPVSLGRRIL Number of specific fragments extracted= 11 number of extra gaps= 0 total=228 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 1qwgA/T0378-1qwgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1qwgA expands to /projects/compbio/data/pdb/1qwg.pdb.gz 1qwgA:Skipped atom 282, because occupancy 0.500 <= existing 0.500 in 1qwgA Skipped atom 284, because occupancy 0.500 <= existing 0.500 in 1qwgA Skipped atom 1754, because occupancy 0.500 <= existing 0.500 in 1qwgA # T0378 read from 1qwgA/T0378-1qwgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qwgA read from 1qwgA/T0378-1qwgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1qwgA to template set # found chain 1qwgA in template set Warning: unaligning (T0378)I174 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1qwgA)M129 Warning: unaligning (T0378)P175 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1qwgA)M129 T0378 23 :QAFAVEG 1qwgA 14 :GLTVVLD T0378 30 :PKLVGEMLPF 1qwgA 25 :PKFVEDYLKV T0378 40 :YR 1qwgA 36 :GD T0378 42 :CRMLVGTAAMLR 1qwgA 39 :IDFVKFGWGTSA T0378 54 :AVSTPHDAEVVEL 1qwgA 62 :NYYKDWGIKVYPG T0378 67 :PESF 1qwgA 83 :SKGK T0378 72 :FKRISTQ 1qwgA 87 :FDEFLNE T0378 121 :ADWFGIRHVWLGTGSADVFS 1qwgA 94 :CEKLGFEAVEISDGSSDISL T0378 160 :KNTVDTLAYFRRQG 1qwgA 114 :EERNNAIKRAKDNG T0378 176 :VYGAFLDGQSLYE 1qwgA 130 :VLTEVGKKMPDKD T0378 192 :PNF 1qwgA 143 :KQL T0378 195 :TEPAILVLGSEG 1qwgA 161 :GADYVIIEGRES T0378 207 :RG 1qwgA 182 :EG T0378 209 :ISPEVAAEIT 1qwgA 185 :VKENELDVLA Number of specific fragments extracted= 14 number of extra gaps= 1 total=242 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 1qwgA/T0378-1qwgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0378 read from 1qwgA/T0378-1qwgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qwgA read from 1qwgA/T0378-1qwgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qwgA in template set Warning: unaligning (T0378)I174 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1qwgA)M129 Warning: unaligning (T0378)P175 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1qwgA)M129 T0378 23 :QAFAVEG 1qwgA 14 :GLTVVLD T0378 30 :PKLVGEMLP 1qwgA 25 :PKFVEDYLK T0378 39 :FYRCRMLVGTAAMLRAVSTPH 1qwgA 36 :GDYIDFVKFGWGTSAVIDRDV T0378 60 :DAEVVEL 1qwgA 68 :GIKVYPG T0378 67 :PESF 1qwgA 83 :SKGK T0378 72 :FKRIST 1qwgA 87 :FDEFLN T0378 120 :TADWFGIRHVWLGTGSADVFS 1qwgA 93 :ECEKLGFEAVEISDGSSDISL T0378 160 :KNTVDTLAYFRRQG 1qwgA 114 :EERNNAIKRAKDNG T0378 176 :VYGAFLDGQSLYEAPLP 1qwgA 130 :VLTEVGKKMPDKDKQLT T0378 197 :PAILVLGSEG 1qwgA 163 :DYVIIEGRES T0378 209 :ISPEVAAEIT 1qwgA 185 :VKENELDVLA Number of specific fragments extracted= 11 number of extra gaps= 1 total=253 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 1qwgA/T0378-1qwgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0378 read from 1qwgA/T0378-1qwgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qwgA read from 1qwgA/T0378-1qwgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1qwgA in template set Warning: unaligning (T0378)I174 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1qwgA)M129 Warning: unaligning (T0378)P175 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1qwgA)M129 T0378 30 :PKLVGEMLPFY 1qwgA 25 :PKFVEDYLKVC T0378 50 :AMLRAVSTPHDAEVVELP 1qwgA 57 :VKEKINYYKDWGIKVYPG T0378 68 :ESFDFKRIST 1qwgA 83 :SKGKFDEFLN T0378 120 :TADWFGIRHVWLGTGSADVFSPK 1qwgA 93 :ECEKLGFEAVEISDGSSDISLEE T0378 162 :TVDTLAYFRRQG 1qwgA 116 :RNNAIKRAKDNG T0378 176 :VYGAFLDGQS 1qwgA 130 :VLTEVGKKMP T0378 197 :PAILVLGSEG 1qwgA 163 :DYVIIEGRES T0378 207 :RGISPEVAAEITD 1qwgA 183 :GKVKENELDVLAK Number of specific fragments extracted= 8 number of extra gaps= 1 total=261 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 1vhyA/T0378-1vhyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1vhyA expands to /projects/compbio/data/pdb/1vhy.pdb.gz 1vhyA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 679, because occupancy 0.350 <= existing 0.650 in 1vhyA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 681, because occupancy 0.350 <= existing 0.650 in 1vhyA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 683, because occupancy 0.350 <= existing 0.650 in 1vhyA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 685, because occupancy 0.350 <= existing 0.650 in 1vhyA Skipped atom 778, because occupancy 0.350 <= existing 0.650 in 1vhyA Skipped atom 780, because occupancy 0.350 <= existing 0.650 in 1vhyA Skipped atom 782, because occupancy 0.350 <= existing 0.650 in 1vhyA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1831, because occupancy 0.350 <= existing 0.650 in 1vhyA Skipped atom 1833, because occupancy 0.350 <= existing 0.650 in 1vhyA Skipped atom 1835, because occupancy 0.350 <= existing 0.650 in 1vhyA Skipped atom 1837, because occupancy 0.350 <= existing 0.650 in 1vhyA Skipped atom 1839, because occupancy 0.350 <= existing 0.650 in 1vhyA # T0378 read from 1vhyA/T0378-1vhyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vhyA read from 1vhyA/T0378-1vhyA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1vhyA to template set # found chain 1vhyA in template set Warning: unaligning (T0378)G107 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vhyA)R91 Warning: unaligning (T0378)G112 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vhyA)R91 T0378 23 :QAFAVE 1vhyA 14 :NQTQCY T0378 47 :GTAAMLR 1vhyA 20 :LSEDAAN T0378 54 :AVSTPHDAEVVELPESFD 1vhyA 31 :VLRMTEGEQLELFDGSNH T0378 79 :TTPQPLMAVF 1vhyA 57 :SNKKSVKVEI T0378 89 :DLPAEPEPVVEGLTLLLD 1vhyA 68 :GRELADKESHLKIHLGQV T0378 113 :NVG 1vhyA 92 :MEF T0378 117 :ILRTADWFGIRHV 1vhyA 95 :TIQKSVELGVNVI T0378 130 :WLGTGSADVFSPK 1vhyA 110 :LWSERCGVKLDAE T0378 143 :VVQASMGALAR 1vhyA 131 :WQKIAIAACEQ T0378 154 :VQPTPLKNTVDTL 1vhyA 148 :PEIRPLMKLQDWC T0378 173 :GIPVYGAFLDGQ 1vhyA 165 :GALKLNLHPRAH T0378 186 :LYEAPLPNF 1vhyA 177 :YSIKTLPTI T0378 195 :TEPAILVLGSEG 1vhyA 187 :AGGVRLLIGSEG T0378 208 :GISPEVAAEITDR 1vhyA 199 :GLSAQEIAQTEQQ T0378 221 :LTIPASGLSVKGHTESLNVAIATAIL 1vhyA 214 :TEILLGKRVLRTETASLAAISALQIC Number of specific fragments extracted= 15 number of extra gaps= 0 total=276 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 1vhyA/T0378-1vhyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0378 read from 1vhyA/T0378-1vhyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vhyA read from 1vhyA/T0378-1vhyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vhyA in template set Warning: unaligning (T0378)G107 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vhyA)R91 Warning: unaligning (T0378)G112 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vhyA)R91 T0378 56 :STP 1vhyA 10 :ISL T0378 60 :DAEVVELPESF 1vhyA 14 :NQTQCYLSEDA T0378 72 :FKRISTQTT 1vhyA 25 :ANHVARVLR T0378 81 :PQPLMA 1vhyA 37 :GEQLEL T0378 100 :GLTLLLD 1vhyA 79 :KIHLGQV T0378 113 :NVGTILRTAD 1vhyA 92 :MEFTIQKSVE T0378 124 :FGIRHVWLGT 1vhyA 102 :LGVNVITPLW T0378 134 :GSADVFSPK 1vhyA 114 :RCGVKLDAE T0378 143 :VVQASMGALA 1vhyA 131 :WQKIAIAACE T0378 153 :RVQPTPLKNTVDTL 1vhyA 147 :VPEIRPLMKLQDWC T0378 173 :GIPVYGAFLDGQSLYEA 1vhyA 165 :GALKLNLHPRAHYSIKT T0378 191 :LPNF 1vhyA 182 :LPTI T0378 195 :TEPAILVLGSEG 1vhyA 187 :AGGVRLLIGSEG T0378 208 :GISPEVAAEITDR 1vhyA 199 :GLSAQEIAQTEQQ T0378 221 :LTIPASGLSVKGH 1vhyA 214 :TEILLGKRVLRTE T0378 238 :NVAIATAILCSE 1vhyA 227 :TASLAAISALQI Number of specific fragments extracted= 16 number of extra gaps= 0 total=292 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 1vhyA/T0378-1vhyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0378 read from 1vhyA/T0378-1vhyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1vhyA read from 1vhyA/T0378-1vhyA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1vhyA in template set Warning: unaligning (T0378)G107 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1vhyA)R91 Warning: unaligning (T0378)G112 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1vhyA)R91 T0378 83 :PLMAVFDLPAEPEPVVE 1vhyA 61 :SVKVEILGRELADKESH T0378 100 :GLTLLLD 1vhyA 79 :KIHLGQV T0378 113 :NVGTILRTA 1vhyA 92 :MEFTIQKSV T0378 123 :WFGIRHVWLGT 1vhyA 101 :ELGVNVITPLW T0378 134 :GSADVFS 1vhyA 114 :RCGVKLD T0378 141 :PKVVQAS 1vhyA 133 :KIAIAAC T0378 148 :MGALARVQPTPLKNTVDTLA 1vhyA 142 :CGRNIVPEIRPLMKLQDWCA T0378 173 :GIPVYGAFLDGQS 1vhyA 165 :GALKLNLHPRAHY T0378 188 :EAPLPN 1vhyA 178 :SIKTLP T0378 194 :FTEPAILVLGSEG 1vhyA 186 :PAGGVRLLIGSEG T0378 208 :GISPEVAAEI 1vhyA 199 :GLSAQEIAQT T0378 218 :TDRLTIPASGLSVKGHTESLNVAIATAI 1vhyA 211 :QGFTEILLGKRVLRTETASLAAISALQI Number of specific fragments extracted= 12 number of extra gaps= 0 total=304 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 2as0A/T0378-2as0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2as0A expands to /projects/compbio/data/pdb/2as0.pdb.gz 2as0A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0378 read from 2as0A/T0378-2as0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2as0A read from 2as0A/T0378-2as0A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2as0A to template set # found chain 2as0A in template set T0378 31 :KLVGEMLPFYRCRMLVGTAAMLRAVSTPHDAEVVELPESF 2as0A 139 :EAIMEVEPGIETVFEKNTGRSRRREGLPEIERVLLGKEKY T0378 83 :PLM 2as0A 179 :RTI T0378 86 :AVFDLPAEPEPVV 2as0A 189 :FIVDMRGQKTGFF T0378 99 :EGLTLLLDGVQ 2as0A 217 :PGDRVLDVFTY T0378 114 :VGTILRTADWFGIRHVWLGTG 2as0A 228 :TGGFAIHAAIAGADEVIGIDK T0378 140 :SPKVVQASMGALAR 2as0A 249 :SPRAIETAKENAKL T0378 154 :VQPTP 2as0A 269 :MKFIV T0378 160 :KNTVDTLAYFRRQGIPVYGAFLDGQSLYEAP 2as0A 274 :GSAFEEMEKLQKKGEKFDIVVLDPPAFVQHE T0378 192 :PN 2as0A 305 :KD T0378 195 :TEPAILVL 2as0A 327 :DGGILVTC Number of specific fragments extracted= 10 number of extra gaps= 0 total=314 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 2as0A/T0378-2as0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0378 read from 2as0A/T0378-2as0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2as0A read from 2as0A/T0378-2as0A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2as0A in template set T0378 30 :PKLVGEMLPFYR 2as0A 135 :LDVAEAIMEVEP T0378 42 :CRMLVG 2as0A 148 :IETVFE T0378 48 :TAAMLRAVSTPHDAEVVELPESF 2as0A 156 :TGRSRRREGLPEIERVLLGKEKY T0378 82 :QPLMAVFDLPAEPEPVVE 2as0A 185 :GRAKFIVDMRGQKTGFFL T0378 100 :GLTLLLDGVQD 2as0A 218 :GDRVLDVFTYT T0378 115 :GTILRTADWFGIRHVWLGTG 2as0A 229 :GGFAIHAAIAGADEVIGIDK T0378 140 :SPKVVQASMGALA 2as0A 249 :SPRAIETAKENAK T0378 153 :RVQPTP 2as0A 268 :RMKFIV T0378 160 :KNTVDTLAYFRRQGIPVYGAFLDGQSLYEAP 2as0A 274 :GSAFEEMEKLQKKGEKFDIVVLDPPAFVQHE T0378 192 :P 2as0A 305 :K Number of specific fragments extracted= 10 number of extra gaps= 0 total=324 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 2as0A/T0378-2as0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0378 read from 2as0A/T0378-2as0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2as0A read from 2as0A/T0378-2as0A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2as0A in template set T0378 23 :QAFAVEGPKLVGEMLPFYRCRMLVGTA 2as0A 149 :ETVFEKNTGRSRRREGLPEIERVLLGK T0378 80 :TPQPLMAVFDLPAEPEPVVE 2as0A 183 :QEGRAKFIVDMRGQKTGFFL T0378 100 :GLTLL 2as0A 219 :DRVLD T0378 106 :DGVQ 2as0A 224 :VFTY T0378 114 :VGTILRTADWFGIRHVWLGTG 2as0A 228 :TGGFAIHAAIAGADEVIGIDK T0378 140 :SPKVVQASMGALA 2as0A 249 :SPRAIETAKENAK T0378 153 :RVQPTP 2as0A 268 :RMKFIV T0378 160 :KNTVDTLAYFRRQG 2as0A 274 :GSAFEEMEKLQKKG T0378 174 :IPVYGAFLDGQS 2as0A 290 :FDIVVLDPPAFV T0378 187 :YEAPLP 2as0A 302 :QHEKDL T0378 211 :PEVAAEI 2as0A 308 :KAGLRAY Number of specific fragments extracted= 11 number of extra gaps= 0 total=335 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 1nxzA/T0378-1nxzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1nxzA expands to /projects/compbio/data/pdb/1nxz.pdb.gz 1nxzA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0378 read from 1nxzA/T0378-1nxzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nxzA read from 1nxzA/T0378-1nxzA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1nxzA to template set # found chain 1nxzA in template set T0378 47 :GTAAMLR 1nxzA 20 :LSEDAAN T0378 54 :AVSTPHDAE 1nxzA 31 :VLRMTEGEQ T0378 63 :VVELPESF 1nxzA 54 :IIESNKKS T0378 84 :LMAVF 1nxzA 62 :VKVEI T0378 89 :DLPAEPEPVVEGLTLLLDGVQDPGNVG 1nxzA 68 :GRELADKESHLKIHLGQVISRGERMEF T0378 117 :ILRTADWFGIRHVWLGT 1nxzA 95 :TIQKSVELGVNVITPLW T0378 134 :GSADVFSPK 1nxzA 114 :RCGVKLDAE T0378 143 :VVQASMGALAR 1nxzA 131 :WQKIAIAACEQ T0378 154 :VQPTPLKNTVDTLA 1nxzA 148 :PEIRPLMKLQDWCA T0378 173 :GIPVYGAFLDGQ 1nxzA 165 :GALKLNLHPRAH T0378 186 :LYEAPLPNFT 1nxzA 177 :YSIKTLPTIP T0378 196 :EPAILVLGSEG 1nxzA 188 :GGVRLLIGSEG T0378 208 :GISPEVAAEITDR 1nxzA 199 :GLSAQEIAQTEQQ T0378 221 :LTIPASGLSVKGHTESLNVAIATAIL 1nxzA 214 :TEILLGKRVLRTETASLAAISALQIC Number of specific fragments extracted= 14 number of extra gaps= 0 total=349 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 1nxzA/T0378-1nxzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0378 read from 1nxzA/T0378-1nxzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nxzA read from 1nxzA/T0378-1nxzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1nxzA in template set T0378 59 :HDAEVVELPESF 1nxzA 13 :ENQTQCYLSEDA T0378 72 :FKRISTQTT 1nxzA 25 :ANHVARVLR T0378 81 :PQPLMAVFD 1nxzA 45 :GSNHIYPAK T0378 100 :GLTLLLDGVQDPGNVGTILRTAD 1nxzA 79 :KIHLGQVISRGERMEFTIQKSVE T0378 124 :FGIRHVWLGT 1nxzA 102 :LGVNVITPLW T0378 134 :GSADVFSPK 1nxzA 114 :RCGVKLDAE T0378 143 :VVQASMGALA 1nxzA 131 :WQKIAIAACE T0378 153 :RVQPTPLKNTVDTLA 1nxzA 147 :VPEIRPLMKLQDWCA T0378 173 :GIPVYGAFLDGQSLYEA 1nxzA 165 :GALKLNLHPRAHYSIKT T0378 191 :LPNF 1nxzA 182 :LPTI T0378 195 :TEPAILVLGSEG 1nxzA 187 :AGGVRLLIGSEG T0378 208 :GISPEVAAEITDR 1nxzA 199 :GLSAQEIAQTEQQ T0378 221 :LTIPASGLSVK 1nxzA 214 :TEILLGKRVLR T0378 236 :SLNVAIATAILCSEW 1nxzA 225 :TETASLAAISALQIC Number of specific fragments extracted= 14 number of extra gaps= 0 total=363 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 1nxzA/T0378-1nxzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0378 read from 1nxzA/T0378-1nxzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1nxzA read from 1nxzA/T0378-1nxzA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1nxzA in template set T0378 84 :LMAVFDLPAEPEPV 1nxzA 62 :VKVEILGRELADKE T0378 100 :GLTLLLDGVQDPG 1nxzA 79 :KIHLGQVISRGER T0378 115 :GTILRT 1nxzA 94 :FTIQKS T0378 122 :DWFGIRHVWLGT 1nxzA 100 :VELGVNVITPLW T0378 134 :GSADV 1nxzA 114 :RCGVK T0378 139 :FSPKVVQAS 1nxzA 131 :WQKIAIAAC T0378 148 :MGALARVQPTPLKNTVDTLA 1nxzA 142 :CGRNIVPEIRPLMKLQDWCA T0378 173 :GIPVYGAFLDGQS 1nxzA 165 :GALKLNLHPRAHY T0378 188 :EAPLPN 1nxzA 178 :SIKTLP T0378 194 :FTEPAILVLGSEG 1nxzA 186 :PAGGVRLLIGSEG T0378 208 :GISPEVAAEITDR 1nxzA 199 :GLSAQEIAQTEQQ T0378 221 :LTIPASGLSVKGHTESLNVAIATAI 1nxzA 214 :TEILLGKRVLRTETASLAAISALQI Number of specific fragments extracted= 12 number of extra gaps= 0 total=375 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 1zxxA/T0378-1zxxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1zxxA expands to /projects/compbio/data/pdb/1zxx.pdb.gz 1zxxA:# T0378 read from 1zxxA/T0378-1zxxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zxxA read from 1zxxA/T0378-1zxxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1zxxA to template set # found chain 1zxxA in template set T0378 32 :LVGEMLPFYRCRMLVGTAAMLR 1zxxA 22 :AVTRVAIANGLEVFGIRYGFAG T0378 62 :EVVELPESF 1zxxA 48 :DIFPLESED T0378 72 :FKRISTQTTPQ 1zxxA 57 :VAHLINVSGTF T0378 90 :LPAEPEPVV 1zxxA 68 :LYSARYPEF T0378 99 :EGLTLLLDGVQDPGNV 1zxxA 161 :HRVFIVNVMGRNCGDI T0378 117 :ILRTADWFGIRHVWLGTGSADV 1zxxA 177 :AMRVGVACGADAIVIPERPYDV T0378 141 :PKVVQASMGALAR 1zxxA 199 :EEIANRLKQAQES T0378 154 :VQPTPL 1zxxA 213 :KDHGLV T0378 160 :KNTVDTLAYFRRQ 1zxxA 225 :MTADQFMAELKKY T0378 173 :GIPV 1zxxA 239 :DFDV T0378 177 :YGAFLDGQSLYEAP 1zxxA 282 :LAVGIENGKVTSHD Number of specific fragments extracted= 11 number of extra gaps= 0 total=386 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 1zxxA/T0378-1zxxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0378 read from 1zxxA/T0378-1zxxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zxxA read from 1zxxA/T0378-1zxxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zxxA in template set T0378 31 :KLVGEMLPFYR 1zxxA 22 :AVTRVAIANGL T0378 44 :MLVGTAAMLRAVSTP 1zxxA 33 :EVFGIRYGFAGLVAG T0378 62 :EVVELPESF 1zxxA 48 :DIFPLESED T0378 72 :FKRISTQTTP 1zxxA 57 :VAHLINVSGT T0378 90 :LPAEPEPVVE 1zxxA 69 :YSARYPEFAE T0378 100 :GLTLLLDGVQDPGNV 1zxxA 162 :RVFIVNVMGRNCGDI T0378 117 :ILRTADWFGIRHVWLGTGSADV 1zxxA 177 :AMRVGVACGADAIVIPERPYDV T0378 160 :KNTVDTLAYFRRQGI 1zxxA 199 :EEIANRLKQAQESGK T0378 195 :TEPAILVL 1zxxA 214 :DHGLVVVA T0378 205 :EGR 1zxxA 222 :EGV T0378 211 :PEVAAEITDR 1zxxA 228 :DQFMAELKKY T0378 221 :LTIPASGLSVKGHT 1zxxA 242 :VRANVLGHMQRGGT Number of specific fragments extracted= 12 number of extra gaps= 0 total=398 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 1zxxA/T0378-1zxxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0378 read from 1zxxA/T0378-1zxxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1zxxA read from 1zxxA/T0378-1zxxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1zxxA in template set T0378 17 :KYRLREQA 1zxxA 87 :EQLKKHGI T0378 25 :FAVEG 1zxxA 97 :VVVIG T0378 30 :PKLVGEMLPFYRCRMLVGTA 1zxxA 106 :YHGALQLTRHGFNSIGLPGT T0378 50 :AMLRAVSTPHDAE 1zxxA 150 :IDKIRDTASSHHR T0378 103 :LLLDGVQDPGNVGTILRTADWFGIRHVWLGTGSADVFS 1zxxA 163 :VFIVNVMGRNCGDIAMRVGVACGADAIVIPERPYDVEE T0378 162 :TVDTLAYFRRQGI 1zxxA 201 :IANRLKQAQESGK T0378 175 :PVYGAFLDGQS 1zxxA 215 :HGLVVVAEGVM T0378 188 :E 1zxxA 226 :T T0378 211 :PEVAAEITDR 1zxxA 228 :DQFMAELKKY T0378 221 :LTIPASGLSVKGHT 1zxxA 242 :VRANVLGHMQRGGT Number of specific fragments extracted= 10 number of extra gaps= 0 total=408 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 1h1yA/T0378-1h1yA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1h1yA expands to /projects/compbio/data/pdb/1h1y.pdb.gz 1h1yA:# T0378 read from 1h1yA/T0378-1h1yA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1h1yA read from 1h1yA/T0378-1h1yA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1h1yA to template set # found chain 1h1yA in template set T0378 27 :VEGPKLVGEMLPFYRCRML 1h1yA 49 :TIGAPVIQSLRKHTKAYLD T0378 104 :LLDGVQDPGN 1h1yA 68 :CHLMVTNPSD T0378 121 :ADWFGIRHVWLGTGSAD 1h1yA 82 :LAKAGASGFTFHIEVSR T0378 160 :KNTVDTLAYFRRQGIPVYGAFLDG 1h1yA 99 :DNWQELIQSIKAKGMRPGVSLRPG T0378 186 :LYEAPL 1h1yA 123 :TPVEEV T0378 195 :TEP 1h1yA 135 :ENP T0378 198 :AILVLGSEG 1h1yA 140 :LVLVMTVEP Number of specific fragments extracted= 7 number of extra gaps= 0 total=415 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 1h1yA/T0378-1h1yA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0378 read from 1h1yA/T0378-1h1yA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1h1yA read from 1h1yA/T0378-1h1yA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1h1yA in template set T0378 28 :EGPKLVGEMLPFYRCRMLVGT 1h1yA 50 :IGAPVIQSLRKHTKAYLDCHL T0378 107 :GVQDPGN 1h1yA 71 :MVTNPSD T0378 119 :R 1h1yA 81 :P T0378 121 :ADWFGIRHVWLGTGSAD 1h1yA 82 :LAKAGASGFTFHIEVSR T0378 160 :KNTVDTLAYFRRQGIPVYGAFLDGQSL 1h1yA 99 :DNWQELIQSIKAKGMRPGVSLRPGTPV T0378 188 :EA 1h1yA 126 :EE T0378 192 :P 1h1yA 128 :V T0378 194 :FTEP 1h1yA 134 :AENP T0378 198 :AILVLGS 1h1yA 140 :LVLVMTV Number of specific fragments extracted= 9 number of extra gaps= 0 total=424 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 1h1yA/T0378-1h1yA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0378 read from 1h1yA/T0378-1h1yA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1h1yA read from 1h1yA/T0378-1h1yA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1h1yA in template set T0378 30 :PKLVGEMLPFYRCRMLVGTA 1h1yA 21 :AAEADRMVRLGADWLHMDIM T0378 66 :LPESFDFKRISTQTTP 1h1yA 49 :TIGAPVIQSLRKHTKA T0378 100 :GLTL 1h1yA 65 :YLDC T0378 105 :LDGVQDPGNV 1h1yA 69 :HLMVTNPSDY T0378 119 :R 1h1yA 81 :P T0378 121 :ADWFGIRHVWLGTGSAD 1h1yA 82 :LAKAGASGFTFHIEVSR T0378 160 :KNTVDTLAYFRRQGIPVYGAFLDGQ 1h1yA 99 :DNWQELIQSIKAKGMRPGVSLRPGT T0378 188 :EAPLPN 1h1yA 124 :PVEEVF T0378 197 :PAILVLGS 1h1yA 139 :ELVLVMTV Number of specific fragments extracted= 9 number of extra gaps= 0 total=433 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 1j8mF/T0378-1j8mF-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1j8mF expands to /projects/compbio/data/pdb/1j8m.pdb.gz 1j8mF:# T0378 read from 1j8mF/T0378-1j8mF-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j8mF read from 1j8mF/T0378-1j8mF-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1j8mF to template set # found chain 1j8mF in template set Warning: unaligning (T0378)N113 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1j8mF)T112 Warning: unaligning (T0378)V114 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1j8mF)T112 T0378 4 :ANQIKFLRSLRERKYRL 1j8mF 22 :DKAVEDFIKELQKSLIS T0378 29 :GPKLVGEMLPF 1j8mF 42 :NVKLVFSLTNK T0378 49 :AAMLRAVSTPHDAE 1j8mF 54 :KERLKNEKPPTYIE T0378 72 :FKRISTQTTP 1j8mF 80 :LSNLFGGDKE T0378 90 :LPA 1j8mF 90 :PKV T0378 95 :EPVVEGLTLLLDGVQDPG 1j8mF 93 :IPDKIPYVIMLVGVQGTG T0378 115 :GTILRTADWF 1j8mF 113 :TTAGKLAYFY T0378 125 :GIR 1j8mF 126 :GFK T0378 128 :HVWLGTGSADVFSPKVVQASMGA 1j8mF 130 :GLVGADVYRPAALEQLQQLGQQI T0378 154 :VQPTPL 1j8mF 154 :VPVYGE T0378 162 :TVDTLAYFRRQGIPVYGAFLDGQ 1j8mF 169 :AKRGVEKFLSEKMEIIIVDTAGR T0378 192 :PNF 1j8mF 192 :HGY T0378 195 :TEPAILVLGS 1j8mF 213 :PDEVTLVIDA T0378 206 :GRG 1j8mF 223 :SIG T0378 213 :VAAEI 1j8mF 235 :FNQAS T0378 219 :DRLTIP 1j8mF 243 :TIIITK T0378 230 :VKGHTESLNVAIATA 1j8mF 249 :MDGTAKGGGALSAVA Number of specific fragments extracted= 17 number of extra gaps= 1 total=450 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 1j8mF/T0378-1j8mF-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0378 read from 1j8mF/T0378-1j8mF-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j8mF read from 1j8mF/T0378-1j8mF-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1j8mF in template set Warning: unaligning (T0378)N113 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1j8mF)T112 Warning: unaligning (T0378)V114 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1j8mF)T112 T0378 4 :ANQIKFLRSLRERKYRLRE 1j8mF 22 :DKAVEDFIKELQKSLISAD T0378 28 :EGPKLVGEMLPF 1j8mF 41 :VNVKLVFSLTNK T0378 48 :TAAMLRAVSTPH 1j8mF 53 :IKERLKNEKPPT T0378 72 :FKRISTQT 1j8mF 80 :LSNLFGGD T0378 91 :PAEPEPVVE 1j8mF 88 :KEPKVIPDK T0378 100 :GLTLLLDGVQDPG 1j8mF 98 :PYVIMLVGVQGTG T0378 115 :GTILRTADWF 1j8mF 113 :TTAGKLAYFY T0378 125 :GIR 1j8mF 126 :GFK T0378 128 :HVWLGTGSADVFSPKVVQASMGA 1j8mF 130 :GLVGADVYRPAALEQLQQLGQQI T0378 153 :RVQPTPLKN 1j8mF 153 :GVPVYGEPG T0378 162 :TVDTLAYFRRQGIPVYGAFLDGQSLYEA 1j8mF 169 :AKRGVEKFLSEKMEIIIVDTAGRHGYGE T0378 192 :P 1j8mF 197 :E T0378 193 :NF 1j8mF 212 :KP T0378 196 :EPAILVL 1j8mF 214 :DEVTLVI T0378 204 :SEGRG 1j8mF 221 :DASIG T0378 213 :VAAEI 1j8mF 235 :FNQAS T0378 220 :RLTI 1j8mF 243 :TIII T0378 224 :P 1j8mF 248 :K T0378 230 :VKGHTESLNVAIATA 1j8mF 249 :MDGTAKGGGALSAVA Number of specific fragments extracted= 19 number of extra gaps= 1 total=469 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 1j8mF/T0378-1j8mF-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0378 read from 1j8mF/T0378-1j8mF-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j8mF read from 1j8mF/T0378-1j8mF-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1j8mF in template set Warning: unaligning (T0378)N113 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1j8mF)T112 Warning: unaligning (T0378)V114 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1j8mF)T112 T0378 3 :SANQIKFLRSL 1j8mF 21 :YDKAVEDFIKE T0378 32 :LVGEMLPFYRCRMLVGTAAMLRAVSTPHDAEV 1j8mF 32 :LQKSLISADVNVKLVFSLTNKIKERLKNEKPP T0378 69 :SFDFKRISTQ 1j8mF 77 :YDELSNLFGG T0378 89 :DLPAEPEPVVEGLTLLLDGVQDPG 1j8mF 87 :DKEPKVIPDKIPYVIMLVGVQGTG T0378 115 :GTILRTADWF 1j8mF 113 :TTAGKLAYFY T0378 125 :GIR 1j8mF 126 :GFK T0378 128 :HVWLGTGSADVFSPKVVQASMG 1j8mF 130 :GLVGADVYRPAALEQLQQLGQQ T0378 154 :VQPTPL 1j8mF 154 :VPVYGE T0378 162 :TVDTLAYFRRQGIPVYGAFLDGQS 1j8mF 169 :AKRGVEKFLSEKMEIIIVDTAGRH T0378 193 :NFTE 1j8mF 193 :GYGE T0378 197 :PAILVLGSEGR 1j8mF 215 :EVTLVIDASIG T0378 213 :VAAEI 1j8mF 235 :FNQAS T0378 220 :RLTIPA 1j8mF 243 :TIIITK T0378 230 :VKGHTESLNVAIATA 1j8mF 249 :MDGTAKGGGALSAVA Number of specific fragments extracted= 14 number of extra gaps= 1 total=483 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 1sdsA/T0378-1sdsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1sdsA expands to /projects/compbio/data/pdb/1sds.pdb.gz 1sdsA:Skipped atom 182, because occupancy 0.500 <= existing 0.500 in 1sdsA Skipped atom 184, because occupancy 0.500 <= existing 0.500 in 1sdsA Skipped atom 186, because occupancy 0.500 <= existing 0.500 in 1sdsA Skipped atom 188, because occupancy 0.500 <= existing 0.500 in 1sdsA Skipped atom 190, because occupancy 0.500 <= existing 0.500 in 1sdsA Skipped atom 192, because occupancy 0.500 <= existing 0.500 in 1sdsA Skipped atom 194, because occupancy 0.500 <= existing 0.500 in 1sdsA Skipped atom 196, because occupancy 0.500 <= existing 0.500 in 1sdsA Skipped atom 198, because occupancy 0.500 <= existing 0.500 in 1sdsA Skipped atom 404, because occupancy 0.500 <= existing 0.500 in 1sdsA Skipped atom 406, because occupancy 0.500 <= existing 0.500 in 1sdsA Skipped atom 408, because occupancy 0.500 <= existing 0.500 in 1sdsA Skipped atom 410, because occupancy 0.500 <= existing 0.500 in 1sdsA Skipped atom 412, because occupancy 0.500 <= existing 0.500 in 1sdsA Skipped atom 414, because occupancy 0.500 <= existing 0.500 in 1sdsA Skipped atom 416, because occupancy 0.500 <= existing 0.500 in 1sdsA Skipped atom 418, because occupancy 0.500 <= existing 0.500 in 1sdsA Skipped atom 420, because occupancy 0.500 <= existing 0.500 in 1sdsA Skipped atom 797, because occupancy 0.500 <= existing 0.500 in 1sdsA Skipped atom 799, because occupancy 0.500 <= existing 0.500 in 1sdsA Skipped atom 801, because occupancy 0.500 <= existing 0.500 in 1sdsA Skipped atom 803, because occupancy 0.500 <= existing 0.500 in 1sdsA Skipped atom 805, because occupancy 0.500 <= existing 0.500 in 1sdsA Skipped atom 807, because occupancy 0.500 <= existing 0.500 in 1sdsA Skipped atom 809, because occupancy 0.500 <= existing 0.500 in 1sdsA Skipped atom 811, because occupancy 0.500 <= existing 0.500 in 1sdsA Skipped atom 813, because occupancy 0.500 <= existing 0.500 in 1sdsA # T0378 read from 1sdsA/T0378-1sdsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sdsA read from 1sdsA/T0378-1sdsA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1sdsA to template set # found chain 1sdsA in template set T0378 1 :MLSANQIKFLRSLRER 1sdsA 8 :KVPEEIQKELLDAVAK T0378 24 :AFAVEGPKLVGEMLPFYRCRMLVGTAAMLR 1sdsA 25 :QKIKKGANEVTKAVERGIAKLVIIAEDVKP T0378 54 :AVSTPHDAEVVELPESFDFKRISTQTTPQPLMAVFDLPA 1sdsA 63 :YLCEEKGIPYAYVASKQDLGKAAGLEVAASSVAIINEGD Number of specific fragments extracted= 3 number of extra gaps= 0 total=486 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 1sdsA/T0378-1sdsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0378 read from 1sdsA/T0378-1sdsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sdsA read from 1sdsA/T0378-1sdsA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1sdsA in template set T0378 1 :MLSANQIKFLRSL 1sdsA 8 :KVPEEIQKELLDA T0378 24 :AFAVEGPKLVGEMLPFYRCRMLVGTAAM 1sdsA 25 :QKIKKGANEVTKAVERGIAKLVIIAEDV T0378 54 :A 1sdsA 53 :K T0378 56 :STPH 1sdsA 54 :PEEV T0378 60 :DAEVVELPESFDFKRISTQTTPQPLMAVFDLP 1sdsA 69 :GIPYAYVASKQDLGKAAGLEVAASSVAIINEG Number of specific fragments extracted= 5 number of extra gaps= 0 total=491 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 1sdsA/T0378-1sdsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0378 read from 1sdsA/T0378-1sdsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1sdsA read from 1sdsA/T0378-1sdsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1sdsA in template set T0378 1 :MLSANQIKFLRSL 1sdsA 8 :KVPEEIQKELLDA T0378 24 :AFAVEGPKLVGEMLPFYRCRMLVGTA 1sdsA 25 :QKIKKGANEVTKAVERGIAKLVIIAE T0378 50 :AMLRAVSTPHDAEVVELP 1sdsA 58 :VAHLPYLCEEKGIPYAYV T0378 68 :ESFDFKRISTQTTPQPLMAVFDLPA 1sdsA 77 :SKQDLGKAAGLEVAASSVAIINEGD Number of specific fragments extracted= 4 number of extra gaps= 0 total=495 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 1j8yF/T0378-1j8yF-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1j8yF expands to /projects/compbio/data/pdb/1j8y.pdb.gz 1j8yF:# T0378 read from 1j8yF/T0378-1j8yF-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j8yF read from 1j8yF/T0378-1j8yF-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1j8yF to template set # found chain 1j8yF in template set Warning: unaligning (T0378)D110 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1j8yF)T113 Warning: unaligning (T0378)P111 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1j8yF)T113 T0378 4 :ANQIKFLRSLRERKYRL 1j8yF 22 :DKAVEDFIKELQKSLIS T0378 22 :EQA 1j8yF 39 :ADV T0378 29 :GPKLVGEMLPF 1j8yF 42 :NVKLVFSLTNK T0378 49 :AAMLRAVSTPHDAE 1j8yF 54 :KERLKNEKPPTYIE T0378 72 :FKRISTQTT 1j8yF 80 :LSNLFGGDK T0378 91 :PAEPEPVVEGLTLLLDGVQ 1j8yF 89 :EPKVIPDKIPYVIMLVGVQ T0378 113 :NVGTILRTADWFGIR 1j8yF 114 :TAGKLAYFYKKKGFK T0378 128 :HVWL 1j8yF 130 :GLVG T0378 136 :ADVFSPKVVQASMGALAR 1j8yF 134 :ADVYRPAALEQLQQLGQQ T0378 154 :VQPTPL 1j8yF 154 :VPVYGE T0378 160 :KN 1j8yF 163 :KD T0378 162 :TVDTLAYFRRQGIPVYGAFLDGQ 1j8yF 169 :AKRGVEKFLSEKMEIIIVDTAGR T0378 192 :PNF 1j8yF 192 :HGY T0378 195 :TEPAILVLG 1j8yF 213 :PDEVTLVID T0378 205 :EGRG 1j8yF 222 :ASIG T0378 213 :VAAEI 1j8yF 235 :FNQAS T0378 220 :RLTIPA 1j8yF 243 :TIIITK T0378 230 :VKGHTESLNVAIATA 1j8yF 249 :MDGTAKGGGALSAVA Number of specific fragments extracted= 18 number of extra gaps= 1 total=513 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 1j8yF/T0378-1j8yF-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0378 read from 1j8yF/T0378-1j8yF-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j8yF read from 1j8yF/T0378-1j8yF-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1j8yF in template set Warning: unaligning (T0378)D110 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1j8yF)T113 Warning: unaligning (T0378)P111 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1j8yF)T113 T0378 4 :ANQIKFLRSLRERKYRLRE 1j8yF 22 :DKAVEDFIKELQKSLISAD T0378 28 :EGPKLVGEMLPF 1j8yF 41 :VNVKLVFSLTNK T0378 48 :TAAMLRAVSTPH 1j8yF 53 :IKERLKNEKPPT T0378 72 :FKRISTQT 1j8yF 80 :LSNLFGGD T0378 91 :PAEPEPVVE 1j8yF 88 :KEPKVIPDK T0378 100 :GLTLLLDGVQ 1j8yF 98 :PYVIMLVGVQ T0378 113 :NVGTILRTADWFGIRH 1j8yF 114 :TAGKLAYFYKKKGFKV T0378 130 :WLGT 1j8yF 130 :GLVG T0378 136 :ADVFSPKVVQASMGALAR 1j8yF 134 :ADVYRPAALEQLQQLGQQ T0378 154 :VQPTPLK 1j8yF 154 :VPVYGEP T0378 162 :TVDTLAYFRRQGIPVYGAFLDGQSLYEA 1j8yF 169 :AKRGVEKFLSEKMEIIIVDTAGRHGYGE T0378 193 :NF 1j8yF 212 :KP T0378 196 :EPAILVL 1j8yF 214 :DEVTLVI T0378 204 :SEGRG 1j8yF 221 :DASIG T0378 213 :VAAEI 1j8yF 235 :FNQAS T0378 220 :RLTIPA 1j8yF 243 :TIIITK T0378 230 :VKGHTESLNVAIATA 1j8yF 249 :MDGTAKGGGALSAVA Number of specific fragments extracted= 17 number of extra gaps= 1 total=530 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 1j8yF/T0378-1j8yF-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0378 read from 1j8yF/T0378-1j8yF-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1j8yF read from 1j8yF/T0378-1j8yF-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1j8yF in template set Warning: unaligning (T0378)D110 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1j8yF)T113 Warning: unaligning (T0378)P111 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1j8yF)T113 T0378 3 :SANQIKFLRSLRE 1j8yF 18 :SSSYDKAVEDFIK T0378 31 :KLVGEMLPFYRCRMLVGTAAMLRAVSTPHDAEV 1j8yF 31 :ELQKSLISADVNVKLVFSLTNKIKERLKNEKPP T0378 69 :SFDFKRISTQ 1j8yF 77 :YDELSNLFGG T0378 89 :DLPAEPEPVVEGLTLLLDGVQ 1j8yF 87 :DKEPKVIPDKIPYVIMLVGVQ T0378 114 :VGTILRTADWFGIRHVWLG 1j8yF 115 :AGKLAYFYKKKGFKVGLVG T0378 136 :ADVFSPKVVQASMGALAR 1j8yF 134 :ADVYRPAALEQLQQLGQQ T0378 154 :VQPTPL 1j8yF 154 :VPVYGE T0378 162 :TVDTLAYFRRQGIPVYGAFLDGQS 1j8yF 169 :AKRGVEKFLSEKMEIIIVDTAGRH T0378 193 :NFTE 1j8yF 193 :GYGE T0378 197 :PAILVLGSEGR 1j8yF 215 :EVTLVIDASIG T0378 213 :VAAEI 1j8yF 235 :FNQAS T0378 219 :DRLTIPA 1j8yF 242 :GTIIITK T0378 230 :VKGHTESLNVAIATA 1j8yF 249 :MDGTAKGGGALSAVA Number of specific fragments extracted= 13 number of extra gaps= 1 total=543 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 1xbiA/T0378-1xbiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1xbiA expands to /projects/compbio/data/pdb/1xbi.pdb.gz 1xbiA:Skipped atom 212, because occupancy 0.350 <= existing 0.650 in 1xbiA Skipped atom 214, because occupancy 0.350 <= existing 0.650 in 1xbiA Skipped atom 216, because occupancy 0.350 <= existing 0.650 in 1xbiA Skipped atom 266, because occupancy 0.350 <= existing 0.650 in 1xbiA Skipped atom 268, because occupancy 0.350 <= existing 0.650 in 1xbiA Skipped atom 270, because occupancy 0.350 <= existing 0.650 in 1xbiA Skipped atom 272, because occupancy 0.350 <= existing 0.650 in 1xbiA Skipped atom 322, because occupancy 0.350 <= existing 0.650 in 1xbiA Skipped atom 324, because occupancy 0.350 <= existing 0.650 in 1xbiA Skipped atom 326, because occupancy 0.350 <= existing 0.650 in 1xbiA Skipped atom 328, because occupancy 0.350 <= existing 0.650 in 1xbiA Skipped atom 330, because occupancy 0.350 <= existing 0.650 in 1xbiA Skipped atom 338, because occupancy 0.350 <= existing 0.650 in 1xbiA Skipped atom 340, because occupancy 0.350 <= existing 0.650 in 1xbiA Skipped atom 342, because occupancy 0.350 <= existing 0.650 in 1xbiA Skipped atom 344, because occupancy 0.350 <= existing 0.650 in 1xbiA Skipped atom 346, because occupancy 0.350 <= existing 0.650 in 1xbiA Skipped atom 393, because occupancy 0.350 <= existing 0.650 in 1xbiA Skipped atom 395, because occupancy 0.350 <= existing 0.650 in 1xbiA Skipped atom 397, because occupancy 0.350 <= existing 0.650 in 1xbiA Skipped atom 399, because occupancy 0.350 <= existing 0.650 in 1xbiA Skipped atom 442, because occupancy 0.350 <= existing 0.650 in 1xbiA Skipped atom 444, because occupancy 0.350 <= existing 0.650 in 1xbiA Skipped atom 446, because occupancy 0.350 <= existing 0.650 in 1xbiA Skipped atom 448, because occupancy 0.350 <= existing 0.650 in 1xbiA Skipped atom 450, because occupancy 0.350 <= existing 0.650 in 1xbiA Skipped atom 464, because occupancy 0.350 <= existing 0.650 in 1xbiA Skipped atom 466, because occupancy 0.350 <= existing 0.650 in 1xbiA Skipped atom 468, because occupancy 0.350 <= existing 0.650 in 1xbiA Skipped atom 470, because occupancy 0.350 <= existing 0.650 in 1xbiA Skipped atom 476, because occupancy 0.350 <= existing 0.650 in 1xbiA Skipped atom 478, because occupancy 0.350 <= existing 0.650 in 1xbiA Skipped atom 480, because occupancy 0.350 <= existing 0.650 in 1xbiA Skipped atom 482, because occupancy 0.350 <= existing 0.650 in 1xbiA Skipped atom 484, because occupancy 0.350 <= existing 0.650 in 1xbiA Skipped atom 490, because occupancy 0.350 <= existing 0.650 in 1xbiA Skipped atom 492, because occupancy 0.350 <= existing 0.650 in 1xbiA Skipped atom 494, because occupancy 0.350 <= existing 0.650 in 1xbiA Skipped atom 594, because occupancy 0.350 <= existing 0.650 in 1xbiA Skipped atom 596, because occupancy 0.350 <= existing 0.650 in 1xbiA Skipped atom 598, because occupancy 0.350 <= existing 0.650 in 1xbiA Skipped atom 600, because occupancy 0.350 <= existing 0.650 in 1xbiA Skipped atom 829, because occupancy 0.350 <= existing 0.650 in 1xbiA Skipped atom 831, because occupancy 0.350 <= existing 0.650 in 1xbiA Skipped atom 833, because occupancy 0.350 <= existing 0.650 in 1xbiA Skipped atom 835, because occupancy 0.350 <= existing 0.650 in 1xbiA Skipped atom 837, because occupancy 0.350 <= existing 0.650 in 1xbiA Skipped atom 843, because occupancy 0.350 <= existing 0.650 in 1xbiA Skipped atom 845, because occupancy 0.350 <= existing 0.650 in 1xbiA Skipped atom 847, because occupancy 0.350 <= existing 0.650 in 1xbiA Skipped atom 849, because occupancy 0.350 <= existing 0.650 in 1xbiA Skipped atom 851, because occupancy 0.350 <= existing 0.650 in 1xbiA # T0378 read from 1xbiA/T0378-1xbiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xbiA read from 1xbiA/T0378-1xbiA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1xbiA to template set # found chain 1xbiA in template set Warning: unaligning (T0378)A4 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1xbiA)E12 Warning: unaligning (T0378)N5 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1xbiA)E12 Warning: unaligning (T0378)E35 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1xbiA)A37 Warning: unaligning (T0378)M36 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1xbiA)A37 T0378 1 :MLS 1xbiA 8 :KVP T0378 6 :QIKFLRSLRER 1xbiA 13 :IQKELLDAVAK T0378 23 :QAFAVEGPKLVG 1xbiA 24 :AQKIKKGANEVT T0378 37 :LPFYRCRMLVGT 1xbiA 38 :VERGIAKLVIIA T0378 49 :AAMLR 1xbiA 55 :EEVVA T0378 54 :AVSTPHDAEVVELPESFDFKRISTQTTPQPLMAVFDLP 1xbiA 63 :YLCEEKGIPYAYVASKQDLGKAAGLEVAASSVAIINEG Number of specific fragments extracted= 6 number of extra gaps= 2 total=549 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 1xbiA/T0378-1xbiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0378 read from 1xbiA/T0378-1xbiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xbiA read from 1xbiA/T0378-1xbiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xbiA in template set Warning: unaligning (T0378)A4 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1xbiA)E12 Warning: unaligning (T0378)N5 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1xbiA)E12 Warning: unaligning (T0378)E35 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1xbiA)A37 Warning: unaligning (T0378)M36 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1xbiA)A37 T0378 1 :MLS 1xbiA 8 :KVP T0378 6 :QIKFLRSL 1xbiA 13 :IQKELLDA T0378 22 :EQAFAVEGPKLVG 1xbiA 23 :KAQKIKKGANEVT T0378 37 :LPFYRCRMLVGTAA 1xbiA 38 :VERGIAKLVIIAED T0378 55 :VSTPH 1xbiA 52 :VKPEE T0378 60 :DAEVVELPESFDFKRISTQTTPQPLMAVFDL 1xbiA 69 :GIPYAYVASKQDLGKAAGLEVAASSVAIINE Number of specific fragments extracted= 6 number of extra gaps= 2 total=555 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 1xbiA/T0378-1xbiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0378 read from 1xbiA/T0378-1xbiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xbiA read from 1xbiA/T0378-1xbiA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xbiA in template set Warning: unaligning (T0378)A4 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1xbiA)E12 Warning: unaligning (T0378)N5 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1xbiA)E12 Warning: unaligning (T0378)E35 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1xbiA)A37 Warning: unaligning (T0378)M36 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1xbiA)A37 T0378 1 :MLS 1xbiA 8 :KVP T0378 6 :QIKFLRSL 1xbiA 13 :IQKELLDA T0378 21 :REQAFAVEGPKLVG 1xbiA 22 :AKAQKIKKGANEVT T0378 37 :LPFYRCRMLVGTA 1xbiA 38 :VERGIAKLVIIAE T0378 50 :AMLRAVSTPHDAEVVELP 1xbiA 58 :VAHLPYLCEEKGIPYAYV T0378 68 :ESFDFKRISTQTTPQPLMAVFDLPA 1xbiA 77 :SKQDLGKAAGLEVAASSVAIINEGD Number of specific fragments extracted= 6 number of extra gaps= 2 total=561 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 1k3rA/T0378-1k3rA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1k3rA expands to /projects/compbio/data/pdb/1k3r.pdb.gz 1k3rA:# T0378 read from 1k3rA/T0378-1k3rA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1k3rA read from 1k3rA/T0378-1k3rA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1k3rA to template set # found chain 1k3rA in template set T0378 100 :GLTLLLDG 1k3rA 5 :DLSLFIPD T0378 108 :VQD 1k3rA 18 :TGD T0378 112 :GNVGTILRTADWFGIRHVWLGTGSADVFSPKVVQASMGALAR 1k3rA 26 :YKVVLIARAASIFGVKRIVIYHDDADGEARFIRDILTYMDTP T0378 167 :AYFR 1k3rA 68 :QYLR T0378 177 :YGAFLDGQSLYEAP 1k3rA 185 :VVVATSRNASPITS T0378 194 :F 1k3rA 199 :I T0378 195 :TEPAILVLGSEGRGISP 1k3rA 210 :AREAAILFGGPYKGLPE T0378 217 :ITDRLTIPASGLSVKGHTESLNVAIATAILCSEW 1k3rA 227 :IDADIWVNTLPGQCTETVRTEEAVLATLSVFNML Number of specific fragments extracted= 8 number of extra gaps= 0 total=569 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 1k3rA/T0378-1k3rA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0378 read from 1k3rA/T0378-1k3rA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1k3rA read from 1k3rA/T0378-1k3rA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1k3rA in template set T0378 100 :GLTLLLD 1k3rA 5 :DLSLFIP T0378 107 :GVQD 1k3rA 17 :ETGD T0378 111 :PGNVGTILRTADWFGIRHVWLGTGSADVFSPKVVQASMGALA 1k3rA 25 :TYKVVLIARAASIFGVKRIVIYHDDADGEARFIRDILTYMDT T0378 153 :RVQPTPL 1k3rA 74 :VFPIMRE T0378 160 :KN 1k3rA 88 :PP T0378 181 :LDGQSLYEAPLP 1k3rA 90 :LRTPHHPTGKPV T0378 193 :NFTEPAILVLGSEGRGISP 1k3rA 208 :RGAREAAILFGGPYKGLPE T0378 217 :ITDRLTIPASGLSVKGHTESLNVAIATAILCSEW 1k3rA 227 :IDADIWVNTLPGQCTETVRTEEAVLATLSVFNML Number of specific fragments extracted= 8 number of extra gaps= 0 total=577 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 1k3rA/T0378-1k3rA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0378 read from 1k3rA/T0378-1k3rA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1k3rA read from 1k3rA/T0378-1k3rA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1k3rA in template set T0378 98 :VEGLTLLLDG 1k3rA 3 :RVDLSLFIPD T0378 112 :G 1k3rA 19 :G T0378 114 :VGTILRTADWFGIRHVWLGTGSADVFSPKVVQASMGALAR 1k3rA 28 :VVLIARAASIFGVKRIVIYHDDADGEARFIRDILTYMDTP T0378 167 :AYFR 1k3rA 68 :QYLR T0378 181 :LDGQ 1k3rA 77 :IMRE T0378 188 :EAPLPNFTE 1k3rA 81 :LKHVGILPP T0378 197 :PAILVLGSEGRGISP 1k3rA 212 :EAAILFGGPYKGLPE T0378 218 :TDRLTIPASGLSVKGHTESLNVAIATAILCS 1k3rA 228 :DADIWVNTLPGQCTETVRTEEAVLATLSVFN Number of specific fragments extracted= 8 number of extra gaps= 0 total=585 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 1xrtA/T0378-1xrtA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1xrtA expands to /projects/compbio/data/pdb/1xrt.pdb.gz 1xrtA:# T0378 read from 1xrtA/T0378-1xrtA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xrtA read from 1xrtA/T0378-1xrtA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1xrtA to template set # found chain 1xrtA in template set Warning: unaligning (T0378)C42 because first residue in template chain is (1xrtA)M1 Warning: unaligning (T0378)A61 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xrtA)E44 Warning: unaligning (T0378)E62 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xrtA)E44 Warning: unaligning (T0378)S185 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xrtA)L186 Warning: unaligning (T0378)L186 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xrtA)L186 Warning: unaligning (T0378)Y187 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xrtA)A187 Warning: unaligning (T0378)E188 because of BadResidue code BAD_PEPTIDE at template residue (1xrtA)Y188 T0378 43 :RMLVGTA 1xrtA 2 :LKLIVKN T0378 50 :AMLR 1xrtA 14 :PSQN T0378 54 :AVSTPHD 1xrtA 36 :KNILVPE T0378 63 :VVELPE 1xrtA 45 :IIDAKG T0378 70 :F 1xrtA 51 :L T0378 84 :LMAV 1xrtA 52 :IVCP T0378 100 :GLTLLLDGVQDPG 1xrtA 56 :GFIDIHVHLRDPG T0378 113 :NVGTILRTADWFGIRHVWLGTGSADVFSPK 1xrtA 74 :DIESGSRCAVAGGFTTIVCMPNTNPPIDNT T0378 143 :VVQASMGALARVQPTPL 1xrtA 105 :VVNYILQKSKSVGLCRV T0378 160 :K 1xrtA 134 :K T0378 162 :TVDTLAYFRRQG 1xrtA 163 :MRKALELASQLG T0378 175 :PVYGAFLDGQ 1xrtA 175 :VPIMDHCEDD T0378 195 :TEPAIL 1xrtA 225 :GGHVHI T0378 210 :SPEVAAEITD 1xrtA 235 :TKLSLEIIEF T0378 220 :RLTI 1xrtA 253 :TCEV Number of specific fragments extracted= 15 number of extra gaps= 2 total=600 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 1xrtA/T0378-1xrtA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0378 read from 1xrtA/T0378-1xrtA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xrtA read from 1xrtA/T0378-1xrtA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xrtA in template set Warning: unaligning (T0378)C42 because first residue in template chain is (1xrtA)M1 Warning: unaligning (T0378)Q82 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xrtA)D23 Warning: unaligning (T0378)P83 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xrtA)D23 Warning: unaligning (T0378)S185 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xrtA)L186 Warning: unaligning (T0378)L186 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xrtA)L186 Warning: unaligning (T0378)Y187 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xrtA)A187 Warning: unaligning (T0378)E188 because of BadResidue code BAD_PEPTIDE at template residue (1xrtA)Y188 T0378 43 :RMLVGTA 1xrtA 2 :LKLIVKN T0378 74 :RISTQTTP 1xrtA 14 :PSQNLEGE T0378 84 :LMAV 1xrtA 24 :ILVE T0378 88 :FDLPAEPEPVVE 1xrtA 31 :IKKIDKNILVPE T0378 100 :GLTLLLDGVQDPG 1xrtA 56 :GFIDIHVHLRDPG T0378 113 :NVGTILRTADWFGIRHVWLGTGSADVFSPK 1xrtA 74 :DIESGSRCAVAGGFTTIVCMPNTNPPIDNT T0378 143 :VVQAS 1xrtA 109 :ILQKS T0378 148 :MGALARV 1xrtA 145 :AGCVAFT T0378 155 :QPTPLKNTVDTLAYFRRQG 1xrtA 156 :PVMDSSVMRKALELASQLG T0378 175 :PVYGAFLDGQ 1xrtA 175 :VPIMDHCEDD T0378 196 :EPAILV 1xrtA 225 :GGHVHI Number of specific fragments extracted= 11 number of extra gaps= 2 total=611 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 1xrtA/T0378-1xrtA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0378 read from 1xrtA/T0378-1xrtA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1xrtA read from 1xrtA/T0378-1xrtA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1xrtA in template set Warning: unaligning (T0378)C42 because first residue in template chain is (1xrtA)M1 Warning: unaligning (T0378)Q82 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xrtA)D23 Warning: unaligning (T0378)P83 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xrtA)D23 Warning: unaligning (T0378)E99 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xrtA)E44 Warning: unaligning (T0378)S185 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xrtA)L186 Warning: unaligning (T0378)E188 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xrtA)L186 Warning: unaligning (T0378)A189 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xrtA)A187 Warning: unaligning (T0378)P190 because of BadResidue code BAD_PEPTIDE at template residue (1xrtA)Y188 Warning: unaligning (T0378)L228 because of BadResidue code BAD_PEPTIDE in next template residue (1xrtA)L262 Warning: unaligning (T0378)S229 because of BadResidue code BAD_PEPTIDE at template residue (1xrtA)L262 T0378 43 :RMLVGTA 1xrtA 2 :LKLIVKN T0378 77 :TQTTP 1xrtA 17 :NLEGE T0378 84 :LMAV 1xrtA 24 :ILVE T0378 88 :FDLPAEPEPVV 1xrtA 32 :KKIDKNILVPE T0378 100 :GLTLLLDGVQDPG 1xrtA 56 :GFIDIHVHLRDPG T0378 113 :NVGTILRTADWFGIRHVWLGTGSADVFS 1xrtA 74 :DIESGSRCAVAGGFTTIVCMPNTNPPID T0378 141 :PKVVQASMG 1xrtA 107 :NYILQKSKS T0378 151 :LARVQPTPLKN 1xrtA 116 :VGLCRVLPTGT T0378 162 :TVDTLAYFRRQGIPV 1xrtA 163 :MRKALELASQLGVPI T0378 178 :GAFLDGQ 1xrtA 178 :MDHCEDD T0378 197 :PAILV 1xrtA 226 :GHVHI T0378 210 :SPEVAAEI 1xrtA 235 :TKLSLEII T0378 218 :TDRLTIPASG 1xrtA 251 :KITCEVNPNH Number of specific fragments extracted= 13 number of extra gaps= 4 total=624 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 1rvgA/T0378-1rvgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1rvgA expands to /projects/compbio/data/pdb/1rvg.pdb.gz 1rvgA:Skipped atom 597, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 599, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 601, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 603, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 605, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 607, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 609, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 611, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 613, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 615, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 617, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 619, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 621, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 623, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 625, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 627, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 629, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 631, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 633, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 635, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 637, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 639, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1021, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1023, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1025, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1027, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1029, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1031, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1033, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1035, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1037, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1326, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1328, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1330, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1332, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1334, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1336, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1338, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1340, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1342, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1344, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1346, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1348, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1350, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1352, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1354, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1356, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1358, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1360, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1362, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1364, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1581, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1583, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1585, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1587, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1589, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1591, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1593, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1595, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1597, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1599, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1601, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1603, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1605, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1607, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1609, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1611, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1613, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1615, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1617, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1619, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1621, because occupancy 0.500 <= existing 0.500 in 1rvgA Skipped atom 1623, because occupancy 0.500 <= existing 0.500 in 1rvgA # T0378 read from 1rvgA/T0378-1rvgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rvgA read from 1rvgA/T0378-1rvgA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1rvgA to template set # found chain 1rvgA in template set Warning: unaligning (T0378)Q184 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1rvgA)K148 T0378 31 :KLVGEMLPFYR 1rvgA 31 :QAVLEAAEEQR T0378 42 :CRMLVGTAAMLR 1rvgA 43 :PVILALSEGAMK T0378 73 :K 1rvgA 69 :K T0378 77 :TQT 1rvgA 70 :EAR T0378 99 :EGLTLLLDGVQDPGNVGT 1rvgA 73 :VPVAVHLDHGSSYESVLR T0378 121 :ADWFGIRHVWLGTGSADV 1rvgA 91 :ALRAGFTSVMIDKSHEDF T0378 141 :PKVVQAS 1rvgA 109 :ETNVRET T0378 163 :VDTLAYFRRQGIPVYGAFLD 1rvgA 116 :RRVVEAAHAVGVTVEAELGR T0378 183 :G 1rvgA 140 :E T0378 195 :TEP 1rvgA 202 :PAP T0378 200 :LVLGS 1rvgA 205 :LVLHG T0378 206 :GRGISPEVAAEITD 1rvgA 210 :ASAVPPELVERFRA T0378 220 :RLTIP 1rvgA 249 :KINTD T0378 237 :LNVAIATAILCSEWRR 1rvgA 254 :TDLRLAFTALIREALN Number of specific fragments extracted= 14 number of extra gaps= 0 total=638 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 1rvgA/T0378-1rvgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0378 read from 1rvgA/T0378-1rvgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rvgA read from 1rvgA/T0378-1rvgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rvgA in template set Warning: unaligning (T0378)E188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1rvgA)K148 T0378 31 :KLVGEMLPFYR 1rvgA 31 :QAVLEAAEEQR T0378 42 :CRMLVGTAAMLRAVSTP 1rvgA 43 :PVILALSEGAMKYGGRA T0378 100 :GLTLLLDGVQDPGNVGTILR 1rvgA 74 :PVAVHLDHGSSYESVLRALR T0378 124 :FGIRHVWLGTGSADV 1rvgA 94 :AGFTSVMIDKSHEDF T0378 141 :PKVVQAS 1rvgA 109 :ETNVRET T0378 163 :VDTLAYFRRQGIPVYGAFLDGQSLY 1rvgA 116 :RRVVEAAHAVGVTVEAELGRLAGIE T0378 194 :FTEP 1rvgA 201 :VPAP T0378 200 :LVLGS 1rvgA 205 :LVLHG T0378 206 :GRGISPEVAAEITD 1rvgA 210 :ASAVPPELVERFRA Number of specific fragments extracted= 9 number of extra gaps= 0 total=647 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 1rvgA/T0378-1rvgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0378 read from 1rvgA/T0378-1rvgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1rvgA read from 1rvgA/T0378-1rvgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1rvgA in template set Warning: unaligning (T0378)E188 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1rvgA)K148 Warning: unaligning (T0378)T195 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1rvgA)K148 T0378 28 :EGPKLVGEMLPFYRCRMLVGTA 1rvgA 4 :TGLEILKKAREEGYGVGAFNVN T0378 50 :AMLRAVSTPHDAEVVE 1rvgA 30 :LQAVLEAAEEQRSPVI T0378 66 :LPESFDFKRIST 1rvgA 47 :ALSEGAMKYGGR T0378 100 :GLTLLLDGVQDPG 1rvgA 74 :PVAVHLDHGSSYE T0378 116 :TILR 1rvgA 87 :SVLR T0378 121 :ADWFGIRHVWLGTGSADV 1rvgA 91 :ALRAGFTSVMIDKSHEDF T0378 141 :PKVVQAS 1rvgA 109 :ETNVRET T0378 163 :VDTLAYFRRQGIPVYGAFLDGQSLY 1rvgA 116 :RRVVEAAHAVGVTVEAELGRLAGIE T0378 198 :AILVLGSE 1rvgA 203 :APLVLHGA T0378 207 :RGISPEVAAEIT 1rvgA 211 :SAVPPELVERFR Number of specific fragments extracted= 10 number of extra gaps= 0 total=657 Will force an alignment to be made, even if fragment is small Number of alignments=63 # command:CPU_time= 19.428 sec, elapsed time= 20.866 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 63 Adding 32131 constraints to all_contacts Done adding distance constraints # command:CPU_time= 19.533 sec, elapsed time= 20.979 sec. # command:Reading probabilities from T0378.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 18.440 Optimizing... Probability sum: -438.873, CN propb: -438.873 weights: 0.389 constraints: 746 # command:CPU_time= 171.531 sec, elapsed time= 173.097 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 746 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 746 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 2536 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 2536 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 26853 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 26853 # command:CPU_time= 172.079 sec, elapsed time= 174.040 sec. # command: