parameters: 0.6 1.3 0.5 200 50 # 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/T0303/ # command:# Making conformation for sequence T0303 numbered 1 through 224 Created new target T0303 from T0303.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0303/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0303//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0303/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0303//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0303/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0303/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0303/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 # T0303 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 (T0303)F9 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1j97A)F12 Warning: unaligning (T0303)L11 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1j97A)F12 T0303 2 :TQFKLIG 1j97A 3 :KKKKLIL # choosing archetypes in rotamer library T0303 12 :DGTLVNSL 1j97A 13 :DSTLVNNE T0303 25 :SINSALKDVNL 1j97A 21 :TIDEIAREAGV T0303 40 :ENLVMTWI 1j97A 32 :EEEVKKIT T0303 48 :GNGADVLSQRAVDWA 1j97A 46 :KLNFEQSLRKRVSLL T0303 68 :KELTEDEFKYFK 1j97A 61 :KDLPIEKVEKAI T0303 92 :NISRLYPNVKETLEALKAQGYILAVVTNKPTKHVQPILTAFGIDHLFSEMLGGQSL 1j97A 73 :KRITPTEGAEETIKELKNRGYVVAVVSGGFDIAVNKIKEKLGLDYAFANRLIVKDG T0303 148 :PEIKPH 1j97A 137 :EVLKEN T0303 154 :PAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCA 1j97A 145 :GEILEKIAKIEGINLEDTVAVGDGANDISMFKKAGLK T0303 192 :VGLTYG 1j97A 182 :IAFCAK T0303 202 :IPIAQS 1j97A 188 :PILKEK T0303 209 :PDWIFD 1j97A 194 :ADICIE T0303 215 :DFADILKI 1j97A 202 :DLREILKY Number of specific fragments extracted= 13 number of extra gaps= 0 total=13 Number of alignments=1 # 1j97A read from 1j97A/merged-good-all-a2m # found chain 1j97A in template set Warning: unaligning (T0303)F9 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1j97A)F12 Warning: unaligning (T0303)L11 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1j97A)F12 T0303 2 :TQFKLIG 1j97A 3 :KKKKLIL T0303 12 :DGTLVNSLP 1j97A 13 :DSTLVNNET T0303 26 :INSALKDVNL 1j97A 22 :IDEIAREAGV T0303 40 :ENLVMTWI 1j97A 32 :EEEVKKIT T0303 48 :GNGADVLSQRA 1j97A 46 :KLNFEQSLRKR T0303 63 :CTQAE 1j97A 57 :VSLLK T0303 69 :ELTEDEFKYFK 1j97A 62 :DLPIEKVEKAI T0303 92 :NISRLYPNVKETLEALKAQGYILAVVTNKPTKHVQPILTAFGIDHLFSEMLGGQ 1j97A 73 :KRITPTEGAEETIKELKNRGYVVAVVSGGFDIAVNKIKEKLGLDYAFANRLIVK T0303 146 :SLPEIK 1j97A 139 :LKENAK T0303 154 :PAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAG 1j97A 145 :GEILEKIAKIEGINLEDTVAVGDGANDISMFKKAG T0303 190 :AVVGLTY 1j97A 180 :LKIAFCA T0303 201 :NIPIAQS 1j97A 187 :KPILKEK T0303 209 :PDWIFD 1j97A 194 :ADICIE T0303 215 :DFADILKI 1j97A 202 :DLREILKY Number of specific fragments extracted= 14 number of extra gaps= 0 total=27 Number of alignments=2 # 1j97A read from 1j97A/merged-good-all-a2m # found chain 1j97A in template set Warning: unaligning (T0303)F9 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1j97A)F12 Warning: unaligning (T0303)L11 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1j97A)F12 T0303 2 :TQFKLIG 1j97A 3 :KKKKLIL T0303 12 :DGTLVNSLP 1j97A 13 :DSTLVNNET T0303 26 :INSALKDVNLPQASENLVMTWIGNGA 1j97A 22 :IDEIAREAGVEEEVKKITKEAMEGKL T0303 52 :DVLSQRAVD 1j97A 51 :QSLRKRVSL T0303 67 :EKELTEDEFKYFKR 1j97A 60 :LKDLPIEKVEKAIK T0303 93 :ISRLYPNVKETLEALKAQGYILAVVTNKPTKHVQPILTAFGIDHLFSEMLGGQS 1j97A 74 :RITPTEGAEETIKELKNRGYVVAVVSGGFDIAVNKIKEKLGLDYAFANRLIVKD T0303 148 :P 1j97A 140 :K T0303 150 :IKPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVVG 1j97A 141 :ENAKGEILEKIAKIEGINLEDTVAVGDGANDISMFKKAGLKIAF T0303 195 :T 1j97A 185 :C T0303 201 :NIPIAQSKPDWIFD 1j97A 186 :AKPILKEKADICIE T0303 215 :DFADILKIT 1j97A 202 :DLREILKYI Number of specific fragments extracted= 11 number of extra gaps= 0 total=38 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:# T0303 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 (T0303)V16 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c4nA)H16 Warning: unaligning (T0303)N17 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2c4nA)H16 T0303 1 :M 2c4nA 1 :M T0303 3 :QFKLIGFDLDGTL 2c4nA 2 :TIKNVICDIDGVL T0303 18 :SLPDLALSINSALKD 2c4nA 20 :AVPGAAEFLHGIMDK T0303 34 :NLPQ 2c4nA 35 :GLPL T0303 48 :GNGADVLSQRAVD 2c4nA 46 :SQTGQDLANRFAT T0303 66 :AEKELTEDE 2c4nA 59 :AGVDVPDSV T0303 82 :FGFYYGENLCNISR 2c4nA 71 :SAMATADFLRRQEG T0303 96 :LYPNV 2c4nA 90 :VGEGA T0303 103 :TLEALKAQGYIL 2c4nA 95 :LIHELYKAGFTI T0303 115 :AVVTN 2c4nA 113 :FVIVG T0303 120 :KPTKHVQPILTAF 2c4nA 121 :SYNWDMMHKAAYF T0303 133 :G 2c4nA 137 :G T0303 138 :FSEMLGGQSL 2c4nA 138 :ARFIATNPDT T0303 149 :EIKPHPAPFYYLCGKFGLYPKQILFVGDSQ 2c4nA 174 :VGKPSPWIIRAALNKMQAHSEETVIVGDNL T0303 179 :NDIFAAHSAGCAVVGLTYGYNYNIPIAQSK 2c4nA 205 :TDILAGFQAGLETILVLSGVSSLDDIDSMP T0303 209 :PDWIFDDFAD 2c4nA 237 :PSWIYPSVAE Number of specific fragments extracted= 16 number of extra gaps= 1 total=54 Number of alignments=4 # 2c4nA read from 2c4nA/merged-good-all-a2m # found chain 2c4nA in template set Warning: unaligning (T0303)T2 because first residue in template chain is (2c4nA)M1 Warning: unaligning (T0303)V16 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c4nA)H16 Warning: unaligning (T0303)N92 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2c4nA)H16 T0303 3 :QFKLIGFDLDGTL 2c4nA 2 :TIKNVICDIDGVL T0303 93 :ISRLYPNVKETLEALKAQGYILAVVTNKP 2c4nA 17 :DNVAVPGAAEFLHGIMDKGLPLVLLTNYP T0303 122 :TKHVQPILTAFGID 2c4nA 49 :GQDLANRFATAGVD T0303 136 :HLF 2c4nA 66 :SVF T0303 146 :S 2c4nA 171 :P T0303 150 :IKPHPAPFYYLCGKFGLYPKQILFVGDSQN 2c4nA 175 :GKPSPWIIRAALNKMQAHSEETVIVGDNLR T0303 180 :DIFAAHSAGCAVVGLTYGYNYNIPIAQSK 2c4nA 206 :DILAGFQAGLETILVLSGVSSLDDIDSMP T0303 209 :PDWIFDDFADI 2c4nA 237 :PSWIYPSVAEI Number of specific fragments extracted= 8 number of extra gaps= 1 total=62 Number of alignments=5 # 2c4nA read from 2c4nA/merged-good-all-a2m # found chain 2c4nA in template set Warning: unaligning (T0303)T2 because first residue in template chain is (2c4nA)M1 Warning: unaligning (T0303)V16 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c4nA)H16 T0303 3 :QFKLIGFDLDGTL 2c4nA 2 :TIKNVICDIDGVL T0303 95 :RLYPNVKETLEALKAQGYILAVVTNKP 2c4nA 19 :VAVPGAAEFLHGIMDKGLPLVLLTNYP T0303 122 :TKHVQPILTAFGIDHLFSEML 2c4nA 49 :GQDLANRFATAGVDVPDSVFY T0303 143 :GGQSLPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQ 2c4nA 168 :GRKPFYVGKPSPWIIRAALNKMQAHSEETVIVGDNL T0303 179 :NDIFAAHSAGCAVVGLTYGYNYNIPIA 2c4nA 205 :TDILAGFQAGLETILVLSGVSSLDDID T0303 206 :QSKPDWIFDDFAD 2c4nA 234 :PFRPSWIYPSVAE Number of specific fragments extracted= 6 number of extra gaps= 1 total=68 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 # T0303 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 (T0303)F9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gfhA)D12 Warning: unaligning (T0303)D10 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gfhA)D12 Warning: unaligning (T0303)N49 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gfhA)C67 T0303 1 :MTQFKLIG 2gfhA 3 :LSRVRAVF T0303 11 :LDGTLVNSLPDLALSINSALKDV 2gfhA 13 :LDNTLIDTAGASRRGMLEVIKLL T0303 34 :NLP 2gfhA 40 :HYK T0303 38 :ASENLVMTWI 2gfhA 43 :EEAEIICDKV T0303 50 :GADVLSQRAVDWACTQAEKELTEDEFKYFKRQFGFYYG 2gfhA 68 :ITDVRTSHWEEAIQETKGGADNRKLAEECYFLWKSTRL T0303 92 :NISRLYPNVKETLEALKAQ 2gfhA 106 :QHMILADDVKAMLTELRKE T0303 112 :YILAVVTNKPTKHVQPILTAFGIDHLFSEMLGGQSLPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQ 2gfhA 125 :VRLLLLTNGDRQTQREKIEACACQSYFDAIVIGGEQKEEKPAPSIFYHCCDLLGVQPGDCVMVGDTL T0303 179 :NDIFAAHSAGCA 2gfhA 193 :TDIQGGLNAGLK T0303 191 :VVGLTYGYN 2gfhA 206 :TVWINKSGR T0303 201 :NIPIAQSKPDWIFDDFADILKI 2gfhA 215 :VPLTSSPMPHYMVSSVLELPAL Number of specific fragments extracted= 10 number of extra gaps= 1 total=78 Number of alignments=7 # 2gfhA read from 2gfhA/merged-good-all-a2m # found chain 2gfhA in template set Warning: unaligning (T0303)F9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gfhA)D12 Warning: unaligning (T0303)D10 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gfhA)D12 Warning: unaligning (T0303)N49 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gfhA)C67 T0303 1 :MTQFKLIG 2gfhA 3 :LSRVRAVF T0303 11 :LDGTLVNSLPDLALSINSALKDV 2gfhA 13 :LDNTLIDTAGASRRGMLEVIKLL T0303 34 :NLPQASENLVMTWI 2gfhA 40 :HYKEEAEIICDKVQ T0303 50 :GADVLSQRAVDWACTQAEKELTEDEFKYFKRQFGFYYG 2gfhA 68 :ITDVRTSHWEEAIQETKGGADNRKLAEECYFLWKSTRL T0303 92 :NISRLYPNVKETLEALKAQ 2gfhA 106 :QHMILADDVKAMLTELRKE T0303 112 :YILAVVTNKPTKHVQPILTAFGIDHLFSEMLGGQSLPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQN 2gfhA 125 :VRLLLLTNGDRQTQREKIEACACQSYFDAIVIGGEQKEEKPAPSIFYHCCDLLGVQPGDCVMVGDTLE T0303 180 :DIFAAHSAGCA 2gfhA 194 :DIQGGLNAGLK T0303 191 :VVGLTYGYNYNIPIAQS 2gfhA 206 :TVWINKSGRVPLTSSPM T0303 209 :PDWIFDDFADILKI 2gfhA 223 :PHYMVSSVLELPAL Number of specific fragments extracted= 9 number of extra gaps= 1 total=87 Number of alignments=8 # 2gfhA read from 2gfhA/merged-good-all-a2m # found chain 2gfhA in template set Warning: unaligning (T0303)F9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gfhA)D12 Warning: unaligning (T0303)D10 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gfhA)D12 Warning: unaligning (T0303)V53 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gfhA)C67 T0303 1 :MTQFKLIG 2gfhA 3 :LSRVRAVF T0303 11 :LDGTLVNSLPDLALSINSALKDV 2gfhA 13 :LDNTLIDTAGASRRGMLEVIKLL T0303 34 :NLPQASENLVMTWIGNGA 2gfhA 40 :HYKEEAEIICDKVQVKLS T0303 54 :LSQRAVDWACTQAEKELTEDEFKYFKRQFGFYYGENLCNISRLYPNVKETLEALKAQ 2gfhA 68 :ITDVRTSHWEEAIQETKGGADNRKLAEECYFLWKSTRLQHMILADDVKAMLTELRKE T0303 112 :YILAVVTNKPTKHVQPILTAFGIDHLFSEMLGGQSLPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQ 2gfhA 125 :VRLLLLTNGDRQTQREKIEACACQSYFDAIVIGGEQKEEKPAPSIFYHCCDLLGVQPGDCVMVGDTL T0303 179 :NDIFAAHSAGCAVVGLTYGYNYNIPIAQSKPDWIFDDFADILKITQ 2gfhA 193 :TDIQGGLNAGLKATVWINKSGRVPLTSSPMPHYMVSSVLELPALLQ Number of specific fragments extracted= 6 number of extra gaps= 1 total=93 Number of alignments=9 # 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 # T0303 read from 1wr8A/merged-good-all-a2m # 1wr8A read from 1wr8A/merged-good-all-a2m # found chain 1wr8A in training set Warning: unaligning (T0303)Q3 because first residue in template chain is (1wr8A)K2 T0303 4 :FKLIGFDLDGTLVN 1wr8A 3 :IKAISIDIDGTITY T0303 18 :SLPDLALSINSALKD 1wr8A 21 :IHEKALEAIRRAESL T0303 34 :NLPQ 1wr8A 36 :GIPI T0303 38 :ASENLVMTW 1wr8A 45 :NTVQFAEAA T0303 55 :SQRAV 1wr8A 54 :SILIG T0303 71 :TEDEFKYFKRQFGFYY 1wr8A 82 :SMDEEWILWNEIRKRF T0303 92 :NISRLYPNVKE 1wr8A 98 :PNARTSYTMPD T0303 110 :QG 1wr8A 117 :RE T0303 119 :NKPTKHVQPILTAFGID 1wr8A 119 :TINVETVREIINELNLN T0303 137 :LFSEMLGGQSLP 1wr8A 142 :GFAIHVKKPWIN T0303 153 :HPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVV 1wr8A 154 :KGSGIEKASEFLGIKPKEVAHVGDGENDLDAFKVVGYKVA T0303 194 :L 1wr8A 194 :V T0303 198 :YNYNIPIAQS 1wr8A 195 :AQAPKILKEN T0303 209 :PDWIFDD 1wr8A 205 :ADYVTKK T0303 216 :FADILKIT 1wr8A 221 :IYHILEKF Number of specific fragments extracted= 15 number of extra gaps= 0 total=108 Number of alignments=10 # 1wr8A read from 1wr8A/merged-good-all-a2m # found chain 1wr8A in training set Warning: unaligning (T0303)Q3 because first residue in template chain is (1wr8A)K2 T0303 4 :FKLIGFDLDGTLVN 1wr8A 3 :IKAISIDIDGTITY T0303 92 :NISRLYPNVKETLEALKAQGYILAVVTNKPTKHVQPILTAFGIDHLF 1wr8A 17 :PNRMIHEKALEAIRRAESLGIPIMLVTGNTVQFAEAASILIGTSGPV T0303 146 :SLPEIK 1wr8A 149 :KPWINK T0303 154 :PAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVV 1wr8A 155 :GSGIEKASEFLGIKPKEVAHVGDGENDLDAFKVVGYKVA T0303 194 :L 1wr8A 194 :V T0303 198 :YNYNIPIAQS 1wr8A 195 :AQAPKILKEN T0303 209 :PDWIFDD 1wr8A 205 :ADYVTKK Number of specific fragments extracted= 7 number of extra gaps= 0 total=115 Number of alignments=11 # 1wr8A read from 1wr8A/merged-good-all-a2m # found chain 1wr8A in training set Warning: unaligning (T0303)Q3 because first residue in template chain is (1wr8A)K2 T0303 4 :FKLIGFDLDGTLV 1wr8A 3 :IKAISIDIDGTIT T0303 92 :NISRLYPNVKETLEALKAQGYILAVVTNKPTKHVQPILTAFGIDHLF 1wr8A 17 :PNRMIHEKALEAIRRAESLGIPIMLVTGNTVQFAEAASILIGTSGPV T0303 139 :SE 1wr8A 67 :DG T0303 147 :LPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVV 1wr8A 148 :KKPWINKGSGIEKASEFLGIKPKEVAHVGDGENDLDAFKVVGYKVA T0303 198 :YNYNIPIAQSKPDWIFDD 1wr8A 194 :VAQAPKILKENADYVTKK T0303 216 :FADI 1wr8A 221 :IYHI Number of specific fragments extracted= 6 number of extra gaps= 0 total=121 Number of alignments=12 # 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 # T0303 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 T0303 1 :M 1qyiA 1 :M T0303 5 :KLIGFDLDGTLVNSLPD 1qyiA 2 :KKILFDVDGVFLSEERC T0303 23 :ALSINSALKDV 1qyiA 19 :FDVSALTVYEL T0303 35 :LPQ 1qyiA 42 :IDW T0303 38 :ASENLVMTWIGN 1qyiA 47 :LTDNDIQDIRNR T0303 50 :GADVLSQRAV 1qyiA 61 :QKDKILNKLK T0303 60 :DWACTQAE 1qyiA 153 :EFATTELH T0303 68 :KELT 1qyiA 162 :SDAT T0303 73 :DEFKYFKRQFGFYYGEN 1qyiA 172 :ALWTLAQEVYQEWYLGS T0303 90 :LCN 1qyiA 191 :YED T0303 93 :ISRLYPNVKETLEALKAQGYILAVVTNKPTKHVQPILTAFGIDHLF 1qyiA 213 :ILRPVDEVKVLLNDLKGAGFELGIATGRPYTETVVPFENLGLLPYF T0303 139 :SEMLGG 1qyiA 261 :DFIATA T0303 145 :QSLPEIKPHPAPFYYLCG 1qyiA 278 :QARPLGKPNPFSYIAALY T0303 165 :G 1qyiA 296 :G T0303 166 :LYPKQILFVGDSQNDIFAAHSAGCAVVGLTYGYNYNI 1qyiA 313 :VNKDDVFIVGDSLADLLSAQKIGATFIGTLTGLKGKD T0303 204 :IAQSKPDWIFDDFADILKITQ 1qyiA 354 :LEAHHADYVINHLGELRGVLD Number of specific fragments extracted= 16 number of extra gaps= 0 total=137 Number of alignments=13 # 1qyiA read from 1qyiA/merged-good-all-a2m # found chain 1qyiA in template set T0303 5 :KLIGFDLDGTLVN 1qyiA 2 :KKILFDVDGVFLS T0303 18 :SLPDLALSINSA 1qyiA 48 :TDNDIQDIRNRI T0303 30 :LKDVNLP 1qyiA 69 :LKSLGLN T0303 38 :A 1qyiA 76 :S T0303 39 :SENLVMTWI 1qyiA 97 :SHDEIEAFM T0303 48 :GNGADVLSQRAVDWACTQ 1qyiA 141 :KVGKNNIYAALEEFATTE T0303 66 :AEKEL 1qyiA 167 :FSLKG T0303 73 :DEFKYFKRQFGFYYGENL 1qyiA 172 :ALWTLAQEVYQEWYLGSK T0303 91 :CNIS 1qyiA 195 :EKKI T0303 95 :RLYPNVKETLEALKAQGYILAVVTNKPTKHVQPILTAFGIDHLF 1qyiA 215 :RPVDEVKVLLNDLKGAGFELGIATGRPYTETVVPFENLGLLPYF T0303 139 :SEMLGGQ 1qyiA 261 :DFIATAS T0303 146 :SLPEIKPHPAPFYYLCGKF 1qyiA 279 :ARPLGKPNPFSYIAALYGN T0303 166 :LYPKQILFVGDSQNDIFAAHSAGCAVVGLTYGYN 1qyiA 313 :VNKDDVFIVGDSLADLLSAQKIGATFIGTLTGLK T0303 200 :YNIPIAQSKPDWIFDDFADILKI 1qyiA 350 :AAGELEAHHADYVINHLGELRGV Number of specific fragments extracted= 14 number of extra gaps= 0 total=151 Number of alignments=14 # 1qyiA read from 1qyiA/merged-good-all-a2m # found chain 1qyiA in template set T0303 5 :KLIGFDLDGTLV 1qyiA 2 :KKILFDVDGVFL T0303 17 :NSLPDLALSINSALKDV 1qyiA 142 :VGKNNIYAALEEFATTE T0303 34 :NLPQAS 1qyiA 160 :HVSDAT T0303 68 :KELTEDEFKYFKRQFGFYYGENLCNI 1qyiA 167 :FSLKGALWTLAQEVYQEWYLGSKLYE T0303 94 :SRLYPNVKETLEALKAQGYILAVVTNKPTKHVQPILTAFGIDHLF 1qyiA 214 :LRPVDEVKVLLNDLKGAGFELGIATGRPYTETVVPFENLGLLPYF T0303 139 :SEML 1qyiA 261 :DFIA T0303 143 :GGQSLPEIKPHPAPFYYLC 1qyiA 276 :YPQARPLGKPNPFSYIAAL T0303 166 :LYPKQILFVGDSQNDIFAAHSAGCAVVGLTYGYNYNIP 1qyiA 313 :VNKDDVFIVGDSLADLLSAQKIGATFIGTLTGLKGKDA T0303 204 :IAQSKPDWIFDDFADILKITQ 1qyiA 354 :LEAHHADYVINHLGELRGVLD Number of specific fragments extracted= 9 number of extra gaps= 0 total=160 Number of alignments=15 # 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:# T0303 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 (T0303)Q3 because first residue in template chain is (1rqlA)K5 T0303 4 :FKLIGFDLDGTLVNSL 1rqlA 6 :IEAVIFDWAGTTVDYG T0303 20 :PDLALSINSALKDVNLP 1rqlA 23 :FAPLEVFMEIFHKRGVA T0303 38 :ASENLVMTWIGNGADVLSQRAV 1rqlA 40 :ITAEEARKPMGLLKIDHVRALT T0303 60 :DWACTQAEKELTEDEFKYFKRQFGFYYGENLCNISRLYPNVKETLEALKAQGYILAVVTNKPTKHVQPILTAF 1rqlA 68 :SEWNRVFRQLPTEADIQEMYEEFEEILFAILPRYASPINAVKEVIASLRERGIKIGSTTGYTREMMDIVAKEA T0303 133 :GID 1rqlA 144 :GYK T0303 138 :FSEMLGGQSLPEIKPHPAPFYYLCGKFGL 1rqlA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMELGV T0303 167 :YPKQILFVGDSQNDIFAAHSAGCAVVGLTYGYNYNIP 1rqlA 177 :PMNHMIKVGDTVSDMKEGRNAGMWTVGVILGSSELGL T0303 204 :IAQSKPDWIFDDFADILKI 1rqlA 237 :FVENGAHFTIETMQELESV Number of specific fragments extracted= 8 number of extra gaps= 0 total=168 Number of alignments=16 # 1rqlA read from 1rqlA/merged-good-all-a2m # found chain 1rqlA in template set Warning: unaligning (T0303)Q3 because first residue in template chain is (1rqlA)K5 T0303 4 :FKLIGFDLDGTLVN 1rqlA 6 :IEAVIFDWAGTTVD T0303 18 :SLPDLALSINSALKDVNLP 1rqlA 21 :GCFAPLEVFMEIFHKRGVA T0303 38 :ASENLVMTWIGNGADVLSQRA 1rqlA 40 :ITAEEARKPMGLLKIDHVRAL T0303 59 :VDWACTQAEKELTEDEFKYFKRQFGFYYGENLCNISRLYPNVKETLEALKAQGYILAVVTNKPTKHVQPILTAF 1rqlA 67 :ASEWNRVFRQLPTEADIQEMYEEFEEILFAILPRYASPINAVKEVIASLRERGIKIGSTTGYTREMMDIVAKEA T0303 133 :GID 1rqlA 144 :GYK T0303 138 :FSEMLGGQSLPEIKPHPAPFYYLCGKFGL 1rqlA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMELGV T0303 167 :YPKQILFVGDSQNDIFAAHSAGCAVVGLTYGYN 1rqlA 177 :PMNHMIKVGDTVSDMKEGRNAGMWTVGVILGSS T0303 200 :YNIPIAQSK 1rqlA 214 :TEEEVENMD T0303 209 :PDWIFDDFADILKI 1rqlA 242 :AHFTIETMQELESV Number of specific fragments extracted= 9 number of extra gaps= 0 total=177 Number of alignments=17 # 1rqlA read from 1rqlA/merged-good-all-a2m # found chain 1rqlA in template set Warning: unaligning (T0303)Q3 because first residue in template chain is (1rqlA)K5 T0303 4 :FKLIGFDLDGTLVNSL 1rqlA 6 :IEAVIFDWAGTTVDYG T0303 20 :PDLALSINSALKDVNLPQASENLVMTWIGNGADVLSQR 1rqlA 23 :FAPLEVFMEIFHKRGVAITAEEARKPMGLLKIDHVRAL T0303 58 :AVDWACTQAEKELTEDEFKYFKRQFGFYYGENLCNISRLYPNVKETLEALKAQGYILAVVTNKPTKHVQPILTAF 1rqlA 66 :IASEWNRVFRQLPTEADIQEMYEEFEEILFAILPRYASPINAVKEVIASLRERGIKIGSTTGYTREMMDIVAKEA T0303 133 :GID 1rqlA 144 :GYK T0303 138 :FSEMLGGQSLPEIKPHPAPFYYLCGKFGL 1rqlA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMELGV T0303 167 :YPKQILFVGDSQNDIFAAHSAGCAVVGLTYGYNYNIP 1rqlA 177 :PMNHMIKVGDTVSDMKEGRNAGMWTVGVILGSSELGL T0303 204 :IAQSKPDWIFDDFADILKITQ 1rqlA 237 :FVENGAHFTIETMQELESVME Number of specific fragments extracted= 7 number of extra gaps= 0 total=184 Number of alignments=18 # 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:# T0303 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 (T0303)K5 because first residue in template chain is (1ek1A)R4 Warning: unaligning (T0303)L19 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ek1A)G48 Warning: unaligning (T0303)N49 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ek1A)G48 Warning: unaligning (T0303)E69 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ek1A)Q90 Warning: unaligning (T0303)R95 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ek1A)Q90 T0303 6 :LIGFDLDGTLVN 1ek1A 5 :VAAFDLDGVLAL T0303 18 :S 1ek1A 18 :S T0303 50 :GADVLSQRA 1ek1A 49 :PTEQLMKGK T0303 60 :D 1ek1A 65 :P T0303 96 :LYPN 1ek1A 91 :IFSQ T0303 100 :VKETLE 1ek1A 102 :NRPMLQ T0303 106 :ALKAQGYILAVVTN 1ek1A 111 :ALKKKGFTTCIVTN T0303 120 :KPTKHVQPILTAF 1ek1A 131 :DKRDSLAQMMCEL T0303 135 :DHLFSEMLGGQSLPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCA 1ek1A 144 :SQHFDFLIESCQVGMIKPEPQIYNFLLDTLKAKPNEVVFLDDFGSNLKPARDMGMV Number of specific fragments extracted= 9 number of extra gaps= 0 total=193 Number of alignments=19 # 1ek1A read from 1ek1A/merged-good-all-a2m # found chain 1ek1A in template set Warning: unaligning (T0303)K5 because first residue in template chain is (1ek1A)R4 Warning: unaligning (T0303)Y85 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ek1A)Q90 T0303 6 :LIGFDLDGTLVN 1ek1A 5 :VAAFDLDGVLAL T0303 86 :YGENLCNISRLYPNVKETLEALKAQGYILAVVTNKP 1ek1A 91 :IFSQAMAARSINRPMLQAAIALKKKGFTTCIVTNNW T0303 122 :TKHVQPILTAFG 1ek1A 133 :RDSLAQMMCELS T0303 136 :HLFSEMLGGQSLPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCA 1ek1A 145 :QHFDFLIESCQVGMIKPEPQIYNFLLDTLKAKPNEVVFLDDFGSNLKPARDMGMV Number of specific fragments extracted= 4 number of extra gaps= 0 total=197 Number of alignments=20 # 1ek1A read from 1ek1A/merged-good-all-a2m # found chain 1ek1A in template set Warning: unaligning (T0303)K5 because first residue in template chain is (1ek1A)R4 Warning: unaligning (T0303)E40 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ek1A)G48 Warning: unaligning (T0303)R95 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ek1A)Q90 T0303 6 :LIGFDLDGTLV 1ek1A 5 :VAAFDLDGVLA T0303 41 :NLVMTWIGNGA 1ek1A 49 :PTEQLMKGKIT T0303 96 :LYPN 1ek1A 91 :IFSQ T0303 100 :VKETLEALKAQGYILAVVTNKP 1ek1A 105 :MLQAAIALKKKGFTTCIVTNNW T0303 122 :TKHVQPILTAF 1ek1A 133 :RDSLAQMMCEL T0303 135 :DHLFSEMLGGQSLPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGC 1ek1A 144 :SQHFDFLIESCQVGMIKPEPQIYNFLLDTLKAKPNEVVFLDDFGSNLKPARDMGM Number of specific fragments extracted= 6 number of extra gaps= 0 total=203 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bduA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2bduA expands to /projects/compbio/data/pdb/2bdu.pdb.gz 2bduA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1944, because occupancy 0.350 <= existing 0.650 in 2bduA Skipped atom 1946, because occupancy 0.350 <= existing 0.650 in 2bduA Skipped atom 1948, because occupancy 0.350 <= existing 0.650 in 2bduA Skipped atom 1950, because occupancy 0.350 <= existing 0.650 in 2bduA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0303 read from 2bduA/merged-good-all-a2m # 2bduA read from 2bduA/merged-good-all-a2m # adding 2bduA to template set # found chain 2bduA in template set Warning: unaligning (T0303)V117 because of BadResidue code BAD_PEPTIDE in next template residue (2bduA)S164 Warning: unaligning (T0303)T118 because of BadResidue code BAD_PEPTIDE at template residue (2bduA)S164 Warning: unaligning (T0303)I171 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bduA)I234 Warning: unaligning (T0303)L172 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bduA)I234 Warning: unaligning (T0303)F213 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bduA)D263 Warning: unaligning (T0303)D214 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bduA)D263 T0303 6 :LIGFDLDGTLVN 2bduA 45 :QIITDFDMTLSR T0303 18 :SLPDLALSINSALKDV 2bduA 77 :VTDECRRKLLQLKEQY T0303 34 :NLPQASENLVMTWIGNGADVLSQRAVD 2bduA 97 :VDPVLTVEEKFPYMVEWYTKSHGLLIE T0303 68 :KELTEDEFKYFKRQ 2bduA 124 :QGIPKAKLKEIVAD T0303 92 :NISRLYPNVKETLEALKAQGYILAV 2bduA 138 :SDVMLKEGYENFFGKLQQHGIPVFI T0303 119 :NKPTKHVQPILTAFGID 2bduA 165 :AGIGDVLEEVIRQAGVY T0303 136 :HLFSEMLGG 2bduA 183 :SNVKVVSNF T0303 145 :QSLPEIK 2bduA 195 :DENGVLK T0303 154 :PAPFY 2bduA 214 :HDGAL T0303 161 :CGKFG 2bduA 224 :FSQLK T0303 168 :PKQ 2bduA 230 :NSN T0303 173 :FVGDSQND 2bduA 235 :LLGDSQGD T0303 186 :SAGC 2bduA 246 :ADGV T0303 190 :AVVGLT 2bduA 254 :HILKIG T0303 211 :WI 2bduA 260 :YL T0303 215 :DFADILKI 2bduA 264 :RVDELLEK Number of specific fragments extracted= 16 number of extra gaps= 3 total=219 Number of alignments=22 # 2bduA read from 2bduA/merged-good-all-a2m # found chain 2bduA in template set Warning: unaligning (T0303)V117 because of BadResidue code BAD_PEPTIDE in next template residue (2bduA)S164 Warning: unaligning (T0303)T118 because of BadResidue code BAD_PEPTIDE at template residue (2bduA)S164 Warning: unaligning (T0303)I171 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bduA)I234 Warning: unaligning (T0303)L172 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bduA)I234 Warning: unaligning (T0303)F213 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bduA)D263 Warning: unaligning (T0303)D214 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bduA)D263 T0303 6 :LIGFDLDGTLVN 2bduA 45 :QIITDFDMTLSR T0303 18 :SLPDLALSINSALKDV 2bduA 77 :VTDECRRKLLQLKEQY T0303 34 :NLPQASENLVMTWIGNGADVLSQRAVDW 2bduA 97 :VDPVLTVEEKFPYMVEWYTKSHGLLIEQ T0303 69 :ELTEDEFKYFKRQ 2bduA 125 :GIPKAKLKEIVAD T0303 92 :NISRLYPNVKETLEALKAQGYILAV 2bduA 138 :SDVMLKEGYENFFGKLQQHGIPVFI T0303 119 :NKPTKHVQPILTAFGIDHLFSEMLGGQ 2bduA 165 :AGIGDVLEEVIRQAGVYHSNVKVVSNF T0303 154 :PAP 2bduA 221 :TDY T0303 161 :CGKFG 2bduA 224 :FSQLK T0303 167 :YPKQ 2bduA 229 :DNSN T0303 173 :FVGDSQNDIFA 2bduA 235 :LLGDSQGDLRM T0303 187 :A 2bduA 246 :A T0303 188 :G 2bduA 248 :G T0303 189 :CAVVGLTY 2bduA 252 :VEHILKIG T0303 211 :WI 2bduA 260 :YL T0303 215 :DFADILKI 2bduA 264 :RVDELLEK Number of specific fragments extracted= 15 number of extra gaps= 3 total=234 Number of alignments=23 # 2bduA read from 2bduA/merged-good-all-a2m # found chain 2bduA in template set Warning: unaligning (T0303)V117 because of BadResidue code BAD_PEPTIDE in next template residue (2bduA)S164 Warning: unaligning (T0303)T118 because of BadResidue code BAD_PEPTIDE at template residue (2bduA)S164 Warning: unaligning (T0303)I171 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bduA)I234 Warning: unaligning (T0303)L172 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bduA)I234 Warning: unaligning (T0303)F213 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bduA)D263 Warning: unaligning (T0303)D214 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bduA)D263 T0303 6 :LIGFDLDGTLV 2bduA 45 :QIITDFDMTLS T0303 18 :SLPDLALSINSALKDVNLPQASENLVMTWIGNGADVLSQRAVDW 2bduA 81 :CRRKLLQLKEQYYAIEVDPVLTVEEKFPYMVEWYTKSHGLLIEQ T0303 69 :ELTEDEFKYFKRQFG 2bduA 125 :GIPKAKLKEIVADSD T0303 94 :SRLYPNVKETLEALKAQGYILAV 2bduA 140 :VMLKEGYENFFGKLQQHGIPVFI T0303 119 :NKPTKHVQPILTAFGIDHLFSEML 2bduA 165 :AGIGDVLEEVIRQAGVYHSNVKVV T0303 143 :GGQSLPEIK 2bduA 204 :KGELIHVFN T0303 157 :FYYLC 2bduA 213 :KHDGA T0303 162 :GKFG 2bduA 225 :SQLK T0303 168 :PKQ 2bduA 230 :NSN T0303 173 :FVGDSQND 2bduA 235 :LLGDSQGD T0303 186 :SAGCA 2bduA 246 :ADGVA T0303 191 :VVGLT 2bduA 257 :KIGYL T0303 215 :DFADIL 2bduA 264 :RVDELL Number of specific fragments extracted= 13 number of extra gaps= 3 total=247 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 # T0303 read from 1nnlA/merged-good-all-a2m # 1nnlA read from 1nnlA/merged-good-all-a2m # found chain 1nnlA in training set Warning: unaligning (T0303)S39 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1nnlA)P57 Warning: unaligning (T0303)G50 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1nnlA)P57 T0303 4 :FKLIGFDLDGTLVNSL 1nnlA 14 :ADAVCFDVDSTVIREE T0303 25 :SINSALKDVNLPQA 1nnlA 30 :GIDELAKICGVEDA T0303 51 :ADVLSQRAVDWA 1nnlA 58 :FKAALTERLALI T0303 69 :ELTEDEFKYFKRQ 1nnlA 70 :QPSREQVQRLIAE T0303 92 :NISRLYPNVKETLEALKAQGYILAVVTNKPTKHVQPILTAFGIDHLFSEMLGGQSLPEI 1nnlA 83 :QPPHLTPGIRELVSRLQERNVQVFLISGGFRSIVEHVASKLNIPATNVFANRLKFYFNG T0303 153 :HPAPFYYLCGKF 1nnlA 154 :ESGGKGKVIKLL T0303 167 :YPKQILFVGDSQNDIFAA 1nnlA 170 :HFKKIIMIGDGATDMEAC T0303 188 :GCAVVGLTYGYNYNIPIAQS 1nnlA 189 :PADAFIGFGGNVIRQQVKDN T0303 209 :PDWIFDDFADI 1nnlA 209 :AKWYITDFVEL Number of specific fragments extracted= 9 number of extra gaps= 0 total=256 Number of alignments=25 # 1nnlA read from 1nnlA/merged-good-all-a2m # found chain 1nnlA in training set Warning: unaligning (T0303)S39 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1nnlA)P57 Warning: unaligning (T0303)G50 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1nnlA)P57 T0303 4 :FKLIGFDLDGTLVNSLP 1nnlA 14 :ADAVCFDVDSTVIREEG T0303 26 :INSALKDVNLPQA 1nnlA 31 :IDELAKICGVEDA T0303 51 :ADVLSQRAVDWA 1nnlA 58 :FKAALTERLALI T0303 69 :ELTEDEFKYFKRQ 1nnlA 70 :QPSREQVQRLIAE T0303 92 :NISRLYPNVKETLEALKAQGYILAVVTNKPTKHVQPILTAFGID 1nnlA 83 :QPPHLTPGIRELVSRLQERNVQVFLISGGFRSIVEHVASKLNIP T0303 138 :FSEMLGGQ 1nnlA 127 :ATNVFANR T0303 146 :SLPEIK 1nnlA 153 :AESGGK T0303 154 :PAPFYYLCGKFGL 1nnlA 159 :GKVIKLLKEKFHF T0303 169 :KQILFVGDSQNDIFAAHSAG 1nnlA 172 :KKIIMIGDGATDMEACPPAD T0303 190 :AVVGLT 1nnlA 192 :AFIGFG T0303 197 :GYNYNIPIAQS 1nnlA 198 :GNVIRQQVKDN T0303 209 :PDWIFDDFADI 1nnlA 209 :AKWYITDFVEL Number of specific fragments extracted= 12 number of extra gaps= 0 total=268 Number of alignments=26 # 1nnlA read from 1nnlA/merged-good-all-a2m # found chain 1nnlA in training set Warning: unaligning (T0303)S39 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1nnlA)P57 Warning: unaligning (T0303)D52 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1nnlA)P57 T0303 5 :KLIGFDLDGTLVNSL 1nnlA 15 :DAVCFDVDSTVIREE T0303 25 :SINSALKDVNLPQA 1nnlA 30 :GIDELAKICGVEDA T0303 53 :VLSQRAVD 1nnlA 58 :FKAALTER T0303 65 :QAEKELTEDEFKYFKRQ 1nnlA 66 :LALIQPSREQVQRLIAE T0303 92 :NISRLYPNVKETLEALKAQGYILAVVTNKPTKHVQPILTAFGIDHLF 1nnlA 83 :QPPHLTPGIRELVSRLQERNVQVFLISGGFRSIVEHVASKLNIPATN T0303 141 :ML 1nnlA 130 :VF T0303 148 :PEIK 1nnlA 151 :PTAE T0303 154 :PAPFYYLCGKF 1nnlA 155 :SGGKGKVIKLL T0303 167 :YPKQILFVGDSQNDI 1nnlA 170 :HFKKIIMIGDGATDM T0303 188 :GCAVVGLTYGYNYNIPI 1nnlA 189 :PADAFIGFGGNVIRQQV T0303 206 :QSKPDWIFDDFADI 1nnlA 206 :KDNAKWYITDFVEL Number of specific fragments extracted= 11 number of extra gaps= 0 total=279 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:# T0303 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 (T0303)Q3 because first residue in template chain is (1zd3A)T2 T0303 4 :FKLIGFDLDGTLVNSL 1zd3A 3 :LRAAVFDLDGVLALPA T0303 24 :LSINSALKDVNLPQASENLV 1zd3A 21 :GVLGRTEEALALPRGLLNDA T0303 44 :MTWI 1zd3A 51 :TRLM T0303 48 :GNGADVLSQRAVDWACTQAE 1zd3A 57 :EITLSQWIPLMEENCRKCSE T0303 68 :KELTED 1zd3A 80 :VCLPKN T0303 82 :FGFYYGENL 1zd3A 88 :IKEIFDKAI T0303 92 :NISRLYPNVKETLEALKAQGYILAVVTN 1zd3A 97 :SARKINRPMLQAALMLRKKGFTTAILTN T0303 120 :KPTKHVQPILTAFGI 1zd3A 131 :AERDGLAQLMCELKM T0303 137 :LFSEMLGGQSLPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVVGL 1zd3A 146 :HFDFLIESCQVGMVKPEPQIYKFLLDTLKASPSEVVFLDDIGANLKPARDLGMVTILV T0303 214 :DD 1zd3A 204 :QD T0303 216 :FADILKI 1zd3A 210 :LKELEKV Number of specific fragments extracted= 11 number of extra gaps= 0 total=290 Number of alignments=28 # 1zd3A read from 1zd3A/merged-good-all-a2m # found chain 1zd3A in template set Warning: unaligning (T0303)Q3 because first residue in template chain is (1zd3A)T2 T0303 4 :FKLIGFDLDGTLVNSLP 1zd3A 3 :LRAAVFDLDGVLALPAV T0303 23 :ALSINSALKDVNLPQA 1zd3A 20 :FGVLGRTEEALALPRG T0303 48 :GNGADVLSQRAVDWACTQ 1zd3A 57 :EITLSQWIPLMEENCRKC T0303 66 :AEKELT 1zd3A 82 :LPKNFS T0303 78 :FKRQFGFYY 1zd3A 88 :IKEIFDKAI T0303 92 :NISRLYPNVKETLEALKAQGYILAVVTNKP 1zd3A 97 :SARKINRPMLQAALMLRKKGFTTAILTNTW T0303 122 :TKHVQPILTAFG 1zd3A 133 :RDGLAQLMCELK T0303 136 :HLFSEMLGGQSLPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVV 1zd3A 145 :MHFDFLIESCQVGMVKPEPQIYKFLLDTLKASPSEVVFLDDIGANLKPARDLGMVTI T0303 212 :IFDDFADILK 1zd3A 202 :LVQDTDTALK Number of specific fragments extracted= 9 number of extra gaps= 0 total=299 Number of alignments=29 # 1zd3A read from 1zd3A/merged-good-all-a2m # found chain 1zd3A in template set Warning: unaligning (T0303)Q3 because first residue in template chain is (1zd3A)T2 T0303 4 :FKLIGFDLDGTLV 1zd3A 3 :LRAAVFDLDGVLA T0303 25 :SINSALKDVNLPQASENLVMTWIGNGADVLSQRAVDWACTQAEKEL 1zd3A 22 :VLGRTEEALALPRGLLNDAFQKGGPEGATTRLMKGEITLSQWIPLM T0303 72 :EDEFKYFKRQFG 1zd3A 68 :EENCRKCSETAK T0303 84 :FYYGENLCNISRLYPNVKETLEALKAQGYILAVVTNKP 1zd3A 89 :KEIFDKAISARKINRPMLQAALMLRKKGFTTAILTNTW T0303 122 :TKHVQPILTAFG 1zd3A 133 :RDGLAQLMCELK T0303 136 :HLFSEMLGGQSLPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVVG 1zd3A 145 :MHFDFLIESCQVGMVKPEPQIYKFLLDTLKASPSEVVFLDDIGANLKPARDLGMVTIL T0303 213 :FDDFADILKIT 1zd3A 203 :VQDTDTALKEL Number of specific fragments extracted= 7 number of extra gaps= 0 total=306 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 # T0303 read from 1l7mA/merged-good-all-a2m # 1l7mA read from 1l7mA/merged-good-all-a2m # found chain 1l7mA in training set Warning: unaligning (T0303)T2 because first residue in template chain is (1l7mA)K3 T0303 3 :QFKLIGFDLDGTLVNSL 1l7mA 4 :KKKLILFDFDSTLVNNE T0303 25 :SINSALKDVNL 1l7mA 21 :TIDEIAREAGV T0303 40 :ENLVMTWI 1l7mA 32 :EEEVKKIT T0303 48 :GNGADVLSQRAVDWA 1l7mA 46 :KLNFEQSLRKRVSLL T0303 68 :KELTEDEFKYFK 1l7mA 61 :KDLPIEKVEKAI T0303 92 :NISRLYPNVKETLEALKAQGYILAVVTNKPTKHVQPILTAFGIDHLFSEMLGGQSL 1l7mA 73 :KRITPTEGAEETIKELKNRGYVVAVVSGGFDIAVNKIKEKLGLDYAFANRLIVKDG T0303 148 :PEIKPH 1l7mA 137 :EVLKEN T0303 154 :PAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCA 1l7mA 145 :GEILEKIAKIEGINLEDTVAVGDGANDISMFKKAGLK T0303 192 :VGLTYG 1l7mA 182 :IAFCAK T0303 202 :IPIAQS 1l7mA 188 :PILKEK T0303 209 :PDWIFD 1l7mA 194 :ADICIE T0303 215 :DFADILKI 1l7mA 202 :DLREILKY Number of specific fragments extracted= 12 number of extra gaps= 0 total=318 Number of alignments=31 # 1l7mA read from 1l7mA/merged-good-all-a2m # found chain 1l7mA in training set Warning: unaligning (T0303)T2 because first residue in template chain is (1l7mA)K3 T0303 3 :QFKLIGFDLDGTLVNSLP 1l7mA 4 :KKKLILFDFDSTLVNNET T0303 26 :INSALKDVNL 1l7mA 22 :IDEIAREAGV T0303 40 :ENLVMTWI 1l7mA 32 :EEEVKKIT T0303 48 :GNGADVLSQRA 1l7mA 46 :KLNFEQSLRKR T0303 63 :CTQAE 1l7mA 57 :VSLLK T0303 69 :ELTEDEFKYFK 1l7mA 62 :DLPIEKVEKAI T0303 92 :NISRLYPNVKETLEALKAQGYILAVVTNKPTKHVQPILTAFGIDHLFSEMLGGQ 1l7mA 73 :KRITPTEGAEETIKELKNRGYVVAVVSGGFDIAVNKIKEKLGLDYAFANRLIVK T0303 146 :SLPEIK 1l7mA 139 :LKENAK T0303 154 :PAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAG 1l7mA 145 :GEILEKIAKIEGINLEDTVAVGDGANDISMFKKAG T0303 190 :AVVGLTY 1l7mA 180 :LKIAFCA T0303 201 :NIPIAQS 1l7mA 187 :KPILKEK T0303 209 :PDWIFD 1l7mA 194 :ADICIE T0303 215 :DFADILKI 1l7mA 202 :DLREILKY Number of specific fragments extracted= 13 number of extra gaps= 0 total=331 Number of alignments=32 # 1l7mA read from 1l7mA/merged-good-all-a2m # found chain 1l7mA in training set Warning: unaligning (T0303)T2 because first residue in template chain is (1l7mA)K3 T0303 3 :QFKLIGFDLDGTLVNSL 1l7mA 4 :KKKLILFDFDSTLVNNE T0303 25 :SINSALKDVNLPQASENLVMTWIGNGA 1l7mA 21 :TIDEIAREAGVEEEVKKITKEAMEGKL T0303 52 :DVLSQRAVD 1l7mA 51 :QSLRKRVSL T0303 67 :EKELTEDEFKYFKR 1l7mA 60 :LKDLPIEKVEKAIK T0303 93 :ISRLYPNVKETLEALKAQGYILAVVTNKPTKHVQPILTAFGIDHLFSEMLGGQS 1l7mA 74 :RITPTEGAEETIKELKNRGYVVAVVSGGFDIAVNKIKEKLGLDYAFANRLIVKD T0303 153 :HPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVVG 1l7mA 144 :KGEILEKIAKIEGINLEDTVAVGDGANDISMFKKAGLKIAF T0303 195 :T 1l7mA 185 :C T0303 201 :NIPIAQSKPDWIFD 1l7mA 186 :AKPILKEKADICIE T0303 215 :DFADILKIT 1l7mA 202 :DLREILKYI Number of specific fragments extracted= 9 number of extra gaps= 0 total=340 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:# T0303 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 (T0303)K5 because first residue in template chain is (1cqzA)R4 Warning: unaligning (T0303)E72 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cqzA)Q90 T0303 6 :LIGFDLDGTLVNSL 1cqzA 5 :VAAFDLDGVLALPS T0303 73 :DEF 1cqzA 91 :IFS T0303 88 :ENLCN 1cqzA 94 :QAMAA T0303 94 :SRLYPNVKETLEALKAQGYILAVVTN 1cqzA 99 :RSINRPMLQAAIALKKKGFTTCIVTN T0303 120 :KPTKHVQPILTAF 1cqzA 131 :DKRDSLAQMMCEL T0303 135 :DHLFSEMLGGQSLPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVVGLTYGY 1cqzA 144 :SQHFDFLIESCQVGMIKPEPQIYNFLLDTLKAKPNEVVFLDDFGSNLKPARDMGMVTILVHNTA Number of specific fragments extracted= 6 number of extra gaps= 0 total=346 Number of alignments=34 # 1cqzA read from 1cqzA/merged-good-all-a2m # found chain 1cqzA in template set Warning: unaligning (T0303)K5 because first residue in template chain is (1cqzA)R4 Warning: unaligning (T0303)S18 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cqzA)Q90 Warning: unaligning (T0303)E67 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cqzA)Q90 T0303 6 :LIGFDLDGTLVN 1cqzA 5 :VAAFDLDGVLAL T0303 68 :KEL 1cqzA 91 :IFS T0303 76 :KYF 1cqzA 94 :QAM T0303 92 :NISRLYPNVKETLEALKAQGYILAVVTNKP 1cqzA 97 :AARSINRPMLQAAIALKKKGFTTCIVTNNW T0303 122 :TKHVQPILTAFG 1cqzA 133 :RDSLAQMMCELS T0303 136 :HLFSEMLGGQSLPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVVGLTYGY 1cqzA 145 :QHFDFLIESCQVGMIKPEPQIYNFLLDTLKAKPNEVVFLDDFGSNLKPARDMGMVTILVHNTA Number of specific fragments extracted= 6 number of extra gaps= 0 total=352 Number of alignments=35 # 1cqzA read from 1cqzA/merged-good-all-a2m # found chain 1cqzA in template set Warning: unaligning (T0303)K5 because first residue in template chain is (1cqzA)R4 Warning: unaligning (T0303)S18 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cqzA)Q90 Warning: unaligning (T0303)G48 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cqzA)Q90 T0303 6 :LIGFDLDGTLV 1cqzA 5 :VAAFDLDGVLA T0303 17 :N 1cqzA 62 :Q T0303 49 :NGADVLSQR 1cqzA 91 :IFSQAMAAR T0303 97 :YPNVKETLEALKAQGYILAVVTNKP 1cqzA 102 :NRPMLQAAIALKKKGFTTCIVTNNW T0303 122 :TKHVQPILTAF 1cqzA 133 :RDSLAQMMCEL T0303 135 :DHLFSEMLGGQSLPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVVGLTYGY 1cqzA 144 :SQHFDFLIESCQVGMIKPEPQIYNFLLDTLKAKPNEVVFLDDFGSNLKPARDMGMVTILVHNTA Number of specific fragments extracted= 6 number of extra gaps= 0 total=358 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:# T0303 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 (T0303)Q3 because first residue in template chain is (1wviA)T1002 T0303 4 :FKLIGFDLDGTLV 1wviA 1003 :YKGYLIDLDGTIY T0303 17 :NSLPDLALSINSALKDV 1wviA 1019 :DRIPAGEDFVKRLQERQ T0303 34 :NL 1wviA 1044 :NT T0303 48 :GNGADVLSQRAVD 1wviA 1046 :TRTPEMVQEMLAT T0303 65 :QAEKELTEDE 1wviA 1059 :SFNIKTPLET T0303 78 :FKRQFGFYYGENLCN 1wviA 1072 :ATLATIDYMNDMKRG T0303 96 :LYPNVKET 1wviA 1093 :GETGLKKA T0303 107 :LKAQGYI 1wviA 1101 :VAEAGYR T0303 114 :LAVVTN 1wviA 1115 :YVVVGL T0303 120 :KPTKHVQPILTAF 1wviA 1123 :NLTYEKLTLATLA T0303 133 :G 1wviA 1139 :G T0303 138 :FSEMLGGQSL 1wviA 1140 :AVFIGTNPDL T0303 149 :EIKPHPAPFYYLCGKFGLYPKQILFVGDSQ 1wviA 1179 :IGKPEAVIMNKALDRLGVKRHEAIMVGDNY T0303 179 :NDIFAAHSAGCAVVGLTYGYNYNIPIAQSK 1wviA 1210 :TDITAGIKNDIATLLVTTGFTKPEEVPALP T0303 209 :PDWIFDDFAD 1wviA 1242 :PDFVLSSLAE Number of specific fragments extracted= 15 number of extra gaps= 0 total=373 Number of alignments=37 # 1wviA read from 1wviA/merged-good-all-a2m # found chain 1wviA in template set Warning: unaligning (T0303)Q3 because first residue in template chain is (1wviA)T1002 T0303 4 :FKLIGFDLDGTLVN 1wviA 1003 :YKGYLIDLDGTIYK T0303 93 :ISRLYPNVKETLEALKAQGYILAVVTNKP 1wviA 1017 :GKDRIPAGEDFVKRLQERQLPYILVTNNT T0303 122 :TKHVQPILTAF 1wviA 1049 :PEMVQEMLATS T0303 133 :GIDHLFSEMLGGQ 1wviA 1061 :NIKTPLETIYTAT T0303 146 :SLPE 1wviA 1173 :RVKP T0303 150 :IKPHPAPFYYLCGKFGLYPKQILFVGDSQN 1wviA 1180 :GKPEAVIMNKALDRLGVKRHEAIMVGDNYL T0303 180 :DIFAAHSAGCAVVGLTYGYNYNIPIAQSK 1wviA 1211 :DITAGIKNDIATLLVTTGFTKPEEVPALP T0303 209 :PDWIFDDFAD 1wviA 1242 :PDFVLSSLAE Number of specific fragments extracted= 8 number of extra gaps= 0 total=381 Number of alignments=38 # 1wviA read from 1wviA/merged-good-all-a2m # found chain 1wviA in template set Warning: unaligning (T0303)Q3 because first residue in template chain is (1wviA)T1002 T0303 4 :FKLIGFDLDGTLV 1wviA 1003 :YKGYLIDLDGTIY T0303 18 :SLPDLALSINSALKDV 1wviA 1020 :RIPAGEDFVKRLQERQ T0303 34 :NLPQASENLVMTWIGNGA 1wviA 1044 :NTTRTPEMVQEMLATSFN T0303 52 :DVLSQR 1wviA 1095 :TGLKKA T0303 58 :AVD 1wviA 1120 :LDT T0303 69 :ELTEDEFKYFKRQF 1wviA 1123 :NLTYEKLTLATLAI T0303 109 :AQGYIL 1wviA 1137 :QKGAVF T0303 116 :VVTNKP 1wviA 1143 :IGTNPD T0303 122 :TKHVQPILTAFGIDHLF 1wviA 1162 :GAILFLLEKATRVKPII T0303 150 :IKPHPAPFYYLCGKFGLYPKQILFVGDSQ 1wviA 1180 :GKPEAVIMNKALDRLGVKRHEAIMVGDNY T0303 179 :NDIFAAHSAGCAVVGLTYGYNYNIPIAQSK 1wviA 1210 :TDITAGIKNDIATLLVTTGFTKPEEVPALP T0303 209 :PDWIFDDFAD 1wviA 1242 :PDFVLSSLAE Number of specific fragments extracted= 12 number of extra gaps= 0 total=393 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:# T0303 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 T0303 5 :KLIGFDLDGTLVN 1zjjA 2 :VAIIFDMDGVLYR T0303 93 :ISRLYPNVKETLEALKAQGYILAVVTN 1zjjA 15 :GNRAIPGVRELIEFLKERGIPFAFLTN T0303 120 :KPTKHVQPILTAFGID 1zjjA 45 :KTPEMYREKLLKMGID T0303 138 :F 1zjjA 61 :V T0303 139 :SEMLGG 1zjjA 64 :SIIITS T0303 146 :SLPEIK 1zjjA 80 :HLDPGK T0303 153 :HPAPFYYLCGKFG 1zjjA 90 :GGEGLVKEMQALG T0303 166 :LYPKQILFVGDSQ 1zjjA 200 :FPGEELWMVGDRL T0303 179 :NDIFAAHSAGCAVVGLTYGYNYNIPIAQSK 1zjjA 214 :TDIAFAKKFGMKAIMVLTGVSSLEDIKKSE T0303 209 :PDWIFDDFADILKITQ 1zjjA 246 :PDLVLPSVYELIDYLK Number of specific fragments extracted= 10 number of extra gaps= 0 total=403 Number of alignments=40 # 1zjjA read from 1zjjA/merged-good-all-a2m # found chain 1zjjA in template set T0303 6 :LIGFDLDGTLV 1zjjA 3 :AIIFDMDGVLY T0303 92 :NISRLYPNVKETLEALKAQGYILAVVTNKP 1zjjA 14 :RGNRAIPGVRELIEFLKERGIPFAFLTNNS T0303 122 :TKHVQPILTAFGIDHLFSEMLGGQ 1zjjA 47 :PEMYREKLLKMGIDVSSSIIITSG T0303 146 :SLPE 1zjjA 179 :NVEP T0303 150 :IKPHPAPFYYLCGKFG 1zjjA 186 :GKPNEPMYEVVREMFP T0303 168 :PKQILFVGDSQN 1zjjA 202 :GEELWMVGDRLD T0303 180 :DIFAAHSAGCAVVGLTYGYNYNIPIAQSK 1zjjA 215 :DIAFAKKFGMKAIMVLTGVSSLEDIKKSE T0303 209 :PDWIFDDFADILKI 1zjjA 246 :PDLVLPSVYELIDY Number of specific fragments extracted= 8 number of extra gaps= 0 total=411 Number of alignments=41 # 1zjjA read from 1zjjA/merged-good-all-a2m # found chain 1zjjA in template set T0303 5 :KLIGFDLDGTLV 1zjjA 2 :VAIIFDMDGVLY T0303 94 :SRLYPNVKETLEALKAQGYILAVVTNKP 1zjjA 16 :NRAIPGVRELIEFLKERGIPFAFLTNNS T0303 122 :TKHVQPILTAFGIDHLFSEML 1zjjA 47 :PEMYREKLLKMGIDVSSSIII T0303 151 :KP 1zjjA 187 :KP T0303 154 :PAPFYYLCGKF 1zjjA 189 :NEPMYEVVREM T0303 166 :LYPKQILFVGDSQ 1zjjA 200 :FPGEELWMVGDRL T0303 179 :NDIFAAHSAGCAVVGLTYGYNYNIPIA 1zjjA 214 :TDIAFAKKFGMKAIMVLTGVSSLEDIK T0303 206 :QSKPDWIFDDFADILKITQ 1zjjA 243 :EYKPDLVLPSVYELIDYLK Number of specific fragments extracted= 8 number of extra gaps= 0 total=419 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 # T0303 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 (T0303)Q3 because first residue in template chain is (2go7A)K3 Warning: unaligning (T0303)F9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2go7A)D9 Warning: unaligning (T0303)D10 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2go7A)D9 Warning: unaligning (T0303)V116 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2go7A)Y106 Warning: unaligning (T0303)V117 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2go7A)Y106 T0303 5 :KLIG 2go7A 4 :TAFI T0303 11 :LDGTLVNSLPDLALSINSALKDVNLP 2go7A 10 :LDGTLLDSYEAILSGIEETFAQFSIP T0303 38 :ASENLVMTWI 2go7A 36 :YDKEKVREFI T0303 48 :GNGADVLSQRAVD 2go7A 47 :KYSVQDLLVRVAE T0303 67 :EKELTEDEFK 2go7A 60 :DRNLDVEVLN T0303 80 :RQFGFYYGENL 2go7A 70 :QVRAQSLAEKN T0303 92 :NISRLYPNVKETLEALKAQGYILA 2go7A 81 :AQVVLMPGAREVLAWADESGIQQF T0303 118 :TNKP 2go7A 107 :THKG T0303 123 :KHVQPILTAFGIDHLFSEMLGGQSLPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVVGLT 2go7A 111 :NNAFTILKDLGVESYFTEILTSQSGFVRKPSPEAATYLLDKYQLNSDNTYYIGDRTLDVEFAQNSGIQSINFL T0303 199 :NYNI 2go7A 184 :ESTY T0303 205 :A 2go7A 188 :E T0303 209 :PDWIFDDFADILKIT 2go7A 189 :GNHRIQALADISRIF Number of specific fragments extracted= 12 number of extra gaps= 2 total=431 Number of alignments=43 # 2go7A read from 2go7A/merged-good-all-a2m # found chain 2go7A in template set Warning: unaligning (T0303)F4 because first residue in template chain is (2go7A)K3 Warning: unaligning (T0303)F9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2go7A)D9 Warning: unaligning (T0303)D10 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2go7A)D9 Warning: unaligning (T0303)V116 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2go7A)Y106 Warning: unaligning (T0303)V117 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2go7A)Y106 T0303 5 :KLIG 2go7A 4 :TAFI T0303 11 :LDGTLVNSLPDLALSINSALKDVNLPQASENLVMTWIGNGADVLSQRAVDWA 2go7A 10 :LDGTLLDSYEAILSGIEETFAQFSIPYDKEKVREFIFKYSVQDLLVRVAEDR T0303 69 :ELTEDEFKYFKRQFGFYYG 2go7A 62 :NLDVEVLNQVRAQSLAEKN T0303 92 :NISRLYPNVKETLEALKAQGYILA 2go7A 81 :AQVVLMPGAREVLAWADESGIQQF T0303 118 :TNKP 2go7A 107 :THKG T0303 123 :KHVQPILTAFGIDHLFSEMLGGQSLPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVVGLTY 2go7A 111 :NNAFTILKDLGVESYFTEILTSQSGFVRKPSPEAATYLLDKYQLNSDNTYYIGDRTLDVEFAQNSGIQSINFLE T0303 200 :YNIP 2go7A 185 :STYE T0303 209 :PDWIFDDFADILKI 2go7A 189 :GNHRIQALADISRI Number of specific fragments extracted= 8 number of extra gaps= 2 total=439 Number of alignments=44 # 2go7A read from 2go7A/merged-good-all-a2m # found chain 2go7A in template set Warning: unaligning (T0303)F9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2go7A)D9 Warning: unaligning (T0303)D10 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2go7A)D9 Warning: unaligning (T0303)V116 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2go7A)Y106 Warning: unaligning (T0303)V117 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2go7A)Y106 T0303 5 :KLIG 2go7A 4 :TAFI T0303 11 :LDGTLVNSLPDLALSINSALKDVNLPQASENLVMTWIGNGADVLSQRAVDW 2go7A 10 :LDGTLLDSYEAILSGIEETFAQFSIPYDKEKVREFIFKYSVQDLLVRVAED T0303 68 :KELTEDEFKYFKRQ 2go7A 61 :RNLDVEVLNQVRAQ T0303 86 :YGENLCNISRLYPNVKETLEALKAQGYILA 2go7A 75 :SLAEKNAQVVLMPGAREVLAWADESGIQQF T0303 118 :TNKP 2go7A 107 :THKG T0303 123 :KHVQPILTAFGIDHLFSEMLGGQSLPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVVG 2go7A 111 :NNAFTILKDLGVESYFTEILTSQSGFVRKPSPEAATYLLDKYQLNSDNTYYIGDRTLDVEFAQNSGIQSIN T0303 197 :GYNY 2go7A 182 :FLES T0303 206 :QSKPDWIFDDFADILKITQ 2go7A 186 :TYEGNHRIQALADISRIFE Number of specific fragments extracted= 8 number of extra gaps= 2 total=447 Number of alignments=45 # 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 # T0303 read from 1nrwA/merged-good-all-a2m # 1nrwA read from 1nrwA/merged-good-all-a2m # found chain 1nrwA in training set Warning: unaligning (T0303)F4 because first residue in template chain is (1nrwA)M1 T0303 5 :KLIGFDLDGTLVN 1nrwA 2 :KLIAIDLDGTLLN T0303 18 :SLPDLALSINSALKDV 1nrwA 19 :VSLENENALRQAQRDG T0303 36 :PQASENLVMTWI 1nrwA 80 :ETIDKKRAYDIL T0303 56 :QRAV 1nrwA 92 :SWLE T0303 60 :DWACTQAEKELTEDEFKYFKRQFGF 1nrwA 123 :LDRFRSANPEADLSVLKQAAEVQYS T0303 110 :Q 1nrwA 148 :Q T0303 112 :YILA 1nrwA 149 :SGFA T0303 119 :NKPTKHVQPILTAFGIDHLFSEMLGGQS 1nrwA 176 :SFFKEKLEAGWKRYEHAEDLTLVSSAEH T0303 148 :PEIK 1nrwA 211 :KASK T0303 154 :PAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAG 1nrwA 215 :GQALKRLAKQLNIPLEETAAVGDSLNDKSMLEAAG T0303 190 :AVVGL 1nrwA 250 :KGVAM T0303 197 :G 1nrwA 255 :G T0303 199 :NYNIPIAQS 1nrwA 256 :NAREDIKSI T0303 209 :PDWIFDDFAD 1nrwA 265 :ADAVTLTNDE Number of specific fragments extracted= 14 number of extra gaps= 0 total=461 Number of alignments=46 # 1nrwA read from 1nrwA/merged-good-all-a2m # found chain 1nrwA in training set Warning: unaligning (T0303)F4 because first residue in template chain is (1nrwA)M1 T0303 5 :KLIGFDLDGTLVN 1nrwA 2 :KLIAIDLDGTLLN T0303 92 :NISRLYPNVKETLEALKAQGYILAVVTNKPTKHVQPILTAFGID 1nrwA 15 :SKHQVSLENENALRQAQRDGIEVVVSTGRAHFDVMSIFEPLGIK T0303 139 :SEMLGGQ 1nrwA 59 :TWVISAN T0303 146 :SLPEIK 1nrwA 209 :SRKASK T0303 154 :PAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAG 1nrwA 215 :GQALKRLAKQLNIPLEETAAVGDSLNDKSMLEAAG T0303 192 :VGLTYGYN 1nrwA 250 :KGVAMGNA T0303 201 :NIPIAQS 1nrwA 258 :REDIKSI T0303 209 :PDWIFDDFAD 1nrwA 265 :ADAVTLTNDE Number of specific fragments extracted= 8 number of extra gaps= 0 total=469 Number of alignments=47 # 1nrwA read from 1nrwA/merged-good-all-a2m # found chain 1nrwA in training set Warning: unaligning (T0303)F4 because first residue in template chain is (1nrwA)M1 T0303 5 :KLIGFDLDGTLVN 1nrwA 2 :KLIAIDLDGTLLN T0303 92 :NISRLYPNVKETLEALKAQGYILAVVTNKPTKHVQPILTAFGIDHLF 1nrwA 15 :SKHQVSLENENALRQAQRDGIEVVVSTGRAHFDVMSIFEPLGIKTWV T0303 139 :SEM 1nrwA 64 :ANG T0303 143 :GGQS 1nrwA 200 :SAEH T0303 151 :KPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAG 1nrwA 212 :ASKGQALKRLAKQLNIPLEETAAVGDSLNDKSMLEAAG T0303 192 :VGLTYGYNY 1nrwA 250 :KGVAMGNAR Number of specific fragments extracted= 6 number of extra gaps= 0 total=475 Number of alignments=48 # 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:# T0303 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 (T0303)Q3 because first residue in template chain is (1rdfA)K5 Warning: unaligning (T0303)Y167 because of BadResidue code BAD_PEPTIDE at template residue (1rdfA)P177 T0303 4 :FKLIGFDLDGTLVNSL 1rdfA 6 :IEAVIFDWAGTTVDYG T0303 20 :PDLALSINSALKDVNLP 1rdfA 23 :FAPLEVFMEIFHKRGVA T0303 38 :ASENLVMTWIGN 1rdfA 40 :ITAEEARKPMPL T0303 50 :GADVLSQRAVD 1rdfA 62 :EMPRIASEWNR T0303 65 :QAEKELTEDEFKYFKRQFGFYYGENLCNISRLYPNVKETLEALKAQGYILAVVTNKPTKHVQPILTAF 1rdfA 73 :VFRQLPTEADIQEMYEEFEEILFAILPRYASPINAVKEVIASLRERGIKIGSTTGYTREMMDIVAKEA T0303 133 :GID 1rdfA 144 :GYK T0303 138 :FSEMLGGQSLPEIKPHPAPFYYLCGKFGL 1rdfA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMELGV T0303 168 :PKQILFVGDSQNDIFAAHSAGCAVVGLTY 1rdfA 178 :MNHMIKVGDTVSDMKEGRNAGMWTVGVIL T0303 204 :IAQSKPDWIFDDFADILKI 1rdfA 237 :FVENGAHFTIETMQELESV Number of specific fragments extracted= 9 number of extra gaps= 1 total=484 Number of alignments=49 # 1rdfA read from 1rdfA/merged-good-all-a2m # found chain 1rdfA in template set Warning: unaligning (T0303)Q3 because first residue in template chain is (1rdfA)K5 Warning: unaligning (T0303)Y167 because of BadResidue code BAD_PEPTIDE at template residue (1rdfA)P177 T0303 4 :FKLIGFDLDGTLVN 1rdfA 6 :IEAVIFDWAGTTVD T0303 18 :SLPDLALSINSALKDVNLP 1rdfA 21 :GCFAPLEVFMEIFHKRGVA T0303 38 :ASENLVMTWI 1rdfA 40 :ITAEEARKPM T0303 48 :GNGADVLSQRAVDWA 1rdfA 60 :LTEMPRIASEWNRVF T0303 67 :EKELTEDEFKYFKRQFGFYYGENLCNISRLYPNVKETLEALKAQGYILAVVTNKPTKHVQPILTAF 1rdfA 75 :RQLPTEADIQEMYEEFEEILFAILPRYASPINAVKEVIASLRERGIKIGSTTGYTREMMDIVAKEA T0303 133 :GID 1rdfA 144 :GYK T0303 138 :FSEMLGGQSLPEIKPHPAPFYYLCGKFGL 1rdfA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMELGV T0303 168 :PKQILFVGDSQNDIFAAHSAGCAVVGLTYGYN 1rdfA 178 :MNHMIKVGDTVSDMKEGRNAGMWTVGVILGSS T0303 200 :YNIPIAQSK 1rdfA 211 :LGLTEEEVE T0303 209 :PDWIFDDFADILKI 1rdfA 242 :AHFTIETMQELESV Number of specific fragments extracted= 10 number of extra gaps= 1 total=494 Number of alignments=50 # 1rdfA read from 1rdfA/merged-good-all-a2m # found chain 1rdfA in template set Warning: unaligning (T0303)Q3 because first residue in template chain is (1rdfA)K5 Warning: unaligning (T0303)Y167 because of BadResidue code BAD_PEPTIDE at template residue (1rdfA)P177 T0303 4 :FKLIGFDLDGTLVNSL 1rdfA 6 :IEAVIFDWAGTTVDYG T0303 20 :PDLALSINSALKDVNLPQASENLVMTWIGN 1rdfA 23 :FAPLEVFMEIFHKRGVAITAEEARKPMPLL T0303 52 :DVLSQR 1rdfA 68 :SEWNRV T0303 66 :AEKELTEDEFKYFKRQFGFYYGENLCNISRLYPNVKETLEALKAQGYILAVVTNKPTKHVQPILTAF 1rdfA 74 :FRQLPTEADIQEMYEEFEEILFAILPRYASPINAVKEVIASLRERGIKIGSTTGYTREMMDIVAKEA T0303 133 :GID 1rdfA 144 :GYK T0303 138 :FSEMLGGQSLPEIKPHPAPFYYLCGKFGL 1rdfA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMELGV T0303 168 :PKQILFVGDSQNDIFAAHSAGCAVVGLTYGYN 1rdfA 178 :MNHMIKVGDTVSDMKEGRNAGMWTVGVILGSS T0303 200 :YNIPIAQSK 1rdfA 214 :TEEEVENMD T0303 209 :PDWIFDDFADILKITQ 1rdfA 242 :AHFTIETMQELESVME Number of specific fragments extracted= 9 number of extra gaps= 1 total=503 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 # T0303 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 (T0303)Q3 because first residue in template chain is (2fdrA)G3 Warning: unaligning (T0303)F9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fdrA)D10 Warning: unaligning (T0303)D10 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fdrA)D10 T0303 4 :FKLIG 2fdrA 4 :FDLII T0303 11 :LDGTLVNSLPDLALSINSALKDVNLPQASENLVMTWIGNGADVLSQRAVD 2fdrA 11 :CDGVLVDSEIIAAQVESRLLTEAGYPISVEEMGERFAGMTWKNILLQVES T0303 65 :QAEKELTEDEFKYFKRQFGFYYGEN 2fdrA 61 :EASIPLSASLLDKSEKLLDMRLERD T0303 94 :SRLYPNVKETLEAL 2fdrA 86 :VKIIDGVKFALSRL T0303 112 :YILAVVTNKPTKHVQPILTAFGIDHLF 2fdrA 101 :TPRCICSNSSSHRLDMMLTKVGLKPYF T0303 139 :SEMLGGQSLP 2fdrA 129 :PHIYSAKDLG T0303 149 :EIKPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVVGLTY 2fdrA 141 :RVKPKPDIFLHGAAQFGVSPDRVVVVEDSVHGIHGARAAGMRVIGFTG T0303 198 :YNYNIP 2fdrA 189 :ASHTYP T0303 204 :IAQSKPDWIFDDFADILKI 2fdrA 200 :LTDAGAETVISRMQDLPAV Number of specific fragments extracted= 9 number of extra gaps= 1 total=512 Number of alignments=52 # 2fdrA read from 2fdrA/merged-good-all-a2m # found chain 2fdrA in template set Warning: unaligning (T0303)Q3 because first residue in template chain is (2fdrA)G3 Warning: unaligning (T0303)F9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fdrA)D10 Warning: unaligning (T0303)D10 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fdrA)D10 T0303 4 :FKLIG 2fdrA 4 :FDLII T0303 11 :LDGTLVNSLPDLALSINSALKDVNLPQASENLVMTWIGNGADVLSQRAVDWA 2fdrA 11 :CDGVLVDSEIIAAQVESRLLTEAGYPISVEEMGERFAGMTWKNILLQVESEA T0303 67 :EKELTEDEFKYFKRQFGFYYG 2fdrA 63 :SIPLSASLLDKSEKLLDMRLE T0303 92 :NISRLYPNVKETLEAL 2fdrA 84 :RDVKIIDGVKFALSRL T0303 112 :YILAVVTNKPTKHVQPILTAFGIDHLF 2fdrA 101 :TPRCICSNSSSHRLDMMLTKVGLKPYF T0303 139 :SEMLGGQSLPE 2fdrA 129 :PHIYSAKDLGA T0303 150 :IKPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVVGLTYGYN 2fdrA 142 :VKPKPDIFLHGAAQFGVSPDRVVVVEDSVHGIHGARAAGMRVIGFTGASH T0303 200 :YNIPIAQSKPDWIFDDFADILKI 2fdrA 196 :HADRLTDAGAETVISRMQDLPAV Number of specific fragments extracted= 8 number of extra gaps= 1 total=520 Number of alignments=53 # 2fdrA read from 2fdrA/merged-good-all-a2m # found chain 2fdrA in template set Warning: unaligning (T0303)Q3 because first residue in template chain is (2fdrA)G3 Warning: unaligning (T0303)F9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fdrA)D10 Warning: unaligning (T0303)D10 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fdrA)D10 T0303 4 :FKLIG 2fdrA 4 :FDLII T0303 11 :LDGTLVNSLPDLALSINSALKDVNLPQASENLVMTWIGNGADVLSQRAVD 2fdrA 11 :CDGVLVDSEIIAAQVESRLLTEAGYPISVEEMGERFAGMTWKNILLQVES T0303 65 :QAEKELTEDEFKYFKRQFGFYYGE 2fdrA 61 :EASIPLSASLLDKSEKLLDMRLER T0303 93 :ISRLYPNVKETLEAL 2fdrA 85 :DVKIIDGVKFALSRL T0303 112 :YILAVVTNKPTKHVQPILTAFGIDHLF 2fdrA 101 :TPRCICSNSSSHRLDMMLTKVGLKPYF T0303 139 :SEMLGG 2fdrA 129 :PHIYSA T0303 147 :LPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVVGLTYGYNYNIP 2fdrA 139 :ADRVKPKPDIFLHGAAQFGVSPDRVVVVEDSVHGIHGARAAGMRVIGFTGASHTYPS T0303 204 :IAQSKPDWIFDDFADILKIT 2fdrA 200 :LTDAGAETVISRMQDLPAVI Number of specific fragments extracted= 8 number of extra gaps= 1 total=528 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 # T0303 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 (T0303)F9 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1lvhA)L9 Warning: unaligning (T0303)L11 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1lvhA)L9 T0303 1 :M 1lvhA 1 :M T0303 4 :FKLIG 1lvhA 2 :FKAVL T0303 12 :DGTLVNSLPDLALSINSALKDVNLPQASENLVMTWIGNGADVLSQRAVD 1lvhA 10 :DGVITDTAEYHFRAWKALAEEIGINGVDRQFNEQLKGVSREDSLQKILD T0303 65 :QAEKELTEDEFKYFKRQFGFYYGENL 1lvhA 59 :LADKKVSAEEFKELAKRKNDNYVKMI T0303 92 :NISR 1lvhA 85 :QDVS T0303 96 :LYPNVKETLEALKAQGYILAVVTNK 1lvhA 92 :VYPGILQLLKDLRSNKIKIALASAS T0303 123 :KHVQPILTAFGIDHLFSEMLGGQSLPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVVGLTY 1lvhA 117 :KNGPFLLERMNLTGYFDAIADPAEVAASKPAPDIFIAAAHAVGVAPSESIGLEDSQAGIQAIKDSGALPIGVGR T0303 206 :Q 1lvhA 196 :D T0303 209 :PDWIFDDFAD 1lvhA 197 :DIVIVPDTSH T0303 219 :ILKI 1lvhA 212 :LKEV Number of specific fragments extracted= 10 number of extra gaps= 0 total=538 Number of alignments=55 # 1lvhA read from 1lvhA/merged-good-all-a2m # found chain 1lvhA in template set Warning: unaligning (T0303)F9 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1lvhA)L9 Warning: unaligning (T0303)L11 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1lvhA)L9 T0303 1 :M 1lvhA 1 :M T0303 4 :FKLIG 1lvhA 2 :FKAVL T0303 12 :DGTLVNSLPDLALSINSALKDVNLPQASENLVMTWIGNGADVLSQRAVDWA 1lvhA 10 :DGVITDTAEYHFRAWKALAEEIGINGVDRQFNEQLKGVSREDSLQKILDLA T0303 67 :EKELTEDEFKYFKRQFGFYYGENL 1lvhA 61 :DKKVSAEEFKELAKRKNDNYVKMI T0303 91 :CNISRLYPNVKETLEALKAQGYILAVVTNK 1lvhA 87 :VSPADVYPGILQLLKDLRSNKIKIALASAS T0303 123 :KHVQPILTAFGIDHLFSEMLGGQSLPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVVGLTY 1lvhA 117 :KNGPFLLERMNLTGYFDAIADPAEVAASKPAPDIFIAAAHAVGVAPSESIGLEDSQAGIQAIKDSGALPIGVGR T0303 201 :NIPIAQ 1lvhA 191 :PEDLGD T0303 209 :PDWIFDDFAD 1lvhA 197 :DIVIVPDTSH T0303 219 :ILKI 1lvhA 212 :LKEV Number of specific fragments extracted= 9 number of extra gaps= 0 total=547 Number of alignments=56 # 1lvhA read from 1lvhA/merged-good-all-a2m # found chain 1lvhA in template set Warning: unaligning (T0303)Q3 because first residue in template chain is (1lvhA)M1 Warning: unaligning (T0303)F9 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1lvhA)L9 Warning: unaligning (T0303)L11 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1lvhA)L9 T0303 4 :FKLIG 1lvhA 2 :FKAVL T0303 12 :DGTLVNSLPDLALSINSALKDVNLPQASENLVMTWIGNGADVLSQRAVDW 1lvhA 10 :DGVITDTAEYHFRAWKALAEEIGINGVDRQFNEQLKGVSREDSLQKILDL T0303 66 :AEKELTEDEFKYFKRQFGFYYGENLCNISR 1lvhA 60 :ADKKVSAEEFKELAKRKNDNYVKMIQDVSP T0303 96 :LYPNVKETLEALKAQGYILAVVTNK 1lvhA 92 :VYPGILQLLKDLRSNKIKIALASAS T0303 123 :KHVQPILTAFGIDHLFSEMLGGQSLPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVVGLT 1lvhA 117 :KNGPFLLERMNLTGYFDAIADPAEVAASKPAPDIFIAAAHAVGVAPSESIGLEDSQAGIQAIKDSGALPIGVG T0303 200 :YNIPI 1lvhA 190 :RPEDL T0303 207 :SKPDWIFDDFA 1lvhA 195 :GDDIVIVPDTS Number of specific fragments extracted= 7 number of extra gaps= 0 total=554 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 # T0303 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 T0303 2 :TQFKLIGFDLDGTLVNSL 1f5sA 3 :KKKKLILFDFDSTLVNNE T0303 25 :SINSALKDVNL 1f5sA 21 :TIDEIAREAGV T0303 40 :ENLVMTWI 1f5sA 32 :EEEVKKIT T0303 48 :GNGADVLSQRAVDWA 1f5sA 46 :KLNFEQSLRKRVSLL T0303 68 :KELTEDEFKYFK 1f5sA 61 :KDLPIEKVEKAI T0303 92 :NISRLYPNVKETLEALKAQGYILAVVTNKPTKHVQPILTAFGIDHLFSEMLGGQSL 1f5sA 73 :KRITPTEGAEETIKELKNRGYVVAVVSGGFDIAVNKIKEKLGLDYAFANRLIVKDG T0303 148 :PEIK 1f5sA 141 :ENAK T0303 154 :PAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCA 1f5sA 145 :GEILEKIAKIEGINLEDTVAVGDGANDISMFKKAGLK T0303 192 :VGLTYG 1f5sA 182 :IAFCAK T0303 202 :IPIAQS 1f5sA 188 :PILKEK T0303 209 :PDWIFD 1f5sA 194 :ADICIE T0303 215 :DFADILKITQ 1f5sA 202 :DLREILKYIK Number of specific fragments extracted= 12 number of extra gaps= 0 total=566 Number of alignments=58 # 1f5sA read from 1f5sA/merged-good-all-a2m # found chain 1f5sA in template set T0303 2 :TQFKLIGFDLDGTLVNSLP 1f5sA 3 :KKKKLILFDFDSTLVNNET T0303 26 :INSALKDVNLPQASENLVMTW 1f5sA 22 :IDEIAREAGVEEEVKKITKEA T0303 49 :NGADVLSQRAVDWACTQAE 1f5sA 43 :MEGKLNFEQSLRKRVSLLK T0303 69 :ELTEDEFKYFK 1f5sA 62 :DLPIEKVEKAI T0303 92 :NISRLYPNVKETLEALKAQGYILAVVTNKPTKHVQPILTAFGIDHLF 1f5sA 73 :KRITPTEGAEETIKELKNRGYVVAVVSGGFDIAVNKIKEKLGLDYAF T0303 139 :SEMLGGQSLPEI 1f5sA 131 :TGDVEGEVLKEN T0303 151 :K 1f5sA 144 :K T0303 154 :PAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCA 1f5sA 145 :GEILEKIAKIEGINLEDTVAVGDGANDISMFKKAGLK T0303 192 :VGLTY 1f5sA 182 :IAFCA T0303 201 :NIPIAQS 1f5sA 187 :KPILKEK T0303 209 :PDWIFD 1f5sA 194 :ADICIE T0303 215 :DFADILKI 1f5sA 202 :DLREILKY Number of specific fragments extracted= 12 number of extra gaps= 0 total=578 Number of alignments=59 # 1f5sA read from 1f5sA/merged-good-all-a2m # found chain 1f5sA in template set T0303 2 :TQFKLIGFDLDGTLVNSLP 1f5sA 3 :KKKKLILFDFDSTLVNNET T0303 26 :INSALKDVNLPQASENLVMTWIGNGA 1f5sA 22 :IDEIAREAGVEEEVKKITKEAMEGKL T0303 52 :DVLSQRAVD 1f5sA 51 :QSLRKRVSL T0303 67 :EKELTEDEFKYFKR 1f5sA 60 :LKDLPIEKVEKAIK T0303 93 :ISRLYPNVKETLEALKAQGYILAVVTNKPTKHVQPILTAFGIDHLFSEMLGGQS 1f5sA 74 :RITPTEGAEETIKELKNRGYVVAVVSGGFDIAVNKIKEKLGLDYAFANRLIVKD T0303 148 :P 1f5sA 140 :K T0303 150 :IKPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVVG 1f5sA 141 :ENAKGEILEKIAKIEGINLEDTVAVGDGANDISMFKKAGLKIAF T0303 195 :T 1f5sA 185 :C T0303 201 :NIPIAQSKPDWIFD 1f5sA 186 :AKPILKEKADICIE T0303 215 :DFADILKIT 1f5sA 202 :DLREILKYI Number of specific fragments extracted= 10 number of extra gaps= 0 total=588 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 # T0303 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 (T0303)Q178 because of BadResidue code BAD_PEPTIDE in next template residue (2b8eA)N621 Warning: unaligning (T0303)N179 because of BadResidue code BAD_PEPTIDE at template residue (2b8eA)N621 Warning: unaligning (T0303)D180 because of BadResidue code BAD_PEPTIDE at template residue (2b8eA)D622 Warning: unaligning (T0303)T195 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b8eA)S645 Warning: unaligning (T0303)Y196 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b8eA)S645 T0303 4 :FKLIGFD 2b8eA 418 :VTAVIFD T0303 15 :LVNSLPDLALSINSALKDV 2b8eA 439 :LVPLNGDERELLRLAAIAE T0303 34 :NLP 2b8eA 459 :RSE T0303 52 :DVLSQRAV 2b8eA 462 :HPIAEAIV T0303 60 :DWACTQAEKELTED 2b8eA 503 :KRLMEDFGVAVSNE T0303 75 :FKYFKRQFGF 2b8eA 517 :VELALEKLER T0303 92 :NI 2b8eA 527 :EA T0303 94 :SRLYPNVKETLEALKAQGYILAVVTNKPTKHVQPILTAFGID 2b8eA 548 :DTLKESAKPAVQELKRMGIKVGMITGDNWRSAEAISRELNLD T0303 141 :MLGGQSL 2b8eA 590 :LVIAEVL T0303 154 :PAPFYYLCGKFG 2b8eA 597 :PHQKSEEVKKLQ T0303 168 :PKQILFVGDS 2b8eA 610 :KEVVAFVGDG T0303 181 :IFAAHSAG 2b8eA 623 :APALAQAD T0303 190 :AVVGL 2b8eA 631 :LGIAV T0303 197 :G 2b8eA 646 :G T0303 210 :DWIF 2b8eA 647 :DIVL T0303 214 :DDFADILKITQ 2b8eA 653 :DDLRDVVAAIQ Number of specific fragments extracted= 16 number of extra gaps= 2 total=604 Number of alignments=61 # 2b8eA read from 2b8eA/merged-good-all-a2m # found chain 2b8eA in template set Warning: unaligning (T0303)Q178 because of BadResidue code BAD_PEPTIDE in next template residue (2b8eA)N621 Warning: unaligning (T0303)N179 because of BadResidue code BAD_PEPTIDE at template residue (2b8eA)N621 Warning: unaligning (T0303)D180 because of BadResidue code BAD_PEPTIDE at template residue (2b8eA)D622 Warning: unaligning (T0303)T195 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b8eA)S645 Warning: unaligning (T0303)Y196 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b8eA)S645 T0303 4 :FKLIGFDLDGTLVN 2b8eA 418 :VTAVIFDKTGTLTK T0303 18 :SLPDLALSINSALKDVNLPQA 2b8eA 460 :SEHPIAEAIVKKALEHGIELG T0303 39 :SE 2b8eA 502 :NK T0303 61 :WACTQAEKELTEDEFKYFKRQFG 2b8eA 504 :RLMEDFGVAVSNEVELALEKLER T0303 92 :NIS 2b8eA 527 :EAK T0303 95 :RLYPNVKETLEALKAQGYILAVVTNKPTKHVQPILTAFGID 2b8eA 549 :TLKESAKPAVQELKRMGIKVGMITGDNWRSAEAISRELNLD T0303 141 :MLGGQSL 2b8eA 590 :LVIAEVL T0303 154 :PAPFYYLCGKFGL 2b8eA 597 :PHQKSEEVKKLQA T0303 168 :PKQILFVGDS 2b8eA 610 :KEVVAFVGDG T0303 181 :IFAAHSAG 2b8eA 623 :APALAQAD T0303 190 :AVVGL 2b8eA 631 :LGIAV T0303 197 :G 2b8eA 646 :G T0303 210 :DWIF 2b8eA 647 :DIVL T0303 214 :DDFADILKI 2b8eA 653 :DDLRDVVAA Number of specific fragments extracted= 14 number of extra gaps= 2 total=618 Number of alignments=62 # 2b8eA read from 2b8eA/merged-good-all-a2m # found chain 2b8eA in template set Warning: unaligning (T0303)Q178 because of BadResidue code BAD_PEPTIDE in next template residue (2b8eA)N621 Warning: unaligning (T0303)N179 because of BadResidue code BAD_PEPTIDE at template residue (2b8eA)N621 Warning: unaligning (T0303)D180 because of BadResidue code BAD_PEPTIDE at template residue (2b8eA)D622 Warning: unaligning (T0303)T195 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b8eA)S645 Warning: unaligning (T0303)Y196 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b8eA)S645 T0303 4 :FKLIGFDLDGTLV 2b8eA 418 :VTAVIFDKTGTLT T0303 17 :NSLPDLALSINSALKDVNLPQAS 2b8eA 459 :RSEHPIAEAIVKKALEHGIELGE T0303 52 :DVLSQRAVD 2b8eA 504 :RLMEDFGVA T0303 70 :LTEDEFKYFKRQFG 2b8eA 513 :VSNEVELALEKLER T0303 94 :SRLYPNVKETLEALKAQGYILAVVTNKPTKHVQPILTAFGIDHLFSEM 2b8eA 548 :DTLKESAKPAVQELKRMGIKVGMITGDNWRSAEAISRELNLDLVIAEV T0303 153 :HPAPFYYLCGKFG 2b8eA 596 :LPHQKSEEVKKLQ T0303 168 :PKQILFVGDS 2b8eA 610 :KEVVAFVGDG T0303 181 :IFAAHSAG 2b8eA 623 :APALAQAD T0303 190 :AVVGL 2b8eA 631 :LGIAV T0303 197 :G 2b8eA 646 :G T0303 210 :DWIF 2b8eA 647 :DIVL T0303 214 :DDFADILKITQ 2b8eA 653 :DDLRDVVAAIQ Number of specific fragments extracted= 12 number of extra gaps= 2 total=630 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:# T0303 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 (T0303)Q3 because first residue in template chain is (1vj5A)T2 T0303 4 :FKLIGFDLDGTLVNSL 1vj5A 3 :LRAAVFDLDGVLALPA T0303 25 :SINSALKDVNLPQ 1vj5A 22 :VLGRTEEALALPR T0303 39 :SENLV 1vj5A 36 :LLNDA T0303 44 :MTWI 1vj5A 51 :TRLM T0303 48 :GNGADVLSQRAVDWACTQAE 1vj5A 57 :EITLSQWIPLMEENCRKCSE T0303 68 :KELTED 1vj5A 80 :VCLPKN T0303 82 :FGFYYGENL 1vj5A 88 :IKEIFDKAI T0303 92 :NISRLYPNVKETLEALKAQGYILAVVTN 1vj5A 97 :SARKINRPMLQAALMLRKKGFTTAILTN T0303 120 :KPTKHVQPILTAFGI 1vj5A 131 :AERDGLAQLMCELKM T0303 137 :LFSEMLGGQSLPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVVGLT 1vj5A 146 :HFDFLIESCQVGMVKPEPQIYKFLLDTLKASPSEVVFLDDIGANLKPARDLGMVTILVQ T0303 215 :D 1vj5A 205 :D T0303 216 :FADILKITQ 1vj5A 210 :LKELEKVTG Number of specific fragments extracted= 12 number of extra gaps= 0 total=642 Number of alignments=64 # 1vj5A read from 1vj5A/merged-good-all-a2m # found chain 1vj5A in template set Warning: unaligning (T0303)Q3 because first residue in template chain is (1vj5A)T2 T0303 4 :FKLIGFDLDGTLVNSLP 1vj5A 3 :LRAAVFDLDGVLALPAV T0303 23 :ALSINSALKDVNLPQA 1vj5A 20 :FGVLGRTEEALALPRG T0303 39 :SENLVMTWI 1vj5A 46 :PEGATTRLM T0303 49 :NGADVLSQRAVDWACTQ 1vj5A 58 :ITLSQWIPLMEENCRKC T0303 66 :AEKELT 1vj5A 82 :LPKNFS T0303 78 :FKRQFGFYY 1vj5A 88 :IKEIFDKAI T0303 92 :NISRLYPNVKETLEALKAQGYILAVVTNKP 1vj5A 97 :SARKINRPMLQAALMLRKKGFTTAILTNTW T0303 122 :TKHVQPILTAFG 1vj5A 133 :RDGLAQLMCELK T0303 136 :HLFSEMLGGQSLPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVVGLT 1vj5A 145 :MHFDFLIESCQVGMVKPEPQIYKFLLDTLKASPSEVVFLDDIGANLKPARDLGMVTILVQ T0303 215 :DFADILK 1vj5A 205 :DTDTALK Number of specific fragments extracted= 10 number of extra gaps= 0 total=652 Number of alignments=65 # 1vj5A read from 1vj5A/merged-good-all-a2m # found chain 1vj5A in template set Warning: unaligning (T0303)Q3 because first residue in template chain is (1vj5A)T2 T0303 4 :FKLIGFDLDGTLV 1vj5A 3 :LRAAVFDLDGVLA T0303 25 :SINSALKDVNLPQASENLVMTWIGNGADVLSQRAVDWACTQAEKELTEDEFKYFKRQFG 1vj5A 22 :VLGRTEEALALPRGLLNDAFQKGGPEGATTRLMKGEITLSQWIPLMEENCRKCSETAKV T0303 84 :FYYGENLCNISRLYPNVKETLEALKAQGYILAVVTNKP 1vj5A 89 :KEIFDKAISARKINRPMLQAALMLRKKGFTTAILTNTW T0303 122 :TKHVQPILTAFG 1vj5A 133 :RDGLAQLMCELK T0303 136 :HLFSEMLGGQSLPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVVG 1vj5A 145 :MHFDFLIESCQVGMVKPEPQIYKFLLDTLKASPSEVVFLDDIGANLKPARDLGMVTIL T0303 213 :FDDFADILKIT 1vj5A 203 :VQDTDTALKEL Number of specific fragments extracted= 6 number of extra gaps= 0 total=658 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 # T0303 read from 1o08A/merged-good-all-a2m # 1o08A read from 1o08A/merged-good-all-a2m # found chain 1o08A in training set Warning: unaligning (T0303)F9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o08A)D1008 Warning: unaligning (T0303)D10 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o08A)D1008 T0303 1 :M 1o08A 1001 :M T0303 4 :FKLIG 1o08A 1002 :FKAVL T0303 11 :LDGTLVNSLPDLALSINSALKDVNLPQASENLVMTWIGNGADVLSQRAVD 1o08A 1009 :LDGVITDTAEYHFRAWKALAEEIGINGVDRQFNEQLKGVSREDSLQKILD T0303 65 :QAEKELTEDEFKYFKRQFGFYYGENLCNISR 1o08A 1059 :LADKKVSAEEFKELAKRKNDNYVKMIQDVSP T0303 96 :LYPNVKETLEALKAQGYILAVVTNK 1o08A 1092 :VYPGILQLLKDLRSNKIKIALASAS T0303 123 :KHVQPILTAFGIDHLFSEMLGGQSLPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVVGLTY 1o08A 1117 :KNGPFLLERMNLTGYFDAIADPAEVAASKPAPDIFIAAAHAVGVAPSESIGLEDSQAGIQAIKDSGALPIGVGR T0303 204 :IAQ 1o08A 1194 :LGD T0303 209 :PDWIFDDFAD 1o08A 1197 :DIVIVPDTSH T0303 219 :ILKI 1o08A 1212 :LKEV Number of specific fragments extracted= 9 number of extra gaps= 1 total=667 Number of alignments=67 # 1o08A read from 1o08A/merged-good-all-a2m # found chain 1o08A in training set Warning: unaligning (T0303)F9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o08A)D1008 Warning: unaligning (T0303)D10 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o08A)D1008 T0303 1 :M 1o08A 1001 :M T0303 4 :FKLIG 1o08A 1002 :FKAVL T0303 11 :LDGTLVNSLPDLALSINSALKDVNLPQASENLVMTWIGNGADVLSQRAVDWA 1o08A 1009 :LDGVITDTAEYHFRAWKALAEEIGINGVDRQFNEQLKGVSREDSLQKILDLA T0303 67 :EKELTEDEFKYFKRQFGFYYGENL 1o08A 1061 :DKKVSAEEFKELAKRKNDNYVKMI T0303 91 :CNISRLYPNVKETLEALKAQGYILAVVTNK 1o08A 1087 :VSPADVYPGILQLLKDLRSNKIKIALASAS T0303 123 :KHVQPILTAFGIDHLFSEMLGGQSLPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVVGLTY 1o08A 1117 :KNGPFLLERMNLTGYFDAIADPAEVAASKPAPDIFIAAAHAVGVAPSESIGLEDSQAGIQAIKDSGALPIGVGR T0303 201 :NIPIAQ 1o08A 1191 :PEDLGD T0303 209 :PDWIFDDFAD 1o08A 1197 :DIVIVPDTSH T0303 219 :ILKI 1o08A 1212 :LKEV Number of specific fragments extracted= 9 number of extra gaps= 1 total=676 Number of alignments=68 # 1o08A read from 1o08A/merged-good-all-a2m # found chain 1o08A in training set Warning: unaligning (T0303)Q3 because first residue in template chain is (1o08A)M1001 Warning: unaligning (T0303)F9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o08A)D1008 Warning: unaligning (T0303)D10 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o08A)D1008 T0303 4 :FKLIG 1o08A 1002 :FKAVL T0303 11 :LDGTLVNSLPDLALSINSALKDVNLPQASENLVMTWIGNGADVLSQRAVDW 1o08A 1009 :LDGVITDTAEYHFRAWKALAEEIGINGVDRQFNEQLKGVSREDSLQKILDL T0303 66 :AEKELTEDEFKYFKRQFGFYYGENLCN 1o08A 1060 :ADKKVSAEEFKELAKRKNDNYVKMIQD T0303 93 :ISRLYPNVKETLEALKAQGYILAVVTNK 1o08A 1089 :PADVYPGILQLLKDLRSNKIKIALASAS T0303 123 :KHVQPILTAFGIDHLFSEMLGGQSLPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVVGLTY 1o08A 1117 :KNGPFLLERMNLTGYFDAIADPAEVAASKPAPDIFIAAAHAVGVAPSESIGLEDSQAGIQAIKDSGALPIGVGR T0303 202 :IPI 1o08A 1191 :PED T0303 206 :QSKPDWIFDDFAD 1o08A 1194 :LGDDIVIVPDTSH Number of specific fragments extracted= 7 number of extra gaps= 1 total=683 Number of alignments=69 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2g09A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2g09A expands to /projects/compbio/data/pdb/2g09.pdb.gz 2g09A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1940, because occupancy 0.500 <= existing 0.500 in 2g09A Skipped atom 1942, because occupancy 0.500 <= existing 0.500 in 2g09A Skipped atom 1944, because occupancy 0.500 <= existing 0.500 in 2g09A Skipped atom 1946, because occupancy 0.500 <= existing 0.500 in 2g09A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0303 read from 2g09A/merged-good-all-a2m # 2g09A read from 2g09A/merged-good-all-a2m # adding 2g09A to template set # found chain 2g09A in template set Warning: unaligning (T0303)L6 because of BadResidue code BAD_PEPTIDE at template residue (2g09A)Q45 T0303 7 :IGFDLDGTLVN 2g09A 46 :IITDFDMTLSR T0303 18 :SLPDLALSINSALKDV 2g09A 77 :VTDECRRKLLQLKEQY T0303 34 :NLPQASENLVMTWIGNGADVLSQRAVD 2g09A 97 :VDPVLTVEEKFPYMVEWYTKSHGLLIE T0303 68 :KELTEDEFKYFKRQ 2g09A 124 :QGIPKAKLKEIVAD T0303 92 :NISRLYPNVKETLEALKAQGYILAVVTNKPTKHVQPILTAFGID 2g09A 138 :SDVMLKEGYENFFGKLQQHGIPVFIFSAGIGDVLEEVIRQAGVY T0303 136 :HLFSEMLGG 2g09A 183 :SNVKVVSNF T0303 145 :QSLPEIK 2g09A 195 :DENGVLK T0303 153 :HPAPFYYLC 2g09A 209 :HVFNKHDGA T0303 162 :GKFG 2g09A 225 :SQLK T0303 168 :PKQILFVGDSQNDIFA 2g09A 230 :NSNIILLGDSQGDLRM T0303 186 :SAGC 2g09A 246 :ADGV T0303 190 :AVVGLTYG 2g09A 256 :LKIGYLND T0303 215 :DFADIL 2g09A 264 :RVDELL Number of specific fragments extracted= 13 number of extra gaps= 1 total=696 Number of alignments=70 # 2g09A read from 2g09A/merged-good-all-a2m # found chain 2g09A in template set Warning: unaligning (T0303)L6 because of BadResidue code BAD_PEPTIDE at template residue (2g09A)Q45 T0303 7 :IGFDLDGTLVN 2g09A 46 :IITDFDMTLSR T0303 18 :SLPDLALSINSALKDV 2g09A 77 :VTDECRRKLLQLKEQY T0303 34 :NLPQASENLVMTWIGNGADVLSQRAVDW 2g09A 97 :VDPVLTVEEKFPYMVEWYTKSHGLLIEQ T0303 69 :ELTEDEFKYFKRQ 2g09A 125 :GIPKAKLKEIVAD T0303 92 :NISRLYPNVKETLEALKAQGYILAVVTNKPTKHVQPILTAFGIDHLFSEMLGGQ 2g09A 138 :SDVMLKEGYENFFGKLQQHGIPVFIFSAGIGDVLEEVIRQAGVYHSNVKVVSNF T0303 154 :PAPF 2g09A 221 :TDYF T0303 162 :GKFG 2g09A 225 :SQLK T0303 167 :YPKQILFVGDSQNDIFA 2g09A 229 :DNSNIILLGDSQGDLRM T0303 187 :AG 2g09A 246 :AD T0303 189 :CAVVG 2g09A 255 :ILKIG T0303 211 :WIFDDFADILK 2g09A 260 :YLNDRVDELLE Number of specific fragments extracted= 11 number of extra gaps= 1 total=707 Number of alignments=71 # 2g09A read from 2g09A/merged-good-all-a2m # found chain 2g09A in template set Warning: unaligning (T0303)L6 because of BadResidue code BAD_PEPTIDE at template residue (2g09A)Q45 T0303 7 :IGFDLDGTLV 2g09A 46 :IITDFDMTLS T0303 18 :SLPDLALSINSALKDVNLPQASENLVMTWIGNGADVLSQRAVDW 2g09A 81 :CRRKLLQLKEQYYAIEVDPVLTVEEKFPYMVEWYTKSHGLLIEQ T0303 69 :ELTEDEFKYFKRQFG 2g09A 125 :GIPKAKLKEIVADSD T0303 94 :SRLYPNVKETLEALKAQGYILAVVTNKPTKHVQPILTAFGIDH 2g09A 140 :VMLKEGYENFFGKLQQHGIPVFIFSAGIGDVLEEVIRQAGVYH T0303 137 :LFSEML 2g09A 184 :NVKVVS T0303 143 :GGQSLPEIK 2g09A 204 :KGELIHVFN T0303 157 :FYYLC 2g09A 213 :KHDGA T0303 162 :GKFG 2g09A 225 :SQLK T0303 168 :PKQILFVGDSQND 2g09A 230 :NSNIILLGDSQGD T0303 187 :AGCA 2g09A 247 :DGVA T0303 191 :VVGLTYG 2g09A 257 :KIGYLND T0303 215 :DFADI 2g09A 264 :RVDEL Number of specific fragments extracted= 12 number of extra gaps= 1 total=719 Number of alignments=72 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b82A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2b82A expands to /projects/compbio/data/pdb/2b82.pdb.gz 2b82A:# T0303 read from 2b82A/merged-good-all-a2m # 2b82A read from 2b82A/merged-good-all-a2m # adding 2b82A to template set # found chain 2b82A in template set Warning: unaligning (T0303)F9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b82A)D44 Warning: unaligning (T0303)D10 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b82A)D44 T0303 2 :TQFKLIG 2b82A 36 :RPPMAVG T0303 11 :LDGTLVNSLPDLALSIN 2b82A 45 :IDDTVLFSSPGFWRGKK T0303 32 :DV 2b82A 62 :TF T0303 59 :VD 2b82A 64 :SP T0303 64 :TQAEKELTEDEFKYFK 2b82A 66 :ESEDYLKNPVFWEKMN T0303 88 :ENLCNISRLYPNVKETLEALKAQGYILAVVTNKPT 2b82A 82 :NGWDEFSIPKEVARQLIDMHVRRGDAIFFVTGRSP T0303 124 :HVQPIL 2b82A 121 :TVSKTL T0303 130 :TAFGIDH 2b82A 128 :DNFHIPA T0303 137 :LFSEMLGGQSLPEIKPHPA 2b82A 136 :NMNPVIFAGDKPGQNTKSQ T0303 160 :LCGKFGLY 2b82A 155 :WLQDKNIR T0303 172 :LFVGDSQNDIFAAHSAGCAVVGLTY 2b82A 163 :IFYGDSDNDITAARDVGARGIRILR T0303 197 :GYNYNIPIAQSKPDWI 2b82A 192 :TYKPLPQAGAFGEEVI Number of specific fragments extracted= 12 number of extra gaps= 1 total=731 Number of alignments=73 # 2b82A read from 2b82A/merged-good-all-a2m # found chain 2b82A in template set Warning: unaligning (T0303)F9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b82A)D44 Warning: unaligning (T0303)D10 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b82A)D44 T0303 2 :TQFKLIG 2b82A 36 :RPPMAVG T0303 11 :LDGTLVNS 2b82A 45 :IDDTVLFS T0303 23 :ALSINSALKDV 2b82A 53 :SPGFWRGKKTF T0303 34 :NLP 2b82A 66 :ESE T0303 67 :EKELTEDEFKYFK 2b82A 69 :DYLKNPVFWEKMN T0303 88 :ENLCNISRLYPNVKETLEALKAQGYILAVVTNKP 2b82A 82 :NGWDEFSIPKEVARQLIDMHVRRGDAIFFVTGRS T0303 123 :KHVQPILTAF 2b82A 120 :ETVSKTLADN T0303 133 :GID 2b82A 131 :HIP T0303 136 :HLFSEMLGGQSLPE 2b82A 136 :NMNPVIFAGDKPGQ T0303 150 :IK 2b82A 151 :TK T0303 158 :YYLCGKFGLY 2b82A 153 :SQWLQDKNIR T0303 172 :LFVGDSQNDIFAAHSAGCAVVGLTY 2b82A 163 :IFYGDSDNDITAARDVGARGIRILR T0303 197 :GYNYNIPIAQSKPDWI 2b82A 192 :TYKPLPQAGAFGEEVI Number of specific fragments extracted= 13 number of extra gaps= 1 total=744 Number of alignments=74 # 2b82A read from 2b82A/merged-good-all-a2m # found chain 2b82A in template set Warning: unaligning (T0303)F9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b82A)D44 Warning: unaligning (T0303)D10 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b82A)D44 T0303 2 :TQFKLIG 2b82A 36 :RPPMAVG T0303 11 :LDGTLVNSLPDLALSINSA 2b82A 45 :IDDTVLFSSPGFWRGKKTF T0303 47 :I 2b82A 64 :S T0303 49 :NGADVL 2b82A 65 :PESEDY T0303 69 :ELTED 2b82A 71 :LKNPV T0303 82 :FGFYYGENLCNISRLYPNVKETLEALKAQGYILAVVTNKP 2b82A 76 :FWEKMNNGWDEFSIPKEVARQLIDMHVRRGDAIFFVTGRS T0303 123 :KHVQPILTAFGIDH 2b82A 121 :TVSKTLADNFHIPA T0303 137 :LFSEMLGGQSLPEIKPHP 2b82A 136 :NMNPVIFAGDKPGQNTKS T0303 159 :YLCGKFGLY 2b82A 154 :QWLQDKNIR T0303 172 :LFVGDSQNDIFAAHSAGCAVVGLTY 2b82A 163 :IFYGDSDNDITAARDVGARGIRILR T0303 197 :GYNYNIPIAQSKPDWI 2b82A 192 :TYKPLPQAGAFGEEVI Number of specific fragments extracted= 11 number of extra gaps= 1 total=755 Number of alignments=75 # 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 # T0303 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 (T0303)N119 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ah5A)K108 Warning: unaligning (T0303)K120 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ah5A)K108 T0303 1 :MTQFKLIGFDLDGTLVNSLPDLALSINSALKDVNLPQASENLVMTWIGNGADVLSQR 2ah5A 1 :MTSITAIFFDLDGTLVDSSIGIHNAFTYTFKELGVPSPDAKTIRGFMGPPLESSFAT T0303 69 :ELTEDEFKYFKRQFGFYYGENLCNISRLYPNVKETLEALKAQ 2ah5A 58 :CLSKDQISEAVQIYRSYYKAKGIYEAQLFPQIIDLLEELSSS T0303 112 :YILAVVT 2ah5A 100 :YPLYITT T0303 121 :PTKHVQPILTAFGIDHLFSEMLGGQSLPEIK 2ah5A 109 :DTSTAQDMAKNLEIHHFFDGIYGSSPEAPHK T0303 154 :PAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVVGLTYGYNYNIPIAQSKPDWIFDDFADILKITQ 2ah5A 140 :ADVIHQALQTHQLAPEQAIIIGDTKFDMLGARETGIQKLAITWGFGEQADLLNYQPDYIAHKPLEVLAYFQ Number of specific fragments extracted= 5 number of extra gaps= 1 total=760 Number of alignments=76 # 2ah5A read from 2ah5A/merged-good-all-a2m # found chain 2ah5A in template set Warning: unaligning (T0303)N119 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ah5A)K108 Warning: unaligning (T0303)K120 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ah5A)K108 T0303 1 :MTQFKLIGFDLDGTLVNSLPDLALSINSALKDVNLPQASENLVMTWIGNGADVLSQ 2ah5A 1 :MTSITAIFFDLDGTLVDSSIGIHNAFTYTFKELGVPSPDAKTIRGFMGPPLESSFA T0303 68 :KELTEDEFKYFKRQFGFYYGENLCNISRLYPNVKETLEALKAQ 2ah5A 57 :TCLSKDQISEAVQIYRSYYKAKGIYEAQLFPQIIDLLEELSSS T0303 112 :YILAVVT 2ah5A 100 :YPLYITT T0303 121 :PTKHVQPILTAFGIDHLFSEMLGGQSLPEIK 2ah5A 109 :DTSTAQDMAKNLEIHHFFDGIYGSSPEAPHK T0303 154 :PAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVVGLTYGYNYNIPIAQSKPDWIFDDFADILKI 2ah5A 140 :ADVIHQALQTHQLAPEQAIIIGDTKFDMLGARETGIQKLAITWGFGEQADLLNYQPDYIAHKPLEVLAY Number of specific fragments extracted= 5 number of extra gaps= 1 total=765 Number of alignments=77 # 2ah5A read from 2ah5A/merged-good-all-a2m # found chain 2ah5A in template set Warning: unaligning (T0303)N119 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ah5A)K108 Warning: unaligning (T0303)K120 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ah5A)K108 T0303 1 :MTQFKLIGFDLDGTLVNSLPDLALSINSALKDVNLPQASENLVMTWIGNGADVLSQRAV 2ah5A 1 :MTSITAIFFDLDGTLVDSSIGIHNAFTYTFKELGVPSPDAKTIRGFMGPPLESSFATCL T0303 71 :TEDEFKYFKRQFGFYYGENLCNISRLYPNVKETLEALKAQ 2ah5A 60 :SKDQISEAVQIYRSYYKAKGIYEAQLFPQIIDLLEELSSS T0303 112 :YILAVVT 2ah5A 100 :YPLYITT T0303 121 :PTKHVQPILTAFGIDHLFSEML 2ah5A 109 :DTSTAQDMAKNLEIHHFFDGIY T0303 143 :GGQSLP 2ah5A 132 :SSPEAP T0303 150 :IK 2ah5A 138 :HK T0303 154 :PAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVVGLTYGYNYNIPIAQSKPDWIFDDFADILKI 2ah5A 140 :ADVIHQALQTHQLAPEQAIIIGDTKFDMLGARETGIQKLAITWGFGEQADLLNYQPDYIAHKPLEVLAY Number of specific fragments extracted= 7 number of extra gaps= 1 total=772 Number of alignments=78 # 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 # T0303 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 (T0303)E69 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1zs9A)K106 Warning: unaligning (T0303)T71 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1zs9A)K106 T0303 3 :QFKLIGFDLDGTLVN 1zs9A 9 :EVTVILLDIEGTTTP T0303 18 :SLPDLALSINSALKDV 1zs9A 31 :LFPYIEENVKEYLQTH T0303 34 :NLPQASENLVMTW 1zs9A 77 :AASGNGVDDLQQM T0303 55 :SQRAVDWACTQAEK 1zs9A 90 :IQAVVDNVCWQMSL T0303 72 :EDEFKYFKRQFGFYYGENLCNISRLYPNVKETLEALKAQGYILAVVTNKPTKHVQPILTAF 1zs9A 107 :TTALKQLQGHMWRAAFTAGRMKAEFFADVVPAVRKWREAGMKVYIYSSGSVEAQKLLFGHS T0303 133 :GIDHLFSEMLGGQSLP 1zs9A 171 :DILELVDGHFDTKIGH T0303 151 :KPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVVGLTYGYNYNIP 1zs9A 187 :KVESESYRKIADSIGCSTNNILFLTDVTREASAAEEADVHVAVVVRPGNAGLT T0303 210 :DWIFDDFADI 1zs9A 246 :YSLITSFSEL Number of specific fragments extracted= 8 number of extra gaps= 0 total=780 Number of alignments=79 # 1zs9A read from 1zs9A/merged-good-all-a2m # found chain 1zs9A in template set Warning: unaligning (T0303)E69 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1zs9A)K106 Warning: unaligning (T0303)T71 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1zs9A)K106 T0303 3 :QFKLIGFDLDGTLVN 1zs9A 9 :EVTVILLDIEGTTTP T0303 18 :SLPDLALSINSALKDVNLPQASENLVMTWI 1zs9A 31 :LFPYIEENVKEYLQTHWEEEECQQDVSLLR T0303 48 :GNGADVLSQRAVDWACTQ 1zs9A 79 :SGNGVDDLQQMIQAVVDN T0303 66 :AEK 1zs9A 101 :MSL T0303 72 :EDEFKYFKRQFGFYYGENLCNISRLYPNVKETLEALKAQGYILAVVTNKPTKHVQPILTAF 1zs9A 107 :TTALKQLQGHMWRAAFTAGRMKAEFFADVVPAVRKWREAGMKVYIYSSGSVEAQKLLFGHS T0303 133 :GIDHLFSEMLGGQSLP 1zs9A 171 :DILELVDGHFDTKIGH T0303 151 :KPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVVGLTYGYNYNIPIAQSKPDWIFDDFADI 1zs9A 187 :KVESESYRKIADSIGCSTNNILFLTDVTREASAAEEADVHVAVVVRPGNAGLTDDEKTYYSLITSFSEL Number of specific fragments extracted= 7 number of extra gaps= 0 total=787 Number of alignments=80 # 1zs9A read from 1zs9A/merged-good-all-a2m # found chain 1zs9A in template set Warning: unaligning (T0303)E69 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1zs9A)K106 Warning: unaligning (T0303)T71 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1zs9A)K106 T0303 3 :QFKLIGFDLDGTLV 1zs9A 9 :EVTVILLDIEGTTT T0303 17 :NSLPDLALSINSALKDVNLPQASENLVMTWIGNGA 1zs9A 30 :ILFPYIEENVKEYLQTHWEEEECQQDVSLLRKQAE T0303 52 :DVLSQRAVDWACTQAEK 1zs9A 87 :QQMIQAVVDNVCWQMSL T0303 72 :EDEFKYFKRQFGFYYGENLCNISRLYPNVKETLEALKAQGYILAVVTNKPTKHVQPILTAF 1zs9A 107 :TTALKQLQGHMWRAAFTAGRMKAEFFADVVPAVRKWREAGMKVYIYSSGSVEAQKLLFGHS T0303 133 :GIDHLFSEMLGGQSLPEI 1zs9A 171 :DILELVDGHFDTKIGHKV T0303 153 :HPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVVGLTYGYNYNIP 1zs9A 189 :ESESYRKIADSIGCSTNNILFLTDVTREASAAEEADVHVAVVVRPGNAGLT T0303 210 :DWIFDDFAD 1zs9A 246 :YSLITSFSE Number of specific fragments extracted= 7 number of extra gaps= 0 total=794 Number of alignments=81 # 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 # T0303 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 T0303 1 :M 1x42A 1 :M T0303 4 :FKLIGFDLDGTLV 1x42A 2 :IRAVFFDFVGTLL T0303 18 :SLPDLALSINSALKDV 1x42A 15 :SVEGEAKTHLKIMEEV T0303 34 :NLP 1x42A 33 :DYP T0303 38 :ASENLVMTWIGNGADVLSQRAV 1x42A 36 :LNPKTLLDEYEKLTREAFSNYA T0303 69 :ELT 1x42A 60 :PYR T0303 72 :EDEFKYFKRQ 1x42A 69 :EEVMRKLAEK T0303 82 :FGFYYGENLCNISRLYPNVKETLEALKAQ 1x42A 87 :FWEIHLRMHQRYGELYPEVVEVLKSLKGK T0303 112 :YILAVVTNKPTKHVQPILTAFGIDHLFSEMLGGQSLPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQ 1x42A 116 :YHVGMITDSDTEYLMAHLDALGIKDLFDSITTSEEAGFFKPHPRIFELALKKAGVKGEEAVYVGDNP T0303 179 :NDIFAAHSAGCAVVGLTYGYNYNIPIAQ 1x42A 184 :KDCGGSKNLGMTSILLDRKGEKREFWDK T0303 209 :PDWIFDDFADILKI 1x42A 212 :CDFIVSDLREVIKI Number of specific fragments extracted= 11 number of extra gaps= 0 total=805 Number of alignments=82 # 1x42A read from 1x42A/merged-good-all-a2m # found chain 1x42A in template set T0303 1 :M 1x42A 1 :M T0303 4 :FKLIGFDLDGTLV 1x42A 2 :IRAVFFDFVGTLL T0303 18 :SLPDLALSINSALKDV 1x42A 15 :SVEGEAKTHLKIMEEV T0303 34 :NLPQASENLVMTWI 1x42A 33 :DYPLNPKTLLDEYE T0303 48 :GNGADVLSQRAVDWACTQAEKELTEDEFKYFKRQFG 1x42A 61 :YRPIRDIEEEVMRKLAEKYGFKYPENFWEIHLRMHQ T0303 92 :NISRLYPNVKETLEALKAQ 1x42A 97 :RYGELYPEVVEVLKSLKGK T0303 112 :YILAVVTNKPTKHVQPILTAFGIDHLFSEMLGGQSLPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQN 1x42A 116 :YHVGMITDSDTEYLMAHLDALGIKDLFDSITTSEEAGFFKPHPRIFELALKKAGVKGEEAVYVGDNPV T0303 180 :DIFAAHSAGCAVVGLTYGYNYNIPIAQ 1x42A 185 :DCGGSKNLGMTSILLDRKGEKREFWDK T0303 209 :PDWIFDDFADILKI 1x42A 212 :CDFIVSDLREVIKI Number of specific fragments extracted= 9 number of extra gaps= 0 total=814 Number of alignments=83 # 1x42A read from 1x42A/merged-good-all-a2m # found chain 1x42A in template set Warning: unaligning (T0303)Q3 because first residue in template chain is (1x42A)M1 T0303 4 :FKLIGFDLDGTLV 1x42A 2 :IRAVFFDFVGTLL T0303 18 :SLPDLALSINSALKDV 1x42A 15 :SVEGEAKTHLKIMEEV T0303 34 :NLPQASENLVMTWIGNGADVLSQR 1x42A 33 :DYPLNPKTLLDEYEKLTREAFSNY T0303 59 :VD 1x42A 62 :RP T0303 67 :EKELTEDEFKYFKRQF 1x42A 64 :IRDIEEEVMRKLAEKY T0303 83 :GFYYGENLCNISRLYPNVKETLEALKAQ 1x42A 88 :WEIHLRMHQRYGELYPEVVEVLKSLKGK T0303 112 :YILAVVTNKPTKHVQPILTAFGIDHLFSEMLGGQSLPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQ 1x42A 116 :YHVGMITDSDTEYLMAHLDALGIKDLFDSITTSEEAGFFKPHPRIFELALKKAGVKGEEAVYVGDNP T0303 179 :NDIFAAHSAGCAVVGLTYGYNYNIP 1x42A 184 :KDCGGSKNLGMTSILLDRKGEKREF T0303 206 :QSKPDWIFDDFADILKITQ 1x42A 209 :WDKCDFIVSDLREVIKIVD Number of specific fragments extracted= 9 number of extra gaps= 0 total=823 Number of alignments=84 # 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:# T0303 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 T0303 5 :KLIGFDLDGTLVNS 2b0cA 8 :MLYIFDLGNVIVDI T0303 19 :LPDLALSINSAL 2b0cA 23 :FNRVLGAWSDLT T0303 37 :QASENLVMTWIGNGADVLS 2b0cA 35 :RIPLASLKKSFHMGEAFHQ T0303 56 :QRAVDWACTQAEKELTEDEFKYFKR 2b0cA 62 :EAFAEALCHEMALPLSYEQFSHGWQ T0303 91 :CNISRLYPNVKETLEALKAQGYILAVVTNKPT 2b0cA 87 :AVFVALRPEVIAIMHKLREQGHRVVVLSNTNR T0303 123 :KHVQPI 2b0cA 129 :PEIRDA T0303 138 :FSEMLGGQSLPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVVGLTYG 2b0cA 135 :ADHIYLSQDLGMRKPEARIYQHVLQAEGFSPSDTVFFDDNADNIEGANQLGITSILVKDK Number of specific fragments extracted= 7 number of extra gaps= 0 total=830 Number of alignments=85 # 2b0cA read from 2b0cA/merged-good-all-a2m # found chain 2b0cA in template set T0303 5 :KLIGFDLDGTLVN 2b0cA 8 :MLYIFDLGNVIVD T0303 18 :SLPDLALSINSAL 2b0cA 22 :DFNRVLGAWSDLT T0303 37 :QASENLVMTWI 2b0cA 35 :RIPLASLKKSF T0303 48 :GNGADVLSQRAVDW 2b0cA 58 :EISDEAFAEALCHE T0303 66 :AEKELTEDEFKYFKRQ 2b0cA 72 :MALPLSYEQFSHGWQA T0303 92 :NISRLYPNVKETLEALKAQGYILAVVTNKP 2b0cA 88 :VFVALRPEVIAIMHKLREQGHRVVVLSNTN T0303 122 :TKHVQPI 2b0cA 128 :YPEIRDA T0303 138 :FSEMLGGQSLPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVVGLT 2b0cA 135 :ADHIYLSQDLGMRKPEARIYQHVLQAEGFSPSDTVFFDDNADNIEGANQLGITSILVK T0303 215 :DFADILKI 2b0cA 193 :DKTTIPDY Number of specific fragments extracted= 9 number of extra gaps= 0 total=839 Number of alignments=86 # 2b0cA read from 2b0cA/merged-good-all-a2m # found chain 2b0cA in template set T0303 6 :LIGFDLDGTLVNSLPD 2b0cA 9 :LYIFDLGNVIVDIDFN T0303 24 :LSINSALKDVN 2b0cA 25 :RVLGAWSDLTR T0303 37 :QASENLVMTWIGNGADVLSQR 2b0cA 36 :IPLASLKKSFHMGEAFHQHER T0303 58 :AVDWACTQAEKELTEDEFKYFKRQ 2b0cA 64 :FAEALCHEMALPLSYEQFSHGWQA T0303 94 :SR 2b0cA 88 :VF T0303 96 :LYPNVKETLEALKAQGYILAVVTNKP 2b0cA 92 :LRPEVIAIMHKLREQGHRVVVLSNTN T0303 122 :TKHVQPI 2b0cA 128 :YPEIRDA T0303 138 :FSEMLGGQSLPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVVG 2b0cA 135 :ADHIYLSQDLGMRKPEARIYQHVLQAEGFSPSDTVFFDDNADNIEGANQLGITSIL T0303 213 :FDDFADILKIT 2b0cA 191 :VKDKTTIPDYF Number of specific fragments extracted= 9 number of extra gaps= 0 total=848 Number of alignments=87 # 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 # T0303 read from 1rkqA/merged-good-all-a2m # 1rkqA read from 1rkqA/merged-good-all-a2m # found chain 1rkqA in training set T0303 92 :NISRLYPNVKETLEALKAQGYILAVVTNKPTKHVQPILTAFGIDHLFSEMLGGQSL 1rkqA 18 :PDHTISPAVKNAIAAARARGVNVVLTTGRPYAGVHNYLKELHMEQPGDYCITYNGA T0303 148 :PEIK 1rkqA 195 :RVNK T0303 154 :PAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVV 1rkqA 199 :GTGVKSLADVLGIKPEEIMAIGDQENDIAMIEYAGVGVA T0303 194 :L 1rkqA 238 :V T0303 198 :YNYNIPIAQS 1rkqA 239 :DNAIPSVKEV T0303 209 :PDWIFDD 1rkqA 249 :ANFVTKS Number of specific fragments extracted= 6 number of extra gaps= 0 total=854 Number of alignments=88 # 1rkqA read from 1rkqA/merged-good-all-a2m # found chain 1rkqA in training set T0303 3 :QFKLIGFDLDGTLVN 1rkqA 3 :AIKLIAIDMDGTLLL T0303 92 :NISRLYPNVKETLEALKAQGYILAVVTNKPTKHVQPILTAFGIDHLFSEMLGGQ 1rkqA 18 :PDHTISPAVKNAIAAARARGVNVVLTTGRPYAGVHNYLKELHMEQPGDYCITYN T0303 146 :SLPEIK 1rkqA 193 :DKRVNK T0303 154 :PAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVV 1rkqA 199 :GTGVKSLADVLGIKPEEIMAIGDQENDIAMIEYAGVGVA T0303 196 :Y 1rkqA 238 :V T0303 198 :YNYNIPIAQS 1rkqA 239 :DNAIPSVKEV T0303 209 :PDWIFDDFA 1rkqA 249 :ANFVTKSNL Number of specific fragments extracted= 7 number of extra gaps= 0 total=861 Number of alignments=89 # 1rkqA read from 1rkqA/merged-good-all-a2m # found chain 1rkqA in training set T0303 2 :TQFKLIGFDLDG 1rkqA 2 :LAIKLIAIDMDG T0303 88 :ENLCNISRLYPNVKETLEALKAQGYILAVVTNKPTKHVQPILTAFGIDHLFSEML 1rkqA 14 :TLLLPDHTISPAVKNAIAAARARGVNVVLTTGRPYAGVHNYLKELHMEQPGDYCI T0303 153 :HPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVV 1rkqA 198 :KGTGVKSLADVLGIKPEEIMAIGDQENDIAMIEYAGVGVA Number of specific fragments extracted= 3 number of extra gaps= 0 total=864 Number of alignments=90 # 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:# T0303 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 (T0303)Q3 because first residue in template chain is (1swvA)K5 T0303 4 :FKLIGFDLDGTLVNSL 1swvA 6 :IEAVIFAWAGTTVDYG T0303 23 :ALSINSALKDVNLP 1swvA 26 :LEVFMEIFHKRGVA T0303 38 :ASENLVMTWIGNGADVLSQRAV 1swvA 40 :ITAEEARKPMGLLKIDHVRALT T0303 60 :DWACTQAEKELTEDEFKYFKRQFGFYYGENLCNISRLYPNVKETLEALKAQGYILAVVTNKPTKHVQPILTAF 1swvA 68 :SEWNRVFRQLPTEADIQEMYEEFEEILFAILPRYASPINGVKEVIASLRERGIKIGSTTGYTREMMDIVAKEA T0303 133 :GID 1swvA 144 :GYK T0303 138 :FSEMLGGQSLPEIKPHPAPFYYLCGKFGLYP 1swvA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMELGVYP T0303 169 :KQILFVGDSQNDIFAAHSAGCAVVGLTYGYNYNIP 1swvA 179 :NHMIKVGDTVSDMKEGRNAGMWTVGVILGSSELGL T0303 204 :IAQSKPDWIFDDFADILKI 1swvA 237 :FVENGAHFTIETMQELESV Number of specific fragments extracted= 8 number of extra gaps= 0 total=872 Number of alignments=91 # 1swvA read from 1swvA/merged-good-all-a2m # found chain 1swvA in template set Warning: unaligning (T0303)Q3 because first residue in template chain is (1swvA)K5 T0303 4 :FKLIGFDLDGTLVN 1swvA 6 :IEAVIFAWAGTTVD T0303 22 :LALSINSALKDVNLP 1swvA 25 :PLEVFMEIFHKRGVA T0303 38 :ASENLVMTWIGNGADVLSQ 1swvA 40 :ITAEEARKPMGLLKIDHVR T0303 57 :RAVDWACTQAEKELTEDEFKYFKRQFGFYYGENLCNISRLYPNVKETLEALKAQGYILAVVTNKPTKHVQPILTAF 1swvA 65 :RIASEWNRVFRQLPTEADIQEMYEEFEEILFAILPRYASPINGVKEVIASLRERGIKIGSTTGYTREMMDIVAKEA T0303 133 :GID 1swvA 144 :GYK T0303 138 :FSEMLGGQSLPEIKPHPAPFYYLCGKFGL 1swvA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMELGV T0303 167 :YPKQILFVGDSQNDIFAAHSAGCAVVGLTYGYN 1swvA 177 :PMNHMIKVGDTVSDMKEGRNAGMWTVGVILGSS T0303 200 :YNIPIAQSK 1swvA 214 :TEEEVENMD T0303 209 :PDWIFDDFADILKI 1swvA 242 :AHFTIETMQELESV Number of specific fragments extracted= 9 number of extra gaps= 0 total=881 Number of alignments=92 # 1swvA read from 1swvA/merged-good-all-a2m # found chain 1swvA in template set Warning: unaligning (T0303)Q3 because first residue in template chain is (1swvA)K5 T0303 4 :FKLIGFDLDGTLV 1swvA 6 :IEAVIFAWAGTTV T0303 23 :ALSINSALKDVNLPQASENLVMTWIGNGADVLSQR 1swvA 26 :LEVFMEIFHKRGVAITAEEARKPMGLLKIDHVRAL T0303 58 :AVDWACTQAEKELTEDEFKYFKRQFGFYYGENLCNISRLYPNVKETLEALKAQGYILAVVTNKPTKHVQPILTAF 1swvA 66 :IASEWNRVFRQLPTEADIQEMYEEFEEILFAILPRYASPINGVKEVIASLRERGIKIGSTTGYTREMMDIVAKEA T0303 133 :GID 1swvA 144 :GYK T0303 138 :FSEMLGGQSLPEIKPHPAPFYYLCGKFGLYP 1swvA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMELGVYP T0303 169 :KQILFVGDSQNDIFAAHSAGCAVVGLTYGYNYNIP 1swvA 179 :NHMIKVGDTVSDMKEGRNAGMWTVGVILGSSELGL T0303 204 :IAQSKPDWIFDDFADILKITQ 1swvA 237 :FVENGAHFTIETMQELESVME Number of specific fragments extracted= 7 number of extra gaps= 0 total=888 Number of alignments=93 # 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 # T0303 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 (T0303)Q3 because first residue in template chain is (1jud)Y3 Warning: unaligning (T0303)T223 because last residue in template chain is (1jud)F222 T0303 4 :FKLIGFDLDGTLVNSLPDLALS 1jud 4 :IKGIAFDLYGTLFDVHSVVGRC T0303 26 :INSALKDV 1jud 37 :SALWRQKQ T0303 40 :ENLVMTWI 1jud 45 :LEYTWLRS T0303 48 :GNGADVLSQRAVDWACTQAEKELTEDEFKYFKR 1jud 57 :YVNFQQATEDALRFTCRHLGLDLDARTRSTLCD T0303 90 :LCNISRLYPNVKETLEALKAQGYILAVVTNKPTKHVQPILTAFGIDHLFSEMLGGQSLPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVVGLTYG 1jud 90 :AYLRLAPFSEVPDSLRELKRRGLKLAILSNGSPQSIDAVVSHAGLRDGFDHLLSVDPVQVYKPDNRVYELAEQALGLDRSAILFVSSNAWDATGARYFGFPTCWINRT T0303 199 :NYNIPIAQSKPDWIFDDFADILKI 1jud 198 :GNVFEEMGQTPDWEVTSLRAVVEL Number of specific fragments extracted= 6 number of extra gaps= 0 total=894 Number of alignments=94 # 1jud read from 1jud/merged-good-all-a2m # found chain 1jud in template set Warning: unaligning (T0303)Q3 because first residue in template chain is (1jud)Y3 T0303 4 :FKLIGFDLDGTLVN 1jud 4 :IKGIAFDLYGTLFD T0303 18 :SLPDLALSINSALKDV 1jud 32 :RGREISALWRQKQLEY T0303 39 :SENLVMTWIGNGADVLSQRAVDWACTQAEKELTEDEFKYFKRQF 1jud 48 :TWLRSLMNRYVNFQQATEDALRFTCRHLGLDLDARTRSTLCDAY T0303 92 :NISRLYPNVKETLEALKAQGYILAVVTNKPTKHVQPILTAFGIDHLFSEMLGGQSLPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVVGLTYGYN 1jud 92 :LRLAPFSEVPDSLRELKRRGLKLAILSNGSPQSIDAVVSHAGLRDGFDHLLSVDPVQVYKPDNRVYELAEQALGLDRSAILFVSSNAWDATGARYFGFPTCWINRTGN T0303 201 :NIPIAQSKPDWIFDDFADILKI 1jud 200 :VFEEMGQTPDWEVTSLRAVVEL Number of specific fragments extracted= 5 number of extra gaps= 0 total=899 Number of alignments=95 # 1jud read from 1jud/merged-good-all-a2m # found chain 1jud in template set Warning: unaligning (T0303)Q3 because first residue in template chain is (1jud)Y3 Warning: unaligning (T0303)T223 because last residue in template chain is (1jud)F222 T0303 4 :FKLIGFDLDGTLVNSLPDLALSINS 1jud 4 :IKGIAFDLYGTLFDVHSVVGRCDEA T0303 35 :LPQASENLVMTWIGNGADVLSQR 1jud 29 :FPGRGREISALWRQKQLEYTWLR T0303 58 :AVDWACTQAEKELTEDEFKYFKR 1jud 67 :ALRFTCRHLGLDLDARTRSTLCD T0303 90 :LCNISRLYPNVKETLEALKAQGYILAVVTNKPTKHVQPILTAFGIDHLFSEMLGGQSLPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVVGLTYGYNYNIPI 1jud 90 :AYLRLAPFSEVPDSLRELKRRGLKLAILSNGSPQSIDAVVSHAGLRDGFDHLLSVDPVQVYKPDNRVYELAEQALGLDRSAILFVSSNAWDATGARYFGFPTCWINRTGNVFEEM T0303 206 :QSKPDWIFDDFADILKI 1jud 205 :GQTPDWEVTSLRAVVEL Number of specific fragments extracted= 5 number of extra gaps= 0 total=904 Number of alignments=96 # 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 # T0303 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 T0303 2 :TQFKLIGFDLDGTLV 1vjrA 3 :DKIELFILDMDGTFY T0303 18 :SLPDLALSINS 1vjrA 22 :LLPGSLEFLET T0303 30 :LKDVNLPQ 1vjrA 33 :LKEKNKRF T0303 48 :GNGADVLSQRAVD 1vjrA 48 :SLGAQDYVRKLRN T0303 66 :AEKELTEDE 1vjrA 61 :MGVDVPDDA T0303 78 :FKRQFGFYYGENL 1vjrA 73 :SGEITAEHMLKRF T0303 92 :NISR 1vjrA 86 :GRCR T0303 96 :LYPNVKETLE 1vjrA 94 :GTPQLKKVFE T0303 109 :AQGYIL 1vjrA 104 :AYGHVI T0303 115 :AVVTN 1vjrA 116 :FVVLG T0303 120 :KPTKHVQPILTAF 1vjrA 124 :TLTYERLKKACIL T0303 134 :IDHLFSEMLGGQSL 1vjrA 137 :LRKGKFYIATHPDI T0303 149 :EIKPHPAPFYYLCGKFGLYPKQILFVGDSQ 1vjrA 181 :AGKPNPLVVDVISEKFGVPKERMAMVGDRL T0303 179 :NDIFAAHSAGCAVVGLTYGYNYNIPIAQSK 1vjrA 212 :TDVKLGKNAGIVSILVLTGETTPEDLERAE T0303 209 :PDWIFDDFADILKITQ 1vjrA 244 :PDFVFKNLGELAKAVQ Number of specific fragments extracted= 15 number of extra gaps= 0 total=919 Number of alignments=97 # 1vjrA read from 1vjrA/merged-good-all-a2m # found chain 1vjrA in template set T0303 2 :TQFKLIGFDLDGTLV 1vjrA 3 :DKIELFILDMDGTFY T0303 92 :NISRLYPNVKETLEALKAQGYILAVVTNKP 1vjrA 18 :LDDSLLPGSLEFLETLKEKNKRFVFFTNNS T0303 122 :TKHVQPILTAFGIDHLFSEMLGGQ 1vjrA 51 :AQDYVRKLRNMGVDVPDDAVVTSG T0303 146 :SLPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQN 1vjrA 178 :DLIAGKPNPLVVDVISEKFGVPKERMAMVGDRLY T0303 180 :DIFAAHSAGCAVVGLTYGYNYNIPIAQSK 1vjrA 213 :DVKLGKNAGIVSILVLTGETTPEDLERAE T0303 209 :PDWIFDDFADILKI 1vjrA 244 :PDFVFKNLGELAKA Number of specific fragments extracted= 6 number of extra gaps= 0 total=925 Number of alignments=98 # 1vjrA read from 1vjrA/merged-good-all-a2m # found chain 1vjrA in template set T0303 2 :TQFKLIGFDLDGTLV 1vjrA 3 :DKIELFILDMDGTFY T0303 95 :RLYPNVKETLEALKAQGYILAVVTNKP 1vjrA 21 :SLLPGSLEFLETLKEKNKRFVFFTNNS T0303 122 :TKHVQPILTAFGIDHLFSEML 1vjrA 51 :AQDYVRKLRNMGVDVPDDAVV T0303 149 :EIKPHPAPFYYLCGKFGLYPKQILFVGDSQ 1vjrA 181 :AGKPNPLVVDVISEKFGVPKERMAMVGDRL T0303 179 :NDIFAAHSAGCAVVGLTYGYNYNIPIAQSK 1vjrA 212 :TDVKLGKNAGIVSILVLTGETTPEDLERAE T0303 209 :PDWIFDDFADILKITQ 1vjrA 244 :PDFVFKNLGELAKAVQ Number of specific fragments extracted= 6 number of extra gaps= 0 total=931 Number of alignments=99 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bdeA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2bdeA expands to /projects/compbio/data/pdb/2bde.pdb.gz 2bdeA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0303 read from 2bdeA/merged-good-all-a2m # 2bdeA read from 2bdeA/merged-good-all-a2m # adding 2bdeA to template set # found chain 2bdeA in template set T0303 1 :MTQFKLIGFDLDGTLVNSL 2bdeA 14 :MRKIKLIGLDMDHTLIRYN T0303 20 :PDLALSINSALKDV 2bdeA 35 :NFESLVYDLVKERL T0303 34 :NLPQASENLVMTWI 2bdeA 96 :GTKQISFSDQKKIY T0303 51 :ADVLSQRAVDWACTQAEKELTEDEFKYFKRQFGF 2bdeA 132 :FCILYGQLVDLKDTNPDKMPSYQAIAQDVQYCVD T0303 85 :YYGENLCNISR 2bdeA 172 :TLKNIIIKNLK T0303 96 :LYPNVKETLEALKAQGYILAVVTNKPTKHVQPILTAF 2bdeA 187 :REKEVVEGLKHFIRYGKKIFILTNSEYSYSKLLLDYA T0303 133 :GIDHLFSEMLG 2bdeA 233 :HWQGLFEFVIT T0303 157 :FYYLCGKFGLYPKQILFVGDSQ 2bdeA 284 :AKKFTEDLGVGGDEILYIGDHI T0303 179 :NDIFAAHSAGCAVVGLTY 2bdeA 308 :DILRLKKDCNWRTALVVE Number of specific fragments extracted= 9 number of extra gaps= 0 total=940 Number of alignments=100 # 2bdeA read from 2bdeA/merged-good-all-a2m # found chain 2bdeA in template set T0303 1 :MTQFKLIGFDLDGTLVN 2bdeA 14 :MRKIKLIGLDMDHTLIR T0303 18 :SLPDLALSIN 2bdeA 36 :FESLVYDLVK T0303 28 :SALKDVNLPQA 2bdeA 47 :RLAESFHYPEE T0303 39 :SENLVMTWI 2bdeA 101 :SFSDQKKIY T0303 48 :GNGADVLSQRAVDWACTQAE 2bdeA 150 :MPSYQAIAQDVQYCVDKVHS T0303 75 :FKYFKRQFGFYYG 2bdeA 170 :DGTLKNIIIKNLK T0303 92 :NISRLYPNVKETLEALKAQGYILAVVTNKPTKHVQPILTAF 2bdeA 183 :KYVIREKEVVEGLKHFIRYGKKIFILTNSEYSYSKLLLDYA T0303 133 :GIDHLFSEMLGGQ 2bdeA 233 :HWQGLFEFVITLA T0303 147 :L 2bdeA 274 :I T0303 150 :IK 2bdeA 282 :GN T0303 157 :FYYLCGKFGLYPKQILFVGDSQN 2bdeA 284 :AKKFTEDLGVGGDEILYIGDHIY T0303 180 :DIFAAHSAGCAVVGLTY 2bdeA 309 :ILRLKKDCNWRTALVVE Number of specific fragments extracted= 12 number of extra gaps= 0 total=952 Number of alignments=101 # 2bdeA read from 2bdeA/merged-good-all-a2m # found chain 2bdeA in template set T0303 1 :MTQFKLIGFDLDGTLV 2bdeA 14 :MRKIKLIGLDMDHTLI T0303 17 :NSLPDLALSINSALKDV 2bdeA 127 :SFSIAFCILYGQLVDLK T0303 34 :NLPQASENLVM 2bdeA 148 :DKMPSYQAIAQ T0303 57 :RAV 2bdeA 159 :DVQ T0303 73 :DEFKYFK 2bdeA 162 :YCVDKVH T0303 80 :RQFGFYYGENLCNISRLYPNVKETLEALKAQGYILAVVTNKPTKHVQPILTAF 2bdeA 171 :GTLKNIIIKNLKKYVIREKEVVEGLKHFIRYGKKIFILTNSEYSYSKLLLDYA T0303 133 :GIDHLFSEML 2bdeA 233 :HWQGLFEFVI T0303 143 :GGQSLPEI 2bdeA 270 :VHGPIVPG T0303 157 :FYYLCGKFGLYPKQILFVGDSQ 2bdeA 284 :AKKFTEDLGVGGDEILYIGDHI T0303 179 :NDIFAAHSAGCAVVGLTYG 2bdeA 308 :DILRLKKDCNWRTALVVEE T0303 216 :FADILK 2bdeA 327 :LGEEIA Number of specific fragments extracted= 11 number of extra gaps= 0 total=963 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 # T0303 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 (T0303)Q3 because first residue in template chain is (1zrn)Y3 Warning: unaligning (T0303)T223 because last residue in template chain is (1zrn)F222 T0303 4 :FKLIGFDLDGTLVNSLPDLALS 1zrn 4 :IKGIAFDLYGTLFDVHSVVGRC T0303 26 :INSALKDV 1zrn 37 :SALWRQKQ T0303 40 :ENLVMTWI 1zrn 45 :LEYTWLRS T0303 48 :GNGADVLSQRAVDWACTQAEKELTEDEFKYFKR 1zrn 57 :YVNFQQATEDALRFTCRHLGLDLDARTRSTLCD T0303 90 :LCNISRLYPNVKETLEALKAQGYILAVVTNKPTKHVQPILTAFGIDHLFSEMLGGQSLPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVVGLTYG 1zrn 90 :AYLRLAPFSEVPDSLRELKRRGLKLAILSNGSPQSIDAVVSHAGLRDGFDHLLSVDPVQVYKPDNRVYELAEQALGLDRSAILFVASNAWDATGARYFGFPTCWINRT T0303 199 :NYNIPIAQSKPDWIFDDFADILKI 1zrn 198 :GNVFEEMGQTPDWEVTSLRAVVEL Number of specific fragments extracted= 6 number of extra gaps= 0 total=969 Number of alignments=103 # 1zrn read from 1zrn/merged-good-all-a2m # found chain 1zrn in template set Warning: unaligning (T0303)Q3 because first residue in template chain is (1zrn)Y3 T0303 4 :FKLIGFDLDGTLVN 1zrn 4 :IKGIAFDLYGTLFD T0303 18 :SLPDLALSINSALKDV 1zrn 32 :RGREISALWRQKQLEY T0303 39 :SENLVMTWIGNGADVLSQRAVDWACTQAEKELTEDEFKYFKRQF 1zrn 48 :TWLRSLMNRYVNFQQATEDALRFTCRHLGLDLDARTRSTLCDAY T0303 92 :NISRLYPNVKETLEALKAQGYILAVVTNKPTKHVQPILTAFGIDHLFSEMLGGQSLPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVVGLTYGYN 1zrn 92 :LRLAPFSEVPDSLRELKRRGLKLAILSNGSPQSIDAVVSHAGLRDGFDHLLSVDPVQVYKPDNRVYELAEQALGLDRSAILFVASNAWDATGARYFGFPTCWINRTGN T0303 201 :NIPIAQSKPDWIFDDFADILKI 1zrn 200 :VFEEMGQTPDWEVTSLRAVVEL Number of specific fragments extracted= 5 number of extra gaps= 0 total=974 Number of alignments=104 # 1zrn read from 1zrn/merged-good-all-a2m # found chain 1zrn in template set Warning: unaligning (T0303)Q3 because first residue in template chain is (1zrn)Y3 Warning: unaligning (T0303)T223 because last residue in template chain is (1zrn)F222 T0303 4 :FKLIGFDLDGTLVNSLPDLALSINS 1zrn 4 :IKGIAFDLYGTLFDVHSVVGRCDEA T0303 35 :LPQASENLVMTWIGNGADVLSQR 1zrn 29 :FPGRGREISALWRQKQLEYTWLR T0303 58 :AVDWACTQAEKELTEDEFKYFKR 1zrn 67 :ALRFTCRHLGLDLDARTRSTLCD T0303 90 :LCNISRLYPNVKETLEALKAQGYILAVVTNKPTKHVQPILTAFGIDHLFSEMLGGQSLPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVVGLTYGYNYNIPI 1zrn 90 :AYLRLAPFSEVPDSLRELKRRGLKLAILSNGSPQSIDAVVSHAGLRDGFDHLLSVDPVQVYKPDNRVYELAEQALGLDRSAILFVASNAWDATGARYFGFPTCWINRTGNVFEEM T0303 206 :QSKPDWIFDDFADILKI 1zrn 205 :GQTPDWEVTSLRAVVEL Number of specific fragments extracted= 5 number of extra gaps= 0 total=979 Number of alignments=105 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1k1eA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0303 read from 1k1eA/merged-good-all-a2m # 1k1eA read from 1k1eA/merged-good-all-a2m # found chain 1k1eA in training set T0303 2 :TQFKLIGFDLDGTLVN 1k1eA 6 :ENIKFVITDVDGVLTD T0303 98 :PNVKETLEALKAQGYILAVVTNKPTKHVQPILTAFGID 1k1eA 38 :VRDGLGIKMLMDADIQVAVLSGRDSPILRRRIADLGIK T0303 141 :MLGGQSLP 1k1eA 76 :LFFLGKLE T0303 153 :HPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAG 1k1eA 84 :KETACFDLMKQAGVTAEQTAYIGDDSVDLPAFAACG T0303 190 :AVVGL 1k1eA 120 :TSFAV T0303 198 :YNYNIPIAQS 1k1eA 125 :ADAPIYVKNA T0303 209 :PDWIFDD 1k1eA 135 :VDHVLST T0303 216 :FADILKI 1k1eA 148 :FREMSDM Number of specific fragments extracted= 8 number of extra gaps= 0 total=987 Number of alignments=106 # 1k1eA read from 1k1eA/merged-good-all-a2m # found chain 1k1eA in training set T0303 2 :TQFKLIGFDLDGTLVN 1k1eA 6 :ENIKFVITDVDGVLTD T0303 20 :P 1k1eA 38 :V T0303 99 :NVKETLEALKAQGYILAVVTNKPTKHVQPILTAFGID 1k1eA 39 :RDGLGIKMLMDADIQVAVLSGRDSPILRRRIADLGIK T0303 141 :MLGGQSLP 1k1eA 76 :LFFLGKLE T0303 151 :K 1k1eA 84 :K T0303 154 :PAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAG 1k1eA 85 :ETACFDLMKQAGVTAEQTAYIGDDSVDLPAFAACG T0303 190 :AVVGLTY 1k1eA 120 :TSFAVAD T0303 200 :YNIPIAQS 1k1eA 127 :APIYVKNA T0303 209 :PDWIFDD 1k1eA 135 :VDHVLST Number of specific fragments extracted= 9 number of extra gaps= 0 total=996 Number of alignments=107 # 1k1eA read from 1k1eA/merged-good-all-a2m # found chain 1k1eA in training set T0303 2 :TQFKLIGFDLDGTLV 1k1eA 6 :ENIKFVITDVDGVLT T0303 98 :PNVKETLEALKAQGYILAVVTNKPTKHVQPILTAFGIDHLF 1k1eA 38 :VRDGLGIKMLMDADIQVAVLSGRDSPILRRRIADLGIKLFF T0303 150 :IKPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAG 1k1eA 81 :KLEKETACFDLMKQAGVTAEQTAYIGDDSVDLPAFAACG T0303 190 :AVVGL 1k1eA 120 :TSFAV T0303 199 :NYNIPIAQSKPDWIFDD 1k1eA 125 :ADAPIYVKNAVDHVLST T0303 216 :FADILKIT 1k1eA 148 :FREMSDMI Number of specific fragments extracted= 6 number of extra gaps= 0 total=1002 Number of alignments=108 # 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:# T0303 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 T0303 1 :MT 1u7pA 1 :MT T0303 3 :QFKLIGFDLDGTLVNSL 1u7pA 4 :LPKLAVFDLDYTLWPFW T0303 32 :DVNLP 1u7pA 22 :DTHVD T0303 38 :AS 1u7pA 27 :PP T0303 68 :KELT 1u7pA 33 :SDGT T0303 90 :LCNISRLYPNVKETLEALKAQGYILAVVTN 1u7pA 41 :RGQNIQLYPEVPEVLGRLQSLGVPVAAASR T0303 120 :KPTKHVQPILTAFGIDHLFSEMLGGQS 1u7pA 72 :SEIQGANQLLELFDLGKYFIQREIYPG T0303 150 :IK 1u7pA 99 :SK T0303 154 :PAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVVGLTYG 1u7pA 101 :VTHFERLHHKTGVPFSQMVFFDDENRNIIDVGRLGVTCIHIRDG T0303 202 :IP 1u7pA 145 :MS Number of specific fragments extracted= 10 number of extra gaps= 0 total=1012 Number of alignments=109 # 1u7pA read from 1u7pA/merged-good-all-a2m # found chain 1u7pA in template set T0303 2 :TQFKLIGFDLDGTLVN 1u7pA 3 :RLPKLAVFDLDYTLWP T0303 34 :NLPQA 1u7pA 24 :HVDPP T0303 69 :E 1u7pA 42 :G T0303 92 :NISRLYPNVKETLEALKAQGYILAVVTN 1u7pA 43 :QNIQLYPEVPEVLGRLQSLGVPVAAASR T0303 120 :KPTKHVQPILTAFGIDHLFSEMLGGQ 1u7pA 72 :SEIQGANQLLELFDLGKYFIQREIYP T0303 149 :EIK 1u7pA 98 :GSK T0303 154 :PAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVVGLTYGYN 1u7pA 101 :VTHFERLHHKTGVPFSQMVFFDDENRNIIDVGRLGVTCIHIRDGMS Number of specific fragments extracted= 7 number of extra gaps= 0 total=1019 Number of alignments=110 # 1u7pA read from 1u7pA/merged-good-all-a2m # found chain 1u7pA in template set T0303 2 :TQFKLIGFDLDGTLV 1u7pA 3 :RLPKLAVFDLDYTLW T0303 94 :SRLYPNVKETLEALKAQGYILAVVTN 1u7pA 45 :IQLYPEVPEVLGRLQSLGVPVAAASR T0303 120 :KPTKHVQPILTAFGIDHLFSEMLGGQS 1u7pA 72 :SEIQGANQLLELFDLGKYFIQREIYPG T0303 152 :PHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVVGLTYGYN 1u7pA 99 :SKVTHFERLHHKTGVPFSQMVFFDDENRNIIDVGRLGVTCIHIRDGMS T0303 216 :FADILKIT 1u7pA 147 :LQTLTQGL Number of specific fragments extracted= 5 number of extra gaps= 0 total=1024 Number of alignments=111 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rkuA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0303 read from 1rkuA/merged-good-all-a2m # 1rkuA read from 1rkuA/merged-good-all-a2m # found chain 1rkuA in training set Warning: unaligning (T0303)F9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rkuA)D7 Warning: unaligning (T0303)D10 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rkuA)D7 T0303 5 :KLIG 1rkuA 2 :EIAC T0303 11 :LDGTLVNS 1rkuA 8 :LEGVLVPE T0303 25 :SINSALKDVNLPQ 1rkuA 16 :IWIAFAEKTGIDA T0303 38 :ASENLVM 1rkuA 37 :PDYDVLM T0303 52 :DVLSQRAVD 1rkuA 44 :KQRLRILDE T0303 68 :KELTEDEFKYFK 1rkuA 53 :HGLKLGDIQEVI T0303 92 :NISRLYPNVKETLEALKAQ 1rkuA 65 :ATLKPLEGAVEFVDWLRER T0303 112 :YILAVVTNKPTKHVQPILTAFGIDHLFSEMLGGQSLPEI 1rkuA 84 :FQVVILSDTFYEFSQPLMRQLGFPTLLCHKLEIDDSDRV T0303 151 :KPHPAPFYYLCGKF 1rkuA 127 :LRQKDPKRQSVIAF T0303 169 :KQILFVGDSQNDIFAAHSAG 1rkuA 145 :YRVIAAGDSYNDTTMLSEAH T0303 190 :AVVGLTYGYNYNIPIAQSK 1rkuA 165 :AGILFHAPENVIREFPQFP T0303 212 :IFDDFADILKI 1rkuA 184 :AVHTYEDLKRE Number of specific fragments extracted= 12 number of extra gaps= 1 total=1036 Number of alignments=112 # 1rkuA read from 1rkuA/merged-good-all-a2m # found chain 1rkuA in training set Warning: unaligning (T0303)F9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rkuA)D7 Warning: unaligning (T0303)D10 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rkuA)D7 T0303 4 :FKLIG 1rkuA 1 :MEIAC T0303 11 :LDGTLVNS 1rkuA 8 :LEGVLVPE T0303 25 :SINSALKDVNLPQA 1rkuA 16 :IWIAFAEKTGIDAL T0303 49 :NGADVLSQRAVDWACT 1rkuA 37 :PDYDVLMKQRLRILDE T0303 68 :KELTEDEFKYFK 1rkuA 53 :HGLKLGDIQEVI T0303 92 :NISRLYPNVKETLEALKAQ 1rkuA 65 :ATLKPLEGAVEFVDWLRER T0303 112 :YILAVVTNKPTKHVQPILTAFGIDHLFSEMLGGQSLPE 1rkuA 84 :FQVVILSDTFYEFSQPLMRQLGFPTLLCHKLEIDDSDR T0303 150 :I 1rkuA 128 :R T0303 153 :HPAPFYYLCGKF 1rkuA 129 :QKDPKRQSVIAF T0303 168 :PKQILFVGDSQNDIFAAHSAG 1rkuA 144 :YYRVIAAGDSYNDTTMLSEAH T0303 190 :AVVGLTYGYNYNIPIAQSK 1rkuA 165 :AGILFHAPENVIREFPQFP T0303 212 :IFDDFADILKI 1rkuA 184 :AVHTYEDLKRE Number of specific fragments extracted= 12 number of extra gaps= 1 total=1048 Number of alignments=113 # 1rkuA read from 1rkuA/merged-good-all-a2m # found chain 1rkuA in training set Warning: unaligning (T0303)F9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rkuA)D7 Warning: unaligning (T0303)D10 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rkuA)D7 T0303 5 :KLIG 1rkuA 2 :EIAC T0303 11 :LDGTLVNS 1rkuA 8 :LEGVLVPE T0303 25 :SINSALKDVNLP 1rkuA 16 :IWIAFAEKTGID T0303 68 :KELTEDEFKYFKRQFG 1rkuA 36 :IPDYDVLMKQRLRILD T0303 84 :FYYGENLCNISRLYPNVKETLEALKAQ 1rkuA 57 :LGDIQEVIATLKPLEGAVEFVDWLRER T0303 112 :YILAVVTNKPTKHVQPILTAFGIDHLFSEMLGGQS 1rkuA 84 :FQVVILSDTFYEFSQPLMRQLGFPTLLCHKLEIDD T0303 147 :LP 1rkuA 127 :LR T0303 153 :HPAPFYYLCGKF 1rkuA 129 :QKDPKRQSVIAF T0303 170 :QILFVGDSQNDIFAAHSAG 1rkuA 146 :RVIAAGDSYNDTTMLSEAH T0303 190 :AVVGLTYG 1rkuA 165 :AGILFHAP T0303 201 :NIPIAQSKPDWIFDDFADILKIT 1rkuA 173 :ENVIREFPQFPAVHTYEDLKREF Number of specific fragments extracted= 11 number of extra gaps= 1 total=1059 Number of alignments=114 # 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 # T0303 read from 1te2A/merged-good-all-a2m # 1te2A read from 1te2A/merged-good-all-a2m # found chain 1te2A in training set Warning: unaligning (T0303)A131 because of BadResidue code BAD_PEPTIDE in next template residue (1te2A)F129 Warning: unaligning (T0303)F132 because of BadResidue code BAD_PEPTIDE at template residue (1te2A)F129 T0303 3 :QFKLIGFDLDGTLVNSLPDLALSINSALKDVNLPQASENL 1te2A 6 :QILAAIFDMDGLLIDSEPLWDRAELDVMASLGVDISRRNE T0303 46 :WIGNGADVLSQRAVD 1te2A 49 :TLGLRIDMVVDLWYA T0303 65 :QAE 1te2A 64 :RQP T0303 68 :KELTEDE 1te2A 68 :NGPSRQE T0303 78 :FKRQFGFYYGENLCNISRLYPNVKETLEALKAQGYILAVVTNKPTKHVQPILT 1te2A 75 :VVERVIARAISLVEETRPLLPGVREAVALCKEQGLLVGLASASPLHMLEKVLT T0303 133 :GIDHLFSEMLGGQSLPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVVGLTYGYNYNIPIAQS 1te2A 130 :DLRDSFDALASAEKLPYSKPHPQVYLDCAAKLGVDPLTCVALEDSVNGMIASKAARMRSIVVPAPEAQNDPRFVL T0303 209 :PDWIFDDFADI 1te2A 205 :ANVKLSSLTEL Number of specific fragments extracted= 7 number of extra gaps= 1 total=1066 Number of alignments=115 # 1te2A read from 1te2A/merged-good-all-a2m # found chain 1te2A in training set Warning: unaligning (T0303)T2 because first residue in template chain is (1te2A)R5 Warning: unaligning (T0303)A131 because of BadResidue code BAD_PEPTIDE in next template residue (1te2A)F129 Warning: unaligning (T0303)F132 because of BadResidue code BAD_PEPTIDE at template residue (1te2A)F129 T0303 3 :QFKLIGFDLDGTLVNSLPDLALSINSALKDVNLPQASENLVMTWIGNGADVLSQRAVDWA 1te2A 6 :QILAAIFDMDGLLIDSEPLWDRAELDVMASLGVDISRRNELPDTLGLRIDMVVDLWYARQ T0303 65 :QAE 1te2A 66 :PWN T0303 69 :ELTEDE 1te2A 69 :GPSRQE T0303 75 :FKYFKRQFGFYYG 1te2A 76 :VERVIARAISLVE T0303 92 :NISRLYPNVKETLEALKAQGYILAVVTNKPTKHVQPILT 1te2A 89 :ETRPLLPGVREAVALCKEQGLLVGLASASPLHMLEKVLT T0303 133 :GIDHLFSEMLGGQSLPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVVGLTYGYNYNIPIAQS 1te2A 130 :DLRDSFDALASAEKLPYSKPHPQVYLDCAAKLGVDPLTCVALEDSVNGMIASKAARMRSIVVPAPEAQNDPRFVL T0303 209 :PDWIFDDFADI 1te2A 205 :ANVKLSSLTEL Number of specific fragments extracted= 7 number of extra gaps= 1 total=1073 Number of alignments=116 # 1te2A read from 1te2A/merged-good-all-a2m # found chain 1te2A in training set Warning: unaligning (T0303)A131 because of BadResidue code BAD_PEPTIDE in next template residue (1te2A)F129 Warning: unaligning (T0303)F132 because of BadResidue code BAD_PEPTIDE at template residue (1te2A)F129 T0303 3 :QFKLIGFDLDGTLVNSLPDLALSINSALKDVNLPQASENLVMTWIGNGADVLSQRAVDW 1te2A 6 :QILAAIFDMDGLLIDSEPLWDRAELDVMASLGVDISRRNELPDTLGLRIDMVVDLWYAR T0303 68 :KELTEDEFKYFKRQFGFYYGENLCNISRLYPNVKETLEALKAQGYILAVVTNKPTKHVQPILT 1te2A 65 :QPWNGPSRQEVVERVIARAISLVEETRPLLPGVREAVALCKEQGLLVGLASASPLHMLEKVLT T0303 133 :GIDHLFSEMLGGQSLPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVVGLTYGYNYNIP 1te2A 130 :DLRDSFDALASAEKLPYSKPHPQVYLDCAAKLGVDPLTCVALEDSVNGMIASKAARMRSIVVPAPEAQNDP T0303 205 :AQSKPDWIFDDFAD 1te2A 201 :RFVLANVKLSSLTE Number of specific fragments extracted= 4 number of extra gaps= 1 total=1077 Number of alignments=117 # 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:# T0303 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 (T0303)Q3 because first residue in template chain is (1fezA)K5 T0303 4 :FKLIGFDLDGTLVNSL 1fezA 6 :IEAVIFDWAGTTVDYG T0303 20 :PDLALSINSALKDVNLP 1fezA 23 :FAPLEVFMEIFHKRGVA T0303 38 :ASENLVMTWIGNGADVLSQRAV 1fezA 40 :ITAEEARKPMGLLKIDHVRALT T0303 60 :DWACTQAEKELTEDEFKYFKRQFGFYYGENLCNISRLYPNVKETLEALKAQGYILAVVTNKPTKHVQPILTAF 1fezA 68 :SEWNRVFRQLPTEADIQEMYEEFEEILFAILPRYASPINAVKEVIASLRERGIKIGSTTGYTREMMDIVAKEA T0303 133 :GID 1fezA 144 :GYK T0303 138 :FSEMLGGQSLPEIKPHPAPFYYLCGKFGL 1fezA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMELGV T0303 167 :YPKQILFVGDSQNDIFAAHSAGCAVVGLTY 1fezA 177 :PMNHMIKVGDTVSDMKEGRNAGMWTVGVIL T0303 197 :G 1fezA 216 :E T0303 204 :IAQSKPDWIFDDFADILKI 1fezA 237 :FVENGAHFTIETMQELESV Number of specific fragments extracted= 9 number of extra gaps= 0 total=1086 Number of alignments=118 # 1fezA read from 1fezA/merged-good-all-a2m # found chain 1fezA in template set Warning: unaligning (T0303)Q3 because first residue in template chain is (1fezA)K5 T0303 4 :FKLIGFDLDGTLVN 1fezA 6 :IEAVIFDWAGTTVD T0303 18 :SLPDLALSINSALKDVNLP 1fezA 21 :GCFAPLEVFMEIFHKRGVA T0303 38 :ASENLVMTWIGNGADVLSQRAVD 1fezA 40 :ITAEEARKPMGLLKIDHVRALTE T0303 61 :WACTQAEKELTEDEFKYFKRQFGFYYGENLCNISRLYPNVKETLEALKAQGYILAVVTNKPTKHVQPILTAF 1fezA 69 :EWNRVFRQLPTEADIQEMYEEFEEILFAILPRYASPINAVKEVIASLRERGIKIGSTTGYTREMMDIVAKEA T0303 133 :GID 1fezA 144 :GYK T0303 138 :FSEMLGGQSLPEIKPHPAPFYYLCGKFGL 1fezA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMELGV T0303 167 :YPKQILFVGDSQNDIFAAHSAGCAVVGLTYGYN 1fezA 177 :PMNHMIKVGDTVSDMKEGRNAGMWTVGVILGSS T0303 200 :YNIPIAQSK 1fezA 214 :TEEEVENMD T0303 209 :PDWIFDDFADILKI 1fezA 242 :AHFTIETMQELESV Number of specific fragments extracted= 9 number of extra gaps= 0 total=1095 Number of alignments=119 # 1fezA read from 1fezA/merged-good-all-a2m # found chain 1fezA in template set Warning: unaligning (T0303)Q3 because first residue in template chain is (1fezA)K5 T0303 4 :FKLIGFDLDGTLVNSLPD 1fezA 6 :IEAVIFDWAGTTVDYGCF T0303 22 :LALSINSALKDVNLPQASENLVMTWIGNGADVLSQR 1fezA 25 :PLEVFMEIFHKRGVAITAEEARKPMGLLKIDHVRAL T0303 58 :AVDWACTQAEKELTEDEFKYFKRQFGFYYGENLCNISRLYPNVKETLEALKAQGYILAVVTNKPTKHVQPILTAF 1fezA 66 :IASEWNRVFRQLPTEADIQEMYEEFEEILFAILPRYASPINAVKEVIASLRERGIKIGSTTGYTREMMDIVAKEA T0303 133 :GID 1fezA 144 :GYK T0303 138 :FSEMLGGQSLPEIKPHPAPFYYLCGKFGL 1fezA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMELGV T0303 167 :YPKQILFVGDSQNDIFAAHSAGCAVVGLTYGYN 1fezA 177 :PMNHMIKVGDTVSDMKEGRNAGMWTVGVILGSS T0303 201 :N 1fezA 216 :E T0303 204 :IAQSKPDWIFDDFADILKITQ 1fezA 237 :FVENGAHFTIETMQELESVME Number of specific fragments extracted= 8 number of extra gaps= 0 total=1103 Number of alignments=120 # 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:# T0303 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 (T0303)K5 because first residue in template chain is (1cr6B)R4 T0303 6 :LIGFDLDGTLVNSL 1cr6B 5 :VAAFDLDGVLALPS T0303 22 :LALSINSALKDV 1cr6B 19 :IAGAFRRSEEAL T0303 37 :QAS 1cr6B 45 :FPE T0303 41 :NLVMTWIGN 1cr6B 48 :GPTEQLMKG T0303 50 :GADVLSQRAVDWACTQAE 1cr6B 59 :TFSQWVPLMDESYRKSSK T0303 68 :KELTED 1cr6B 80 :ANLPEN T0303 82 :FGFYYGENLCN 1cr6B 88 :ISQIFSQAMAA T0303 94 :SRLYPNVKETLEALKAQGYILAVVTN 1cr6B 99 :RSINRPMLQAAIALKKKGFTTCIVTN T0303 120 :KPTKHVQPILTAFG 1cr6B 131 :DKRDSLAQMMCELS T0303 136 :HLFSEMLGGQSLPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVVGLTYGYN 1cr6B 145 :QHFDFLIESCQVGMIKPEPQIYNFLLDTLKAKPNEVVFLDDFGSNLKPARDMGMVTILVHNTAS Number of specific fragments extracted= 10 number of extra gaps= 0 total=1113 Number of alignments=121 # 1cr6B read from 1cr6B/merged-good-all-a2m # found chain 1cr6B in template set Warning: unaligning (T0303)K5 because first residue in template chain is (1cr6B)R4 T0303 6 :LIGFDLDGTLVNSLP 1cr6B 5 :VAAFDLDGVLALPSI T0303 23 :ALSINSALKDVNLPQA 1cr6B 20 :AGAFRRSEEALALPRD T0303 40 :ENLVMTWI 1cr6B 47 :EGPTEQLM T0303 48 :G 1cr6B 56 :G T0303 49 :NGADVLSQRAVDWACTQ 1cr6B 58 :ITFSQWVPLMDESYRKS T0303 66 :AEKELT 1cr6B 82 :LPENFS T0303 72 :EDEFKYFK 1cr6B 89 :SQIFSQAM T0303 92 :NISRLYPNVKETLEALKAQGYILAVVTNKP 1cr6B 97 :AARSINRPMLQAAIALKKKGFTTCIVTNNW T0303 122 :TKHVQPILTAFG 1cr6B 133 :RDSLAQMMCELS T0303 136 :HLFSEMLGGQSLPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVVGLTYGYNYN 1cr6B 145 :QHFDFLIESCQVGMIKPEPQIYNFLLDTLKAKPNEVVFLDDFGSNLKPARDMGMVTILVHNTASAL Number of specific fragments extracted= 10 number of extra gaps= 0 total=1123 Number of alignments=122 # 1cr6B read from 1cr6B/merged-good-all-a2m # found chain 1cr6B in template set Warning: unaligning (T0303)K5 because first residue in template chain is (1cr6B)R4 T0303 6 :LIGFDLDGTLVNSL 1cr6B 5 :VAAFDLDGVLALPS T0303 22 :LALSINSALKDVNLP 1cr6B 19 :IAGAFRRSEEALALP T0303 37 :QASENLVMTWIGNGADV 1cr6B 45 :FPEGPTEQLMKGKITFS T0303 69 :ELTEDEFKYFKRQFG 1cr6B 62 :QWVPLMDESYRKSSK T0303 84 :FYYGENLCNISRLYPNVKETLEALKAQGYILAVVTNKP 1cr6B 89 :SQIFSQAMAARSINRPMLQAAIALKKKGFTTCIVTNNW T0303 122 :TKHVQPILTAFG 1cr6B 133 :RDSLAQMMCELS T0303 136 :HLFSEMLGGQSLPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVVGLTYGYNYNI 1cr6B 145 :QHFDFLIESCQVGMIKPEPQIYNFLLDTLKAKPNEVVFLDDFGSNLKPARDMGMVTILVHNTASALR Number of specific fragments extracted= 7 number of extra gaps= 0 total=1130 Number of alignments=123 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2feaA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2feaA expands to /projects/compbio/data/pdb/2fea.pdb.gz 2feaA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 517, because occupancy 0.500 <= existing 0.500 in 2feaA Skipped atom 521, because occupancy 0.500 <= existing 0.500 in 2feaA Skipped atom 523, because occupancy 0.500 <= existing 0.500 in 2feaA Skipped atom 552, because occupancy 0.500 <= existing 0.500 in 2feaA Skipped atom 556, because occupancy 0.500 <= existing 0.500 in 2feaA Skipped atom 558, because occupancy 0.500 <= existing 0.500 in 2feaA Skipped atom 560, because occupancy 0.500 <= existing 0.500 in 2feaA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1319, because occupancy 0.500 <= existing 0.500 in 2feaA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1323, because occupancy 0.500 <= existing 0.500 in 2feaA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1325, because occupancy 0.500 <= existing 0.500 in 2feaA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1329, because occupancy 0.500 <= existing 0.500 in 2feaA Skipped atom 1566, because occupancy 0.300 <= existing 0.700 in 2feaA Skipped atom 1570, because occupancy 0.300 <= existing 0.700 in 2feaA Skipped atom 1572, because occupancy 0.300 <= existing 0.700 in 2feaA Skipped atom 1574, because occupancy 0.300 <= existing 0.700 in 2feaA Skipped atom 1576, because occupancy 0.300 <= existing 0.700 in 2feaA # T0303 read from 2feaA/merged-good-all-a2m # 2feaA read from 2feaA/merged-good-all-a2m # adding 2feaA to template set # found chain 2feaA in template set Warning: unaligning (T0303)V117 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2feaA)S99 Warning: unaligning (T0303)T118 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2feaA)S99 T0303 5 :KLIGFDLDGTLVNSL 2feaA 6 :PFIICDFDGTITMND T0303 25 :SINSALKDV 2feaA 21 :NIINIMKTF T0303 35 :LPQASENLVMTWIGN 2feaA 30 :APPEWMALKDGVLSK T0303 50 :GADVLSQRAVD 2feaA 47 :SIKEGVGRMFG T0303 69 :ELTEDEFKYFKRQFGF 2feaA 58 :LLPSSLKEEITSFVLE T0303 93 :ISRLYPNVKETLEALKAQGYILAV 2feaA 74 :DAKIREGFREFVAFINEHEIPFYV T0303 119 :NKPTKHVQPILTAF 2feaA 100 :GGMDFFVYPLLEGI T0303 133 :GIDHLFSEMLGGQSL 2feaA 115 :EKDRIYCNHASFDND T0303 156 :PFYYLCGKF 2feaA 150 :CKPSVIHEL T0303 166 :LYPK 2feaA 159 :SEPN T0303 170 :QILFVGDSQNDIFAAHS 2feaA 164 :YIIMIGDSVTDVEAAKL T0303 189 :CAVVGLTY 2feaA 181 :SDLCFARD T0303 202 :IPIAQSKPDWI 2feaA 192 :NECREQNLNHL T0303 213 :FDDFADILKI 2feaA 204 :YQDFYEIRKE Number of specific fragments extracted= 14 number of extra gaps= 1 total=1144 Number of alignments=124 # 2feaA read from 2feaA/merged-good-all-a2m # found chain 2feaA in template set Warning: unaligning (T0303)T2 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2feaA)T3 Warning: unaligning (T0303)V117 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2feaA)S99 Warning: unaligning (T0303)T118 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2feaA)S99 Warning: unaligning (T0303)P148 because of BadResidue code BAD_PEPTIDE in next template residue (2feaA)C149 Warning: unaligning (T0303)E149 because of BadResidue code BAD_PEPTIDE at template residue (2feaA)C149 T0303 3 :QFKLIGFDLDGTLVNSLP 2feaA 4 :RKPFIICDFDGTITMNDN T0303 26 :INSALKDV 2feaA 22 :IINIMKTF T0303 36 :PQASENLVMTWIGNG 2feaA 31 :PPEWMALKDGVLSKT T0303 51 :ADVLSQRAV 2feaA 48 :IKEGVGRMF T0303 67 :E 2feaA 57 :G T0303 69 :ELTEDEFKYFKRQFG 2feaA 58 :LLPSSLKEEITSFVL T0303 92 :NISRLYPNVKETLEALKAQGYILAV 2feaA 73 :EDAKIREGFREFVAFINEHEIPFYV T0303 119 :NKPTKHVQPILTAF 2feaA 100 :GGMDFFVYPLLEGI T0303 133 :GIDHLFSEMLGGQ 2feaA 115 :EKDRIYCNHASFD T0303 146 :SL 2feaA 146 :QC T0303 150 :IK 2feaA 150 :CK T0303 158 :YYLCGKF 2feaA 152 :PSVIHEL T0303 166 :LYPK 2feaA 159 :SEPN T0303 170 :QILFVGDSQNDIFAAHSAG 2feaA 164 :YIIMIGDSVTDVEAAKLSD T0303 192 :VGLTY 2feaA 183 :LCFAR T0303 201 :NIPIAQSKPDWI 2feaA 191 :LNECREQNLNHL T0303 213 :FDDFADILKI 2feaA 204 :YQDFYEIRKE Number of specific fragments extracted= 17 number of extra gaps= 3 total=1161 Number of alignments=125 # 2feaA read from 2feaA/merged-good-all-a2m # found chain 2feaA in template set Warning: unaligning (T0303)V117 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2feaA)S99 Warning: unaligning (T0303)T118 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2feaA)S99 Warning: unaligning (T0303)P148 because of BadResidue code BAD_PEPTIDE in next template residue (2feaA)C149 Warning: unaligning (T0303)E149 because of BadResidue code BAD_PEPTIDE at template residue (2feaA)C149 T0303 3 :QFKLIGFDLDGTLVNSLP 2feaA 4 :RKPFIICDFDGTITMNDN T0303 26 :INSALKDV 2feaA 22 :IINIMKTF T0303 35 :LPQASENLVMTWIGNGADVLSQRA 2feaA 30 :APPEWMALKDGVLSKTLSIKEGVG T0303 65 :QAEKELTEDEFKYFKRQFGF 2feaA 54 :RMFGLLPSSLKEEITSFVLE T0303 93 :ISRLYPNVKETLEALKAQGYILAV 2feaA 74 :DAKIREGFREFVAFINEHEIPFYV T0303 119 :NKPTKHVQPILTAF 2feaA 100 :GGMDFFVYPLLEGI T0303 133 :GIDHLFSEMLGGQS 2feaA 115 :EKDRIYCNHASFDN T0303 147 :L 2feaA 147 :C T0303 156 :PFYYLCGKF 2feaA 150 :CKPSVIHEL T0303 166 :LYPKQ 2feaA 159 :SEPNQ T0303 171 :ILFVGDSQNDIFAAHSAG 2feaA 165 :IIMIGDSVTDVEAAKLSD T0303 192 :VGLTY 2feaA 183 :LCFAR T0303 202 :I 2feaA 188 :D T0303 204 :IAQSKPDWI 2feaA 194 :CREQNLNHL T0303 213 :FDDFADILKITQ 2feaA 204 :YQDFYEIRKEIE Number of specific fragments extracted= 15 number of extra gaps= 2 total=1176 Number of alignments=126 # 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:# T0303 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 (T0303)F4 because first residue in template chain is (1ymqA)T2 T0303 5 :KLIGFDLDGTLVNS 1ymqA 3 :KALFFDIDGTLVSF T0303 92 :NISRLYPNVKETLEALKAQGYILAVVTNKPTKHVQ 1ymqA 17 :ETHRIPSSTIEALEAAHAKGLKIFIATGRPKAIIN T0303 127 :PILTAFGI 1ymqA 54 :SELQDRNL T0303 138 :FSEMLGGQSL 1ymqA 62 :IDGYITMNGA T0303 148 :PEIK 1ymqA 185 :GDTK T0303 154 :PAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAG 1ymqA 189 :QKGIDEIIRHFGIKLEETMSFGDGGNDISMLRHAA T0303 190 :AVVGL 1ymqA 224 :IGVAM T0303 198 :YNYNIPIAQS 1ymqA 229 :GQAKEDVKAA T0303 209 :PDWIFDDFAD 1ymqA 239 :ADYVTAPIDE Number of specific fragments extracted= 9 number of extra gaps= 0 total=1185 Number of alignments=127 # 1ymqA read from 1ymqA/merged-good-all-a2m # found chain 1ymqA in template set Warning: unaligning (T0303)F4 because first residue in template chain is (1ymqA)T2 T0303 5 :KLIGFDLDGTLVNS 1ymqA 3 :KALFFDIDGTLVSF T0303 92 :NISRLYPNVKETLEALKAQGYILAVVTNKPTKHVQ 1ymqA 17 :ETHRIPSSTIEALEAAHAKGLKIFIATGRPKAIIN T0303 127 :PILTAFGI 1ymqA 54 :SELQDRNL T0303 138 :FSEMLGGQ 1ymqA 62 :IDGYITMN T0303 146 :SLPEIK 1ymqA 183 :AKGDTK T0303 154 :PAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAG 1ymqA 189 :QKGIDEIIRHFGIKLEETMSFGDGGNDISMLRHAA T0303 192 :VGLTYGYN 1ymqA 224 :IGVAMGQA T0303 201 :NIPIAQS 1ymqA 232 :KEDVKAA T0303 209 :PDWIFDDFAD 1ymqA 239 :ADYVTAPIDE T0303 219 :IL 1ymqA 251 :IS Number of specific fragments extracted= 10 number of extra gaps= 0 total=1195 Number of alignments=128 # 1ymqA read from 1ymqA/merged-good-all-a2m # found chain 1ymqA in template set Warning: unaligning (T0303)F4 because first residue in template chain is (1ymqA)T2 T0303 5 :KLIGFDLDGTLVNS 1ymqA 3 :KALFFDIDGTLVSF T0303 92 :NISRLYPNVKETLEALKAQGYILAVVTNKPTKHVQ 1ymqA 17 :ETHRIPSSTIEALEAAHAKGLKIFIATGRPKAIIN T0303 127 :PILTAFGI 1ymqA 54 :SELQDRNL T0303 138 :FSEML 1ymqA 62 :IDGYI T0303 147 :LPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAG 1ymqA 182 :TAKGDTKQKGIDEIIRHFGIKLEETMSFGDGGNDISMLRHAA T0303 192 :VGLTYGYN 1ymqA 224 :IGVAMGQA T0303 201 :NIPI 1ymqA 232 :KEDV T0303 206 :QSKPDWIFDDFAD 1ymqA 236 :KAAADYVTAPIDE Number of specific fragments extracted= 8 number of extra gaps= 0 total=1203 Number of alignments=129 # 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:# T0303 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 T0303 1 :M 1nf2A 1 :M T0303 4 :FKLIGFDLDGTLVN 1nf2A 2 :YRVFVFDLDGTLLN T0303 18 :SLPDLALSINSALKDV 1nf2A 20 :ISEKDRRNIEKLSRKC T0303 69 :ELTEDE 1nf2A 82 :KIPPEV T0303 100 :VKETLEALKAQGYI 1nf2A 88 :AKDIIEYIKPLNVH T0303 116 :VVTNKPTKHVQPILTAFGID 1nf2A 110 :LYSEKDNEEIKSYARHSNVD T0303 141 :MLGGQSL 1nf2A 130 :YRVEPNL T0303 148 :PEIKPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVV 1nf2A 186 :PKNVDKGKALRFLRERMNWKKEEIVVFGDNENDLFMFEEAGLRVA Number of specific fragments extracted= 8 number of extra gaps= 0 total=1211 Number of alignments=130 # 1nf2A read from 1nf2A/merged-good-all-a2m # found chain 1nf2A in template set T0303 1 :M 1nf2A 1 :M T0303 4 :FKLIGFDLDGTLVN 1nf2A 2 :YRVFVFDLDGTLLN T0303 92 :NISRLYPNVKETLEALKAQ 1nf2A 16 :DNLEISEKDRRNIEKLSRK T0303 112 :YILAVVTNKP 1nf2A 35 :CYVVFASGRM T0303 146 :SLPEIK 1nf2A 186 :PKNVDK T0303 154 :PAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVV 1nf2A 192 :GKALRFLRERMNWKKEEIVVFGDNENDLFMFEEAGLRVA T0303 197 :GYNYNIPIAQS 1nf2A 231 :MENAIEKVKEA T0303 209 :PDWIFDDF 1nf2A 242 :SDIVTLTN Number of specific fragments extracted= 8 number of extra gaps= 0 total=1219 Number of alignments=131 # 1nf2A read from 1nf2A/merged-good-all-a2m # found chain 1nf2A in template set Warning: unaligning (T0303)Q3 because first residue in template chain is (1nf2A)M1 T0303 4 :FKLIGFDLDG 1nf2A 2 :YRVFVFDLDG T0303 88 :ENLCNISRLYPNVKETLEALKAQ 1nf2A 12 :TLLNDNLEISEKDRRNIEKLSRK T0303 112 :YILAVVTNKP 1nf2A 35 :CYVVFASGRM T0303 122 :TKHVQPILTAFGID 1nf2A 116 :NEEIKSYARHSNVD T0303 147 :LPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVV 1nf2A 185 :VPKNVDKGKALRFLRERMNWKKEEIVVFGDNENDLFMFEEAGLRVA Number of specific fragments extracted= 5 number of extra gaps= 0 total=1224 Number of alignments=132 # 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 # T0303 read from 1qq5A/merged-good-all-a2m # 1qq5A read from 1qq5A/merged-good-all-a2m # found chain 1qq5A in training set T0303 1 :M 1qq5A 1 :M T0303 4 :FKLIGFDLDGTLVN 1qq5A 2 :IKAVVFDAYGTLFD T0303 18 :SLPDLALSINSALKDV 1qq5A 30 :RGEYITQVWRQKQLEY T0303 41 :NLVMTWIGN 1qq5A 46 :SWLRALMGR T0303 50 :GADVLSQRAVDWACTQAEKELTEDEFKYFK 1qq5A 57 :DFWSVTREALAYTLGTLGLEPDESFLADMA T0303 88 :ENL 1qq5A 87 :QAY T0303 92 :NISRLYPNVKETLEAL 1qq5A 90 :NRLTPYPDAAQCLAEL T0303 110 :QGYILAVVTNKPTKHVQPILTAFGIDHLFSEMLGGQSLPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVVGLTY 1qq5A 106 :APLKRAILSNGAPDMLQALVANAGLTDSFDAVISVDAKRVFKPHPDSYALVEEVLGVTPAEVLFVSSNGFDVGGAKNFGFSVARVAR T0303 198 :YN 1qq5A 205 :GT T0303 202 :IP 1qq5A 207 :IA T0303 204 :IAQSKPDWIFDDFADILKI 1qq5A 222 :TYAEAPDFVVPALGDLPRL Number of specific fragments extracted= 11 number of extra gaps= 0 total=1235 Number of alignments=133 # 1qq5A read from 1qq5A/merged-good-all-a2m # found chain 1qq5A in training set T0303 1 :M 1qq5A 1 :M T0303 4 :FKLIGFDLDGTLVN 1qq5A 2 :IKAVVFDAYGTLFD T0303 18 :SLPDLALSINSALKDV 1qq5A 30 :RGEYITQVWRQKQLEY T0303 39 :SENLVMTWIGNGADVLSQRAVDWACTQAEKELTEDEFKYFKRQF 1qq5A 46 :SWLRALMGRYADFWSVTREALAYTLGTLGLEPDESFLADMAQAY T0303 92 :NISRLYPNVKETLEAL 1qq5A 90 :NRLTPYPDAAQCLAEL T0303 110 :QGYILAVVTNKPTKHVQPILTAFGIDHLFSEMLGGQSLPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVVGLTYGYN 1qq5A 106 :APLKRAILSNGAPDMLQALVANAGLTDSFDAVISVDAKRVFKPHPDSYALVEEVLGVTPAEVLFVSSNGFDVGGAKNFGFSVARVARLSQ T0303 201 :NIPIAQSK 1qq5A 218 :MREETYAE T0303 209 :PDWIFDDFADILKI 1qq5A 227 :PDFVVPALGDLPRL Number of specific fragments extracted= 8 number of extra gaps= 0 total=1243 Number of alignments=134 # 1qq5A read from 1qq5A/merged-good-all-a2m # found chain 1qq5A in training set Warning: unaligning (T0303)Q3 because first residue in template chain is (1qq5A)M1 T0303 4 :FKLIGFDLDGTLV 1qq5A 2 :IKAVVFDAYGTLF T0303 17 :NSLPDLALSINSALKDVNLPQASENLVM 1qq5A 57 :DFWSVTREALAYTLGTLGLEPDESFLAD T0303 78 :F 1qq5A 85 :M T0303 88 :ENLCNISRLYPNVKETLEAL 1qq5A 86 :AQAYNRLTPYPDAAQCLAEL T0303 110 :QGYILAVVTNKPTKHVQPILTAFGIDHLFSEMLGGQSLPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVVGLTYGY 1qq5A 106 :APLKRAILSNGAPDMLQALVANAGLTDSFDAVISVDAKRVFKPHPDSYALVEEVLGVTPAEVLFVSSNGFDVGGAKNFGFSVARVARLS T0303 200 :YNIPIAQSKPDWIFDDFADILKITQ 1qq5A 218 :MREETYAEAPDFVVPALGDLPRLVR Number of specific fragments extracted= 6 number of extra gaps= 0 total=1249 Number of alignments=135 # 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:# T0303 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 T0303 1 :M 2fi1A 4 :M T0303 3 :QFKLIGFDLDGTLVNSLPDLALSINSALKDVNLP 2fi1A 5 :KYHDYIWDLGGTLLDNYETSTAAFVETLALYGIT T0303 38 :ASENLVMTWIGNGADVLSQRAVD 2fi1A 39 :QDHDSVYQALKVSTPFAIETFAP T0303 69 :ELTE 2fi1A 62 :NLEN T0303 78 :FKRQFGFYYGENL 2fi1A 66 :FLEKYKENEAREL T0303 92 :NISRLYPNVKETLEALKAQGYILAVVTNKPTK 2fi1A 79 :EHPILFEGVSDLLEDISNQGGRHFLVSHRNDQ T0303 125 :VQPILTAFGIDHLFSEMLGGQSLPEIKPHPAPFYYLCGKFGL 2fi1A 111 :VLEILEKTSIAAYFTEVVTSSSGFKRKPNPESMLYLREKYQI T0303 169 :KQILFVGDSQNDIFAAHSAGCAV 2fi1A 153 :SSGLVIGDRPIDIEAGQAAGLDT T0303 211 :WIFDDFADILKIT 2fi1A 176 :HLFTSIVNLRQVL Number of specific fragments extracted= 9 number of extra gaps= 0 total=1258 Number of alignments=136 # 2fi1A read from 2fi1A/merged-good-all-a2m # found chain 2fi1A in template set Warning: unaligning (T0303)T2 because first residue in template chain is (2fi1A)M4 T0303 3 :QFKLIGFDLDGTLVNSLPDLALSINSALKDVNLP 2fi1A 5 :KYHDYIWDLGGTLLDNYETSTAAFVETLALYGIT T0303 38 :ASENLVMTWIGNGADVLSQRAVD 2fi1A 39 :QDHDSVYQALKVSTPFAIETFAP T0303 67 :EKELTEDEFKYFKRQF 2fi1A 62 :NLENFLEKYKENEARE T0303 86 :Y 2fi1A 78 :L T0303 92 :NISRLYPNVKETLEALKAQGYILAVVTNKPTK 2fi1A 79 :EHPILFEGVSDLLEDISNQGGRHFLVSHRNDQ T0303 125 :VQPILTAFGIDHLFSEMLGGQSLPEIKPHPAPFYYLCGKFGL 2fi1A 111 :VLEILEKTSIAAYFTEVVTSSSGFKRKPNPESMLYLREKYQI T0303 169 :KQILFVGDSQNDIFAAHSAGCAV 2fi1A 153 :SSGLVIGDRPIDIEAGQAAGLDT T0303 211 :WIFDDFADILKI 2fi1A 176 :HLFTSIVNLRQV Number of specific fragments extracted= 8 number of extra gaps= 0 total=1266 Number of alignments=137 # 2fi1A read from 2fi1A/merged-good-all-a2m # found chain 2fi1A in template set Warning: unaligning (T0303)T2 because first residue in template chain is (2fi1A)M4 T0303 3 :QFKLIGFDLDGTLVNSLPDLALSINSALKDVNLPQASENLVMTWIGNGADVLSQRAVD 2fi1A 5 :KYHDYIWDLGGTLLDNYETSTAAFVETLALYGITQDHDSVYQALKVSTPFAIETFAPN T0303 71 :TEDEFKYFKRQFGF 2fi1A 63 :LENFLEKYKENEAR T0303 90 :LCNISRLYPNVKETLEALKAQGYILAVVTNKPTK 2fi1A 77 :ELEHPILFEGVSDLLEDISNQGGRHFLVSHRNDQ T0303 125 :VQPILTAFGIDHLFSEMLGGQSLPEIKPHPAPFYYLCGKFGLY 2fi1A 111 :VLEILEKTSIAAYFTEVVTSSSGFKRKPNPESMLYLREKYQIS T0303 170 :QILFVGDSQNDIFAAHSAGCAV 2fi1A 154 :SGLVIGDRPIDIEAGQAAGLDT T0303 211 :WIFDDFADILKIT 2fi1A 176 :HLFTSIVNLRQVL Number of specific fragments extracted= 6 number of extra gaps= 0 total=1272 Number of alignments=138 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1q92A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0303 read from 1q92A/merged-good-all-a2m # 1q92A read from 1q92A/merged-good-all-a2m # found chain 1q92A in training set Warning: unaligning (T0303)T2 because first residue in template chain is (1q92A)G33 Warning: unaligning (T0303)A29 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)F61 Warning: unaligning (T0303)L30 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)F61 Warning: unaligning (T0303)E40 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)E70 Warning: unaligning (T0303)N41 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)E70 Warning: unaligning (T0303)G48 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)G74 Warning: unaligning (T0303)Q56 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)R83 Warning: unaligning (T0303)R57 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)R83 Warning: unaligning (T0303)Y97 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)P109 Warning: unaligning (T0303)P98 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)P109 Warning: unaligning (T0303)L107 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)A119 Warning: unaligning (T0303)K108 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)A119 Warning: unaligning (T0303)F132 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)F151 Warning: unaligning (T0303)C189 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1q92A)E190 Warning: unaligning (T0303)A190 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1q92A)E190 Warning: unaligning (T0303)T195 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)A196 Warning: unaligning (T0303)Y196 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)A196 Warning: unaligning (T0303)I212 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1q92A)L211 Warning: unaligning (T0303)F213 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1q92A)L211 T0303 3 :QFKLIGFDLDGTLVNSLPDLALSINS 1q92A 34 :RALRVLVDMDGVLADFEGGFLRKFRA T0303 34 :NLPQAS 1q92A 63 :DQPFIA T0303 49 :NGADVLS 1q92A 75 :FWVSEQY T0303 58 :AVD 1q92A 84 :LRP T0303 73 :DEFKYFKRQFG 1q92A 87 :GLSEKAISIWE T0303 88 :ENLCNISRL 1q92A 99 :KNFFFELEP T0303 99 :NVKETLEA 1q92A 110 :GAVEAVKE T0303 109 :AQ 1q92A 120 :SL T0303 111 :GYILAVVTN 1q92A 123 :NTDVFICTS T0303 120 :KPTKHVQPILTA 1q92A 138 :YCPYEKYAWVEK T0303 134 :IDHLFSEMLGGQSLPEIKPH 1q92A 152 :GPDFLEQIVLTRDKTVVSAD T0303 172 :LFVGDSQ 1q92A 172 :LLIDDRP T0303 188 :G 1q92A 188 :S T0303 191 :VVGL 1q92A 191 :HVLF T0303 197 :GYNYNIPIAQ 1q92A 197 :CHNQHLQLQP T0303 209 :PDW 1q92A 207 :PRR T0303 214 :D 1q92A 212 :H T0303 215 :DFADILK 1q92A 217 :DWKAILD Number of specific fragments extracted= 18 number of extra gaps= 10 total=1290 Number of alignments=139 # 1q92A read from 1q92A/merged-good-all-a2m # found chain 1q92A in training set Warning: unaligning (T0303)T2 because first residue in template chain is (1q92A)G33 Warning: unaligning (T0303)V33 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)F61 Warning: unaligning (T0303)T45 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)R83 Warning: unaligning (T0303)W46 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)R83 Warning: unaligning (T0303)Y97 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)P109 Warning: unaligning (T0303)P98 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)P109 Warning: unaligning (T0303)L107 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)A119 Warning: unaligning (T0303)K108 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)A119 Warning: unaligning (T0303)F132 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)F151 Warning: unaligning (T0303)C189 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1q92A)E190 Warning: unaligning (T0303)A190 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1q92A)E190 Warning: unaligning (T0303)T195 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)A196 Warning: unaligning (T0303)Y196 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)A196 Warning: unaligning (T0303)I212 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1q92A)L211 Warning: unaligning (T0303)F213 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1q92A)L211 T0303 3 :QFKLIGFDLDGTLVNSLPDLALSINS 1q92A 34 :RALRVLVDMDGVLADFEGGFLRKFRA T0303 34 :NLPQA 1q92A 63 :DQPFI T0303 39 :SENLVM 1q92A 76 :WVSEQY T0303 47 :IGNGADVLSQRAV 1q92A 84 :LRPGLSEKAISIW T0303 67 :E 1q92A 97 :E T0303 87 :GENLCNISRL 1q92A 98 :SKNFFFELEP T0303 99 :NVKETLEA 1q92A 110 :GAVEAVKE T0303 109 :AQG 1q92A 120 :SLQ T0303 112 :YILAVVTNKP 1q92A 124 :TDVFICTSPI T0303 122 :TKHVQPILTA 1q92A 140 :PYEKYAWVEK T0303 133 :G 1q92A 152 :G T0303 135 :DHLFSEMLGGQSLPEIKPH 1q92A 153 :PDFLEQIVLTRDKTVVSAD T0303 172 :LFVGDSQN 1q92A 172 :LLIDDRPD T0303 188 :G 1q92A 188 :S T0303 191 :VVGL 1q92A 191 :HVLF T0303 197 :GYNYNIPIAQ 1q92A 197 :CHNQHLQLQP T0303 209 :PDW 1q92A 207 :PRR T0303 214 :D 1q92A 212 :H T0303 215 :DFADILK 1q92A 217 :DWKAILD Number of specific fragments extracted= 19 number of extra gaps= 8 total=1309 Number of alignments=140 # 1q92A read from 1q92A/merged-good-all-a2m # found chain 1q92A in training set Warning: unaligning (T0303)A29 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)F61 Warning: unaligning (T0303)L30 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)F61 Warning: unaligning (T0303)A38 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)E70 Warning: unaligning (T0303)S39 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)E70 Warning: unaligning (T0303)V59 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)G74 Warning: unaligning (T0303)D60 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)G74 Warning: unaligning (T0303)K68 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)R83 Warning: unaligning (T0303)E69 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)R83 Warning: unaligning (T0303)Y97 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)P109 Warning: unaligning (T0303)P98 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)P109 Warning: unaligning (T0303)L107 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)A119 Warning: unaligning (T0303)K108 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)A119 Warning: unaligning (T0303)F132 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)F151 Warning: unaligning (T0303)G133 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)F151 Warning: unaligning (T0303)C189 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1q92A)E190 Warning: unaligning (T0303)A190 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1q92A)E190 Warning: unaligning (T0303)T195 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)A196 Warning: unaligning (T0303)Y196 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)A196 Warning: unaligning (T0303)W211 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1q92A)L211 Warning: unaligning (T0303)I212 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1q92A)L211 T0303 5 :KLIGFDLDGTLVNSLPDLALSINS 1q92A 36 :LRVLVDMDGVLADFEGGFLRKFRA T0303 31 :KDVNLPQ 1q92A 62 :PDQPFIA T0303 57 :RA 1q92A 71 :DR T0303 61 :WACTQAE 1q92A 75 :FWVSEQY T0303 70 :LTEDEFKYFKRQFG 1q92A 84 :LRPGLSEKAISIWE T0303 88 :ENLCNISRL 1q92A 99 :KNFFFELEP T0303 99 :NVKETLEA 1q92A 110 :GAVEAVKE T0303 109 :AQ 1q92A 120 :SL T0303 111 :GYILAVVTNKP 1q92A 123 :NTDVFICTSPI T0303 122 :TKHVQPILTA 1q92A 140 :PYEKYAWVEK T0303 134 :IDHLFSEMLGGQSLPEIKPH 1q92A 152 :GPDFLEQIVLTRDKTVVSAD T0303 172 :LFVGDSQ 1q92A 172 :LLIDDRP T0303 188 :G 1q92A 188 :S T0303 191 :VVGL 1q92A 191 :HVLF T0303 197 :GYNYNIPI 1q92A 197 :CHNQHLQL T0303 206 :QSKPD 1q92A 205 :QPPRR T0303 213 :F 1q92A 212 :H T0303 214 :DDFADILK 1q92A 216 :DDWKAILD Number of specific fragments extracted= 18 number of extra gaps= 10 total=1327 Number of alignments=141 # 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 # T0303 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 (T0303)F9 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1qq7A)A9 Warning: unaligning (T0303)L11 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1qq7A)A9 T0303 1 :M 1qq7A 1 :M T0303 4 :FKLIG 1qq7A 2 :IKAVV T0303 12 :DGTLVN 1qq7A 10 :YGTLFD T0303 18 :SLPDLALS 1qq7A 19 :VADATERA T0303 26 :INSALKDV 1qq7A 35 :TQVWRQKQ T0303 38 :ASENLVMTWIGN 1qq7A 43 :LEYSWLRALMGR T0303 50 :GADVLSQRAVDWACTQAEKELTEDEFKYF 1qq7A 57 :DFWSVTREALAYTLGTLGLEPDESFLADM T0303 87 :GENL 1qq7A 86 :AQAY T0303 92 :NISRLYPNVKETLEAL 1qq7A 90 :NRLTPYPDAAQCLAEL T0303 110 :QGYILAVVTNKPTKHVQPILTAFGIDHLFSEMLGGQSLPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVVGLTY 1qq7A 106 :APLKRAILSNGAPDMLQALVANAGLTDSFDAVISVDAKRVFKPHPDSYALVEEVLGVTPAEVLFVSSNGFDVGGAKNFGFSVARVAR T0303 201 :NIP 1qq7A 206 :TIA T0303 204 :IAQSKPDWIFDDFADILKI 1qq7A 222 :TYAEAPDFVVPALGDLPRL Number of specific fragments extracted= 12 number of extra gaps= 0 total=1339 Number of alignments=142 # 1qq7A read from 1qq7A/merged-good-all-a2m # found chain 1qq7A in template set Warning: unaligning (T0303)F9 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1qq7A)A9 Warning: unaligning (T0303)L11 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1qq7A)A9 T0303 1 :M 1qq7A 1 :M T0303 4 :FKLIG 1qq7A 2 :IKAVV T0303 12 :DGTLVN 1qq7A 10 :YGTLFD T0303 18 :SLPDLALSINSALKDV 1qq7A 30 :RGEYITQVWRQKQLEY T0303 39 :SENLVMTWIGNGADVLSQRAVDWACTQAEKELTEDEFKYFKRQF 1qq7A 46 :SWLRALMGRYADFWSVTREALAYTLGTLGLEPDESFLADMAQAY T0303 92 :NISRLYPNVKETLEAL 1qq7A 90 :NRLTPYPDAAQCLAEL T0303 110 :QGYILAVVTNKPTKHVQPILTAFGIDHLFSEMLGGQSLPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVVGLTYGYN 1qq7A 106 :APLKRAILSNGAPDMLQALVANAGLTDSFDAVISVDAKRVFKPHPDSYALVEEVLGVTPAEVLFVSSNGFDVGGAKNFGFSVARVARLSQ T0303 200 :YNIPIAQSKPDWIFDDFADILKI 1qq7A 218 :MREETYAEAPDFVVPALGDLPRL Number of specific fragments extracted= 8 number of extra gaps= 0 total=1347 Number of alignments=143 # 1qq7A read from 1qq7A/merged-good-all-a2m # found chain 1qq7A in template set Warning: unaligning (T0303)Q3 because first residue in template chain is (1qq7A)M1 Warning: unaligning (T0303)F9 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1qq7A)A9 Warning: unaligning (T0303)L11 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1qq7A)A9 T0303 4 :FKLIG 1qq7A 2 :IKAVV T0303 12 :DGTLV 1qq7A 10 :YGTLF T0303 17 :NSLPDLALSINSALKDVNLPQASENLVM 1qq7A 57 :DFWSVTREALAYTLGTLGLEPDESFLAD T0303 87 :GENLCNISRLYPNVKETLEAL 1qq7A 85 :MAQAYNRLTPYPDAAQCLAEL T0303 110 :QGYILAVVTNKPTKHVQPILTAFGIDHLFSEMLGGQSLPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVVGLTYGY 1qq7A 106 :APLKRAILSNGAPDMLQALVANAGLTDSFDAVISVDAKRVFKPHPDSYALVEEVLGVTPAEVLFVSSNGFDVGGAKNFGFSVARVARLS T0303 200 :YNIPIAQSKPDWIFDDFADILKITQ 1qq7A 218 :MREETYAEAPDFVVPALGDLPRLVR Number of specific fragments extracted= 6 number of extra gaps= 0 total=1353 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:# T0303 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 T0303 1 :M 1aq6A 1 :M T0303 4 :FKLIGFDLDGTLVN 1aq6A 2 :IKAVVFDAYGTLFD T0303 18 :SLPDLALS 1aq6A 19 :VADATERA T0303 26 :INSALKDV 1aq6A 35 :TQVWRQKQ T0303 38 :ASENLVMTWIGN 1aq6A 43 :LEYSWLRALMGR T0303 50 :GADVLSQRAVDWACTQAEKELTEDEFKYFK 1aq6A 57 :DFWGVTREALAYTLGTLGLEPDESFLADMA T0303 88 :ENL 1aq6A 87 :QAY T0303 92 :NISRLYPNVKETLEAL 1aq6A 90 :NRLTPYPDAAQCLAEL T0303 110 :QGYILAVVTNKPTKHVQPILTAFGIDHLFSEMLGGQSLPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVVGLTY 1aq6A 106 :APLKRAILSNGAPDMLQALVANAGLTDSFDAVISVDAKRVFKPHPDSYALVEEVLGVTPAEVLFVSSNGFDVGGAKNFGFSVARVAR T0303 201 :NIPIAQSKPDWIFDDFADILKI 1aq6A 219 :REETYAEAPDFVVPALGDLPRL Number of specific fragments extracted= 10 number of extra gaps= 0 total=1363 Number of alignments=145 # 1aq6A read from 1aq6A/merged-good-all-a2m # found chain 1aq6A in template set T0303 1 :M 1aq6A 1 :M T0303 4 :FKLIGFDLDGTLVN 1aq6A 2 :IKAVVFDAYGTLFD T0303 18 :SLPDLALSINSALKDV 1aq6A 30 :RGEYITQVWRQKQLEY T0303 39 :SENLVMTWIGNGADVLSQRAVDWACTQAEKELTEDEFKYFKRQF 1aq6A 46 :SWLRALMGRYADFWGVTREALAYTLGTLGLEPDESFLADMAQAY T0303 92 :NISRLYPNVKETLEAL 1aq6A 90 :NRLTPYPDAAQCLAEL T0303 110 :QGYILAVVTNKPTKHVQPILTAFGIDHLFSEMLGGQSLPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVVGLTYGYN 1aq6A 106 :APLKRAILSNGAPDMLQALVANAGLTDSFDAVISVDAKRVFKPHPDSYALVEEVLGVTPAEVLFVSSNGFDVGGAKNFGFSVARVARLSQ T0303 201 :NIPIAQSK 1aq6A 218 :MREETYAE T0303 209 :PDWIFDDFADILKI 1aq6A 227 :PDFVVPALGDLPRL Number of specific fragments extracted= 8 number of extra gaps= 0 total=1371 Number of alignments=146 # 1aq6A read from 1aq6A/merged-good-all-a2m # found chain 1aq6A in template set Warning: unaligning (T0303)Q3 because first residue in template chain is (1aq6A)M1 T0303 4 :FKLIGFDLDGTLV 1aq6A 2 :IKAVVFDAYGTLF T0303 17 :NSLPDLALSINSALKDVNLPQASENLVM 1aq6A 57 :DFWGVTREALAYTLGTLGLEPDESFLAD T0303 87 :GENLCNISRLYPNVKETLEAL 1aq6A 85 :MAQAYNRLTPYPDAAQCLAEL T0303 110 :QGYILAVVTNKPTKHVQPILTAFGIDHLFSEMLGGQSLPEIKPHPAPFYYLCGKFGLYPKQILFVGDSQNDIFAAHSAGCAVVGLTYGY 1aq6A 106 :APLKRAILSNGAPDMLQALVANAGLTDSFDAVISVDAKRVFKPHPDSYALVEEVLGVTPAEVLFVSSNGFDVGGAKNFGFSVARVARLS T0303 200 :YNIPIAQSKPDWIFDDFADILKITQ 1aq6A 218 :MREETYAEAPDFVVPALGDLPRLVR Number of specific fragments extracted= 5 number of extra gaps= 0 total=1376 Number of alignments=147 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mh9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1mh9A expands to /projects/compbio/data/pdb/1mh9.pdb.gz 1mh9A:# T0303 read from 1mh9A/merged-good-all-a2m # 1mh9A read from 1mh9A/merged-good-all-a2m # adding 1mh9A to template set # found chain 1mh9A in template set Warning: unaligning (T0303)A205 because of BadResidue code BAD_PEPTIDE in next template residue (1mh9A)P206 Warning: unaligning (T0303)Q206 because of BadResidue code BAD_PEPTIDE at template residue (1mh9A)P206 T0303 3 :Q 1mh9A 35 :A T0303 5 :KLIGFDLDGTLVNSLPDLALSINSA 1mh9A 36 :LRVLVDMDGVLADFEGGFLRKFRAR T0303 34 :NLPQASEN 1mh9A 63 :DQPFIALE T0303 49 :NGADVLSQRAVD 1mh9A 72 :RRGFWVSEQYGR T0303 70 :LTEDEFKYFKRQFG 1mh9A 84 :LRPGLSEKAISIWE T0303 88 :ENLCNISRLYPNVKETLEALKAQ 1mh9A 99 :KNFFFELEPLPGAVEAVKEMASL T0303 111 :GYILAVVTN 1mh9A 123 :NTDVFICTS T0303 120 :KPTKHVQPILTAF 1mh9A 134 :KMFKYCPYEKYAW T0303 133 :G 1mh9A 152 :G T0303 135 :DHLFSEMLGGQSLPEIKPH 1mh9A 153 :PDFLEQIVLTRDKTVVSAD T0303 172 :LFVGDSQ 1mh9A 172 :LLIDDRP T0303 188 :GCAVVGLTYGYNYNIPI 1mh9A 188 :SWEHVLFTACHNQHLQL T0303 209 :PDWIFD 1mh9A 207 :PRRRLH T0303 215 :DFADILK 1mh9A 217 :DWKAILD Number of specific fragments extracted= 14 number of extra gaps= 1 total=1390 Number of alignments=148 # 1mh9A read from 1mh9A/merged-good-all-a2m # found chain 1mh9A in template set Warning: unaligning (T0303)A205 because of BadResidue code BAD_PEPTIDE in next template residue (1mh9A)P206 Warning: unaligning (T0303)Q206 because of BadResidue code BAD_PEPTIDE at template residue (1mh9A)P206 T0303 5 :KLIGFDLDGTLVNSLPD 1mh9A 36 :LRVLVDMDGVLADFEGG T0303 26 :INSALKDV 1mh9A 53 :FLRKFRAR T0303 34 :NLPQA 1mh9A 63 :DQPFI T0303 39 :SENLVMTWIGNGADVLSQRAV 1mh9A 76 :WVSEQYGRLRPGLSEKAISIW T0303 83 :GF 1mh9A 97 :ES T0303 88 :ENLCNISRLYPNVKETLEALKAQ 1mh9A 99 :KNFFFELEPLPGAVEAVKEMASL T0303 111 :GYILAVVTNKP 1mh9A 123 :NTDVFICTSPI T0303 122 :TKHVQPILTAF 1mh9A 140 :PYEKYAWVEKY T0303 133 :G 1mh9A 152 :G T0303 135 :DHLFSEMLGGQSLPEIKPH 1mh9A 153 :PDFLEQIVLTRDKTVVSAD T0303 172 :LFVGDSQN 1mh9A 172 :LLIDDRPD T0303 188 :GCAVVGLTYGYNYNIPI 1mh9A 188 :SWEHVLFTACHNQHLQL T0303 209 :PDWIFD 1mh9A 207 :PRRRLH T0303 215 :DFADILK 1mh9A 217 :DWKAILD Number of specific fragments extracted= 14 number of extra gaps= 1 total=1404 Number of alignments=149 # 1mh9A read from 1mh9A/merged-good-all-a2m # found chain 1mh9A in template set Warning: unaligning (T0303)Q206 because of BadResidue code BAD_PEPTIDE in next template residue (1mh9A)P206 Warning: unaligning (T0303)S207 because of BadResidue code BAD_PEPTIDE at template residue (1mh9A)P206 T0303 6 :LIGFDLDGTLVNSLPDLALSINSALKDVNLPQAS 1mh9A 37 :RVLVDMDGVLADFEGGFLRKFRARFPDQPFIALE T0303 57 :RAVDWACTQAEKELTEDEFKYFKRQFG 1mh9A 71 :DRRGFWVSEQYGRLRPGLSEKAISIWE T0303 88 :ENLCNISRLYPNVKETLEALKAQ 1mh9A 99 :KNFFFELEPLPGAVEAVKEMASL T0303 111 :GYILAVVTNKP 1mh9A 123 :NTDVFICTSPI T0303 122 :TKHVQPILTAF 1mh9A 140 :PYEKYAWVEKY T0303 134 :IDHLFSEMLGGQSLPEIKPH 1mh9A 152 :GPDFLEQIVLTRDKTVVSAD T0303 172 :LFVGDSQ 1mh9A 172 :LLIDDRP T0303 188 :GCAVVGLTYGYNYNIPI 1mh9A 188 :SWEHVLFTACHNQHLQL T0303 208 :KPDWIFD 1mh9A 207 :PRRRLHS T0303 215 :DFADILK 1mh9A 217 :DWKAILD Number of specific fragments extracted= 10 number of extra gaps= 1 total=1414 Number of alignments=150 # command:# PrintAlignmentsContacts allconstraints.under Using radius: 8.0000 NUMB_ALIGNS: 150 Done printing distance constraints # command: