# command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading dunbrack-2191.atoms # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 53157 examples # computed average trans backbone unit before proline from 2010 examples # computed average cis backbone unit from 97 examples # trans (non-proline) backbone unit: # CA= -2.2087 1.0126 -0.0030 # O= -0.1499 2.2440 0.0016 # C= -0.6889 1.1368 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4581 -0.0000 0.0000 # cis backbone unit: # CA= -0.1436 2.4534 -0.0002 # O= -2.0284 0.9742 0.0015 # C= -0.8018 1.0771 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4668 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2100 1.0631 -0.0014 # O= -0.1236 2.2458 0.0075 # C= -0.6872 1.1517 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4660 0.0000 0.0000 # After reading dunbrack-2191.atoms have 2191 chains in training database # Count of chains,residues,atoms: 2191,500310,3902258 # 493341 residues have no bad marker # 3226 residues lack atoms needed to compute omega # 1453 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 4 # HAS_OXT 1167 # TOO_MANY_ATOMS 1 # TOO_FEW_ATOMS 3052 # HAS_UNKNOWN_ATOMS 9 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 979 # NON_PLANAR_PEPTIDE 888 # BAD_PEPTIDE 2680 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-2191.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 /projects/compbio/experiments/protein-predict/casp7/T0371/ # command:# Making conformation for sequence T0371 numbered 1 through 283 Created new target T0371 from T0371.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0371/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0371//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0371/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0371//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0371/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0371/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0371/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j97A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1j97A expands to /projects/compbio/data/pdb/1j97.pdb.gz 1j97A:Bad short name: BE for alphabet: pdb_atoms Bad short name: F1 for alphabet: pdb_atoms Bad short name: F2 for alphabet: pdb_atoms Bad short name: F3 for alphabet: pdb_atoms # T0371 read from 1j97A/merged-good-all-a2m # 1j97A read from 1j97A/merged-good-all-a2m # adding 1j97A to template set # found chain 1j97A in template set Warning: unaligning (T0371)F18 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1j97A)F12 Warning: unaligning (T0371)A20 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1j97A)F12 T0371 11 :PKYKCIF 1j97A 3 :KKKKLIL # choosing archetypes in rotamer library T0371 21 :FGVLKTYN 1j97A 13 :DSTLVNNE T0371 61 :QLADSYHKLGL 1j97A 21 :TIDEIAREAGV T0371 76 :ADKI 1j97A 32 :EEEV T0371 83 :GMITKEYIDLKV 1j97A 36 :KKITKEAMEGKL T0371 103 :GTANSANYLVSD 1j97A 48 :NFEQSLRKRVSL T0371 115 :GIKM 1j97A 62 :DLPI T0371 130 :GEVNALVL 1j97A 66 :EKVEKAIK T0371 142 :GFNWFHDLNKTVNLLRKRTIPA 1j97A 74 :RITPTEGAEETIKELKNRGYVV T0371 164 :IVANT 1j97A 97 :VVSGG T0371 174 :L 1j97A 102 :F T0371 183 :IGGVATMIES 1j97A 103 :DIAVNKIKEK T0371 194 :LGRRFIR 1j97A 113 :LGLDYAF T0371 203 :K 1j97A 144 :K T0371 206 :SQMFMFAYDML 1j97A 145 :GEILEKIAKIE T0371 221 :EISKREILMVGDT 1j97A 156 :GINLEDTVAVGDG T0371 235 :HTDILGGNKFGLDTAL 1j97A 169 :ANDISMFKKAGLKIAF T0371 256 :TRIDD 1j97A 185 :CAKPI T0371 265 :IKST 1j97A 190 :LKEK T0371 272 :PTHICESA 1j97A 194 :ADICIEKR T0371 280 :VIEL 1j97A 203 :LREI Number of specific fragments extracted= 21 number of extra gaps= 0 total=21 Number of alignments=1 # 1j97A read from 1j97A/merged-good-all-a2m # found chain 1j97A in template set Warning: unaligning (T0371)F18 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1j97A)F12 Warning: unaligning (T0371)A20 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1j97A)F12 T0371 11 :PKYKCIF 1j97A 3 :KKKKLIL T0371 21 :FGVLKTYN 1j97A 13 :DSTLVNNE T0371 37 :TFDYLKAQ 1j97A 21 :TIDEIARE T0371 45 :GQ 1j97A 30 :GV T0371 59 :PEQLADSYHKLGLFSITAD 1j97A 32 :EEEVKKITKEAMEGKLNFE T0371 105 :ANSANYLV 1j97A 51 :QSLRKRVS T0371 123 :AIDDSNIGEVNALVL 1j97A 59 :LLKDLPIEKVEKAIK T0371 142 :GFNWFHDLNKTVNLLRKRTIPAIVANTDNTYPLTKTDVAIAI 1j97A 74 :RITPTEGAEETIKELKNRGYVVAVVSGGFDIAVNKIKEKLGL T0371 191 :ESI 1j97A 116 :DYA T0371 194 :LGRRFIRF 1j97A 130 :LTGDVEGE T0371 203 :KPDSQMFMFAYDMLRQKMEISKREILMVGDTLH 1j97A 138 :VLKENAKGEILEKIAKIEGINLEDTVAVGDGAN T0371 237 :DILGGNKFG 1j97A 171 :DISMFKKAG T0371 247 :DTALV 1j97A 180 :LKIAF T0371 256 :TRIDDAETK 1j97A 185 :CAKPILKEK T0371 272 :PTHICESA 1j97A 194 :ADICIEKR T0371 280 :VIEL 1j97A 203 :LREI Number of specific fragments extracted= 16 number of extra gaps= 0 total=37 Number of alignments=2 # 1j97A read from 1j97A/merged-good-all-a2m # found chain 1j97A in template set Warning: unaligning (T0371)F18 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1j97A)F12 Warning: unaligning (T0371)A20 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1j97A)F12 T0371 14 :KCIF 1j97A 6 :KLIL T0371 21 :FGVLKTYNGLLPGI 1j97A 13 :DSTLVNNETIDEIA T0371 42 :KAQG 1j97A 27 :REAG T0371 58 :SPEQLADSYHKLGLFSIT 1j97A 31 :VEEEVKKITKEAMEGKLN T0371 82 :SGMITKEYIDLK 1j97A 49 :FEQSLRKRVSLL T0371 125 :DDSNIGEVNALV 1j97A 61 :KDLPIEKVEKAI T0371 141 :EGFNWFHDLNKTVNLLRKRTIPAIVANTD 1j97A 73 :KRITPTEGAEETIKELKNRGYVVAVVSGG T0371 186 :VATMIESIL 1j97A 102 :FDIAVNKIK T0371 195 :GRRFIR 1j97A 135 :EGEVLK T0371 205 :DSQMFMFAYDML 1j97A 144 :KGEILEKIAKIE T0371 221 :EISKREILMVGDTLH 1j97A 156 :GINLEDTVAVGDGAN T0371 237 :DILGGNKFGLDTAL 1j97A 171 :DISMFKKAGLKIAF T0371 256 :TRIDDAET 1j97A 185 :CAKPILKE T0371 267 :STGIVPT 1j97A 193 :KADICIE T0371 274 :HICESAVIEL 1j97A 202 :DLREILKYIK Number of specific fragments extracted= 15 number of extra gaps= 0 total=52 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2c4nA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2c4nA expands to /projects/compbio/data/pdb/2c4n.pdb.gz 2c4nA:# T0371 read from 2c4nA/merged-good-all-a2m # 2c4nA read from 2c4nA/merged-good-all-a2m # adding 2c4nA to template set # found chain 2c4nA in template set Warning: unaligning (T0371)K25 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c4nA)H16 Warning: unaligning (T0371)T26 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2c4nA)H16 T0371 12 :KYKCIFFDAFGVL 2c4nA 2 :TIKNVICDIDGVL T0371 27 :YNGLLPGIENTFDYLKAQGQDYYIVTNDASRSPEQLADSYHKLGL 2c4nA 17 :DNVAVPGAAEFLHGIMDKGLPLVLLTNYPSQTGQDLANRFATAGV T0371 73 :SITADKIISSGMITKEYI 2c4nA 62 :DVPDSVFYTSAMATADFL T0371 91 :DLKV 2c4nA 81 :RQEG T0371 97 :GIVAYLGTANSANYLVSDGIKM 2c4nA 85 :KKAYVVGEGALIHELYKAGFTI T0371 122 :S 2c4nA 107 :T T0371 129 :IGEVNALVLLDDEGFN 2c4nA 108 :DVNPDFVIVGETRSYN T0371 146 :FHDLNKTVNLLRK 2c4nA 124 :WDMMHKAAYFVAN T0371 160 :TIPAIVANTDNTY 2c4nA 137 :GARFIATNPDTHG T0371 175 :TKTDVAIAI 2c4nA 150 :RGFYPACGA T0371 186 :VATMIESILGRRFIRFGKPDSQMFMFAYDML 2c4nA 159 :LCAGIEKISGRKPFYVGKPSPWIIRAALNKM T0371 221 :EISKREILMVGDTLHTDILGGNKFGLDTALVLTGNTRIDD 2c4nA 190 :QAHSEETVIVGDNLRTDILAGFQAGLETILVLSGVSSLDD T0371 265 :IKSTGIVPTHICES 2c4nA 230 :IDSMPFRPSWIYPS T0371 280 :VIEL 2c4nA 244 :VAEI Number of specific fragments extracted= 14 number of extra gaps= 1 total=66 Number of alignments=4 # 2c4nA read from 2c4nA/merged-good-all-a2m # found chain 2c4nA in template set Warning: unaligning (T0371)K25 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c4nA)H16 Warning: unaligning (T0371)T26 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2c4nA)H16 T0371 12 :KYKCIFFDAFGVL 2c4nA 2 :TIKNVICDIDGVL T0371 27 :YNGLLPGIENTFDYLKAQGQDYYIVTNDASRSPEQLADSYHKLGL 2c4nA 17 :DNVAVPGAAEFLHGIMDKGLPLVLLTNYPSQTGQDLANRFATAGV T0371 73 :SITADKIISSGMITKEYIDLK 2c4nA 62 :DVPDSVFYTSAMATADFLRRQ T0371 95 :DGGIVAYLGTANSANYLVSDGIKMLP 2c4nA 83 :EGKKAYVVGEGALIHELYKAGFTITD T0371 130 :GEVNALVLLDDEGFN 2c4nA 109 :VNPDFVIVGETRSYN T0371 146 :FHDLNKTVNLLRK 2c4nA 124 :WDMMHKAAYFVAN T0371 160 :TIPAIVANTDNTY 2c4nA 137 :GARFIATNPDTHG T0371 175 :TKTDVAIA 2c4nA 150 :RGFYPACG T0371 185 :GVATMIESILGRRFIRFGKPDSQMFMFAYDML 2c4nA 158 :ALCAGIEKISGRKPFYVGKPSPWIIRAALNKM T0371 221 :EISKREILMVGDTLHTDILGGNKFGLDTALVLTGNTRIDDAETK 2c4nA 190 :QAHSEETVIVGDNLRTDILAGFQAGLETILVLSGVSSLDDIDSM T0371 269 :GIVPTHICES 2c4nA 234 :PFRPSWIYPS T0371 280 :VIEL 2c4nA 244 :VAEI Number of specific fragments extracted= 12 number of extra gaps= 1 total=78 Number of alignments=5 # 2c4nA read from 2c4nA/merged-good-all-a2m # found chain 2c4nA in template set Warning: unaligning (T0371)K25 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c4nA)H16 Warning: unaligning (T0371)T26 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2c4nA)H16 T0371 13 :YKCIFFDAFGVL 2c4nA 3 :IKNVICDIDGVL T0371 27 :YNGLLPGIENTFDYLKAQGQDYYIVTNDASRSPEQLADSYHKLGL 2c4nA 17 :DNVAVPGAAEFLHGIMDKGLPLVLLTNYPSQTGQDLANRFATAGV T0371 73 :SITADKIISSGMITKEYIDLK 2c4nA 62 :DVPDSVFYTSAMATADFLRRQ T0371 95 :DGGIVAYLGTANSANYLVSDGIKMLP 2c4nA 83 :EGKKAYVVGEGALIHELYKAGFTITD T0371 130 :GEVNALVLLDDEGFN 2c4nA 109 :VNPDFVIVGETRSYN T0371 147 :HDLNKTVNLLRKRTIPAIVANTD 2c4nA 124 :WDMMHKAAYFVANGARFIATNPD T0371 173 :PLTKT 2c4nA 147 :THGRG T0371 179 :VAIAIGGVATMIESILGRRFIRFGKPDSQMFMFAYDML 2c4nA 152 :FYPACGALCAGIEKISGRKPFYVGKPSPWIIRAALNKM T0371 221 :EISKREILMVGDTLHTDILGGNKFGLDTALVLTGNTRIDDAETKIKSTGIVPTHICES 2c4nA 190 :QAHSEETVIVGDNLRTDILAGFQAGLETILVLSGVSSLDDIDSMPFRPSWIYPSVAEI Number of specific fragments extracted= 9 number of extra gaps= 1 total=87 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gfhA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2gfhA expands to /projects/compbio/data/pdb/2gfh.pdb.gz 2gfhA:Skipped atom 62, because occupancy 0.5 <= existing 0.500 in 2gfhA Skipped atom 66, because occupancy 0.500 <= existing 0.500 in 2gfhA Skipped atom 68, because occupancy 0.500 <= existing 0.500 in 2gfhA Skipped atom 70, because occupancy 0.500 <= existing 0.500 in 2gfhA Skipped atom 72, because occupancy 0.500 <= existing 0.500 in 2gfhA Skipped atom 74, because occupancy 0.500 <= existing 0.500 in 2gfhA Skipped atom 76, because occupancy 0.500 <= existing 0.500 in 2gfhA Skipped atom 78, because occupancy 0.500 <= existing 0.500 in 2gfhA Skipped atom 789, because occupancy 0.500 <= existing 0.500 in 2gfhA Skipped atom 793, because occupancy 0.500 <= existing 0.500 in 2gfhA Skipped atom 795, because occupancy 0.500 <= existing 0.500 in 2gfhA # T0371 read from 2gfhA/merged-good-all-a2m # 2gfhA read from 2gfhA/merged-good-all-a2m # adding 2gfhA to template set # found chain 2gfhA in template set Warning: unaligning (T0371)F18 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gfhA)D12 Warning: unaligning (T0371)D19 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gfhA)D12 Warning: unaligning (T0371)D95 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2gfhA)C67 Warning: unaligning (T0371)A100 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gfhA)C67 T0371 11 :PKYKCIF 2gfhA 4 :SRVRAVF T0371 20 :AFGVLKTYNGLL 2gfhA 13 :LDNTLIDTAGAS T0371 32 :PG 2gfhA 26 :RG T0371 59 :PEQLADSYHK 2gfhA 28 :MLEVIKLLQS T0371 69 :LGL 2gfhA 39 :YHY T0371 75 :T 2gfhA 42 :K T0371 77 :DKIISSGMITKEYI 2gfhA 43 :EEAEIICDKVQVKL T0371 91 :DLKV 2gfhA 58 :KECF T0371 101 :Y 2gfhA 68 :I T0371 102 :LGTANSANYLVSD 2gfhA 71 :VRTSHWEEAIQET T0371 115 :GI 2gfhA 85 :GG T0371 122 :SAIDDSNIGEVNALVLLDDEGFNWFHDLNKTVNLLRKRTIPAIVANTDNTYP 2gfhA 87 :ADNRKLAEECYFLWKSTRLQHMILADDVKAMLTELRKEVRLLLLTNGDRQTQ T0371 175 :TKTDVAIA 2gfhA 139 :REKIEACA T0371 186 :VATMIESILGRRFIRFGKPDSQMFMFAYDML 2gfhA 147 :CQSYFDAIVIGGEQKEEKPAPSIFYHCCDLL T0371 221 :EISKREILMVGDTLHTDILGGNKFGLD 2gfhA 178 :GVQPGDCVMVGDTLETDIQGGLNAGLK T0371 248 :TALVL 2gfhA 206 :TVWIN T0371 254 :GNTRIDD 2gfhA 211 :KSGRVPL T0371 267 :STGIVPTHICES 2gfhA 218 :TSSPMPHYMVSS T0371 280 :VIEL 2gfhA 230 :VLEL Number of specific fragments extracted= 19 number of extra gaps= 1 total=106 Number of alignments=7 # 2gfhA read from 2gfhA/merged-good-all-a2m # found chain 2gfhA in template set Warning: unaligning (T0371)F18 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gfhA)D12 Warning: unaligning (T0371)D19 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gfhA)D12 Warning: unaligning (T0371)F72 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2gfhA)C67 Warning: unaligning (T0371)I98 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gfhA)C67 T0371 10 :LPKYKCIF 2gfhA 3 :LSRVRAVF T0371 20 :AFGVLKTYNGLL 2gfhA 13 :LDNTLIDTAGAS T0371 32 :PGIENTFDYLKAQ 2gfhA 26 :RGMLEVIKLLQSK T0371 54 :DASRSPEQLADSYHKL 2gfhA 40 :HYKEEAEIICDKVQVK T0371 70 :GL 2gfhA 60 :CF T0371 99 :VAYLGTANSANYLVSD 2gfhA 68 :ITDVRTSHWEEAIQET T0371 119 :L 2gfhA 84 :K T0371 121 :VSAIDDSNIGEVNAL 2gfhA 85 :GGADNRKLAEECYFL T0371 136 :VLLDDEGFNWFHDLNKTVNLLRKR 2gfhA 101 :KSTRLQHMILADDVKAMLTELRKE T0371 161 :IPAIVANTDNTYPLTKTDVAIAIGGVATMI 2gfhA 125 :VRLLLLTNGDRQTQREKIEACACQSYFDAI T0371 194 :LGRRFIRFGKPDSQMFMFAYDML 2gfhA 155 :VIGGEQKEEKPAPSIFYHCCDLL T0371 221 :EISKREILMVGDTLHTDILGGNKFGLDTALVLTGNTRID 2gfhA 178 :GVQPGDCVMVGDTLETDIQGGLNAGLKATVWINKSGRVP T0371 266 :KSTGIVPTHICES 2gfhA 217 :LTSSPMPHYMVSS T0371 280 :VIEL 2gfhA 230 :VLEL Number of specific fragments extracted= 14 number of extra gaps= 1 total=120 Number of alignments=8 # 2gfhA read from 2gfhA/merged-good-all-a2m # found chain 2gfhA in template set Warning: unaligning (T0371)F18 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gfhA)D12 Warning: unaligning (T0371)D19 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gfhA)D12 Warning: unaligning (T0371)F72 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2gfhA)C67 Warning: unaligning (T0371)L102 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gfhA)C67 T0371 12 :KYKCIF 2gfhA 5 :RVRAVF T0371 20 :AFGVLKTYNGLLPGIENTFDYLK 2gfhA 13 :LDNTLIDTAGASRRGMLEVIKLL T0371 59 :PEQLADSYHKLGL 2gfhA 49 :CDKVQVKLSKECF T0371 103 :GTANSANYLVSDGIKMLPVSAIDDSNIGEVNALVLLDDEGFNWFHDLNKTVNLLRKRTIPAIVANT 2gfhA 68 :ITDVRTSHWEEAIQETKGGADNRKLAEECYFLWKSTRLQHMILADDVKAMLTELRKEVRLLLLTNG T0371 182 :AIGGVATMIESIL 2gfhA 134 :DRQTQREKIEACA T0371 195 :GRRFIRFGKPDSQMFMFAYDML 2gfhA 156 :IGGEQKEEKPAPSIFYHCCDLL T0371 221 :EISKREILMVGDTLHTDILGGNKFGLD 2gfhA 178 :GVQPGDCVMVGDTLETDIQGGLNAGLK T0371 248 :TALVLTGNTRID 2gfhA 206 :TVWINKSGRVPL T0371 263 :TKIKSTGIVPTHICESA 2gfhA 218 :TSSPMPHYMVSSVLELP Number of specific fragments extracted= 9 number of extra gaps= 1 total=129 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1s2oA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0371 read from 1s2oA/merged-good-all-a2m # 1s2oA read from 1s2oA/merged-good-all-a2m # found chain 1s2oA in training set T0371 14 :KCIFFDAFGVLKTYN 1s2oA 4 :LLLISDLDNTWVGDQ T0371 32 :PGIENTFDYLKAQ 1s2oA 19 :QALEHLQEYLGDR T0371 46 :QDYYIVT 1s2oA 35 :FYLAYAT T0371 56 :SRSPEQLADSYHKLGLFSIT 1s2oA 42 :GRSYHSARELQKQVGLMEPD T0371 78 :KIISSGM 1s2oA 62 :YWLTAVG T0371 97 :GIVAY 1s2oA 69 :SEIYH T0371 102 :LGTANSANYLVS 1s2oA 76 :GLDQHWADYLSE T0371 115 :GIKM 1s2oA 88 :HWQR T0371 122 :SAIDDSNI 1s2oA 92 :DILQAIAD T0371 134 :A 1s2oA 117 :I T0371 136 :VLLDDEGFNW 1s2oA 118 :SYHLDPQACP T0371 147 :HDLNKTVNLLRKRTIPA 1s2oA 128 :TVIDQLTEMLKETGIPV T0371 164 :IVANTDNTY 1s2oA 146 :VIFSSGKDV T0371 175 :TKTDVAIA 1s2oA 155 :DLLPQRSN T0371 203 :K 1s2oA 163 :K T0371 206 :SQMFMFAYDML 1s2oA 164 :GNATQYLQQHL T0371 221 :EISKREILMVGDT 1s2oA 175 :AMEPSQTLVCGDS T0371 235 :HTDILG 1s2oA 188 :GNDIGL T0371 242 :NKFGLDTALVL 1s2oA 194 :FETSARGVIVR T0371 256 :TRIDDAETKIKST 1s2oA 205 :NAQPELLHWYDQW T0371 269 :G 1s2oA 220 :S T0371 272 :PTHICE 1s2oA 221 :RHYRAQ Number of specific fragments extracted= 22 number of extra gaps= 0 total=151 Number of alignments=10 # 1s2oA read from 1s2oA/merged-good-all-a2m # found chain 1s2oA in training set T0371 14 :KCIFFDAFGVLKTYN 1s2oA 4 :LLLISDLDNTWVGDQ T0371 32 :PGIENTFDYLKAQ 1s2oA 19 :QALEHLQEYLGDR T0371 45 :GQDYYIVTNDA 1s2oA 34 :NFYLAYATGRS T0371 59 :PEQLADSYHKLGLFSITA 1s2oA 45 :YHSARELQKQVGLMEPDY T0371 78 :KIISSGMITKE 1s2oA 63 :WLTAVGSEIYH T0371 90 :IDLKVDG 1s2oA 81 :WADYLSE T0371 101 :YLGTANSANYLVSDG 1s2oA 88 :HWQRDILQAIADGFE T0371 116 :IKMLPVSAIDDSN 1s2oA 104 :LKPQSPLEQNPWK T0371 135 :LVLLDDEGFN 1s2oA 117 :ISYHLDPQAC T0371 146 :FHDLNKTVNLLRKRTIPAIVANTDNTYP 1s2oA 127 :PTVIDQLTEMLKETGIPVQVIFSSGKDV T0371 199 :IRFGK 1s2oA 157 :LPQRS T0371 208 :MFMFAYDMLRQKMEISKREILMVGDT 1s2oA 162 :NKGNATQYLQQHLAMEPSQTLVCGDS T0371 235 :HTDILGG 1s2oA 188 :GNDIGLF T0371 243 :KFGLDTALVLTGN 1s2oA 195 :ETSARGVIVRNAQ T0371 259 :DDAETKIKSTGIVPTHICES 1s2oA 208 :PELLHWYDQWGDSRHYRAQS Number of specific fragments extracted= 15 number of extra gaps= 0 total=166 Number of alignments=11 # 1s2oA read from 1s2oA/merged-good-all-a2m # found chain 1s2oA in training set T0371 15 :CIFFDAFGVLKTYNGLLP 1s2oA 5 :LLISDLDNTWVGDQQALE T0371 36 :NTFDYLKAQGQDYYIVTNDA 1s2oA 23 :HLQEYLGDRRGNFYLAYATG T0371 57 :RSPEQLADSYHKLGLFSIT 1s2oA 43 :RSYHSARELQKQVGLMEPD T0371 84 :MITKEYIDLKV 1s2oA 79 :QHWADYLSEHW T0371 103 :GTANSANYLVSDG 1s2oA 90 :QRDILQAIADGFE T0371 116 :IKMLP 1s2oA 104 :LKPQS T0371 125 :DDSNIGEVNALVLLDDEGFNWFHDLNK 1s2oA 109 :PLEQNPWKISYHLDPQACPTVIDQLTE T0371 155 :LLRKRTIPA 1s2oA 136 :MLKETGIPV T0371 170 :NTYPLTK 1s2oA 145 :QVIFSSG T0371 179 :VAIAIGGVATMIE 1s2oA 156 :LLPQRSNKGNATQ T0371 211 :FAYDML 1s2oA 169 :YLQQHL T0371 221 :EISKREILMVGDTLH 1s2oA 175 :AMEPSQTLVCGDSGN T0371 237 :D 1s2oA 190 :D T0371 239 :LGGNKFGLDTALV 1s2oA 191 :IGLFETSARGVIV T0371 254 :GNTRIDDAE 1s2oA 204 :RNAQPELLH T0371 263 :TKIKSTGIVPT 1s2oA 216 :QWGDSRHYRAQ Number of specific fragments extracted= 16 number of extra gaps= 0 total=182 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wr8A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0371 read from 1wr8A/merged-good-all-a2m # 1wr8A read from 1wr8A/merged-good-all-a2m # found chain 1wr8A in training set Warning: unaligning (T0371)K12 because first residue in template chain is (1wr8A)K2 T0371 13 :YKCIFFDAFGVLKTYNGLL 1wr8A 3 :IKAISIDIDGTITYPNRMI T0371 32 :PGIENTFDYLKAQGQDYYIVT 1wr8A 23 :EKALEAIRRAESLGIPIMLVT T0371 56 :SRSPEQLADSYHKLGL 1wr8A 44 :GNTVQFAEAASILIGT T0371 73 :SIT 1wr8A 60 :SGP T0371 79 :IISSGMITK 1wr8A 63 :VVAEDGGAI T0371 93 :KVDGGIVAYLG 1wr8A 72 :SYKKKRIFLAS T0371 104 :TANSANYLVSD 1wr8A 86 :EWILWNEIRKR T0371 115 :GIKM 1wr8A 99 :NART T0371 126 :DSNIGEVNALVLLDDEGFN 1wr8A 103 :SYTMPDRRAGLVIMRETIN T0371 146 :FHDLNKTVN 1wr8A 122 :VETVREIIN T0371 158 :KRTI 1wr8A 131 :ELNL T0371 175 :TKTDVAIAIG 1wr8A 135 :NLVAVDSGFA T0371 196 :RRFIRFGK 1wr8A 147 :VKKPWINK T0371 206 :SQMFMFAYDML 1wr8A 155 :GSGIEKASEFL T0371 221 :EISKREILMVGDT 1wr8A 166 :GIKPKEVAHVGDG T0371 235 :HTDILGGNKFG 1wr8A 179 :ENDLDAFKVVG T0371 248 :TALVL 1wr8A 190 :YKVAV T0371 254 :GN 1wr8A 195 :AQ T0371 257 :RIDDAETK 1wr8A 197 :APKILKEN T0371 272 :PTHICES 1wr8A 205 :ADYVTKK Number of specific fragments extracted= 20 number of extra gaps= 0 total=202 Number of alignments=13 # 1wr8A read from 1wr8A/merged-good-all-a2m # found chain 1wr8A in training set Warning: unaligning (T0371)K12 because first residue in template chain is (1wr8A)K2 T0371 13 :YKCIFFDAFGVLKTYNGLL 1wr8A 3 :IKAISIDIDGTITYPNRMI T0371 32 :PGIENTFDYLKAQGQDYYIVTNDA 1wr8A 23 :EKALEAIRRAESLGIPIMLVTGNT T0371 59 :PEQLADSYHKLGLF 1wr8A 47 :VQFAEAASILIGTS T0371 74 :I 1wr8A 61 :G T0371 77 :DKIISSGMIT 1wr8A 62 :PVVAEDGGAI T0371 93 :KVDGGIVAYLGTA 1wr8A 72 :SYKKKRIFLASMD T0371 106 :NSANYLVSD 1wr8A 88 :ILWNEIRKR T0371 115 :GIKMLP 1wr8A 99 :NARTSY T0371 128 :NIGEVNALVLLDDEGFN 1wr8A 105 :TMPDRRAGLVIMRETIN T0371 146 :FHDLNKTVN 1wr8A 122 :VETVREIIN T0371 158 :KRT 1wr8A 131 :ELN T0371 194 :LGRRFIRFGKPDSQMFMFAYDML 1wr8A 143 :FAIHVKKPWINKGSGIEKASEFL T0371 221 :EISKREILMVGDT 1wr8A 166 :GIKPKEVAHVGDG T0371 235 :HTDILGGNKFG 1wr8A 179 :ENDLDAFKVVG T0371 247 :DTALV 1wr8A 190 :YKVAV T0371 255 :NTRIDDAETK 1wr8A 195 :AQAPKILKEN T0371 272 :PTHICES 1wr8A 205 :ADYVTKK Number of specific fragments extracted= 17 number of extra gaps= 0 total=219 Number of alignments=14 # 1wr8A read from 1wr8A/merged-good-all-a2m # found chain 1wr8A in training set Warning: unaligning (T0371)K12 because first residue in template chain is (1wr8A)K2 T0371 13 :YKCIFFDAFGVLKTYNG 1wr8A 3 :IKAISIDIDGTITYPNR T0371 30 :LLPGIENTFDYLKAQGQDYYIVTNDA 1wr8A 21 :IHEKALEAIRRAESLGIPIMLVTGNT T0371 59 :PEQLADSYHKLGL 1wr8A 47 :VQFAEAASILIGT T0371 72 :FSITA 1wr8A 81 :ASMDE T0371 105 :ANSANYLVSD 1wr8A 87 :WILWNEIRKR T0371 115 :GIKML 1wr8A 99 :NARTS T0371 127 :SNIGEVNALVLLDDEGFN 1wr8A 104 :YTMPDRRAGLVIMRETIN T0371 146 :FHDLNKTVN 1wr8A 122 :VETVREIIN T0371 158 :KRT 1wr8A 131 :ELN T0371 167 :NTDNTYPLTKT 1wr8A 141 :SGFAIHVKKPW T0371 181 :IAI 1wr8A 152 :INK T0371 206 :SQMFMFAYDML 1wr8A 155 :GSGIEKASEFL T0371 221 :EISKREILMVGDTLH 1wr8A 166 :GIKPKEVAHVGDGEN T0371 237 :DILGGNKFGLDTA 1wr8A 181 :DLDAFKVVGYKVA T0371 251 :V 1wr8A 194 :V Number of specific fragments extracted= 15 number of extra gaps= 0 total=234 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qyiA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1qyiA expands to /projects/compbio/data/pdb/1qyi.pdb.gz 1qyiA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0371 read from 1qyiA/merged-good-all-a2m # 1qyiA read from 1qyiA/merged-good-all-a2m # adding 1qyiA to template set # found chain 1qyiA in template set T0371 14 :KCIFFDAFGVLKTY 1qyiA 2 :KKILFDVDGVFLSE T0371 28 :NGLL 1qyiA 45 :ETLT T0371 32 :PGIEN 1qyiA 50 :NDIQD T0371 37 :TFDYLKAQG 1qyiA 65 :ILNKLKSLG T0371 56 :SRSPEQLADSYH 1qyiA 95 :KLSHDEIEAFMY T0371 68 :KLG 1qyiA 114 :KLQ T0371 71 :L 1qyiA 126 :F T0371 73 :SITADKI 1qyiA 127 :NLNEQLP T0371 87 :KEYIDLKVDG 1qyiA 134 :LQFLDNVKVG T0371 130 :GEVNALVLLDDEGFN 1qyiA 189 :KLYEDVEKKIARTTF T0371 145 :WFHDLNKTVNLLRKRTIPA 1qyiA 216 :PVDEVKVLLNDLKGAGFEL T0371 164 :IVANTD 1qyiA 236 :IATGRP T0371 176 :KTDVAIAIG 1qyiA 253 :GLLPYFEAD T0371 185 :GVATMIESILGRRF 1qyiA 264 :ATASDVLEAENMYP T0371 199 :IRFGKPDSQMFMFAYD 1qyiA 280 :RPLGKPNPFSYIAALY T0371 221 :EISKRE 1qyiA 296 :GNNRDK T0371 227 :ILMVGDT 1qyiA 318 :VFIVGDS T0371 235 :HTDILGGNKFGLDTALVLTGNTR 1qyiA 325 :LADLLSAQKIGATFIGTLTGLKG T0371 259 :DDAETKIKSTG 1qyiA 348 :KDAAGELEAHH T0371 272 :PTHICES 1qyiA 359 :ADYVINH T0371 280 :VIEL 1qyiA 366 :LGEL Number of specific fragments extracted= 21 number of extra gaps= 0 total=255 Number of alignments=16 # 1qyiA read from 1qyiA/merged-good-all-a2m # found chain 1qyiA in template set T0371 14 :KCIFFDAFGVLKT 1qyiA 2 :KKILFDVDGVFLS T0371 27 :YNGLL 1qyiA 44 :WETLT T0371 32 :PGIENTFDYLKA 1qyiA 50 :NDIQDIRNRIFQ T0371 61 :QLADSYHKLGL 1qyiA 64 :KILNKLKSLGL T0371 73 :SITADKIISSGMITKE 1qyiA 75 :NSNWDMLFIVFSIHLI T0371 89 :YIDLKVDGG 1qyiA 136 :FLDNVKVGK T0371 101 :YLGTANSANYLVSD 1qyiA 145 :NNIYAALEEFATTE T0371 116 :IKMLPVSAIDDSNI 1qyiA 159 :LHVSDATLFSLKGA T0371 130 :GEVNALVLLDDEGFN 1qyiA 189 :KLYEDVEKKIARTTF T0371 145 :WFHDLNKTVNLLRKRTIPAIVANTDNTYPLTKTDVAIAIGGVA 1qyiA 216 :PVDEVKVLLNDLKGAGFELGIATGRPYTETVVPFENLGLLPYF T0371 188 :TMI 1qyiA 261 :DFI T0371 194 :LGRRFIR 1qyiA 264 :ATASDVL T0371 201 :FGKPDSQMFMFAYD 1qyiA 282 :LGKPNPFSYIAALY T0371 221 :EISKRE 1qyiA 296 :GNNRDK T0371 227 :ILMVGDTLH 1qyiA 318 :VFIVGDSLA T0371 237 :DILGGNKFGLDTALVLTGNTR 1qyiA 327 :DLLSAQKIGATFIGTLTGLKG T0371 259 :DDAETKIKSTG 1qyiA 348 :KDAAGELEAHH T0371 272 :PTHICES 1qyiA 359 :ADYVINH T0371 280 :VIEL 1qyiA 366 :LGEL Number of specific fragments extracted= 19 number of extra gaps= 0 total=274 Number of alignments=17 # 1qyiA read from 1qyiA/merged-good-all-a2m # found chain 1qyiA in template set T0371 14 :KCIFFDAFGVLKTYNGLLPGIENTFDYLK 1qyiA 2 :KKILFDVDGVFLSEERCFDVSALTVYELL T0371 56 :SRSPEQLAD 1qyiA 46 :TLTDNDIQD T0371 65 :SYHKLGL 1qyiA 68 :KLKSLGL T0371 73 :SITADKIISSGMITKEYIDLK 1qyiA 75 :NSNWDMLFIVFSIHLIDILKK T0371 103 :GTANSANYLVSDGIKMLPVS 1qyiA 96 :LSHDEIEAFMYQDEPVELKL T0371 123 :AIDDSNIGEVNALVLLDDEGFNWFHDLNKTVNLLRKRTIPAIVANTD 1qyiA 194 :VEKKIARTTFKTGYIYQEIILRPVDEVKVLLNDLKGAGFELGIATGR T0371 182 :AIGGVATMIESIL 1qyiA 241 :PYTETVVPFENLG T0371 195 :GRRFIRFGKPDSQMFMFAYD 1qyiA 276 :YPQARPLGKPNPFSYIAALY T0371 220 :ME 1qyiA 310 :DN T0371 222 :ISKREILMVGDTLH 1qyiA 313 :VNKDDVFIVGDSLA T0371 237 :DILGGNKFGLDTALVLTGNTRIDDAE 1qyiA 327 :DLLSAQKIGATFIGTLTGLKGKDAAG T0371 264 :KIKSTGIVPTHICESAV 1qyiA 355 :EAHHADYVINHLGELRG Number of specific fragments extracted= 12 number of extra gaps= 0 total=286 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rqlA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1rqlA expands to /projects/compbio/data/pdb/1rql.pdb.gz 1rqlA:# T0371 read from 1rqlA/merged-good-all-a2m # 1rqlA read from 1rqlA/merged-good-all-a2m # adding 1rqlA to template set # found chain 1rqlA in template set Warning: unaligning (T0371)K12 because first residue in template chain is (1rqlA)K5 T0371 13 :YKCIFFDAFGVLKTYNGLL 1rqlA 6 :IEAVIFDWAGTTVDYGCFA T0371 59 :PEQLADSYHKLGL 1rqlA 26 :LEVFMEIFHKRGV T0371 73 :SITADKIISS 1rqlA 39 :AITAEEARKP T0371 83 :GMITKEYI 1rqlA 54 :IDHVRALT T0371 103 :GTANSANYLVSDGIKMLPVSAIDDSNIGEVNALVLLDDEGFNWFHDLNKTVNLLRKRTIPAIVANT 1rqlA 62 :EMPRIASEWNRVFRQLPTEADIQEMYEEFEEILFAILPRYASPINAVKEVIASLRERGIKIGSTTG T0371 174 :LTKTDVAI 1rqlA 128 :YTREMMDI T0371 186 :VATMIES 1rqlA 136 :VAKEAAL T0371 195 :GRRFIRFGKPDSQMFMFAYDML 1rqlA 152 :TPDDVPAGRPYPWMCYKNAMEL T0371 221 :EI 1rqlA 174 :GV T0371 223 :SKREILMVGDT 1rqlA 177 :PMNHMIKVGDT T0371 235 :HTDILGGNKFGLDTALVLTGNTR 1rqlA 188 :VSDMKEGRNAGMWTVGVILGSSE T0371 258 :IDDAETKIKSTG 1rqlA 230 :IEVVRNRFVENG T0371 272 :PTHICES 1rqlA 242 :AHFTIET T0371 280 :VIEL 1rqlA 249 :MQEL Number of specific fragments extracted= 14 number of extra gaps= 0 total=300 Number of alignments=19 # 1rqlA read from 1rqlA/merged-good-all-a2m # found chain 1rqlA in template set Warning: unaligning (T0371)P11 because first residue in template chain is (1rqlA)K5 T0371 13 :YKCIFFDAFGVLKTYNGL 1rqlA 6 :IEAVIFDWAGTTVDYGCF T0371 57 :RSPEQLADSYHKLGL 1rqlA 24 :APLEVFMEIFHKRGV T0371 73 :SITADKIISSG 1rqlA 39 :AITAEEARKPM T0371 84 :MITKEYI 1rqlA 51 :LLKIDHV T0371 99 :VAYLGTANSANYLVSDGIKMLPVSAIDDSN 1rqlA 58 :RALTEMPRIASEWNRVFRQLPTEADIQEMY T0371 130 :GEVNALVL 1rqlA 88 :EEFEEILF T0371 138 :LDDEGFNWFHDLNKTVNLLRKRTIPAIVANTDNTYPLTKTDVAIAIGGVA 1rqlA 97 :ILPRYASPINAVKEVIASLRERGIKIGSTTGYTREMMDIVAKEAALQGYK T0371 188 :TMI 1rqlA 148 :DFL T0371 194 :LGRRFIRFGKPDSQMFMFAYDML 1rqlA 151 :VTPDDVPAGRPYPWMCYKNAMEL T0371 221 :EI 1rqlA 174 :GV T0371 223 :SKREILMVGDT 1rqlA 177 :PMNHMIKVGDT T0371 235 :HTDILGGNKFGLDTALVLTGNTR 1rqlA 188 :VSDMKEGRNAGMWTVGVILGSSE T0371 258 :IDDAETKIKSTG 1rqlA 230 :IEVVRNRFVENG T0371 272 :PTHICES 1rqlA 242 :AHFTIET T0371 280 :VIEL 1rqlA 249 :MQEL Number of specific fragments extracted= 15 number of extra gaps= 0 total=315 Number of alignments=20 # 1rqlA read from 1rqlA/merged-good-all-a2m # found chain 1rqlA in template set Warning: unaligning (T0371)K12 because first residue in template chain is (1rqlA)K5 T0371 13 :YKCIFFDAFGVLKTYNGLLP 1rqlA 6 :IEAVIFDWAGTTVDYGCFAP T0371 59 :PEQLADSYHKLGL 1rqlA 26 :LEVFMEIFHKRGV T0371 73 :SITADKII 1rqlA 39 :AITAEEAR T0371 81 :SSGMITKEYI 1rqlA 52 :LKIDHVRALT T0371 103 :GTANSANYLVSDGIKMLPVSAIDDSNIGEVNALVLLDDEGFNWFHDLNKTVNLLRKRTIPAIVANT 1rqlA 62 :EMPRIASEWNRVFRQLPTEADIQEMYEEFEEILFAILPRYASPINAVKEVIASLRERGIKIGSTTG T0371 182 :AIGGVATMIESIL 1rqlA 128 :YTREMMDIVAKEA T0371 195 :GRRFIRFGKPDSQMFMFAYDML 1rqlA 152 :TPDDVPAGRPYPWMCYKNAMEL T0371 221 :EI 1rqlA 174 :GV T0371 223 :SKREILMVGDTLH 1rqlA 177 :PMNHMIKVGDTVS T0371 237 :DILGGNKFGLDTALVLTG 1rqlA 190 :DMKEGRNAGMWTVGVILG T0371 255 :NTRIDDAE 1rqlA 212 :GLTEEEVE T0371 265 :IKSTGIVPTHICESAV 1rqlA 239 :ENGAHFTIETMQELES Number of specific fragments extracted= 12 number of extra gaps= 0 total=327 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ek1A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ek1A expands to /projects/compbio/data/pdb/1ek1.pdb.gz 1ek1A:# T0371 read from 1ek1A/merged-good-all-a2m # 1ek1A read from 1ek1A/merged-good-all-a2m # adding 1ek1A to template set # found chain 1ek1A in template set Warning: unaligning (T0371)D260 because of BadResidue code BAD_PEPTIDE in next template residue (1ek1A)P369 Warning: unaligning (T0371)A261 because of BadResidue code BAD_PEPTIDE at template residue (1ek1A)P369 T0371 32 :PGIENTFDYLKAQGQDYYIVTNDASRS 1ek1A 103 :RPMLQAAIALKKKGFTTCIVTNNWLDD T0371 59 :PEQLADSYHKL 1ek1A 136 :LAQMMCELSQH T0371 71 :L 1ek1A 147 :F T0371 77 :DKIISS 1ek1A 148 :DFLIES T0371 83 :GMITKEYIDLKVD 1ek1A 166 :YNFLLDTLKAKPN T0371 97 :GIVAYLGTANSANYLVSDGIKMLPVSAIDDSNI 1ek1A 179 :EVVFLDDFGSNLKPARDMGMVTILVHNTASALR T0371 143 :FNWFH 1ek1A 267 :ESWFS T0371 152 :TVNLLRKRTIPAIVANT 1ek1A 275 :QIPALAQAGFRVLAIDM T0371 169 :DNT 1ek1A 296 :DSS T0371 174 :LTKTDVAIA 1ek1A 299 :SPPEIEEYA T0371 186 :VATMIES 1ek1A 308 :MELLCKE T0371 209 :FMFAYDML 1ek1A 315 :MVTFLDKL T0371 221 :EI 1ek1A 323 :GI T0371 225 :REILMVGDT 1ek1A 325 :PQAVFIGHD T0371 235 :HTDILGGNKF 1ek1A 334 :WAGVMVWNMA T0371 246 :LD 1ek1A 350 :VR T0371 248 :TALVLTGNTRID 1ek1A 353 :VASLNTPFMPPD T0371 262 :ETKIKSTG 1ek1A 370 :MKVIRSIP Number of specific fragments extracted= 18 number of extra gaps= 1 total=345 Number of alignments=22 # 1ek1A read from 1ek1A/merged-good-all-a2m # found chain 1ek1A in template set Warning: unaligning (T0371)K14 because first residue in template chain is (1ek1A)R4 Warning: unaligning (T0371)R257 because of BadResidue code BAD_PEPTIDE in next template residue (1ek1A)P369 Warning: unaligning (T0371)I258 because of BadResidue code BAD_PEPTIDE at template residue (1ek1A)P369 T0371 15 :CIFFDAFGVLKT 1ek1A 5 :VAAFDLDGVLAL T0371 27 :YNGLL 1ek1A 97 :AARSI T0371 32 :PGIENTFDYLKAQGQDYYIVTNDASRS 1ek1A 103 :RPMLQAAIALKKKGFTTCIVTNNWLDD T0371 59 :PEQLADSYHKL 1ek1A 136 :LAQMMCELSQH T0371 73 :SIT 1ek1A 155 :QVG T0371 76 :ADKII 1ek1A 162 :EPQIY T0371 84 :MITKEYIDLK 1ek1A 167 :NFLLDTLKAK T0371 95 :DGGIVAYLGTANSANYLVSDGIKMLPVSAIDDSNI 1ek1A 177 :PNEVVFLDDFGSNLKPARDMGMVTILVHNTASALR T0371 130 :GEVNALVLLDDEGFNW 1ek1A 233 :NDVSHGYVTVKPGIRL T0371 160 :TIPAIVANTDNTYP 1ek1A 255 :SGPALCLCHGFPES T0371 180 :AIAIGGVATMIESI 1ek1A 269 :WFSWRYQIPALAQA T0371 199 :IR 1ek1A 306 :YA T0371 209 :FMFAYDML 1ek1A 308 :MELLCKEM T0371 217 :RQKMEIS 1ek1A 319 :LDKLGIP T0371 226 :EILMVGDTLH 1ek1A 326 :QAVFIGHDWA T0371 237 :DILGGNKF 1ek1A 336 :GVMVWNMA T0371 245 :GLDTALVLT 1ek1A 349 :RVRAVASLN T0371 254 :GNT 1ek1A 365 :PDV T0371 259 :DDAETKI 1ek1A 370 :MKVIRSI Number of specific fragments extracted= 19 number of extra gaps= 1 total=364 Number of alignments=23 # 1ek1A read from 1ek1A/merged-good-all-a2m # found chain 1ek1A in template set Warning: unaligning (T0371)K14 because first residue in template chain is (1ek1A)R4 Warning: unaligning (T0371)L31 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ek1A)G48 Warning: unaligning (T0371)N106 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ek1A)G48 T0371 15 :CIFFDAFGVLKT 1ek1A 5 :VAAFDLDGVLAL T0371 29 :GL 1ek1A 17 :PS T0371 107 :SANYLVSDGIKMLPVS 1ek1A 49 :PTEQLMKGKITFSQWV T0371 127 :SNIG 1ek1A 91 :IFSQ T0371 139 :DDEGFNWFHDLNKTVNLLRKRTIPAIVANTD 1ek1A 95 :AMAARSINRPMLQAAIALKKKGFTTCIVTNN T0371 173 :PLTKTDVAIAIGGVATMIESIL 1ek1A 126 :WLDDGDKRDSLAQMMCELSQHF T0371 195 :GRRFIRFGKPDSQMFMFAYDML 1ek1A 152 :ESCQVGMIKPEPQIYNFLLDTL T0371 221 :EISKREILMVGDTLH 1ek1A 174 :KAKPNEVVFLDDFGS T0371 237 :DILGGNKFGLD 1ek1A 189 :NLKPARDMGMV Number of specific fragments extracted= 9 number of extra gaps= 0 total=373 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nnlA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0371 read from 1nnlA/merged-good-all-a2m # 1nnlA read from 1nnlA/merged-good-all-a2m # found chain 1nnlA in training set Warning: unaligning (T0371)E4 because first residue in template chain is (1nnlA)S5 Warning: unaligning (T0371)I79 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1nnlA)P57 Warning: unaligning (T0371)S122 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1nnlA)P57 T0371 5 :SFKSLLPKYKCIFFDAFGVLKTYNG 1nnlA 6 :ELRKLFYSADAVCFDVDSTVIREEG T0371 59 :PEQLADS 1nnlA 31 :IDELAKI T0371 69 :LGL 1nnlA 38 :CGV T0371 76 :ADK 1nnlA 41 :EDA T0371 123 :AIDDSNI 1nnlA 58 :FKAALTE T0371 130 :GEVNALV 1nnlA 74 :EQVQRLI T0371 139 :DDEGFNWFHDLNKTVNLLRKRTIPA 1nnlA 81 :AEQPPHLTPGIRELVSRLQERNVQV T0371 164 :IVANT 1nnlA 107 :LISGG T0371 186 :VATMIESILGRRFIR 1nnlA 112 :FRSIVEHVASKLNIP T0371 207 :QMFMFAYDMLRQKM 1nnlA 156 :GGKGKVIKLLKEKF T0371 223 :SKREILMVGDT 1nnlA 170 :HFKKIIMIGDG T0371 235 :HTDILG 1nnlA 181 :ATDMEA T0371 244 :F 1nnlA 187 :C T0371 245 :GLDTALVLTGNTRIDDAETK 1nnlA 189 :PADAFIGFGGNVIRQQVKDN T0371 272 :PTHICES 1nnlA 209 :AKWYITD T0371 280 :VIEL 1nnlA 216 :FVEL Number of specific fragments extracted= 16 number of extra gaps= 0 total=389 Number of alignments=25 # 1nnlA read from 1nnlA/merged-good-all-a2m # found chain 1nnlA in training set Warning: unaligning (T0371)E4 because first residue in template chain is (1nnlA)S5 Warning: unaligning (T0371)L62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1nnlA)P57 Warning: unaligning (T0371)T75 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1nnlA)P57 T0371 5 :SFKSLLPKYKCIFFDAFGVLKTYN 1nnlA 6 :ELRKLFYSADAVCFDVDSTVIREE T0371 37 :TFDYLKAQ 1nnlA 30 :GIDELAKI T0371 45 :GQ 1nnlA 39 :GV T0371 59 :PEQ 1nnlA 41 :EDA T0371 76 :A 1nnlA 58 :F T0371 104 :TANSANYLVSDGIK 1nnlA 59 :KAALTERLALIQPS T0371 130 :GEVNALV 1nnlA 74 :EQVQRLI T0371 139 :DDEGFNWFHDLNKTVNLLRKRTIPAIVANTDNTYPLTKTDVAIAIGG 1nnlA 81 :AEQPPHLTPGIRELVSRLQERNVQVFLISGGFRSIVEHVASKLNIPA T0371 191 :ESI 1nnlA 128 :TNV T0371 205 :DSQMFMFAYDMLRQKM 1nnlA 154 :ESGGKGKVIKLLKEKF T0371 223 :SKREILMVGDT 1nnlA 170 :HFKKIIMIGDG T0371 235 :HTDILGGNKFG 1nnlA 181 :ATDMEACPPAD T0371 247 :DTALV 1nnlA 192 :AFIGF T0371 253 :TGNTRIDDAETK 1nnlA 197 :GGNVIRQQVKDN T0371 272 :PTHICES 1nnlA 209 :AKWYITD T0371 280 :VIEL 1nnlA 216 :FVEL Number of specific fragments extracted= 16 number of extra gaps= 0 total=405 Number of alignments=26 # 1nnlA read from 1nnlA/merged-good-all-a2m # found chain 1nnlA in training set Warning: unaligning (T0371)E4 because first residue in template chain is (1nnlA)S5 Warning: unaligning (T0371)R57 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1nnlA)P57 Warning: unaligning (T0371)V280 because last residue in template chain is (1nnlA)G221 T0371 5 :SFKSLLPKYKCIFFDAFGVLKTYN 1nnlA 6 :ELRKLFYSADAVCFDVDSTVIREE T0371 37 :TFDYLK 1nnlA 30 :GIDELA T0371 58 :SPEQLADSYHKLGL 1nnlA 58 :FKAALTERLALIQP T0371 104 :TANSANYLV 1nnlA 72 :SREQVQRLI T0371 139 :DDEGFNWFHDLNKTVNLLRKRTIPAIVANTD 1nnlA 81 :AEQPPHLTPGIRELVSRLQERNVQVFLISGG T0371 186 :VATMIESIL 1nnlA 112 :FRSIVEHVA T0371 195 :GRRFIRFG 1nnlA 140 :NGEYAGFD T0371 205 :DSQMFMFAYDMLRQKM 1nnlA 154 :ESGGKGKVIKLLKEKF T0371 223 :SKREILMVGDTLH 1nnlA 170 :HFKKIIMIGDGAT T0371 237 :DIL 1nnlA 183 :DME T0371 244 :F 1nnlA 186 :A T0371 245 :GLD 1nnlA 189 :PAD T0371 248 :TALVLTGNTRIDDAET 1nnlA 193 :FIGFGGNVIRQQVKDN T0371 268 :TGIVPTHICESA 1nnlA 209 :AKWYITDFVELL Number of specific fragments extracted= 14 number of extra gaps= 0 total=419 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zd3A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zd3A expands to /projects/compbio/data/pdb/1zd3.pdb.gz 1zd3A:# T0371 read from 1zd3A/merged-good-all-a2m # 1zd3A read from 1zd3A/merged-good-all-a2m # adding 1zd3A to template set # found chain 1zd3A in template set Warning: unaligning (T0371)K12 because first residue in template chain is (1zd3A)T2 T0371 13 :YKCIFFDAFGVLKTYNGLL 1zd3A 3 :LRAAVFDLDGVLALPAVFG T0371 61 :QLADSYHKLGL 1zd3A 22 :VLGRTEEALAL T0371 75 :TADKIISSG 1zd3A 33 :PRGLLNDAF T0371 84 :MITKEYI 1zd3A 48 :GATTRLM T0371 91 :DLK 1zd3A 56 :GEI T0371 103 :GTANSANYLVS 1zd3A 59 :TLSQWIPLMEE T0371 115 :GIKMLPVSAIDDSNIGEVNA 1zd3A 79 :KVCLPKNFSIKEIFDKAISA T0371 143 :FNWFHDLNKTVNLLRKRTIPA 1zd3A 99 :RKINRPMLQAALMLRKKGFTT T0371 164 :IVANTDN 1zd3A 121 :ILTNTWL T0371 175 :TKTDVAIA 1zd3A 128 :DDRAERDG T0371 186 :VATMIESI 1zd3A 136 :LAQLMCEL T0371 194 :LGRRFIRFGKPDSQMFMFAYDML 1zd3A 151 :IESCQVGMVKPEPQIYKFLLDTL T0371 221 :EISKREILMVGDT 1zd3A 174 :KASPSEVVFLDDI T0371 235 :HTDILGGNKFGLDTA 1zd3A 187 :GANLKPARDLGMVTI T0371 254 :GNTRIDDAETKIKS 1zd3A 202 :LVQDTDTALKELEK Number of specific fragments extracted= 15 number of extra gaps= 0 total=434 Number of alignments=28 # 1zd3A read from 1zd3A/merged-good-all-a2m # found chain 1zd3A in template set Warning: unaligning (T0371)P11 because first residue in template chain is (1zd3A)T2 T0371 13 :YKCIFFDAFGVLKT 1zd3A 3 :LRAAVFDLDGVLAL T0371 29 :GLLPGIENTF 1zd3A 45 :GPEGATTRLM T0371 54 :DASRSPEQLADSY 1zd3A 55 :KGEITLSQWIPLM T0371 104 :TANSANYLVSDGIKMLPV 1zd3A 68 :EENCRKCSETAKVCLPKN T0371 130 :GEVNALVLLDDEGFNWFHDLNKTVNLLRKRTIPAIVANT 1zd3A 86 :FSIKEIFDKAISARKINRPMLQAALMLRKKGFTTAILTN T0371 169 :DNT 1zd3A 131 :AER T0371 175 :TKTDVAI 1zd3A 134 :DGLAQLM T0371 182 :AIGGVATMI 1zd3A 142 :ELKMHFDFL T0371 194 :LGRRFIRFGKPDSQMFMFAYDML 1zd3A 151 :IESCQVGMVKPEPQIYKFLLDTL T0371 221 :EISKREILMVGDT 1zd3A 174 :KASPSEVVFLDDI T0371 235 :HTDILGGNKFGLDTALV 1zd3A 187 :GANLKPARDLGMVTILV T0371 256 :TRIDDAETKIKS 1zd3A 204 :QDTDTALKELEK Number of specific fragments extracted= 12 number of extra gaps= 0 total=446 Number of alignments=29 # 1zd3A read from 1zd3A/merged-good-all-a2m # found chain 1zd3A in template set T0371 13 :YKCIFFDAFGVLKT 1zd3A 3 :LRAAVFDLDGVLAL T0371 27 :YNGLLPGIEN 1zd3A 19 :VFGVLGRTEE T0371 37 :TFDYLK 1zd3A 36 :LLNDAF T0371 55 :ASRSPEQLADSYHK 1zd3A 56 :GEITLSQWIPLMEE T0371 106 :NSANYLVSDGIKMLP 1zd3A 70 :NCRKCSETAKVCLPK T0371 129 :IGEVNALVLLDDEGFNWFHDLNKTVNLLRKRTIPAIVANTD 1zd3A 85 :NFSIKEIFDKAISARKINRPMLQAALMLRKKGFTTAILTNT T0371 172 :YPLTKT 1zd3A 126 :WLDDRA T0371 182 :AIGGVATMIESIL 1zd3A 132 :ERDGLAQLMCELK T0371 199 :IRFGKPDSQMFMFAYDML 1zd3A 156 :VGMVKPEPQIYKFLLDTL T0371 221 :EISKREILMVGDTLH 1zd3A 174 :KASPSEVVFLDDIGA T0371 237 :DILGGNKFGLDTALV 1zd3A 189 :NLKPARDLGMVTILV Number of specific fragments extracted= 11 number of extra gaps= 0 total=457 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1l7mA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0371 read from 1l7mA/merged-good-all-a2m # 1l7mA read from 1l7mA/merged-good-all-a2m # found chain 1l7mA in training set Warning: unaligning (T0371)P11 because first residue in template chain is (1l7mA)K3 T0371 12 :KYKCIFFDAFGVLKTYN 1l7mA 4 :KKKLILFDFDSTLVNNE T0371 61 :QLADSYHKLGL 1l7mA 21 :TIDEIAREAGV T0371 76 :ADKI 1l7mA 32 :EEEV T0371 83 :GMITKEYIDLKV 1l7mA 36 :KKITKEAMEGKL T0371 103 :GTANSANYLVSD 1l7mA 48 :NFEQSLRKRVSL T0371 115 :GIKM 1l7mA 62 :DLPI T0371 130 :GEVNALVL 1l7mA 66 :EKVEKAIK T0371 142 :GFNWFHDLNKTVNLLRKRTIPA 1l7mA 74 :RITPTEGAEETIKELKNRGYVV T0371 164 :IVANT 1l7mA 97 :VVSGG T0371 174 :L 1l7mA 102 :F T0371 183 :IGGVATMIES 1l7mA 103 :DIAVNKIKEK T0371 194 :LGRRFIR 1l7mA 113 :LGLDYAF T0371 203 :K 1l7mA 144 :K T0371 206 :SQMFMFAYDML 1l7mA 145 :GEILEKIAKIE T0371 221 :EISKREILMVGDT 1l7mA 156 :GINLEDTVAVGDG T0371 235 :HTDILGGNKFGLDTAL 1l7mA 169 :ANDISMFKKAGLKIAF T0371 256 :TRIDD 1l7mA 185 :CAKPI T0371 265 :IKST 1l7mA 190 :LKEK T0371 272 :PTHICESA 1l7mA 194 :ADICIEKR T0371 280 :VIEL 1l7mA 203 :LREI Number of specific fragments extracted= 20 number of extra gaps= 0 total=477 Number of alignments=31 # 1l7mA read from 1l7mA/merged-good-all-a2m # found chain 1l7mA in training set Warning: unaligning (T0371)P11 because first residue in template chain is (1l7mA)K3 T0371 12 :KYKCIFFDAFGVLKTYN 1l7mA 4 :KKKLILFDFDSTLVNNE T0371 37 :TFDYLKAQ 1l7mA 21 :TIDEIARE T0371 45 :GQ 1l7mA 30 :GV T0371 59 :PEQLADSYHKLGLFSITAD 1l7mA 32 :EEEVKKITKEAMEGKLNFE T0371 109 :NYLVSD 1l7mA 51 :QSLRKR T0371 121 :VSAIDDSNIGEVNALVL 1l7mA 57 :VSLLKDLPIEKVEKAIK T0371 142 :GFNWFHDLNKTVNLLRKRTIPAIVANTDNTYPLTKTDVAIAI 1l7mA 74 :RITPTEGAEETIKELKNRGYVVAVVSGGFDIAVNKIKEKLGL T0371 191 :ESI 1l7mA 116 :DYA T0371 194 :LGRRFIRF 1l7mA 130 :LTGDVEGE T0371 203 :KPDSQMFMFAYDMLRQKMEISKREILMVGDTLH 1l7mA 138 :VLKENAKGEILEKIAKIEGINLEDTVAVGDGAN T0371 237 :DILGGNKFG 1l7mA 171 :DISMFKKAG T0371 247 :DTALV 1l7mA 180 :LKIAF T0371 256 :TRIDDAETK 1l7mA 185 :CAKPILKEK T0371 272 :PTHICESA 1l7mA 194 :ADICIEKR T0371 280 :VIEL 1l7mA 203 :LREI Number of specific fragments extracted= 15 number of extra gaps= 0 total=492 Number of alignments=32 # 1l7mA read from 1l7mA/merged-good-all-a2m # found chain 1l7mA in training set T0371 14 :KCIFFDAFGVLKTYNGLLPGI 1l7mA 6 :KLILFDFDSTLVNNETIDEIA T0371 42 :KAQG 1l7mA 27 :REAG T0371 58 :SPEQLADSYHKLGLFSIT 1l7mA 31 :VEEEVKKITKEAMEGKLN T0371 82 :SGMITKEYIDLK 1l7mA 49 :FEQSLRKRVSLL T0371 125 :DDSNIGEVNALV 1l7mA 61 :KDLPIEKVEKAI T0371 141 :EGFNWFHDLNKTVNLLRKRTIPAIVANTD 1l7mA 73 :KRITPTEGAEETIKELKNRGYVVAVVSGG T0371 186 :VATMIESIL 1l7mA 102 :FDIAVNKIK T0371 195 :GRRFIR 1l7mA 135 :EGEVLK T0371 205 :DSQMFMFAYDML 1l7mA 144 :KGEILEKIAKIE T0371 221 :EISKREILMVGDTLH 1l7mA 156 :GINLEDTVAVGDGAN T0371 237 :DILGGNKFGLDTAL 1l7mA 171 :DISMFKKAGLKIAF T0371 256 :TRIDDAET 1l7mA 185 :CAKPILKE T0371 267 :STGIVPT 1l7mA 193 :KADICIE T0371 274 :HICESAVIE 1l7mA 202 :DLREILKYI Number of specific fragments extracted= 14 number of extra gaps= 0 total=506 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cqzA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1cqzA expands to /projects/compbio/data/pdb/1cqz.pdb.gz 1cqzA:# T0371 read from 1cqzA/merged-good-all-a2m # 1cqzA read from 1cqzA/merged-good-all-a2m # adding 1cqzA to template set # found chain 1cqzA in template set Warning: unaligning (T0371)K14 because first residue in template chain is (1cqzA)R4 Warning: unaligning (T0371)G29 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cqzA)G48 Warning: unaligning (T0371)I74 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cqzA)G48 Warning: unaligning (T0371)I98 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cqzA)Q90 Warning: unaligning (T0371)I129 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cqzA)Q90 T0371 15 :CIFFDAFGVLKTYN 1cqzA 5 :VAAFDLDGVLALPS T0371 75 :TADKI 1cqzA 49 :PTEQL T0371 90 :I 1cqzA 54 :M T0371 91 :DLKVDGG 1cqzA 56 :GKITFSQ T0371 130 :GEVNALVL 1cqzA 91 :IFSQAMAA T0371 143 :FNWFHDLNKTVNLLRKRTIPA 1cqzA 99 :RSINRPMLQAAIALKKKGFTT T0371 164 :IVANTDNTYP 1cqzA 121 :IVTNNWLDDG T0371 175 :TKTDVAIAI 1cqzA 131 :DKRDSLAQM T0371 184 :GGVATMIESILGRRFIRFGKPDSQMFMFAYDML 1cqzA 141 :CELSQHFDFLIESCQVGMIKPEPQIYNFLLDTL T0371 221 :EISKREILMVGDT 1cqzA 174 :KAKPNEVVFLDDF T0371 235 :HTDILGGNKFGLDTALVL 1cqzA 187 :GSNLKPARDMGMVTILVH T0371 256 :TRIDDAETKIKST 1cqzA 205 :NTASALRELEKVT Number of specific fragments extracted= 12 number of extra gaps= 0 total=518 Number of alignments=34 # 1cqzA read from 1cqzA/merged-good-all-a2m # found chain 1cqzA in template set Warning: unaligning (T0371)K14 because first residue in template chain is (1cqzA)R4 Warning: unaligning (T0371)G29 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cqzA)G48 Warning: unaligning (T0371)I90 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cqzA)G48 Warning: unaligning (T0371)V99 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cqzA)Q90 Warning: unaligning (T0371)D126 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cqzA)Q90 T0371 15 :CIFFDAFGVLKTYN 1cqzA 5 :VAAFDLDGVLALPS T0371 91 :DLKVDG 1cqzA 51 :EQLMKG T0371 97 :GI 1cqzA 61 :SQ T0371 127 :SNIGEVNALV 1cqzA 91 :IFSQAMAARS T0371 145 :WFHDLNKTVNLLRKRTIPAIVANT 1cqzA 101 :INRPMLQAAIALKKKGFTTCIVTN T0371 169 :DNTYPLTKTDVA 1cqzA 131 :DKRDSLAQMMCE T0371 183 :IGGVATMI 1cqzA 143 :LSQHFDFL T0371 194 :LGRRFIRFGKPDSQMFMFAYDML 1cqzA 151 :IESCQVGMIKPEPQIYNFLLDTL T0371 221 :EISKREILMVGDTLH 1cqzA 174 :KAKPNEVVFLDDFGS T0371 237 :DILGGNKFGLDTALV 1cqzA 189 :NLKPARDMGMVTILV T0371 255 :NTRIDDAETKIKSTGIV 1cqzA 204 :HNTASALRELEKVTGTQ Number of specific fragments extracted= 11 number of extra gaps= 0 total=529 Number of alignments=35 # 1cqzA read from 1cqzA/merged-good-all-a2m # found chain 1cqzA in template set Warning: unaligning (T0371)K14 because first residue in template chain is (1cqzA)R4 Warning: unaligning (T0371)L31 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cqzA)G48 Warning: unaligning (T0371)D126 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cqzA)Q90 T0371 15 :CIFFDAFGVLKT 1cqzA 5 :VAAFDLDGVLAL T0371 29 :GL 1cqzA 17 :PS T0371 127 :SNIGEVN 1cqzA 91 :IFSQAMA T0371 142 :GFNWFHDLNKTVNLLRKRTIPAIVANTD 1cqzA 98 :ARSINRPMLQAAIALKKKGFTTCIVTNN T0371 173 :PLTKTDVAIAIGGVATMIESIL 1cqzA 126 :WLDDGDKRDSLAQMMCELSQHF T0371 199 :IRFGKPDSQMFMFAYDML 1cqzA 156 :VGMIKPEPQIYNFLLDTL T0371 221 :EISKREILMVGDTLH 1cqzA 174 :KAKPNEVVFLDDFGS T0371 237 :DILGGNKFGLDTALV 1cqzA 189 :NLKPARDMGMVTILV T0371 254 :GNTR 1cqzA 204 :HNTA Number of specific fragments extracted= 9 number of extra gaps= 0 total=538 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wviA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wviA expands to /projects/compbio/data/pdb/1wvi.pdb.gz 1wviA:# T0371 read from 1wviA/merged-good-all-a2m # 1wviA read from 1wviA/merged-good-all-a2m # adding 1wviA to template set # found chain 1wviA in template set Warning: unaligning (T0371)K12 because first residue in template chain is (1wviA)T1002 T0371 13 :YKCIFFDAFGVLKTYNGLLPGIENTFDYLKAQGQDYYIVTNDASRSPEQLADSYHK 1wviA 1003 :YKGYLIDLDGTIYKGKDRIPAGEDFVKRLQERQLPYILVTNNTTRTPEMVQEMLAT T0371 69 :LGL 1wviA 1060 :FNI T0371 73 :SITADKIISSGMITKEYIDLKVDGGIVAYLGTANSANYLVSDGIKML 1wviA 1063 :KTPLETIYTATLATIDYMNDMKRGKTAYVIGETGLKKAVAEAGYRED T0371 129 :IGEVNALVLLDDEGFN 1wviA 1110 :SENPAYVVVGLDTNLT T0371 146 :FHDLNKTVNLL 1wviA 1126 :YEKLTLATLAI T0371 158 :KRTIPAIVANTDNTYP 1wviA 1137 :QKGAVFIGTNPDLNIP T0371 175 :TKTDVAIAIGGVATMIESILGRRFIRFGKPDSQMFMFAYDML 1wviA 1153 :TERGLLPGAGAILFLLEKATRVKPIIIGKPEAVIMNKALDRL T0371 221 :EISKREILMVGDTLHTDILGGNKFGLDTALVLTGNTRIDD 1wviA 1195 :GVKRHEAIMVGDNYLTDITAGIKNDIATLLVTTGFTKPEE T0371 265 :IKSTGIVPTHICES 1wviA 1235 :VPALPIQPDFVLSS T0371 280 :VIEL 1wviA 1249 :LAEW Number of specific fragments extracted= 10 number of extra gaps= 0 total=548 Number of alignments=37 # 1wviA read from 1wviA/merged-good-all-a2m # found chain 1wviA in template set Warning: unaligning (T0371)P11 because first residue in template chain is (1wviA)T1002 T0371 13 :YKCIFFDAFGVLKTYNGLLPGIENTFDYLKAQGQDYYIVTNDASRSPEQLADSYHK 1wviA 1003 :YKGYLIDLDGTIYKGKDRIPAGEDFVKRLQERQLPYILVTNNTTRTPEMVQEMLAT T0371 69 :LGL 1wviA 1060 :FNI T0371 73 :SITADKIISSGMITKEYIDLKVDGGIVAYLGTANSANYLVSDGIKMLP 1wviA 1063 :KTPLETIYTATLATIDYMNDMKRGKTAYVIGETGLKKAVAEAGYREDS T0371 130 :GEVNALVLLDDEGFN 1wviA 1111 :ENPAYVVVGLDTNLT T0371 146 :FHDLNKTVNLL 1wviA 1126 :YEKLTLATLAI T0371 158 :KRTIPAIVANTDNTYPLTKTD 1wviA 1137 :QKGAVFIGTNPDLNIPTERGL T0371 180 :AIAIGGVATMIESILGRRFIRFGKPDSQMFMFAYDML 1wviA 1158 :LPGAGAILFLLEKATRVKPIIIGKPEAVIMNKALDRL T0371 221 :EISKREILMVGDTLHTDILGGNKFGLDTALVLTGNTRIDDAETK 1wviA 1195 :GVKRHEAIMVGDNYLTDITAGIKNDIATLLVTTGFTKPEEVPAL T0371 269 :GIVPTHICES 1wviA 1239 :PIQPDFVLSS T0371 280 :VIEL 1wviA 1249 :LAEW Number of specific fragments extracted= 10 number of extra gaps= 0 total=558 Number of alignments=38 # 1wviA read from 1wviA/merged-good-all-a2m # found chain 1wviA in template set T0371 13 :YKCIFFDAFGVLKTYNGLLPGIENTFDYLKAQGQDYYIVTNDASRSPEQLADSYHKLGLFSITADKIISSGMITKEYIDLKVDGGIVAYLGTANSANYLVSDGIKMLP 1wviA 1003 :YKGYLIDLDGTIYKGKDRIPAGEDFVKRLQERQLPYILVTNNTTRTPEMVQEMLATSFNIKTPLETIYTATLATIDYMNDMKRGKTAYVIGETGLKKAVAEAGYREDS T0371 130 :GEVNALVLLDDEGFN 1wviA 1111 :ENPAYVVVGLDTNLT T0371 147 :HDLNKTVNLLRKRTIPAIVANTDNTYPLTKT 1wviA 1126 :YEKLTLATLAIQKGAVFIGTNPDLNIPTERG T0371 179 :VAIAIGGVATMIESILGRRFIRFGKPDSQMFMFAYDML 1wviA 1157 :LLPGAGAILFLLEKATRVKPIIIGKPEAVIMNKALDRL T0371 221 :EISKREILMVGDTLHTDILGGNKFGLDTALVLTGNTRIDDAETKIKSTGIVPTHICES 1wviA 1195 :GVKRHEAIMVGDNYLTDITAGIKNDIATLLVTTGFTKPEEVPALPIQPDFVLSSLAEW Number of specific fragments extracted= 5 number of extra gaps= 0 total=563 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zjjA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zjjA expands to /projects/compbio/data/pdb/1zjj.pdb.gz 1zjjA:# T0371 read from 1zjjA/merged-good-all-a2m # 1zjjA read from 1zjjA/merged-good-all-a2m # adding 1zjjA to template set # found chain 1zjjA in template set T0371 14 :KCIFFDAFGVLKTYNGLLPGIENTFDYLKAQGQDYYIVTNDASRSPEQLADSYHKLGL 1zjjA 2 :VAIIFDMDGVLYRGNRAIPGVRELIEFLKERGIPFAFLTNNSTKTPEMYREKLLKMGI T0371 73 :SITADKIISSGMITKEYIDLKVDGGIVAYLGTANSANYLVSDGIKMLPVSAIDDSNIGEVNALVLLDDEGFN 1zjjA 60 :DVSSSIIITSGLATRLYMSKHLDPGKIFVIGGEGLVKEMQALGWGIVTLDEARQGSWKEVKHVVVGLDPDLT T0371 147 :HDLNKTVNLLRKRTIPAIVANTDNTYP 1zjjA 132 :YEKLKYATLAIRNGATFIGTNPDATLP T0371 175 :TKTDVAIAIGGVATMIESILGRRFIRFGKPDSQMFMFAYDML 1zjjA 159 :GEEGIYPGAGSIIAALKVATNVEPIIIGKPNEPMYEVVREMF T0371 221 :E 1zjjA 201 :P T0371 224 :KREILMVGDTLHTDILGGNKFGLDTALVLTGNTRIDD 1zjjA 202 :GEELWMVGDRLDTDIAFAKKFGMKAIMVLTGVSSLED T0371 265 :IKSTGIVPTHICES 1zjjA 239 :IKKSEYKPDLVLPS T0371 280 :VIEL 1zjjA 253 :VYEL Number of specific fragments extracted= 8 number of extra gaps= 0 total=571 Number of alignments=40 # 1zjjA read from 1zjjA/merged-good-all-a2m # found chain 1zjjA in template set T0371 14 :KCIFFDAFGVLKTYNGLLPGIENTFDYLKAQGQDYYIVTNDASRSPEQLADSYHKLGL 1zjjA 2 :VAIIFDMDGVLYRGNRAIPGVRELIEFLKERGIPFAFLTNNSTKTPEMYREKLLKMGI T0371 73 :SITADKIISSGMITKEYIDLKVDGGIVAYLGTANSANYLVSDGIKMLPVSAIDDSNIGEVNALVLLDDEGFN 1zjjA 60 :DVSSSIIITSGLATRLYMSKHLDPGKIFVIGGEGLVKEMQALGWGIVTLDEARQGSWKEVKHVVVGLDPDLT T0371 147 :HDLNKTVNLLRKRTIPAIVANTDNTYPLTKT 1zjjA 132 :YEKLKYATLAIRNGATFIGTNPDATLPGEEG T0371 179 :VAIAIGGVATMIESILGRRFIRFGKPDSQMFMFAYDML 1zjjA 163 :IYPGAGSIIAALKVATNVEPIIIGKPNEPMYEVVREMF T0371 223 :SKREILMVGDTLHTDILGGNKFGLDTALVLTGNTRIDDAE 1zjjA 201 :PGEELWMVGDRLDTDIAFAKKFGMKAIMVLTGVSSLEDIK T0371 267 :STGIVPTHICES 1zjjA 241 :KSEYKPDLVLPS T0371 280 :VIEL 1zjjA 253 :VYEL Number of specific fragments extracted= 7 number of extra gaps= 0 total=578 Number of alignments=41 # 1zjjA read from 1zjjA/merged-good-all-a2m # found chain 1zjjA in template set T0371 15 :CIFFDAFGVLKTYNGLLPGIENTFDYLKAQGQDYYIVTNDASRSPEQLADSYHKLGL 1zjjA 3 :AIIFDMDGVLYRGNRAIPGVRELIEFLKERGIPFAFLTNNSTKTPEMYREKLLKMGI T0371 73 :SITADKIISSGMITKEYIDLKVDGGIVAYLGTANSANYLVSDGIKMLPVSAIDDSNIGEVNALVLLDDEGFN 1zjjA 60 :DVSSSIIITSGLATRLYMSKHLDPGKIFVIGGEGLVKEMQALGWGIVTLDEARQGSWKEVKHVVVGLDPDLT T0371 147 :HDLNKTVNLLRKRTIPAIVANTDNTYPLTKT 1zjjA 132 :YEKLKYATLAIRNGATFIGTNPDATLPGEEG T0371 179 :VAIAIGGVATMIESILGRRFIRFGKPDSQMFMFAYDML 1zjjA 163 :IYPGAGSIIAALKVATNVEPIIIGKPNEPMYEVVREMF T0371 223 :SKREILMVGDTLHTDILGGNKFGLDTALVLTGNTRIDDAETKIKSTGIVPTHICESAV 1zjjA 201 :PGEELWMVGDRLDTDIAFAKKFGMKAIMVLTGVSSLEDIKKSEYKPDLVLPSVYELID Number of specific fragments extracted= 5 number of extra gaps= 0 total=583 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2go7A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2go7A expands to /projects/compbio/data/pdb/2go7.pdb.gz 2go7A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0371 read from 2go7A/merged-good-all-a2m # 2go7A read from 2go7A/merged-good-all-a2m # adding 2go7A to template set # found chain 2go7A in template set Warning: unaligning (T0371)F18 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2go7A)D9 Warning: unaligning (T0371)D19 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2go7A)D9 Warning: unaligning (T0371)V165 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2go7A)Y106 Warning: unaligning (T0371)A166 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2go7A)Y106 T0371 14 :KCIF 2go7A 4 :TAFI T0371 20 :AFGVLKTYNGLL 2go7A 10 :LDGTLLDSYEAI T0371 59 :PEQLADSYHKLGL 2go7A 22 :LSGIEETFAQFSI T0371 73 :SITADKI 2go7A 35 :PYDKEKV T0371 87 :KEYIDLK 2go7A 42 :REFIFKY T0371 103 :GTANSANYLV 2go7A 49 :SVQDLLVRVA T0371 113 :SDGIKM 2go7A 60 :DRNLDV T0371 126 :DSNIGEVNALVLLDDEGFNWFHDLNKTVNLLRKRTIPAI 2go7A 66 :EVLNQVRAQSLAEKNAQVVLMPGAREVLAWADESGIQQF T0371 167 :NTDNTYP 2go7A 107 :THKGNNA T0371 175 :TKTDVAIA 2go7A 114 :FTILKDLG T0371 186 :VATMIESILGRRFIRFGKPDSQMFMFAYDML 2go7A 122 :VESYFTEILTSQSGFVRKPSPEAATYLLDKY T0371 221 :EISKREILMVGDT 2go7A 153 :QLNSDNTYYIGDR T0371 235 :HTDILGGNKFGLDTAL 2go7A 166 :TLDVEFAQNSGIQSIN T0371 265 :IKSTGIVPTHICES 2go7A 182 :FLESTYEGNHRIQA T0371 280 :VIEL 2go7A 196 :LADI Number of specific fragments extracted= 15 number of extra gaps= 2 total=598 Number of alignments=43 # 2go7A read from 2go7A/merged-good-all-a2m # found chain 2go7A in template set Warning: unaligning (T0371)F18 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2go7A)D9 Warning: unaligning (T0371)D19 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2go7A)D9 Warning: unaligning (T0371)V165 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2go7A)Y106 Warning: unaligning (T0371)A166 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2go7A)Y106 T0371 14 :KCIF 2go7A 4 :TAFI T0371 20 :AFGVLKTYNGLL 2go7A 10 :LDGTLLDSYEAI T0371 32 :PGIENTFDYL 2go7A 23 :SGIEETFAQF T0371 45 :G 2go7A 33 :S T0371 55 :ASRSPEQLADSY 2go7A 34 :IPYDKEKVREFI T0371 91 :DLK 2go7A 46 :FKY T0371 103 :GTANSANYLVSD 2go7A 49 :SVQDLLVRVAED T0371 121 :VSAIDDSNIGEVNALVLLDDEGFNWFHDLNKTVNLLRKRTIPAI 2go7A 61 :RNLDVEVLNQVRAQSLAEKNAQVVLMPGAREVLAWADESGIQQF T0371 167 :NTDNTYP 2go7A 107 :THKGNNA T0371 175 :TKTDVAIAIGGVATMI 2go7A 114 :FTILKDLGVESYFTEI T0371 194 :LGRRFIRFGKPDSQMFMFAYDML 2go7A 130 :LTSQSGFVRKPSPEAATYLLDKY T0371 221 :EISKREILMVGDT 2go7A 153 :QLNSDNTYYIGDR T0371 235 :HTDILGGNKFGLDTALV 2go7A 166 :TLDVEFAQNSGIQSINF T0371 266 :KSTGIVPTHICES 2go7A 183 :LESTYEGNHRIQA T0371 280 :VIEL 2go7A 196 :LADI Number of specific fragments extracted= 15 number of extra gaps= 2 total=613 Number of alignments=44 # 2go7A read from 2go7A/merged-good-all-a2m # found chain 2go7A in template set Warning: unaligning (T0371)F18 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2go7A)D9 Warning: unaligning (T0371)D19 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2go7A)D9 Warning: unaligning (T0371)V165 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2go7A)Y106 Warning: unaligning (T0371)A166 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2go7A)Y106 T0371 14 :KCIF 2go7A 4 :TAFI T0371 20 :AFGVLKTYNGLLPG 2go7A 10 :LDGTLLDSYEAILS T0371 34 :IENTFDYL 2go7A 25 :IEETFAQF T0371 45 :GQD 2go7A 33 :SIP T0371 57 :RSPEQLADSYHKLGL 2go7A 36 :YDKEKVREFIFKYSV T0371 83 :GMITKEYIDLKVDG 2go7A 51 :QDLLVRVAEDRNLD T0371 104 :TANSANYLVS 2go7A 65 :VEVLNQVRAQ T0371 135 :LVLLDDEGFNWFHDLNKTVNLLRKRTIPAI 2go7A 75 :SLAEKNAQVVLMPGAREVLAWADESGIQQF T0371 167 :NT 2go7A 107 :TH T0371 182 :AIGGVATMIESIL 2go7A 109 :KGNNAFTILKDLG T0371 195 :GRRFIRFGKPDSQMFMFAYDML 2go7A 131 :TSQSGFVRKPSPEAATYLLDKY T0371 221 :EISKREILMVGDTLH 2go7A 153 :QLNSDNTYYIGDRTL T0371 237 :DILGGNKFGLDTAL 2go7A 168 :DVEFAQNSGIQSIN T0371 261 :AETKIKSTGIVPTHICESAV 2go7A 182 :FLESTYEGNHRIQALADISR Number of specific fragments extracted= 14 number of extra gaps= 2 total=627 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ys9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0371/1ys9A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0371/1ys9A/merged-good-all-a2m.gz for input Trying 1ys9A/merged-good-all-a2m Error: Couldn't open file 1ys9A/merged-good-all-a2m or 1ys9A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nrwA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0371 read from 1nrwA/merged-good-all-a2m # 1nrwA read from 1nrwA/merged-good-all-a2m # found chain 1nrwA in training set Warning: unaligning (T0371)Y13 because first residue in template chain is (1nrwA)M1 T0371 14 :KCIFFDAFGVLKTYNGLL 1nrwA 2 :KLIAIDLDGTLLNSKHQV T0371 32 :PGIENTFDYLKAQGQDYYIVT 1nrwA 21 :LENENALRQAQRDGIEVVVST T0371 56 :SRSPEQLADSYHKLGL 1nrwA 42 :GRAHFDVMSIFEPLGI T0371 73 :SIT 1nrwA 58 :KTW T0371 79 :IISSGMITKEYI 1nrwA 61 :VISANGAVIHDP T0371 91 :DLKVDGGIVAYLGTANSANYLVSDGI 1nrwA 74 :GRLYHHETIDKKRAYDILSWLESENY T0371 117 :KMLPVSAIDDSNIGEVNALVLLDDE 1nrwA 108 :AIYTPQNGRELLDVELDRFRSANPE T0371 143 :FN 1nrwA 133 :AD T0371 146 :FHDLNKTVNLLRKR 1nrwA 135 :LSVLKQAAEVQYSQ T0371 174 :LTKTDVAIAIG 1nrwA 154 :INSFQELFEAD T0371 185 :GVATMIESILGRRFIR 1nrwA 181 :KLEAGWKRYEHAEDLT T0371 201 :FGK 1nrwA 212 :ASK T0371 206 :SQMFMFAYDML 1nrwA 215 :GQALKRLAKQL T0371 221 :EISKREILMVGDT 1nrwA 226 :NIPLEETAAVGDS T0371 235 :HTDILGGNKFGLDTA 1nrwA 239 :LNDKSMLEAAGKGVA T0371 254 :GNTRIDDAETK 1nrwA 254 :MGNAREDIKSI T0371 272 :PTHICE 1nrwA 265 :ADAVTL Number of specific fragments extracted= 17 number of extra gaps= 0 total=644 Number of alignments=46 # 1nrwA read from 1nrwA/merged-good-all-a2m # found chain 1nrwA in training set Warning: unaligning (T0371)Y13 because first residue in template chain is (1nrwA)M1 T0371 14 :KCIFFDAFGVLKTYNGLL 1nrwA 2 :KLIAIDLDGTLLNSKHQV T0371 32 :PGIENTFDYLKAQGQDYYIVTNDA 1nrwA 21 :LENENALRQAQRDGIEVVVSTGRA T0371 59 :PEQLADSYHKLGL 1nrwA 45 :HFDVMSIFEPLGI T0371 73 :SI 1nrwA 58 :KT T0371 78 :KIISSGMITKEYIDLKVDGGIVAYLGTANSANYLVSDGIKM 1nrwA 61 :VISANGAVIHDPEGRLYHHETIDKKRAYDILSWLESENYYY T0371 119 :LPVSAIDDSNIGEVNALVLLDDEGFN 1nrwA 109 :IYTPQNGRELLDVELDRFRSANPEAD T0371 146 :FHDLNKTVNLLRKRT 1nrwA 135 :LSVLKQAAEVQYSQS T0371 161 :IPAIVANTDNTYPLTKTDVAIAIGGVATMI 1nrwA 169 :FYNILGFSFFKEKLEAGWKRYEHAEDLTLV T0371 194 :LGRRFIR 1nrwA 199 :SSAEHNF T0371 201 :FGKPD 1nrwA 209 :SRKAS T0371 209 :FMFAYDMLRQKMEISKREILMVGDTLH 1nrwA 214 :KGQALKRLAKQLNIPLEETAAVGDSLN T0371 237 :DILGGNKFG 1nrwA 241 :DKSMLEAAG T0371 247 :DTALVL 1nrwA 250 :KGVAMG T0371 256 :TRIDDAETK 1nrwA 256 :NAREDIKSI T0371 272 :PTHICE 1nrwA 265 :ADAVTL Number of specific fragments extracted= 15 number of extra gaps= 0 total=659 Number of alignments=47 # 1nrwA read from 1nrwA/merged-good-all-a2m # found chain 1nrwA in training set Warning: unaligning (T0371)Y13 because first residue in template chain is (1nrwA)M1 T0371 14 :KCIFFDAFGVLKTYNG 1nrwA 2 :KLIAIDLDGTLLNSKH T0371 30 :LLPGIENTFDYLKAQGQDYYIVTNDA 1nrwA 19 :VSLENENALRQAQRDGIEVVVSTGRA T0371 59 :PEQLADSYHKLGL 1nrwA 45 :HFDVMSIFEPLGI T0371 98 :IVAYLG 1nrwA 58 :KTWVIS T0371 132 :VNALVLLDDEG 1nrwA 64 :ANGAVIHDPEG T0371 144 :NWF 1nrwA 75 :RLY T0371 147 :HDLNKTVNLLRKRTIPAIVANTDNTYPLTKTDVAIAI 1nrwA 85 :KRAYDILSWLESENYYYEVFTGSAIYTPQNGRELLDV T0371 186 :VATMIESIL 1nrwA 122 :ELDRFRSAN T0371 206 :SQMFMFAYDML 1nrwA 179 :KEKLEAGWKRY T0371 220 :MEISKREILMVGDTLH 1nrwA 225 :LNIPLEETAAVGDSLN T0371 237 :DILGGNKFG 1nrwA 241 :DKSMLEAAG T0371 247 :DT 1nrwA 250 :KG T0371 251 :VLTGNTRID 1nrwA 252 :VAMGNARED T0371 261 :AETK 1nrwA 261 :IKSI T0371 268 :TGIVPTHICE 1nrwA 265 :ADAVTLTNDE Number of specific fragments extracted= 15 number of extra gaps= 0 total=674 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yv9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0371/1yv9A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0371/1yv9A/merged-good-all-a2m.gz for input Trying 1yv9A/merged-good-all-a2m Error: Couldn't open file 1yv9A/merged-good-all-a2m or 1yv9A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rdfA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1rdfA expands to /projects/compbio/data/pdb/1rdf.pdb.gz 1rdfA:# T0371 read from 1rdfA/merged-good-all-a2m # 1rdfA read from 1rdfA/merged-good-all-a2m # adding 1rdfA to template set # found chain 1rdfA in template set Warning: unaligning (T0371)K12 because first residue in template chain is (1rdfA)K5 Warning: unaligning (T0371)S223 because of BadResidue code BAD_PEPTIDE at template residue (1rdfA)P177 T0371 13 :YKCIFFDAFGVLKTYNGLL 1rdfA 6 :IEAVIFDWAGTTVDYGCFA T0371 59 :PEQLADSYHKLGL 1rdfA 26 :LEVFMEIFHKRGV T0371 73 :SITADKII 1rdfA 39 :AITAEEAR T0371 97 :GIVA 1rdfA 47 :KPMP T0371 101 :YLGTANSANYLVSDGIKMLPVSAIDDSNIGEVNALVLLDDEGFNWFHDLNKTVNLLRKRTIPAIVANT 1rdfA 60 :LTEMPRIASEWNRVFRQLPTEADIQEMYEEFEEILFAILPRYASPINAVKEVIASLRERGIKIGSTTG T0371 174 :LTKTDVAI 1rdfA 128 :YTREMMDI T0371 186 :VATMIES 1rdfA 136 :VAKEAAL T0371 195 :GRRFIRFGKPDSQMFMFAYDML 1rdfA 152 :TPDDVPAGRPYPWMCYKNAMEL T0371 221 :EI 1rdfA 174 :GV T0371 224 :KREILMVGDT 1rdfA 178 :MNHMIKVGDT T0371 235 :HTDILGGNKFGLDTALVLTGNTR 1rdfA 188 :VSDMKEGRNAGMWTVGVILGSSE T0371 258 :IDDAETKIKSTG 1rdfA 230 :IEVVRNRFVENG T0371 272 :PTHICES 1rdfA 242 :AHFTIET T0371 280 :VIEL 1rdfA 249 :MQEL Number of specific fragments extracted= 14 number of extra gaps= 1 total=688 Number of alignments=49 # 1rdfA read from 1rdfA/merged-good-all-a2m # found chain 1rdfA in template set Warning: unaligning (T0371)P11 because first residue in template chain is (1rdfA)K5 Warning: unaligning (T0371)S223 because of BadResidue code BAD_PEPTIDE at template residue (1rdfA)P177 T0371 13 :YKCIFFDAFGVLKTYNGLL 1rdfA 6 :IEAVIFDWAGTTVDYGCFA T0371 59 :PEQLADSYHKLGL 1rdfA 26 :LEVFMEIFHKRGV T0371 73 :SITADKIISSG 1rdfA 39 :AITAEEARKPM T0371 91 :DLKVDGGIVAYLGTANSANYLVSDGIKMLPVSAIDDSNIGEVNALVLLDDEGFNWFHDLNKTVNLLRKRTIPAIVANTDNTYPLTKTDVAIAIGGVA 1rdfA 50 :PLLKIDHVRALTEMPRIASEWNRVFRQLPTEADIQEMYEEFEEILFAILPRYASPINAVKEVIASLRERGIKIGSTTGYTREMMDIVAKEAALQGYK T0371 188 :TMI 1rdfA 148 :DFL T0371 194 :LGRRFIRFGKPDSQMFMFAYDML 1rdfA 151 :VTPDDVPAGRPYPWMCYKNAMEL T0371 221 :EI 1rdfA 174 :GV T0371 224 :KREILMVGDTLH 1rdfA 178 :MNHMIKVGDTVS T0371 237 :DILGGNKFGLDTALVLTGNTR 1rdfA 190 :DMKEGRNAGMWTVGVILGSSE T0371 258 :IDDAETKIKSTG 1rdfA 230 :IEVVRNRFVENG T0371 272 :PTHICES 1rdfA 242 :AHFTIET T0371 280 :VIEL 1rdfA 249 :MQEL Number of specific fragments extracted= 12 number of extra gaps= 1 total=700 Number of alignments=50 # 1rdfA read from 1rdfA/merged-good-all-a2m # found chain 1rdfA in template set Warning: unaligning (T0371)K12 because first residue in template chain is (1rdfA)K5 Warning: unaligning (T0371)S223 because of BadResidue code BAD_PEPTIDE at template residue (1rdfA)P177 T0371 13 :YKCIFFDAFGVLKTYNGLLP 1rdfA 6 :IEAVIFDWAGTTVDYGCFAP T0371 59 :PEQLADSYHKLGL 1rdfA 26 :LEVFMEIFHKRGV T0371 73 :SITADKIISSG 1rdfA 39 :AITAEEARKPM T0371 94 :VD 1rdfA 50 :PL T0371 100 :AYLGTANSANYLVSDGIKMLPVSAIDDSNIGEVNALVLLDDEGFNWFHDLNKTVNLLRKRTIPAIVANT 1rdfA 59 :ALTEMPRIASEWNRVFRQLPTEADIQEMYEEFEEILFAILPRYASPINAVKEVIASLRERGIKIGSTTG T0371 181 :IAIGGVATMIESIL 1rdfA 128 :YTREMMDIVAKEAA T0371 195 :GRRFIRFGKPDSQMFMFAYDML 1rdfA 152 :TPDDVPAGRPYPWMCYKNAMEL T0371 221 :EI 1rdfA 174 :GV T0371 224 :KREILMVGDTLH 1rdfA 178 :MNHMIKVGDTVS T0371 237 :DILGGNKFGLDTALVLTG 1rdfA 190 :DMKEGRNAGMWTVGVILG T0371 255 :NTRIDDAE 1rdfA 212 :GLTEEEVE T0371 266 :KSTGIVPTHICESAV 1rdfA 240 :NGAHFTIETMQELES Number of specific fragments extracted= 12 number of extra gaps= 1 total=712 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fdrA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fdrA expands to /projects/compbio/data/pdb/2fdr.pdb.gz 2fdrA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 600, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 602, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 604, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 606, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 608, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 610, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 612, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 614, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 616, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 618, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 620, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 709, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 711, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 713, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 715, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 717, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 719, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 721, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 723, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 725, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 751, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 753, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 755, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 757, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 759, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 761, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 763, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 765, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 767, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 769, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 771, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 773, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 775, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 777, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 779, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 781, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 783, because occupancy 0.500 <= existing 0.500 in 2fdrA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1330, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 1332, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 1334, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 1336, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 1338, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 1340, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 1342, because occupancy 0.500 <= existing 0.500 in 2fdrA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0371 read from 2fdrA/merged-good-all-a2m # 2fdrA read from 2fdrA/merged-good-all-a2m # adding 2fdrA to template set # found chain 2fdrA in template set Warning: unaligning (T0371)K12 because first residue in template chain is (2fdrA)G3 Warning: unaligning (T0371)F18 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fdrA)D10 Warning: unaligning (T0371)D19 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fdrA)D10 T0371 13 :YKCIF 2fdrA 4 :FDLII T0371 20 :AFGVLKTYNGLL 2fdrA 11 :CDGVLVDSEIIA T0371 59 :PEQLADSYHKLGL 2fdrA 23 :AQVESRLLTEAGY T0371 73 :SITADKII 2fdrA 36 :PISVEEMG T0371 97 :GIVAYLGTANSANYLV 2fdrA 44 :ERFAGMTWKNILLQVE T0371 113 :SDGI 2fdrA 61 :EASI T0371 122 :SAIDDSNIGEVNALVLLDDEGFNWFHDLNKTVNLL 2fdrA 65 :PLSASLLDKSEKLLDMRLERDVKIIDGVKFALSRL T0371 160 :TIPA 2fdrA 100 :TTPR T0371 164 :IVANTDNTY 2fdrA 105 :ICSNSSSHR T0371 174 :LTKTDVAIA 2fdrA 114 :LDMMLTKVG T0371 186 :VATMI 2fdrA 123 :LKPYF T0371 192 :SILGRRFIRFG 2fdrA 130 :HIYSAKDLGAD T0371 203 :KPDSQMFMFAYDML 2fdrA 143 :KPKPDIFLHGAAQF T0371 221 :EISKREILMVGDT 2fdrA 157 :GVSPDRVVVVEDS T0371 235 :HTDILGGNKFGLDTALVLTGNTRIDDAETKIKSTG 2fdrA 170 :VHGIHGARAAGMRVIGFTGASHTYPSHADRLTDAG T0371 272 :PTHICES 2fdrA 205 :AETVISR T0371 280 :VIEL 2fdrA 212 :MQDL Number of specific fragments extracted= 17 number of extra gaps= 1 total=729 Number of alignments=52 # 2fdrA read from 2fdrA/merged-good-all-a2m # found chain 2fdrA in template set Warning: unaligning (T0371)K12 because first residue in template chain is (2fdrA)G3 Warning: unaligning (T0371)F18 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fdrA)D10 Warning: unaligning (T0371)D19 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fdrA)D10 T0371 13 :YKCIF 2fdrA 4 :FDLII T0371 20 :AFGVLKTYN 2fdrA 11 :CDGVLVDSE T0371 32 :PGIENTF 2fdrA 20 :IIAAQVE T0371 39 :DYLKAQGQD 2fdrA 28 :RLLTEAGYP T0371 57 :RSPEQLADSY 2fdrA 37 :ISVEEMGERF T0371 100 :AYLGTANSANYLV 2fdrA 47 :AGMTWKNILLQVE T0371 113 :SDGIKML 2fdrA 61 :EASIPLS T0371 126 :DSNIGEVNALVL 2fdrA 68 :ASLLDKSEKLLD T0371 138 :LDDEGFNWFHDLNKTVNLL 2fdrA 81 :RLERDVKIIDGVKFALSRL T0371 160 :TIPAIVANTDNTYPLTKTDVAIAIGGVAT 2fdrA 100 :TTPRCICSNSSSHRLDMMLTKVGLKPYFA T0371 191 :ESILGRRFIR 2fdrA 129 :PHIYSAKDLG T0371 201 :FGKPDSQMFMFAYDML 2fdrA 141 :RVKPKPDIFLHGAAQF T0371 221 :EISKREILMVGDTLH 2fdrA 157 :GVSPDRVVVVEDSVH T0371 237 :DILGGNKFGLDTALVLTGNTRIDDAETKIKSTG 2fdrA 172 :GIHGARAAGMRVIGFTGASHTYPSHADRLTDAG T0371 272 :PTHICES 2fdrA 205 :AETVISR T0371 280 :VIEL 2fdrA 212 :MQDL Number of specific fragments extracted= 16 number of extra gaps= 1 total=745 Number of alignments=53 # 2fdrA read from 2fdrA/merged-good-all-a2m # found chain 2fdrA in template set Warning: unaligning (T0371)K12 because first residue in template chain is (2fdrA)G3 Warning: unaligning (T0371)F18 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fdrA)D10 Warning: unaligning (T0371)D19 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fdrA)D10 T0371 13 :YKCIF 2fdrA 4 :FDLII T0371 20 :AFGVLKTYN 2fdrA 11 :CDGVLVDSE T0371 31 :LPGIENTFDYLKAQGQDY 2fdrA 20 :IIAAQVESRLLTEAGYPI T0371 55 :ASRSPEQLADSYHKLGLFSITADKIISSGMITKEYIDL 2fdrA 47 :AGMTWKNILLQVESEASIPLSASLLDKSEKLLDMRLER T0371 142 :GFNWFHDLNKTVNLL 2fdrA 85 :DVKIIDGVKFALSRL T0371 161 :IPAIVANTD 2fdrA 101 :TPRCICSNS T0371 182 :AIGGVATMIESIL 2fdrA 110 :SSHRLDMMLTKVG T0371 195 :GRRF 2fdrA 138 :GADR T0371 202 :GKPDSQMFMFAYDML 2fdrA 142 :VKPKPDIFLHGAAQF T0371 221 :EISKREILMVGDTLH 2fdrA 157 :GVSPDRVVVVEDSVH T0371 237 :DILGGNKFGLDTALVLTGNTRIDDAE 2fdrA 172 :GIHGARAAGMRVIGFTGASHTYPSHA T0371 263 :T 2fdrA 202 :D T0371 266 :KSTGIVPTHICESA 2fdrA 203 :AGAETVISRMQDLP Number of specific fragments extracted= 13 number of extra gaps= 1 total=758 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lvhA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1lvhA expands to /projects/compbio/data/pdb/1lvh.pdb.gz 1lvhA:Bad short name: P for alphabet: pdb_atoms Bad short name: OP1 for alphabet: pdb_atoms Bad short name: OP2 for alphabet: pdb_atoms Bad short name: OP3 for alphabet: pdb_atoms # T0371 read from 1lvhA/merged-good-all-a2m # 1lvhA read from 1lvhA/merged-good-all-a2m # adding 1lvhA to template set # found chain 1lvhA in template set Warning: unaligning (T0371)K12 because first residue in template chain is (1lvhA)M1 Warning: unaligning (T0371)F18 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1lvhA)L9 Warning: unaligning (T0371)A20 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1lvhA)L9 T0371 13 :YKCIF 1lvhA 2 :FKAVL T0371 21 :FGVLKTYNGLL 1lvhA 10 :DGVITDTAEYH T0371 59 :PEQLADSYHKLGLFSITADKI 1lvhA 21 :FRAWKALAEEIGINGVDRQFN T0371 97 :GIVAYLGTANSANYLVSD 1lvhA 42 :EQLKGVSREDSLQKILDL T0371 115 :GIKMLP 1lvhA 61 :DKKVSA T0371 122 :SAIDDSNIGEVNALVLLDDE 1lvhA 67 :EEFKELAKRKNDNYVKMIQD T0371 142 :G 1lvhA 89 :P T0371 145 :WFHDLNKTVNLLRKRTIPAIVANTDNTY 1lvhA 92 :VYPGILQLLKDLRSNKIKIALASASKNG T0371 175 :TKTDVAIA 1lvhA 120 :PFLLERMN T0371 186 :VATMIESILGRRFIRFGKPDSQMFMFAYDML 1lvhA 128 :LTGYFDAIADPAEVAASKPAPDIFIAAAHAV T0371 221 :EISKREILMVGDT 1lvhA 159 :GVAPSESIGLEDS T0371 235 :HTDILGGNKFGLDTALVL 1lvhA 172 :QAGIQAIKDSGALPIGVG T0371 257 :RIDD 1lvhA 190 :RPED T0371 265 :IKS 1lvhA 194 :LGD T0371 272 :PTHICES 1lvhA 197 :DIVIVPD T0371 280 :VIEL 1lvhA 204 :TSHY Number of specific fragments extracted= 16 number of extra gaps= 0 total=774 Number of alignments=55 # 1lvhA read from 1lvhA/merged-good-all-a2m # found chain 1lvhA in template set Warning: unaligning (T0371)K12 because first residue in template chain is (1lvhA)M1 Warning: unaligning (T0371)F18 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1lvhA)L9 Warning: unaligning (T0371)A20 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1lvhA)L9 T0371 13 :YKCIF 1lvhA 2 :FKAVL T0371 21 :FGVLKTYNGLL 1lvhA 10 :DGVITDTAEYH T0371 32 :PGIENTF 1lvhA 22 :RAWKALA T0371 42 :KAQGQD 1lvhA 29 :EEIGIN T0371 55 :ASRSPEQLADSYHKLGLFSITADK 1lvhA 45 :KGVSREDSLQKILDLADKKVSAEE T0371 104 :TANSA 1lvhA 69 :FKELA T0371 130 :GEVNALVLLDDEGFN 1lvhA 74 :KRKNDNYVKMIQDVS T0371 145 :WFHDLNKTVNLLRKRTIPAIVANTDNTY 1lvhA 92 :VYPGILQLLKDLRSNKIKIALASASKNG T0371 175 :TKTDVAIAIGGVATMI 1lvhA 120 :PFLLERMNLTGYFDAI T0371 194 :LGRRFIRFGKPDSQMFMFAYDML 1lvhA 136 :ADPAEVAASKPAPDIFIAAAHAV T0371 221 :EISKREILMVGDTLH 1lvhA 159 :GVAPSESIGLEDSQA T0371 237 :DILGGNKFGLDTALV 1lvhA 174 :GIQAIKDSGALPIGV T0371 256 :TRIDDAET 1lvhA 189 :GRPEDLGD T0371 272 :PTHICES 1lvhA 197 :DIVIVPD T0371 280 :VIE 1lvhA 204 :TSH Number of specific fragments extracted= 15 number of extra gaps= 0 total=789 Number of alignments=56 # 1lvhA read from 1lvhA/merged-good-all-a2m # found chain 1lvhA in template set Warning: unaligning (T0371)F18 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1lvhA)L9 Warning: unaligning (T0371)A20 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1lvhA)L9 T0371 13 :YKCIF 1lvhA 2 :FKAVL T0371 21 :FGVLKTY 1lvhA 10 :DGVITDT T0371 31 :LPGIENTFDYLK 1lvhA 17 :AEYHFRAWKALA T0371 43 :AQGQD 1lvhA 30 :EIGIN T0371 55 :ASRSPEQLADSYHKLGLFSITADKIISSGMITKEYIDLKVDGG 1lvhA 45 :KGVSREDSLQKILDLADKKVSAEEFKELAKRKNDNYVKMIQDV T0371 141 :EGFNWFHDLNKTVNLLRKRTIPAIVANT 1lvhA 88 :SPADVYPGILQLLKDLRSNKIKIALASA T0371 174 :LTKT 1lvhA 116 :SKNG T0371 187 :ATMIESIL 1lvhA 120 :PFLLERMN T0371 195 :GRRFIRFGKPDSQMFMFAYDML 1lvhA 137 :DPAEVAASKPAPDIFIAAAHAV T0371 221 :EISKREILMVGDTLH 1lvhA 159 :GVAPSESIGLEDSQA T0371 237 :DILGGNKFGLDTALV 1lvhA 174 :GIQAIKDSGALPIGV T0371 256 :TRIDDAETKI 1lvhA 189 :GRPEDLGDDI T0371 270 :IVPTHICE 1lvhA 199 :VIVPDTSH Number of specific fragments extracted= 13 number of extra gaps= 0 total=802 Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f5sA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1f5sA expands to /projects/compbio/data/pdb/1f5s.pdb.gz 1f5sA:Skipped atom 82, because occupancy 0.500 <= existing 0.500 in 1f5sA Skipped atom 84, because occupancy 0.500 <= existing 0.500 in 1f5sA Skipped atom 86, because occupancy 0.500 <= existing 0.500 in 1f5sA Skipped atom 88, because occupancy 0.500 <= existing 0.500 in 1f5sA Skipped atom 90, because occupancy 0.500 <= existing 0.500 in 1f5sA Skipped atom 92, because occupancy 0.500 <= existing 0.500 in 1f5sA Skipped atom 94, because occupancy 0.500 <= existing 0.500 in 1f5sA Skipped atom 96, because occupancy 0.500 <= existing 0.500 in 1f5sA # T0371 read from 1f5sA/merged-good-all-a2m # 1f5sA read from 1f5sA/merged-good-all-a2m # adding 1f5sA to template set # found chain 1f5sA in template set T0371 11 :PKYKCIFFDAFGVLKTYN 1f5sA 3 :KKKKLILFDFDSTLVNNE T0371 61 :QLADSYHKLGL 1f5sA 21 :TIDEIAREAGV T0371 76 :ADKI 1f5sA 32 :EEEV T0371 83 :GMITKEYIDLKV 1f5sA 36 :KKITKEAMEGKL T0371 103 :GTANSANYLVSD 1f5sA 48 :NFEQSLRKRVSL T0371 115 :GIKM 1f5sA 62 :DLPI T0371 130 :GEVNALVL 1f5sA 66 :EKVEKAIK T0371 142 :GFNWFHDLNKTVNLLRKRTIPA 1f5sA 74 :RITPTEGAEETIKELKNRGYVV T0371 164 :IVANT 1f5sA 97 :VVSGG T0371 174 :L 1f5sA 102 :F T0371 183 :IGGVATMIES 1f5sA 103 :DIAVNKIKEK T0371 194 :LGRRFIR 1f5sA 113 :LGLDYAF T0371 203 :K 1f5sA 144 :K T0371 206 :SQMFMFAYDML 1f5sA 145 :GEILEKIAKIE T0371 221 :EISKREILMVGDT 1f5sA 156 :GINLEDTVAVGDG T0371 235 :HTDILGGNKFGLDTAL 1f5sA 169 :ANDISMFKKAGLKIAF T0371 256 :TRIDD 1f5sA 185 :CAKPI T0371 265 :IKST 1f5sA 190 :LKEK T0371 272 :PTHICESA 1f5sA 194 :ADICIEKR T0371 280 :VIEL 1f5sA 203 :LREI Number of specific fragments extracted= 20 number of extra gaps= 0 total=822 Number of alignments=58 # 1f5sA read from 1f5sA/merged-good-all-a2m # found chain 1f5sA in template set T0371 11 :PKYKCIFFDAFGVLKTYN 1f5sA 3 :KKKKLILFDFDSTLVNNE T0371 37 :TFDYLKAQ 1f5sA 21 :TIDEIARE T0371 45 :GQ 1f5sA 30 :GV T0371 59 :PEQLADSYHKLGLFSITAD 1f5sA 32 :EEEVKKITKEAMEGKLNFE T0371 105 :ANSANYLV 1f5sA 51 :QSLRKRVS T0371 123 :AIDDSNIGEVNALVL 1f5sA 59 :LLKDLPIEKVEKAIK T0371 142 :GFNWFHDLNKTVNLLRKRTIPAIVANTDNTYPLTKTDVAIAI 1f5sA 74 :RITPTEGAEETIKELKNRGYVVAVVSGGFDIAVNKIKEKLGL T0371 191 :ESI 1f5sA 116 :DYA T0371 194 :LGRRFIRF 1f5sA 130 :LTGDVEGE T0371 203 :KPDSQMFMFAYDMLRQKMEISKREILMVGDTLH 1f5sA 138 :VLKENAKGEILEKIAKIEGINLEDTVAVGDGAN T0371 237 :DILGGNKFG 1f5sA 171 :DISMFKKAG T0371 247 :DTALV 1f5sA 180 :LKIAF T0371 256 :TRIDDAETK 1f5sA 185 :CAKPILKEK T0371 272 :PTHICESA 1f5sA 194 :ADICIEKR T0371 280 :VIEL 1f5sA 203 :LREI Number of specific fragments extracted= 15 number of extra gaps= 0 total=837 Number of alignments=59 # 1f5sA read from 1f5sA/merged-good-all-a2m # found chain 1f5sA in template set T0371 14 :KCIFFDAFGVLKTYNGLLPGI 1f5sA 6 :KLILFDFDSTLVNNETIDEIA T0371 42 :KAQG 1f5sA 27 :REAG T0371 58 :SPEQLADSYHKLGLFSIT 1f5sA 31 :VEEEVKKITKEAMEGKLN T0371 82 :SGMITKEYIDLK 1f5sA 49 :FEQSLRKRVSLL T0371 125 :DDSNIGEVNALV 1f5sA 61 :KDLPIEKVEKAI T0371 141 :EGFNWFHDLNKTVNLLRKRTIPAIVANTD 1f5sA 73 :KRITPTEGAEETIKELKNRGYVVAVVSGG T0371 186 :VATMIESIL 1f5sA 102 :FDIAVNKIK T0371 195 :GRRFIR 1f5sA 135 :EGEVLK T0371 205 :DSQMFMFAYDML 1f5sA 144 :KGEILEKIAKIE T0371 221 :EISKREILMVGDTLH 1f5sA 156 :GINLEDTVAVGDGAN T0371 237 :DILGGNKFGLDTAL 1f5sA 171 :DISMFKKAGLKIAF T0371 256 :TRIDDAET 1f5sA 185 :CAKPILKE T0371 267 :STGIVPT 1f5sA 193 :KADICIE T0371 274 :HICESAVI 1f5sA 202 :DLREILKY Number of specific fragments extracted= 14 number of extra gaps= 0 total=851 Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b8eA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2b8eA expands to /projects/compbio/data/pdb/2b8e.pdb.gz 2b8eA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0371 read from 2b8eA/merged-good-all-a2m # 2b8eA read from 2b8eA/merged-good-all-a2m # adding 2b8eA to template set # found chain 2b8eA in template set Warning: unaligning (T0371)Y101 because of BadResidue code BAD_PEPTIDE in next template residue (2b8eA)D496 Warning: unaligning (T0371)L102 because of BadResidue code BAD_PEPTIDE at template residue (2b8eA)D496 Warning: unaligning (T0371)G103 because of BadResidue code BAD_PEPTIDE at template residue (2b8eA)G497 Warning: unaligning (T0371)H235 because of BadResidue code BAD_PEPTIDE in next template residue (2b8eA)N621 Warning: unaligning (T0371)T236 because of BadResidue code BAD_PEPTIDE at template residue (2b8eA)N621 Warning: unaligning (T0371)D237 because of BadResidue code BAD_PEPTIDE at template residue (2b8eA)D622 Warning: unaligning (T0371)V251 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b8eA)S645 Warning: unaligning (T0371)L252 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b8eA)S645 T0371 12 :KYKCIFFDAFGVLKTYNG 2b8eA 417 :KVTAVIFDKTGTLTKGKP T0371 30 :LL 2b8eA 441 :PL T0371 32 :PGIENTFDYLK 2b8eA 444 :GDERELLRLAA T0371 59 :PEQLADSYHKLGL 2b8eA 465 :AEAIVKKALEHGI T0371 73 :SITA 2b8eA 478 :ELGE T0371 77 :DKI 2b8eA 483 :EKV T0371 92 :LKVDGGIVA 2b8eA 486 :EVIAGEGVV T0371 108 :ANYLVSDGIKM 2b8eA 503 :KRLMEDFGVAV T0371 122 :SAIDDSNI 2b8eA 514 :SNEVELAL T0371 135 :LVLLDDE 2b8eA 532 :VIVARNG T0371 142 :GFNWFHDLNKTVNLLRKRTIPA 2b8eA 547 :SDTLKESAKPAVQELKRMGIKV T0371 164 :IVANT 2b8eA 570 :MITGD T0371 174 :L 2b8eA 575 :N T0371 184 :GGVATMIESILGRRFIRFG 2b8eA 576 :WRSAEAISRELNLDLVIAE T0371 206 :SQMFMFAYDMLRQ 2b8eA 597 :PHQKSEEVKKLQA T0371 221 :E 2b8eA 610 :K T0371 225 :REILMVGDT 2b8eA 611 :EVVAFVGDG T0371 238 :ILGGNKFGLDTAL 2b8eA 623 :APALAQADLGIAV T0371 253 :T 2b8eA 646 :G T0371 273 :THIC 2b8eA 647 :DIVL T0371 277 :ES 2b8eA 653 :DD T0371 280 :VIE 2b8eA 655 :LRD Number of specific fragments extracted= 22 number of extra gaps= 3 total=873 Number of alignments=61 # 2b8eA read from 2b8eA/merged-good-all-a2m # found chain 2b8eA in template set Warning: unaligning (T0371)L234 because of BadResidue code BAD_PEPTIDE in next template residue (2b8eA)N621 Warning: unaligning (T0371)H235 because of BadResidue code BAD_PEPTIDE at template residue (2b8eA)N621 Warning: unaligning (T0371)D237 because of BadResidue code BAD_PEPTIDE at template residue (2b8eA)D622 Warning: unaligning (T0371)L252 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b8eA)S645 Warning: unaligning (T0371)T253 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b8eA)S645 T0371 8 :SLLPKYKCIFFDAFGVLKT 2b8eA 413 :EVAEKVTAVIFDKTGTLTK T0371 27 :YNGLL 2b8eA 460 :SEHPI T0371 59 :PEQLADSYHKLGL 2b8eA 465 :AEAIVKKALEHGI T0371 73 :SIT 2b8eA 478 :ELG T0371 120 :PVSAIDDSNI 2b8eA 481 :EPEKVEVIAG T0371 130 :GEVNALVLLD 2b8eA 538 :GRVEGIIAVS T0371 143 :FNWFHDLNKTVNLLRKRTIPAIVANTDNTYPLTKTDVAIAIG 2b8eA 548 :DTLKESAKPAVQELKRMGIKVGMITGDNWRSAEAISRELNLD T0371 189 :MI 2b8eA 590 :LV T0371 194 :LG 2b8eA 592 :IA T0371 203 :KPDSQMFMFAYDMLRQ 2b8eA 594 :EVLPHQKSEEVKKLQA T0371 221 :EI 2b8eA 610 :KE T0371 226 :EILMVGDT 2b8eA 612 :VVAFVGDG T0371 238 :ILGGNKFGL 2b8eA 623 :APALAQADL T0371 248 :TALV 2b8eA 632 :GIAV T0371 254 :G 2b8eA 646 :G T0371 273 :THIC 2b8eA 647 :DIVL T0371 277 :ES 2b8eA 653 :DD T0371 280 :VIE 2b8eA 655 :LRD Number of specific fragments extracted= 18 number of extra gaps= 2 total=891 Number of alignments=62 # 2b8eA read from 2b8eA/merged-good-all-a2m # found chain 2b8eA in template set Warning: unaligning (T0371)L234 because of BadResidue code BAD_PEPTIDE in next template residue (2b8eA)N621 Warning: unaligning (T0371)H235 because of BadResidue code BAD_PEPTIDE at template residue (2b8eA)N621 Warning: unaligning (T0371)D237 because of BadResidue code BAD_PEPTIDE at template residue (2b8eA)D622 Warning: unaligning (T0371)L252 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b8eA)S645 Warning: unaligning (T0371)T253 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b8eA)S645 T0371 7 :KSLLPKYKCIFFDAFGVLKTYNG 2b8eA 412 :LEVAEKVTAVIFDKTGTLTKGKP T0371 35 :ENTFDYLK 2b8eA 447 :RELLRLAA T0371 104 :TANSANYLVSDGIKMLPVS 2b8eA 465 :AEAIVKKALEHGIELGEPE T0371 123 :AIDDSNIGEVNALVLLDDEG 2b8eA 520 :ALEKLEREAKTAVIVARNGR T0371 143 :FNWFHDLNKTVNLLRKRTIPAIVANT 2b8eA 548 :DTLKESAKPAVQELKRMGIKVGMITG T0371 182 :AIGGVATMIESILGRRFIRFGKPDSQMFMFAYDML 2b8eA 574 :DNWRSAEAISRELNLDLVIAEVLPHQKSEEVKKLQ T0371 223 :SKREILMVGDT 2b8eA 609 :AKEVVAFVGDG T0371 239 :LGGNKFGLDTALV 2b8eA 623 :APALAQADLGIAV T0371 254 :G 2b8eA 646 :G T0371 269 :GIVP 2b8eA 647 :DIVL T0371 273 :THICESA 2b8eA 653 :DDLRDVV Number of specific fragments extracted= 11 number of extra gaps= 2 total=902 Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vj5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vj5A expands to /projects/compbio/data/pdb/1vj5.pdb.gz 1vj5A:# T0371 read from 1vj5A/merged-good-all-a2m # 1vj5A read from 1vj5A/merged-good-all-a2m # adding 1vj5A to template set # found chain 1vj5A in template set Warning: unaligning (T0371)K12 because first residue in template chain is (1vj5A)T2 T0371 13 :YKCIFFDAFGVLKTYNGLL 1vj5A 3 :LRAAVFDLDGVLALPAVFG T0371 61 :QLADSYHKLGL 1vj5A 22 :VLGRTEEALAL T0371 75 :TADKIISSG 1vj5A 33 :PRGLLNDAF T0371 84 :MITKEYI 1vj5A 48 :GATTRLM T0371 91 :DLK 1vj5A 56 :GEI T0371 103 :GTANSANYLVSD 1vj5A 59 :TLSQWIPLMEEN T0371 115 :GIKMLPVSAIDDSNIGEVNA 1vj5A 79 :KVCLPKNFSIKEIFDKAISA T0371 143 :FNWFHDLNKTVNLLRKRTIPA 1vj5A 99 :RKINRPMLQAALMLRKKGFTT T0371 164 :IVANTDN 1vj5A 121 :ILTNTWL T0371 175 :TKTDVAIA 1vj5A 128 :DDRAERDG T0371 186 :VATMIESI 1vj5A 136 :LAQLMCEL T0371 194 :LGRRFIRFGKPDSQMFMFAYDML 1vj5A 151 :IESCQVGMVKPEPQIYKFLLDTL T0371 221 :EISKREILMVGDT 1vj5A 174 :KASPSEVVFLDDI T0371 235 :HTDILGGNKFGLDTA 1vj5A 187 :GANLKPARDLGMVTI T0371 254 :GNTRIDDAETKIKS 1vj5A 202 :LVQDTDTALKELEK Number of specific fragments extracted= 15 number of extra gaps= 0 total=917 Number of alignments=64 # 1vj5A read from 1vj5A/merged-good-all-a2m # found chain 1vj5A in template set Warning: unaligning (T0371)P11 because first residue in template chain is (1vj5A)T2 T0371 13 :YKCIFFDAFGVLKT 1vj5A 3 :LRAAVFDLDGVLAL T0371 27 :YNGL 1vj5A 44 :GGPE T0371 32 :PGIENTF 1vj5A 48 :GATTRLM T0371 54 :DASRSPEQLADSY 1vj5A 55 :KGEITLSQWIPLM T0371 104 :TANSANYLVSDGIKMLPV 1vj5A 68 :EENCRKCSETAKVCLPKN T0371 130 :GEVNALVLLDDEGFNWFHDLNKTVNLLRKRTIPAIVANT 1vj5A 86 :FSIKEIFDKAISARKINRPMLQAALMLRKKGFTTAILTN T0371 169 :DNTYPLTKTDVAIA 1vj5A 131 :AERDGLAQLMCELK T0371 185 :GVATMI 1vj5A 145 :MHFDFL T0371 194 :LGRRFIRFGKPDSQMFMFAYDML 1vj5A 151 :IESCQVGMVKPEPQIYKFLLDTL T0371 221 :EISKREILMVGDT 1vj5A 174 :KASPSEVVFLDDI T0371 235 :HTDILGGNKFGLDTALV 1vj5A 187 :GANLKPARDLGMVTILV T0371 256 :TRIDDAETKIKS 1vj5A 204 :QDTDTALKELEK Number of specific fragments extracted= 12 number of extra gaps= 0 total=929 Number of alignments=65 # 1vj5A read from 1vj5A/merged-good-all-a2m # found chain 1vj5A in template set T0371 13 :YKCIFFDAFGVLKT 1vj5A 3 :LRAAVFDLDGVLAL T0371 27 :YNGLLPGIEN 1vj5A 19 :VFGVLGRTEE T0371 37 :TFDYLKAQG 1vj5A 36 :LLNDAFQKG T0371 55 :ASRSPEQLADSYHK 1vj5A 56 :GEITLSQWIPLMEE T0371 106 :NSANYLVSDGIKMLP 1vj5A 70 :NCRKCSETAKVCLPK T0371 129 :IGEVNALVLLDDEGFNWFHDLNKTVNLLRKRTIPAIVANT 1vj5A 85 :NFSIKEIFDKAISARKINRPMLQAALMLRKKGFTTAILTN T0371 171 :TYPLTKT 1vj5A 125 :TWLDDRA T0371 182 :AIGGVATMIESIL 1vj5A 132 :ERDGLAQLMCELK T0371 199 :IRFGKPDSQMFMFAYDML 1vj5A 156 :VGMVKPEPQIYKFLLDTL T0371 221 :EISKREILMVGDTLH 1vj5A 174 :KASPSEVVFLDDIGA T0371 237 :DILGGNKFGLDTALV 1vj5A 189 :NLKPARDLGMVTILV Number of specific fragments extracted= 11 number of extra gaps= 0 total=940 Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o08A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0371 read from 1o08A/merged-good-all-a2m # 1o08A read from 1o08A/merged-good-all-a2m # found chain 1o08A in training set Warning: unaligning (T0371)K12 because first residue in template chain is (1o08A)M1001 Warning: unaligning (T0371)F18 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o08A)D1008 Warning: unaligning (T0371)D19 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o08A)D1008 T0371 13 :YKCIF 1o08A 1002 :FKAVL T0371 20 :AFGVLKTYNGLL 1o08A 1009 :LDGVITDTAEYH T0371 59 :PEQLADSYHKLGLFSITADKI 1o08A 1021 :FRAWKALAEEIGINGVDRQFN T0371 97 :GIVAYLGTANSANYLVSDGIKMLPVSAIDDSNIGEVNALVLLDDE 1o08A 1042 :EQLKGVSREDSLQKILDLADKKVSAEEFKELAKRKNDNYVKMIQD T0371 142 :GFNWFHDLNKTVNLLRKRTIPAIVANTDNTY 1o08A 1089 :PADVYPGILQLLKDLRSNKIKIALASASKNG T0371 175 :TKTDVAIA 1o08A 1120 :PFLLERMN T0371 186 :VATMIESILGRRFIRFGKPDSQMFMFAYDML 1o08A 1128 :LTGYFDAIADPAEVAASKPAPDIFIAAAHAV T0371 221 :EISKREILMVGDT 1o08A 1159 :GVAPSESIGLEDS T0371 235 :HTDILGGNKFGLDTALVL 1o08A 1172 :QAGIQAIKDSGALPIGVG T0371 257 :RIDD 1o08A 1190 :RPED T0371 265 :IKS 1o08A 1194 :LGD T0371 272 :PTHICES 1o08A 1197 :DIVIVPD T0371 280 :VIEL 1o08A 1204 :TSHY Number of specific fragments extracted= 13 number of extra gaps= 1 total=953 Number of alignments=67 # 1o08A read from 1o08A/merged-good-all-a2m # found chain 1o08A in training set Warning: unaligning (T0371)K12 because first residue in template chain is (1o08A)M1001 Warning: unaligning (T0371)F18 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o08A)D1008 Warning: unaligning (T0371)D19 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o08A)D1008 T0371 13 :YKCIF 1o08A 1002 :FKAVL T0371 20 :AFGVLKTYN 1o08A 1009 :LDGVITDTA T0371 32 :PGIENTFDYL 1o08A 1018 :EYHFRAWKAL T0371 66 :YHKLGLFSITADKI 1o08A 1028 :AEEIGINGVDRQFN T0371 97 :GIVAYLGTANSANYLVSD 1o08A 1042 :EQLKGVSREDSLQKILDL T0371 121 :VSAIDDSNI 1o08A 1060 :ADKKVSAEE T0371 130 :GEVNALVLLDDEGFN 1o08A 1074 :KRKNDNYVKMIQDVS T0371 145 :WFHDLNKTVNLLRKRTIPAIVANTDNTY 1o08A 1092 :VYPGILQLLKDLRSNKIKIALASASKNG T0371 175 :TKTDVAIAIGGVATMI 1o08A 1120 :PFLLERMNLTGYFDAI T0371 194 :LGRRFIRFGKPDSQMFMFAYDML 1o08A 1136 :ADPAEVAASKPAPDIFIAAAHAV T0371 221 :EISKREILMVGDTLH 1o08A 1159 :GVAPSESIGLEDSQA T0371 237 :DILGGNKFGLDTALV 1o08A 1174 :GIQAIKDSGALPIGV T0371 256 :TRIDDAET 1o08A 1189 :GRPEDLGD T0371 272 :PTHICES 1o08A 1197 :DIVIVPD T0371 280 :VIEL 1o08A 1204 :TSHY Number of specific fragments extracted= 15 number of extra gaps= 1 total=968 Number of alignments=68 # 1o08A read from 1o08A/merged-good-all-a2m # found chain 1o08A in training set Warning: unaligning (T0371)F18 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o08A)D1008 Warning: unaligning (T0371)D19 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o08A)D1008 T0371 13 :YKCIF 1o08A 1002 :FKAVL T0371 20 :AFGVLKT 1o08A 1009 :LDGVITD T0371 30 :LLPGIENTFDYLK 1o08A 1016 :TAEYHFRAWKALA T0371 43 :AQGQD 1o08A 1030 :EIGIN T0371 55 :ASRSPEQLADSYHKLGLFSITADKIISSGMITKEYIDLKVDGG 1o08A 1045 :KGVSREDSLQKILDLADKKVSAEEFKELAKRKNDNYVKMIQDV T0371 141 :EGFNWFHDLNKTVNLLRKRTIPAIVANT 1o08A 1088 :SPADVYPGILQLLKDLRSNKIKIALASA T0371 174 :LTK 1o08A 1116 :SKN T0371 186 :VATMIESIL 1o08A 1119 :GPFLLERMN T0371 195 :GRRFIRFGKPDSQMFMFAYDML 1o08A 1137 :DPAEVAASKPAPDIFIAAAHAV T0371 221 :EISKREILMVGDTLH 1o08A 1159 :GVAPSESIGLEDSQA T0371 237 :DILGGNKFGLDTALV 1o08A 1174 :GIQAIKDSGALPIGV T0371 256 :TRIDDAETKI 1o08A 1189 :GRPEDLGDDI T0371 270 :IVPTHICE 1o08A 1199 :VIVPDTSH Number of specific fragments extracted= 13 number of extra gaps= 1 total=981 Number of alignments=69 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xviA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1xviA expands to /projects/compbio/data/pdb/1xvi.pdb.gz 1xviA:Skipped atom 342, because occupancy 0.500 <= existing 0.500 in 1xviA Skipped atom 346, because occupancy 0.500 <= existing 0.500 in 1xviA Skipped atom 348, because occupancy 0.500 <= existing 0.500 in 1xviA Skipped atom 633, because occupancy 0.500 <= existing 0.500 in 1xviA Skipped atom 637, because occupancy 0.500 <= existing 0.500 in 1xviA Skipped atom 639, because occupancy 0.500 <= existing 0.500 in 1xviA Skipped atom 641, because occupancy 0.500 <= existing 0.500 in 1xviA Skipped atom 643, because occupancy 0.500 <= existing 0.500 in 1xviA Skipped atom 645, because occupancy 0.500 <= existing 0.500 in 1xviA Skipped atom 656, because occupancy 0.500 <= existing 0.500 in 1xviA Skipped atom 660, because occupancy 0.500 <= existing 0.500 in 1xviA Skipped atom 662, because occupancy 0.500 <= existing 0.500 in 1xviA Skipped atom 664, because occupancy 0.500 <= existing 0.500 in 1xviA Skipped atom 666, because occupancy 0.500 <= existing 0.500 in 1xviA Skipped atom 718, because occupancy 0.500 <= existing 0.500 in 1xviA Skipped atom 722, because occupancy 0.500 <= existing 0.500 in 1xviA Skipped atom 724, because occupancy 0.500 <= existing 0.500 in 1xviA Skipped atom 1061, because occupancy 0.500 <= existing 0.500 in 1xviA Skipped atom 1065, because occupancy 0.500 <= existing 0.500 in 1xviA Skipped atom 1067, because occupancy 0.500 <= existing 0.500 in 1xviA Skipped atom 1069, because occupancy 0.500 <= existing 0.500 in 1xviA Skipped atom 1071, because occupancy 0.500 <= existing 0.500 in 1xviA Skipped atom 1073, because occupancy 0.500 <= existing 0.500 in 1xviA Skipped atom 1392, because occupancy 0.500 <= existing 0.500 in 1xviA Skipped atom 1396, because occupancy 0.500 <= existing 0.500 in 1xviA Skipped atom 1398, because occupancy 0.500 <= existing 0.500 in 1xviA Skipped atom 1400, because occupancy 0.500 <= existing 0.500 in 1xviA Skipped atom 1402, because occupancy 0.500 <= existing 0.500 in 1xviA Skipped atom 1404, because occupancy 0.500 <= existing 0.500 in 1xviA Skipped atom 1406, because occupancy 0.500 <= existing 0.500 in 1xviA Skipped atom 1408, because occupancy 0.500 <= existing 0.500 in 1xviA # T0371 read from 1xviA/merged-good-all-a2m # 1xviA read from 1xviA/merged-good-all-a2m # adding 1xviA to template set # found chain 1xviA in template set Warning: unaligning (T0371)L10 because first residue in template chain is (1xviA)I4 Warning: unaligning (T0371)G29 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xviA)Y24 Warning: unaligning (T0371)L30 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xviA)Y24 Warning: unaligning (T0371)I90 because of BadResidue code BAD_PEPTIDE in next template residue (1xviA)E80 Warning: unaligning (T0371)D91 because of BadResidue code BAD_PEPTIDE at template residue (1xviA)E80 T0371 11 :PKYKCIFFDAFGVLKTYN 1xviA 5 :QQPLLVFSDLDGTLLDSH T0371 31 :L 1xviA 25 :D T0371 32 :PGIENTFDYLKAQGQDYYIVT 1xviA 27 :QPAAPWLTRLREANVPVILCS T0371 56 :SRSPEQLADSYHKLGLFSIT 1xviA 48 :SKTSAEMLYLQKTLGLQGLP T0371 79 :IISSGMITKEY 1xviA 68 :LIAENGAVIQL T0371 92 :LKV 1xviA 81 :QWQ T0371 95 :DGGIVAYLGTANSANYLVSD 1xviA 88 :FPRIISGISHGEISLVLNTL T0371 115 :GIKMLPVSAIDDSNI 1xviA 112 :HFKFTTFDDVDDATI T0371 130 :GEVNALVLLDDEGFN 1xviA 141 :QLHEASVTLIWRDSD T0371 147 :HDLNKTVNLLRKRTIPA 1xviA 156 :ERMAQFTARLNELGLQF T0371 173 :PLTKTDVAI 1xviA 174 :QGARFWHVL T0371 198 :FIRFGK 1xviA 183 :DASAGK T0371 206 :SQMFMFAYDMLRQKMEISKR 1xviA 189 :DQAANWIIATYQQLSGKRPT T0371 227 :ILMVGDT 1xviA 209 :TLGLGDG T0371 235 :HTDILG 1xviA 216 :PNDAPL Number of specific fragments extracted= 15 number of extra gaps= 2 total=996 Number of alignments=70 # 1xviA read from 1xviA/merged-good-all-a2m # found chain 1xviA in template set Warning: unaligning (T0371)L10 because first residue in template chain is (1xviA)I4 Warning: unaligning (T0371)Y89 because of BadResidue code BAD_PEPTIDE in next template residue (1xviA)E80 Warning: unaligning (T0371)I90 because of BadResidue code BAD_PEPTIDE at template residue (1xviA)E80 T0371 11 :PKYKCIFFDAFGVLKTYN 1xviA 5 :QQPLLVFSDLDGTLLDSH T0371 29 :GLLPGIENT 1xviA 28 :PAAPWLTRL T0371 42 :KAQGQDYYIVTNDA 1xviA 37 :REANVPVILCSSKT T0371 59 :PEQLADSYHKLGLFSITA 1xviA 51 :SAEMLYLQKTLGLQGLPL T0371 79 :IISSGMITKE 1xviA 69 :IAENGAVIQL T0371 91 :DLK 1xviA 81 :QWQ T0371 94 :VDGGIVAYLGTANSANYLVSD 1xviA 87 :GFPRIISGISHGEISLVLNTL T0371 115 :GIKMLPVSAIDDSNI 1xviA 112 :HFKFTTFDDVDDATI T0371 132 :VNALVLLDDEGF 1xviA 143 :HEASVTLIWRDS T0371 146 :FHDLNKTVNLLRKRT 1xviA 155 :DERMAQFTARLNELG T0371 161 :IPAIVANTDNTYP 1xviA 176 :ARFWHVLDASAGK T0371 206 :SQMFMFAYDMLRQKMEISKR 1xviA 189 :DQAANWIIATYQQLSGKRPT T0371 227 :ILMVGDTLH 1xviA 209 :TLGLGDGPN T0371 237 :DILGGNKF 1xviA 218 :DAPLLEVM Number of specific fragments extracted= 14 number of extra gaps= 1 total=1010 Number of alignments=71 # 1xviA read from 1xviA/merged-good-all-a2m # found chain 1xviA in template set Warning: unaligning (T0371)G29 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xviA)Y24 T0371 12 :KYKCIFFDAFGVLKTYN 1xviA 6 :QPLLVFSDLDGTLLDSH T0371 30 :LLPGIE 1xviA 29 :AAPWLT T0371 40 :YLKAQGQDYYIVTNDA 1xviA 35 :RLREANVPVILCSSKT T0371 83 :GMITKEYIDLK 1xviA 51 :SAEMLYLQKTL T0371 94 :VDGGIVAYLG 1xviA 63 :LQGLPLIAEN T0371 125 :DDSNIGEVNALVLLDDEG 1xviA 136 :QAALTQLHEASVTLIWRD T0371 145 :WFHDLNKTVNLLRKRT 1xviA 154 :SDERMAQFTARLNELG T0371 167 :NTDNTYPLTKT 1xviA 175 :GARFWHVLDAS T0371 184 :GGV 1xviA 186 :AGK T0371 206 :SQMFMFAYDMLRQKMEISK 1xviA 189 :DQAANWIIATYQQLSGKRP T0371 227 :ILMVGDTLH 1xviA 209 :TLGLGDGPN Number of specific fragments extracted= 11 number of extra gaps= 1 total=1021 Number of alignments=72 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wzcA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wzcA expands to /projects/compbio/data/pdb/1wzc.pdb.gz 1wzcA:# T0371 read from 1wzcA/merged-good-all-a2m # 1wzcA read from 1wzcA/merged-good-all-a2m # adding 1wzcA to template set # found chain 1wzcA in template set Warning: unaligning (T0371)K12 because first residue in template chain is (1wzcA)M1 Warning: unaligning (T0371)D95 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1wzcA)Y87 Warning: unaligning (T0371)G97 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1wzcA)Y87 T0371 13 :YKCIFFDAFGVLKTYNG 1wzcA 2 :IRLIFLDIDKTLIPGYE T0371 31 :LPGIENTFDYLKAQGQDYYIVT 1wzcA 19 :PDPAKPIIEELKDMGFEIIFNS T0371 56 :SRSPEQLADSYHKLGL 1wzcA 41 :SKTRAEQEYYRKELEV T0371 73 :SIT 1wzcA 57 :ETP T0371 79 :IISSGMITKEYIDLKV 1wzcA 60 :FISENGSAIFIPKGYF T0371 98 :IVA 1wzcA 88 :IVI T0371 101 :YLGTANSANYLVSD 1wzcA 93 :GIRVEKIREELKKL T0371 115 :GIKMLPVSAIDDSNI 1wzcA 111 :GLKYYGNSTKEEIEK T0371 130 :GEVNALVLLDDEGF 1wzcA 141 :EYSETIFEWSRDGW T0371 150 :N 1wzcA 155 :E T0371 154 :NLLRKRTIPA 1wzcA 156 :EVLVEGGFKV T0371 173 :PLTKTDVAIA 1wzcA 167 :MGSRFYTVHG T0371 200 :RFGK 1wzcA 177 :NSDK T0371 206 :SQMFMFAYDMLRQKME 1wzcA 181 :GKAAKILLDFYKRLGQ T0371 226 :EILMVGDT 1wzcA 198 :ESYAVGDS T0371 235 :HTDILGGNK 1wzcA 206 :YNDFPMFEV T0371 246 :LDTALVL 1wzcA 215 :VDKVFIV T0371 254 :GNTRIDD 1wzcA 222 :GSLKHKK T0371 272 :PTHI 1wzcA 229 :AQNV T0371 277 :ES 1wzcA 233 :SS T0371 280 :VIE 1wzcA 235 :IID Number of specific fragments extracted= 21 number of extra gaps= 0 total=1042 Number of alignments=73 # 1wzcA read from 1wzcA/merged-good-all-a2m # found chain 1wzcA in template set Warning: unaligning (T0371)K12 because first residue in template chain is (1wzcA)M1 Warning: unaligning (T0371)S267 because last residue in template chain is (1wzcA)H244 T0371 13 :YKCIFFDAFGVLKTYNGL 1wzcA 2 :IRLIFLDIDKTLIPGYEP T0371 32 :PGIENTFDYLKAQGQDYYIVTNDASRSPEQLADSY 1wzcA 20 :DPAKPIIEELKDMGFEIIFNSSKTRAEQEYYRKEL T0371 73 :SITADKIISSGMITKE 1wzcA 55 :EVETPFISENGSAIFI T0371 97 :GIVAYL 1wzcA 88 :IVIELG T0371 103 :GTANSANYLVSD 1wzcA 95 :RVEKIREELKKL T0371 115 :GIKMLPVSAI 1wzcA 111 :GLKYYGNSTK T0371 130 :GEVNALVLLDDEGFN 1wzcA 121 :EEIEKFTGMPPELVP T0371 146 :FHDLNK 1wzcA 151 :RDGWEE T0371 155 :LLRKRTIPA 1wzcA 157 :VLVEGGFKV T0371 194 :LGRRFIRFGKPD 1wzcA 168 :GSRFYTVHGNSD T0371 209 :FMFAYDMLRQKM 1wzcA 180 :KGKAAKILLDFY T0371 221 :E 1wzcA 196 :Q T0371 226 :EILMVGDTLH 1wzcA 198 :ESYAVGDSYN T0371 237 :DILGGNKFG 1wzcA 208 :DFPMFEVVD T0371 247 :DTALVLTGNTR 1wzcA 217 :KVFIVGSLKHK T0371 258 :IDDAETKIK 1wzcA 235 :IIDVLEVIK Number of specific fragments extracted= 16 number of extra gaps= 0 total=1058 Number of alignments=74 # 1wzcA read from 1wzcA/merged-good-all-a2m # found chain 1wzcA in template set T0371 14 :KCIFFDAFGVLKTYNGL 1wzcA 3 :RLIFLDIDKTLIPGYEP T0371 32 :PGIENTFDYLKAQGQDYYIVTNDA 1wzcA 20 :DPAKPIIEELKDMGFEIIFNSSKT T0371 83 :GMITKEYIDLK 1wzcA 44 :RAEQEYYRKEL T0371 123 :AIDDSNIGEVNALVLLDDEGFNWFH 1wzcA 132 :ELVPLAMEREYSETIFEWSRDGWEE T0371 155 :LLRKRTIP 1wzcA 157 :VLVEGGFK T0371 171 :TYPLTKTDVAIAIGGVATMI 1wzcA 165 :VTMGSRFYTVHGNSDKGKAA T0371 210 :MFAYDMLRQKMEI 1wzcA 185 :KILLDFYKRLGQI T0371 226 :EILMVGDTLH 1wzcA 198 :ESYAVGDSYN T0371 237 :DILG 1wzcA 208 :DFPM T0371 246 :LDTALVLTGNTRI 1wzcA 215 :VDKVFIVGSLKHK T0371 268 :TGIVPTHICESAVI 1wzcA 228 :KAQNVSSIIDVLEV Number of specific fragments extracted= 11 number of extra gaps= 0 total=1069 Number of alignments=75 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1l6rA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0371 read from 1l6rA/merged-good-all-a2m # 1l6rA read from 1l6rA/merged-good-all-a2m # found chain 1l6rA in training set Warning: unaligning (T0371)P11 because first residue in template chain is (1l6rA)H0 T0371 12 :KYKCIFFDAFGVLKTYNGLL 1l6rA 1 :MIRLAAIDVDGNLTDRDRLI T0371 32 :PGIENTFDYLKAQGQDYYIVT 1l6rA 22 :TKAIESIRSAEKKGLTVSLLS T0371 56 :SRSPEQLADSYHKLGL 1l6rA 43 :GNVIPVVYALKIFLGI T0371 73 :SIT 1l6rA 59 :NGP T0371 79 :IISSGMITKEY 1l6rA 62 :VFGENGGIMFD T0371 94 :VDGGIVAYLGTANSANYLVSD 1l6rA 73 :NDGSIKKFFSNEGTNKFLEEM T0371 115 :GIKM 1l6rA 96 :RTSM T0371 124 :IDDSNIGEVNALVLLDDEG 1l6rA 100 :RSILTNRWREASTGFDIDP T0371 144 :NWFHDLN 1l6rA 119 :EDVDYVR T0371 154 :NLLRKRTI 1l6rA 126 :KEAESRGF T0371 199 :IR 1l6rA 134 :VI T0371 201 :FGK 1l6rA 147 :RGE T0371 209 :FMFAYDMLRQKMEISKREILMVGDT 1l6rA 151 :KAFAVNKLKEMYSLEYDEILVIGDS T0371 235 :HTDILGG 1l6rA 176 :NNDMPMF T0371 245 :GLDTALVL 1l6rA 183 :QLPVRKAC T0371 254 :GNTRIDDAETK 1l6rA 191 :PANATDNIKAV T0371 272 :PTHICE 1l6rA 202 :SDFVSD Number of specific fragments extracted= 17 number of extra gaps= 0 total=1086 Number of alignments=76 # 1l6rA read from 1l6rA/merged-good-all-a2m # found chain 1l6rA in training set Warning: unaligning (T0371)P11 because first residue in template chain is (1l6rA)H0 T0371 12 :KYKCIFFDAFGVLKTYNGLL 1l6rA 1 :MIRLAAIDVDGNLTDRDRLI T0371 32 :PGIENTFDYLKAQGQDYYIVTNDA 1l6rA 22 :TKAIESIRSAEKKGLTVSLLSGNV T0371 59 :PEQLADSYHKLGLF 1l6rA 46 :IPVVYALKIFLGIN T0371 74 :IT 1l6rA 60 :GP T0371 78 :KIISSGMITKE 1l6rA 62 :VFGENGGIMFD T0371 94 :VDGGIVAYLGTANSANYLVSDG 1l6rA 73 :NDGSIKKFFSNEGTNKFLEEMS T0371 116 :IKMLPVSAI 1l6rA 99 :MRSILTNRW T0371 130 :GEVNALVLLDDEG 1l6rA 108 :REASTGFDIDPED T0371 146 :FHDLN 1l6rA 121 :VDYVR T0371 154 :NLLRKRT 1l6rA 126 :KEAESRG T0371 165 :VANTDNTY 1l6rA 143 :HLMNRGED T0371 209 :FMFAYDMLRQKMEISKREILMVGDT 1l6rA 151 :KAFAVNKLKEMYSLEYDEILVIGDS T0371 235 :HTDILGGN 1l6rA 176 :NNDMPMFQ T0371 244 :FGLDTAL 1l6rA 184 :LPVRKAC T0371 254 :GNTRIDDAETK 1l6rA 191 :PANATDNIKAV T0371 272 :PTHICES 1l6rA 202 :SDFVSDY Number of specific fragments extracted= 16 number of extra gaps= 0 total=1102 Number of alignments=77 # 1l6rA read from 1l6rA/merged-good-all-a2m # found chain 1l6rA in training set T0371 13 :YKCIFFDAFGVLKTYNG 1l6rA 2 :IRLAAIDVDGNLTDRDR T0371 30 :LLPGIENTFDYLKAQGQDYYIVTNDA 1l6rA 20 :ISTKAIESIRSAEKKGLTVSLLSGNV T0371 59 :PEQLADSYHKLGL 1l6rA 46 :IPVVYALKIFLGI T0371 96 :GGIVAY 1l6rA 59 :NGPVFG T0371 132 :VNALVLLDDEG 1l6rA 65 :ENGGIMFDNDG T0371 143 :FNWFHDLNKTVNLLRKRT 1l6rA 80 :FFSNEGTNKFLEEMSKRT T0371 168 :TDNTYPLTKT 1l6rA 110 :ASTGFDIDPE T0371 182 :AIGGVATMIESIL 1l6rA 120 :DVDYVRKEAESRG T0371 196 :RRF 1l6rA 147 :RGE T0371 209 :FMFAYDMLRQKMEISKREILMVGDTLH 1l6rA 151 :KAFAVNKLKEMYSLEYDEILVIGDSNN T0371 237 :D 1l6rA 178 :D T0371 239 :LGGNKFGLDTAL 1l6rA 179 :MPMFQLPVRKAC Number of specific fragments extracted= 12 number of extra gaps= 0 total=1114 Number of alignments=78 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ah5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2ah5A expands to /projects/compbio/data/pdb/2ah5.pdb.gz 2ah5A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0371 read from 2ah5A/merged-good-all-a2m # 2ah5A read from 2ah5A/merged-good-all-a2m # adding 2ah5A to template set # found chain 2ah5A in template set Warning: unaligning (T0371)L10 because first residue in template chain is (2ah5A)M1 Warning: unaligning (T0371)N167 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ah5A)K108 Warning: unaligning (T0371)T168 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ah5A)K108 T0371 11 :PKYKCIFFDAFGVLKTYNGLL 2ah5A 2 :TSITAIFFDLDGTLVDSSIGI T0371 59 :PEQLADSYHKLGLFSITADKIISS 2ah5A 23 :HNAFTYTFKELGVPSPDAKTIRGF T0371 83 :GMITKEYIDLKVDG 2ah5A 48 :GPPLESSFATCLSK T0371 102 :LGTANSANYLVS 2ah5A 62 :DQISEAVQIYRS T0371 134 :ALVLLDDEGFNWFHDLNKTVNLLRKRTIPAIVA 2ah5A 74 :YYKAKGIYEAQLFPQIIDLLEELSSSYPLYITT T0371 169 :DNTY 2ah5A 109 :DTST T0371 174 :LTKTDVAIA 2ah5A 113 :AQDMAKNLE T0371 186 :VATMIESILGRRFIRFGK 2ah5A 122 :IHHFFDGIYGSSPEAPHK T0371 206 :SQMFMFAYDML 2ah5A 140 :ADVIHQALQTH T0371 221 :EISKREILMVGDT 2ah5A 151 :QLAPEQAIIIGDT T0371 235 :HTDILGGNKFGLDTALVLTGNTRIDD 2ah5A 164 :KFDMLGARETGIQKLAITWGFGEQAD T0371 265 :IKSTG 2ah5A 190 :LLNYQ T0371 272 :PTHICESAVI 2ah5A 195 :PDYIAHKPLE Number of specific fragments extracted= 13 number of extra gaps= 1 total=1127 Number of alignments=79 # 2ah5A read from 2ah5A/merged-good-all-a2m # found chain 2ah5A in template set Warning: unaligning (T0371)L10 because first residue in template chain is (2ah5A)M1 Warning: unaligning (T0371)T168 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ah5A)K108 Warning: unaligning (T0371)D169 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ah5A)K108 T0371 11 :PKYKCIFFDAFGVLKTYN 2ah5A 2 :TSITAIFFDLDGTLVDSS T0371 32 :PGIENTFDYL 2ah5A 20 :IGIHNAFTYT T0371 63 :ADSY 2ah5A 30 :FKEL T0371 70 :GLFSITADKIISSGMITKE 2ah5A 34 :GVPSPDAKTIRGFMGPPLE T0371 89 :YIDLKVD 2ah5A 54 :SFATCLS T0371 101 :YLGTANSANYLVSD 2ah5A 61 :KDQISEAVQIYRSY T0371 135 :LVLLDDEGFNWFHDLNKTVNLLRKR 2ah5A 75 :YKAKGIYEAQLFPQIIDLLEELSSS T0371 161 :IPAIVAN 2ah5A 100 :YPLYITT T0371 170 :NTYPLTKTDVAIAIGGVATMI 2ah5A 109 :DTSTAQDMAKNLEIHHFFDGI T0371 194 :LGRRF 2ah5A 130 :YGSSP T0371 202 :GKPD 2ah5A 135 :EAPH T0371 209 :FMFAYDMLRQKMEISKREILMVGDTLH 2ah5A 139 :KADVIHQALQTHQLAPEQAIIIGDTKF T0371 237 :DILGGNKFGLDTALVLTGNTRIDDAETKI 2ah5A 166 :DMLGARETGIQKLAITWGFGEQADLLNYQ T0371 272 :PTHICESAV 2ah5A 195 :PDYIAHKPL Number of specific fragments extracted= 14 number of extra gaps= 1 total=1141 Number of alignments=80 # 2ah5A read from 2ah5A/merged-good-all-a2m # found chain 2ah5A in template set Warning: unaligning (T0371)N167 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ah5A)K108 Warning: unaligning (T0371)T168 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ah5A)K108 T0371 11 :PKYKCIFFDAFGVLKT 2ah5A 2 :TSITAIFFDLDGTLVD T0371 30 :LLPGIENTFDYLK 2ah5A 18 :SSIGIHNAFTYTF T0371 43 :AQGQD 2ah5A 32 :ELGVP T0371 56 :SRSPEQLAD 2ah5A 37 :SPDAKTIRG T0371 66 :YHKLGLFSITADKIISSGMITKEYIDLK 2ah5A 51 :LESSFATCLSKDQISEAVQIYRSYYKAK T0371 139 :DDEGFNWFHDLNKTVNLLRKRTIPAIVA 2ah5A 79 :GIYEAQLFPQIIDLLEELSSSYPLYITT T0371 182 :AIGGVATMIESIL 2ah5A 109 :DTSTAQDMAKNLE T0371 195 :GRRF 2ah5A 133 :SPEA T0371 205 :D 2ah5A 138 :H T0371 206 :SQMFMFAYDML 2ah5A 140 :ADVIHQALQTH T0371 221 :EISKREILMVGDTLH 2ah5A 151 :QLAPEQAIIIGDTKF T0371 237 :DILGGNKFGLDTALVLTGNTRIDDAET 2ah5A 166 :DMLGARETGIQKLAITWGFGEQADLLN T0371 266 :KSTGIVPTHICESA 2ah5A 193 :YQPDYIAHKPLEVL Number of specific fragments extracted= 13 number of extra gaps= 1 total=1154 Number of alignments=81 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zs9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zs9A expands to /projects/compbio/data/pdb/1zs9.pdb.gz 1zs9A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0371 read from 1zs9A/merged-good-all-a2m # 1zs9A read from 1zs9A/merged-good-all-a2m # adding 1zs9A to template set # found chain 1zs9A in template set Warning: unaligning (T0371)G115 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1zs9A)K106 Warning: unaligning (T0371)K117 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1zs9A)K106 T0371 11 :PKYKCIFFDAFGVLKTYNGL 1zs9A 8 :AEVTVILLDIEGTTTPIAFV T0371 32 :PGIENTF 1zs9A 29 :DILFPYI T0371 59 :PEQLADSYHK 1zs9A 36 :EENVKEYLQT T0371 69 :LGL 1zs9A 47 :WEE T0371 77 :DKIISSGMITKEYI 1zs9A 50 :EECQQDVSLLRKQA T0371 91 :DLKVDGGIVAY 1zs9A 65 :EDAHLDGAVPI T0371 102 :LGTANSANYLV 1zs9A 88 :QMIQAVVDNVC T0371 113 :SD 1zs9A 102 :SL T0371 118 :M 1zs9A 107 :T T0371 122 :SAIDDSNIGEVNALVLLDDEGFNWFHDLNKTVNLLRKRTIPAIVANT 1zs9A 108 :TALKQLQGHMWRAAFTAGRMKAEFFADVVPAVRKWREAGMKVYIYSS T0371 174 :L 1zs9A 155 :G T0371 186 :VATMIESILGRRFIR 1zs9A 156 :SVEAQKLLFGHSTEG T0371 201 :FGKPDSQMFMFAYDML 1zs9A 185 :GHKVESESYRKIADSI T0371 221 :EISKREILMVGDT 1zs9A 201 :GCSTNNILFLTDV T0371 235 :HTDILGGNKFGLDTALVLTGNTR 1zs9A 214 :TREASAAEEADVHVAVVVRPGNA T0371 258 :IDDAETKIK 1zs9A 239 :TDDEKTYYS T0371 275 :ICES 1zs9A 248 :LITS T0371 280 :VIEL 1zs9A 252 :FSEL Number of specific fragments extracted= 18 number of extra gaps= 0 total=1172 Number of alignments=82 # 1zs9A read from 1zs9A/merged-good-all-a2m # found chain 1zs9A in template set T0371 10 :LPKYKCIFFDAFGVLKT 1zs9A 7 :PAEVTVILLDIEGTTTP T0371 32 :PGIENTF 1zs9A 29 :DILFPYI T0371 59 :PEQLADSYHKL 1zs9A 36 :EENVKEYLQTH T0371 95 :DGGIVAYLGTANSANYLVSDG 1zs9A 47 :WEEEECQQDVSLLRKQAEEDA T0371 116 :IKMLPVSAIDDSNI 1zs9A 73 :VPIPAASGNGVDDL T0371 130 :GEVNALVLLDDEGFNWFHDLNKTVNLLRKRTIPAIVANTDNTYPLTKTDVAIAIGGVATMIESILGRRFIRFGK 1zs9A 116 :HMWRAAFTAGRMKAEFFADVVPAVRKWREAGMKVYIYSSGSVEAQKLLFGHSTEGDILELVDGHFDTKIGHKVE T0371 206 :SQMFMFAYDML 1zs9A 190 :SESYRKIADSI T0371 221 :EISKREILMVGDTLH 1zs9A 201 :GCSTNNILFLTDVTR T0371 237 :DILGGNKFGLDTALVLTGNTR 1zs9A 216 :EASAAEEADVHVAVVVRPGNA T0371 258 :IDDAETKI 1zs9A 239 :TDDEKTYY T0371 274 :HICES 1zs9A 247 :SLITS T0371 280 :VIEL 1zs9A 252 :FSEL Number of specific fragments extracted= 12 number of extra gaps= 0 total=1184 Number of alignments=83 # 1zs9A read from 1zs9A/merged-good-all-a2m # found chain 1zs9A in template set T0371 11 :PKYKCIFFDAFGVLKTYNGLLPGIENTFDY 1zs9A 8 :AEVTVILLDIEGTTTPIAFVKDILFPYIEE T0371 61 :QLADSYHKLGL 1zs9A 38 :NVKEYLQTHWE T0371 76 :ADKIISSGMITKEYIDLK 1zs9A 49 :EEECQQDVSLLRKQAEED T0371 119 :LPVS 1zs9A 67 :AHLD T0371 123 :AIDDSNIGEVNALVLLDDEGFNWFHDLNKTVNLLRKRTIPAIVANT 1zs9A 109 :ALKQLQGHMWRAAFTAGRMKAEFFADVVPAVRKWREAGMKVYIYSS T0371 182 :AIGGVATMIESILGRRFIR 1zs9A 155 :GSVEAQKLLFGHSTEGDIL T0371 201 :FGKPDSQMFMFAYDML 1zs9A 185 :GHKVESESYRKIADSI T0371 221 :EISKREILMVGDTLH 1zs9A 201 :GCSTNNILFLTDVTR T0371 237 :DILGGNKFGLDTALVLTGNT 1zs9A 216 :EASAAEEADVHVAVVVRPGN T0371 257 :RIDDAETK 1zs9A 239 :TDDEKTYY T0371 270 :IVPTHICES 1zs9A 247 :SLITSFSEL Number of specific fragments extracted= 11 number of extra gaps= 0 total=1195 Number of alignments=84 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1x42A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1x42A expands to /projects/compbio/data/pdb/1x42.pdb.gz 1x42A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0371 read from 1x42A/merged-good-all-a2m # 1x42A read from 1x42A/merged-good-all-a2m # adding 1x42A to template set # found chain 1x42A in template set Warning: unaligning (T0371)K12 because first residue in template chain is (1x42A)M1 T0371 13 :YKCIFFDAFGVLKTYNGLLPGIENTFDYLKA 1x42A 2 :IRAVFFDFVGTLLSVEGEAKTHLKIMEEVLG T0371 45 :GQ 1x42A 33 :DY T0371 56 :SRSPEQLADSYHKL 1x42A 35 :PLNPKTLLDEYEKL T0371 82 :SGMITKEYIDLKV 1x42A 49 :TREAFSNYAGKPY T0371 97 :GIVAYLGTANSANYLVSDGIKM 1x42A 62 :RPIRDIEEEVMRKLAEKYGFKY T0371 128 :NIGEVNALVLLDDEGFNWFHDLNKTVNLLRK 1x42A 84 :PENFWEIHLRMHQRYGELYPEVVEVLKSLKG T0371 160 :TIPA 1x42A 115 :KYHV T0371 164 :IVANTDNTY 1x42A 120 :MITDSDTEY T0371 174 :LTKTDVAIA 1x42A 129 :LMAHLDALG T0371 186 :VATMIESILGRRFIRFGKPDSQMFMFAYDML 1x42A 138 :IKDLFDSITTSEEAGFFKPHPRIFELALKKA T0371 221 :EISKREILMVGDTLHTDILGGNKFGLDTALVL 1x42A 169 :GVKGEEAVYVGDNPVKDCGGSKNLGMTSILLD T0371 254 :GNTRIDDAETK 1x42A 201 :RKGEKREFWDK T0371 272 :PTHICES 1x42A 212 :CDFIVSD T0371 280 :VIEL 1x42A 219 :LREV Number of specific fragments extracted= 14 number of extra gaps= 0 total=1209 Number of alignments=85 # 1x42A read from 1x42A/merged-good-all-a2m # found chain 1x42A in template set Warning: unaligning (T0371)K12 because first residue in template chain is (1x42A)M1 T0371 13 :YKCIFFDAFGVLKTYNGLLPGIENTFDYLKAQ 1x42A 2 :IRAVFFDFVGTLLSVEGEAKTHLKIMEEVLGD T0371 55 :ASRSPEQLADSYHKL 1x42A 34 :YPLNPKTLLDEYEKL T0371 84 :MITKEYIDLKV 1x42A 51 :EAFSNYAGKPY T0371 97 :GIVAYLGTANSANYLVSDGIKMLP 1x42A 62 :RPIRDIEEEVMRKLAEKYGFKYPE T0371 130 :GEVNALVLLDDEGFNWFHDLNKTVNLLRKR 1x42A 86 :NFWEIHLRMHQRYGELYPEVVEVLKSLKGK T0371 161 :IPAIVANTDNTYPLTKTDVAIAIGGVATMI 1x42A 116 :YHVGMITDSDTEYLMAHLDALGIKDLFDSI T0371 194 :LGRRFIRFGKPDSQMFMFAYDML 1x42A 146 :TTSEEAGFFKPHPRIFELALKKA T0371 221 :EISKREILMVGDTLHTDILGGNKFGLDTALVLT 1x42A 169 :GVKGEEAVYVGDNPVKDCGGSKNLGMTSILLDR T0371 255 :NTRIDDAETK 1x42A 202 :KGEKREFWDK T0371 272 :PTHICES 1x42A 212 :CDFIVSD T0371 280 :VIEL 1x42A 219 :LREV Number of specific fragments extracted= 11 number of extra gaps= 0 total=1220 Number of alignments=86 # 1x42A read from 1x42A/merged-good-all-a2m # found chain 1x42A in template set T0371 13 :YKCIFFDAFGVLKTYNGLLPGIENTFDYLKA 1x42A 2 :IRAVFFDFVGTLLSVEGEAKTHLKIMEEVLG T0371 45 :GQD 1x42A 33 :DYP T0371 57 :RSPEQLADSYHK 1x42A 36 :LNPKTLLDEYEK T0371 85 :ITKEYIDLKVDGGI 1x42A 48 :LTREAFSNYAGKPY T0371 104 :TANSANYLVSDGIKMLP 1x42A 69 :EEVMRKLAEKYGFKYPE T0371 130 :GEVNALVLLDDEGFNWFHDLNKTVNLLRK 1x42A 86 :NFWEIHLRMHQRYGELYPEVVEVLKSLKG T0371 160 :TIPAIVANTD 1x42A 115 :KYHVGMITDS T0371 182 :AIGGVATMIESIL 1x42A 125 :DTEYLMAHLDALG T0371 201 :FGKPDSQMFMFAYDML 1x42A 153 :FFKPHPRIFELALKKA T0371 221 :EISKREILMVGDTLHTDILGGNKFGLDTALVLTGNTRIDDAE 1x42A 169 :GVKGEEAVYVGDNPVKDCGGSKNLGMTSILLDRKGEKREFWD T0371 267 :STGIVPTHICESAVI 1x42A 211 :KCDFIVSDLREVIKI Number of specific fragments extracted= 11 number of extra gaps= 0 total=1231 Number of alignments=87 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b0cA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2b0cA expands to /projects/compbio/data/pdb/2b0c.pdb.gz 2b0cA:# T0371 read from 2b0cA/merged-good-all-a2m # 2b0cA read from 2b0cA/merged-good-all-a2m # adding 2b0cA to template set # found chain 2b0cA in template set T0371 15 :CIFFDAFGVLKTYN 2b0cA 9 :LYIFDLGNVIVDID T0371 59 :PEQLADSYHKL 2b0cA 23 :FNRVLGAWSDL T0371 73 :SITADKIISS 2b0cA 35 :RIPLASLKKS T0371 83 :GMITKEYIDLKV 2b0cA 48 :GEAFHQHERGEI T0371 103 :GTANSANYLVSD 2b0cA 60 :SDEAFAEALCHE T0371 115 :GI 2b0cA 73 :AL T0371 122 :SAIDDSNIGEVNALV 2b0cA 75 :PLSYEQFSHGWQAVF T0371 143 :FNWFHDLNKTVNLLRKRTIPA 2b0cA 90 :VALRPEVIAIMHKLREQGHRV T0371 164 :IVANTDNTYPLTKTDVAIA 2b0cA 112 :VLSNTNRLHTTFWPEEYPE T0371 186 :VATMIESILGRRFIRFGKPDSQMFMFAYDML 2b0cA 131 :IRDAADHIYLSQDLGMRKPEARIYQHVLQAE T0371 221 :EISKREILMVGDT 2b0cA 162 :GFSPSDTVFFDDN T0371 235 :HTDILGGNKFGLDTA 2b0cA 175 :ADNIEGANQLGITSI T0371 254 :GNTRIDDAETKIKS 2b0cA 190 :LVKDKTTIPDYFAK Number of specific fragments extracted= 13 number of extra gaps= 0 total=1244 Number of alignments=88 # 2b0cA read from 2b0cA/merged-good-all-a2m # found chain 2b0cA in template set Warning: unaligning (T0371)T268 because last residue in template chain is (2b0cA)V204 T0371 13 :YKCIFFDAFGVLKTYN 2b0cA 7 :KMLYIFDLGNVIVDID T0371 34 :IENTFDYLKAQ 2b0cA 23 :FNRVLGAWSDL T0371 55 :ASRSPEQLADSY 2b0cA 34 :TRIPLASLKKSF T0371 73 :SITADK 2b0cA 46 :HMGEAF T0371 87 :KEYIDL 2b0cA 52 :HQHERG T0371 101 :YLGTANSANYLVSD 2b0cA 58 :EISDEAFAEALCHE T0371 115 :GIKMLP 2b0cA 73 :ALPLSY T0371 130 :GEVNALVLLD 2b0cA 79 :EQFSHGWQAV T0371 142 :GFNWFHDLNKTVNLLRKRTIPAIVANTDNTYPLTKTDVAIA 2b0cA 89 :FVALRPEVIAIMHKLREQGHRVVVLSNTNRLHTTFWPEEYP T0371 185 :GVATMIESILGRRFIRFGKPDSQMFMFAYDML 2b0cA 130 :EIRDAADHIYLSQDLGMRKPEARIYQHVLQAE T0371 221 :EISKREILMVGDTLH 2b0cA 162 :GFSPSDTVFFDDNAD T0371 237 :DILGGNKFGLDTALV 2b0cA 177 :NIEGANQLGITSILV T0371 256 :TRIDDAETKIKS 2b0cA 192 :KDKTTIPDYFAK Number of specific fragments extracted= 13 number of extra gaps= 0 total=1257 Number of alignments=89 # 2b0cA read from 2b0cA/merged-good-all-a2m # found chain 2b0cA in template set T0371 15 :CIFFDAFGVLKTYN 2b0cA 9 :LYIFDLGNVIVDID T0371 31 :LPGIENTFDYLK 2b0cA 23 :FNRVLGAWSDLT T0371 43 :AQGQ 2b0cA 55 :ERGE T0371 57 :RSPEQLADSYHKLGLFSITADKII 2b0cA 59 :ISDEAFAEALCHEMALPLSYEQFS T0371 88 :EYIDLK 2b0cA 83 :HGWQAV T0371 142 :GFNWFHDLNKTVNLLRKRTIPAIVANTD 2b0cA 89 :FVALRPEVIAIMHKLREQGHRVVVLSNT T0371 172 :YPLTKTDVAIAIGGVATMIESILGRRFIRFGKPDSQMFMFAYDML 2b0cA 117 :NRLHTTFWPEEYPEIRDAADHIYLSQDLGMRKPEARIYQHVLQAE T0371 221 :EISKREILMVGDTLH 2b0cA 162 :GFSPSDTVFFDDNAD T0371 237 :DILGGNKFGLDTALV 2b0cA 177 :NIEGANQLGITSILV Number of specific fragments extracted= 9 number of extra gaps= 0 total=1266 Number of alignments=90 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rkqA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0371 read from 1rkqA/merged-good-all-a2m # 1rkqA read from 1rkqA/merged-good-all-a2m # found chain 1rkqA in training set Warning: unaligning (T0371)Y110 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1rkqA)S101 Warning: unaligning (T0371)L111 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1rkqA)S101 T0371 12 :KYKCIFFDAFGVLKTYNGLL 1rkqA 3 :AIKLIAIDMDGTLLLPDHTI T0371 32 :PGIENTFDYLKAQGQDYYIVT 1rkqA 24 :PAVKNAIAAARARGVNVVLTT T0371 56 :SRSPEQLADSYHKLGL 1rkqA 45 :GRPYAGVHNYLKELHM T0371 73 :SITADKIISSGMITKEYI 1rkqA 61 :EQPGDYCITYNGALVQKA T0371 91 :DLKVDGGIVAYLGTANSAN 1rkqA 81 :GSTVAQTALSYDDYRFLEK T0371 112 :VSDGIKMLPVSAID 1rkqA 102 :REVGSHFHALDRTT T0371 135 :LVLLDDE 1rkqA 116 :LYTANRD T0371 145 :WFHDLNKTVNL 1rkqA 123 :ISYYTVHESFV T0371 159 :RTIPA 1rkqA 134 :ATIPL T0371 168 :TDNTYPLTKTDVAI 1rkqA 140 :FCEAEKMDPNTQFL T0371 182 :AIGGVATMIESI 1rkqA 160 :EPAILDQAIARI T0371 201 :FGK 1rkqA 196 :VNK T0371 206 :SQMFMFAYDML 1rkqA 199 :GTGVKSLADVL T0371 221 :EISKREILMVGDT 1rkqA 210 :GIKPEEIMAIGDQ T0371 235 :HTDILGGNKFGLDTA 1rkqA 223 :ENDIAMIEYAGVGVA T0371 254 :GNTRIDDAETK 1rkqA 238 :VDNAIPSVKEV T0371 272 :PTHICESAVIE 1rkqA 249 :ANFVTKSNLED Number of specific fragments extracted= 17 number of extra gaps= 1 total=1283 Number of alignments=91 # 1rkqA read from 1rkqA/merged-good-all-a2m # found chain 1rkqA in training set Warning: unaligning (T0371)Y110 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1rkqA)S101 Warning: unaligning (T0371)L111 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1rkqA)S101 T0371 12 :KYKCIFFDAFGVLKTYNGLL 1rkqA 3 :AIKLIAIDMDGTLLLPDHTI T0371 32 :PGIENTFDYLKAQGQDYYIVTNDASRSPEQLADSY 1rkqA 24 :PAVKNAIAAARARGVNVVLTTGRPYAGVHNYLKEL T0371 73 :SITADK 1rkqA 59 :HMEQPG T0371 79 :IISSGMITKEYI 1rkqA 68 :ITYNGALVQKAA T0371 91 :DLKVDGGIVAYLGTANSAN 1rkqA 81 :GSTVAQTALSYDDYRFLEK T0371 112 :VSDGIKMLPVSAI 1rkqA 102 :REVGSHFHALDRT T0371 170 :N 1rkqA 115 :T T0371 171 :TYPLTKTDVAIA 1rkqA 161 :PAILDQAIARIP T0371 184 :GGVATMIESILGRRF 1rkqA 173 :QEVKEKYTVLKSAPY T0371 199 :IRFGKPDSQMFMFAYDML 1rkqA 192 :LDKRVNKGTGVKSLADVL T0371 221 :EISKREILMVGDT 1rkqA 210 :GIKPEEIMAIGDQ T0371 235 :HTDILGGNKFGL 1rkqA 223 :ENDIAMIEYAGV T0371 248 :TALVLT 1rkqA 235 :GVAVDN T0371 257 :RIDDAETK 1rkqA 241 :AIPSVKEV T0371 272 :PTHICESAVI 1rkqA 249 :ANFVTKSNLE Number of specific fragments extracted= 15 number of extra gaps= 1 total=1298 Number of alignments=92 # 1rkqA read from 1rkqA/merged-good-all-a2m # found chain 1rkqA in training set Warning: unaligning (T0371)L155 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1rkqA)S101 Warning: unaligning (T0371)L156 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1rkqA)S101 T0371 12 :KYKCIFFDAFGVLKTYNG 1rkqA 3 :AIKLIAIDMDGTLLLPDH T0371 30 :LLPGIENTFDYLKAQGQDYYIVTNDASR 1rkqA 22 :ISPAVKNAIAAARARGVNVVLTTGRPYA T0371 61 :QLADSYHKLGL 1rkqA 50 :GVHNYLKELHM T0371 93 :KVDGGIVAY 1rkqA 61 :EQPGDYCIT T0371 132 :VNALVLLDDEGFNW 1rkqA 70 :YNGALVQKAADGST T0371 146 :FHDLNKTVN 1rkqA 91 :YDDYRFLEK T0371 157 :RKRTIPAIVANTDNTYPLTKT 1rkqA 102 :REVGSHFHALDRTTLYTANRD T0371 182 :AIGGVATMIESIL 1rkqA 123 :ISYYTVHESFVAT T0371 205 :DSQMFMFAYDML 1rkqA 160 :EPAILDQAIARI T0371 217 :RQK 1rkqA 176 :KEK T0371 220 :MEISKREILMVGDTLH 1rkqA 209 :LGIKPEEIMAIGDQEN T0371 237 :DILGGNKFGLDTA 1rkqA 225 :DIAMIEYAGVGVA T0371 253 :TGNTRID 1rkqA 238 :VDNAIPS T0371 261 :AET 1rkqA 245 :VKE T0371 267 :STGIVPTHI 1rkqA 248 :VANFVTKSN Number of specific fragments extracted= 15 number of extra gaps= 1 total=1313 Number of alignments=93 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1swvA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1swvA expands to /projects/compbio/data/pdb/1swv.pdb.gz 1swvA:# T0371 read from 1swvA/merged-good-all-a2m # 1swvA read from 1swvA/merged-good-all-a2m # adding 1swvA to template set # found chain 1swvA in template set Warning: unaligning (T0371)K12 because first residue in template chain is (1swvA)K5 T0371 13 :YKCIFFDAFGVLKTYNGLL 1swvA 6 :IEAVIFAWAGTTVDYGCFA T0371 58 :SPEQLADSYHKLGL 1swvA 25 :PLEVFMEIFHKRGV T0371 73 :SITADKIISSGMITKEYI 1swvA 39 :AITAEEARKPMGLLKIDH T0371 91 :DLK 1swvA 58 :RAL T0371 102 :LGTANSANYLVSDGIKMLPVSAIDDSNIGEVNALVLLDDEGFNWFHDLNKTVNLLRKRTIPAIVANT 1swvA 61 :TEMPRIASEWNRVFRQLPTEADIQEMYEEFEEILFAILPRYASPINGVKEVIASLRERGIKIGSTTG T0371 174 :LTKTDVAI 1swvA 128 :YTREMMDI T0371 186 :VATMIES 1swvA 136 :VAKEAAL T0371 194 :LGRRFIRFGKPDSQMFMFAYDML 1swvA 151 :VTPDDVPAGRPYPWMCYKNAMEL T0371 221 :EI 1swvA 174 :GV T0371 223 :SKREILMVGDT 1swvA 177 :PMNHMIKVGDT T0371 235 :HTDILGGNKFGLDTALVLTGNTR 1swvA 188 :VSDMKEGRNAGMWTVGVILGSSE T0371 258 :IDDAETKIKSTG 1swvA 230 :IEVVRNRFVENG T0371 272 :PTHICES 1swvA 242 :AHFTIET T0371 280 :VIEL 1swvA 249 :MQEL Number of specific fragments extracted= 14 number of extra gaps= 0 total=1327 Number of alignments=94 # 1swvA read from 1swvA/merged-good-all-a2m # found chain 1swvA in template set Warning: unaligning (T0371)P11 because first residue in template chain is (1swvA)K5 T0371 13 :YKCIFFDAFGVLKTYN 1swvA 6 :IEAVIFAWAGTTVDYG T0371 55 :ASRSPEQLADSYHKLGL 1swvA 22 :CFAPLEVFMEIFHKRGV T0371 73 :SITADKIISSGMITKEYIDLK 1swvA 39 :AITAEEARKPMGLLKIDHVRA T0371 101 :YLGTANSANYLVSDGIKMLPVSAIDDSNIGEVNALVLLDDEGFNWFHDLNKTVNLLRKRTIPAIVANTDNTYPLTKTDVAIAIGGVA 1swvA 60 :LTEMPRIASEWNRVFRQLPTEADIQEMYEEFEEILFAILPRYASPINGVKEVIASLRERGIKIGSTTGYTREMMDIVAKEAALQGYK T0371 188 :TMI 1swvA 148 :DFL T0371 194 :LGRRFIRFGKPDSQMFMFAYDML 1swvA 151 :VTPDDVPAGRPYPWMCYKNAMEL T0371 221 :EI 1swvA 174 :GV T0371 223 :SKREILMVGDTLH 1swvA 177 :PMNHMIKVGDTVS T0371 237 :DILGGNKFGLDTALVLTGNTR 1swvA 190 :DMKEGRNAGMWTVGVILGSSE T0371 258 :IDDAETKIKSTG 1swvA 230 :IEVVRNRFVENG T0371 272 :PTHICES 1swvA 242 :AHFTIET T0371 280 :VIEL 1swvA 249 :MQEL Number of specific fragments extracted= 12 number of extra gaps= 0 total=1339 Number of alignments=95 # 1swvA read from 1swvA/merged-good-all-a2m # found chain 1swvA in template set Warning: unaligning (T0371)K12 because first residue in template chain is (1swvA)K5 T0371 13 :YKCIFFDAFGVLKTYNGLL 1swvA 6 :IEAVIFAWAGTTVDYGCFA T0371 58 :SPEQLADSYHKLGL 1swvA 25 :PLEVFMEIFHKRGV T0371 73 :SITADK 1swvA 39 :AITAEE T0371 79 :IISSGMITKEYIDLK 1swvA 49 :MGLLKIDHVRALTEM T0371 105 :ANSANYLVSDGIKMLPVSAIDDSNIGEVNALVLLDDEGFNWFHDLNKTVNLLRKRTIPAIVANT 1swvA 64 :PRIASEWNRVFRQLPTEADIQEMYEEFEEILFAILPRYASPINGVKEVIASLRERGIKIGSTTG T0371 181 :IAIG 1swvA 128 :YTRE T0371 186 :VATMIESIL 1swvA 132 :MMDIVAKEA T0371 195 :GRRFIRFGKPDSQMFMFAYDML 1swvA 152 :TPDDVPAGRPYPWMCYKNAMEL T0371 221 :EI 1swvA 174 :GV T0371 223 :SKREILMVGDTLH 1swvA 177 :PMNHMIKVGDTVS T0371 237 :DILGGNKFGLDTALVLTG 1swvA 190 :DMKEGRNAGMWTVGVILG T0371 255 :NTRIDDAE 1swvA 212 :GLTEEEVE T0371 263 :T 1swvA 239 :E T0371 266 :KSTGIVPTHICESA 1swvA 240 :NGAHFTIETMQELE Number of specific fragments extracted= 14 number of extra gaps= 0 total=1353 Number of alignments=96 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jud/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1jud expands to /projects/compbio/data/pdb/1jud.pdb.gz 1jud:Warning: there is no chain 1jud will retry with 1judA # T0371 read from 1jud/merged-good-all-a2m # 1jud read from 1jud/merged-good-all-a2m # adding 1jud to template set # found chain 1jud in template set Warning: unaligning (T0371)K12 because first residue in template chain is (1jud)Y3 T0371 13 :YKCIFFDAFGVLKTYNGLL 1jud 4 :IKGIAFDLYGTLFDVHSVV T0371 39 :DYLKAQ 1jud 23 :GRCDEA T0371 56 :SR 1jud 31 :GR T0371 59 :PEQLADSYHKL 1jud 33 :GREISALWRQK T0371 79 :I 1jud 44 :Q T0371 83 :GMITKEYI 1jud 45 :LEYTWLRS T0371 91 :DLKV 1jud 54 :MNRY T0371 97 :GIVAYLGTANSANYLVSDGI 1jud 58 :VNFQQATEDALRFTCRHLGL T0371 122 :SAID 1jud 78 :DLDA T0371 130 :GEVNALVLLDDE 1jud 82 :RTRSTLCDAYLR T0371 143 :FNWFHDLNKTVNLLRKRTIPA 1jud 94 :LAPFSEVPDSLRELKRRGLKL T0371 164 :IVANTDNTY 1jud 116 :ILSNGSPQS T0371 174 :LTKTDVAIA 1jud 125 :IDAVVSHAG T0371 186 :VATMIESILGRRFIRFGKPDSQMFMFAYDML 1jud 134 :LRDGFDHLLSVDPVQVYKPDNRVYELAEQAL T0371 221 :EISKREILMVGDT 1jud 165 :GLDRSAILFVSSN T0371 235 :HTDILGGNKFGLDTALVLTGNTR 1jud 178 :AWDATGARYFGFPTCWINRTGNV T0371 265 :IKSTGIVPTHICES 1jud 201 :FEEMGQTPDWEVTS T0371 280 :VIE 1jud 215 :LRA Number of specific fragments extracted= 18 number of extra gaps= 0 total=1371 Number of alignments=97 # 1jud read from 1jud/merged-good-all-a2m # found chain 1jud in template set Warning: unaligning (T0371)K12 because first residue in template chain is (1jud)Y3 T0371 13 :YKCIFFDAFGVLKTYNGLLPGIENT 1jud 4 :IKGIAFDLYGTLFDVHSVVGRCDEA T0371 55 :ASRSPEQLADSYHKLG 1jud 29 :FPGRGREISALWRQKQ T0371 83 :GMITKEYI 1jud 45 :LEYTWLRS T0371 94 :VDG 1jud 53 :LMN T0371 97 :GIVAYLGTANSANYLVSDGIKML 1jud 58 :VNFQQATEDALRFTCRHLGLDLD T0371 130 :GEVNALVLLDDEGFNWFHDLNKTVNLLRKRTIPAIVANTDNTYPLTKTDVAIAIGGVATMI 1jud 81 :ARTRSTLCDAYLRLAPFSEVPDSLRELKRRGLKLAILSNGSPQSIDAVVSHAGLRDGFDHL T0371 194 :LGRRFIRFGKPDSQMFMFAYDML 1jud 142 :LSVDPVQVYKPDNRVYELAEQAL T0371 221 :EISKREILMVGDTLH 1jud 165 :GLDRSAILFVSSNAW T0371 237 :DILGGNKFGLDTALVLTGNTR 1jud 180 :DATGARYFGFPTCWINRTGNV T0371 265 :IKSTGIVPTHICES 1jud 201 :FEEMGQTPDWEVTS T0371 280 :VIEL 1jud 215 :LRAV Number of specific fragments extracted= 11 number of extra gaps= 0 total=1382 Number of alignments=98 # 1jud read from 1jud/merged-good-all-a2m # found chain 1jud in template set Warning: unaligning (T0371)K12 because first residue in template chain is (1jud)Y3 Warning: unaligning (T0371)E282 because last residue in template chain is (1jud)F222 T0371 13 :YKCIFFDAFGVLKTYNGLLPGIENT 1jud 4 :IKGIAFDLYGTLFDVHSVVGRCDEA T0371 56 :SRSPEQLADSYHKLGL 1jud 30 :PGRGREISALWRQKQL T0371 84 :MITKEYIDLK 1jud 46 :EYTWLRSLMN T0371 103 :GTANSANYLVSDGIKM 1jud 64 :TEDALRFTCRHLGLDL T0371 129 :IGEVNALVLLDDEGFNWFHDLNKTVNLLRKRTIPAIVANTD 1jud 80 :DARTRSTLCDAYLRLAPFSEVPDSLRELKRRGLKLAILSNG T0371 182 :AIGGVATMIESIL 1jud 121 :SPQSIDAVVSHAG T0371 195 :GRRFIRFGKPDSQMFMFAYDML 1jud 143 :SVDPVQVYKPDNRVYELAEQAL T0371 221 :EISKREILMVGDTLH 1jud 165 :GLDRSAILFVSSNAW T0371 237 :DILGGNKFGLDTALVLTGNTRI 1jud 180 :DATGARYFGFPTCWINRTGNVF T0371 262 :ETKIKSTGIVPTHICESAVI 1jud 202 :EEMGQTPDWEVTSLRAVVEL Number of specific fragments extracted= 10 number of extra gaps= 0 total=1392 Number of alignments=99 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vjrA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vjrA expands to /projects/compbio/data/pdb/1vjr.pdb.gz 1vjrA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 172, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 173, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 177, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 178, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 180, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 181, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 183, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 184, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 186, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 187, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 237, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 241, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 243, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 245, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 247, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 249, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 271, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 275, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 277, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 279, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 281, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 283, because occupancy 0.500 <= existing 0.500 in 1vjrA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1601, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1605, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1607, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1609, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1611, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1613, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1616, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1620, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1622, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1624, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1626, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1628, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1630, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1632, because occupancy 0.500 <= existing 0.500 in 1vjrA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1868, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1872, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1874, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1876, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1878, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1880, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1912, because occupancy 0.350 <= existing 0.650 in 1vjrA Skipped atom 1914, because occupancy 0.350 <= existing 0.650 in 1vjrA Skipped atom 1916, because occupancy 0.350 <= existing 0.650 in 1vjrA Skipped atom 1918, because occupancy 0.350 <= existing 0.650 in 1vjrA Skipped atom 1920, because occupancy 0.350 <= existing 0.650 in 1vjrA Skipped atom 1922, because occupancy 0.350 <= existing 0.650 in 1vjrA Skipped atom 1930, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1934, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1936, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1938, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1940, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1942, because occupancy 0.500 <= existing 0.500 in 1vjrA # T0371 read from 1vjrA/merged-good-all-a2m # 1vjrA read from 1vjrA/merged-good-all-a2m # adding 1vjrA to template set # found chain 1vjrA in template set Warning: unaligning (T0371)S8 because of BadResidue code BAD_PEPTIDE at template residue (1vjrA)H0 T0371 9 :LLPKYKCIFFDAFGVLKTYNGLLPGIENTFDYLKAQGQDYYIVTNDASRSPEQLADSYHKLGL 1vjrA 1 :VLDKIELFILDMDGTFYLDDSLLPGSLEFLETLKEKNKRFVFFTNNSSLGAQDYVRKLRNMGV T0371 73 :SITADKIISSGMITKEYIDLKVDGGIVAYLGTANSANYLVSDGIKML 1vjrA 64 :DVPDDAVVTSGEITAEHMLKRFGRCRIFLLGTPQLKKVFEAYGHVID T0371 129 :IGEVNALVLLDDEGFN 1vjrA 111 :EENPDFVVLGFDKTLT T0371 146 :FHDLNKTVNLLR 1vjrA 127 :YERLKKACILLR T0371 159 :RTIPAIVANTDNTYP 1vjrA 139 :KGKFYIATHPDINCP T0371 175 :TKTDVAIAIGGVATMIESILGRRF 1vjrA 154 :SKEGPVPDAGSIMAAIEASTGRKP T0371 199 :IRFGKPDSQMFMFAYDML 1vjrA 179 :LIAGKPNPLVVDVISEKF T0371 221 :EISKREILMVGDTLHTDILGGNKFGLDTALVLTGNTRIDD 1vjrA 197 :GVPKERMAMVGDRLYTDVKLGKNAGIVSILVLTGETTPED T0371 265 :IKSTGIVPTHICES 1vjrA 237 :LERAETKPDFVFKN T0371 280 :VIEL 1vjrA 251 :LGEL Number of specific fragments extracted= 10 number of extra gaps= 1 total=1402 Number of alignments=100 # 1vjrA read from 1vjrA/merged-good-all-a2m # found chain 1vjrA in template set T0371 9 :LLPKYKCIFFDAFGVLKTYNGLLPGIENTFDYLKAQGQDYYIVTNDASRSPEQLADSYHKLGL 1vjrA 1 :VLDKIELFILDMDGTFYLDDSLLPGSLEFLETLKEKNKRFVFFTNNSSLGAQDYVRKLRNMGV T0371 73 :SITADKIISSGMITKEYIDLKVDGGIVAYLGTANSANYLVSDGIKMLP 1vjrA 64 :DVPDDAVVTSGEITAEHMLKRFGRCRIFLLGTPQLKKVFEAYGHVIDE T0371 130 :GEVNALVLLDDEGFN 1vjrA 112 :ENPDFVVLGFDKTLT T0371 146 :FHDLNKTVNLL 1vjrA 127 :YERLKKACILL T0371 158 :KRTIPAIVANTDNTYP 1vjrA 138 :RKGKFYIATHPDINCP T0371 175 :TKTDVAIAIGGVATMIESILGRRF 1vjrA 154 :SKEGPVPDAGSIMAAIEASTGRKP T0371 199 :IRFGKPDSQMFMFAYDML 1vjrA 179 :LIAGKPNPLVVDVISEKF T0371 221 :EISKREILMVGDTLHTDILGGNKFGLDTALVLTGNTRIDDAETK 1vjrA 197 :GVPKERMAMVGDRLYTDVKLGKNAGIVSILVLTGETTPEDLERA T0371 269 :GIVPTHICES 1vjrA 241 :ETKPDFVFKN T0371 280 :VIEL 1vjrA 251 :LGEL Number of specific fragments extracted= 10 number of extra gaps= 0 total=1412 Number of alignments=101 # 1vjrA read from 1vjrA/merged-good-all-a2m # found chain 1vjrA in template set T0371 10 :LPKYKCIFFDAFGVLKTYNGLLPGIENTFDYLKAQGQDYYIVTNDASRSPEQLADSYHKLGL 1vjrA 2 :LDKIELFILDMDGTFYLDDSLLPGSLEFLETLKEKNKRFVFFTNNSSLGAQDYVRKLRNMGV T0371 73 :SITADKIISSGMITKEYIDLKVDGGIVAYLGTANSANYLVSDGIKMLP 1vjrA 64 :DVPDDAVVTSGEITAEHMLKRFGRCRIFLLGTPQLKKVFEAYGHVIDE T0371 130 :GEVNALVLLDDEGFN 1vjrA 112 :ENPDFVVLGFDKTLT T0371 147 :HDLNKTVNLLRKRTIPAIVANTDNTYPLTKT 1vjrA 127 :YERLKKACILLRKGKFYIATHPDINCPSKEG T0371 179 :VAIAIGGVATMIESILGRRF 1vjrA 158 :PVPDAGSIMAAIEASTGRKP T0371 199 :IRFGKPDSQMFMFAYDML 1vjrA 179 :LIAGKPNPLVVDVISEKF T0371 221 :EISKREILMVGDTLHTDILGGNKFGLDTALVLTGNTRIDDAETKIKSTGIVPTHICESAVI 1vjrA 197 :GVPKERMAMVGDRLYTDVKLGKNAGIVSILVLTGETTPEDLERAETKPDFVFKNLGELAKA Number of specific fragments extracted= 7 number of extra gaps= 0 total=1419 Number of alignments=102 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zrn/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zrn expands to /projects/compbio/data/pdb/1zrn.pdb.gz 1zrn:Warning: there is no chain 1zrn will retry with 1zrnA # T0371 read from 1zrn/merged-good-all-a2m # 1zrn read from 1zrn/merged-good-all-a2m # adding 1zrn to template set # found chain 1zrn in template set Warning: unaligning (T0371)K12 because first residue in template chain is (1zrn)Y3 T0371 13 :YKCIFFDAFGVLKTYN 1zrn 4 :IKGIAFDLYGTLFDVH T0371 29 :GLL 1zrn 27 :EAF T0371 32 :PGIENTFDYLKAQ 1zrn 31 :GRGREISALWRQK T0371 59 :PEQLADSYHK 1zrn 45 :LEYTWLRSLM T0371 70 :GL 1zrn 55 :NR T0371 73 :SITADKI 1zrn 57 :YVNFQQA T0371 104 :TANSANYLV 1zrn 64 :TEDALRFTC T0371 113 :SDGI 1zrn 74 :HLGL T0371 122 :SAIDDSNIGEVNAL 1zrn 78 :DLDARTRSTLCDAY T0371 140 :D 1zrn 92 :L T0371 142 :GFNWFHDLNKTVNLLRKRTIPA 1zrn 93 :RLAPFSEVPDSLRELKRRGLKL T0371 164 :IVANTDNTY 1zrn 116 :ILSNGSPQS T0371 174 :LTKTDVAIA 1zrn 125 :IDAVVSHAG T0371 186 :VATMIESILGRRFIRFGKPDSQMFMFAYDML 1zrn 134 :LRDGFDHLLSVDPVQVYKPDNRVYELAEQAL T0371 221 :EISKREILMVGDT 1zrn 165 :GLDRSAILFVASN T0371 235 :HTDILGGNKFGLDTALVL 1zrn 178 :AWDATGARYFGFPTCWIN T0371 254 :GNTRI 1zrn 196 :RTGNV T0371 265 :IKSTGIVPTHICES 1zrn 201 :FEEMGQTPDWEVTS T0371 280 :VIE 1zrn 215 :LRA Number of specific fragments extracted= 19 number of extra gaps= 0 total=1438 Number of alignments=103 # 1zrn read from 1zrn/merged-good-all-a2m # found chain 1zrn in template set Warning: unaligning (T0371)K12 because first residue in template chain is (1zrn)Y3 T0371 13 :YKCIFFDAFGVLKTYNGLLPGIENTF 1zrn 4 :IKGIAFDLYGTLFDVHSVVGRCDEAF T0371 56 :SRSPEQLADSYHKLG 1zrn 30 :PGRGREISALWRQKQ T0371 83 :GMITKEYI 1zrn 45 :LEYTWLRS T0371 91 :DL 1zrn 54 :MN T0371 96 :G 1zrn 56 :R T0371 97 :GIVAYLGTANSANYLVSDGIKML 1zrn 58 :VNFQQATEDALRFTCRHLGLDLD T0371 130 :GEVNALVLLDDEGFNWFHDLNKTVNLLRKRTIPAIVANTDNTYPLTKTDVAIAIGGVATMI 1zrn 81 :ARTRSTLCDAYLRLAPFSEVPDSLRELKRRGLKLAILSNGSPQSIDAVVSHAGLRDGFDHL T0371 194 :LGRRFIRFGKPDSQMFMFAYDML 1zrn 142 :LSVDPVQVYKPDNRVYELAEQAL T0371 221 :EISKREILMVGDTLH 1zrn 165 :GLDRSAILFVASNAW T0371 237 :DILGGNKFGLDTALVLTGNTR 1zrn 180 :DATGARYFGFPTCWINRTGNV T0371 265 :IKSTGIVPTHICES 1zrn 201 :FEEMGQTPDWEVTS T0371 280 :VIEL 1zrn 215 :LRAV Number of specific fragments extracted= 12 number of extra gaps= 0 total=1450 Number of alignments=104 # 1zrn read from 1zrn/merged-good-all-a2m # found chain 1zrn in template set Warning: unaligning (T0371)K12 because first residue in template chain is (1zrn)Y3 Warning: unaligning (T0371)E282 because last residue in template chain is (1zrn)F222 T0371 13 :YKCIFFDAFGVLKTYNGLLPGIE 1zrn 4 :IKGIAFDLYGTLFDVHSVVGRCD T0371 36 :NTFDYLKA 1zrn 35 :EISALWRQ T0371 57 :RSPEQLADSYHKLGLF 1zrn 43 :KQLEYTWLRSLMNRYV T0371 81 :SSGMIT 1zrn 59 :NFQQAT T0371 104 :TANSANYLVSDGIKM 1zrn 65 :EDALRFTCRHLGLDL T0371 129 :IGEVNALVLLDDEGFNWFHDLNKTVNLLRKRTIPAIVANTD 1zrn 80 :DARTRSTLCDAYLRLAPFSEVPDSLRELKRRGLKLAILSNG T0371 182 :AIGGVATMIESIL 1zrn 121 :SPQSIDAVVSHAG T0371 195 :GRRFIRFGKPDSQMFMFAYDML 1zrn 143 :SVDPVQVYKPDNRVYELAEQAL T0371 221 :EISKREILMVGDTLH 1zrn 165 :GLDRSAILFVASNAW T0371 237 :DILGGNKFGLDTALVLTGNTRI 1zrn 180 :DATGARYFGFPTCWINRTGNVF T0371 262 :ETKIKSTGIVPTHICESAVI 1zrn 202 :EEMGQTPDWEVTSLRAVVEL Number of specific fragments extracted= 11 number of extra gaps= 0 total=1461 Number of alignments=105 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pw5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0371/1pw5A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0371/1pw5A/merged-good-all-a2m.gz for input Trying 1pw5A/merged-good-all-a2m Error: Couldn't open file 1pw5A/merged-good-all-a2m or 1pw5A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1u7pA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1u7pA expands to /projects/compbio/data/pdb/1u7p.pdb.gz 1u7pA:# T0371 read from 1u7pA/merged-good-all-a2m # 1u7pA read from 1u7pA/merged-good-all-a2m # adding 1u7pA to template set # found chain 1u7pA in template set T0371 13 :YKCIFFDAFGVLKTYNGLL 1u7pA 5 :PKLAVFDLDYTLWPFWVDT T0371 70 :GL 1u7pA 24 :HV T0371 73 :SIT 1u7pA 26 :DPP T0371 79 :I 1u7pA 29 :F T0371 97 :GI 1u7pA 30 :HK T0371 122 :SAID 1u7pA 32 :SSDG T0371 134 :ALVLLDDEGFNWFHDLNKTVNLLRKRTIPAIVANTDNTYP 1u7pA 36 :TVRDRRGQNIQLYPEVPEVLGRLQSLGVPVAAASRTSEIQ T0371 174 :LTKTDVAIA 1u7pA 77 :ANQLLELFD T0371 186 :VATMI 1u7pA 86 :LGKYF T0371 194 :LGRRFIRFGK 1u7pA 91 :IQREIYPGSK T0371 206 :SQMFMFAYDML 1u7pA 101 :VTHFERLHHKT T0371 221 :EISKREILMVGDT 1u7pA 112 :GVPFSQMVFFDDE T0371 235 :HTDILGGNKFGLDTALVL 1u7pA 125 :NRNIIDVGRLGVTCIHIR T0371 254 :GNTRIDDAETKIK 1u7pA 143 :DGMSLQTLTQGLE Number of specific fragments extracted= 14 number of extra gaps= 0 total=1475 Number of alignments=106 # 1u7pA read from 1u7pA/merged-good-all-a2m # found chain 1u7pA in template set T0371 12 :KYKCIFFDAFGVLKTYNGLL 1u7pA 4 :LPKLAVFDLDYTLWPFWVDT T0371 73 :SITAD 1u7pA 24 :HVDPP T0371 118 :MLPVSAI 1u7pA 29 :FHKSSDG T0371 134 :ALVLLDDEGFNWFHDLNKTVNLLRKRTIPAIVANT 1u7pA 36 :TVRDRRGQNIQLYPEVPEVLGRLQSLGVPVAAASR T0371 169 :DNTYPLTKTDVAIAIGGVATMI 1u7pA 72 :SEIQGANQLLELFDLGKYFIQR T0371 198 :FIRFGK 1u7pA 94 :EIYPGS T0371 209 :FMFAYDMLRQKMEISKREILMVGDT 1u7pA 100 :KVTHFERLHHKTGVPFSQMVFFDDE T0371 235 :HTDILGGNKFGL 1u7pA 125 :NRNIIDVGRLGV T0371 248 :TALVLTGNTRIDDAETKI 1u7pA 137 :TCIHIRDGMSLQTLTQGL Number of specific fragments extracted= 9 number of extra gaps= 0 total=1484 Number of alignments=107 # 1u7pA read from 1u7pA/merged-good-all-a2m # found chain 1u7pA in template set T0371 13 :YKCIFFDAFGVLKTYNG 1u7pA 5 :PKLAVFDLDYTLWPFWV T0371 73 :SIT 1u7pA 24 :HVD T0371 114 :DGIKMLP 1u7pA 27 :PPFHKSS T0371 132 :VNALVLLDDEGFNWFHDLNKTVNLLRKRTIPAIVANT 1u7pA 34 :DGTVRDRRGQNIQLYPEVPEVLGRLQSLGVPVAAASR T0371 173 :PL 1u7pA 71 :TS T0371 182 :AIGGVATMIESIL 1u7pA 73 :EIQGANQLLELFD T0371 195 :GRRFIRFGKPDSQMFMFAYDML 1u7pA 90 :FIQREIYPGSKVTHFERLHHKT T0371 221 :EISKREILMVGDTLH 1u7pA 112 :GVPFSQMVFFDDENR T0371 237 :DILGGNKFGLDTALV 1u7pA 127 :NIIDVGRLGVTCIHI T0371 253 :TGNTRIDDA 1u7pA 142 :RDGMSLQTL Number of specific fragments extracted= 10 number of extra gaps= 0 total=1494 Number of alignments=108 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1te2A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0371 read from 1te2A/merged-good-all-a2m # 1te2A read from 1te2A/merged-good-all-a2m # found chain 1te2A in training set Warning: unaligning (T0371)L10 because first residue in template chain is (1te2A)R5 Warning: unaligning (T0371)A180 because of BadResidue code BAD_PEPTIDE in next template residue (1te2A)F129 Warning: unaligning (T0371)I181 because of BadResidue code BAD_PEPTIDE at template residue (1te2A)F129 T0371 12 :KYKCIFFDAFGVLKTYNGLL 1te2A 6 :QILAAIFDMDGLLIDSEPLW T0371 59 :PEQLADSYHKLGL 1te2A 26 :DRAELDVMASLGV T0371 73 :SIT 1te2A 39 :DIS T0371 76 :ADKI 1te2A 43 :RNEL T0371 97 :GIVAYLGTANSANYLVSDG 1te2A 47 :PDTLGLRIDMVVDLWYARQ T0371 118 :MLPVSAIDDSNIGEVNALVLLDDEGFNWFHDLNKTVNLLRKRTIPA 1te2A 66 :PWNGPSRQEVVERVIARAISLVEETRPLLPGVREAVALCKEQGLLV T0371 164 :IVANTDNTY 1te2A 113 :LASASPLHM T0371 174 :LTKTDV 1te2A 122 :LEKVLT T0371 182 :A 1te2A 130 :D T0371 186 :VATMIESILGRRFIRFGKPDSQMFMFAYDML 1te2A 131 :LRDSFDALASAEKLPYSKPHPQVYLDCAAKL T0371 221 :EISKREILMVGDT 1te2A 162 :GVDPLTCVALEDS T0371 235 :HTDILGGNKFGLDTALVLTGNT 1te2A 175 :VNGMIASKAARMRSIVVPAPEA T0371 257 :RIDD 1te2A 198 :NDPR T0371 265 :IKS 1te2A 202 :FVL T0371 272 :PTHICES 1te2A 205 :ANVKLSS T0371 280 :VIEL 1te2A 212 :LTEL Number of specific fragments extracted= 16 number of extra gaps= 1 total=1510 Number of alignments=109 # 1te2A read from 1te2A/merged-good-all-a2m # found chain 1te2A in training set Warning: unaligning (T0371)P11 because first residue in template chain is (1te2A)R5 Warning: unaligning (T0371)A180 because of BadResidue code BAD_PEPTIDE in next template residue (1te2A)F129 Warning: unaligning (T0371)I181 because of BadResidue code BAD_PEPTIDE at template residue (1te2A)F129 T0371 12 :KYKCIFFDAFGVLKTYN 1te2A 6 :QILAAIFDMDGLLIDSE T0371 32 :PGIENTF 1te2A 23 :PLWDRAE T0371 39 :DYLKAQG 1te2A 31 :DVMASLG T0371 55 :ASRSPEQLADSYHKLG 1te2A 50 :LGLRIDMVVDLWYARQ T0371 71 :LFSITADKIISS 1te2A 67 :WNGPSRQEVVER T0371 103 :GTANSANYLVSD 1te2A 79 :VIARAISLVEET T0371 143 :FNWFHDLNKTVNLLRKRTIPAIVANTDNTYPLTKTDV 1te2A 91 :RPLLPGVREAVALCKEQGLLVGLASASPLHMLEKVLT T0371 182 :AIGGVATMI 1te2A 130 :DLRDSFDAL T0371 194 :LGRRFIRFGKPDSQMFMFAYDML 1te2A 139 :ASAEKLPYSKPHPQVYLDCAAKL T0371 221 :EISKREILMVGDTLH 1te2A 162 :GVDPLTCVALEDSVN T0371 237 :DILGGNKFGLDTALVLTGNT 1te2A 177 :GMIASKAARMRSIVVPAPEA T0371 257 :RIDDAET 1te2A 198 :NDPRFVL T0371 272 :PTHICES 1te2A 205 :ANVKLSS T0371 280 :VIEL 1te2A 212 :LTEL Number of specific fragments extracted= 14 number of extra gaps= 1 total=1524 Number of alignments=110 # 1te2A read from 1te2A/merged-good-all-a2m # found chain 1te2A in training set Warning: unaligning (T0371)S192 because of BadResidue code BAD_PEPTIDE in next template residue (1te2A)F129 Warning: unaligning (T0371)I193 because of BadResidue code BAD_PEPTIDE at template residue (1te2A)F129 T0371 13 :YKCIFFDAFGVLKT 1te2A 7 :ILAAIFDMDGLLID T0371 30 :LLPGIENTF 1te2A 21 :SEPLWDRAE T0371 63 :ADSYHKLGL 1te2A 30 :LDVMASLGV T0371 73 :SITAD 1te2A 39 :DISRR T0371 78 :KIISSGMITKEYIDLKVDGGI 1te2A 50 :LGLRIDMVVDLWYARQPWNGP T0371 103 :GTANSANYLVSD 1te2A 71 :SRQEVVERVIAR T0371 135 :LVLLDDEGFNWFHDLNKTVNLLRKRTIPAIVANTD 1te2A 83 :AISLVEETRPLLPGVREAVALCKEQGLLVGLASAS T0371 182 :AIGGVATMIE 1te2A 118 :PLHMLEKVLT T0371 194 :L 1te2A 130 :D T0371 195 :GRRFIRFGKPDSQMFMFAYDML 1te2A 140 :SAEKLPYSKPHPQVYLDCAAKL T0371 221 :EISKREILMVGDTLH 1te2A 162 :GVDPLTCVALEDSVN T0371 237 :DILGGNKFGLDTALVLT 1te2A 177 :GMIASKAARMRSIVVPA T0371 259 :DDAE 1te2A 194 :PEAQ T0371 263 :TKIKSTGIVPTHICES 1te2A 200 :PRFVLANVKLSSLTEL Number of specific fragments extracted= 14 number of extra gaps= 1 total=1538 Number of alignments=111 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fezA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1fezA expands to /projects/compbio/data/pdb/1fez.pdb.gz 1fezA:# T0371 read from 1fezA/merged-good-all-a2m # 1fezA read from 1fezA/merged-good-all-a2m # adding 1fezA to template set # found chain 1fezA in template set Warning: unaligning (T0371)K12 because first residue in template chain is (1fezA)K5 T0371 13 :YKCIFFDAFGVLKTYNGLL 1fezA 6 :IEAVIFDWAGTTVDYGCFA T0371 59 :PEQLADSYHKLGL 1fezA 26 :LEVFMEIFHKRGV T0371 73 :SITADKIISS 1fezA 39 :AITAEEARKP T0371 83 :GMITKEYID 1fezA 54 :IDHVRALTE T0371 104 :TANSANYLVSDGIKMLPVSAIDDSNIGEVNALVLLDDEGFNWFHDLNKTVNLLRKRTIPAIVANT 1fezA 63 :MPRIASEWNRVFRQLPTEADIQEMYEEFEEILFAILPRYASPINAVKEVIASLRERGIKIGSTTG T0371 174 :LTKTD 1fezA 128 :YTREM T0371 186 :VATMIESIL 1fezA 133 :MDIVAKEAA T0371 195 :GRRFIRFGKPDSQMFMFAYDML 1fezA 152 :TPDDVPAGRPYPWMCYKNAMEL T0371 221 :EI 1fezA 174 :GV T0371 223 :SKREILMVGDT 1fezA 177 :PMNHMIKVGDT T0371 235 :HTDILGGNKFGLDTALVLTGNTR 1fezA 188 :VSDMKEGRNAGMWTVGVILGSSE T0371 258 :IDDAETKIKSTG 1fezA 230 :IEVVRNRFVENG T0371 272 :PTHICES 1fezA 242 :AHFTIET T0371 280 :VIEL 1fezA 249 :MQEL Number of specific fragments extracted= 14 number of extra gaps= 0 total=1552 Number of alignments=112 # 1fezA read from 1fezA/merged-good-all-a2m # found chain 1fezA in template set Warning: unaligning (T0371)K12 because first residue in template chain is (1fezA)K5 T0371 13 :YKCIFFDAFGVLKTYNGL 1fezA 6 :IEAVIFDWAGTTVDYGCF T0371 57 :RSPEQLADSYHKLGL 1fezA 24 :APLEVFMEIFHKRGV T0371 73 :SITADKIISSGMI 1fezA 39 :AITAEEARKPMGL T0371 93 :KVDGGIVAYLGTANSANYLVSDGIKMLPVSAIDDSNIGEVNALVLLDDEGFNWFHDLNKTVNLLRKRTIPAIVANTDNTYPLTKTDVAIAIGGVA 1fezA 52 :LKIDHVRALTEMPRIASEWNRVFRQLPTEADIQEMYEEFEEILFAILPRYASPINAVKEVIASLRERGIKIGSTTGYTREMMDIVAKEAALQGYK T0371 188 :TMI 1fezA 148 :DFL T0371 194 :LGRRFIRFGKPDSQMFMFAYDML 1fezA 151 :VTPDDVPAGRPYPWMCYKNAMEL T0371 221 :EI 1fezA 174 :GV T0371 223 :SKREILMVGDTLH 1fezA 177 :PMNHMIKVGDTVS T0371 237 :DILGGNKFGLDTALVLTGNTR 1fezA 190 :DMKEGRNAGMWTVGVILGSSE T0371 258 :IDDAETKIKSTG 1fezA 230 :IEVVRNRFVENG T0371 272 :PTHICES 1fezA 242 :AHFTIET T0371 280 :VIEL 1fezA 249 :MQEL Number of specific fragments extracted= 12 number of extra gaps= 0 total=1564 Number of alignments=113 # 1fezA read from 1fezA/merged-good-all-a2m # found chain 1fezA in template set Warning: unaligning (T0371)K12 because first residue in template chain is (1fezA)K5 T0371 13 :YKCIFFDAFGVLKTYNGLLP 1fezA 6 :IEAVIFDWAGTTVDYGCFAP T0371 59 :PEQLADSYHKLGL 1fezA 26 :LEVFMEIFHKRGV T0371 73 :SITADKI 1fezA 39 :AITAEEA T0371 80 :ISSGMITKEYID 1fezA 51 :LLKIDHVRALTE T0371 104 :TANSANYLVSDGIKMLPVSAIDDSNIGEVNALVLLDDEGFNWFHDLNKTVNLLRKRTIPAIVANT 1fezA 63 :MPRIASEWNRVFRQLPTEADIQEMYEEFEEILFAILPRYASPINAVKEVIASLRERGIKIGSTTG T0371 181 :IAIGGVATMIESIL 1fezA 128 :YTREMMDIVAKEAA T0371 195 :GRRFIRFGKPDSQMFMFAYDML 1fezA 152 :TPDDVPAGRPYPWMCYKNAMEL T0371 221 :EI 1fezA 174 :GV T0371 223 :SKREILMVGDTLH 1fezA 177 :PMNHMIKVGDTVS T0371 237 :DILGGNKFGLDTALVLTGNT 1fezA 190 :DMKEGRNAGMWTVGVILGSS T0371 257 :RIDDAE 1fezA 214 :TEEEVE T0371 266 :KSTGIVPTHICESAV 1fezA 240 :NGAHFTIETMQELES Number of specific fragments extracted= 12 number of extra gaps= 0 total=1576 Number of alignments=114 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cr6B/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1cr6B expands to /projects/compbio/data/pdb/1cr6.pdb.gz 1cr6B:# T0371 read from 1cr6B/merged-good-all-a2m # 1cr6B read from 1cr6B/merged-good-all-a2m # adding 1cr6B to template set # found chain 1cr6B in template set Warning: unaligning (T0371)K14 because first residue in template chain is (1cr6B)R4 T0371 15 :CIFFDAFGVLKT 1cr6B 5 :VAAFDLDGVLAL T0371 29 :GLL 1cr6B 17 :PSI T0371 59 :PEQLADSYHKL 1cr6B 20 :AGAFRRSEEAL T0371 73 :SITADKIISSG 1cr6B 31 :ALPRDFLLGAY T0371 84 :MITKEYIDLK 1cr6B 48 :GPTEQLMKGK T0371 98 :IVAYLGTANSANYLVSD 1cr6B 58 :ITFSQWVPLMDESYRKS T0371 115 :GIKM 1cr6B 79 :GANL T0371 122 :SAIDDSNIGEVNALV 1cr6B 83 :PENFSISQIFSQAMA T0371 142 :GFNWFHDLNKTVNLLRKRTIPA 1cr6B 98 :ARSINRPMLQAAIALKKKGFTT T0371 164 :IVANTDNTY 1cr6B 121 :IVTNNWLDD T0371 175 :TKTDVA 1cr6B 130 :GDKRDS T0371 186 :VATMIESI 1cr6B 136 :LAQMMCEL T0371 194 :LGRRFIRFGKPDSQMFMFAYDML 1cr6B 151 :IESCQVGMIKPEPQIYNFLLDTL T0371 221 :EISKREILMVGDT 1cr6B 174 :KAKPNEVVFLDDF T0371 235 :HTDILGGNKFGLDTALVL 1cr6B 187 :GSNLKPARDMGMVTILVH T0371 254 :GNTR 1cr6B 205 :NTAS T0371 258 :IDDAETK 1cr6B 211 :RELEKVT Number of specific fragments extracted= 17 number of extra gaps= 0 total=1593 Number of alignments=115 # 1cr6B read from 1cr6B/merged-good-all-a2m # found chain 1cr6B in template set Warning: unaligning (T0371)K14 because first residue in template chain is (1cr6B)R4 T0371 15 :CIFFDAFGVLKT 1cr6B 5 :VAAFDLDGVLAL T0371 27 :YNGLLPGIENTF 1cr6B 43 :TEFPEGPTEQLM T0371 54 :DASRSPEQLADSY 1cr6B 55 :KGKITFSQWVPLM T0371 104 :TANSANYLVSDGIKMLPV 1cr6B 68 :DESYRKSSKACGANLPEN T0371 130 :GEVNALVLLDDEGFNWFHDLNKTVNLLRKRTIPAIVANT 1cr6B 86 :FSISQIFSQAMAARSINRPMLQAAIALKKKGFTTCIVTN T0371 169 :DNTYPLTKTDVAIA 1cr6B 131 :DKRDSLAQMMCELS T0371 185 :GVATMI 1cr6B 145 :QHFDFL T0371 194 :LGRRFIRFGKPDSQMFMFAYDML 1cr6B 151 :IESCQVGMIKPEPQIYNFLLDTL T0371 221 :EISKREILMVGDT 1cr6B 174 :KAKPNEVVFLDDF T0371 235 :HTDILGGNKFGLDTALVLT 1cr6B 187 :GSNLKPARDMGMVTILVHN T0371 254 :GNTRIDDAETKIKSTGIVP 1cr6B 207 :ASALRELEKVTGTQFPEAP Number of specific fragments extracted= 11 number of extra gaps= 0 total=1604 Number of alignments=116 # 1cr6B read from 1cr6B/merged-good-all-a2m # found chain 1cr6B in template set Warning: unaligning (T0371)K14 because first residue in template chain is (1cr6B)R4 T0371 15 :CIFFDAFGVLKT 1cr6B 5 :VAAFDLDGVLAL T0371 29 :GLLPGIEN 1cr6B 17 :PSIAGAFR T0371 72 :FSITADKIISSG 1cr6B 30 :LALPRDFLLGAY T0371 84 :MITKEYIDLKV 1cr6B 48 :GPTEQLMKGKI T0371 103 :GTANSANYLVSDGIKMLPVSAIDDSNIGEVNALVLLDDEGFNWFHDLNKTVNLLRKRTIPAIVANTDN 1cr6B 59 :TFSQWVPLMDESYRKSSKACGANLPENFSISQIFSQAMAARSINRPMLQAAIALKKKGFTTCIVTNNW T0371 173 :PLTKT 1cr6B 127 :LDDGD T0371 182 :AIGGVATMIESIL 1cr6B 132 :KRDSLAQMMCELS T0371 199 :IRFGKPDSQMFMFAYDML 1cr6B 156 :VGMIKPEPQIYNFLLDTL T0371 221 :EISKREILMVGDTLH 1cr6B 174 :KAKPNEVVFLDDFGS T0371 237 :DILGGNKFGLDTALVLTGNT 1cr6B 189 :NLKPARDMGMVTILVHNTAS Number of specific fragments extracted= 10 number of extra gaps= 0 total=1614 Number of alignments=117 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b30A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2b30A expands to /projects/compbio/data/pdb/2b30.pdb.gz 2b30A:# T0371 read from 2b30A/merged-good-all-a2m # 2b30A read from 2b30A/merged-good-all-a2m # adding 2b30A to template set # found chain 2b30A in template set Warning: unaligning (T0371)H147 because of BadResidue code BAD_PEPTIDE in next template residue (2b30A)E190 Warning: unaligning (T0371)D148 because of BadResidue code BAD_PEPTIDE at template residue (2b30A)E190 T0371 3 :IESFKSLL 2b30A 18 :VEEALKGA T0371 12 :KYKCIFFDAFGVLKTYNGLL 2b30A 26 :DIKLLLIDFDGTLFVDKDIK T0371 32 :PGIENTFDYLKAQGQDYYIVT 2b30A 48 :SENIDAIKEAIEKGYMVSICT T0371 56 :SRSPEQLADSY 2b30A 69 :GRSKVGILSAF T0371 67 :HKLGLFSIT 2b30A 85 :KKMNFYGMP T0371 79 :IISSGMITKEYI 2b30A 94 :GVYINGTIVYDQ T0371 91 :DLKVDGGIVAYLGTANSANYLVSDGI 2b30A 107 :GYTLLDETIETDVYAELISYLVEKNL T0371 130 :GEVNALVLLDDE 2b30A 177 :RTMNKLMIVLDP T0371 149 :LNKTVNLLRKR 2b30A 191 :SKTVIGNLKQK T0371 168 :TDNTYPLT 2b30A 203 :KNKLTIFT T0371 181 :IAIGG 2b30A 211 :TYNGH T0371 198 :FIRFGK 2b30A 220 :KLGHDK T0371 206 :SQMFMFAYDML 2b30A 226 :YTGINYLLKHY T0371 221 :EISKREILMVGDT 2b30A 237 :NISNDQVLVVGDA T0371 235 :HTDILGGN 2b30A 250 :ENDIAMLS T0371 245 :GLDTALVL 2b30A 258 :NFKYSFAV T0371 255 :NTRIDDAETK 2b30A 266 :ANATDSAKSH T0371 272 :PTHICE 2b30A 276 :AKCVLP Number of specific fragments extracted= 18 number of extra gaps= 1 total=1632 Number of alignments=118 # 2b30A read from 2b30A/merged-good-all-a2m # found chain 2b30A in template set Warning: unaligning (T0371)Q2 because first residue in template chain is (2b30A)K17 Warning: unaligning (T0371)G142 because of BadResidue code BAD_PEPTIDE in next template residue (2b30A)E190 Warning: unaligning (T0371)D148 because of BadResidue code BAD_PEPTIDE at template residue (2b30A)E190 T0371 3 :IESFKSLLP 2b30A 18 :VEEALKGAD T0371 13 :YKCIFFDAFGVL 2b30A 27 :IKLLLIDFDGTL T0371 25 :KTYNGLL 2b30A 40 :VDKDIKV T0371 32 :PGIENTFDYLKAQGQDYYIVTNDASRSP 2b30A 48 :SENIDAIKEAIEKGYMVSICTGRSKVGI T0371 60 :EQLADSY 2b30A 81 :EENLKKM T0371 73 :SIT 2b30A 88 :NFY T0371 76 :ADKIISSGMITKEYIDLKVDGGIVAYLGTANSANYLVSDGI 2b30A 92 :MPGVYINGTIVYDQIGYTLLDETIETDVYAELISYLVEKNL T0371 117 :KMLPVSAIDDSNI 2b30A 143 :SNYVTEDNKYADF T0371 130 :GEVNALVLLDDE 2b30A 177 :RTMNKLMIVLDP T0371 149 :LNKTVNLLRKR 2b30A 191 :SKTVIGNLKQK T0371 161 :I 2b30A 202 :F T0371 169 :DNTYP 2b30A 203 :KNKLT T0371 180 :AI 2b30A 208 :IF T0371 194 :LGRRF 2b30A 210 :TTYNG T0371 199 :IRFGK 2b30A 219 :TKLGH T0371 208 :MFMFAYDMLRQKMEISKREILMVGDTLH 2b30A 224 :DKYTGINYLLKHYNISNDQVLVVGDAEN T0371 237 :DILGGNKFGL 2b30A 252 :DIAMLSNFKY T0371 248 :TALV 2b30A 262 :SFAV T0371 255 :NTRIDDAETK 2b30A 266 :ANATDSAKSH T0371 272 :PTHICE 2b30A 276 :AKCVLP Number of specific fragments extracted= 20 number of extra gaps= 1 total=1652 Number of alignments=119 # 2b30A read from 2b30A/merged-good-all-a2m # found chain 2b30A in template set Warning: unaligning (T0371)S5 because first residue in template chain is (2b30A)K17 Warning: unaligning (T0371)G142 because of BadResidue code BAD_PEPTIDE in next template residue (2b30A)E190 Warning: unaligning (T0371)D148 because of BadResidue code BAD_PEPTIDE at template residue (2b30A)E190 T0371 6 :FKSLLPK 2b30A 18 :VEEALKG T0371 13 :YKCIFFDAFGVLKTYNG 2b30A 27 :IKLLLIDFDGTLFVDKD T0371 30 :LLPGIENTFDYLKAQGQDYYIVTNDA 2b30A 46 :VPSENIDAIKEAIEKGYMVSICTGRS T0371 63 :ADSYHKLGL 2b30A 72 :KVGILSAFG T0371 72 :FSITADKI 2b30A 113 :ETIETDVY T0371 105 :ANSANYLVSDGIK 2b30A 121 :AELISYLVEKNLV T0371 123 :AIDDSNIGEVNALVLLDDE 2b30A 170 :HNEMLKYRTMNKLMIVLDP T0371 149 :LNKTVNLLRKR 2b30A 191 :SKTVIGNLKQK T0371 199 :IRFGKPDSQMFMFAYDML 2b30A 219 :TKLGHDKYTGINYLLKHY T0371 221 :EISKREILMVGDTLH 2b30A 237 :NISNDQVLVVGDAEN T0371 237 :DILGGNKFGLDTA 2b30A 252 :DIAMLSNFKYSFA Number of specific fragments extracted= 11 number of extra gaps= 1 total=1663 Number of alignments=120 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ymqA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ymqA expands to /projects/compbio/data/pdb/1ymq.pdb.gz 1ymqA:# T0371 read from 1ymqA/merged-good-all-a2m # 1ymqA read from 1ymqA/merged-good-all-a2m # adding 1ymqA to template set # found chain 1ymqA in template set Warning: unaligning (T0371)Y13 because first residue in template chain is (1ymqA)T2 T0371 14 :KCIFFDAFGVLKTYNGLL 1ymqA 3 :KALFFDIDGTLVSFETHR T0371 32 :PGIENTFDYLKAQGQDYYIVT 1ymqA 23 :SSTIEALEAAHAKGLKIFIAT T0371 56 :SRS 1ymqA 44 :GRP T0371 64 :DSYHKLGLFS 1ymqA 54 :SELQDRNLID T0371 78 :KIISSGMITKEYIDLKVDGGIVAYLGTANSANYLVSDGIK 1ymqA 64 :GYITMNGAYCFVGEEVIYKSAIPQEEVKAMAAFCEKKGVP T0371 135 :LVLLDDEG 1ymqA 104 :CIFVEEHN T0371 143 :FNWFHDLNK 1ymqA 115 :CQPNEMVKK T0371 155 :LLRKR 1ymqA 124 :IFYDF T0371 160 :TI 1ymqA 168 :TC T0371 201 :FGKPDSQMFMFAYDML 1ymqA 184 :KGDTKQKGIDEIIRHF T0371 221 :EISKREILMVGDT 1ymqA 200 :GIKLEETMSFGDG T0371 235 :HTDILGGNKF 1ymqA 213 :GNDISMLRHA T0371 247 :DTALVL 1ymqA 223 :AIGVAM T0371 254 :GNTR 1ymqA 229 :GQAK T0371 259 :DDAETK 1ymqA 233 :EDVKAA T0371 272 :PTHICES 1ymqA 239 :ADYVTAP T0371 280 :VIE 1ymqA 246 :IDE Number of specific fragments extracted= 17 number of extra gaps= 0 total=1680 Number of alignments=121 # 1ymqA read from 1ymqA/merged-good-all-a2m # found chain 1ymqA in template set Warning: unaligning (T0371)Y13 because first residue in template chain is (1ymqA)T2 T0371 14 :KCIFFDAFGVLKTYN 1ymqA 3 :KALFFDIDGTLVSFE T0371 29 :GLL 1ymqA 19 :HRI T0371 32 :PGIENTFDYLKAQGQDYYIVTNDASR 1ymqA 23 :SSTIEALEAAHAKGLKIFIATGRPKA T0371 64 :DSYHKLGLFSI 1ymqA 54 :SELQDRNLIDG T0371 78 :KIISS 1ymqA 65 :YITMN T0371 84 :MITKEYIDLKVDGGIVA 1ymqA 70 :GAYCFVGEEVIYKSAIP T0371 146 :FHDLNKTVNLLRKRTIPAIVANTDN 1ymqA 87 :QEEVKAMAAFCEKKGVPCIFVEEHN T0371 182 :AIGGVAT 1ymqA 116 :QPNEMVK T0371 191 :ESI 1ymqA 123 :KIF T0371 194 :LGRRFIRFGK 1ymqA 177 :AFADVTAKGD T0371 208 :MFMFAYDMLRQKMEISKREILMVGDT 1ymqA 187 :TKQKGIDEIIRHFGIKLEETMSFGDG T0371 235 :HTDILGGNKFG 1ymqA 213 :GNDISMLRHAA T0371 247 :DTALVLTGN 1ymqA 224 :IGVAMGQAK T0371 259 :DDAETK 1ymqA 233 :EDVKAA T0371 272 :PTHICES 1ymqA 239 :ADYVTAP T0371 280 :VIE 1ymqA 246 :IDE Number of specific fragments extracted= 16 number of extra gaps= 0 total=1696 Number of alignments=122 # 1ymqA read from 1ymqA/merged-good-all-a2m # found chain 1ymqA in template set Warning: unaligning (T0371)Y13 because first residue in template chain is (1ymqA)T2 T0371 14 :KCIFFDAFGVLKTYNG 1ymqA 3 :KALFFDIDGTLVSFET T0371 30 :LLPGIENTFDYLKAQGQDYYIVTNDA 1ymqA 21 :IPSSTIEALEAAHAKGLKIFIATGRP T0371 77 :DKIISSG 1ymqA 47 :KAIINNL T0371 109 :NYLVSDGIKMLP 1ymqA 54 :SELQDRNLIDGY T0371 129 :IGEVNALVLLDDEGFN 1ymqA 66 :ITMNGAYCFVGEEVIY T0371 145 :WFHDLNKTVNLLRKRTIPAIVANTDNT 1ymqA 86 :PQEEVKAMAAFCEKKGVPCIFVEEHNI T0371 178 :DVAIAIGGVATMIESIL 1ymqA 113 :SVCQPNEMVKKIFYDFL T0371 204 :PDSQMFMFAYDML 1ymqA 187 :TKQKGIDEIIRHF T0371 221 :EISKREILMVGDTLH 1ymqA 200 :GIKLEETMSFGDGGN T0371 237 :DILGGNKFG 1ymqA 215 :DISMLRHAA T0371 249 :ALVLTGNTRIDDAE 1ymqA 224 :IGVAMGQAKEDVKA T0371 267 :STGIVPTHICE 1ymqA 238 :AADYVTAPIDE Number of specific fragments extracted= 12 number of extra gaps= 0 total=1708 Number of alignments=123 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nf2A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1nf2A expands to /projects/compbio/data/pdb/1nf2.pdb.gz 1nf2A:# T0371 read from 1nf2A/merged-good-all-a2m # 1nf2A read from 1nf2A/merged-good-all-a2m # adding 1nf2A to template set # found chain 1nf2A in template set Warning: unaligning (T0371)K12 because first residue in template chain is (1nf2A)M1 T0371 13 :YKCIFFDAFGVLKTYNGLL 1nf2A 2 :YRVFVFDLDGTLLNDNLEI T0371 32 :PGIENTFDYLKAQ 1nf2A 22 :EKDRRNIEKLSRK T0371 46 :QDYYIVT 1nf2A 35 :CYVVFAS T0371 56 :SRSPEQLADSYHKL 1nf2A 42 :GRMLVSTLNVEKKY T0371 72 :FSIT 1nf2A 58 :RTFP T0371 79 :IISSGMITKEYI 1nf2A 62 :TIAYNGAIVYLP T0371 91 :DLKVDGGIVAYLGTANSANYLVSDGIKMLPVSAID 1nf2A 75 :EGVILNEKIPPEVAKDIIEYIKPLNVHWQAYIDDV T0371 130 :GEVNALVLLDDEGFNWFHDLNKTV 1nf2A 117 :EEIKSYARHSNVDYRVEPNLSELV T0371 157 :RKRTIPA 1nf2A 141 :SKMGTTK T0371 164 :IVANT 1nf2A 149 :LLIDT T0371 175 :TKT 1nf2A 154 :PER T0371 186 :VATMIESILGRR 1nf2A 157 :LDELKEILSERF T0371 201 :FGK 1nf2A 189 :VDK T0371 206 :SQMFMFAYDML 1nf2A 192 :GKALRFLRERM T0371 221 :EISKREILMVGDT 1nf2A 203 :NWKKEEIVVFGDN T0371 235 :HTDILGGNKFGLDTA 1nf2A 216 :ENDLFMFEEAGLRVA T0371 252 :L 1nf2A 231 :M T0371 255 :NTRIDDAETK 1nf2A 232 :ENAIEKVKEA T0371 272 :PTHI 1nf2A 242 :SDIV Number of specific fragments extracted= 19 number of extra gaps= 0 total=1727 Number of alignments=124 # 1nf2A read from 1nf2A/merged-good-all-a2m # found chain 1nf2A in template set Warning: unaligning (T0371)K12 because first residue in template chain is (1nf2A)M1 T0371 13 :YKCIFFDAFGVLKTYNGLL 1nf2A 2 :YRVFVFDLDGTLLNDNLEI T0371 32 :PGIENTFDYLKAQ 1nf2A 22 :EKDRRNIEKLSRK T0371 46 :QDYYIVTNDA 1nf2A 35 :CYVVFASGRM T0371 59 :PEQLADSYHKLGLFSITA 1nf2A 45 :LVSTLNVEKKYFKRTFPT T0371 79 :IISSGMITKEYIDLKVDGGIVAYLGTANSANYLVSDGIKM 1nf2A 63 :IAYNGAIVYLPEEGVILNEKIPPEVAKDIIEYIKPLNVHW T0371 120 :PVSAID 1nf2A 111 :YSEKDN T0371 130 :GEVNALVLLDDEGFNWFHDLNK 1nf2A 117 :EEIKSYARHSNVDYRVEPNLSE T0371 155 :LLRKRTIPAIVANTDNTYP 1nf2A 139 :LVSKMGTTKLLLIDTPERL T0371 175 :TKTDVAIA 1nf2A 158 :DELKEILS T0371 191 :ESI 1nf2A 166 :ERF T0371 209 :FMFAYDMLRQKMEISKREILMVGDT 1nf2A 191 :KGKALRFLRERMNWKKEEIVVFGDN T0371 235 :HTDILGGNKFG 1nf2A 216 :ENDLFMFEEAG T0371 247 :DTALVLTG 1nf2A 227 :LRVAMENA T0371 258 :IDDAETK 1nf2A 235 :IEKVKEA T0371 272 :PTHIC 1nf2A 242 :SDIVT Number of specific fragments extracted= 15 number of extra gaps= 0 total=1742 Number of alignments=125 # 1nf2A read from 1nf2A/merged-good-all-a2m # found chain 1nf2A in template set T0371 13 :YKCIFFDAFGVLKTYNG 1nf2A 2 :YRVFVFDLDGTLLNDNL T0371 30 :LLPGIENTFDYLKA 1nf2A 20 :ISEKDRRNIEKLSR T0371 45 :GQDYYIVTNDA 1nf2A 34 :KCYVVFASGRM T0371 83 :GMITKEYIDLKVDGGIVAYL 1nf2A 45 :LVSTLNVEKKYFKRTFPTIA T0371 132 :VNALVLLDDEG 1nf2A 65 :YNGAIVYLPEE T0371 143 :FNWFHDLNKTVNLLRKRTIPAIVANTDNTYPLT 1nf2A 82 :KIPPEVAKDIIEYIKPLNVHWQAYIDDVLYSEK T0371 182 :AIGGVATMIESIL 1nf2A 115 :DNEEIKSYARHSN T0371 203 :KPDSQMFMFAYDML 1nf2A 189 :VDKGKALRFLRERM T0371 221 :EISKREILMVGDTLH 1nf2A 203 :NWKKEEIVVFGDNEN T0371 237 :DILGGNKFGLDTA 1nf2A 218 :DLFMFEEAGLRVA Number of specific fragments extracted= 10 number of extra gaps= 0 total=1752 Number of alignments=126 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qq5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0371 read from 1qq5A/merged-good-all-a2m # 1qq5A read from 1qq5A/merged-good-all-a2m # found chain 1qq5A in training set Warning: unaligning (T0371)K12 because first residue in template chain is (1qq5A)M1 T0371 13 :YKCIFFDAFGVLKTYNGLLPGIENT 1qq5A 2 :IKAVVFDAYGTLFDVQSVADATERA T0371 56 :SR 1qq5A 29 :GR T0371 59 :PEQLADSYHKL 1qq5A 31 :GEYITQVWRQK T0371 79 :I 1qq5A 42 :Q T0371 83 :GMITKEYI 1qq5A 43 :LEYSWLRA T0371 91 :DLKV 1qq5A 52 :MGRY T0371 97 :GIVAYLGTANSANYLVSDGI 1qq5A 56 :ADFWSVTREALAYTLGTLGL T0371 122 :SAIDDSNIGEVNAL 1qq5A 76 :EPDESFLADMAQAY T0371 141 :EGFNWFHDLNKTVNLLR 1qq5A 90 :NRLTPYPDAAQCLAELA T0371 160 :TIPA 1qq5A 107 :PLKR T0371 164 :IVANTDNTY 1qq5A 112 :ILSNGAPDM T0371 174 :LTKTDVAIA 1qq5A 121 :LQALVANAG T0371 186 :VATMIESILGRRFIRFGKPDSQMFMFAYDML 1qq5A 130 :LTDSFDAVISVDAKRVFKPHPDSYALVEEVL T0371 221 :EISKREILMVGDT 1qq5A 161 :GVTPAEVLFVSSN T0371 235 :HTDILGGNKFGLDTALVL 1qq5A 174 :GFDVGGAKNFGFSVARVA T0371 255 :NTRIDDAETKIKSTGI 1qq5A 192 :RLSQEALARELVSGTI T0371 272 :PTHICES 1qq5A 227 :PDFVVPA T0371 280 :VIEL 1qq5A 234 :LGDL Number of specific fragments extracted= 18 number of extra gaps= 0 total=1770 Number of alignments=127 # 1qq5A read from 1qq5A/merged-good-all-a2m # found chain 1qq5A in training set Warning: unaligning (T0371)K12 because first residue in template chain is (1qq5A)M1 T0371 13 :YKCIFFDAFGVLKTYNGLLPGIENT 1qq5A 2 :IKAVVFDAYGTLFDVQSVADATERA T0371 55 :ASRSPEQLADSYHK 1qq5A 27 :YPGRGEYITQVWRQ T0371 84 :MITKEYIDLKVDG 1qq5A 41 :KQLEYSWLRALMG T0371 97 :GIVAYLGTANSANYLVSDGIKML 1qq5A 56 :ADFWSVTREALAYTLGTLGLEPD T0371 130 :GEVNALVLLDDEGFNWFHDLNKTVNLL 1qq5A 79 :ESFLADMAQAYNRLTPYPDAAQCLAEL T0371 159 :RTIPAIVANTDNTYPLTKTDVAIAIGGVATMI 1qq5A 106 :APLKRAILSNGAPDMLQALVANAGLTDSFDAV T0371 194 :LGRRFIRFGKPDSQMFMFAYDML 1qq5A 138 :ISVDAKRVFKPHPDSYALVEEVL T0371 221 :EISKREILMVGDTLH 1qq5A 161 :GVTPAEVLFVSSNGF T0371 237 :DILGGNKFGLDTALVLT 1qq5A 176 :DVGGAKNFGFSVARVAR T0371 256 :TRIDDAETKIKSTGIV 1qq5A 193 :LSQEALARELVSGTIA T0371 272 :PTHICES 1qq5A 227 :PDFVVPA T0371 280 :VIEL 1qq5A 234 :LGDL Number of specific fragments extracted= 12 number of extra gaps= 0 total=1782 Number of alignments=128 # 1qq5A read from 1qq5A/merged-good-all-a2m # found chain 1qq5A in training set T0371 13 :YKCIFFDAFGVLKTYNGLLPGIENT 1qq5A 2 :IKAVVFDAYGTLFDVQSVADATERA T0371 38 :FDYLKA 1qq5A 35 :TQVWRQ T0371 57 :RSPEQLADSYHKLGL 1qq5A 41 :KQLEYSWLRALMGRY T0371 80 :ISSGMITKEY 1qq5A 56 :ADFWSVTREA T0371 107 :SANYLVSDGIKM 1qq5A 66 :LAYTLGTLGLEP T0371 129 :IGEVNALVLLDDEGFNWFHDLNKTVNLL 1qq5A 78 :DESFLADMAQAYNRLTPYPDAAQCLAEL T0371 159 :RTIPAIVANTD 1qq5A 106 :APLKRAILSNG T0371 182 :AIGGVATMIESIL 1qq5A 117 :APDMLQALVANAG T0371 201 :FGKPDSQMFMFAYDML 1qq5A 145 :VFKPHPDSYALVEEVL T0371 221 :EISKREILMVGDTLH 1qq5A 161 :GVTPAEVLFVSSNGF T0371 237 :DILGGNKFGLDTALVLT 1qq5A 176 :DVGGAKNFGFSVARVAR T0371 256 :TRIDDAE 1qq5A 193 :LSQEALA T0371 263 :TKIKSTGIVPTHICESAVI 1qq5A 222 :TYAEAPDFVVPALGDLPRL Number of specific fragments extracted= 13 number of extra gaps= 0 total=1795 Number of alignments=129 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fi1A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fi1A expands to /projects/compbio/data/pdb/2fi1.pdb.gz 2fi1A:# T0371 read from 2fi1A/merged-good-all-a2m # 2fi1A read from 2fi1A/merged-good-all-a2m # adding 2fi1A to template set # found chain 2fi1A in template set Warning: unaligning (T0371)L10 because first residue in template chain is (2fi1A)M4 T0371 12 :KYKCIFFDAFGVLKTYNGLL 2fi1A 5 :KYHDYIWDLGGTLLDNYETS T0371 59 :PEQLADSYHKLGL 2fi1A 25 :TAAFVETLALYGI T0371 73 :SITADKI 2fi1A 38 :TQDHDSV T0371 83 :GMITK 2fi1A 45 :YQALK T0371 102 :LGTANSANYLVS 2fi1A 50 :VSTPFAIETFAP T0371 115 :GI 2fi1A 62 :NL T0371 126 :DSNIGEVNALVLLDDEGFNWFHDLNKTVNLLRKRTIPAIVANTDNTY 2fi1A 64 :ENFLEKYKENEARELEHPILFEGVSDLLEDISNQGGRHFLVSHRNDQ T0371 174 :LTKTDVAIA 2fi1A 111 :VLEILEKTS T0371 186 :VATMIESILGRRFIRFGKPDSQMFMFAYDML 2fi1A 120 :IAAYFTEVVTSSSGFKRKPNPESMLYLREKY T0371 221 :EI 2fi1A 151 :QI T0371 225 :REILMVGDT 2fi1A 153 :SSGLVIGDR T0371 235 :HTDILGGNKFGLDTA 2fi1A 162 :PIDIEAGQAAGLDTH T0371 254 :GNTRIDDAETKI 2fi1A 177 :LFTSIVNLRQVL Number of specific fragments extracted= 13 number of extra gaps= 0 total=1808 Number of alignments=130 # 2fi1A read from 2fi1A/merged-good-all-a2m # found chain 2fi1A in template set Warning: unaligning (T0371)L10 because first residue in template chain is (2fi1A)M4 T0371 11 :P 2fi1A 5 :K T0371 13 :YKCIFFDAFGVLKTYNGLL 2fi1A 6 :YHDYIWDLGGTLLDNYETS T0371 32 :PGIENTFDY 2fi1A 26 :AAFVETLAL T0371 44 :QGQ 2fi1A 35 :YGI T0371 56 :SRSPEQLADSY 2fi1A 38 :TQDHDSVYQAL T0371 73 :SITAD 2fi1A 49 :KVSTP T0371 106 :NSANYL 2fi1A 54 :FAIETF T0371 122 :SAIDDSNIGEVNALVLLDDEGFNWFHDLNKTVNLLRKRTIPAIVANTDNTYP 2fi1A 60 :APNLENFLEKYKENEARELEHPILFEGVSDLLEDISNQGGRHFLVSHRNDQV T0371 175 :TKTDVAIAIGGVATMI 2fi1A 112 :LEILEKTSIAAYFTEV T0371 194 :LGRRFIRFGKPDSQMFMFAYDML 2fi1A 128 :VTSSSGFKRKPNPESMLYLREKY T0371 221 :EI 2fi1A 151 :QI T0371 225 :REILMVGDTLH 2fi1A 153 :SSGLVIGDRPI T0371 237 :DILGGNKFGLDTALV 2fi1A 164 :DIEAGQAAGLDTHLF T0371 256 :TRIDDAETKI 2fi1A 179 :TSIVNLRQVL Number of specific fragments extracted= 14 number of extra gaps= 0 total=1822 Number of alignments=131 # 2fi1A read from 2fi1A/merged-good-all-a2m # found chain 2fi1A in template set T0371 12 :KYKCIFFDAFGVLKTYNGL 2fi1A 5 :KYHDYIWDLGGTLLDNYET T0371 33 :GIENTFDYLKAQGQD 2fi1A 24 :STAAFVETLALYGIT T0371 57 :RSPEQLADSYHK 2fi1A 39 :QDHDSVYQALKV T0371 107 :SANYLVSDGIKMLP 2fi1A 51 :STPFAIETFAPNLE T0371 127 :SNIGEVNALVLLDDEGFNWFHDLNKTVNLLRKRTIPAIVANTD 2fi1A 65 :NFLEKYKENEARELEHPILFEGVSDLLEDISNQGGRHFLVSHR T0371 183 :IGGVATMIESIL 2fi1A 108 :NDQVLEILEKTS T0371 195 :GRRFIRFGKPDSQMFMFAYDML 2fi1A 129 :TSSSGFKRKPNPESMLYLREKY T0371 221 :EI 2fi1A 151 :QI T0371 225 :REILMVGDTLH 2fi1A 153 :SSGLVIGDRPI T0371 237 :DILGGNKFGLDT 2fi1A 164 :DIEAGQAAGLDT T0371 270 :IVPTHICESAV 2fi1A 176 :HLFTSIVNLRQ Number of specific fragments extracted= 11 number of extra gaps= 0 total=1833 Number of alignments=132 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rlmA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1rlmA expands to /projects/compbio/data/pdb/1rlm.pdb.gz 1rlmA:# T0371 read from 1rlmA/merged-good-all-a2m # 1rlmA read from 1rlmA/merged-good-all-a2m # adding 1rlmA to template set # found chain 1rlmA in template set Warning: unaligning (T0371)K12 because first residue in template chain is (1rlmA)A2 T0371 13 :YKCIFFDAFGVLKTYNGLL 1rlmA 3 :VKVIVTDMDGTFLNDAKTY T0371 32 :PGIENTFDYLKAQGQDYYIVT 1rlmA 24 :PRFMAQYQELKKRGIKFVVAS T0371 56 :SRSPEQL 1rlmA 45 :GNQYYQL T0371 71 :L 1rlmA 82 :G T0371 73 :SITADKI 1rlmA 83 :ELTRHES T0371 83 :GMITKEYID 1rlmA 90 :RIVIGELLK T0371 94 :VDGGIVAY 1rlmA 99 :DKQLNFVA T0371 102 :LGTANSANYLVSDGIKMLPVSAIDDSNIGEVNALVLLDDEG 1rlmA 117 :NAPEAFVALMAKHYHRLKPVKDYQEIDDVLFKFSLNLPDEQ T0371 146 :FHDLN 1rlmA 158 :IPLVI T0371 154 :NLLRK 1rlmA 163 :DKLHV T0371 169 :DNTY 1rlmA 170 :DGIM T0371 175 :TKTDVAIA 1rlmA 174 :KPVTSGFG T0371 198 :FIRFGK 1rlmA 187 :IPGLHK T0371 206 :SQMFMFAYDML 1rlmA 193 :ANGISRLLKRW T0371 221 :EISKREILMVGDT 1rlmA 204 :DLSPQNVVAIGDS T0371 235 :HTDILGGNK 1rlmA 217 :GNDAEMLKM T0371 246 :LDTALVL 1rlmA 226 :ARYSFAM T0371 254 :GN 1rlmA 233 :GN T0371 257 :RIDDAETK 1rlmA 235 :AAENIKQI T0371 272 :PTHICES 1rlmA 243 :ARYATDD T0371 280 :VIE 1rlmA 250 :NNH Number of specific fragments extracted= 21 number of extra gaps= 0 total=1854 Number of alignments=133 # 1rlmA read from 1rlmA/merged-good-all-a2m # found chain 1rlmA in template set Warning: unaligning (T0371)K12 because first residue in template chain is (1rlmA)A2 T0371 13 :YKCIFFDAFGVLKTYNGLL 1rlmA 3 :VKVIVTDMDGTFLNDAKTY T0371 32 :PGIENTFDYLKAQGQDYYIVTNDA 1rlmA 24 :PRFMAQYQELKKRGIKFVVASGNQ T0371 63 :ADSY 1rlmA 48 :YYQL T0371 76 :ADK 1rlmA 52 :ISF T0371 79 :IISSGMITK 1rlmA 65 :VAENGALVY T0371 89 :YIDLKVDGGIVAYLGTANSANYLVSDG 1rlmA 74 :EHGKQLFHGELTRHESRIVIGELLKDK T0371 116 :IKM 1rlmA 102 :LNF T0371 119 :LPVSAIDDSNI 1rlmA 113 :YVSENAPEAFV T0371 130 :GEVNALVLLDDE 1rlmA 144 :DVLFKFSLNLPD T0371 147 :HDLNKTVNLLRKR 1rlmA 156 :EQIPLVIDKLHVA T0371 183 :IGGVATMI 1rlmA 169 :LDGIMKPV T0371 194 :LGRRF 1rlmA 177 :TSGFG T0371 199 :IRFGK 1rlmA 186 :IIPGL T0371 208 :MFMFAYDMLRQKMEISKREILMVGDTLH 1rlmA 191 :HKANGISRLLKRWDLSPQNVVAIGDSGN T0371 237 :DILGGNKFGL 1rlmA 219 :DAEMLKMARY T0371 248 :TALVL 1rlmA 229 :SFAMG T0371 256 :TRIDDAETK 1rlmA 234 :NAAENIKQI T0371 272 :PTHICES 1rlmA 243 :ARYATDD T0371 280 :VI 1rlmA 250 :NN Number of specific fragments extracted= 19 number of extra gaps= 0 total=1873 Number of alignments=134 # 1rlmA read from 1rlmA/merged-good-all-a2m # found chain 1rlmA in template set T0371 13 :YKCIFFDAFGVLKTYNG 1rlmA 3 :VKVIVTDMDGTFLNDAK T0371 30 :LLPGIENTFDYLKAQGQDYYIVTNDA 1rlmA 22 :NQPRFMAQYQELKKRGIKFVVASGNQ T0371 63 :ADSYHKLGL 1rlmA 48 :YYQLISFFP T0371 72 :FSITADKII 1rlmA 82 :GELTRHESR T0371 85 :ITKEYIDLK 1rlmA 91 :IVIGELLKD T0371 95 :D 1rlmA 100 :K T0371 96 :GGIVAYL 1rlmA 109 :LQSAYVS T0371 103 :GTANSANYLVSDGIKMLPVSAIDDSNIGEVNALVLLDDEG 1rlmA 118 :APEAFVALMAKHYHRLKPVKDYQEIDDVLFKFSLNLPDEQ T0371 146 :FHDLNKTVN 1rlmA 158 :IPLVIDKLH T0371 160 :TIP 1rlmA 171 :GIM T0371 170 :NTYPLTKTDV 1rlmA 174 :KPVTSGFGFI T0371 199 :IRFGKPDSQMFMFAYDML 1rlmA 186 :IIPGLHKANGISRLLKRW T0371 221 :EISKREILMVGDTLH 1rlmA 204 :DLSPQNVVAIGDSGN T0371 237 :DILGGNKFGLDTA 1rlmA 219 :DAEMLKMARYSFA T0371 253 :TGNTRID 1rlmA 232 :MGNAAEN T0371 261 :AET 1rlmA 239 :IKQ T0371 267 :STGIVPTHICE 1rlmA 242 :IARYATDDNNH Number of specific fragments extracted= 17 number of extra gaps= 0 total=1890 Number of alignments=135 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rlmB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1rlmB expands to /projects/compbio/data/pdb/1rlm.pdb.gz 1rlmB:# T0371 read from 1rlmB/merged-good-all-a2m # 1rlmB read from 1rlmB/merged-good-all-a2m # adding 1rlmB to template set # found chain 1rlmB in template set Warning: unaligning (T0371)K12 because first residue in template chain is (1rlmB)A2 T0371 13 :YKCIFFDAFGVLKTYNGLL 1rlmB 3 :VKVIVTDMDGTFLNDAKTY T0371 32 :PGIENTFDYLKAQGQDYYIVT 1rlmB 24 :PRFMAQYQELKKRGIKFVVAS T0371 56 :SRSPEQL 1rlmB 45 :GNQYYQL T0371 71 :L 1rlmB 82 :G T0371 73 :SITADKI 1rlmB 83 :ELTRHES T0371 83 :GMITKEYID 1rlmB 90 :RIVIGELLK T0371 94 :VDGGIVAY 1rlmB 99 :DKQLNFVA T0371 102 :LGTANSANYLVSDGIKMLPVSAIDDSNIGEVNALVLLDDEG 1rlmB 117 :NAPEAFVALMAKHYHRLKPVKDYQEIDDVLFKFSLNLPDEQ T0371 146 :FHDLNK 1rlmB 158 :IPLVID T0371 155 :LLRKR 1rlmB 164 :KLHVA T0371 169 :DNTY 1rlmB 170 :DGIM T0371 175 :TKTDVAIA 1rlmB 174 :KPVTSGFG T0371 198 :FIRFGK 1rlmB 187 :IPGLHK T0371 206 :SQMFMFAYDML 1rlmB 193 :ANGISRLLKRW T0371 221 :EISKREILMVGDT 1rlmB 204 :DLSPQNVVAIGDS T0371 235 :HTDILGGNKF 1rlmB 217 :GNDAEMLKMA T0371 247 :DTALVL 1rlmB 227 :RYSFAM T0371 254 :GNT 1rlmB 233 :GNA T0371 258 :IDDAETK 1rlmB 236 :AENIKQI T0371 272 :PTHICES 1rlmB 243 :ARYATDD T0371 280 :VIE 1rlmB 250 :NNH Number of specific fragments extracted= 21 number of extra gaps= 0 total=1911 Number of alignments=136 # 1rlmB read from 1rlmB/merged-good-all-a2m # found chain 1rlmB in template set Warning: unaligning (T0371)K12 because first residue in template chain is (1rlmB)A2 T0371 13 :YKCIFFDAFGVLKTYNGLL 1rlmB 3 :VKVIVTDMDGTFLNDAKTY T0371 32 :PGIENTFDYLKAQGQDYYIVTNDA 1rlmB 24 :PRFMAQYQELKKRGIKFVVASGNQ T0371 63 :ADSY 1rlmB 48 :YYQL T0371 76 :ADK 1rlmB 52 :ISF T0371 79 :IISSGMITKEYIDLKVDGGIVAYLGTANSANYLVSD 1rlmB 64 :FVAENGALVYEHGKQLFHGELTRHESRIVIGELLKD T0371 130 :GEVNALVLLDD 1rlmB 100 :KQLNFVACGLQ T0371 141 :EGFN 1rlmB 116 :ENAP T0371 150 :NKTVNLLRKR 1rlmB 120 :EAFVALMAKH T0371 161 :I 1rlmB 130 :Y T0371 171 :TYPLTKTDVAIA 1rlmB 155 :DEQIPLVIDKLH T0371 183 :IGGVATMI 1rlmB 169 :LDGIMKPV T0371 194 :LGRRF 1rlmB 177 :TSGFG T0371 199 :IRFGKP 1rlmB 186 :IIPGLH T0371 209 :FMFAYDMLRQKMEISKREILMVGDT 1rlmB 192 :KANGISRLLKRWDLSPQNVVAIGDS T0371 235 :HTDILGGNKFGL 1rlmB 217 :GNDAEMLKMARY T0371 248 :TALVLTG 1rlmB 229 :SFAMGNA T0371 258 :IDDAETK 1rlmB 236 :AENIKQI T0371 272 :PTHICES 1rlmB 243 :ARYATDD T0371 280 :VI 1rlmB 250 :NN Number of specific fragments extracted= 19 number of extra gaps= 0 total=1930 Number of alignments=137 # 1rlmB read from 1rlmB/merged-good-all-a2m # found chain 1rlmB in template set T0371 13 :YKCIFFDAFGVLKTYNG 1rlmB 3 :VKVIVTDMDGTFLNDAK T0371 30 :LLPGIENTFDYLKAQGQDYYIVTNDA 1rlmB 22 :NQPRFMAQYQELKKRGIKFVVASGNQ T0371 63 :ADSYHKLGL 1rlmB 48 :YYQLISFFP T0371 72 :FSITADKI 1rlmB 82 :GELTRHES T0371 87 :KEYIDLK 1rlmB 90 :RIVIGEL T0371 94 :VD 1rlmB 99 :DK T0371 96 :GGIVAYL 1rlmB 109 :LQSAYVS T0371 103 :GTANSANYLVSDGIKMLPVSAIDDSNIGEVNALVLLDDEG 1rlmB 118 :APEAFVALMAKHYHRLKPVKDYQEIDDVLFKFSLNLPDEQ T0371 146 :FHDLNKTVN 1rlmB 158 :IPLVIDKLH T0371 170 :NTYPLTKTDV 1rlmB 174 :KPVTSGFGFI T0371 199 :IRFGKPDSQMFMFAYDML 1rlmB 186 :IIPGLHKANGISRLLKRW T0371 221 :EISKREILMVGDTLH 1rlmB 204 :DLSPQNVVAIGDSGN T0371 237 :DILGGNKFGLDTA 1rlmB 219 :DAEMLKMARYSFA T0371 253 :TGNTRIDDAE 1rlmB 232 :MGNAAENIKQ T0371 267 :STGIVPTHICE 1rlmB 242 :IARYATDDNNH Number of specific fragments extracted= 15 number of extra gaps= 0 total=1945 Number of alignments=138 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ydfA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0371/1ydfA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0371/1ydfA/merged-good-all-a2m.gz for input Trying 1ydfA/merged-good-all-a2m Error: Couldn't open file 1ydfA/merged-good-all-a2m or 1ydfA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qq7A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1qq7A expands to /projects/compbio/data/pdb/1qq7.pdb.gz 1qq7A:Bad short name: C2 for alphabet: pdb_atoms Bad short name: C1 for alphabet: pdb_atoms Bad short name: O1 for alphabet: pdb_atoms Bad short name: O2 for alphabet: pdb_atoms Skipped atom 191, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 193, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 195, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 197, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 199, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 201, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 203, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 763, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 765, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 767, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 882, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 884, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 886, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 888, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 890, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1206, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1208, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1357, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1359, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1459, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1461, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1619, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1621, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1623, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1625, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1627, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1629, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1631, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1633, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1635, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1637, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1639, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1641, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1643, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1645, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1647, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1649, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1651, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1653, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1655, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1657, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1659, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1661, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1663, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1665, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1667, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1669, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1671, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1673, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1675, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1677, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1679, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1681, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1683, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1685, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1687, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1689, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1691, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1693, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1695, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1697, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1699, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1701, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1703, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1705, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1707, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1709, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1748, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1750, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1752, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1754, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1789, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1791, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1793, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1816, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1818, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1820, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1822, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1824, because occupancy 0.500 <= existing 0.500 in 1qq7A # T0371 read from 1qq7A/merged-good-all-a2m # 1qq7A read from 1qq7A/merged-good-all-a2m # adding 1qq7A to template set # found chain 1qq7A in template set Warning: unaligning (T0371)K12 because first residue in template chain is (1qq7A)M1 Warning: unaligning (T0371)F18 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1qq7A)A9 Warning: unaligning (T0371)A20 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1qq7A)A9 T0371 13 :YKCIF 1qq7A 2 :IKAVV T0371 21 :FGVLKTYNGLLPGIENT 1qq7A 10 :YGTLFDVQSVADATERA T0371 56 :SR 1qq7A 29 :GR T0371 59 :PEQLADSYHKL 1qq7A 31 :GEYITQVWRQK T0371 79 :I 1qq7A 42 :Q T0371 83 :GMITKEYI 1qq7A 43 :LEYSWLRA T0371 91 :DLKV 1qq7A 52 :MGRY T0371 97 :GIVAYLGTANSANYLVSDGI 1qq7A 56 :ADFWSVTREALAYTLGTLGL T0371 122 :SAIDDSNIGEVNAL 1qq7A 76 :EPDESFLADMAQAY T0371 141 :EGFNWFHDLNKTVNLLR 1qq7A 90 :NRLTPYPDAAQCLAELA T0371 160 :TIPA 1qq7A 107 :PLKR T0371 164 :IVANTDNTY 1qq7A 112 :ILSNGAPDM T0371 174 :LTKTDVAIA 1qq7A 121 :LQALVANAG T0371 186 :VATMIESILGRRFIRFGKPDSQMFMFAYDML 1qq7A 130 :LTDSFDAVISVDAKRVFKPHPDSYALVEEVL T0371 221 :EISKREILMVGDT 1qq7A 161 :GVTPAEVLFVSSN T0371 235 :HTDILGGNKFGLDTALVL 1qq7A 174 :GFDVGGAKNFGFSVARVA T0371 255 :NTRIDDAETKIKSTGI 1qq7A 192 :RLSQEALARELVSGTI T0371 272 :PTHICES 1qq7A 227 :PDFVVPA T0371 280 :VIEL 1qq7A 234 :LGDL Number of specific fragments extracted= 19 number of extra gaps= 0 total=1964 Number of alignments=139 # 1qq7A read from 1qq7A/merged-good-all-a2m # found chain 1qq7A in template set Warning: unaligning (T0371)K12 because first residue in template chain is (1qq7A)M1 Warning: unaligning (T0371)F18 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1qq7A)A9 Warning: unaligning (T0371)A20 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1qq7A)A9 T0371 13 :YKCIF 1qq7A 2 :IKAVV T0371 21 :FGVLKTYNGLLPGIENT 1qq7A 10 :YGTLFDVQSVADATERA T0371 55 :ASRSPEQLADSYH 1qq7A 27 :YPGRGEYITQVWR T0371 83 :GMITKEYIDLKVDG 1qq7A 40 :QKQLEYSWLRALMG T0371 97 :GIVAYLGTANSANYLVSDGIKML 1qq7A 56 :ADFWSVTREALAYTLGTLGLEPD T0371 130 :GEVNALVLLDDEGFNWFHDLNKTVNLL 1qq7A 79 :ESFLADMAQAYNRLTPYPDAAQCLAEL T0371 159 :RTIPAIVANTDNTYPLTKTDVAIAIGGVATMI 1qq7A 106 :APLKRAILSNGAPDMLQALVANAGLTDSFDAV T0371 194 :LGRRFIRFGKPDSQMFMFAYDML 1qq7A 138 :ISVDAKRVFKPHPDSYALVEEVL T0371 221 :EISKREILMVGDT 1qq7A 161 :GVTPAEVLFVSSN T0371 235 :HTDILGGNKFGLDTALVLT 1qq7A 174 :GFDVGGAKNFGFSVARVAR T0371 256 :TRIDDAETKIKSTGIV 1qq7A 193 :LSQEALARELVSGTIA T0371 272 :PTHICES 1qq7A 227 :PDFVVPA T0371 280 :VIEL 1qq7A 234 :LGDL Number of specific fragments extracted= 13 number of extra gaps= 0 total=1977 Number of alignments=140 # 1qq7A read from 1qq7A/merged-good-all-a2m # found chain 1qq7A in template set Warning: unaligning (T0371)F18 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1qq7A)A9 Warning: unaligning (T0371)A20 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1qq7A)A9 T0371 13 :YKCIF 1qq7A 2 :IKAVV T0371 21 :FGVLKTYNGLLPGIENT 1qq7A 10 :YGTLFDVQSVADATERA T0371 38 :FDYLKA 1qq7A 35 :TQVWRQ T0371 57 :RSPEQLADSYHKLGL 1qq7A 41 :KQLEYSWLRALMGRY T0371 80 :ISSGMITKEY 1qq7A 56 :ADFWSVTREA T0371 107 :SANYLVSDGIKM 1qq7A 66 :LAYTLGTLGLEP T0371 129 :IGEVNALVLLDDEGFNWFHDLNKTVNLL 1qq7A 78 :DESFLADMAQAYNRLTPYPDAAQCLAEL T0371 159 :RTIPAIVANTD 1qq7A 106 :APLKRAILSNG T0371 182 :AIGGVATMIESIL 1qq7A 117 :APDMLQALVANAG T0371 201 :FGKPDSQMFMFAYDML 1qq7A 145 :VFKPHPDSYALVEEVL T0371 221 :EISKREILMVGDTLH 1qq7A 161 :GVTPAEVLFVSSNGF T0371 237 :DILGGNKFGLDTALVLT 1qq7A 176 :DVGGAKNFGFSVARVAR T0371 256 :TRIDDAE 1qq7A 193 :LSQEALA T0371 263 :TKIKSTGIVPTHICESAV 1qq7A 222 :TYAEAPDFVVPALGDLPR Number of specific fragments extracted= 14 number of extra gaps= 0 total=1991 Number of alignments=141 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rloA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1rloA expands to /projects/compbio/data/pdb/1rlo.pdb.gz 1rloA:Bad short name: BE for alphabet: pdb_atoms Bad short name: F1 for alphabet: pdb_atoms Bad short name: F2 for alphabet: pdb_atoms Bad short name: F3 for alphabet: pdb_atoms # T0371 read from 1rloA/merged-good-all-a2m # 1rloA read from 1rloA/merged-good-all-a2m # adding 1rloA to template set # found chain 1rloA in template set Warning: unaligning (T0371)Y13 because first residue in template chain is (1rloA)V3 Warning: unaligning (T0371)F18 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1rloA)M10 Warning: unaligning (T0371)A20 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1rloA)M10 T0371 14 :KCIF 1rloA 4 :KVIV T0371 21 :FGVLKTYNGLL 1rloA 11 :DGTFLNDAKTY T0371 32 :PGIENTFDYLKAQGQDYYIVT 1rloA 24 :PRFMAQYQELKKRGIKFVVAS T0371 56 :SRSPEQL 1rloA 45 :GNQYYQL T0371 68 :KLGL 1rloA 57 :ELKD T0371 73 :SIT 1rloA 61 :EIS T0371 79 :IISSGMITKEYIDLKVDGGIVAYLGTANSANYLVSD 1rloA 64 :FVAENGALVYEHGKQLFHGELTRHESRIVIGELLKD T0371 115 :GIK 1rloA 101 :QLN T0371 134 :ALVLLDD 1rloA 104 :FVACGLQ T0371 141 :EGFN 1rloA 116 :ENAP T0371 150 :NKTVNLLRKRTIPA 1rloA 120 :EAFVALMAKHYHRL T0371 167 :NTDNTY 1rloA 136 :VKDYQE T0371 174 :LTKTDV 1rloA 142 :IDDVLF T0371 180 :AIAIG 1rloA 152 :NLPDE T0371 185 :GVATMIESILGRRFIR 1rloA 160 :LVIDKLHVALDGIMKP T0371 201 :FGK 1rloA 190 :LHK T0371 206 :SQMFMFAYDML 1rloA 193 :ANGISRLLKRW T0371 221 :EISKREILMVGDT 1rloA 204 :DLSPQNVVAIGDS T0371 235 :HTDILGGNK 1rloA 217 :GNDAEMLKM T0371 246 :LDTALVL 1rloA 226 :ARYSFAM T0371 254 :G 1rloA 233 :G T0371 256 :TRIDDAETK 1rloA 234 :NAAENIKQI T0371 272 :PTHICES 1rloA 243 :ARYATDD T0371 280 :VI 1rloA 250 :NN Number of specific fragments extracted= 24 number of extra gaps= 0 total=2015 Number of alignments=142 # 1rloA read from 1rloA/merged-good-all-a2m # found chain 1rloA in template set Warning: unaligning (T0371)Y13 because first residue in template chain is (1rloA)V3 Warning: unaligning (T0371)F18 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1rloA)M10 Warning: unaligning (T0371)A20 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1rloA)M10 T0371 14 :KCIF 1rloA 4 :KVIV T0371 21 :FGVLKTYNGLL 1rloA 11 :DGTFLNDAKTY T0371 32 :PGIENTFDYLKAQGQDYYIVTNDA 1rloA 24 :PRFMAQYQELKKRGIKFVVASGNQ T0371 63 :ADSYH 1rloA 48 :YYQLI T0371 68 :KLGL 1rloA 57 :ELKD T0371 73 :SIT 1rloA 61 :EIS T0371 79 :IIS 1rloA 65 :VAE T0371 83 :GMITKEYIDLKVDGGIVAYLGTANSANYLVSD 1rloA 68 :NGALVYEHGKQLFHGELTRHESRIVIGELLKD T0371 130 :GEVNALVLLDD 1rloA 100 :KQLNFVACGLQ T0371 141 :EGFN 1rloA 116 :ENAP T0371 150 :NKTVNLLRKR 1rloA 120 :EAFVALMAKH T0371 161 :I 1rloA 130 :Y T0371 171 :TYPLTKTDVAIA 1rloA 155 :DEQIPLVIDKLH T0371 183 :IGGVATMI 1rloA 169 :LDGIMKPV T0371 194 :LGRRF 1rloA 178 :SGFGF T0371 199 :IRFGKP 1rloA 186 :IIPGLH T0371 209 :FMFAYDMLRQKMEISKREILMVGDTLH 1rloA 192 :KANGISRLLKRWDLSPQNVVAIGDSGN T0371 237 :DILGGNKFGL 1rloA 219 :DAEMLKMARY T0371 248 :TALVL 1rloA 229 :SFAMG T0371 256 :TRIDDAETK 1rloA 234 :NAAENIKQI T0371 272 :PTHICES 1rloA 243 :ARYATDD T0371 280 :V 1rloA 250 :N Number of specific fragments extracted= 22 number of extra gaps= 0 total=2037 Number of alignments=143 # 1rloA read from 1rloA/merged-good-all-a2m # found chain 1rloA in template set Warning: unaligning (T0371)Y13 because first residue in template chain is (1rloA)V3 Warning: unaligning (T0371)F18 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1rloA)M10 Warning: unaligning (T0371)A20 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1rloA)M10 T0371 14 :KCIF 1rloA 4 :KVIV T0371 21 :FGVLKTYNG 1rloA 11 :DGTFLNDAK T0371 30 :LLPGIENTFDYLKAQGQDYYIVTNDA 1rloA 22 :NQPRFMAQYQELKKRGIKFVVASGNQ T0371 63 :ADSYHKLGL 1rloA 48 :YYQLISFFP T0371 72 :F 1rloA 82 :G T0371 80 :ISSGMITKEYIDLK 1rloA 83 :ELTRHESRIVIGEL T0371 94 :VD 1rloA 99 :DK T0371 96 :GGIVAYL 1rloA 109 :LQSAYVS T0371 103 :GTANSANYLVSDGIKMLPVSAIDDSNIGEVNALVLLDDEG 1rloA 118 :APEAFVALMAKHYHRLKPVKDYQEIDDVLFKFSLNLPDEQ T0371 146 :FHDLNKTVN 1rloA 158 :IPLVIDKLH T0371 155 :LL 1rloA 168 :AL T0371 168 :TDNTYPLTKTD 1rloA 170 :DGIMKPVTSGF T0371 179 :VAIAIGGVAT 1rloA 185 :LIIPGLHKAN T0371 208 :MFMFAYDML 1rloA 195 :GISRLLKRW T0371 221 :EISKREILMVGDTLH 1rloA 204 :DLSPQNVVAIGDSGN T0371 237 :DILGGNKFGLDTA 1rloA 219 :DAEMLKMARYSFA T0371 253 :TGNTR 1rloA 232 :MGNAA T0371 259 :DDAETK 1rloA 237 :ENIKQI T0371 268 :TGIVPTHICE 1rloA 243 :ARYATDDNNH Number of specific fragments extracted= 19 number of extra gaps= 0 total=2056 Number of alignments=144 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1aq6A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1aq6A expands to /projects/compbio/data/pdb/1aq6.pdb.gz 1aq6A:# T0371 read from 1aq6A/merged-good-all-a2m # 1aq6A read from 1aq6A/merged-good-all-a2m # adding 1aq6A to template set # found chain 1aq6A in template set Warning: unaligning (T0371)K12 because first residue in template chain is (1aq6A)M1 T0371 13 :YKCIFFDAFGVLKTYNGLLPGIENT 1aq6A 2 :IKAVVFDAYGTLFDVQSVADATERA T0371 56 :SR 1aq6A 29 :GR T0371 59 :PEQLADSYHKL 1aq6A 31 :GEYITQVWRQK T0371 79 :I 1aq6A 42 :Q T0371 83 :GMITKEYI 1aq6A 43 :LEYSWLRA T0371 91 :DLKV 1aq6A 52 :MGRY T0371 97 :GIVAYLGTANSANYLVSDGI 1aq6A 56 :ADFWGVTREALAYTLGTLGL T0371 122 :SAIDDSNIGEVNAL 1aq6A 76 :EPDESFLADMAQAY T0371 141 :EGFNWFHDLNKTVNLLR 1aq6A 90 :NRLTPYPDAAQCLAELA T0371 160 :TIPA 1aq6A 107 :PLKR T0371 164 :IVANTDNTY 1aq6A 112 :ILSNGAPDM T0371 174 :LTKTDVAIA 1aq6A 121 :LQALVANAG T0371 186 :VATMIESILGRRFIRFGKPDSQMFMFAYDML 1aq6A 130 :LTDSFDAVISVDAKRVFKPHPDSYALVEEVL T0371 221 :EISKREILMVGDT 1aq6A 161 :GVTPAEVLFVSSN T0371 235 :HTDILGGNKFGLDTALVL 1aq6A 174 :GFDVGGAKNFGFSVARVA T0371 255 :NTRIDDAETK 1aq6A 192 :RLSQEALARE T0371 265 :IKSTGIV 1aq6A 219 :REETYAE T0371 272 :PTHICES 1aq6A 227 :PDFVVPA T0371 280 :VIEL 1aq6A 234 :LGDL Number of specific fragments extracted= 19 number of extra gaps= 0 total=2075 Number of alignments=145 # 1aq6A read from 1aq6A/merged-good-all-a2m # found chain 1aq6A in template set Warning: unaligning (T0371)K12 because first residue in template chain is (1aq6A)M1 T0371 13 :YKCIFFDAFGVLKTYNGLLPGIENTF 1aq6A 2 :IKAVVFDAYGTLFDVQSVADATERAY T0371 56 :SRSPEQLADSYHK 1aq6A 28 :PGRGEYITQVWRQ T0371 84 :MITKEYIDLKVDG 1aq6A 41 :KQLEYSWLRALMG T0371 97 :GIVAYLGTANSANYLVSDGIKML 1aq6A 56 :ADFWGVTREALAYTLGTLGLEPD T0371 130 :GEVNALVLLDDEGFNWFHDLNKTVNLL 1aq6A 79 :ESFLADMAQAYNRLTPYPDAAQCLAEL T0371 159 :RTIPAIVANTDNTYPLTKTDVAIAIGGVATMI 1aq6A 106 :APLKRAILSNGAPDMLQALVANAGLTDSFDAV T0371 194 :LGRRFIRFGKPDSQMFMFAYDML 1aq6A 138 :ISVDAKRVFKPHPDSYALVEEVL T0371 221 :EISKREILMVGDTLH 1aq6A 161 :GVTPAEVLFVSSNGF T0371 237 :DILGGNKFGLDTALVLT 1aq6A 176 :DVGGAKNFGFSVARVAR T0371 256 :TRIDDAETKI 1aq6A 193 :LSQEALAREL T0371 266 :KSTGIVPTHICES 1aq6A 221 :ETYAEAPDFVVPA T0371 280 :VIEL 1aq6A 234 :LGDL Number of specific fragments extracted= 12 number of extra gaps= 0 total=2087 Number of alignments=146 # 1aq6A read from 1aq6A/merged-good-all-a2m # found chain 1aq6A in template set T0371 13 :YKCIFFDAFGVLKTYNGLLPGIENT 1aq6A 2 :IKAVVFDAYGTLFDVQSVADATERA T0371 38 :FDYLKA 1aq6A 35 :TQVWRQ T0371 57 :RSPEQLADSYHKLGL 1aq6A 41 :KQLEYSWLRALMGRY T0371 80 :ISSGMITKEY 1aq6A 56 :ADFWGVTREA T0371 107 :SANYLVSDGIK 1aq6A 66 :LAYTLGTLGLE T0371 128 :NIGEVNALVLLDDEGFNWFHDLNKTVNLL 1aq6A 77 :PDESFLADMAQAYNRLTPYPDAAQCLAEL T0371 159 :RTIPAIVANTD 1aq6A 106 :APLKRAILSNG T0371 182 :AIGGVATMIESIL 1aq6A 117 :APDMLQALVANAG T0371 198 :FIRFGKPDSQMFMFAYDML 1aq6A 142 :AKRVFKPHPDSYALVEEVL T0371 221 :EISKREILMVGDTLH 1aq6A 161 :GVTPAEVLFVSSNGF T0371 237 :DILGGNKFGLDTALVLT 1aq6A 176 :DVGGAKNFGFSVARVAR T0371 256 :TRIDDAE 1aq6A 193 :LSQEALA T0371 263 :TKIKSTGIVPTHICESAV 1aq6A 222 :TYAEAPDFVVPALGDLPR Number of specific fragments extracted= 13 number of extra gaps= 0 total=2100 Number of alignments=147 # command:Using radius: 8.0000 Alignment mode NUMB_ALIGNS: 147 Adding 7211 constraints to all.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all.constraints maxweight: 1.0000 Optimizing... Probability sum: -505.6558, CN propb: -505.6558 weights: 0.2396 constraints: 810 # command:Found ConstraintSet # PrintContacts align.constraints_v3 Number of constraints in align.constraints 810 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_v3 Number of constraints in align.constraints.bonus 810 # command:Found ConstraintSet # PrintContacts rejected.constraints_v3 Number of constraints in rejected.constraints 6401 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_v3 Number of constraints in rejected.constraints.bonus 6401 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_v3 Number of constraints in noncontact.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_v3 Number of constraints in noncontact.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_v3 Number of constraints in all.constraints 7211 # command: