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/T0324/ # command:# Making conformation for sequence T0324 numbered 1 through 208 Created new target T0324 from T0324.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0324/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0324//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0324/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0324//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0324/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0324/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0324/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 # T0324 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 (T0324)F8 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1j97A)F12 Warning: unaligning (T0324)I10 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1j97A)F12 T0324 2 :TYQALM 1j97A 4 :KKKLIL # choosing archetypes in rotamer library T0324 11 :DGTLTNSQ 1j97A 13 :DSTLVNNE T0324 24 :VMREVLATYGK 1j97A 21 :TIDEIAREAGV T0324 38 :PAQAQKTF 1j97A 32 :EEEVKKIT T0324 46 :PMAAEQAMTEL 1j97A 46 :KLNFEQSLRKR T0324 57 :GIAASEFDHFQA 1j97A 62 :DLPIEKVEKAIK T0324 80 :QIELYPGITSLFEQLPS 1j97A 74 :RITPTEGAEETIKELKN T0324 97 :ELRLGIVTSQRRNELESGMRSYPFMMRMAVTISADDT 1j97A 92 :GYVVAVVSGGFDIAVNKIKEKLGLDYAFANRLIVKDG T0324 134 :PKRK 1j97A 137 :EVLK T0324 140 :PLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAAN 1j97A 145 :GEILEKIAKIEGINLEDTVAVGDGANDISMFKKAG T0324 176 :DFGLAVWG 1j97A 180 :LKIAFCAK T0324 188 :ADH 1j97A 188 :PIL T0324 191 :QKVAHRFQ 1j97A 192 :EKADICIE T0324 199 :KPLDILELF 1j97A 202 :DLREILKYI Number of specific fragments extracted= 14 number of extra gaps= 0 total=14 Number of alignments=1 # 1j97A read from 1j97A/merged-good-all-a2m # found chain 1j97A in template set Warning: unaligning (T0324)F8 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1j97A)F12 Warning: unaligning (T0324)I10 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1j97A)F12 T0324 3 :YQALM 1j97A 5 :KKLIL T0324 11 :DGTLTNSQ 1j97A 13 :DSTLVNNE T0324 24 :VMREVLATYGK 1j97A 21 :TIDEIAREAGV T0324 38 :PAQAQKT 1j97A 32 :EEEVKKI T0324 50 :EQAMTEL 1j97A 39 :TKEAMEG T0324 63 :FDHFQAQYEDVMASHYDQIELYPGITSLFEQLP 1j97A 57 :VSLLKDLPIEKVEKAIKRITPTEGAEETIKELK T0324 96 :SELRLGIVTSQRRNELESGMRSYPFMMRMAVTISADDT 1j97A 91 :RGYVVAVVSGGFDIAVNKIKEKLGLDYAFANRLIVKDG T0324 134 :PKR 1j97A 140 :KEN T0324 137 :K 1j97A 144 :K T0324 140 :PLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAAN 1j97A 145 :GEILEKIAKIEGINLEDTVAVGDGANDISMFKKAG T0324 176 :DFGLA 1j97A 180 :LKIAF T0324 184 :MDPNADHQKVAHRF 1j97A 185 :CAKPILKEKADICI T0324 198 :QKPLDILELF 1j97A 201 :RDLREILKYI Number of specific fragments extracted= 13 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 (T0324)F8 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1j97A)F12 Warning: unaligning (T0324)I10 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1j97A)F12 T0324 2 :TYQALM 1j97A 4 :KKKLIL T0324 11 :DGTLTNSQ 1j97A 13 :DSTLVNNE T0324 24 :VMREVLATYGK 1j97A 21 :TIDEIAREAGV T0324 38 :PAQAQKTF 1j97A 32 :EEEVKKIT T0324 46 :PMAAEQAMTELGI 1j97A 46 :KLNFEQSLRKRVS T0324 59 :AASEFDHFQAQY 1j97A 61 :KDLPIEKVEKAI T0324 79 :DQIELYPGITSLFEQLPS 1j97A 73 :KRITPTEGAEETIKELKN T0324 97 :ELRLGIVTSQRRNELESGMRSYPFMMRMAVTISADD 1j97A 92 :GYVVAVVSGGFDIAVNKIKEKLGLDYAFANRLIVKD T0324 135 :KRK 1j97A 138 :VLK T0324 138 :PDPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAAN 1j97A 143 :AKGEILEKIAKIEGINLEDTVAVGDGANDISMFKKAG T0324 176 :DFGLAVWG 1j97A 180 :LKIAFCAK T0324 188 :ADH 1j97A 188 :PIL T0324 191 :QKVAHRFQK 1j97A 192 :EKADICIEK Number of specific fragments extracted= 13 number of extra gaps= 0 total=40 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:# T0324 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 (T0324)T15 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c4nA)H16 Warning: unaligning (T0324)N16 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2c4nA)H16 T0324 1 :MTYQALMFDIDGTL 2c4nA 1 :MTIKNVICDIDGVL T0324 17 :SQPAYTTVMREVLAT 2c4nA 20 :AVPGAAEFLHGIMDK T0324 33 :GKP 2c4nA 35 :GLP T0324 36 :FSPAQAQKTF 2c4nA 47 :QTGQDLANRF T0324 46 :PMAAEQAMTEL 2c4nA 92 :EGALIHELYKA T0324 57 :GIAASEFDHFQAQYE 2c4nA 121 :SYNWDMMHKAAYFVA T0324 96 :SELRL 2c4nA 136 :NGARF T0324 102 :IVTS 2c4nA 141 :IATN T0324 131 :DDT 2c4nA 145 :PDT T0324 135 :KRKPDPLPLLTALEKVNVAPQNALFIGDSV 2c4nA 174 :VGKPSPWIIRAALNKMQAHSEETVIVGDNL T0324 165 :SDEQTAQAANVDFGLAVWGMDPNADH 2c4nA 205 :TDILAGFQAGLETILVLSGVSSLDDI T0324 191 :QKVAHRFQKPLD 2c4nA 235 :FRPSWIYPSVAE Number of specific fragments extracted= 12 number of extra gaps= 1 total=52 Number of alignments=4 # 2c4nA read from 2c4nA/merged-good-all-a2m # found chain 2c4nA in template set Warning: unaligning (T0324)T15 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c4nA)H16 Warning: unaligning (T0324)N16 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2c4nA)H16 T0324 1 :MTYQALMFDIDGTL 2c4nA 1 :MTIKNVICDIDGVL T0324 80 :QIELYPGITSLFEQLP 2c4nA 17 :DNVAVPGAAEFLHGIM T0324 96 :SELRLGIVTSQ 2c4nA 34 :KGLPLVLLTNY T0324 107 :RRNELESGMRSYPFMMRMAVTIS 2c4nA 48 :TGQDLANRFATAGVDVPDSVFYT T0324 130 :ADDTPKRKPDPLPLLTALEKVNVAPQNALFIGDSV 2c4nA 169 :RKPFYVGKPSPWIIRAALNKMQAHSEETVIVGDNL T0324 165 :SDEQTAQAANVDFGLAVWGMDPNADH 2c4nA 205 :TDILAGFQAGLETILVLSGVSSLDDI T0324 191 :QKVAHRFQKPLD 2c4nA 235 :FRPSWIYPSVAE Number of specific fragments extracted= 7 number of extra gaps= 1 total=59 Number of alignments=5 # 2c4nA read from 2c4nA/merged-good-all-a2m # found chain 2c4nA in template set Warning: unaligning (T0324)T15 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c4nA)H16 Warning: unaligning (T0324)N16 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2c4nA)H16 T0324 1 :MTYQALMFDIDGTL 2c4nA 1 :MTIKNVICDIDGVL T0324 17 :S 2c4nA 17 :D T0324 81 :IELYPGITSLFEQLPS 2c4nA 18 :NVAVPGAAEFLHGIMD T0324 97 :ELRLGIVTSQ 2c4nA 35 :GLPLVLLTNY T0324 107 :RRNELESGMRSYPF 2c4nA 48 :TGQDLANRFATAGV T0324 121 :MMRM 2c4nA 65 :DSVF T0324 125 :AVTISADD 2c4nA 86 :KAYVVGEG T0324 134 :PKRKPDPLPLLTALEKVNVAPQNALFIGDSV 2c4nA 173 :YVGKPSPWIIRAALNKMQAHSEETVIVGDNL T0324 165 :SDEQTAQAANVDFGLAVWGMDPNADH 2c4nA 205 :TDILAGFQAGLETILVLSGVSSLDDI T0324 191 :QKVAHRFQKPLD 2c4nA 235 :FRPSWIYPSVAE Number of specific fragments extracted= 10 number of extra gaps= 1 total=69 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 # T0324 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 (T0324)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gfhA)D12 Warning: unaligning (T0324)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gfhA)D12 T0324 2 :TYQALM 2gfhA 5 :RVRAVF T0324 10 :IDGTLTNSQPAYTTVMREVLATY 2gfhA 13 :LDNTLIDTAGASRRGMLEVIKLL T0324 33 :GKPFSP 2gfhA 38 :KYHYKE T0324 39 :AQAQKTF 2gfhA 46 :EIICDKV T0324 46 :PMAAEQA 2gfhA 73 :TSHWEEA T0324 57 :GIAASEFDHFQAQYEDVMAS 2gfhA 87 :ADNRKLAEECYFLWKSTRLQ T0324 80 :QIELYPGITSLFEQLPSELRLGIVTSQRRNELESGMRSYPFMMRMAVTISADDTPKRKPDPLPLLTALEKVNVAPQNALFIGDSV 2gfhA 107 :HMILADDVKAMLTELRKEVRLLLLTNGDRQTQREKIEACACQSYFDAIVIGGEQKEEKPAPSIFYHCCDLLGVQPGDCVMVGDTL T0324 165 :SDEQTAQAANV 2gfhA 193 :TDIQGGLNAGL T0324 176 :DFGLAVWGMDPNADH 2gfhA 205 :ATVWINKSGRVPLTS T0324 191 :QKVAHRFQKPLDILELFK 2gfhA 221 :PMPHYMVSSVLELPALLQ Number of specific fragments extracted= 10 number of extra gaps= 1 total=79 Number of alignments=7 # 2gfhA read from 2gfhA/merged-good-all-a2m # found chain 2gfhA in template set Warning: unaligning (T0324)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gfhA)D12 Warning: unaligning (T0324)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gfhA)D12 T0324 2 :TYQALM 2gfhA 5 :RVRAVF T0324 10 :IDGTLTNSQPAYTTVMREVLATY 2gfhA 13 :LDNTLIDTAGASRRGMLEVIKLL T0324 41 :AQKTFPMAAEQAMTEL 2gfhA 36 :QSKYHYKEEAEIICDK T0324 57 :GIAASEFDHFQAQYEDVMASH 2gfhA 87 :ADNRKLAEECYFLWKSTRLQH T0324 81 :IELYPGITSLFEQLPSELRLGIVTSQRRNELESGMRSYPFMMRMAVTISADDTPKRKPDPLPLLTALEKVNVAPQNALFIGDSV 2gfhA 108 :MILADDVKAMLTELRKEVRLLLLTNGDRQTQREKIEACACQSYFDAIVIGGEQKEEKPAPSIFYHCCDLLGVQPGDCVMVGDTL T0324 165 :SDEQTAQAANVD 2gfhA 193 :TDIQGGLNAGLK T0324 177 :FGLAVWGMDPNADH 2gfhA 206 :TVWINKSGRVPLTS T0324 191 :QKVAHRFQKPLDILELFK 2gfhA 221 :PMPHYMVSSVLELPALLQ Number of specific fragments extracted= 8 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 (T0324)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gfhA)D12 Warning: unaligning (T0324)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gfhA)D12 Warning: unaligning (T0324)Q40 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gfhA)C67 T0324 2 :TYQALM 2gfhA 5 :RVRAVF T0324 10 :IDGTLTNSQPAYTTVMREVLATY 2gfhA 13 :LDNTLIDTAGASRRGMLEVIKLL T0324 41 :AQKTFPMAAEQAMTELGIAASEFDHFQAQYEDVMASHYDQIELYPGITSLFEQLPSELRLGIVTSQRRNELESGMRSYPFMMRMAVTISADDTPKRKPDPLPLLTALEKVNVAPQNALFIGDSV 2gfhA 68 :ITDVRTSHWEEAIQETKGGADNRKLAEECYFLWKSTRLQHMILADDVKAMLTELRKEVRLLLLTNGDRQTQREKIEACACQSYFDAIVIGGEQKEEKPAPSIFYHCCDLLGVQPGDCVMVGDTL T0324 165 :SDEQTAQAANVDFGLAVWGMDPNADH 2gfhA 193 :TDIQGGLNAGLKATVWINKSGRVPLT T0324 191 :QKVAHRFQKPLDILELFK 2gfhA 221 :PMPHYMVSSVLELPALLQ Number of specific fragments extracted= 5 number of extra gaps= 1 total=92 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 # T0324 read from 1wr8A/merged-good-all-a2m # 1wr8A read from 1wr8A/merged-good-all-a2m # found chain 1wr8A in training set Warning: unaligning (T0324)T2 because first residue in template chain is (1wr8A)K2 T0324 3 :YQALMFDIDGTLTN 1wr8A 3 :IKAISIDIDGTITY T0324 17 :SQPAYTTVMREVLA 1wr8A 21 :IHEKALEAIRRAES T0324 32 :YGKPF 1wr8A 35 :LGIPI T0324 37 :SPAQAQK 1wr8A 46 :TVQFAEA T0324 52 :AMTEL 1wr8A 53 :ASILI T0324 57 :GIAASEFDHFQAQYED 1wr8A 80 :LASMDEEWILWNEIRK T0324 77 :HYDQIELYPGITS 1wr8A 96 :RFPNARTSYTMPD T0324 95 :PSE 1wr8A 117 :RET T0324 106 :QRRNELESGMRSYPFMMR 1wr8A 120 :INVETVREIINELNLNLV T0324 124 :MAVTISADDTP 1wr8A 143 :FAIHVKKPWIN T0324 139 :DPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFG 1wr8A 154 :KGSGIEKASEFLGIKPKEVAHVGDGENDLDAFKVVGYKVA T0324 180 :A 1wr8A 194 :V T0324 186 :PNADH 1wr8A 195 :AQAPK T0324 191 :QKVAHRFQK 1wr8A 203 :ENADYVTKK T0324 200 :PLDILELF 1wr8A 221 :IYHILEKF Number of specific fragments extracted= 15 number of extra gaps= 0 total=107 Number of alignments=10 # 1wr8A read from 1wr8A/merged-good-all-a2m # found chain 1wr8A in training set Warning: unaligning (T0324)T2 because first residue in template chain is (1wr8A)K2 T0324 3 :YQALMFDIDGTLTN 1wr8A 3 :IKAISIDIDGTITY T0324 79 :DQIELYPGITSLFEQLP 1wr8A 17 :PNRMIHEKALEAIRRAE T0324 96 :SELRLGIVTSQR 1wr8A 35 :LGIPIMLVTGNT T0324 108 :RNELESGMRSYPFMMRM 1wr8A 122 :VETVREIINELNLNLVA T0324 125 :AVTISADDTPKRK 1wr8A 142 :GFAIHVKKPWINK T0324 140 :PLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAAN 1wr8A 155 :GSGIEKASEFLGIKPKEVAHVGDGENDLDAFKVVG T0324 178 :GLAVWGMDPNADHQKVAHRFQK 1wr8A 190 :YKVAVAQAPKILKENADYVTKK T0324 201 :LD 1wr8A 214 :GE T0324 203 :ILELF 1wr8A 217 :GAEAI Number of specific fragments extracted= 9 number of extra gaps= 0 total=116 Number of alignments=11 # 1wr8A read from 1wr8A/merged-good-all-a2m # found chain 1wr8A in training set Warning: unaligning (T0324)T2 because first residue in template chain is (1wr8A)K2 T0324 3 :YQALMFDIDGTLT 1wr8A 3 :IKAISIDIDGTIT T0324 17 :SQPAYTTVMREVLATY 1wr8A 21 :IHEKALEAIRRAESLG T0324 46 :PMAAEQAMTELGI 1wr8A 43 :TGNTVQFAEAASI T0324 59 :AASEFDHFQAQYE 1wr8A 82 :SMDEEWILWNEIR T0324 76 :SHYDQIELYPGITS 1wr8A 95 :KRFPNARTSYTMPD T0324 107 :RRNELESGMRSYPFMMRM 1wr8A 121 :NVETVREIINELNLNLVA T0324 125 :AVTISADDTP 1wr8A 144 :AIHVKKPWIN T0324 139 :DPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQA 1wr8A 154 :KGSGIEKASEFLGIKPKEVAHVGDGENDLDAFKV T0324 175 :VDFGLAVWGM 1wr8A 188 :VGYKVAVAQA T0324 187 :NADH 1wr8A 198 :PKIL T0324 191 :QKVAHRFQK 1wr8A 203 :ENADYVTKK T0324 200 :PL 1wr8A 221 :IY Number of specific fragments extracted= 12 number of extra gaps= 0 total=128 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 # T0324 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 T0324 1 :M 1qyiA 1 :M T0324 4 :QALMFDIDGTLTNSQPAYTTVMREVLATY 1qyiA 2 :KKILFDVDGVFLSEERCFDVSALTVYELL T0324 33 :G 1qyiA 41 :H T0324 35 :P 1qyiA 43 :D T0324 36 :FSPAQAQKTF 1qyiA 47 :LTDNDIQDIR T0324 46 :PMAAEQAMTEL 1qyiA 141 :KVGKNNIYAAL T0324 59 :AA 1qyiA 170 :KG T0324 65 :HFQAQYEDVMASHY 1qyiA 172 :ALWTLAQEVYQEWY T0324 79 :DQIEL 1qyiA 209 :YQEII T0324 84 :YPGITSLFEQLPS 1qyiA 217 :VDEVKVLLNDLKG T0324 97 :ELRLGIVTSQRRNELESGMRSYPFMMRM 1qyiA 231 :GFELGIATGRPYTETVVPFENLGLLPYF T0324 125 :AVTIS 1qyiA 261 :DFIAT T0324 130 :ADDTPKRKPDPLPLLTALE 1qyiA 277 :PQARPLGKPNPFSYIAALY T0324 152 :VAPQNALFIGDSVSDEQTAQAANVDFGLAVWGMDPNADH 1qyiA 313 :VNKDDVFIVGDSLADLLSAQKIGATFIGTLTGLKGKDAA T0324 191 :QKVAHRFQKPLDILELFK 1qyiA 357 :HHADYVINHLGELRGVLD Number of specific fragments extracted= 15 number of extra gaps= 0 total=143 Number of alignments=13 # 1qyiA read from 1qyiA/merged-good-all-a2m # found chain 1qyiA in template set T0324 1 :M 1qyiA 1 :M T0324 4 :QALMFDIDGTLTN 1qyiA 2 :KKILFDVDGVFLS T0324 17 :SQPAYTTVMREV 1qyiA 48 :TDNDIQDIRNRI T0324 29 :LATYGKPFSPA 1qyiA 69 :LKSLGLNSNWD T0324 40 :QAQKTFPMAAEQAMTEL 1qyiA 91 :DILKKLSHDEIEAFMYQ T0324 57 :GIAASEFDHFQAQYEDVMASHYD 1qyiA 138 :DNVKVGKNNIYAALEEFATTELH T0324 82 :ELYPGITSLFEQLP 1qyiA 215 :RPVDEVKVLLNDLK T0324 96 :SELRLGIVTSQRRNELESGMRSYPFMMRM 1qyiA 230 :AGFELGIATGRPYTETVVPFENLGLLPYF T0324 125 :AVTIS 1qyiA 261 :DFIAT T0324 130 :ADDTPKRKPDPLPLLTALE 1qyiA 277 :PQARPLGKPNPFSYIAALY T0324 152 :VAPQNALFIGDSVSDEQTAQAANVDFGLAVWGMDPNADH 1qyiA 313 :VNKDDVFIVGDSLADLLSAQKIGATFIGTLTGLKGKDAA T0324 191 :QKVAHRFQKPLDILELFK 1qyiA 357 :HHADYVINHLGELRGVLD Number of specific fragments extracted= 12 number of extra gaps= 0 total=155 Number of alignments=14 # 1qyiA read from 1qyiA/merged-good-all-a2m # found chain 1qyiA in template set T0324 4 :QALMFDIDGTLTNSQPAYTTVMREVLATY 1qyiA 2 :KKILFDVDGVFLSEERCFDVSALTVYELL T0324 33 :GKPFSPAQAQKT 1qyiA 139 :NVKVGKNNIYAA T0324 49 :AEQAMTELGI 1qyiA 151 :LEEFATTELH T0324 59 :AASEFDHFQAQYEDVMA 1qyiA 170 :KGALWTLAQEVYQEWYL T0324 76 :SHYDQIELYPGITSLFEQLPS 1qyiA 209 :YQEIILRPVDEVKVLLNDLKG T0324 97 :ELRLGIVTSQRRNELESGMRSYPFMMRM 1qyiA 231 :GFELGIATGRPYTETVVPFENLGLLPYF T0324 125 :AVTIS 1qyiA 261 :DFIAT T0324 130 :ADDTPKRKPDPLPLLTALE 1qyiA 277 :PQARPLGKPNPFSYIAALY T0324 152 :VAPQNALFIGDSVSDEQTAQAANVDFGLAVWGMDPNADH 1qyiA 313 :VNKDDVFIVGDSLADLLSAQKIGATFIGTLTGLKGKDAA T0324 191 :QKVAHRFQKPLDILELFK 1qyiA 357 :HHADYVINHLGELRGVLD Number of specific fragments extracted= 10 number of extra gaps= 0 total=165 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:# T0324 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 (T0324)T2 because first residue in template chain is (1rqlA)K5 T0324 3 :YQALMFDIDGTLTNS 1rqlA 6 :IEAVIFDWAGTTVDY T0324 19 :PAYTTVMREVLATYGKPFSPAQAQKTFPMAAEQAMTEL 1rqlA 23 :FAPLEVFMEIFHKRGVAITAEEARKPMGLLKIDHVRAL T0324 57 :GIAASEFDHFQAQYEDVMASHYD 1rqlA 77 :LPTEADIQEMYEEFEEILFAILP T0324 80 :QIELYPGITSLFEQLPS 1rqlA 101 :YASPINAVKEVIASLRE T0324 97 :ELRLGIVTSQRR 1rqlA 119 :GIKIGSTTGYTR T0324 109 :NELESGMRSYPFM 1rqlA 134 :DIVAKEAALQGYK T0324 124 :MAVTISADDTPKRKPDPLPLLTALEKVNV 1rqlA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMELGV T0324 153 :APQNALFIGDSVSDEQTAQAANVDFGLAVWGMDPNADH 1rqlA 177 :PMNHMIKVGDTVSDMKEGRNAGMWTVGVILGSSELGLT T0324 191 :QKVAHRFQKPLDILELFK 1rqlA 240 :NGAHFTIETMQELESVME Number of specific fragments extracted= 9 number of extra gaps= 0 total=174 Number of alignments=16 # 1rqlA read from 1rqlA/merged-good-all-a2m # found chain 1rqlA in template set Warning: unaligning (T0324)T2 because first residue in template chain is (1rqlA)K5 T0324 3 :YQALMFDIDGTLTN 1rqlA 6 :IEAVIFDWAGTTVD T0324 20 :AYTTVMREVLATYGKPFSPAQAQKTFPMAAEQAMTEL 1rqlA 24 :APLEVFMEIFHKRGVAITAEEARKPMGLLKIDHVRAL T0324 57 :GIAASEFDHFQAQYEDVMASHYD 1rqlA 77 :LPTEADIQEMYEEFEEILFAILP T0324 80 :QIELYPGITSLFEQLP 1rqlA 101 :YASPINAVKEVIASLR T0324 96 :SELRLGIVTSQRRNELESGMRSY 1rqlA 118 :RGIKIGSTTGYTREMMDIVAKEA T0324 119 :PFM 1rqlA 144 :GYK T0324 124 :MAVTISADDTPKRKPDPLPLLTALEKVNV 1rqlA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMELGV T0324 153 :APQNALFIGDSVSDEQTAQAANVDFGLAVWGMDPNADH 1rqlA 177 :PMNHMIKVGDTVSDMKEGRNAGMWTVGVILGSSELGLT T0324 191 :QKVAHRFQKPLDILELFK 1rqlA 240 :NGAHFTIETMQELESVME Number of specific fragments extracted= 9 number of extra gaps= 0 total=183 Number of alignments=17 # 1rqlA read from 1rqlA/merged-good-all-a2m # found chain 1rqlA in template set Warning: unaligning (T0324)T2 because first residue in template chain is (1rqlA)K5 T0324 3 :YQALMFDIDGTLTNSQ 1rqlA 6 :IEAVIFDWAGTTVDYG T0324 20 :AYTTVMREVLATYGKPFSPAQAQKTFPMAAEQAMTELGI 1rqlA 24 :APLEVFMEIFHKRGVAITAEEARKPMGLLKIDHVRALTE T0324 59 :AASEFDHFQAQYED 1rqlA 79 :TEADIQEMYEEFEE T0324 73 :VMASHYDQIELYPGITSLFEQLPS 1rqlA 94 :LFAILPRYASPINAVKEVIASLRE T0324 97 :ELRLGIVTSQRR 1rqlA 119 :GIKIGSTTGYTR T0324 109 :NELESGMRSYPFM 1rqlA 134 :DIVAKEAALQGYK T0324 124 :MAVTISADDTPKRKPDPLPLLTALEKVNV 1rqlA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMELGV T0324 153 :APQNALFIGDSVSDEQTAQAANVDFGLAVWGMDPNADH 1rqlA 177 :PMNHMIKVGDTVSDMKEGRNAGMWTVGVILGSSELGLT T0324 191 :QKVAHRFQKPLDILELFK 1rqlA 240 :NGAHFTIETMQELESVME Number of specific fragments extracted= 9 number of extra gaps= 0 total=192 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:# T0324 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 (T0324)Q4 because first residue in template chain is (1ek1A)R4 Warning: unaligning (T0324)Q18 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ek1A)G48 Warning: unaligning (T0324)A48 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ek1A)G48 Warning: unaligning (T0324)I58 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ek1A)Q90 Warning: unaligning (T0324)E82 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ek1A)Q90 T0324 5 :ALMFDIDGTLT 1ek1A 5 :VAAFDLDGVLA T0324 16 :NS 1ek1A 17 :PS T0324 49 :AEQAMTEL 1ek1A 49 :PTEQLMKG T0324 57 :G 1ek1A 65 :P T0324 83 :LYPG 1ek1A 91 :IFSQ T0324 87 :ITSLFEQ 1ek1A 102 :NRPMLQA T0324 94 :LPS 1ek1A 112 :LKK T0324 97 :ELRLGIVTS 1ek1A 116 :GFTTCIVTN T0324 106 :QRRNELESGMRSYP 1ek1A 131 :DKRDSLAQMMCELS T0324 122 :MRMAVTISADDTPKRKPDPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVD 1ek1A 145 :QHFDFLIESCQVGMIKPEPQIYNFLLDTLKAKPNEVVFLDDFGSNLKPARDMGMV Number of specific fragments extracted= 10 number of extra gaps= 0 total=202 Number of alignments=19 # 1ek1A read from 1ek1A/merged-good-all-a2m # found chain 1ek1A in template set Warning: unaligning (T0324)Q4 because first residue in template chain is (1ek1A)R4 Warning: unaligning (T0324)P19 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ek1A)G48 Warning: unaligning (T0324)A48 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ek1A)G48 Warning: unaligning (T0324)A60 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ek1A)Q90 T0324 5 :ALMFDIDGTLTNSQ 1ek1A 5 :VAAFDLDGVLALPS T0324 49 :AEQAMTEL 1ek1A 49 :PTEQLMKG T0324 61 :SEF 1ek1A 91 :IFS T0324 76 :SHYDQIELYPGITSLFEQLP 1ek1A 94 :QAMAARSINRPMLQAAIALK T0324 96 :SELRLGIVTSQR 1ek1A 115 :KGFTTCIVTNNW T0324 108 :RNELESGMRSYP 1ek1A 133 :RDSLAQMMCELS T0324 122 :MRMAVTISADDTPKRKPDPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANV 1ek1A 145 :QHFDFLIESCQVGMIKPEPQIYNFLLDTLKAKPNEVVFLDDFGSNLKPARDMGM Number of specific fragments extracted= 7 number of extra gaps= 0 total=209 Number of alignments=20 # 1ek1A read from 1ek1A/merged-good-all-a2m # found chain 1ek1A in template set Warning: unaligning (T0324)Q4 because first residue in template chain is (1ek1A)R4 Warning: unaligning (T0324)S17 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ek1A)G48 Warning: unaligning (T0324)A48 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ek1A)G48 Warning: unaligning (T0324)A60 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ek1A)Q90 T0324 5 :ALMFDIDGTLT 1ek1A 5 :VAAFDLDGVLA T0324 16 :N 1ek1A 18 :S T0324 49 :AEQAMTEL 1ek1A 49 :PTEQLMKG T0324 61 :SE 1ek1A 91 :IF T0324 75 :ASHYDQIELYPGITSLFEQLPS 1ek1A 93 :SQAMAARSINRPMLQAAIALKK T0324 97 :ELRLGIVTS 1ek1A 116 :GFTTCIVTN T0324 106 :QRRNELESGMRSY 1ek1A 131 :DKRDSLAQMMCEL T0324 122 :MRMAVTISADDTPKRKPDPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANV 1ek1A 145 :QHFDFLIESCQVGMIKPEPQIYNFLLDTLKAKPNEVVFLDDFGSNLKPARDMGM Number of specific fragments extracted= 8 number of extra gaps= 0 total=217 Number of alignments=21 # 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 # T0324 read from 1nnlA/merged-good-all-a2m # 1nnlA read from 1nnlA/merged-good-all-a2m # found chain 1nnlA in training set Warning: unaligning (T0324)F36 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1nnlA)P57 T0324 4 :QALMFDIDGTLTNSQ 1nnlA 15 :DAVCFDVDSTVIREE T0324 24 :VMREVLATYGK 1nnlA 30 :GIDELAKICGV T0324 35 :P 1nnlA 43 :A T0324 48 :AAEQAMTELGIAASEFDHFQAQ 1nnlA 61 :ALTERLALIQPSREQVQRLIAE T0324 79 :DQIELYPGITSLFEQLPS 1nnlA 83 :QPPHLTPGIRELVSRLQE T0324 97 :ELRLGIVTSQRRNELESGMRSYPFMMRMAVTISADDTPKR 1nnlA 102 :NVQVFLISGGFRSIVEHVASKLNIPATNVFANRLKFYFNG T0324 139 :DPLPLLTALEKV 1nnlA 154 :ESGGKGKVIKLL T0324 153 :APQNALFIGDSVSDE 1nnlA 170 :HFKKIIMIGDGATDM T0324 174 :NVDFGLAVWGMDPNADH 1nnlA 189 :PADAFIGFGGNVIRQQV T0324 191 :QKVAHRFQKPLDI 1nnlA 207 :DNAKWYITDFVEL Number of specific fragments extracted= 10 number of extra gaps= 0 total=227 Number of alignments=22 # 1nnlA read from 1nnlA/merged-good-all-a2m # found chain 1nnlA in training set Warning: unaligning (T0324)P38 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1nnlA)P57 Warning: unaligning (T0324)Q51 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1nnlA)P57 T0324 4 :QALMFDIDGTLTNSQ 1nnlA 15 :DAVCFDVDSTVIREE T0324 24 :VMREVLATYGKPFS 1nnlA 30 :GIDELAKICGVEDA T0324 52 :AMTELGIAASEFDHFQAQYEDVM 1nnlA 58 :FKAALTERLALIQPSREQVQRLI T0324 79 :D 1nnlA 81 :A T0324 80 :QIELYPGITSLFEQLP 1nnlA 84 :PPHLTPGIRELVSRLQ T0324 96 :SELRLGIVTSQRRNELESGMRSYPFM 1nnlA 101 :RNVQVFLISGGFRSIVEHVASKLNIP T0324 122 :MRMAVTISADDTPKR 1nnlA 129 :NVFANRLKFYFNGEY T0324 137 :K 1nnlA 158 :K T0324 140 :PLPLLTALEKV 1nnlA 159 :GKVIKLLKEKF T0324 153 :APQNALFIGDSVSDE 1nnlA 170 :HFKKIIMIGDGATDM T0324 174 :NVDFGLAVWGMDPNADH 1nnlA 189 :PADAFIGFGGNVIRQQV T0324 191 :QKVAHRFQKPLDI 1nnlA 207 :DNAKWYITDFVEL Number of specific fragments extracted= 12 number of extra gaps= 0 total=239 Number of alignments=23 # 1nnlA read from 1nnlA/merged-good-all-a2m # found chain 1nnlA in training set Warning: unaligning (T0324)P38 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1nnlA)P57 Warning: unaligning (T0324)A48 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1nnlA)P57 T0324 4 :QALMFDIDGTLTNSQ 1nnlA 15 :DAVCFDVDSTVIREE T0324 24 :VMREVLATYGKPFS 1nnlA 30 :GIDELAKICGVEDA T0324 49 :AEQAMTELGI 1nnlA 58 :FKAALTERLA T0324 59 :AASEFDHFQAQYED 1nnlA 69 :IQPSREQVQRLIAE T0324 79 :DQIELYPGITSLFEQLPS 1nnlA 83 :QPPHLTPGIRELVSRLQE T0324 97 :ELRLGIVTSQRRNELESGMRSYPFMMRMAVTISA 1nnlA 102 :NVQVFLISGGFRSIVEHVASKLNIPATNVFANRL T0324 131 :DD 1nnlA 139 :FN T0324 137 :KPDPLPLLTALEKV 1nnlA 152 :TAESGGKGKVIKLL T0324 153 :APQNALFIGDSVSDEQ 1nnlA 170 :HFKKIIMIGDGATDME T0324 174 :NVDFGLAVWGMDPNADH 1nnlA 189 :PADAFIGFGGNVIRQQV T0324 191 :QKVAHRFQKPLDI 1nnlA 207 :DNAKWYITDFVEL Number of specific fragments extracted= 11 number of extra gaps= 0 total=250 Number of alignments=24 # 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:# T0324 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 (T0324)T2 because first residue in template chain is (1zd3A)T2 T0324 3 :YQALMFDIDGTLTNS 1zd3A 3 :LRAAVFDLDGVLALP T0324 18 :QP 1zd3A 20 :FG T0324 24 :VMREVLATYGKP 1zd3A 22 :VLGRTEEALALP T0324 38 :PAQAQKTF 1zd3A 34 :RGLLNDAF T0324 46 :PMAAEQAMTE 1zd3A 47 :EGATTRLMKG T0324 60 :ASEFDHFQAQYEDVMASHYD 1zd3A 57 :EITLSQWIPLMEENCRKCSE T0324 80 :QIELYPG 1zd3A 79 :KVCLPKN T0324 87 :ITSLFEQLPS 1zd3A 105 :MLQAALMLRK T0324 97 :ELRLGIVTS 1zd3A 116 :GFTTAILTN T0324 106 :QRRNELESGMRSYPF 1zd3A 131 :AERDGLAQLMCELKM T0324 123 :RMAVTISADDTPKRKPDPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFG 1zd3A 146 :HFDFLIESCQVGMVKPEPQIYKFLLDTLKASPSEVVFLDDIGANLKPARDLGMVTI T0324 196 :RFQKPLDILELFK 1zd3A 202 :LVQDTDTALKELE Number of specific fragments extracted= 12 number of extra gaps= 0 total=262 Number of alignments=25 # 1zd3A read from 1zd3A/merged-good-all-a2m # found chain 1zd3A in template set Warning: unaligning (T0324)T2 because first residue in template chain is (1zd3A)T2 T0324 3 :YQALMFDIDGTLTN 1zd3A 3 :LRAAVFDLDGVLAL T0324 17 :SQPAYTTVMREVLATYGKPFSPA 1zd3A 63 :WIPLMEENCRKCSETAKVCLPKN T0324 69 :QYEDVMASHYDQIELYPGITSLFEQLP 1zd3A 87 :SIKEIFDKAISARKINRPMLQAALMLR T0324 96 :SELRLGIVTSQR 1zd3A 115 :KGFTTAILTNTW T0324 108 :RNELESGMRSYPFM 1zd3A 133 :RDGLAQLMCELKMH T0324 124 :MAVTISADDTPKRKPDPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFG 1zd3A 147 :FDFLIESCQVGMVKPEPQIYKFLLDTLKASPSEVVFLDDIGANLKPARDLGMVTI T0324 196 :RFQKPLDILELFK 1zd3A 202 :LVQDTDTALKELE Number of specific fragments extracted= 7 number of extra gaps= 0 total=269 Number of alignments=26 # 1zd3A read from 1zd3A/merged-good-all-a2m # found chain 1zd3A in template set Warning: unaligning (T0324)T2 because first residue in template chain is (1zd3A)T2 T0324 3 :YQALMFDIDGTLTNSQ 1zd3A 3 :LRAAVFDLDGVLALPA T0324 24 :VMREVLATYGKPFSPAQAQKTFPMAAEQAMTELGI 1zd3A 22 :VLGRTEEALALPRGLLNDAFQKGGPEGATTRLMKG T0324 59 :AASEFDHFQAQYEDVMASHYDQIE 1zd3A 60 :LSQWIPLMEENCRKCSETAKVCLP T0324 83 :LYPGITSLFEQLPS 1zd3A 101 :INRPMLQAALMLRK T0324 97 :ELRLGIVTS 1zd3A 116 :GFTTAILTN T0324 106 :QRRNELESGMRSYPF 1zd3A 131 :AERDGLAQLMCELKM T0324 123 :RMAVTISADDTPKRKPDPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFG 1zd3A 146 :HFDFLIESCQVGMVKPEPQIYKFLLDTLKASPSEVVFLDDIGANLKPARDLGMVTI T0324 196 :RFQKPLDILELFK 1zd3A 202 :LVQDTDTALKELE Number of specific fragments extracted= 8 number of extra gaps= 0 total=277 Number of alignments=27 # 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 # T0324 read from 1l7mA/merged-good-all-a2m # 1l7mA read from 1l7mA/merged-good-all-a2m # found chain 1l7mA in training set T0324 2 :TYQALMFDIDGTLTNSQ 1l7mA 4 :KKKLILFDFDSTLVNNE T0324 24 :VMREVLATYGK 1l7mA 21 :TIDEIAREAGV T0324 38 :PAQAQKTF 1l7mA 32 :EEEVKKIT T0324 46 :PMAAEQAMTEL 1l7mA 46 :KLNFEQSLRKR T0324 57 :GIAASEFDHFQA 1l7mA 62 :DLPIEKVEKAIK T0324 80 :QIELYPGITSLFEQLPS 1l7mA 74 :RITPTEGAEETIKELKN T0324 97 :ELRLGIVTSQRRNELESGMRSYPFMMRMAVTISADDT 1l7mA 92 :GYVVAVVSGGFDIAVNKIKEKLGLDYAFANRLIVKDG T0324 134 :PKRK 1l7mA 137 :EVLK T0324 140 :PLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAAN 1l7mA 145 :GEILEKIAKIEGINLEDTVAVGDGANDISMFKKAG T0324 176 :DFGLAVWG 1l7mA 180 :LKIAFCAK T0324 188 :ADH 1l7mA 188 :PIL T0324 191 :QKVAHRFQ 1l7mA 192 :EKADICIE T0324 199 :KPLDILELF 1l7mA 202 :DLREILKYI Number of specific fragments extracted= 13 number of extra gaps= 0 total=290 Number of alignments=28 # 1l7mA read from 1l7mA/merged-good-all-a2m # found chain 1l7mA in training set T0324 2 :TYQALMFDIDGTLTNSQ 1l7mA 4 :KKKLILFDFDSTLVNNE T0324 24 :VMREVLATYGK 1l7mA 21 :TIDEIAREAGV T0324 38 :PAQAQKT 1l7mA 32 :EEEVKKI T0324 50 :EQAMTEL 1l7mA 39 :TKEAMEG T0324 65 :HFQAQYEDVMASHYDQIELYPGITSLFEQLP 1l7mA 59 :LLKDLPIEKVEKAIKRITPTEGAEETIKELK T0324 96 :SELRLGIVTSQRRNELESGMRSYPFMMRMAVTISADDT 1l7mA 91 :RGYVVAVVSGGFDIAVNKIKEKLGLDYAFANRLIVKDG T0324 134 :PK 1l7mA 140 :KE T0324 137 :K 1l7mA 144 :K T0324 140 :PLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAAN 1l7mA 145 :GEILEKIAKIEGINLEDTVAVGDGANDISMFKKAG T0324 176 :DFGLA 1l7mA 180 :LKIAF T0324 184 :MDPNADHQKVAHRF 1l7mA 185 :CAKPILKEKADICI T0324 198 :QKPLDILELF 1l7mA 201 :RDLREILKYI Number of specific fragments extracted= 12 number of extra gaps= 0 total=302 Number of alignments=29 # 1l7mA read from 1l7mA/merged-good-all-a2m # found chain 1l7mA in training set T0324 2 :TYQALMFDIDGTLTNSQ 1l7mA 4 :KKKLILFDFDSTLVNNE T0324 24 :VMREVLATYGK 1l7mA 21 :TIDEIAREAGV T0324 38 :PAQAQKTF 1l7mA 32 :EEEVKKIT T0324 46 :PMAAEQAMTELGI 1l7mA 46 :KLNFEQSLRKRVS T0324 59 :AASEFDHFQAQY 1l7mA 61 :KDLPIEKVEKAI T0324 79 :DQIELYPGITSLFEQLPS 1l7mA 73 :KRITPTEGAEETIKELKN T0324 97 :ELRLGIVTSQRRNELESGMRSYPFMMRMAVTISADD 1l7mA 92 :GYVVAVVSGGFDIAVNKIKEKLGLDYAFANRLIVKD T0324 135 :KRK 1l7mA 138 :VLK T0324 138 :PDPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAAN 1l7mA 143 :AKGEILEKIAKIEGINLEDTVAVGDGANDISMFKKAG T0324 176 :DFGLAVWG 1l7mA 180 :LKIAFCAK T0324 188 :ADH 1l7mA 188 :PIL T0324 191 :QKVAHRFQK 1l7mA 192 :EKADICIEK Number of specific fragments extracted= 12 number of extra gaps= 0 total=314 Number of alignments=30 # 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:# T0324 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 (T0324)Q4 because first residue in template chain is (1cqzA)R4 Warning: unaligning (T0324)Q18 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cqzA)G48 Warning: unaligning (T0324)A60 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cqzA)Q90 T0324 5 :ALMFDIDGTLTN 1cqzA 5 :VAAFDLDGVLAL T0324 17 :S 1cqzA 18 :S T0324 61 :SEFDHFQ 1cqzA 91 :IFSQAMA T0324 80 :QIELYPGITSLFEQLPS 1cqzA 98 :ARSINRPMLQAAIALKK T0324 97 :ELRLGIVTS 1cqzA 116 :GFTTCIVTN T0324 106 :QRRNELESGMRSYP 1cqzA 131 :DKRDSLAQMMCELS T0324 122 :MRMAVTISADDTPKRKPDPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFGLAVW 1cqzA 145 :QHFDFLIESCQVGMIKPEPQIYNFLLDTLKAKPNEVVFLDDFGSNLKPARDMGMVTILVHN T0324 199 :KPLDILEL 1cqzA 206 :TASALREL Number of specific fragments extracted= 8 number of extra gaps= 0 total=322 Number of alignments=31 # 1cqzA read from 1cqzA/merged-good-all-a2m # found chain 1cqzA in template set Warning: unaligning (T0324)Q4 because first residue in template chain is (1cqzA)R4 Warning: unaligning (T0324)A60 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cqzA)Q90 T0324 5 :ALMFDIDGTLTN 1cqzA 5 :VAAFDLDGVLAL T0324 61 :SEFDH 1cqzA 91 :IFSQA T0324 78 :YDQIELYPGITSLFEQLP 1cqzA 96 :MAARSINRPMLQAAIALK T0324 96 :SELRLGIVTSQR 1cqzA 115 :KGFTTCIVTNNW T0324 108 :RNELESGMRSY 1cqzA 136 :LAQMMCELSQH T0324 124 :MAVTISADDTPKRKPDPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFGLA 1cqzA 147 :FDFLIESCQVGMIKPEPQIYNFLLDTLKAKPNEVVFLDDFGSNLKPARDMGMVTILV T0324 198 :QKPLDILELF 1cqzA 205 :NTASALRELE Number of specific fragments extracted= 7 number of extra gaps= 0 total=329 Number of alignments=32 # 1cqzA read from 1cqzA/merged-good-all-a2m # found chain 1cqzA in template set Warning: unaligning (T0324)Q4 because first residue in template chain is (1cqzA)R4 Warning: unaligning (T0324)S17 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cqzA)G48 Warning: unaligning (T0324)A60 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cqzA)Q90 T0324 5 :ALMFDIDGTLT 1cqzA 5 :VAAFDLDGVLA T0324 16 :N 1cqzA 18 :S T0324 61 :SEFDHFQ 1cqzA 91 :IFSQAMA T0324 80 :QIELYPGITSLFEQLPS 1cqzA 98 :ARSINRPMLQAAIALKK T0324 97 :ELRLGIVTS 1cqzA 116 :GFTTCIVTN T0324 106 :QRRNELESGMRSYP 1cqzA 131 :DKRDSLAQMMCELS T0324 122 :MRMAVTISADDTPKRKPDPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFGLAVW 1cqzA 145 :QHFDFLIESCQVGMIKPEPQIYNFLLDTLKAKPNEVVFLDDFGSNLKPARDMGMVTILVHN T0324 199 :K 1cqzA 206 :T Number of specific fragments extracted= 8 number of extra gaps= 0 total=337 Number of alignments=33 # 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:# T0324 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 (T0324)T2 because first residue in template chain is (1wviA)T1002 T0324 3 :YQALMFDIDGTLT 1wviA 1003 :YKGYLIDLDGTIY T0324 16 :NSQPAYTTVMREVLATY 1wviA 1019 :DRIPAGEDFVKRLQERQ T0324 33 :GKPFSPAQAQKTF 1wviA 1044 :NTTRTPEMVQEML T0324 46 :PMAAEQAMTEL 1wviA 1094 :ETGLKKAVAEA T0324 57 :GIAASEFDHFQAQYE 1wviA 1123 :NLTYEKLTLATLAIQ T0324 96 :SELRL 1wviA 1138 :KGAVF T0324 102 :IVTSQ 1wviA 1143 :IGTNP T0324 107 :RRNELESGMRSY 1wviA 1160 :GAGAILFLLEKA T0324 119 :PFMMRM 1wviA 1173 :RVKPII T0324 136 :RKPDPLPLLTALEKVNVAPQNALFIGDSV 1wviA 1180 :GKPEAVIMNKALDRLGVKRHEAIMVGDNY T0324 165 :SDEQTAQAANVDFGLAVWGMDPNADH 1wviA 1210 :TDITAGIKNDIATLLVTTGFTKPEEV T0324 191 :QKVAHRFQKPLD 1wviA 1240 :IQPDFVLSSLAE Number of specific fragments extracted= 12 number of extra gaps= 0 total=349 Number of alignments=34 # 1wviA read from 1wviA/merged-good-all-a2m # found chain 1wviA in template set Warning: unaligning (T0324)T2 because first residue in template chain is (1wviA)T1002 T0324 3 :YQALMFDIDGTLT 1wviA 1003 :YKGYLIDLDGTIY T0324 16 :NSQPAYTTVMREVLAT 1wviA 1019 :DRIPAGEDFVKRLQER T0324 33 :GKP 1wviA 1035 :QLP T0324 62 :EFDHFQAQYEDVMASHYD 1wviA 1044 :NTTRTPEMVQEMLATSFN T0324 80 :QIEL 1wviA 1063 :KTPL T0324 87 :ITSLFEQLPSELRLGIVT 1wviA 1076 :TIDYMNDMKRGKTAYVIG T0324 108 :RNELESGMRSYPFMMR 1wviA 1094 :ETGLKKAVAEAGYRED T0324 124 :MAVTIS 1wviA 1113 :PAYVVV T0324 130 :ADDTPKRKPDPLPLLTALEKVNVAPQNALFIGDSV 1wviA 1174 :VKPIIIGKPEAVIMNKALDRLGVKRHEAIMVGDNY T0324 165 :SDEQTAQAANVDFGLAVWGMDPNADH 1wviA 1210 :TDITAGIKNDIATLLVTTGFTKPEEV T0324 191 :QKVAHRFQKPLD 1wviA 1240 :IQPDFVLSSLAE Number of specific fragments extracted= 11 number of extra gaps= 0 total=360 Number of alignments=35 # 1wviA read from 1wviA/merged-good-all-a2m # found chain 1wviA in template set Warning: unaligning (T0324)T2 because first residue in template chain is (1wviA)T1002 T0324 3 :YQALMFDIDGTLT 1wviA 1003 :YKGYLIDLDGTIY T0324 16 :NSQPAYTTVMREVLATY 1wviA 1019 :DRIPAGEDFVKRLQERQ T0324 36 :FS 1wviA 1047 :RT T0324 50 :EQAMTELGI 1wviA 1049 :PEMVQEMLA T0324 59 :AASEFDHFQAQYEDVMASHYDQIELY 1wviA 1065 :PLETIYTATLATIDYMNDMKRGKTAY T0324 85 :PGITSLFEQL 1wviA 1095 :TGLKKAVAEA T0324 96 :S 1wviA 1110 :S T0324 97 :ELRLGIVTSQRR 1wviA 1112 :NPAYVVVGLDTN T0324 109 :NELESGMRSY 1wviA 1130 :TLATLAIQKG T0324 124 :MAVTISADD 1wviA 1140 :AVFIGTNPD T0324 135 :KRKPDPLPLLTALEKVNVAPQNALFIGDSV 1wviA 1179 :IGKPEAVIMNKALDRLGVKRHEAIMVGDNY T0324 165 :SDEQTAQAANVDFGLAVWGMDPNADH 1wviA 1210 :TDITAGIKNDIATLLVTTGFTKPEEV T0324 191 :QKVAHRFQKPLD 1wviA 1240 :IQPDFVLSSLAE Number of specific fragments extracted= 13 number of extra gaps= 0 total=373 Number of alignments=36 # 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:# T0324 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 T0324 4 :QALMFDIDGTLTN 1zjjA 2 :VAIIFDMDGVLYR T0324 17 :SQPAYTTVMRE 1zjjA 18 :AIPGVRELIEF T0324 29 :LATYGKPF 1zjjA 29 :LKERGIPF T0324 37 :SPAQAQKTF 1zjjA 46 :TPEMYREKL T0324 46 :PMAAEQAMTELGIAASEFDHFQA 1zjjA 91 :GEGLVKEMQALGWGIVTLDEARQ T0324 76 :SHYDQIE 1zjjA 114 :GSWKEVK T0324 83 :LYPGI 1zjjA 126 :LDPDL T0324 88 :TSLFEQL 1zjjA 132 :YEKLKYA T0324 95 :PSELRL 1zjjA 143 :RNGATF T0324 102 :IVTSQ 1zjjA 149 :IGTNP T0324 107 :RRNELESGMRSY 1zjjA 166 :GAGSIIAALKVA T0324 119 :PFMMRM 1zjjA 179 :NVEPII T0324 136 :RKPD 1zjjA 186 :GKPN T0324 141 :LPLLTALEKV 1zjjA 190 :EPMYEVVREM T0324 153 :APQNALFIGDSV 1zjjA 201 :PGEELWMVGDRL T0324 165 :SDEQTAQAANVDFGLAVWGMDPNADH 1zjjA 214 :TDIAFAKKFGMKAIMVLTGVSSLEDI T0324 191 :QKVAHRFQKPLDILELFK 1zjjA 244 :YKPDLVLPSVYELIDYLK Number of specific fragments extracted= 17 number of extra gaps= 0 total=390 Number of alignments=37 # 1zjjA read from 1zjjA/merged-good-all-a2m # found chain 1zjjA in template set T0324 4 :QALMFDIDGTLTN 1zjjA 2 :VAIIFDMDGVLYR T0324 80 :QIELYPGITSLFEQLP 1zjjA 15 :GNRAIPGVRELIEFLK T0324 96 :SELRLGIVTSQ 1zjjA 32 :RGIPFAFLTNN T0324 107 :RRNELESGMRSYPFMMRMAVTIS 1zjjA 46 :TPEMYREKLLKMGIDVSSSIIIT T0324 130 :ADDTPKRKPDP 1zjjA 180 :VEPIIIGKPNE T0324 142 :PLLTALEKV 1zjjA 191 :PMYEVVREM T0324 152 :VAPQNALFIGDSV 1zjjA 200 :FPGEELWMVGDRL T0324 165 :SDEQTAQAANVDFGLAVWGMDPNADH 1zjjA 214 :TDIAFAKKFGMKAIMVLTGVSSLEDI T0324 191 :QKVAHRFQKPLDILELFK 1zjjA 244 :YKPDLVLPSVYELIDYLK Number of specific fragments extracted= 9 number of extra gaps= 0 total=399 Number of alignments=38 # 1zjjA read from 1zjjA/merged-good-all-a2m # found chain 1zjjA in template set T0324 4 :QALMFDIDGTLTN 1zjjA 2 :VAIIFDMDGVLYR T0324 80 :QIELYPGITSLFEQLPS 1zjjA 15 :GNRAIPGVRELIEFLKE T0324 97 :ELRLGIVTS 1zjjA 33 :GIPFAFLTN T0324 106 :QRRNELESGMRSYPFM 1zjjA 45 :KTPEMYREKLLKMGID T0324 128 :ISADD 1zjjA 61 :VSSSI T0324 133 :TPKRK 1zjjA 81 :LDPGK T0324 139 :DPLPLLTALEKVN 1zjjA 90 :GGEGLVKEMQALG T0324 152 :VAPQNALFIGDSV 1zjjA 200 :FPGEELWMVGDRL T0324 165 :SDEQTAQAANVDFGLAVWGMDPNADH 1zjjA 214 :TDIAFAKKFGMKAIMVLTGVSSLEDI T0324 191 :QKVAHRFQKPLDILELFK 1zjjA 244 :YKPDLVLPSVYELIDYLK Number of specific fragments extracted= 10 number of extra gaps= 0 total=409 Number of alignments=39 # 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 # T0324 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 (T0324)Y3 because first residue in template chain is (2go7A)K3 Warning: unaligning (T0324)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2go7A)D9 Warning: unaligning (T0324)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2go7A)D9 Warning: unaligning (T0324)I102 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2go7A)Y106 Warning: unaligning (T0324)V103 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2go7A)Y106 T0324 4 :QALM 2go7A 4 :TAFI T0324 10 :IDGTLTNSQPAYTTVMREVLATYGKPFSPAQAQKTF 2go7A 10 :LDGTLLDSYEAILSGIEETFAQFSIPYDKEKVREFI T0324 46 :PMAAEQAMTEL 2go7A 47 :KYSVQDLLVRV T0324 57 :GIAA 2go7A 62 :NLDV T0324 64 :DHFQAQYEDVMASHYDQIELYPGITSLFEQLPS 2go7A 66 :EVLNQVRAQSLAEKNAQVVLMPGAREVLAWADE T0324 97 :ELRLG 2go7A 100 :GIQQF T0324 104 :TSQR 2go7A 107 :THKG T0324 109 :NELESGMRSYPFMMRMAVTISADDTPKRKPDPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFGL 2go7A 111 :NNAFTILKDLGVESYFTEILTSQSGFVRKPSPEAATYLLDKYQLNSDNTYYIGDRTLDVEFAQNSGIQSIN T0324 186 :PNADHQKVAHRFQKPLDILELFK 2go7A 182 :FLESTYEGNHRIQALADISRIFE Number of specific fragments extracted= 9 number of extra gaps= 2 total=418 Number of alignments=40 # 2go7A read from 2go7A/merged-good-all-a2m # found chain 2go7A in template set Warning: unaligning (T0324)Y3 because first residue in template chain is (2go7A)K3 Warning: unaligning (T0324)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2go7A)D9 Warning: unaligning (T0324)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2go7A)D9 Warning: unaligning (T0324)I102 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2go7A)Y106 Warning: unaligning (T0324)V103 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2go7A)Y106 T0324 4 :QALM 2go7A 4 :TAFI T0324 10 :IDGTLTNSQPAYTTVMREVLATYGKPFSPAQAQKTFPMAAEQAMTEL 2go7A 10 :LDGTLLDSYEAILSGIEETFAQFSIPYDKEKVREFIFKYSVQDLLVR T0324 57 :GIAASEFDHFQAQYEDVMASHYDQIELYPGITSLFEQLP 2go7A 59 :EDRNLDVEVLNQVRAQSLAEKNAQVVLMPGAREVLAWAD T0324 96 :SELRLG 2go7A 99 :SGIQQF T0324 104 :TSQRRN 2go7A 107 :THKGNN T0324 111 :LESGMRSYPFMMRMAVTISADDTPKRKPDPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFGL 2go7A 113 :AFTILKDLGVESYFTEILTSQSGFVRKPSPEAATYLLDKYQLNSDNTYYIGDRTLDVEFAQNSGIQSIN T0324 182 :WGMDP 2go7A 182 :FLEST T0324 191 :QKVAHRFQKPLDILELFK 2go7A 187 :YEGNHRIQALADISRIFE Number of specific fragments extracted= 8 number of extra gaps= 2 total=426 Number of alignments=41 # 2go7A read from 2go7A/merged-good-all-a2m # found chain 2go7A in template set Warning: unaligning (T0324)Y3 because first residue in template chain is (2go7A)K3 Warning: unaligning (T0324)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2go7A)D9 Warning: unaligning (T0324)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2go7A)D9 Warning: unaligning (T0324)I102 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2go7A)Y106 Warning: unaligning (T0324)V103 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2go7A)Y106 T0324 4 :QALM 2go7A 4 :TAFI T0324 10 :IDGTLTNSQPAYTTVMREVLATYGKPFSPAQAQKTFPMAAEQAMTELGI 2go7A 10 :LDGTLLDSYEAILSGIEETFAQFSIPYDKEKVREFIFKYSVQDLLVRVA T0324 59 :AASEFDHFQAQYEDVMASHYDQIELYPGITSLFEQLPS 2go7A 61 :RNLDVEVLNQVRAQSLAEKNAQVVLMPGAREVLAWADE T0324 97 :ELRLG 2go7A 100 :GIQQF T0324 104 :TSQRRN 2go7A 107 :THKGNN T0324 111 :LESGMRSYPFMMRMAVTISADDTPKRKPDPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFGL 2go7A 113 :AFTILKDLGVESYFTEILTSQSGFVRKPSPEAATYLLDKYQLNSDNTYYIGDRTLDVEFAQNSGIQSIN T0324 186 :PNAD 2go7A 182 :FLES T0324 191 :QKVAHRFQKPLDILELFK 2go7A 187 :YEGNHRIQALADISRIFE Number of specific fragments extracted= 8 number of extra gaps= 2 total=434 Number of alignments=42 # 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 # T0324 read from 1nrwA/merged-good-all-a2m # 1nrwA read from 1nrwA/merged-good-all-a2m # found chain 1nrwA in training set Warning: unaligning (T0324)Y3 because first residue in template chain is (1nrwA)M1 T0324 4 :QALMFDIDGTLTN 1nrwA 2 :KLIAIDLDGTLLN T0324 17 :SQPAYTTVMREVLAT 1nrwA 19 :VSLENENALRQAQRD T0324 33 :GKP 1nrwA 34 :GIE T0324 36 :FSPAQAQKTF 1nrwA 43 :RAHFDVMSIF T0324 46 :PMAAEQAMTEL 1nrwA 84 :KKRAYDILSWL T0324 57 :GIAASEFDHFQAQYED 1nrwA 132 :EADLSVLKQAAEVQYS T0324 79 :D 1nrwA 148 :Q T0324 80 :QIELYPGITSL 1nrwA 150 :GFAYINSFQEL T0324 95 :PS 1nrwA 161 :FE T0324 97 :E 1nrwA 164 :D T0324 105 :SQRRNELESGMRSYPFMMRMAVTISADD 1nrwA 176 :SFFKEKLEAGWKRYEHAEDLTLVSSAEH T0324 134 :PKRK 1nrwA 211 :KASK T0324 140 :PLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAAN 1nrwA 215 :GQALKRLAKQLNIPLEETAAVGDSLNDKSMLEAAG T0324 178 :GLAVWGMDP 1nrwA 250 :KGVAMGNAR T0324 201 :LDILELF 1nrwA 259 :EDIKSIA Number of specific fragments extracted= 15 number of extra gaps= 0 total=449 Number of alignments=43 # 1nrwA read from 1nrwA/merged-good-all-a2m # found chain 1nrwA in training set Warning: unaligning (T0324)Y3 because first residue in template chain is (1nrwA)M1 T0324 4 :QALMFDIDGTLTN 1nrwA 2 :KLIAIDLDGTLLN T0324 79 :DQIELYPGITSLFEQLP 1nrwA 15 :SKHQVSLENENALRQAQ T0324 96 :SELRLGIVTSQRRNELESGMRSYPFM 1nrwA 33 :DGIEVVVSTGRAHFDVMSIFEPLGIK T0324 125 :AVTIS 1nrwA 59 :TWVIS T0324 130 :AD 1nrwA 209 :SR T0324 134 :PKRK 1nrwA 211 :KASK T0324 140 :PLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAAN 1nrwA 215 :GQALKRLAKQLNIPLEETAAVGDSLNDKSMLEAAG T0324 178 :GLAVWGMDPNADHQKVAHRFQKPLD 1nrwA 250 :KGVAMGNAREDIKSIADAVTLTNDE T0324 203 :ILELFK 1nrwA 277 :VAHMMK Number of specific fragments extracted= 9 number of extra gaps= 0 total=458 Number of alignments=44 # 1nrwA read from 1nrwA/merged-good-all-a2m # found chain 1nrwA in training set Warning: unaligning (T0324)Y3 because first residue in template chain is (1nrwA)M1 T0324 4 :QALMFDIDGTLTNSQ 1nrwA 2 :KLIAIDLDGTLLNSK T0324 19 :PAYTTVMREVLATY 1nrwA 21 :LENENALRQAQRDG T0324 35 :PFSPAQAQKT 1nrwA 112 :PQNGRELLDV T0324 50 :EQAMTELGIAASEFDHFQAQYEDVMASHY 1nrwA 122 :ELDRFRSANPEADLSVLKQAAEVQYSQSG T0324 81 :IELYPGITSLFEQ 1nrwA 151 :FAYINSFQELFEA T0324 96 :S 1nrwA 164 :D T0324 97 :ELR 1nrwA 166 :PID T0324 105 :SQRRNELESGMRSYPFMMRMAVTISADD 1nrwA 176 :SFFKEKLEAGWKRYEHAEDLTLVSSAEH T0324 135 :KRKPDPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAAN 1nrwA 210 :RKASKGQALKRLAKQLNIPLEETAAVGDSLNDKSMLEAAG T0324 178 :GLAVWGMDPNADHQKVA 1nrwA 250 :KGVAMGNAREDIKSIAD Number of specific fragments extracted= 10 number of extra gaps= 0 total=468 Number of alignments=45 # 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:# T0324 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 (T0324)T2 because first residue in template chain is (1rdfA)K5 Warning: unaligning (T0324)A153 because of BadResidue code BAD_PEPTIDE at template residue (1rdfA)P177 T0324 3 :YQALMFDIDGTLTNS 1rdfA 6 :IEAVIFDWAGTTVDY T0324 19 :PAYTTVMREVLATYGKPFSPAQAQKTF 1rdfA 23 :FAPLEVFMEIFHKRGVAITAEEARKPM T0324 47 :M 1rdfA 63 :M T0324 48 :AAEQAMTEL 1rdfA 65 :RIASEWNRV T0324 57 :GIAASEFDHFQAQYEDVMASHYD 1rdfA 77 :LPTEADIQEMYEEFEEILFAILP T0324 80 :QIELYPGITSLFEQLPS 1rdfA 101 :YASPINAVKEVIASLRE T0324 97 :ELRLGIVTSQRRNELE 1rdfA 119 :GIKIGSTTGYTREMMD T0324 113 :SGMRSYPFM 1rdfA 138 :KEAALQGYK T0324 124 :MAVTISADDTPKRKPDPLPLLTALEKVNV 1rdfA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMELGV T0324 154 :PQNALFIGDSVSDEQTAQAANVDFGLAVW 1rdfA 178 :MNHMIKVGDTVSDMKEGRNAGMWTVGVIL T0324 183 :GMDPNADHQKVA 1rdfA 211 :LGLTEEEVENMD T0324 200 :PLDILELFK 1rdfA 223 :SVELREKIE Number of specific fragments extracted= 12 number of extra gaps= 1 total=480 Number of alignments=46 # 1rdfA read from 1rdfA/merged-good-all-a2m # found chain 1rdfA in template set Warning: unaligning (T0324)T2 because first residue in template chain is (1rdfA)K5 Warning: unaligning (T0324)A153 because of BadResidue code BAD_PEPTIDE at template residue (1rdfA)P177 T0324 3 :YQALMFDIDGTLTN 1rdfA 6 :IEAVIFDWAGTTVD T0324 20 :AYTTVMREVLATYGKPFSPAQAQKTF 1rdfA 24 :APLEVFMEIFHKRGVAITAEEARKPM T0324 46 :PMAAEQAMTEL 1rdfA 63 :MPRIASEWNRV T0324 57 :GIAASEFDHFQAQYEDVMASHYD 1rdfA 77 :LPTEADIQEMYEEFEEILFAILP T0324 80 :QIELYPGITSLFEQLP 1rdfA 101 :YASPINAVKEVIASLR T0324 96 :SELRLGIVTSQRRNELESGMRSY 1rdfA 118 :RGIKIGSTTGYTREMMDIVAKEA T0324 119 :PFM 1rdfA 144 :GYK T0324 124 :MAVTISADDTPKRKPDPLPLLTALEKVNV 1rdfA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMELGV T0324 154 :PQNALFIGDSVSDEQTAQAANVDFGLAVWG 1rdfA 178 :MNHMIKVGDTVSDMKEGRNAGMWTVGVILG T0324 184 :MDPNADH 1rdfA 212 :GLTEEEV T0324 191 :QKVAHRFQKPLDILELFK 1rdfA 240 :NGAHFTIETMQELESVME Number of specific fragments extracted= 11 number of extra gaps= 1 total=491 Number of alignments=47 # 1rdfA read from 1rdfA/merged-good-all-a2m # found chain 1rdfA in template set Warning: unaligning (T0324)T2 because first residue in template chain is (1rdfA)K5 Warning: unaligning (T0324)A153 because of BadResidue code BAD_PEPTIDE at template residue (1rdfA)P177 T0324 3 :YQALMFDIDGTLTNSQ 1rdfA 6 :IEAVIFDWAGTTVDYG T0324 20 :AYTTVMREVLATYGKPFSPAQAQKTFPM 1rdfA 24 :APLEVFMEIFHKRGVAITAEEARKPMPL T0324 48 :AAEQAMTELGI 1rdfA 65 :RIASEWNRVFR T0324 59 :AASEFDHF 1rdfA 79 :TEADIQEM T0324 67 :QAQYEDVMASHYDQIELYPGITSLFEQLPS 1rdfA 88 :EEFEEILFAILPRYASPINAVKEVIASLRE T0324 97 :ELRLGIVTSQRRNELE 1rdfA 119 :GIKIGSTTGYTREMMD T0324 113 :SGMRSYPFM 1rdfA 138 :KEAALQGYK T0324 124 :MAVTISADDTPKRKPDPLPLLTALEKVNV 1rdfA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMELGV T0324 154 :PQNALFIGDSVSDEQTAQAANVDFGLAVWG 1rdfA 178 :MNHMIKVGDTVSDMKEGRNAGMWTVGVILG T0324 184 :MDPNADHQKVA 1rdfA 212 :GLTEEEVENMD Number of specific fragments extracted= 10 number of extra gaps= 1 total=501 Number of alignments=48 # 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 # T0324 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 (T0324)T2 because first residue in template chain is (2fdrA)G3 Warning: unaligning (T0324)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fdrA)D10 Warning: unaligning (T0324)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fdrA)D10 T0324 3 :YQALM 2fdrA 4 :FDLII T0324 10 :IDGTLTNSQPAYTTVMREVLATYGKPFSPAQA 2fdrA 11 :CDGVLVDSEIIAAQVESRLLTEAGYPISVEEM T0324 42 :QKTFPMAAEQAMTEL 2fdrA 44 :ERFAGMTWKNILLQV T0324 57 :GIAASEFDHFQAQYEDVMAS 2fdrA 65 :PLSASLLDKSEKLLDMRLER T0324 80 :QIELYPGITSLFEQLP 2fdrA 85 :DVKIIDGVKFALSRLT T0324 98 :LRLGIVTSQRRNELESGMRSYPFMMRM 2fdrA 101 :TPRCICSNSSSHRLDMMLTKVGLKPYF T0324 126 :VTISAD 2fdrA 130 :HIYSAK T0324 132 :DTPKRKPDPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFGLAVWGMDPNADH 2fdrA 138 :GADRVKPKPDIFLHGAAQFGVSPDRVVVVEDSVHGIHGARAAGMRVIGFTGASHTYPSH T0324 191 :QKVAHRFQKPLDILELFK 2fdrA 203 :AGAETVISRMQDLPAVIA Number of specific fragments extracted= 9 number of extra gaps= 1 total=510 Number of alignments=49 # 2fdrA read from 2fdrA/merged-good-all-a2m # found chain 2fdrA in template set Warning: unaligning (T0324)T2 because first residue in template chain is (2fdrA)G3 Warning: unaligning (T0324)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fdrA)D10 Warning: unaligning (T0324)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fdrA)D10 T0324 3 :YQALM 2fdrA 4 :FDLII T0324 10 :IDGTLTNSQPAYTTVMREVLATYGKPFSPAQAQKTFPMAAEQAMTEL 2fdrA 11 :CDGVLVDSEIIAAQVESRLLTEAGYPISVEEMGERFAGMTWKNILLQ T0324 57 :GIAASEFDHFQAQYEDVMASH 2fdrA 65 :PLSASLLDKSEKLLDMRLERD T0324 81 :IELYPGITSLFEQLP 2fdrA 86 :VKIIDGVKFALSRLT T0324 98 :LRLGIVTSQRRNELESGMRSYPFMMRM 2fdrA 101 :TPRCICSNSSSHRLDMMLTKVGLKPYF T0324 125 :AVTIS 2fdrA 129 :PHIYS T0324 130 :ADDTPKRK 2fdrA 138 :GADRVKPK T0324 140 :PLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFGLAVWGMDPNADH 2fdrA 146 :PDIFLHGAAQFGVSPDRVVVVEDSVHGIHGARAAGMRVIGFTGASHTYPSH T0324 191 :QKVAHRFQKPLDILELFK 2fdrA 203 :AGAETVISRMQDLPAVIA Number of specific fragments extracted= 9 number of extra gaps= 1 total=519 Number of alignments=50 # 2fdrA read from 2fdrA/merged-good-all-a2m # found chain 2fdrA in template set Warning: unaligning (T0324)T2 because first residue in template chain is (2fdrA)G3 Warning: unaligning (T0324)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fdrA)D10 Warning: unaligning (T0324)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fdrA)D10 T0324 3 :YQALM 2fdrA 4 :FDLII T0324 10 :IDGTLTNSQPAYTTVMREVLATYGKPFSPAQAQKTFPMAAEQAMTELGI 2fdrA 11 :CDGVLVDSEIIAAQVESRLLTEAGYPISVEEMGERFAGMTWKNILLQVE T0324 59 :AASEFDHFQAQYEDVMAS 2fdrA 67 :SASLLDKSEKLLDMRLER T0324 80 :QIELYPGITSLFEQLP 2fdrA 85 :DVKIIDGVKFALSRLT T0324 98 :LRLGIVTSQRRNELESGMRSYPFMMRM 2fdrA 101 :TPRCICSNSSSHRLDMMLTKVGLKPYF T0324 125 :AVTISADD 2fdrA 129 :PHIYSAKD T0324 133 :TPKRKPDPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFGLAVWGMDPNADH 2fdrA 139 :ADRVKPKPDIFLHGAAQFGVSPDRVVVVEDSVHGIHGARAAGMRVIGFTGASHTYPSH T0324 191 :QKVAHRFQKPLDILELFK 2fdrA 203 :AGAETVISRMQDLPAVIA Number of specific fragments extracted= 8 number of extra gaps= 1 total=527 Number of alignments=51 # 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 # T0324 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 (T0324)F8 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1lvhA)L9 Warning: unaligning (T0324)I10 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1lvhA)L9 T0324 1 :M 1lvhA 1 :M T0324 3 :YQALM 1lvhA 2 :FKAVL T0324 11 :DGTLTNSQPAYTTVMREVLATYGK 1lvhA 10 :DGVITDTAEYHFRAWKALAEEIGI T0324 35 :PFSPAQAQKTFPMAAEQAMTEL 1lvhA 35 :GVDRQFNEQLKGVSREDSLQKI T0324 57 :GIAASEFDHFQAQYEDVMASHYDQIEL 1lvhA 63 :KVSAEEFKELAKRKNDNYVKMIQDVSP T0324 84 :YPGITSLFEQLPS 1lvhA 93 :YPGILQLLKDLRS T0324 97 :ELRLGIVTSQ 1lvhA 107 :KIKIALASAS T0324 109 :NELESGMRSYPFMMRMAVTISADDTPKRKPDPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFGLAV 1lvhA 117 :KNGPFLLERMNLTGYFDAIADPAEVAASKPAPDIFIAAAHAVGVAPSESIGLEDSQAGIQAIKDSGALPIGVG T0324 186 :PNADH 1lvhA 190 :RPEDL T0324 191 :QKV 1lvhA 196 :DDI T0324 195 :HRFQ 1lvhA 199 :VIVP T0324 199 :KPLDILELF 1lvhA 208 :TLEFLKEVW Number of specific fragments extracted= 12 number of extra gaps= 0 total=539 Number of alignments=52 # 1lvhA read from 1lvhA/merged-good-all-a2m # found chain 1lvhA in template set Warning: unaligning (T0324)F8 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1lvhA)L9 Warning: unaligning (T0324)I10 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1lvhA)L9 T0324 1 :M 1lvhA 1 :M T0324 3 :YQALM 1lvhA 2 :FKAVL T0324 11 :DGTLTNSQPAYTTVMREVLATYGKPFS 1lvhA 10 :DGVITDTAEYHFRAWKALAEEIGINGV T0324 38 :PAQAQKTFPMAAEQAMTEL 1lvhA 41 :NEQLKGVSREDSLQKILDL T0324 57 :GIAASEFDHFQAQYEDVMASHYDQIEL 1lvhA 63 :KVSAEEFKELAKRKNDNYVKMIQDVSP T0324 84 :YPGITSLFEQLP 1lvhA 93 :YPGILQLLKDLR T0324 96 :SELRLGIVTSQ 1lvhA 106 :NKIKIALASAS T0324 109 :NELESGMRSYPFMMRMAVTISADDTPKRKPDPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFGLA 1lvhA 117 :KNGPFLLERMNLTGYFDAIADPAEVAASKPAPDIFIAAAHAVGVAPSESIGLEDSQAGIQAIKDSGALPIGV T0324 185 :DPNADH 1lvhA 189 :GRPEDL T0324 191 :QKV 1lvhA 196 :DDI T0324 195 :HRFQKPLD 1lvhA 199 :VIVPDTSH T0324 203 :ILELF 1lvhA 212 :LKEVW Number of specific fragments extracted= 12 number of extra gaps= 0 total=551 Number of alignments=53 # 1lvhA read from 1lvhA/merged-good-all-a2m # found chain 1lvhA in template set Warning: unaligning (T0324)T2 because first residue in template chain is (1lvhA)M1 Warning: unaligning (T0324)F8 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1lvhA)L9 Warning: unaligning (T0324)I10 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1lvhA)L9 T0324 3 :YQALM 1lvhA 2 :FKAVL T0324 11 :DGTLTNSQPAYTTVMREVLATYGKPFSPAQAQKTFPMAAEQAMTELGI 1lvhA 10 :DGVITDTAEYHFRAWKALAEEIGINGVDRQFNEQLKGVSREDSLQKIL T0324 59 :AASEFDHFQAQYEDVMASHYDQIEL 1lvhA 65 :SAEEFKELAKRKNDNYVKMIQDVSP T0324 84 :YPGITSLFEQLPS 1lvhA 93 :YPGILQLLKDLRS T0324 97 :ELRLGIVTSQR 1lvhA 107 :KIKIALASASK T0324 110 :ELESGMRSYPFMMRMAVTISADDTPKRKPDPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFGLA 1lvhA 118 :NGPFLLERMNLTGYFDAIADPAEVAASKPAPDIFIAAAHAVGVAPSESIGLEDSQAGIQAIKDSGALPIGV T0324 185 :DPNADH 1lvhA 189 :GRPEDL T0324 191 :QKVAHRFQ 1lvhA 196 :DDIVIVPD T0324 199 :KPLDILELF 1lvhA 208 :TLEFLKEVW Number of specific fragments extracted= 9 number of extra gaps= 0 total=560 Number of alignments=54 # 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 # T0324 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 T0324 2 :TYQALMFDIDGTLTNSQ 1f5sA 4 :KKKLILFDFDSTLVNNE T0324 24 :VMREVLATYGK 1f5sA 21 :TIDEIAREAGV T0324 38 :PAQAQKTF 1f5sA 32 :EEEVKKIT T0324 46 :PMAAEQAMTEL 1f5sA 46 :KLNFEQSLRKR T0324 57 :GIAASEFDHFQA 1f5sA 62 :DLPIEKVEKAIK T0324 80 :QIELYPGITSLFEQLPS 1f5sA 74 :RITPTEGAEETIKELKN T0324 97 :ELRLGIVTSQRRNELESGMRSYPFMMRMAVTISADDT 1f5sA 92 :GYVVAVVSGGFDIAVNKIKEKLGLDYAFANRLIVKDG T0324 134 :PK 1f5sA 140 :KE T0324 140 :PLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAAN 1f5sA 145 :GEILEKIAKIEGINLEDTVAVGDGANDISMFKKAG T0324 176 :DFGLAVWG 1f5sA 180 :LKIAFCAK T0324 188 :ADH 1f5sA 188 :PIL T0324 191 :QKVAHRFQ 1f5sA 192 :EKADICIE T0324 199 :KPLDILELFK 1f5sA 202 :DLREILKYIK Number of specific fragments extracted= 13 number of extra gaps= 0 total=573 Number of alignments=55 # 1f5sA read from 1f5sA/merged-good-all-a2m # found chain 1f5sA in template set T0324 3 :YQALMFDIDGTLTNSQ 1f5sA 5 :KKLILFDFDSTLVNNE T0324 24 :VMREVLATYGK 1f5sA 21 :TIDEIAREAGV T0324 38 :PAQAQKT 1f5sA 32 :EEEVKKI T0324 50 :EQAMTEL 1f5sA 39 :TKEAMEG T0324 63 :FDHFQAQYEDVMASHYDQIELYPGITSLFEQLP 1f5sA 57 :VSLLKDLPIEKVEKAIKRITPTEGAEETIKELK T0324 96 :SELRLGIVTSQRRNELESGMRSYPFMMRMAVTISADDT 1f5sA 91 :RGYVVAVVSGGFDIAVNKIKEKLGLDYAFANRLIVKDG T0324 135 :K 1f5sA 141 :E T0324 137 :K 1f5sA 144 :K T0324 140 :PLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAAN 1f5sA 145 :GEILEKIAKIEGINLEDTVAVGDGANDISMFKKAG T0324 176 :DFGLA 1f5sA 180 :LKIAF T0324 184 :MDPNADHQKVAHRF 1f5sA 185 :CAKPILKEKADICI T0324 198 :QKPLDILELFK 1f5sA 201 :RDLREILKYIK Number of specific fragments extracted= 12 number of extra gaps= 0 total=585 Number of alignments=56 # 1f5sA read from 1f5sA/merged-good-all-a2m # found chain 1f5sA in template set T0324 2 :TYQALMFDIDGTLTNSQ 1f5sA 4 :KKKLILFDFDSTLVNNE T0324 24 :VMREVLATYGK 1f5sA 21 :TIDEIAREAGV T0324 38 :PAQAQKTF 1f5sA 32 :EEEVKKIT T0324 46 :PMAAEQAMTELGI 1f5sA 46 :KLNFEQSLRKRVS T0324 59 :AASEFDHFQAQY 1f5sA 61 :KDLPIEKVEKAI T0324 79 :DQIELYPGITSLFEQLPS 1f5sA 73 :KRITPTEGAEETIKELKN T0324 97 :ELRLGIVTSQRRNELESGMRSYPFMMRMAVTISADD 1f5sA 92 :GYVVAVVSGGFDIAVNKIKEKLGLDYAFANRLIVKD T0324 135 :KRKPDPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAAN 1f5sA 140 :KENAKGEILEKIAKIEGINLEDTVAVGDGANDISMFKKAG T0324 176 :DFGLAVWG 1f5sA 180 :LKIAFCAK T0324 188 :ADH 1f5sA 188 :PIL T0324 191 :QKVAHRFQK 1f5sA 192 :EKADICIEK Number of specific fragments extracted= 11 number of extra gaps= 0 total=596 Number of alignments=57 # 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 # T0324 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 (T0324)V164 because of BadResidue code BAD_PEPTIDE in next template residue (2b8eA)N621 Warning: unaligning (T0324)S165 because of BadResidue code BAD_PEPTIDE at template residue (2b8eA)N621 Warning: unaligning (T0324)D166 because of BadResidue code BAD_PEPTIDE at template residue (2b8eA)D622 Warning: unaligning (T0324)V181 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b8eA)S645 Warning: unaligning (T0324)W182 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b8eA)S645 T0324 3 :YQALMFD 2b8eA 418 :VTAVIFD T0324 14 :LTNSQPAYTTVMREVLATYGK 2b8eA 439 :LVPLNGDERELLRLAAIAERR T0324 35 :PFSP 2b8eA 461 :EHPI T0324 39 :AQAQKTF 2b8eA 466 :EAIVKKA T0324 50 :EQAMTELGIAAS 2b8eA 503 :KRLMEDFGVAVS T0324 64 :DHFQAQYEDVMASHY 2b8eA 515 :NEVELALEKLEREAK T0324 81 :IELYPGITSLFEQLPS 2b8eA 548 :DTLKESAKPAVQELKR T0324 97 :ELRLGIVTSQRRNELESGMRSYPFM 2b8eA 565 :GIKVGMITGDNWRSAEAISRELNLD T0324 127 :TISADDT 2b8eA 590 :LVIAEVL T0324 140 :PLPLLTALEKVN 2b8eA 597 :PHQKSEEVKKLQ T0324 154 :PQNALFIGDS 2b8eA 610 :KEVVAFVGDG T0324 167 :EQTAQAAN 2b8eA 623 :APALAQAD T0324 176 :DFGLA 2b8eA 631 :LGIAV T0324 183 :G 2b8eA 646 :G T0324 194 :AHRF 2b8eA 647 :DIVL T0324 198 :QKPLDILELFK 2b8eA 653 :DDLRDVVAAIQ Number of specific fragments extracted= 16 number of extra gaps= 2 total=612 Number of alignments=58 # 2b8eA read from 2b8eA/merged-good-all-a2m # found chain 2b8eA in template set Warning: unaligning (T0324)V164 because of BadResidue code BAD_PEPTIDE in next template residue (2b8eA)N621 Warning: unaligning (T0324)S165 because of BadResidue code BAD_PEPTIDE at template residue (2b8eA)N621 Warning: unaligning (T0324)D166 because of BadResidue code BAD_PEPTIDE at template residue (2b8eA)D622 Warning: unaligning (T0324)G183 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b8eA)S645 Warning: unaligning (T0324)M184 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b8eA)S645 T0324 3 :YQALMFDIDGTLTN 2b8eA 418 :VTAVIFDKTGTLTK T0324 17 :SQPAYTTVMREVLATYGKPFS 2b8eA 460 :SEHPIAEAIVKKALEHGIELG T0324 50 :EQAMTELGIA 2b8eA 503 :KRLMEDFGVA T0324 66 :FQAQYEDVMASHYDQI 2b8eA 513 :VSNEVELALEKLEREA T0324 82 :ELYPGITSLFEQLP 2b8eA 549 :TLKESAKPAVQELK T0324 96 :SELRLGIVTSQRRNELESGMRSYPFM 2b8eA 564 :MGIKVGMITGDNWRSAEAISRELNLD T0324 127 :TISADDT 2b8eA 590 :LVIAEVL T0324 140 :PLPLLTALEKVN 2b8eA 597 :PHQKSEEVKKLQ T0324 154 :PQNALFIGDS 2b8eA 610 :KEVVAFVGDG T0324 167 :EQTAQAAN 2b8eA 623 :APALAQAD T0324 178 :GLAVW 2b8eA 631 :LGIAV T0324 185 :D 2b8eA 646 :G T0324 194 :AHRF 2b8eA 647 :DIVL T0324 198 :QKPLDILELFK 2b8eA 653 :DDLRDVVAAIQ Number of specific fragments extracted= 14 number of extra gaps= 2 total=626 Number of alignments=59 # 2b8eA read from 2b8eA/merged-good-all-a2m # found chain 2b8eA in template set Warning: unaligning (T0324)V164 because of BadResidue code BAD_PEPTIDE in next template residue (2b8eA)N621 Warning: unaligning (T0324)S165 because of BadResidue code BAD_PEPTIDE at template residue (2b8eA)N621 Warning: unaligning (T0324)D166 because of BadResidue code BAD_PEPTIDE at template residue (2b8eA)D622 Warning: unaligning (T0324)G183 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b8eA)S645 Warning: unaligning (T0324)M184 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b8eA)S645 T0324 3 :YQALMFD 2b8eA 418 :VTAVIFD T0324 14 :LTNSQPAYTTVMREVLA 2b8eA 439 :LVPLNGDERELLRLAAI T0324 41 :AQKTFPMAAEQAMTELGI 2b8eA 456 :AERRSEHPIAEAIVKKAL T0324 59 :AASEFDHFQAQYEDVMASHY 2b8eA 510 :GVAVSNEVELALEKLEREAK T0324 81 :IELYPGITSLFEQLPS 2b8eA 548 :DTLKESAKPAVQELKR T0324 97 :ELRLGIVTSQRRNELESGMRSYPFM 2b8eA 565 :GIKVGMITGDNWRSAEAISRELNLD T0324 127 :TISADDT 2b8eA 590 :LVIAEVL T0324 140 :PLPLLTALEKVN 2b8eA 597 :PHQKSEEVKKLQ T0324 154 :PQNALFIGDS 2b8eA 610 :KEVVAFVGDG T0324 167 :EQTAQAAN 2b8eA 623 :APALAQAD T0324 176 :DFGLA 2b8eA 631 :LGIAV T0324 185 :D 2b8eA 646 :G T0324 194 :AHRF 2b8eA 647 :DIVL T0324 198 :QKPLDILELFK 2b8eA 653 :DDLRDVVAAIQ Number of specific fragments extracted= 14 number of extra gaps= 2 total=640 Number of alignments=60 # 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:# T0324 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 (T0324)T2 because first residue in template chain is (1vj5A)T2 T0324 3 :YQALMFDIDGTLTNS 1vj5A 3 :LRAAVFDLDGVLALP T0324 24 :VMREVLATYGKP 1vj5A 22 :VLGRTEEALALP T0324 38 :PAQAQKTF 1vj5A 34 :RGLLNDAF T0324 46 :PMAAEQAMTEL 1vj5A 57 :EITLSQWIPLM T0324 57 :GIAAS 1vj5A 81 :CLPKN T0324 63 :FD 1vj5A 86 :FS T0324 70 :YEDVMASHYDQIELYPGITSLFEQLPS 1vj5A 88 :IKEIFDKAISARKINRPMLQAALMLRK T0324 97 :ELRLGIVTS 1vj5A 116 :GFTTAILTN T0324 106 :QRRNELESGMRSYPF 1vj5A 131 :AERDGLAQLMCELKM T0324 123 :RMAVTISADDTPKRKPDPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFG 1vj5A 146 :HFDFLIESCQVGMVKPEPQIYKFLLDTLKASPSEVVFLDDIGANLKPARDLGMVTI T0324 196 :RFQKPLDILELFK 1vj5A 202 :LVQDTDTALKELE Number of specific fragments extracted= 11 number of extra gaps= 0 total=651 Number of alignments=61 # 1vj5A read from 1vj5A/merged-good-all-a2m # found chain 1vj5A in template set Warning: unaligning (T0324)T2 because first residue in template chain is (1vj5A)T2 T0324 3 :YQALMFDIDGTLTN 1vj5A 3 :LRAAVFDLDGVLAL T0324 17 :SQPAYTTVMREVLATYGKPFSPA 1vj5A 63 :WIPLMEENCRKCSETAKVCLPKN T0324 63 :F 1vj5A 86 :F T0324 69 :QYEDVMASHYDQIELYPGITSLFEQLP 1vj5A 87 :SIKEIFDKAISARKINRPMLQAALMLR T0324 96 :SELRLGIVTSQR 1vj5A 115 :KGFTTAILTNTW T0324 108 :RNELESGMRSYPFM 1vj5A 133 :RDGLAQLMCELKMH T0324 124 :MAVTISADDTPKRKPDPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFG 1vj5A 147 :FDFLIESCQVGMVKPEPQIYKFLLDTLKASPSEVVFLDDIGANLKPARDLGMVTI T0324 196 :RFQKPLDILELFK 1vj5A 202 :LVQDTDTALKELE Number of specific fragments extracted= 8 number of extra gaps= 0 total=659 Number of alignments=62 # 1vj5A read from 1vj5A/merged-good-all-a2m # found chain 1vj5A in template set Warning: unaligning (T0324)T2 because first residue in template chain is (1vj5A)T2 T0324 3 :YQALMFDIDGTLTNSQ 1vj5A 3 :LRAAVFDLDGVLALPA T0324 24 :VMREVLATYGKPFSPAQAQKTFPMAAEQAMTELGI 1vj5A 22 :VLGRTEEALALPRGLLNDAFQKGGPEGATTRLMKG T0324 59 :AASEFDHFQAQYEDVMASHYDQIE 1vj5A 60 :LSQWIPLMEENCRKCSETAKVCLP T0324 83 :LYPGITSLFEQLPS 1vj5A 101 :INRPMLQAALMLRK T0324 97 :ELRLGIVTS 1vj5A 116 :GFTTAILTN T0324 106 :QRRNELESGMRSYPF 1vj5A 131 :AERDGLAQLMCELKM T0324 123 :RMAVTISADDTPKRKPDPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFG 1vj5A 146 :HFDFLIESCQVGMVKPEPQIYKFLLDTLKASPSEVVFLDDIGANLKPARDLGMVTI T0324 196 :RFQKPLDILELFK 1vj5A 202 :LVQDTDTALKELE Number of specific fragments extracted= 8 number of extra gaps= 0 total=667 Number of alignments=63 # 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 # T0324 read from 1o08A/merged-good-all-a2m # 1o08A read from 1o08A/merged-good-all-a2m # found chain 1o08A in training set Warning: unaligning (T0324)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o08A)D1008 Warning: unaligning (T0324)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o08A)D1008 T0324 1 :M 1o08A 1001 :M T0324 3 :YQALM 1o08A 1002 :FKAVL T0324 10 :IDGTLTNSQPAYTTVMREVLATYGK 1o08A 1009 :LDGVITDTAEYHFRAWKALAEEIGI T0324 35 :PFSPAQAQKTFPMAAEQAMTEL 1o08A 1035 :GVDRQFNEQLKGVSREDSLQKI T0324 57 :GIAASEFDHFQAQYEDVMASHYDQIE 1o08A 1063 :KVSAEEFKELAKRKNDNYVKMIQDVS T0324 83 :LYPGITSLFEQLPS 1o08A 1092 :VYPGILQLLKDLRS T0324 97 :ELRLGIVTSQ 1o08A 1107 :KIKIALASAS T0324 109 :NELESGMRSYPFMMRMAVTISADDTPKRKPDPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFGLAVW 1o08A 1117 :KNGPFLLERMNLTGYFDAIADPAEVAASKPAPDIFIAAAHAVGVAPSESIGLEDSQAGIQAIKDSGALPIGVGR T0324 191 :QKVAHRFQK 1o08A 1195 :GDDIVIVPD T0324 200 :PLDILELF 1o08A 1209 :LEFLKEVW Number of specific fragments extracted= 10 number of extra gaps= 1 total=677 Number of alignments=64 # 1o08A read from 1o08A/merged-good-all-a2m # found chain 1o08A in training set Warning: unaligning (T0324)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o08A)D1008 Warning: unaligning (T0324)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o08A)D1008 T0324 1 :M 1o08A 1001 :M T0324 3 :YQALM 1o08A 1002 :FKAVL T0324 10 :IDGTLTNSQPAYTTVMREVLATYGKPFSPAQAQKTFPMAAEQAMTEL 1o08A 1009 :LDGVITDTAEYHFRAWKALAEEIGINGVDRQFNEQLKGVSREDSLQK T0324 57 :GIAASEFDHFQAQYEDVMASHYDQIE 1o08A 1063 :KVSAEEFKELAKRKNDNYVKMIQDVS T0324 83 :LYPGITSLFEQLP 1o08A 1092 :VYPGILQLLKDLR T0324 96 :SELRLGIVTSQ 1o08A 1106 :NKIKIALASAS T0324 109 :NELESGMRSYPFMMRMAVTISADDTPKRKPDPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFGLAVW 1o08A 1117 :KNGPFLLERMNLTGYFDAIADPAEVAASKPAPDIFIAAAHAVGVAPSESIGLEDSQAGIQAIKDSGALPIGVGR T0324 187 :NADHQKVAHRFQKPLD 1o08A 1191 :PEDLGDDIVIVPDTSH T0324 203 :ILELF 1o08A 1212 :LKEVW Number of specific fragments extracted= 9 number of extra gaps= 1 total=686 Number of alignments=65 # 1o08A read from 1o08A/merged-good-all-a2m # found chain 1o08A in training set Warning: unaligning (T0324)T2 because first residue in template chain is (1o08A)M1001 Warning: unaligning (T0324)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o08A)D1008 Warning: unaligning (T0324)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o08A)D1008 T0324 3 :YQALM 1o08A 1002 :FKAVL T0324 10 :IDGTLTNSQPAYTTVMREVLATYGKPFSPAQAQKTFPMAAEQAMTELGI 1o08A 1009 :LDGVITDTAEYHFRAWKALAEEIGINGVDRQFNEQLKGVSREDSLQKIL T0324 59 :AASEFDHFQAQYEDVMASHYDQIE 1o08A 1065 :SAEEFKELAKRKNDNYVKMIQDVS T0324 83 :LYPGITSLFEQLPS 1o08A 1092 :VYPGILQLLKDLRS T0324 97 :ELRLGIVTSQ 1o08A 1107 :KIKIALASAS T0324 109 :NELESGMRSYPFMMRMAVTISADDTPKRKPDPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFGLAV 1o08A 1117 :KNGPFLLERMNLTGYFDAIADPAEVAASKPAPDIFIAAAHAVGVAPSESIGLEDSQAGIQAIKDSGALPIGVG T0324 186 :PNADHQKVAHRFQK 1o08A 1190 :RPEDLGDDIVIVPD T0324 200 :PLDILELF 1o08A 1209 :LEFLKEVW Number of specific fragments extracted= 8 number of extra gaps= 1 total=694 Number of alignments=66 # 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 # T0324 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 (T0324)A5 because of BadResidue code BAD_PEPTIDE at template residue (2g09A)Q45 T0324 6 :LMFDIDGTLTN 2g09A 46 :IITDFDMTLSR T0324 17 :SQPAYTTVMREVLATY 2g09A 77 :VTDECRRKLLQLKEQY T0324 33 :GKPFSPAQAQKTFPMAAEQAMTEL 2g09A 98 :DPVLTVEEKFPYMVEWYTKSHGLL T0324 57 :GIAASEFDHFQAQ 2g09A 125 :GIPKAKLKEIVAD T0324 80 :QIELYPGITSLFEQLPS 2g09A 139 :DVMLKEGYENFFGKLQQ T0324 97 :ELRLGIVTSQRRNELESGMRSYPFMM 2g09A 157 :GIPVFIFSAGIGDVLEEVIRQAGVYH T0324 123 :RMAVT 2g09A 184 :NVKVV T0324 128 :ISADDT 2g09A 192 :MDFDEN T0324 134 :PKRKPDPLPLLTAL 2g09A 204 :KGELIHVFNKHDGA T0324 148 :EKVN 2g09A 225 :SQLK T0324 155 :QNALFIGDSVSD 2g09A 231 :SNIILLGDSQGD T0324 172 :AANV 2g09A 246 :ADGV T0324 176 :DFGLAV 2g09A 254 :HILKIG T0324 195 :HRFQKPLDILELF 2g09A 260 :YLNDRVDELLEKY Number of specific fragments extracted= 14 number of extra gaps= 1 total=708 Number of alignments=67 # 2g09A read from 2g09A/merged-good-all-a2m # found chain 2g09A in template set Warning: unaligning (T0324)A5 because of BadResidue code BAD_PEPTIDE at template residue (2g09A)Q45 T0324 6 :LMFDIDGTLTN 2g09A 46 :IITDFDMTLSR T0324 17 :SQPAYTTVMREVLATY 2g09A 77 :VTDECRRKLLQLKEQY T0324 33 :GKPFSPAQAQKTF 2g09A 98 :DPVLTVEEKFPYM T0324 46 :PMAAEQAMTELGIAASEFDHFQAQ 2g09A 114 :YTKSHGLLIEQGIPKAKLKEIVAD T0324 80 :QIELYPGITSLFEQLP 2g09A 139 :DVMLKEGYENFFGKLQ T0324 96 :SELRLGIVTSQRRNELESGMRSYPFM 2g09A 156 :HGIPVFIFSAGIGDVLEEVIRQAGVY T0324 122 :MRMAVTIS 2g09A 183 :SNVKVVSN T0324 130 :ADDTPKR 2g09A 194 :FDENGVL T0324 146 :ALEKV 2g09A 223 :YFSQL T0324 151 :NV 2g09A 229 :DN T0324 155 :QNALFIGDSVSD 2g09A 231 :SNIILLGDSQGD T0324 173 :A 2g09A 246 :A T0324 174 :NVD 2g09A 248 :GVA T0324 195 :HRF 2g09A 254 :HIL T0324 198 :QKPLDILELF 2g09A 263 :DRVDELLEKY Number of specific fragments extracted= 15 number of extra gaps= 1 total=723 Number of alignments=68 # 2g09A read from 2g09A/merged-good-all-a2m # found chain 2g09A in template set Warning: unaligning (T0324)A5 because of BadResidue code BAD_PEPTIDE at template residue (2g09A)Q45 T0324 6 :LMFDIDGTLTN 2g09A 46 :IITDFDMTLSR T0324 17 :SQPAYTTVMREVLATY 2g09A 77 :VTDECRRKLLQLKEQY T0324 33 :GKPFSPAQAQKTFPMAAEQAMTELGI 2g09A 98 :DPVLTVEEKFPYMVEWYTKSHGLLIE T0324 59 :AASEFDHFQAQ 2g09A 127 :PKAKLKEIVAD T0324 79 :DQIELYPGITSLFEQLPS 2g09A 138 :SDVMLKEGYENFFGKLQQ T0324 97 :ELRLGIVTSQRRNELESGMRSYPFMM 2g09A 157 :GIPVFIFSAGIGDVLEEVIRQAGVYH T0324 123 :RMAVT 2g09A 184 :NVKVV T0324 128 :ISADD 2g09A 192 :MDFDE T0324 134 :PKR 2g09A 209 :HVF T0324 139 :DPLPLLT 2g09A 212 :NKHDGAL T0324 146 :ALEKVN 2g09A 223 :YFSQLK T0324 155 :QNALFIGDSVSD 2g09A 231 :SNIILLGDSQGD T0324 172 :AANVD 2g09A 246 :ADGVA T0324 177 :FGLAV 2g09A 257 :KIGYL T0324 197 :FQKPLDILELF 2g09A 262 :NDRVDELLEKY Number of specific fragments extracted= 15 number of extra gaps= 1 total=738 Number of alignments=69 # 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 # T0324 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 (T0324)S105 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ah5A)K108 Warning: unaligning (T0324)Q106 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ah5A)K108 T0324 2 :TYQALMFDIDGTLTNSQPAYTTVMREVLATYGKP 2ah5A 3 :SITAIFFDLDGTLVDSSIGIHNAFTYTFKELGVP T0324 36 :FSPAQAQKTFPMAAEQAMTE 2ah5A 38 :PDAKTIRGFMGPPLESSFAT T0324 57 :GIAASEFDHFQAQYEDVMASH 2ah5A 58 :CLSKDQISEAVQIYRSYYKAK T0324 78 :YDQIELYPGITSLFEQLPSELRLGIVT 2ah5A 80 :IYEAQLFPQIIDLLEELSSSYPLYITT T0324 107 :RRNELESGMRSYPFMMRMAVTISADDTPKRK 2ah5A 109 :DTSTAQDMAKNLEIHHFFDGIYGSSPEAPHK T0324 140 :PLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFGLAVWGMDPNADH 2ah5A 140 :ADVIHQALQTHQLAPEQAIIIGDTKFDMLGARETGIQKLAITWGFGEQADL T0324 191 :QKVAHRFQKPLDILELFK 2ah5A 193 :YQPDYIAHKPLEVLAYFQ Number of specific fragments extracted= 7 number of extra gaps= 1 total=745 Number of alignments=70 # 2ah5A read from 2ah5A/merged-good-all-a2m # found chain 2ah5A in template set Warning: unaligning (T0324)S105 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ah5A)K108 Warning: unaligning (T0324)Q106 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ah5A)K108 T0324 1 :MT 2ah5A 1 :MT T0324 3 :YQALMFDIDGTLTNSQPAYTTVMREVLATYGKPFSPAQAQKTFPMAAEQAMTELGIAASEFDHFQAQYEDVMASHYD 2ah5A 4 :ITAIFFDLDGTLVDSSIGIHNAFTYTFKELGVPSPDAKTIRGFMGPPLESSFATCLSKDQISEAVQIYRSYYKAKGI T0324 80 :QIELYPGITSLFEQLPSELRLGIVT 2ah5A 82 :EAQLFPQIIDLLEELSSSYPLYITT T0324 107 :RRNELESGMRSYPFMMRMAVTISADDTPKRK 2ah5A 109 :DTSTAQDMAKNLEIHHFFDGIYGSSPEAPHK T0324 140 :PLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFGLAVWGMDPNADH 2ah5A 140 :ADVIHQALQTHQLAPEQAIIIGDTKFDMLGARETGIQKLAITWGFGEQADL T0324 191 :QKVAHRFQKPLDILELFK 2ah5A 193 :YQPDYIAHKPLEVLAYFQ Number of specific fragments extracted= 6 number of extra gaps= 1 total=751 Number of alignments=71 # 2ah5A read from 2ah5A/merged-good-all-a2m # found chain 2ah5A in template set Warning: unaligning (T0324)S105 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ah5A)K108 Warning: unaligning (T0324)Q106 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ah5A)K108 T0324 3 :YQALMFDIDGTLTNSQPAYTTVMREVLATYGKPFSPAQAQKTFPMAAEQAMTELGIAASEFDHFQAQYEDVMAS 2ah5A 4 :ITAIFFDLDGTLVDSSIGIHNAFTYTFKELGVPSPDAKTIRGFMGPPLESSFATCLSKDQISEAVQIYRSYYKA T0324 77 :HYDQIELYPGITSLFEQLPSELRLGIVT 2ah5A 79 :GIYEAQLFPQIIDLLEELSSSYPLYITT T0324 107 :RRNELESGMRSYPFMMRMAVTISADDTPKRK 2ah5A 109 :DTSTAQDMAKNLEIHHFFDGIYGSSPEAPHK T0324 140 :PLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFGLAVWGMDPNADH 2ah5A 140 :ADVIHQALQTHQLAPEQAIIIGDTKFDMLGARETGIQKLAITWGFGEQADL T0324 191 :QKVAHRFQKPLDILELF 2ah5A 193 :YQPDYIAHKPLEVLAYF Number of specific fragments extracted= 5 number of extra gaps= 1 total=756 Number of alignments=72 # 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 # T0324 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 (T0324)G57 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1zs9A)K106 Warning: unaligning (T0324)A59 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1zs9A)K106 T0324 3 :YQALMFDIDGTLTN 1zs9A 10 :VTVILLDIEGTTTP T0324 17 :SQPAYTTVMREVLATYGKP 1zs9A 31 :LFPYIEENVKEYLQTHWEE T0324 39 :AQAQKTF 1zs9A 50 :EECQQDV T0324 46 :PMAAEQAMTEL 1zs9A 80 :GNGVDDLQQMI T0324 60 :ASEFDHFQAQYEDVMASHYD 1zs9A 107 :TTALKQLQGHMWRAAFTAGR T0324 80 :QIELYPGITSLFEQLPS 1zs9A 128 :KAEFFADVVPAVRKWRE T0324 97 :ELRLGIVTSQRRNELESGMRSY 1zs9A 146 :GMKVYIYSSGSVEAQKLLFGHS T0324 119 :PFMMRMAVTISADDTPKRK 1zs9A 171 :DILELVDGHFDTKIGHKVE T0324 140 :PLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFGLAVWGMDPNADH 1zs9A 190 :SESYRKIADSIGCSTNNILFLTDVTREASAAEEADVHVAVVVRPGNAGLTD T0324 193 :V 1zs9A 246 :Y T0324 195 :HRFQKPLD 1zs9A 247 :SLITSFSE Number of specific fragments extracted= 11 number of extra gaps= 0 total=767 Number of alignments=73 # 1zs9A read from 1zs9A/merged-good-all-a2m # found chain 1zs9A in template set Warning: unaligning (T0324)G57 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1zs9A)K106 Warning: unaligning (T0324)A59 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1zs9A)K106 T0324 3 :YQALMFDIDGTLTN 1zs9A 10 :VTVILLDIEGTTTP T0324 17 :SQPAYTTVMREVLATYGK 1zs9A 31 :LFPYIEENVKEYLQTHWE T0324 47 :MAAEQAMTEL 1zs9A 49 :EEECQQDVSL T0324 60 :ASEFDHFQAQYEDVMASHYD 1zs9A 107 :TTALKQLQGHMWRAAFTAGR T0324 80 :QIELYPGITSLFEQLP 1zs9A 128 :KAEFFADVVPAVRKWR T0324 96 :SELRLGIVTSQRRNELESGMRSY 1zs9A 145 :AGMKVYIYSSGSVEAQKLLFGHS T0324 119 :PFMMRMAVTISADDTPKRK 1zs9A 171 :DILELVDGHFDTKIGHKVE T0324 140 :PLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFGLAVWGMDPNADH 1zs9A 190 :SESYRKIADSIGCSTNNILFLTDVTREASAAEEADVHVAVVVRPGNAGLTD T0324 193 :VA 1zs9A 246 :YS T0324 196 :RFQKPLD 1zs9A 248 :LITSFSE Number of specific fragments extracted= 10 number of extra gaps= 0 total=777 Number of alignments=74 # 1zs9A read from 1zs9A/merged-good-all-a2m # found chain 1zs9A in template set T0324 3 :YQALMFDIDGTLTNSQ 1zs9A 10 :VTVILLDIEGTTTPIA T0324 19 :PAYTTVMREVLATY 1zs9A 33 :PYIEENVKEYLQTH T0324 33 :GKPFSPAQAQKTFPMAAEQAMTELGI 1zs9A 77 :AASGNGVDDLQQMIQAVVDNVCWQMS T0324 59 :AASEFDHFQAQYEDVMASHYDQIELYPGITSLFEQLPS 1zs9A 107 :TTALKQLQGHMWRAAFTAGRMKAEFFADVVPAVRKWRE T0324 97 :ELRLGIVTSQRRNELESGMRSY 1zs9A 146 :GMKVYIYSSGSVEAQKLLFGHS T0324 119 :PFMMRMAVTISADDTPKR 1zs9A 171 :DILELVDGHFDTKIGHKV T0324 139 :DPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFGLAVWGMDPNA 1zs9A 189 :ESESYRKIADSIGCSTNNILFLTDVTREASAAEEADVHVAVVVRPGNAGL Number of specific fragments extracted= 7 number of extra gaps= 0 total=784 Number of alignments=75 # 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 # T0324 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 T0324 1 :M 1x42A 1 :M T0324 3 :YQALMFDIDGTLT 1x42A 2 :IRAVFFDFVGTLL T0324 17 :SQPAYTTVMREVLATY 1x42A 15 :SVEGEAKTHLKIMEEV T0324 33 :GKPFSPAQAQKTFPMAAEQAMTEL 1x42A 33 :DYPLNPKTLLDEYEKLTREAFSNY T0324 57 :GIA 1x42A 80 :GFK T0324 62 :EFDHFQAQYEDVMAS 1x42A 83 :YPENFWEIHLRMHQR T0324 80 :QIELYPGITSLFEQLPSELRLGIVTSQRRNELESGMRSYPFMMRMAVTISADDTPKRKPDPLPLLTALEKVNVAPQNALFIGDSV 1x42A 98 :YGELYPEVVEVLKSLKGKYHVGMITDSDTEYLMAHLDALGIKDLFDSITTSEEAGFFKPHPRIFELALKKAGVKGEEAVYVGDNP T0324 165 :SDEQTAQAANVDFGLAVWGMDPNADHQKVAHRFQKPLDILELFK 1x42A 184 :KDCGGSKNLGMTSILLDRKGEKREFWDKCDFIVSDLREVIKIVD Number of specific fragments extracted= 8 number of extra gaps= 0 total=792 Number of alignments=76 # 1x42A read from 1x42A/merged-good-all-a2m # found chain 1x42A in template set T0324 1 :M 1x42A 1 :M T0324 3 :YQALMFDIDGTLTN 1x42A 2 :IRAVFFDFVGTLLS T0324 18 :QPAYTTVMREVLATY 1x42A 16 :VEGEAKTHLKIMEEV T0324 33 :GKPFSPAQAQKTFPMAAEQAMTEL 1x42A 33 :DYPLNPKTLLDEYEKLTREAFSNY T0324 57 :GIAASEFDHFQAQYEDVMASH 1x42A 78 :KYGFKYPENFWEIHLRMHQRY T0324 81 :IELYPGITSLFEQLPSELRLGIVTSQRRNELESGMRSYPFMMRMAVTISADDTPKRKPDPLPLLTALEKVNVAPQNALFIGDSV 1x42A 99 :GELYPEVVEVLKSLKGKYHVGMITDSDTEYLMAHLDALGIKDLFDSITTSEEAGFFKPHPRIFELALKKAGVKGEEAVYVGDNP T0324 165 :SDEQTAQAANVDFGLAVWGMDPNADHQKVAHRFQKPLDILELFK 1x42A 184 :KDCGGSKNLGMTSILLDRKGEKREFWDKCDFIVSDLREVIKIVD Number of specific fragments extracted= 7 number of extra gaps= 0 total=799 Number of alignments=77 # 1x42A read from 1x42A/merged-good-all-a2m # found chain 1x42A in template set Warning: unaligning (T0324)T2 because first residue in template chain is (1x42A)M1 T0324 3 :YQALMFDIDGTLT 1x42A 2 :IRAVFFDFVGTLL T0324 17 :SQPAYTTVMREVLATY 1x42A 15 :SVEGEAKTHLKIMEEV T0324 33 :GKPFSPAQAQKTFPMAAEQAMTELGI 1x42A 33 :DYPLNPKTLLDEYEKLTREAFSNYAG T0324 59 :AASEFDHFQAQ 1x42A 80 :GFKYPENFWEI T0324 73 :VMASHYDQIELYPGITSLFEQLPSELRLGIVTSQRRNELESGMRSYPFMMRMAVTISADDTPKRKPDPLPLLTALEKVNVAPQNALFIGDSV 1x42A 91 :HLRMHQRYGELYPEVVEVLKSLKGKYHVGMITDSDTEYLMAHLDALGIKDLFDSITTSEEAGFFKPHPRIFELALKKAGVKGEEAVYVGDNP T0324 165 :SDEQTAQAANVDFGLAVWGMDPNADHQKVAHRFQKPLDILELFK 1x42A 184 :KDCGGSKNLGMTSILLDRKGEKREFWDKCDFIVSDLREVIKIVD Number of specific fragments extracted= 6 number of extra gaps= 0 total=805 Number of alignments=78 # 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:# T0324 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 T0324 4 :QALMFDIDGTLTNS 2b0cA 8 :MLYIFDLGNVIVDI T0324 18 :QPAYTTVMREVL 2b0cA 23 :FNRVLGAWSDLT T0324 35 :PFSPAQAQKTFPM 2b0cA 35 :RIPLASLKKSFHM T0324 48 :AAEQAMTELGIAASEF 2b0cA 49 :EAFHQHERGEISDEAF T0324 64 :DHFQAQY 2b0cA 66 :EALCHEM T0324 71 :EDVMASHYD 2b0cA 78 :YEQFSHGWQ T0324 80 :QIELYPGITSLFEQLPS 2b0cA 89 :FVALRPEVIAIMHKLRE T0324 97 :ELRLGIVTSQRR 2b0cA 107 :GHRVVVLSNTNR T0324 115 :MRSYPFMMR 2b0cA 119 :LHTTFWPEE T0324 124 :MAVTISADDTPKRKPDPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFG 2b0cA 135 :ADHIYLSQDLGMRKPEARIYQHVLQAEGFSPSDTVFFDDNADNIEGANQLGITSI T0324 196 :RFQKPLDILELFK 2b0cA 190 :LVKDKTTIPDYFA Number of specific fragments extracted= 11 number of extra gaps= 0 total=816 Number of alignments=79 # 2b0cA read from 2b0cA/merged-good-all-a2m # found chain 2b0cA in template set T0324 3 :YQALMFDIDGTLTNSQ 2b0cA 7 :KMLYIFDLGNVIVDID T0324 19 :PAYTTVMREVL 2b0cA 24 :NRVLGAWSDLT T0324 35 :PFSPAQAQKTFPMAAEQAMTEL 2b0cA 35 :RIPLASLKKSFHMGEAFHQHER T0324 57 :GIAASEFDHFQAQY 2b0cA 59 :ISDEAFAEALCHEM T0324 71 :EDVMASHYDQI 2b0cA 78 :YEQFSHGWQAV T0324 82 :ELYPGITSLFEQLP 2b0cA 91 :ALRPEVIAIMHKLR T0324 96 :SELRLGIVTSQR 2b0cA 106 :QGHRVVVLSNTN T0324 108 :RNELESG 2b0cA 128 :YPEIRDA T0324 124 :MAVTISADDTPKRKPDPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFG 2b0cA 135 :ADHIYLSQDLGMRKPEARIYQHVLQAEGFSPSDTVFFDDNADNIEGANQLGITSI T0324 196 :RFQKPLDILELFK 2b0cA 190 :LVKDKTTIPDYFA Number of specific fragments extracted= 10 number of extra gaps= 0 total=826 Number of alignments=80 # 2b0cA read from 2b0cA/merged-good-all-a2m # found chain 2b0cA in template set T0324 4 :QALMFDIDGTLTNS 2b0cA 8 :MLYIFDLGNVIVDI T0324 18 :QPAYTTVMREVL 2b0cA 23 :FNRVLGAWSDLT T0324 35 :PFSPAQAQKTFPMAAEQAMTELGI 2b0cA 35 :RIPLASLKKSFHMGEAFHQHERGE T0324 59 :AASEFDHFQAQY 2b0cA 61 :DEAFAEALCHEM T0324 71 :EDVMASHYDQ 2b0cA 78 :YEQFSHGWQA T0324 81 :IELYPGITSLFEQLPS 2b0cA 90 :VALRPEVIAIMHKLRE T0324 97 :ELRLGIVTSQRR 2b0cA 107 :GHRVVVLSNTNR T0324 109 :NELESG 2b0cA 129 :PEIRDA T0324 124 :MAVTISADDTPKRKPDPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFG 2b0cA 135 :ADHIYLSQDLGMRKPEARIYQHVLQAEGFSPSDTVFFDDNADNIEGANQLGITSI T0324 196 :RFQKPLDILELFK 2b0cA 190 :LVKDKTTIPDYFA Number of specific fragments extracted= 10 number of extra gaps= 0 total=836 Number of alignments=81 # 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 # T0324 read from 1rkqA/merged-good-all-a2m # 1rkqA read from 1rkqA/merged-good-all-a2m # found chain 1rkqA in training set Warning: unaligning (T0324)Q69 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1rkqA)S101 Warning: unaligning (T0324)Y70 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1rkqA)S101 T0324 2 :TYQALMFDIDGTLT 1rkqA 3 :AIKLIAIDMDGTLL T0324 16 :NSQPAYTTVMREVLATY 1rkqA 21 :TISPAVKNAIAAARARG T0324 37 :SP 1rkqA 47 :PY T0324 50 :EQAMTEL 1rkqA 52 :HNYLKEL T0324 57 :GIAASEFDHFQA 1rkqA 88 :ALSYDDYRFLEK T0324 71 :EDV 1rkqA 102 :REV T0324 74 :MASHYD 1rkqA 127 :TVHESF T0324 80 :QIEL 1rkqA 135 :TIPL T0324 92 :EQLPSELR 1rkqA 144 :EKMDPNTQ T0324 106 :QRRNELESGMRSYP 1rkqA 159 :DEPAILDQAIARIP T0324 120 :FMMRMAVTISADDT 1rkqA 184 :SAPYFLEILDKRVN T0324 140 :PLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANV 1rkqA 199 :GTGVKSLADVLGIKPEEIMAIGDQENDIAMIEYAGV T0324 179 :LAVWGMDPNAD 1rkqA 235 :GVAVDNAIPSV T0324 191 :QKVAHRFQK 1rkqA 247 :EVANFVTKS Number of specific fragments extracted= 14 number of extra gaps= 1 total=850 Number of alignments=82 # 1rkqA read from 1rkqA/merged-good-all-a2m # found chain 1rkqA in training set Warning: unaligning (T0324)T2 because first residue in template chain is (1rkqA)S1 T0324 3 :YQALMFDIDGTLTN 1rkqA 4 :IKLIAIDMDGTLLL T0324 79 :DQIELYPGITSLFEQLP 1rkqA 18 :PDHTISPAVKNAIAAAR T0324 96 :SELRLGIVTSQRRNELESGMRSYPFMMRMAVTIS 1rkqA 36 :RGVNVVLTTGRPYAGVHNYLKELHMEQPGDYCIT T0324 130 :ADDTPKRK 1rkqA 191 :ILDKRVNK T0324 140 :PLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAAN 1rkqA 199 :GTGVKSLADVLGIKPEEIMAIGDQENDIAMIEYAG T0324 178 :GLAVWGMDPNADHQKVAHRFQKPLD 1rkqA 234 :VGVAVDNAIPSVKEVANFVTKSNLE T0324 203 :ILELFK 1rkqA 261 :VAFAIE Number of specific fragments extracted= 7 number of extra gaps= 0 total=857 Number of alignments=83 # 1rkqA read from 1rkqA/merged-good-all-a2m # found chain 1rkqA in training set Warning: unaligning (T0324)A52 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1rkqA)S101 Warning: unaligning (T0324)M53 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1rkqA)S101 T0324 2 :TYQALMFDIDGTLT 1rkqA 3 :AIKLIAIDMDGTLL T0324 16 :NSQPAYTTVMREVLATY 1rkqA 21 :TISPAVKNAIAAARARG T0324 34 :KPFSPAQAQKT 1rkqA 87 :TALSYDDYRFL T0324 50 :EQ 1rkqA 98 :EK T0324 54 :TE 1rkqA 102 :RE T0324 61 :SEF 1rkqA 122 :DIS T0324 68 :AQYEDVMASHYDQIELYP 1rkqA 125 :YYTVHESFVATIPLVFCE T0324 91 :FEQLPSELRL 1rkqA 143 :AEKMDPNTQF T0324 107 :RRNELESGMRSYP 1rkqA 160 :EPAILDQAIARIP T0324 120 :FMMRMAVTISADDT 1rkqA 184 :SAPYFLEILDKRVN T0324 139 :DPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFG 1rkqA 198 :KGTGVKSLADVLGIKPEEIMAIGDQENDIAMIEYAGVGVA T0324 181 :VWGMDP 1rkqA 238 :VDNAIP T0324 191 :QKVAHRFQ 1rkqA 247 :EVANFVTK Number of specific fragments extracted= 13 number of extra gaps= 1 total=870 Number of alignments=84 # 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:# T0324 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 (T0324)T2 because first residue in template chain is (1swvA)K5 T0324 3 :YQALMFDIDGTLTNS 1swvA 6 :IEAVIFAWAGTTVDY T0324 22 :TTVMREVLATYGKPFSPAQAQKTFPMAAEQAMTEL 1swvA 26 :LEVFMEIFHKRGVAITAEEARKPMGLLKIDHVRAL T0324 57 :GIAASEFDHFQAQYEDVMASHYD 1swvA 77 :LPTEADIQEMYEEFEEILFAILP T0324 80 :QIELYPGITSLFEQLPS 1swvA 101 :YASPINGVKEVIASLRE T0324 97 :ELRLGIVTSQRRN 1swvA 119 :GIKIGSTTGYTRE T0324 110 :ELESGMRSYPFM 1swvA 135 :IVAKEAALQGYK T0324 124 :MAVTISADDTPKRKPDPLPLLTALEKVNVAP 1swvA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMELGVYP T0324 155 :QNALFIGDSVSDEQTAQAANVDFGLAVWGMDPNADH 1swvA 179 :NHMIKVGDTVSDMKEGRNAGMWTVGVILGSSELGLT T0324 191 :QKVAHRFQKPLDILELFK 1swvA 240 :NGAHFTIETMQELESVME Number of specific fragments extracted= 9 number of extra gaps= 0 total=879 Number of alignments=85 # 1swvA read from 1swvA/merged-good-all-a2m # found chain 1swvA in template set Warning: unaligning (T0324)T2 because first residue in template chain is (1swvA)K5 T0324 3 :YQALMFDIDGTLTN 1swvA 6 :IEAVIFAWAGTTVD T0324 22 :TTVMREVLATYGKPFSPAQAQKTFPMAAEQAMTEL 1swvA 26 :LEVFMEIFHKRGVAITAEEARKPMGLLKIDHVRAL T0324 57 :GIAASEFDHFQAQYEDVMASHYD 1swvA 77 :LPTEADIQEMYEEFEEILFAILP T0324 80 :QIELYPGITSLFEQLP 1swvA 101 :YASPINGVKEVIASLR T0324 96 :SELRLGIVTSQRRN 1swvA 118 :RGIKIGSTTGYTRE T0324 110 :ELESGMRSYPFM 1swvA 135 :IVAKEAALQGYK T0324 124 :MAVTISADDTPKRKPDPLPLLTALEKVNV 1swvA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMELGV T0324 153 :APQNALFIGDSVSDEQTAQAANVDFGLAVWGMDPNADH 1swvA 177 :PMNHMIKVGDTVSDMKEGRNAGMWTVGVILGSSELGLT T0324 191 :QKVAHRFQKPLDILELFK 1swvA 240 :NGAHFTIETMQELESVME Number of specific fragments extracted= 9 number of extra gaps= 0 total=888 Number of alignments=86 # 1swvA read from 1swvA/merged-good-all-a2m # found chain 1swvA in template set Warning: unaligning (T0324)T2 because first residue in template chain is (1swvA)K5 T0324 3 :YQALMFDIDGTLTNSQ 1swvA 6 :IEAVIFAWAGTTVDYG T0324 22 :TTVMREVLATYGKPFSPAQAQKTFPMAAEQAMTELGI 1swvA 26 :LEVFMEIFHKRGVAITAEEARKPMGLLKIDHVRALTE T0324 59 :AASEFDHFQAQYEDVMASHYDQIELYPGITSLFEQLPS 1swvA 80 :EADIQEMYEEFEEILFAILPRYASPINGVKEVIASLRE T0324 97 :ELRLGIVTSQRR 1swvA 119 :GIKIGSTTGYTR T0324 109 :NELESGMRSYPFM 1swvA 134 :DIVAKEAALQGYK T0324 124 :MAVTISADDTPKRKPDPLPLLTALEKVNV 1swvA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMELGV T0324 153 :APQNALFIGDSVSDEQTAQAANVDFGLAVWGM 1swvA 177 :PMNHMIKVGDTVSDMKEGRNAGMWTVGVILGS T0324 191 :QKVAHRFQKPLDILELFK 1swvA 240 :NGAHFTIETMQELESVME Number of specific fragments extracted= 8 number of extra gaps= 0 total=896 Number of alignments=87 # 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 # T0324 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 (T0324)T2 because first residue in template chain is (1jud)Y3 Warning: unaligning (T0324)F207 because last residue in template chain is (1jud)F222 T0324 3 :YQALMFDIDGTLTNSQPAYTTV 1jud 4 :IKGIAFDLYGTLFDVHSVVGRC T0324 25 :MREVLATY 1jud 40 :WRQKQLEY T0324 33 :GKPFSPAQAQKTF 1jud 55 :NRYVNFQQATEDA T0324 49 :AEQAMTEL 1jud 68 :LRFTCRHL T0324 57 :GIAASEFD 1jud 78 :DLDARTRS T0324 73 :VMASHYDQIELYPGITSLFEQLPS 1jud 86 :TLCDAYLRLAPFSEVPDSLRELKR T0324 97 :ELRLGIVTSQRRNELESGMRSYPFMMRMAVTISADDTPKRKPDPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFGLAVWGMDPNADH 1jud 111 :GLKLAILSNGSPQSIDAVVSHAGLRDGFDHLLSVDPVQVYKPDNRVYELAEQALGLDRSAILFVSSNAWDATGARYFGFPTCWINRTGNVFEEM T0324 191 :QKVAHRFQKPLDILEL 1jud 206 :QTPDWEVTSLRAVVEL Number of specific fragments extracted= 8 number of extra gaps= 0 total=904 Number of alignments=88 # 1jud read from 1jud/merged-good-all-a2m # found chain 1jud in template set Warning: unaligning (T0324)F207 because last residue in template chain is (1jud)F222 T0324 3 :YQALMFDIDGTLTN 1jud 4 :IKGIAFDLYGTLFD T0324 17 :SQPAYTTVMREVLATY 1jud 32 :RGREISALWRQKQLEY T0324 38 :PAQAQKTFPMAAEQAMTEL 1jud 49 :WLRSLMNRYVNFQQATEDA T0324 57 :GIAASEFD 1jud 71 :TCRHLGLD T0324 66 :FQAQYEDVMASHYDQIELYPGITSLFEQLP 1jud 79 :LDARTRSTLCDAYLRLAPFSEVPDSLRELK T0324 96 :SELRLGIVTSQRRNELESGMRSYPFMMRMAVTISADDTPKRKPDPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFGLAVWGMDPNADH 1jud 110 :RGLKLAILSNGSPQSIDAVVSHAGLRDGFDHLLSVDPVQVYKPDNRVYELAEQALGLDRSAILFVSSNAWDATGARYFGFPTCWINRTGNVFEEM T0324 191 :QKVAHRFQKPLDILEL 1jud 206 :QTPDWEVTSLRAVVEL Number of specific fragments extracted= 7 number of extra gaps= 0 total=911 Number of alignments=89 # 1jud read from 1jud/merged-good-all-a2m # found chain 1jud in template set Warning: unaligning (T0324)T2 because first residue in template chain is (1jud)Y3 Warning: unaligning (T0324)F207 because last residue in template chain is (1jud)F222 T0324 3 :YQALMFDIDGTLTNSQPAYTTVMRE 1jud 4 :IKGIAFDLYGTLFDVHSVVGRCDEA T0324 36 :FSPAQAQKTFPMAAEQAMTELGI 1jud 31 :GRGREISALWRQKQLEYTWLRSL T0324 59 :AASEFDHF 1jud 80 :DARTRSTL T0324 75 :ASHYDQIELYPGITSLFEQLPS 1jud 88 :CDAYLRLAPFSEVPDSLRELKR T0324 97 :ELRLGIVTSQRRNELESGMRSYPFMMRMAVTISADDTPKRKPDPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFGLAVWGMDPNADH 1jud 111 :GLKLAILSNGSPQSIDAVVSHAGLRDGFDHLLSVDPVQVYKPDNRVYELAEQALGLDRSAILFVSSNAWDATGARYFGFPTCWINRTGNVFEEM T0324 191 :QKVAHRFQKPLDILEL 1jud 206 :QTPDWEVTSLRAVVEL Number of specific fragments extracted= 6 number of extra gaps= 0 total=917 Number of alignments=90 # 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 # T0324 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 T0324 3 :YQALMFDIDGTLT 1vjrA 5 :IELFILDMDGTFY T0324 17 :SQPAYTTVMRE 1vjrA 22 :LLPGSLEFLET T0324 29 :LATYGKPF 1vjrA 33 :LKEKNKRF T0324 46 :PMAAEQAMTEL 1vjrA 48 :SLGAQDYVRKL T0324 57 :GIAASEF 1vjrA 64 :DVPDDAV T0324 66 :FQAQYEDVMASHYDQIEL 1vjrA 73 :SGEITAEHMLKRFGRCRI T0324 84 :YPGITSLFEQL 1vjrA 95 :TPQLKKVFEAY T0324 96 :SELRLGIVTS 1vjrA 112 :ENPDFVVLGF T0324 106 :QRRNELESGMRS 1vjrA 128 :ERLKKACILLRK T0324 123 :RMAVTISADDT 1vjrA 140 :GKFYIATHPDI T0324 135 :KRKPDPLPLLTALEKVNVAPQNALFIGDSV 1vjrA 181 :AGKPNPLVVDVISEKFGVPKERMAMVGDRL T0324 165 :SDEQTAQAANVDFGLAVWGMDPNADH 1vjrA 212 :TDVKLGKNAGIVSILVLTGETTPEDL T0324 191 :QKVAHRFQKPLDILELFK 1vjrA 242 :TKPDFVFKNLGELAKAVQ Number of specific fragments extracted= 13 number of extra gaps= 0 total=930 Number of alignments=91 # 1vjrA read from 1vjrA/merged-good-all-a2m # found chain 1vjrA in template set T0324 3 :YQALMFDIDGTLTN 1vjrA 5 :IELFILDMDGTFYL T0324 80 :QIELYPGITSLFEQLP 1vjrA 19 :DDSLLPGSLEFLETLK T0324 96 :SELRLGIVTSQ 1vjrA 36 :KNKRFVFFTNN T0324 107 :RRNELESGMRSYPFMMRMAVTIS 1vjrA 50 :GAQDYVRKLRNMGVDVPDDAVVT T0324 137 :KPDPLPLLTALEKVNVAPQNALFIGDSV 1vjrA 183 :KPNPLVVDVISEKFGVPKERMAMVGDRL T0324 165 :SDEQTAQAANVDFGLAVWGMDPNADH 1vjrA 212 :TDVKLGKNAGIVSILVLTGETTPEDL T0324 191 :QKVAHRFQKPLDILELFK 1vjrA 242 :TKPDFVFKNLGELAKAVQ Number of specific fragments extracted= 7 number of extra gaps= 0 total=937 Number of alignments=92 # 1vjrA read from 1vjrA/merged-good-all-a2m # found chain 1vjrA in template set T0324 2 :TYQALMFDIDGTLTNS 1vjrA 4 :KIELFILDMDGTFYLD T0324 81 :IELYPGITSLFEQLPS 1vjrA 20 :DSLLPGSLEFLETLKE T0324 97 :ELRLGIVTSQRR 1vjrA 37 :NKRFVFFTNNSS T0324 109 :NELESGMRSYPF 1vjrA 96 :PQLKKVFEAYGH T0324 121 :MMRMAVTISADD 1vjrA 111 :EENPDFVVLGFD T0324 135 :KRKPDPLPLLTALEKVNVAPQNALFIGDSV 1vjrA 181 :AGKPNPLVVDVISEKFGVPKERMAMVGDRL T0324 165 :SDEQTAQAANVDFGLAVWGMDPNADH 1vjrA 212 :TDVKLGKNAGIVSILVLTGETTPEDL T0324 191 :QKVAHRFQKPLDILELFK 1vjrA 242 :TKPDFVFKNLGELAKAVQ Number of specific fragments extracted= 8 number of extra gaps= 0 total=945 Number of alignments=93 # 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 # T0324 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 T0324 2 :TYQALMFDIDGTLTN 2bdeA 16 :KIKLIGLDMDHTLIR T0324 17 :SQPAYTTVMREVLATY 2bdeA 36 :FESLVYDLVKERLAES T0324 33 :GK 2bdeA 96 :GT T0324 35 :PFSPAQAQKTF 2bdeA 99 :QISFSDQKKIY T0324 47 :MAAEQAMTEL 2bdeA 151 :PSYQAIAQDV T0324 60 :ASEFDHFQAQ 2bdeA 161 :QYCVDKVHSD T0324 70 :YEDVMASHYD 2bdeA 173 :LKNIIIKNLK T0324 80 :QIELYPGITSLFEQLPS 2bdeA 184 :YVIREKEVVEGLKHFIR T0324 97 :ELRLGIVTSQRRNELESGMRSY 2bdeA 202 :GKKIFILTNSEYSYSKLLLDYA T0324 119 :PFMMRMAVTIS 2bdeA 233 :HWQGLFEFVIT T0324 135 :KR 2bdeA 272 :GP T0324 143 :LLTALEKVNVAPQNALFIGDSV 2bdeA 284 :AKKFTEDLGVGGDEILYIGDHI T0324 165 :SDEQTAQAANVDFGLAVWG 2bdeA 308 :DILRLKKDCNWRTALVVEE T0324 200 :PLDILE 2bdeA 327 :LGEEIA Number of specific fragments extracted= 14 number of extra gaps= 0 total=959 Number of alignments=94 # 2bdeA read from 2bdeA/merged-good-all-a2m # found chain 2bdeA in template set T0324 2 :TYQALMFDIDGTLTN 2bdeA 16 :KIKLIGLDMDHTLIR T0324 59 :AASEFDHFQAQYEDVMASHYD 2bdeA 149 :KMPSYQAIAQDVQYCVDKVHS T0324 80 :QI 2bdeA 171 :GT T0324 82 :ELYPGITSLFEQLP 2bdeA 186 :IREKEVVEGLKHFI T0324 96 :SELRLGIVTSQRRNELESGMRSY 2bdeA 201 :YGKKIFILTNSEYSYSKLLLDYA T0324 119 :PFMMRMAVTIS 2bdeA 233 :HWQGLFEFVIT T0324 133 :TPKR 2bdeA 270 :VHGP T0324 143 :LLTALEKVNVAPQNALFIGDSV 2bdeA 284 :AKKFTEDLGVGGDEILYIGDHI T0324 165 :SDEQTAQAANVDFGLAVW 2bdeA 308 :DILRLKKDCNWRTALVVE T0324 199 :KPLDILEL 2bdeA 326 :ELGEEIAS Number of specific fragments extracted= 10 number of extra gaps= 0 total=969 Number of alignments=95 # 2bdeA read from 2bdeA/merged-good-all-a2m # found chain 2bdeA in template set T0324 2 :TYQALMFDIDGTLTNSQ 2bdeA 16 :KIKLIGLDMDHTLIRYN T0324 19 :PAYTTVMREVLATY 2bdeA 34 :KNFESLVYDLVKER T0324 45 :FPMAAEQAMTELGI 2bdeA 148 :DKMPSYQAIAQDVQ T0324 59 :AASEFDHFQAQYEDVMASHYDQIELYPGITSLFEQLPS 2bdeA 163 :CVDKVHSDGTLKNIIIKNLKKYVIREKEVVEGLKHFIR T0324 97 :ELRLGIVTSQRRNELESGMRSY 2bdeA 202 :GKKIFILTNSEYSYSKLLLDYA T0324 119 :PFMMRMAVTISADD 2bdeA 233 :HWQGLFEFVITLAN T0324 133 :TPKRKP 2bdeA 271 :HGPIVP T0324 143 :LLTALEKVNVAPQNALFIGDSV 2bdeA 284 :AKKFTEDLGVGGDEILYIGDHI T0324 165 :SDEQTAQAANVDFGLAVWG 2bdeA 308 :DILRLKKDCNWRTALVVEE T0324 200 :PLDILEL 2bdeA 327 :LGEEIAS Number of specific fragments extracted= 10 number of extra gaps= 0 total=979 Number of alignments=96 # 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 # T0324 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 (T0324)T2 because first residue in template chain is (1zrn)Y3 Warning: unaligning (T0324)F207 because last residue in template chain is (1zrn)F222 T0324 3 :YQALMFDIDGTLTNSQPA 1zrn 4 :IKGIAFDLYGTLFDVHSV T0324 21 :YTTVMREVLATY 1zrn 36 :ISALWRQKQLEY T0324 33 :GKPFSPAQAQKTF 1zrn 55 :NRYVNFQQATEDA T0324 49 :AEQAMTEL 1zrn 68 :LRFTCRHL T0324 57 :GIAASE 1zrn 78 :DLDART T0324 71 :EDVMASHYDQIELYPGITSLFEQLPS 1zrn 84 :RSTLCDAYLRLAPFSEVPDSLRELKR T0324 97 :ELRLGIVTSQRRNELESGMRSYPFMMRMAVTISADDTPKRKPDPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFGLAVWGMDPNADH 1zrn 111 :GLKLAILSNGSPQSIDAVVSHAGLRDGFDHLLSVDPVQVYKPDNRVYELAEQALGLDRSAILFVASNAWDATGARYFGFPTCWINRTGNVFEEM T0324 191 :QKVAHRFQKPLDILEL 1zrn 206 :QTPDWEVTSLRAVVEL Number of specific fragments extracted= 8 number of extra gaps= 0 total=987 Number of alignments=97 # 1zrn read from 1zrn/merged-good-all-a2m # found chain 1zrn in template set Warning: unaligning (T0324)F207 because last residue in template chain is (1zrn)F222 T0324 3 :YQALMFDIDGTLTN 1zrn 4 :IKGIAFDLYGTLFD T0324 17 :SQPAYTTVMREVLATY 1zrn 32 :RGREISALWRQKQLEY T0324 38 :PAQAQKTFPMAAEQAMTEL 1zrn 49 :WLRSLMNRYVNFQQATEDA T0324 57 :GIAASEFD 1zrn 71 :TCRHLGLD T0324 66 :FQAQYEDVMASHYDQIELYPGITSLFEQLP 1zrn 79 :LDARTRSTLCDAYLRLAPFSEVPDSLRELK T0324 96 :SELRLGIVTSQRRNELESGMRSYPFMMRMAVTISADDTPKRKPDPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFGLAVWGMDPNADH 1zrn 110 :RGLKLAILSNGSPQSIDAVVSHAGLRDGFDHLLSVDPVQVYKPDNRVYELAEQALGLDRSAILFVASNAWDATGARYFGFPTCWINRTGNVFEEM T0324 191 :QKVAHRFQKPLDILEL 1zrn 206 :QTPDWEVTSLRAVVEL Number of specific fragments extracted= 7 number of extra gaps= 0 total=994 Number of alignments=98 # 1zrn read from 1zrn/merged-good-all-a2m # found chain 1zrn in template set Warning: unaligning (T0324)T2 because first residue in template chain is (1zrn)Y3 Warning: unaligning (T0324)F207 because last residue in template chain is (1zrn)F222 T0324 3 :YQALMFDIDGTLTNSQPA 1zrn 4 :IKGIAFDLYGTLFDVHSV T0324 21 :YTTVMREVLATY 1zrn 36 :ISALWRQKQLEY T0324 39 :AQAQKTFPMAAEQAMTELGI 1zrn 50 :LRSLMNRYVNFQQATEDALR T0324 59 :AASEFDHF 1zrn 80 :DARTRSTL T0324 75 :ASHYDQIELYPGITSLFEQLPS 1zrn 88 :CDAYLRLAPFSEVPDSLRELKR T0324 97 :ELRLGIVTSQRRNELESGMRSYPFMMRMAVTISADDTPKRKPDPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFGLAVWGMDPNADH 1zrn 111 :GLKLAILSNGSPQSIDAVVSHAGLRDGFDHLLSVDPVQVYKPDNRVYELAEQALGLDRSAILFVASNAWDATGARYFGFPTCWINRTGNVFEEM T0324 191 :QKVAHRFQKPLDILEL 1zrn 206 :QTPDWEVTSLRAVVEL Number of specific fragments extracted= 7 number of extra gaps= 0 total=1001 Number of alignments=99 # 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 # T0324 read from 1k1eA/merged-good-all-a2m # 1k1eA read from 1k1eA/merged-good-all-a2m # found chain 1k1eA in training set T0324 3 :YQALMFDIDGTLTNS 1k1eA 8 :IKFVITDVDGVLTDG T0324 19 :PAYTTVMREVLA 1k1eA 38 :VRDGLGIKMLMD T0324 97 :ELRLGIVTSQRRNELESGMRSYPFM 1k1eA 51 :DIQVAVLSGRDSPILRRRIADLGIK T0324 127 :TISADDTP 1k1eA 76 :LFFLGKLE T0324 139 :DPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAAN 1k1eA 84 :KETACFDLMKQAGVTAEQTAYIGDDSVDLPAFAACG T0324 177 :FGLAVW 1k1eA 120 :TSFAVA T0324 184 :MDPNA 1k1eA 126 :DAPIY T0324 191 :QKVAHRFQK 1k1eA 133 :NAVDHVLST T0324 200 :PLDILELF 1k1eA 148 :FREMSDMI Number of specific fragments extracted= 9 number of extra gaps= 0 total=1010 Number of alignments=100 # 1k1eA read from 1k1eA/merged-good-all-a2m # found chain 1k1eA in training set T0324 3 :YQALMFDIDGTLTN 1k1eA 8 :IKFVITDVDGVLTD T0324 17 :SQPAYTTVMREVLA 1k1eA 36 :FHVRDGLGIKMLMD T0324 96 :SELRLGIVTSQRRNELESGMRSYPFM 1k1eA 50 :ADIQVAVLSGRDSPILRRRIADLGIK T0324 127 :TISADDTP 1k1eA 76 :LFFLGKLE T0324 137 :K 1k1eA 84 :K T0324 140 :PLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAAN 1k1eA 85 :ETACFDLMKQAGVTAEQTAYIGDDSVDLPAFAACG T0324 178 :GLAVWGMDPNADHQKVAHRFQK 1k1eA 120 :TSFAVADAPIYVKNAVDHVLST T0324 200 :PLDILELF 1k1eA 148 :FREMSDMI Number of specific fragments extracted= 8 number of extra gaps= 0 total=1018 Number of alignments=101 # 1k1eA read from 1k1eA/merged-good-all-a2m # found chain 1k1eA in training set T0324 2 :TYQALMFDIDGTLTNSQ 1k1eA 7 :NIKFVITDVDGVLTDGQ T0324 19 :PAYTT 1k1eA 38 :VRDGL T0324 90 :LFEQLPS 1k1eA 43 :GIKMLMD T0324 97 :ELRLGIVTSQRRNELESGMRSYPFM 1k1eA 51 :DIQVAVLSGRDSPILRRRIADLGIK T0324 127 :TISADDTP 1k1eA 76 :LFFLGKLE T0324 139 :DPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQA 1k1eA 84 :KETACFDLMKQAGVTAEQTAYIGDDSVDLPAFAA T0324 175 :VDFGLAVWGMD 1k1eA 118 :CGTSFAVADAP T0324 187 :NA 1k1eA 129 :IY T0324 191 :QKVAHRFQK 1k1eA 133 :NAVDHVLST T0324 200 :PLDILELF 1k1eA 148 :FREMSDMI Number of specific fragments extracted= 10 number of extra gaps= 0 total=1028 Number of alignments=102 # 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:# T0324 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 T0324 3 :YQALMFDIDGTLTNSQ 1u7pA 5 :PKLAVFDLDYTLWPFW T0324 32 :Y 1u7pA 21 :V T0324 33 :GKPFS 1u7pA 24 :HVDPP T0324 76 :SHYDQIELYPGITSLFEQLPS 1u7pA 40 :RRGQNIQLYPEVPEVLGRLQS T0324 97 :ELRLGIVTS 1u7pA 62 :GVPVAAASR T0324 106 :QRRNELESGMRSYPFMMRMAVTISAD 1u7pA 72 :SEIQGANQLLELFDLGKYFIQREIYP T0324 135 :KRK 1u7pA 98 :GSK T0324 140 :PLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFGLAVWGM 1u7pA 101 :VTHFERLHHKTGVPFSQMVFFDDENRNIIDVGRLGVTCIHIRDGM T0324 199 :KPLDILELFK 1u7pA 146 :SLQTLTQGLE Number of specific fragments extracted= 9 number of extra gaps= 0 total=1037 Number of alignments=103 # 1u7pA read from 1u7pA/merged-good-all-a2m # found chain 1u7pA in template set T0324 1 :MT 1u7pA 1 :MT T0324 3 :YQALMFDIDGTLTN 1u7pA 5 :PKLAVFDLDYTLWP T0324 82 :ELYPGITSLFEQLP 1u7pA 46 :QLYPEVPEVLGRLQ T0324 96 :SELRLGIVTS 1u7pA 61 :LGVPVAAASR T0324 106 :QRRNELESGMRSYPFMMRMAVTI 1u7pA 72 :SEIQGANQLLELFDLGKYFIQRE T0324 130 :A 1u7pA 95 :I T0324 133 :TPKRK 1u7pA 96 :YPGSK T0324 140 :PLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFGLAVWGM 1u7pA 101 :VTHFERLHHKTGVPFSQMVFFDDENRNIIDVGRLGVTCIHIRDGM T0324 199 :KPLDILELFK 1u7pA 146 :SLQTLTQGLE Number of specific fragments extracted= 9 number of extra gaps= 0 total=1046 Number of alignments=104 # 1u7pA read from 1u7pA/merged-good-all-a2m # found chain 1u7pA in template set T0324 2 :TYQALMFDIDGTLTNSQ 1u7pA 4 :LPKLAVFDLDYTLWPFW T0324 76 :SHYDQIELYPGITSLFEQLPS 1u7pA 40 :RRGQNIQLYPEVPEVLGRLQS T0324 97 :ELRLGIVTS 1u7pA 62 :GVPVAAASR T0324 106 :QRRNELESGMRSYPFMMRMAVTISADD 1u7pA 72 :SEIQGANQLLELFDLGKYFIQREIYPG T0324 139 :DPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFGLAVWGM 1u7pA 100 :KVTHFERLHHKTGVPFSQMVFFDDENRNIIDVGRLGVTCIHIRDGM T0324 199 :KPLDILELFK 1u7pA 146 :SLQTLTQGLE Number of specific fragments extracted= 6 number of extra gaps= 0 total=1052 Number of alignments=105 # 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 # T0324 read from 1rkuA/merged-good-all-a2m # 1rkuA read from 1rkuA/merged-good-all-a2m # found chain 1rkuA in training set Warning: unaligning (T0324)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rkuA)D7 Warning: unaligning (T0324)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rkuA)D7 T0324 3 :YQALM 1rkuA 1 :MEIAC T0324 10 :IDGTLTNS 1rkuA 8 :LEGVLVPE T0324 24 :VMREVLATYGKP 1rkuA 16 :IWIAFAEKTGID T0324 36 :FSPAQAQKT 1rkuA 37 :PDYDVLMKQ T0324 49 :AEQAMTELGIAASE 1rkuA 46 :RLRILDEHGLKLGD T0324 74 :MASHYDQIELYPGITSLFEQLPSELRLGIVTSQRRNELESGMRSYPFMMRMAVTISADDTPK 1rkuA 60 :IQEVIATLKPLEGAVEFVDWLRERFQVVILSDTFYEFSQPLMRQLGFPTLLCHKLEIDDSDR T0324 137 :KPDPLPLLTALEKV 1rkuA 127 :LRQKDPKRQSVIAF T0324 156 :NALFIGDSVSDEQTAQAAN 1rkuA 146 :RVIAAGDSYNDTTMLSEAH T0324 176 :DFGLAVWG 1rkuA 165 :AGILFHAP T0324 187 :NADH 1rkuA 173 :ENVI T0324 191 :QKVA 1rkuA 180 :PQFP T0324 196 :RFQKPLDILELF 1rkuA 184 :AVHTYEDLKREF Number of specific fragments extracted= 12 number of extra gaps= 1 total=1064 Number of alignments=106 # 1rkuA read from 1rkuA/merged-good-all-a2m # found chain 1rkuA in training set Warning: unaligning (T0324)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rkuA)D7 Warning: unaligning (T0324)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rkuA)D7 T0324 3 :YQALM 1rkuA 1 :MEIAC T0324 10 :IDGTLTN 1rkuA 8 :LEGVLVP T0324 23 :TVMREVLATYGKP 1rkuA 15 :EIWIAFAEKTGID T0324 36 :FSPAQAQKT 1rkuA 37 :PDYDVLMKQ T0324 49 :AEQAMTELGIAAS 1rkuA 46 :RLRILDEHGLKLG T0324 73 :VMASHYDQIELYPGITSLFEQLPSELRLGIVTSQRRNELESGMRSYPFMMRMAVTISADDTPKR 1rkuA 59 :DIQEVIATLKPLEGAVEFVDWLRERFQVVILSDTFYEFSQPLMRQLGFPTLLCHKLEIDDSDRV T0324 137 :KPDPLPLLTALEKV 1rkuA 127 :LRQKDPKRQSVIAF T0324 156 :NALFIGDSVSDEQTAQAAN 1rkuA 146 :RVIAAGDSYNDTTMLSEAH T0324 176 :DFGLA 1rkuA 165 :AGILF T0324 184 :MDPNADH 1rkuA 170 :HAPENVI T0324 191 :QKVA 1rkuA 180 :PQFP T0324 196 :RFQKPLDILELF 1rkuA 184 :AVHTYEDLKREF Number of specific fragments extracted= 12 number of extra gaps= 1 total=1076 Number of alignments=107 # 1rkuA read from 1rkuA/merged-good-all-a2m # found chain 1rkuA in training set Warning: unaligning (T0324)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rkuA)D7 Warning: unaligning (T0324)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rkuA)D7 T0324 4 :QALM 1rkuA 2 :EIAC T0324 10 :IDGTLTNS 1rkuA 8 :LEGVLVPE T0324 24 :VMREVLATYGKP 1rkuA 16 :IWIAFAEKTGID T0324 59 :AASEFDHFQAQYEDVMA 1rkuA 36 :IPDYDVLMKQRLRILDE T0324 76 :SHYDQIELYPGITSLFEQLPSELRLGIVTSQRRNELESGMRSYPFMMRMAVTISADD 1rkuA 62 :EVIATLKPLEGAVEFVDWLRERFQVVILSDTFYEFSQPLMRQLGFPTLLCHKLEIDD T0324 133 :TP 1rkuA 127 :LR T0324 136 :R 1rkuA 129 :Q T0324 140 :PLPLLTALEKV 1rkuA 130 :KDPKRQSVIAF T0324 156 :NALFIGDSVSDEQTAQAAN 1rkuA 146 :RVIAAGDSYNDTTMLSEAH T0324 176 :DFGLAVW 1rkuA 165 :AGILFHA T0324 186 :PNADH 1rkuA 172 :PENVI T0324 191 :QKVAH 1rkuA 180 :PQFPA T0324 197 :FQKPLDILELF 1rkuA 185 :VHTYEDLKREF Number of specific fragments extracted= 13 number of extra gaps= 1 total=1089 Number of alignments=108 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cr6A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0324/1cr6A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0324/1cr6A/merged-good-all-a2m.gz for input Trying 1cr6A/merged-good-all-a2m Error: Couldn't open file 1cr6A/merged-good-all-a2m or 1cr6A/merged-good-all-a2m.gz for input # 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 # T0324 read from 1te2A/merged-good-all-a2m # 1te2A read from 1te2A/merged-good-all-a2m # found chain 1te2A in training set Warning: unaligning (T0324)S117 because of BadResidue code BAD_PEPTIDE in next template residue (1te2A)F129 Warning: unaligning (T0324)Y118 because of BadResidue code BAD_PEPTIDE at template residue (1te2A)F129 T0324 2 :TYQALMFDIDGTLTNSQPAYTTVMREVLATYGKP 1te2A 6 :QILAAIFDMDGLLIDSEPLWDRAELDVMASLGVD T0324 38 :PAQAQKT 1te2A 40 :ISRRNEL T0324 45 :FPMAAEQAMTEL 1te2A 50 :LGLRIDMVVDLW T0324 57 :GIAASE 1te2A 69 :GPSRQE T0324 66 :FQAQYEDVMASHYD 1te2A 75 :VVERVIARAISLVE T0324 80 :QIELYPGITSLFEQLPS 1te2A 90 :TRPLLPGVREAVALCKE T0324 97 :ELRLGIVTSQRRNELESGMR 1te2A 108 :GLLVGLASASPLHMLEKVLT T0324 119 :PFMMRMAVTISADDTPKRKPDPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFGLAVWGMDPNADH 1te2A 130 :DLRDSFDALASAEKLPYSKPHPQVYLDCAAKLGVDPLTCVALEDSVNGMIASKAARMRSIVVPAPEAQNDPR T0324 191 :QKVAHRFQKPLDI 1te2A 203 :VLANVKLSSLTEL Number of specific fragments extracted= 9 number of extra gaps= 1 total=1098 Number of alignments=109 # 1te2A read from 1te2A/merged-good-all-a2m # found chain 1te2A in training set Warning: unaligning (T0324)S117 because of BadResidue code BAD_PEPTIDE in next template residue (1te2A)F129 Warning: unaligning (T0324)Y118 because of BadResidue code BAD_PEPTIDE at template residue (1te2A)F129 T0324 2 :TYQALMFDIDGTLTNSQPAYTTVMREVLATYGKPFSPAQAQKTFPMAAEQAMTEL 1te2A 6 :QILAAIFDMDGLLIDSEPLWDRAELDVMASLGVDISRRNELPDTLGLRIDMVVDL T0324 57 :GIAASEFDHFQAQYEDVMASHYD 1te2A 66 :PWNGPSRQEVVERVIARAISLVE T0324 80 :QIELYPGITSLFEQLP 1te2A 90 :TRPLLPGVREAVALCK T0324 96 :SELRLGIVTSQRRNELESGMR 1te2A 107 :QGLLVGLASASPLHMLEKVLT T0324 119 :PFMMRMAVTISADDTPKRKPDPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFGLAVWGMDPNADH 1te2A 130 :DLRDSFDALASAEKLPYSKPHPQVYLDCAAKLGVDPLTCVALEDSVNGMIASKAARMRSIVVPAPEAQNDPR T0324 191 :QKVAHRFQKPLD 1te2A 203 :VLANVKLSSLTE Number of specific fragments extracted= 6 number of extra gaps= 1 total=1104 Number of alignments=110 # 1te2A read from 1te2A/merged-good-all-a2m # found chain 1te2A in training set Warning: unaligning (T0324)S117 because of BadResidue code BAD_PEPTIDE in next template residue (1te2A)F129 Warning: unaligning (T0324)Y118 because of BadResidue code BAD_PEPTIDE at template residue (1te2A)F129 T0324 2 :TYQALMFDIDGTLTNSQPAYTTVMREVLATYGKPFSPAQAQKTFPMAAEQAMTELGI 1te2A 6 :QILAAIFDMDGLLIDSEPLWDRAELDVMASLGVDISRRNELPDTLGLRIDMVVDLWY T0324 59 :AASEFDHFQAQYEDVMASHYDQIELYPGITSLFEQLPS 1te2A 69 :GPSRQEVVERVIARAISLVEETRPLLPGVREAVALCKE T0324 97 :ELRLGIVTSQRRNELESGMR 1te2A 108 :GLLVGLASASPLHMLEKVLT T0324 119 :PFMMRMAVTISADDTPKRKPDPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFGLAVWGMDPNADH 1te2A 130 :DLRDSFDALASAEKLPYSKPHPQVYLDCAAKLGVDPLTCVALEDSVNGMIASKAARMRSIVVPAPEAQNDPR T0324 191 :QKVAHRFQKPLD 1te2A 203 :VLANVKLSSLTE Number of specific fragments extracted= 5 number of extra gaps= 1 total=1109 Number of alignments=111 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fezA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1fezA expands to /projects/compbio/data/pdb/1fez.pdb.gz 1fezA:# T0324 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 (T0324)T2 because first residue in template chain is (1fezA)K5 T0324 3 :YQALMFDIDGTLTNS 1fezA 6 :IEAVIFDWAGTTVDY T0324 19 :PAYTTVMREVLATYGKPFSPAQAQKTFPMAAEQAMTEL 1fezA 23 :FAPLEVFMEIFHKRGVAITAEEARKPMGLLKIDHVRAL T0324 57 :GIAASEFDHFQAQYEDVMASHYD 1fezA 77 :LPTEADIQEMYEEFEEILFAILP T0324 80 :QIELYPGITSLFEQLPS 1fezA 101 :YASPINAVKEVIASLRE T0324 97 :ELRLGIVTSQRR 1fezA 119 :GIKIGSTTGYTR T0324 109 :NELESGMRSYPFM 1fezA 134 :DIVAKEAALQGYK T0324 124 :MAVTISADDTPKRKPDPLPLLTALEKVNV 1fezA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMELGV T0324 153 :APQNALFIGDSVSDEQTAQAANVDFGLAVW 1fezA 177 :PMNHMIKVGDTVSDMKEGRNAGMWTVGVIL T0324 183 :GMDPNAD 1fezA 212 :GLTEEEV T0324 191 :QKVAHRFQKPLDILELFK 1fezA 240 :NGAHFTIETMQELESVME Number of specific fragments extracted= 10 number of extra gaps= 0 total=1119 Number of alignments=112 # 1fezA read from 1fezA/merged-good-all-a2m # found chain 1fezA in template set Warning: unaligning (T0324)T2 because first residue in template chain is (1fezA)K5 T0324 3 :YQALMFDIDGTLTN 1fezA 6 :IEAVIFDWAGTTVD T0324 21 :YTTVMREVLATYGKPFSPAQAQKTFPMAAEQAMTEL 1fezA 25 :PLEVFMEIFHKRGVAITAEEARKPMGLLKIDHVRAL T0324 57 :GIAASEFDHFQAQYEDVMASHYD 1fezA 77 :LPTEADIQEMYEEFEEILFAILP T0324 80 :QIELYPGITSLFEQLP 1fezA 101 :YASPINAVKEVIASLR T0324 96 :SELRLGIVTSQRRNELESGMRSY 1fezA 118 :RGIKIGSTTGYTREMMDIVAKEA T0324 119 :PFM 1fezA 144 :GYK T0324 124 :MAVTISADDTPKRKPDPLPLLTALEKVNV 1fezA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMELGV T0324 153 :APQNALFIGDSVSDEQTAQAANVDFGLAV 1fezA 177 :PMNHMIKVGDTVSDMKEGRNAGMWTVGVI T0324 182 :WGMDPNAD 1fezA 211 :LGLTEEEV T0324 191 :QKVAHRFQKPLDILELFK 1fezA 240 :NGAHFTIETMQELESVME Number of specific fragments extracted= 10 number of extra gaps= 0 total=1129 Number of alignments=113 # 1fezA read from 1fezA/merged-good-all-a2m # found chain 1fezA in template set Warning: unaligning (T0324)T2 because first residue in template chain is (1fezA)K5 T0324 3 :YQALMFDIDGTLTNSQ 1fezA 6 :IEAVIFDWAGTTVDYG T0324 20 :AYTTVMREVLATYGKPFSPAQAQKTFPMAAEQAMTELGI 1fezA 24 :APLEVFMEIFHKRGVAITAEEARKPMGLLKIDHVRALTE T0324 59 :AASEFDHFQAQYEDVMASHYDQIELYPGITSLFEQLPS 1fezA 80 :EADIQEMYEEFEEILFAILPRYASPINAVKEVIASLRE T0324 97 :ELRLGIVTSQRR 1fezA 119 :GIKIGSTTGYTR T0324 109 :NELESGMRSYPFM 1fezA 134 :DIVAKEAALQGYK T0324 124 :MAVTISADDTPKRKPDPLPLLTALEKVNV 1fezA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMELGV T0324 153 :APQNALFIGDSVSDEQTAQAANVDFGLAV 1fezA 177 :PMNHMIKVGDTVSDMKEGRNAGMWTVGVI T0324 182 :WGMDPNA 1fezA 211 :LGLTEEE T0324 190 :H 1fezA 218 :V T0324 191 :QKVAHRFQKPLDILELFK 1fezA 240 :NGAHFTIETMQELESVME Number of specific fragments extracted= 10 number of extra gaps= 0 total=1139 Number of alignments=114 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cr6B/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1cr6B expands to /projects/compbio/data/pdb/1cr6.pdb.gz 1cr6B:# T0324 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 (T0324)Q4 because first residue in template chain is (1cr6B)R4 T0324 5 :ALMFDIDGTLTNSQ 1cr6B 5 :VAAFDLDGVLALPS T0324 21 :YTTVMREVLATYGKP 1cr6B 19 :IAGAFRRSEEALALP T0324 46 :PMAAEQAMTEL 1cr6B 57 :KITFSQWVPLM T0324 57 :GIAAS 1cr6B 81 :NLPEN T0324 70 :YEDVMASHYDQIELYPGITSLFEQLPS 1cr6B 88 :ISQIFSQAMAARSINRPMLQAAIALKK T0324 97 :ELRLGIVTS 1cr6B 116 :GFTTCIVTN T0324 106 :QRRNELESGMRSYPF 1cr6B 131 :DKRDSLAQMMCELSQ T0324 123 :RMAVTISADDTPKRKPDPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFGLAVWGMDP 1cr6B 146 :HFDFLIESCQVGMIKPEPQIYNFLLDTLKAKPNEVVFLDDFGSNLKPARDMGMVTILVHNTASA Number of specific fragments extracted= 8 number of extra gaps= 0 total=1147 Number of alignments=115 # 1cr6B read from 1cr6B/merged-good-all-a2m # found chain 1cr6B in template set Warning: unaligning (T0324)Q4 because first residue in template chain is (1cr6B)R4 T0324 5 :ALMFDIDGTLTN 1cr6B 5 :VAAFDLDGVLAL T0324 17 :SQPAYTTVMREVLAT 1cr6B 59 :TFSQWVPLMDESYRK T0324 56 :L 1cr6B 74 :S T0324 57 :GIAASEF 1cr6B 81 :NLPENFS T0324 70 :YEDVMASHYDQIELYPGITSLFEQLP 1cr6B 88 :ISQIFSQAMAARSINRPMLQAAIALK T0324 96 :SELRLGIVTS 1cr6B 115 :KGFTTCIVTN T0324 106 :QRRNELESGMRSYPFM 1cr6B 131 :DKRDSLAQMMCELSQH T0324 124 :MAVTISADDTPKRKPDPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFGLAVW 1cr6B 147 :FDFLIESCQVGMIKPEPQIYNFLLDTLKAKPNEVVFLDDFGSNLKPARDMGMVTILVHN Number of specific fragments extracted= 8 number of extra gaps= 0 total=1155 Number of alignments=116 # 1cr6B read from 1cr6B/merged-good-all-a2m # found chain 1cr6B in template set Warning: unaligning (T0324)Q4 because first residue in template chain is (1cr6B)R4 T0324 5 :ALMFDIDGTLTNSQ 1cr6B 5 :VAAFDLDGVLALPS T0324 25 :MREVLATY 1cr6B 19 :IAGAFRRS T0324 33 :GKPFSPAQAQKTFPMAAEQAMTELGI 1cr6B 43 :TEFPEGPTEQLMKGKITFSQWVPLMD T0324 61 :SEF 1cr6B 85 :NFS T0324 70 :YEDVMASHYDQIELYPGITSLFEQLPS 1cr6B 88 :ISQIFSQAMAARSINRPMLQAAIALKK T0324 97 :ELRLGIVTS 1cr6B 116 :GFTTCIVTN T0324 106 :QRRNELESGMRSYPF 1cr6B 131 :DKRDSLAQMMCELSQ T0324 123 :RMAVTISADDTPKRKPDPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFGLAVWGM 1cr6B 146 :HFDFLIESCQVGMIKPEPQIYNFLLDTLKAKPNEVVFLDDFGSNLKPARDMGMVTILVHNTA Number of specific fragments extracted= 8 number of extra gaps= 0 total=1163 Number of alignments=117 # 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 # T0324 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 (T0324)V103 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2feaA)S99 Warning: unaligning (T0324)T104 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2feaA)S99 Warning: unaligning (T0324)P140 because of BadResidue code BAD_PEPTIDE in next template residue (2feaA)C149 Warning: unaligning (T0324)L141 because of BadResidue code BAD_PEPTIDE at template residue (2feaA)C149 T0324 4 :QALMFDIDGTLTNSQ 2feaA 6 :PFIICDFDGTITMND T0324 24 :VMREVLATYGKP 2feaA 21 :NIINIMKTFAPP T0324 37 :SPAQAQKTF 2feaA 33 :EWMALKDGV T0324 46 :PMAAEQAMTEL 2feaA 45 :TLSIKEGVGRM T0324 57 :GIAASEFDHFQAQYEDV 2feaA 58 :LLPSSLKEEITSFVLED T0324 81 :IELYPGITSLFEQLPS 2feaA 75 :AKIREGFREFVAFINE T0324 97 :ELRLGI 2feaA 92 :EIPFYV T0324 105 :SQRRNELESGMRSY 2feaA 100 :GGMDFFVYPLLEGI T0324 119 :PFMMRMAVTISADDT 2feaA 115 :EKDRIYCNHASFDND T0324 136 :RKPD 2feaA 144 :SNQC T0324 142 :PLLTALEKV 2feaA 150 :CKPSVIHEL T0324 152 :VAPQ 2feaA 159 :SEPN T0324 156 :NALFIGDSVSDEQTAQ 2feaA 164 :YIIMIGDSVTDVEAAK T0324 174 :NVDFGLAV 2feaA 180 :LSDLCFAR T0324 191 :QKVAHR 2feaA 197 :QNLNHL T0324 197 :FQKPLDILELFK 2feaA 204 :YQDFYEIRKEIE Number of specific fragments extracted= 16 number of extra gaps= 2 total=1179 Number of alignments=118 # 2feaA read from 2feaA/merged-good-all-a2m # found chain 2feaA in template set Warning: unaligning (T0324)V103 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2feaA)S99 Warning: unaligning (T0324)T104 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2feaA)S99 Warning: unaligning (T0324)P134 because of BadResidue code BAD_PEPTIDE in next template residue (2feaA)C149 Warning: unaligning (T0324)K135 because of BadResidue code BAD_PEPTIDE at template residue (2feaA)C149 T0324 3 :YQALMFDIDGTLTNSQP 2feaA 5 :KPFIICDFDGTITMNDN T0324 25 :MREVLATY 2feaA 22 :IINIMKTF T0324 45 :FP 2feaA 30 :AP T0324 48 :AAEQAMTEL 2feaA 32 :PEWMALKDG T0324 57 :GIAASEFDHFQAQYEDV 2feaA 58 :LLPSSLKEEITSFVLED T0324 81 :IELYPGITSLFEQLP 2feaA 75 :AKIREGFREFVAFIN T0324 96 :SELRLGI 2feaA 91 :HEIPFYV T0324 105 :SQRRNELESGMRSY 2feaA 100 :GGMDFFVYPLLEGI T0324 119 :PFMMRMAVTISADDT 2feaA 115 :EKDRIYCNHASFDND T0324 136 :RK 2feaA 150 :CK T0324 140 :PLPLLTA 2feaA 152 :PSVIHEL T0324 152 :VAPQ 2feaA 159 :SEPN T0324 156 :NALFIGDSVSDEQTAQAAN 2feaA 164 :YIIMIGDSVTDVEAAKLSD T0324 178 :GLAVW 2feaA 183 :LCFAR T0324 191 :QKVAHR 2feaA 197 :QNLNHL T0324 197 :FQKPLDILELFK 2feaA 204 :YQDFYEIRKEIE Number of specific fragments extracted= 16 number of extra gaps= 2 total=1195 Number of alignments=119 # 2feaA read from 2feaA/merged-good-all-a2m # found chain 2feaA in template set Warning: unaligning (T0324)V103 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2feaA)S99 Warning: unaligning (T0324)T104 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2feaA)S99 Warning: unaligning (T0324)P140 because of BadResidue code BAD_PEPTIDE in next template residue (2feaA)C149 Warning: unaligning (T0324)L141 because of BadResidue code BAD_PEPTIDE at template residue (2feaA)C149 T0324 4 :QALMFDIDGTLTNSQ 2feaA 6 :PFIICDFDGTITMND T0324 24 :VMREVLATYGKPFSPAQA 2feaA 21 :NIINIMKTFAPPEWMALK T0324 42 :QKTFPMAAEQAMTELGI 2feaA 41 :VLSKTLSIKEGVGRMFG T0324 59 :AASEFDHFQAQYEDV 2feaA 60 :PSSLKEEITSFVLED T0324 81 :IELYPGITSLFEQLPS 2feaA 75 :AKIREGFREFVAFINE T0324 97 :ELRLGI 2feaA 92 :EIPFYV T0324 105 :SQRRNELESGMRSY 2feaA 100 :GGMDFFVYPLLEGI T0324 119 :PFMMRMAVTISADD 2feaA 115 :EKDRIYCNHASFDN T0324 135 :KRKPD 2feaA 143 :CSNQC T0324 142 :PLLTALEKV 2feaA 150 :CKPSVIHEL T0324 152 :VAPQN 2feaA 159 :SEPNQ T0324 157 :ALFIGDSVSDEQTAQA 2feaA 165 :IIMIGDSVTDVEAAKL T0324 175 :VDFGLAV 2feaA 181 :SDLCFAR T0324 188 :ADH 2feaA 188 :DYL T0324 191 :QKVAHR 2feaA 197 :QNLNHL T0324 197 :FQKPLDILELFK 2feaA 204 :YQDFYEIRKEIE Number of specific fragments extracted= 16 number of extra gaps= 2 total=1211 Number of alignments=120 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ymqA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ymqA expands to /projects/compbio/data/pdb/1ymq.pdb.gz 1ymqA:# T0324 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 (T0324)Y3 because first residue in template chain is (1ymqA)T2 T0324 4 :QALMFDIDGTLTN 1ymqA 3 :KALFFDIDGTLVS T0324 17 :SQPAYTTVMREVLATY 1ymqA 21 :IPSSTIEALEAAHAKG T0324 39 :AQAQKTF 1ymqA 54 :SELQDRN T0324 46 :PMAAEQAMTEL 1ymqA 87 :QEEVKAMAAFC T0324 57 :GIA 1ymqA 116 :QPN T0324 68 :AQYEDVMASHYD 1ymqA 119 :EMVKKIFYDFLH T0324 80 :QIELYP 1ymqA 133 :VIPTVS T0324 91 :FEQLPS 1ymqA 139 :FEEASN T0324 97 :EL 1ymqA 146 :EV T0324 107 :RRNELESGMRSYP 1ymqA 155 :TEEEEKEVLPSIP T0324 120 :FMMRMAVTISADDT 1ymqA 174 :WYPAFADVTAKGDT T0324 140 :PLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAAN 1ymqA 189 :QKGIDEIIRHFGIKLEETMSFGDGGNDISMLRHAA T0324 178 :GLAVWGMDPNADHQKVAHRFQKPLD 1ymqA 224 :IGVAMGQAKEDVKAAADYVTAPIDE T0324 203 :ILELFK 1ymqA 251 :ISKAMK Number of specific fragments extracted= 14 number of extra gaps= 0 total=1225 Number of alignments=121 # 1ymqA read from 1ymqA/merged-good-all-a2m # found chain 1ymqA in template set Warning: unaligning (T0324)Y3 because first residue in template chain is (1ymqA)T2 T0324 4 :QALMFDIDGTLTN 1ymqA 3 :KALFFDIDGTLVS T0324 78 :YDQIELYPGITSLFEQLP 1ymqA 16 :FETHRIPSSTIEALEAAH T0324 96 :SELRLGIVTSQR 1ymqA 35 :KGLKIFIATGRP T0324 108 :RNELESGMRSYPFM 1ymqA 90 :VKAMAAFCEKKGVP T0324 126 :VTIS 1ymqA 104 :CIFV T0324 130 :ADDTPKRK 1ymqA 181 :VTAKGDTK T0324 140 :PLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAAN 1ymqA 189 :QKGIDEIIRHFGIKLEETMSFGDGGNDISMLRHAA T0324 178 :GLAVWGMDPNADHQKVAHRFQKPLD 1ymqA 224 :IGVAMGQAKEDVKAAADYVTAPIDE T0324 203 :ILELFK 1ymqA 251 :ISKAMK Number of specific fragments extracted= 9 number of extra gaps= 0 total=1234 Number of alignments=122 # 1ymqA read from 1ymqA/merged-good-all-a2m # found chain 1ymqA in template set Warning: unaligning (T0324)Y3 because first residue in template chain is (1ymqA)T2 T0324 4 :QALMFDIDGTLTN 1ymqA 3 :KALFFDIDGTLVS T0324 78 :YDQIELYPGITSLFEQLPS 1ymqA 16 :FETHRIPSSTIEALEAAHA T0324 97 :ELRLGIVTSQRR 1ymqA 36 :GLKIFIATGRPK T0324 109 :NELESGMRSYPF 1ymqA 91 :KAMAAFCEKKGV T0324 125 :AVTISADD 1ymqA 103 :PCIFVEEH T0324 133 :TPKRKPDPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAAN 1ymqA 182 :TAKGDTKQKGIDEIIRHFGIKLEETMSFGDGGNDISMLRHAA T0324 178 :GLAVWGMDPNADHQKVAHRFQKPLD 1ymqA 224 :IGVAMGQAKEDVKAAADYVTAPIDE Number of specific fragments extracted= 7 number of extra gaps= 0 total=1241 Number of alignments=123 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nf2A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1nf2A expands to /projects/compbio/data/pdb/1nf2.pdb.gz 1nf2A:# T0324 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 T0324 1 :M 1nf2A 1 :M T0324 3 :YQALMFDIDGTLTN 1nf2A 2 :YRVFVFDLDGTLLN T0324 33 :GKPFSPAQAQKTF 1nf2A 17 :NLEISEKDRRNIE T0324 46 :PMAAEQAMTEL 1nf2A 85 :PEVAKDIIEYI T0324 57 :GIAASEFDHF 1nf2A 113 :EKDNEEIKSY T0324 75 :ASHYD 1nf2A 123 :ARHSN T0324 80 :QIELYPGITSLFEQLP 1nf2A 129 :DYRVEPNLSELVSKMG T0324 106 :QRRNELESGMRSY 1nf2A 152 :DTPERLDELKEIL T0324 121 :MMRMAV 1nf2A 169 :KDVVKV T0324 127 :TISADDTP 1nf2A 183 :EIVPKNVD T0324 140 :PLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFG 1nf2A 192 :GKALRFLRERMNWKKEEIVVFGDNENDLFMFEEAGLRVA Number of specific fragments extracted= 11 number of extra gaps= 0 total=1252 Number of alignments=124 # 1nf2A read from 1nf2A/merged-good-all-a2m # found chain 1nf2A in template set T0324 1 :M 1nf2A 1 :M T0324 3 :YQALMFDIDGTLTN 1nf2A 2 :YRVFVFDLDGTLLN T0324 79 :DQIELYPGITSLFEQLPSELRLGIVTSQRRNELESGMRSY 1nf2A 16 :DNLEISEKDRRNIEKLSRKCYVVFASGRMLVSTLNVEKKY T0324 120 :FMMRMAVTIS 1nf2A 56 :FKRTFPTIAY T0324 130 :AD 1nf2A 186 :PK T0324 134 :PKRK 1nf2A 188 :NVDK T0324 140 :PLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAAN 1nf2A 192 :GKALRFLRERMNWKKEEIVVFGDNENDLFMFEEAG T0324 178 :GLAVWGMDPNADHQKVAHRFQKPLD 1nf2A 227 :LRVAMENAIEKVKEASDIVTLTNND T0324 203 :ILELFK 1nf2A 254 :VSYVLE Number of specific fragments extracted= 9 number of extra gaps= 0 total=1261 Number of alignments=125 # 1nf2A read from 1nf2A/merged-good-all-a2m # found chain 1nf2A in template set Warning: unaligning (T0324)T2 because first residue in template chain is (1nf2A)M1 T0324 3 :YQALMFDIDGTLTN 1nf2A 2 :YRVFVFDLDGTLLN T0324 17 :SQPAYTTVMREVLATY 1nf2A 20 :ISEKDRRNIEKLSRKC T0324 35 :PFSPAQAQK 1nf2A 82 :KIPPEVAKD T0324 52 :AMTELG 1nf2A 91 :IIEYIK T0324 68 :AQYEDVMASHYDQIELYPGITSLFEQLP 1nf2A 117 :EEIKSYARHSNVDYRVEPNLSELVSKMG T0324 107 :RRNELESGMRSY 1nf2A 153 :TPERLDELKEIL T0324 119 :PFMMRM 1nf2A 170 :DVVKVF T0324 125 :AVTISADDTP 1nf2A 181 :YLEIVPKNVD T0324 139 :DPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQ 1nf2A 191 :KGKALRFLRERMNWKKEEIVVFGDNENDLFMFE T0324 174 :NVDFGLAVWG 1nf2A 224 :EAGLRVAMEN Number of specific fragments extracted= 10 number of extra gaps= 0 total=1271 Number of alignments=126 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qq5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0324 read from 1qq5A/merged-good-all-a2m # 1qq5A read from 1qq5A/merged-good-all-a2m # found chain 1qq5A in training set T0324 1 :M 1qq5A 1 :M T0324 3 :YQALMFDIDGTLTN 1qq5A 2 :IKAVVFDAYGTLFD T0324 18 :QPAYTTVMREVLATY 1qq5A 32 :EYITQVWRQKQLEYS T0324 33 :GKPFSPAQAQKTF 1qq5A 53 :GRYADFWSVTREA T0324 49 :AEQAMTELGIAASE 1qq5A 66 :LAYTLGTLGLEPDE T0324 64 :DH 1qq5A 80 :SF T0324 71 :EDVMASHYDQIELYPGITSLFEQLP 1qq5A 82 :LADMAQAYNRLTPYPDAAQCLAELA T0324 97 :ELRLGIVTSQRRNELESGMRSYPFMMRMAVTISADDTPKRKPDPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFGLAVW 1qq5A 107 :PLKRAILSNGAPDMLQALVANAGLTDSFDAVISVDAKRVFKPHPDSYALVEEVLGVTPAEVLFVSSNGFDVGGAKNFGFSVARVAR T0324 184 :MDPNADHQKVAHRFQKPLDILELFK 1qq5A 218 :MREETYAEAPDFVVPALGDLPRLVR Number of specific fragments extracted= 9 number of extra gaps= 0 total=1280 Number of alignments=127 # 1qq5A read from 1qq5A/merged-good-all-a2m # found chain 1qq5A in training set T0324 1 :M 1qq5A 1 :M T0324 3 :YQALMFDIDGTLTN 1qq5A 2 :IKAVVFDAYGTLFD T0324 17 :SQPAYTTVMREVLATYGKPFSPAQA 1qq5A 58 :FWSVTREALAYTLGTLGLEPDESFL T0324 72 :DVMASHYDQIELYPGITSLFEQL 1qq5A 83 :ADMAQAYNRLTPYPDAAQCLAEL T0324 96 :SELRLGIVTSQRRNELESGMRSYPFMMRMAVTISADDTPKRKPDPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFGLAVW 1qq5A 106 :APLKRAILSNGAPDMLQALVANAGLTDSFDAVISVDAKRVFKPHPDSYALVEEVLGVTPAEVLFVSSNGFDVGGAKNFGFSVARVAR T0324 184 :MDPNAD 1qq5A 204 :SGTIAP T0324 191 :QKVAHRFQKPLDILELFK 1qq5A 225 :EAPDFVVPALGDLPRLVR Number of specific fragments extracted= 7 number of extra gaps= 0 total=1287 Number of alignments=128 # 1qq5A read from 1qq5A/merged-good-all-a2m # found chain 1qq5A in training set Warning: unaligning (T0324)T2 because first residue in template chain is (1qq5A)M1 T0324 3 :YQALMFDIDGTLTN 1qq5A 2 :IKAVVFDAYGTLFD T0324 17 :SQPAYTTVMREVLATY 1qq5A 30 :RGEYITQVWRQKQLEY T0324 33 :GKPFSPAQAQKT 1qq5A 53 :GRYADFWSVTRE T0324 56 :LGI 1qq5A 65 :ALA T0324 59 :AASEFDHFQAQ 1qq5A 75 :LEPDESFLADM T0324 75 :ASHYDQIELYPGITSLFEQLPS 1qq5A 86 :AQAYNRLTPYPDAAQCLAELAP T0324 98 :LRLGIVTSQRRNELESGMRSYPFMMRMAVTISADDTPKRKPDPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFGLAVWG 1qq5A 108 :LKRAILSNGAPDMLQALVANAGLTDSFDAVISVDAKRVFKPHPDSYALVEEVLGVTPAEVLFVSSNGFDVGGAKNFGFSVARVARL T0324 184 :MDPNADHQKVAHRFQKPLDILELFK 1qq5A 218 :MREETYAEAPDFVVPALGDLPRLVR Number of specific fragments extracted= 8 number of extra gaps= 0 total=1295 Number of alignments=129 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fi1A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fi1A expands to /projects/compbio/data/pdb/2fi1.pdb.gz 2fi1A:# T0324 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 T0324 1 :MTYQALMFDIDGTLTNSQPAYTTVMREVLATYGKPFSPAQAQKTFPMAAEQAMTEL 2fi1A 4 :MKYHDYIWDLGGTLLDNYETSTAAFVETLALYGITQDHDSVYQALKVSTPFAIETF T0324 61 :SEFDHFQAQYEDVMASHYDQIELYPGITSLFEQLPS 2fi1A 61 :PNLENFLEKYKENEARELEHPILFEGVSDLLEDISN T0324 97 :ELRLGIVTSQR 2fi1A 98 :GGRHFLVSHRN T0324 109 :NELESGMRSYPFMMRMAVTISADDTPKRKPDPLPLLTALEKVNVA 2fi1A 109 :DQVLEILEKTSIAAYFTEVVTSSSGFKRKPNPESMLYLREKYQIS T0324 156 :NALFIGDSVSDEQTAQAANVDF 2fi1A 154 :SGLVIGDRPIDIEAGQAAGLDT T0324 195 :HRFQKPLDILELFK 2fi1A 176 :HLFTSIVNLRQVLD Number of specific fragments extracted= 6 number of extra gaps= 0 total=1301 Number of alignments=130 # 2fi1A read from 2fi1A/merged-good-all-a2m # found chain 2fi1A in template set T0324 1 :MTYQALMFDIDGTLTNSQPAYTTVMREVLATYGKPFSPAQAQKTFPMAAEQAMTEL 2fi1A 4 :MKYHDYIWDLGGTLLDNYETSTAAFVETLALYGITQDHDSVYQALKVSTPFAIETF T0324 60 :ASEFDHFQAQYEDVMASHYDQIELYPGITSLFEQLP 2fi1A 60 :APNLENFLEKYKENEARELEHPILFEGVSDLLEDIS T0324 96 :SELRLGIVTSQRRN 2fi1A 97 :QGGRHFLVSHRNDQ T0324 111 :LESGMRSYPFMMRMAVTISADDTPKRKPDPLPLLTALEKVNVA 2fi1A 111 :VLEILEKTSIAAYFTEVVTSSSGFKRKPNPESMLYLREKYQIS T0324 156 :NALFIGDSVSDEQTAQAANVDF 2fi1A 154 :SGLVIGDRPIDIEAGQAAGLDT T0324 195 :HRFQKPLDILELFK 2fi1A 176 :HLFTSIVNLRQVLD Number of specific fragments extracted= 6 number of extra gaps= 0 total=1307 Number of alignments=131 # 2fi1A read from 2fi1A/merged-good-all-a2m # found chain 2fi1A in template set T0324 1 :MTYQALMFDIDGTLTNSQPAYTTVMREVLATYGKPFSPAQAQKTFPMAAEQAMTELGI 2fi1A 4 :MKYHDYIWDLGGTLLDNYETSTAAFVETLALYGITQDHDSVYQALKVSTPFAIETFAP T0324 62 :EFDHFQAQYEDVMASHYDQIELYPGITSLFEQLPS 2fi1A 62 :NLENFLEKYKENEARELEHPILFEGVSDLLEDISN T0324 97 :ELRLGIVTSQRRN 2fi1A 98 :GGRHFLVSHRNDQ T0324 111 :LESGMRSYPFMMRMAVTISADDTPKRKPDPLPLLTALEKVNVA 2fi1A 111 :VLEILEKTSIAAYFTEVVTSSSGFKRKPNPESMLYLREKYQIS T0324 156 :NALFIGDSVSDEQTAQAANVDF 2fi1A 154 :SGLVIGDRPIDIEAGQAAGLDT T0324 195 :HRFQKPLDILELF 2fi1A 176 :HLFTSIVNLRQVL Number of specific fragments extracted= 6 number of extra gaps= 0 total=1313 Number of alignments=132 # 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 # T0324 read from 1q92A/merged-good-all-a2m # 1q92A read from 1q92A/merged-good-all-a2m # found chain 1q92A in training set Warning: unaligning (T0324)Y32 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)F61 Warning: unaligning (T0324)P38 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)E70 Warning: unaligning (T0324)A39 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)E70 Warning: unaligning (T0324)F45 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)G74 Warning: unaligning (T0324)P46 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)G74 Warning: unaligning (T0324)T54 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)R83 Warning: unaligning (T0324)E55 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)R83 Warning: unaligning (T0324)Y84 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)P109 Warning: unaligning (T0324)P85 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)P109 Warning: unaligning (T0324)L94 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)A119 Warning: unaligning (T0324)P95 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)A119 Warning: unaligning (T0324)Y118 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)F151 Warning: unaligning (T0324)V175 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1q92A)E190 Warning: unaligning (T0324)D176 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1q92A)E190 Warning: unaligning (T0324)V181 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)A196 Warning: unaligning (T0324)W182 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)A196 Warning: unaligning (T0324)R196 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1q92A)L211 Warning: unaligning (T0324)F197 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1q92A)L211 T0324 3 :YQALMFDIDGTLTNSQPAYTTVMR 1q92A 35 :ALRVLVDMDGVLADFEGGFLRKFR T0324 31 :T 1q92A 59 :A T0324 33 :GKP 1q92A 63 :DQP T0324 36 :FS 1q92A 67 :IA T0324 40 :Q 1q92A 71 :D T0324 47 :MAAEQAM 1q92A 75 :FWVSEQY T0324 56 :L 1q92A 84 :L T0324 64 :DHFQAQYEDVMA 1q92A 86 :PGLSEKAISIWE T0324 76 :SHYDQIEL 1q92A 100 :NFFFELEP T0324 86 :GITSLFEQ 1q92A 110 :GAVEAVKE T0324 96 :S 1q92A 120 :S T0324 97 :ELRLGIVTS 1q92A 123 :NTDVFICTS T0324 106 :QRRNELESGMRS 1q92A 138 :YCPYEKYAWVEK T0324 119 :PFMMR 1q92A 154 :DFLEQ T0324 127 :TISADDTPKRKPD 1q92A 159 :IVLTRDKTVVSAD T0324 158 :LFIGDSV 1q92A 172 :LLIDDRP T0324 174 :N 1q92A 188 :S T0324 177 :FGLA 1q92A 191 :HVLF T0324 183 :GMDPNADHQKVAH 1q92A 197 :CHNQHLQLQPPRR T0324 198 :QKPLDILE 1q92A 216 :DDWKAILD Number of specific fragments extracted= 20 number of extra gaps= 10 total=1333 Number of alignments=133 # 1q92A read from 1q92A/merged-good-all-a2m # found chain 1q92A in training set Warning: unaligning (T0324)Y32 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)F61 Warning: unaligning (T0324)A39 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)E70 Warning: unaligning (T0324)Q40 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)E70 Warning: unaligning (T0324)F45 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)G74 Warning: unaligning (T0324)P46 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)G74 Warning: unaligning (T0324)T54 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)R83 Warning: unaligning (T0324)E55 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)R83 Warning: unaligning (T0324)Y84 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)P109 Warning: unaligning (T0324)P85 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)P109 Warning: unaligning (T0324)L94 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)A119 Warning: unaligning (T0324)P95 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)A119 Warning: unaligning (T0324)Y118 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)F151 Warning: unaligning (T0324)V175 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1q92A)E190 Warning: unaligning (T0324)D176 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1q92A)E190 Warning: unaligning (T0324)V181 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)A196 Warning: unaligning (T0324)W182 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)A196 Warning: unaligning (T0324)R196 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1q92A)L211 Warning: unaligning (T0324)F197 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1q92A)L211 T0324 4 :QALMFDIDGTLTNSQPAYT 1q92A 36 :LRVLVDMDGVLADFEGGFL T0324 27 :EVLAT 1q92A 55 :RKFRA T0324 33 :GKPFSP 1q92A 63 :DQPFIA T0324 41 :A 1q92A 71 :D T0324 44 :T 1q92A 72 :R T0324 47 :MAAEQAM 1q92A 75 :FWVSEQY T0324 56 :L 1q92A 84 :L T0324 63 :FDHFQAQYEDVMA 1q92A 85 :RPGLSEKAISIWE T0324 76 :SHYDQIEL 1q92A 100 :NFFFELEP T0324 86 :GITSLFEQ 1q92A 110 :GAVEAVKE T0324 96 :SELRLGIVTSQR 1q92A 122 :QNTDVFICTSPI T0324 108 :RNELESGMRS 1q92A 140 :PYEKYAWVEK T0324 119 :P 1q92A 152 :G T0324 121 :MMRMAVTISADDTPKRKPD 1q92A 153 :PDFLEQIVLTRDKTVVSAD T0324 158 :LFIGDSV 1q92A 172 :LLIDDRP T0324 165 :S 1q92A 181 :T T0324 177 :FGLA 1q92A 191 :HVLF T0324 183 :GMDPNADHQKVAH 1q92A 197 :CHNQHLQLQPPRR T0324 198 :QKPLDILE 1q92A 216 :DDWKAILD Number of specific fragments extracted= 19 number of extra gaps= 10 total=1352 Number of alignments=134 # 1q92A read from 1q92A/merged-good-all-a2m # found chain 1q92A in training set Warning: unaligning (T0324)Y32 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)F61 Warning: unaligning (T0324)K34 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)G74 Warning: unaligning (T0324)P35 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)G74 Warning: unaligning (T0324)K43 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)R83 Warning: unaligning (T0324)T44 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)R83 Warning: unaligning (T0324)Y84 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)P109 Warning: unaligning (T0324)P85 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)P109 Warning: unaligning (T0324)L94 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)A119 Warning: unaligning (T0324)P95 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)A119 Warning: unaligning (T0324)Y118 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)F151 Warning: unaligning (T0324)V175 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1q92A)E190 Warning: unaligning (T0324)D176 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1q92A)E190 Warning: unaligning (T0324)V181 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)A196 Warning: unaligning (T0324)W182 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)A196 Warning: unaligning (T0324)R196 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1q92A)L211 Warning: unaligning (T0324)F197 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1q92A)L211 T0324 6 :LMFDIDGTLTNSQPAYTTVMRE 1q92A 38 :VLVDMDGVLADFEGGFLRKFRA T0324 33 :G 1q92A 72 :R T0324 36 :FSPAQAQ 1q92A 75 :FWVSEQY T0324 45 :FPMAAEQAMTELGI 1q92A 84 :LRPGLSEKAISIWE T0324 76 :SHYDQIEL 1q92A 100 :NFFFELEP T0324 86 :GITSLFEQ 1q92A 110 :GAVEAVKE T0324 96 :S 1q92A 120 :S T0324 97 :ELRLGIVTSQ 1q92A 123 :NTDVFICTSP T0324 107 :RRNELESGMRS 1q92A 139 :CPYEKYAWVEK T0324 119 :PFMMR 1q92A 154 :DFLEQ T0324 127 :TISADDTPKRKPD 1q92A 159 :IVLTRDKTVVSAD T0324 158 :LFIGDSV 1q92A 172 :LLIDDRP T0324 174 :N 1q92A 188 :S T0324 177 :FGLA 1q92A 191 :HVLF T0324 183 :GMDPNADHQKVAH 1q92A 197 :CHNQHLQLQPPRR T0324 198 :QKPLDILE 1q92A 216 :DDWKAILD Number of specific fragments extracted= 16 number of extra gaps= 9 total=1368 Number of alignments=135 # 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 # T0324 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 (T0324)F8 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1qq7A)A9 Warning: unaligning (T0324)I10 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1qq7A)A9 T0324 1 :M 1qq7A 1 :M T0324 3 :YQALM 1qq7A 2 :IKAVV T0324 11 :DGTLTNS 1qq7A 10 :YGTLFDV T0324 18 :QPAYTTV 1qq7A 20 :ADATERA T0324 25 :MREVLATY 1qq7A 39 :RQKQLEYS T0324 33 :GKPFSPAQAQKTF 1qq7A 53 :GRYADFWSVTREA T0324 49 :AEQAMTELGIAASE 1qq7A 66 :LAYTLGTLGLEPDE T0324 64 :D 1qq7A 80 :S T0324 70 :YEDVMASHYDQIELYPGITSLFEQLP 1qq7A 81 :FLADMAQAYNRLTPYPDAAQCLAELA T0324 97 :ELRLGIVTSQRRNELESGMRSYPFMMRMAVTISADDTPKRKPDPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFGLAVW 1qq7A 107 :PLKRAILSNGAPDMLQALVANAGLTDSFDAVISVDAKRVFKPHPDSYALVEEVLGVTPAEVLFVSSNGFDVGGAKNFGFSVARVAR T0324 184 :MDPNADHQKVAHRFQKPLDILELFK 1qq7A 218 :MREETYAEAPDFVVPALGDLPRLVR Number of specific fragments extracted= 11 number of extra gaps= 0 total=1379 Number of alignments=136 # 1qq7A read from 1qq7A/merged-good-all-a2m # found chain 1qq7A in template set Warning: unaligning (T0324)F8 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1qq7A)A9 Warning: unaligning (T0324)I10 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1qq7A)A9 T0324 1 :M 1qq7A 1 :M T0324 3 :YQALM 1qq7A 2 :IKAVV T0324 11 :DGTLTN 1qq7A 10 :YGTLFD T0324 17 :SQPAYTTVMREVLATYGKPFSPAQA 1qq7A 58 :FWSVTREALAYTLGTLGLEPDESFL T0324 72 :DVMASHYDQIELYPGITSLFEQL 1qq7A 83 :ADMAQAYNRLTPYPDAAQCLAEL T0324 96 :SELRLGIVTSQRRNELESGMRSYPFMMRMAVTISADDTPKRKPDPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFGLAVW 1qq7A 106 :APLKRAILSNGAPDMLQALVANAGLTDSFDAVISVDAKRVFKPHPDSYALVEEVLGVTPAEVLFVSSNGFDVGGAKNFGFSVARVAR T0324 185 :DPNA 1qq7A 205 :GTIA T0324 191 :QKVAHRFQKPLDILELFK 1qq7A 225 :EAPDFVVPALGDLPRLVR Number of specific fragments extracted= 8 number of extra gaps= 0 total=1387 Number of alignments=137 # 1qq7A read from 1qq7A/merged-good-all-a2m # found chain 1qq7A in template set Warning: unaligning (T0324)T2 because first residue in template chain is (1qq7A)M1 Warning: unaligning (T0324)F8 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1qq7A)A9 Warning: unaligning (T0324)I10 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1qq7A)A9 T0324 3 :YQALM 1qq7A 2 :IKAVV T0324 11 :DGTLTN 1qq7A 10 :YGTLFD T0324 17 :SQPAYTTVMREVLATY 1qq7A 30 :RGEYITQVWRQKQLEY T0324 40 :QAQKTFPMAAEQAMTELGI 1qq7A 49 :RALMGRYADFWSVTREALA T0324 59 :AASEFDHFQA 1qq7A 75 :LEPDESFLAD T0324 74 :MASHYDQIELYPGITSLFEQLPS 1qq7A 85 :MAQAYNRLTPYPDAAQCLAELAP T0324 98 :LRLGIVTSQRRNELESGMRSYPFMMRMAVTISADDTPKRKPDPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFGLAVWG 1qq7A 108 :LKRAILSNGAPDMLQALVANAGLTDSFDAVISVDAKRVFKPHPDSYALVEEVLGVTPAEVLFVSSNGFDVGGAKNFGFSVARVARL T0324 184 :MDPNADHQKVAHRFQKPLDILELFK 1qq7A 218 :MREETYAEAPDFVVPALGDLPRLVR Number of specific fragments extracted= 8 number of extra gaps= 0 total=1395 Number of alignments=138 # 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:# T0324 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 T0324 1 :M 1aq6A 1 :M T0324 3 :YQALMFDIDGTLTN 1aq6A 2 :IKAVVFDAYGTLFD T0324 18 :QPAYTTV 1aq6A 20 :ADATERA T0324 25 :MREVLATY 1aq6A 39 :RQKQLEYS T0324 33 :GKPFSPAQAQKTF 1aq6A 53 :GRYADFWGVTREA T0324 49 :AEQAMTELGIAASE 1aq6A 66 :LAYTLGTLGLEPDE T0324 64 :D 1aq6A 80 :S T0324 70 :YEDVMASHYDQIELYPGITSLFEQLP 1aq6A 81 :FLADMAQAYNRLTPYPDAAQCLAELA T0324 97 :ELRLGIVTSQRRNELESGMRSYPFMMRMAVTISADDTPKRKPDPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFGLAVW 1aq6A 107 :PLKRAILSNGAPDMLQALVANAGLTDSFDAVISVDAKRVFKPHPDSYALVEEVLGVTPAEVLFVSSNGFDVGGAKNFGFSVARVAR T0324 184 :MDPNADHQKVAHRFQKPLDILELFK 1aq6A 218 :MREETYAEAPDFVVPALGDLPRLVR Number of specific fragments extracted= 10 number of extra gaps= 0 total=1405 Number of alignments=139 # 1aq6A read from 1aq6A/merged-good-all-a2m # found chain 1aq6A in template set T0324 1 :M 1aq6A 1 :M T0324 3 :YQALMFDIDGTLTN 1aq6A 2 :IKAVVFDAYGTLFD T0324 17 :SQPAYTTVMREVLATYGKPFSPAQA 1aq6A 58 :FWGVTREALAYTLGTLGLEPDESFL T0324 72 :DVMASHYDQIELYPGITSLFEQL 1aq6A 83 :ADMAQAYNRLTPYPDAAQCLAEL T0324 96 :SELRLGIVTSQRRNELESGMRSYPFMMRMAVTISADDTPKRKPDPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFGLAVW 1aq6A 106 :APLKRAILSNGAPDMLQALVANAGLTDSFDAVISVDAKRVFKPHPDSYALVEEVLGVTPAEVLFVSSNGFDVGGAKNFGFSVARVAR T0324 184 :MDPNADH 1aq6A 204 :SGTIAPL T0324 191 :QKVAHRFQKPLDILELFK 1aq6A 225 :EAPDFVVPALGDLPRLVR Number of specific fragments extracted= 7 number of extra gaps= 0 total=1412 Number of alignments=140 # 1aq6A read from 1aq6A/merged-good-all-a2m # found chain 1aq6A in template set Warning: unaligning (T0324)T2 because first residue in template chain is (1aq6A)M1 T0324 3 :YQALMFDIDGTLTN 1aq6A 2 :IKAVVFDAYGTLFD T0324 17 :SQPAYTTVMREVLATY 1aq6A 30 :RGEYITQVWRQKQLEY T0324 39 :AQAQKTFPMAAEQAMTELGI 1aq6A 48 :LRALMGRYADFWGVTREALA T0324 59 :AASEFDHFQAQ 1aq6A 75 :LEPDESFLADM T0324 75 :ASHYDQIELYPGITSLFEQLPS 1aq6A 86 :AQAYNRLTPYPDAAQCLAELAP T0324 98 :LRLGIVTSQRRNELESGMRSYPFMMRMAVTISADDTPKRKPDPLPLLTALEKVNVAPQNALFIGDSVSDEQTAQAANVDFGLAVWG 1aq6A 108 :LKRAILSNGAPDMLQALVANAGLTDSFDAVISVDAKRVFKPHPDSYALVEEVLGVTPAEVLFVSSNGFDVGGAKNFGFSVARVARL T0324 184 :MDPNADHQKVAHRFQKPLDILELFK 1aq6A 218 :MREETYAEAPDFVVPALGDLPRLVR Number of specific fragments extracted= 7 number of extra gaps= 0 total=1419 Number of alignments=141 # 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:# T0324 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 (T0324)Q191 because of BadResidue code BAD_PEPTIDE in next template residue (1mh9A)P206 Warning: unaligning (T0324)K192 because of BadResidue code BAD_PEPTIDE at template residue (1mh9A)P206 T0324 3 :YQALMFDIDGTLTNSQPAYTTV 1mh9A 35 :ALRVLVDMDGVLADFEGGFLRK T0324 29 :LATY 1mh9A 57 :FRAR T0324 33 :GKP 1mh9A 63 :DQP T0324 36 :FSPAQ 1mh9A 67 :IALED T0324 45 :FPMAAEQAMTEL 1mh9A 73 :RGFWVSEQYGRL T0324 64 :DHFQAQYEDVMA 1mh9A 86 :PGLSEKAISIWE T0324 76 :SHYDQIELYPGITSLFEQLPS 1mh9A 100 :NFFFELEPLPGAVEAVKEMAS T0324 97 :ELRLGIVTS 1mh9A 123 :NTDVFICTS T0324 106 :QRRNELESGMRSY 1mh9A 138 :YCPYEKYAWVEKY T0324 119 :PFMMR 1mh9A 154 :DFLEQ T0324 127 :TISADDTPKRKPD 1mh9A 159 :IVLTRDKTVVSAD T0324 158 :LFIGDSV 1mh9A 172 :LLIDDRP T0324 165 :S 1mh9A 181 :T T0324 174 :NVDFGLAVWGMDPNADH 1mh9A 188 :SWEHVLFTACHNQHLQL T0324 193 :VAHRF 1mh9A 207 :PRRRL T0324 198 :QKPLDILE 1mh9A 216 :DDWKAILD Number of specific fragments extracted= 16 number of extra gaps= 1 total=1435 Number of alignments=142 # 1mh9A read from 1mh9A/merged-good-all-a2m # found chain 1mh9A in template set Warning: unaligning (T0324)Q191 because of BadResidue code BAD_PEPTIDE in next template residue (1mh9A)P206 Warning: unaligning (T0324)K192 because of BadResidue code BAD_PEPTIDE at template residue (1mh9A)P206 T0324 4 :QALMFDIDGTLTNS 1mh9A 36 :LRVLVDMDGVLADF T0324 22 :TTVMREVLATY 1mh9A 50 :EGGFLRKFRAR T0324 33 :GKPFSPAQ 1mh9A 63 :DQPFIALE T0324 43 :KTFPMAAEQAMTEL 1mh9A 71 :DRRGFWVSEQYGRL T0324 63 :FDHFQAQYEDVMA 1mh9A 85 :RPGLSEKAISIWE T0324 76 :SHYDQIELYPGITSLFEQLP 1mh9A 100 :NFFFELEPLPGAVEAVKEMA T0324 96 :SELRLGIVTSQR 1mh9A 122 :QNTDVFICTSPI T0324 108 :RNELESGMRSY 1mh9A 140 :PYEKYAWVEKY T0324 119 :P 1mh9A 152 :G T0324 121 :MMRMAVTISADDTPKRKPD 1mh9A 153 :PDFLEQIVLTRDKTVVSAD T0324 158 :LFIGDSV 1mh9A 172 :LLIDDRP T0324 165 :S 1mh9A 181 :T T0324 175 :VDFGLAVWGMDPNADH 1mh9A 189 :WEHVLFTACHNQHLQL T0324 193 :VAHRF 1mh9A 207 :PRRRL T0324 198 :QKPLDILE 1mh9A 216 :DDWKAILD Number of specific fragments extracted= 15 number of extra gaps= 1 total=1450 Number of alignments=143 # 1mh9A read from 1mh9A/merged-good-all-a2m # found chain 1mh9A in template set Warning: unaligning (T0324)Q191 because of BadResidue code BAD_PEPTIDE in next template residue (1mh9A)P206 Warning: unaligning (T0324)K192 because of BadResidue code BAD_PEPTIDE at template residue (1mh9A)P206 T0324 6 :LMFDIDGTLTNSQPAYTTVMRE 1mh9A 38 :VLVDMDGVLADFEGGFLRKFRA T0324 32 :Y 1mh9A 60 :R T0324 33 :GKPFSPAQAQKTFPMAAEQAMTELGI 1mh9A 72 :RRGFWVSEQYGRLRPGLSEKAISIWE T0324 76 :SHYDQIELYPGITSLFEQLPS 1mh9A 100 :NFFFELEPLPGAVEAVKEMAS T0324 97 :ELRLGIVTSQ 1mh9A 123 :NTDVFICTSP T0324 107 :RRNELESGMRSY 1mh9A 139 :CPYEKYAWVEKY T0324 119 :PFMMR 1mh9A 154 :DFLEQ T0324 127 :TISADDTPKRKPD 1mh9A 159 :IVLTRDKTVVSAD T0324 158 :LFIGDSV 1mh9A 172 :LLIDDRP T0324 174 :NVDFGLAVWGMDPNADH 1mh9A 188 :SWEHVLFTACHNQHLQL T0324 193 :VAHRF 1mh9A 207 :PRRRL T0324 198 :QKPLDILE 1mh9A 216 :DDWKAILD Number of specific fragments extracted= 12 number of extra gaps= 1 total=1462 Number of alignments=144 # command:# PrintAlignmentsContacts allconstraints.under Using radius: 8.0000 NUMB_ALIGNS: 144 Done printing distance constraints # command: