# 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:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0324//projects/compbio/experiments/protein-predict/casp7/T0324/align.constraints_v3.costfcn or /projects/compbio/experiments/protein-predict/casp7/T0324//projects/compbio/experiments/protein-predict/casp7/T0324/align.constraints_v3.costfcn.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/T0324/align.constraints_v3.costfcn # reading script from file /projects/compbio/experiments/protein-predict/casp7/T0324/align.constraints_v3.costfcn # future Constraint commands -> align # future HelixConstraint commands -> align # future StrandConstraint commands -> align # future SheetConstraint commands -> align # future Hbond commands -> align # future SSbond commands -> align # Constraint # added constraint: constraint((T0324)M7.CB, (T0324)I160.CB) [> 4.2811 = 7.1351 < 9.2757] w=1.0000 to align # Constraint # added constraint: constraint((T0324)M7.CB, (T0324)F159.CB) [> 2.8756 = 4.7926 < 6.2304] w=1.0000 to align # Constraint # added constraint: constraint((T0324)M7.CB, (T0324)L158.CB) [> 4.1660 = 6.9434 < 9.0264] w=1.0000 to align # Constraint # added constraint: constraint((T0324)L6.CB, (T0324)L158.CB) [> 2.9630 = 4.9383 < 6.4198] w=1.0000 to align # Constraint # added constraint: constraint((T0324)T13.CB, (T0324)D162.CB) [> 3.0601 = 5.1002 < 6.6303] w=0.9857 to align # Constraint # added constraint: constraint((T0324)T13.CB, (T0324)G161.CA) [> 2.8803 = 4.8005 < 6.2407] w=0.9857 to align # Constraint # added constraint: constraint((T0324)T13.CB, (T0324)I160.CB) [> 3.5905 = 5.9842 < 7.7795] w=0.9857 to align # Constraint # added constraint: constraint((T0324)G12.CA, (T0324)D162.CB) [> 2.8540 = 4.7566 < 6.1836] w=0.9857 to align # Constraint # added constraint: constraint((T0324)L6.CB, (T0324)I160.CB) [> 4.1027 = 6.8377 < 8.8891] w=0.9787 to align # Constraint # added constraint: constraint((T0324)M7.CB, (T0324)A157.CB) [> 3.6872 = 6.1453 < 7.9889] w=0.9765 to align # Constraint # added constraint: constraint((T0324)L6.CB, (T0324)A157.CB) [> 4.4211 = 7.3685 < 9.5790] w=0.9765 to align # Constraint # added constraint: constraint((T0324)A5.CB, (T0324)L158.CB) [> 4.3597 = 7.2662 < 9.4461] w=0.9712 to align # Constraint # added constraint: constraint((T0324)A5.CB, (T0324)N156.CB) [> 3.8708 = 6.4513 < 8.3867] w=0.9555 to align # Constraint # added constraint: constraint((T0324)A5.CB, (T0324)A157.CB) [> 2.8143 = 4.6905 < 6.0977] w=0.9555 to align # Constraint # added constraint: constraint((T0324)F159.CB, (T0324)G178.CA) [> 3.9077 = 6.5129 < 8.4668] w=0.9218 to align # Constraint # added constraint: constraint((T0324)L158.CB, (T0324)G178.CA) [> 3.9858 = 6.6430 < 8.6359] w=0.9218 to align # Constraint # added constraint: constraint((T0324)F159.CB, (T0324)A170.CB) [> 2.6440 = 4.4067 < 5.7287] w=0.9127 to align # Constraint # added constraint: constraint((T0324)Q4.CB, (T0324)N156.CB) [> 2.6746 = 4.4576 < 5.7949] w=0.8985 to align # Constraint # added constraint: constraint((T0324)M7.CB, (T0324)G101.CA) [> 3.1916 = 5.3193 < 6.9151] w=0.8930 to align # Constraint # added constraint: constraint((T0324)L6.CB, (T0324)G101.CA) [> 4.1181 = 6.8635 < 8.9225] w=0.8930 to align # Constraint # added constraint: constraint((T0324)L6.CB, (T0324)L100.CB) [> 3.2381 = 5.3968 < 7.0158] w=0.8930 to align # Constraint # added constraint: constraint((T0324)L6.CB, (T0324)L98.CB) [> 3.4199 = 5.6999 < 7.4099] w=0.8930 to align # Constraint # added constraint: constraint((T0324)L143.CB, (T0324)T169.CB) [> 3.4468 = 5.7446 < 7.4680] w=0.8842 to align # Constraint # added constraint: constraint((T0324)A5.CB, (T0324)V150.CB) [> 3.3960 = 5.6601 < 7.3581] w=0.8842 to align # Constraint # added constraint: constraint((T0324)F159.CB, (T0324)F177.CB) [> 3.2104 = 5.3506 < 6.9558] w=0.8790 to align # Constraint # added constraint: constraint((T0324)F91.CB, (T0324)L100.CB) [> 3.6669 = 6.1115 < 7.9449] w=0.8788 to align # Constraint # added constraint: constraint((T0324)L6.CB, (T0324)R99.CB) [> 4.3633 = 7.2721 < 9.4537] w=0.8716 to align # Constraint # added constraint: constraint((T0324)A5.CB, (T0324)R99.CB) [> 2.6481 = 4.4135 < 5.7375] w=0.8642 to align # Constraint # added constraint: constraint((T0324)A5.CB, (T0324)V152.CB) [> 2.9584 = 4.9307 < 6.4099] w=0.8628 to align # Constraint # added constraint: constraint((T0324)L6.CB, (T0324)L94.CB) [> 3.5396 = 5.8992 < 7.6690] w=0.8574 to align # Constraint # added constraint: constraint((T0324)L14.CB, (T0324)I87.CB) [> 3.2557 = 5.4262 < 7.0541] w=0.8574 to align # Constraint # added constraint: constraint((T0324)Q4.CB, (T0324)A157.CB) [> 4.3312 = 7.2186 < 9.3842] w=0.8557 to align # Constraint # added constraint: constraint((T0324)L147.CB, (T0324)A157.CB) [> 3.7403 = 6.2337 < 8.1039] w=0.8557 to align # Constraint # added constraint: constraint((T0324)I160.CB, (T0324)G178.CA) [> 3.2273 = 5.3788 < 6.9924] w=0.8506 to align # Constraint # added constraint: constraint((T0324)G161.CA, (T0324)A180.CB) [> 3.4439 = 5.7398 < 7.4617] w=0.8505 to align # Constraint # added constraint: constraint((T0324)M7.CB, (T0324)V103.CB) [> 3.2349 = 5.3914 < 7.0089] w=0.8502 to align # Constraint # added constraint: constraint((T0324)A5.CB, (T0324)L98.CB) [> 3.8609 = 6.4349 < 8.3653] w=0.8485 to align # Constraint # added constraint: constraint((T0324)I160.CB, (T0324)A180.CB) [> 3.5866 = 5.9776 < 7.7709] w=0.8433 to align # Constraint # added constraint: constraint((T0324)L158.CB, (T0324)D176.CB) [> 2.8380 = 4.7300 < 6.1491] w=0.8365 to align # Constraint # added constraint: constraint((T0324)D11.CB, (T0324)T104.CB) [> 4.1166 = 6.8610 < 8.9193] w=0.8359 to align # Constraint # added constraint: constraint((T0324)L143.CB, (T0324)A173.CB) [> 2.9845 = 4.9741 < 6.4663] w=0.8341 to align # Constraint # added constraint: constraint((T0324)G161.CA, (T0324)G178.CA) [> 3.9794 = 6.6323 < 8.6220] w=0.8292 to align # Constraint # added constraint: constraint((T0324)D9.CB, (T0324)D162.CB) [> 3.7923 = 6.3205 < 8.2166] w=0.8288 to align # Constraint # added constraint: constraint((T0324)D9.CB, (T0324)G161.CA) [> 2.4229 = 4.0382 < 5.2496] w=0.8288 to align # Constraint # added constraint: constraint((T0324)D9.CB, (T0324)I160.CB) [> 3.9380 = 6.5634 < 8.5324] w=0.8288 to align # Constraint # added constraint: constraint((T0324)F8.CB, (T0324)G161.CA) [> 4.2661 = 7.1102 < 9.2432] w=0.8288 to align # Constraint # added constraint: constraint((T0324)F8.CB, (T0324)I160.CB) [> 3.1031 = 5.1719 < 6.7235] w=0.8288 to align # Constraint # added constraint: constraint((T0324)A5.CB, (T0324)G101.CA) [> 4.2944 = 7.1574 < 9.3047] w=0.8285 to align # Constraint # added constraint: constraint((T0324)M7.CB, (T0324)A146.CB) [> 3.6759 = 6.1265 < 7.9645] w=0.8200 to align # Constraint # added constraint: constraint((T0324)A157.CB, (T0324)D176.CB) [> 4.0447 = 6.7411 < 8.7635] w=0.8199 to align # Constraint # added constraint: constraint((T0324)G161.CA, (T0324)L179.CB) [> 3.7898 = 6.3163 < 8.2113] w=0.8148 to align # Constraint # added constraint: constraint((T0324)A5.CB, (T0324)L100.CB) [> 4.4401 = 7.4002 < 9.6202] w=0.8142 to align # Constraint # added constraint: constraint((T0324)P140.CB, (T0324)T169.CB) [> 3.4529 = 5.7548 < 7.4812] w=0.8129 to align # Constraint # added constraint: constraint((T0324)P154.CB, (T0324)N174.CB) [> 2.8576 = 4.7626 < 6.1914] w=0.8129 to align # Constraint # added constraint: constraint((T0324)L158.CB, (T0324)F177.CB) [> 4.3333 = 7.2221 < 9.3888] w=0.8112 to align # Constraint # added constraint: constraint((T0324)Q4.CB, (T0324)R99.CB) [> 4.0303 = 6.7171 < 8.7323] w=0.8072 to align # Constraint # added constraint: constraint((T0324)Q4.CB, (T0324)L98.CB) [> 3.6605 = 6.1008 < 7.9310] w=0.8072 to align # Constraint # added constraint: constraint((T0324)I10.CB, (T0324)T104.CB) [> 2.6605 = 4.4341 < 5.7644] w=0.7932 to align # Constraint # added constraint: constraint((T0324)I10.CB, (T0324)I102.CB) [> 3.4611 = 5.7686 < 7.4992] w=0.7932 to align # Constraint # added constraint: constraint((T0324)M7.CB, (T0324)I102.CB) [> 4.3434 = 7.2390 < 9.4108] w=0.7864 to align # Constraint # added constraint: constraint((T0324)L14.CB, (T0324)L83.CB) [> 3.8030 = 6.3383 < 8.2399] w=0.7861 to align # Constraint # added constraint: constraint((T0324)A157.CB, (T0324)V175.CB) [> 2.9111 = 4.8518 < 6.3074] w=0.7842 to align # Constraint # added constraint: constraint((T0324)F159.CB, (T0324)D176.CB) [> 4.0971 = 6.8285 < 8.8770] w=0.7723 to align # Constraint # added constraint: constraint((T0324)T15.CB, (T0324)L83.CB) [> 3.6229 = 6.0382 < 7.8496] w=0.7718 to align # Constraint # added constraint: constraint((T0324)F159.CB, (T0324)V175.CB) [> 3.0150 = 5.0251 < 6.5326] w=0.7653 to align # Constraint # added constraint: constraint((T0324)L158.CB, (T0324)V175.CB) [> 3.9826 = 6.6377 < 8.6290] w=0.7653 to align # Constraint # added constraint: constraint((T0324)D9.CB, (T0324)S163.CB) [> 4.3048 = 7.1747 < 9.3270] w=0.7646 to align # Constraint # added constraint: constraint((T0324)D9.CB, (T0324)D166.CB) [> 3.4935 = 5.8224 < 7.5691] w=0.7626 to align # Constraint # added constraint: constraint((T0324)T15.CB, (T0324)I81.CB) [> 3.2903 = 5.4838 < 7.1290] w=0.7575 to align # Constraint # added constraint: constraint((T0324)P140.CB, (T0324)A172.CB) [> 3.0436 = 5.0727 < 6.5945] w=0.7557 to align # Constraint # added constraint: constraint((T0324)G101.CA, (T0324)M124.CB) [> 3.0765 = 5.1274 < 6.6657] w=0.7554 to align # Constraint # added constraint: constraint((T0324)G12.CA, (T0324)G161.CA) [> 4.5761 = 7.6269 < 9.9150] w=0.7509 to align # Constraint # added constraint: constraint((T0324)D162.CB, (T0324)A180.CB) [> 3.0653 = 5.1088 < 6.6415] w=0.7507 to align # Constraint # added constraint: constraint((T0324)G101.CA, (T0324)T127.CB) [> 3.9262 = 6.5437 < 8.5069] w=0.7434 to align # Constraint # added constraint: constraint((T0324)D11.CB, (T0324)D162.CB) [> 4.5685 = 7.6141 < 9.8983] w=0.7434 to align # Constraint # added constraint: constraint((T0324)I102.CB, (T0324)M124.CB) [> 3.4095 = 5.6825 < 7.3873] w=0.7412 to align # Constraint # added constraint: constraint((T0324)T104.CB, (T0324)I128.CB) [> 4.4213 = 7.3689 < 9.5795] w=0.7365 to align # Constraint # added constraint: constraint((T0324)P154.CB, (T0324)A173.CB) [> 3.4121 = 5.6869 < 7.3930] w=0.7344 to align # Constraint # added constraint: constraint((T0324)L143.CB, (T0324)F159.CB) [> 4.2012 = 7.0021 < 9.1027] w=0.7273 to align # Constraint # added constraint: constraint((T0324)Q4.CB, (T0324)V152.CB) [> 3.2305 = 5.3842 < 6.9994] w=0.7273 to align # Constraint # added constraint: constraint((T0324)Y3.CB, (T0324)N156.CB) [> 3.6256 = 6.0427 < 7.8556] w=0.7273 to align # Constraint # added constraint: constraint((T0324)V103.CB, (T0324)P142.CB) [> 3.5932 = 5.9886 < 7.7852] w=0.7273 to align # Constraint # added constraint: constraint((T0324)D162.CB, (T0324)V181.CB) [> 3.9884 = 6.6473 < 8.6415] w=0.7234 to align # Constraint # added constraint: constraint((T0324)L83.CB, (T0324)Y118.CB) [> 3.4700 = 5.7833 < 7.5183] w=0.7231 to align # Constraint # added constraint: constraint((T0324)L14.CB, (T0324)Y84.CB) [> 3.7412 = 6.2353 < 8.1058] w=0.7220 to align # Constraint # added constraint: constraint((T0324)F8.CB, (T0324)G101.CA) [> 3.7848 = 6.3080 < 8.2004] w=0.7218 to align # Constraint # added constraint: constraint((T0324)F8.CB, (T0324)I102.CB) [> 3.2496 = 5.4160 < 7.0408] w=0.7218 to align # Constraint # added constraint: constraint((T0324)Q155.CB, (T0324)N174.CB) [> 3.3615 = 5.6025 < 7.2832] w=0.7201 to align # Constraint # added constraint: constraint((T0324)N16.CB, (T0324)Y84.CB) [> 3.6493 = 6.0821 < 7.9067] w=0.7161 to align # Constraint # added constraint: constraint((T0324)I102.CB, (T0324)T127.CB) [> 2.9427 = 4.9046 < 6.3760] w=0.7149 to align # Constraint # added constraint: constraint((T0324)L14.CB, (T0324)I102.CB) [> 4.2429 = 7.0716 < 9.1930] w=0.7147 to align # Constraint # added constraint: constraint((T0324)G178.CA, (T0324)A194.CB) [> 3.4810 = 5.8017 < 7.5422] w=0.7080 to align # Constraint # added constraint: constraint((T0324)L179.CB, (T0324)H195.CB) [> 4.0507 = 6.7512 < 8.7766] w=0.7080 to align # Constraint # added constraint: constraint((T0324)I102.CB, (T0324)I128.CB) [> 3.9358 = 6.5596 < 8.5275] w=0.7080 to align # Constraint # added constraint: constraint((T0324)T15.CB, (T0324)Y84.CB) [> 3.9273 = 6.5455 < 8.5091] w=0.7077 to align # Constraint # added constraint: constraint((T0324)G178.CA, (T0324)H195.CB) [> 2.9651 = 4.9418 < 6.4244] w=0.7009 to align # Constraint # added constraint: constraint((T0324)A180.CB, (T0324)F197.CB) [> 3.4713 = 5.7855 < 7.5211] w=0.7008 to align # Constraint # added constraint: constraint((T0324)D9.CB, (T0324)V103.CB) [> 3.8931 = 6.4884 < 8.4350] w=0.7004 to align # Constraint # added constraint: constraint((T0324)D9.CB, (T0324)T104.CB) [> 3.8863 = 6.4773 < 8.4204] w=0.7004 to align # Constraint # added constraint: constraint((T0324)G101.CA, (T0324)V126.CB) [> 2.9739 = 4.9564 < 6.4433] w=0.6993 to align # Constraint # added constraint: constraint((T0324)D162.CB, (T0324)L179.CB) [> 4.1903 = 6.9839 < 9.0790] w=0.6937 to align # Constraint # added constraint: constraint((T0324)F8.CB, (T0324)L100.CB) [> 4.2407 = 7.0678 < 9.1881] w=0.6826 to align # Constraint # added constraint: constraint((T0324)V103.CB, (T0324)I128.CB) [> 2.9621 = 4.9369 < 6.4180] w=0.6795 to align # Constraint # added constraint: constraint((T0324)I10.CB, (T0324)L111.CB) [> 3.8647 = 6.4411 < 8.3734] w=0.6791 to align # Constraint # added constraint: constraint((T0324)T104.CB, (T0324)S129.CB) [> 3.5556 = 5.9261 < 7.7039] w=0.6723 to align # Constraint # added constraint: constraint((T0324)T13.CB, (T0324)A180.CB) [> 3.3367 = 5.5611 < 7.2295] w=0.6652 to align # Constraint # added constraint: constraint((T0324)L6.CB, (T0324)F159.CB) [> 4.6915 = 7.8191 < 10.1648] w=0.6648 to align # Constraint # added constraint: constraint((T0324)I102.CB, (T0324)V126.CB) [> 4.1943 = 6.9904 < 9.0876] w=0.6636 to align # Constraint # added constraint: constraint((T0324)V103.CB, (T0324)A146.CB) [> 3.4214 = 5.7023 < 7.4130] w=0.6632 to align # Constraint # added constraint: constraint((T0324)G178.CA, (T0324)R196.CB) [> 3.9717 = 6.6195 < 8.6053] w=0.6582 to align # Constraint # added constraint: constraint((T0324)F8.CB, (T0324)V103.CB) [> 4.4118 = 7.3531 < 9.5590] w=0.6577 to align # Constraint # added constraint: constraint((T0324)L100.CB, (T0324)M124.CB) [> 3.0058 = 5.0097 < 6.5126] w=0.6558 to align # Constraint # added constraint: constraint((T0324)E167.CB, (T0324)F177.CB) [> 2.9641 = 4.9402 < 6.4223] w=0.6492 to align # Constraint # added constraint: constraint((T0324)P154.CB, (T0324)V175.CB) [> 3.0504 = 5.0841 < 6.6093] w=0.6490 to align # Constraint # added constraint: constraint((T0324)I128.CB, (T0324)A146.CB) [> 3.5295 = 5.8825 < 7.6472] w=0.6490 to align # Constraint # added constraint: constraint((T0324)Y3.CB, (T0324)A157.CB) [> 4.0918 = 6.8196 < 8.8655] w=0.6419 to align # Constraint # added constraint: constraint((T0324)G178.CA, (T0324)F197.CB) [> 4.1101 = 6.8501 < 8.9051] w=0.6368 to align # Constraint # added constraint: constraint((T0324)L179.CB, (T0324)V193.CB) [> 2.5954 = 4.3257 < 5.6234] w=0.6346 to align # Constraint # added constraint: constraint((T0324)L179.CB, (T0324)R196.CB) [> 3.0052 = 5.0087 < 6.5113] w=0.6296 to align # Constraint # added constraint: constraint((T0324)L90.CB, (T0324)P200.CB) [> 2.9898 = 4.9831 < 6.4780] w=0.6272 to align # Constraint # added constraint: constraint((T0324)I160.CB, (T0324)I203.CB) [> 3.8209 = 6.3682 < 8.2787] w=0.6251 to align # Constraint # added constraint: constraint((T0324)L143.CB, (T0324)V175.CB) [> 3.9209 = 6.5348 < 8.4952] w=0.6241 to align # Constraint # added constraint: constraint((T0324)I160.CB, (T0324)L179.CB) [> 4.3478 = 7.2463 < 9.4201] w=0.6237 to align # Constraint # added constraint: constraint((T0324)L179.CB, (T0324)F197.CB) [> 4.2608 = 7.1014 < 9.2318] w=0.6225 to align # Constraint # added constraint: constraint((T0324)Y3.CB, (T0324)L98.CB) [> 4.0664 = 6.7773 < 8.8104] w=0.6210 to align # Constraint # added constraint: constraint((T0324)G178.CA, (T0324)V193.CB) [> 3.1975 = 5.3292 < 6.9280] w=0.6204 to align # Constraint # added constraint: constraint((T0324)M7.CB, (T0324)L143.CB) [> 3.7393 = 6.2322 < 8.1019] w=0.6204 to align # Constraint # added constraint: constraint((T0324)G101.CA, (T0324)A125.CB) [> 3.4615 = 5.7691 < 7.4998] w=0.6201 to align # Constraint # added constraint: constraint((T0324)V103.CB, (T0324)L143.CB) [> 3.8142 = 6.3570 < 8.2642] w=0.6165 to align # Constraint # added constraint: constraint((T0324)P138.CB, (T0324)Q168.CB) [> 3.1907 = 5.3179 < 6.9132] w=0.6133 to align # Constraint # added constraint: constraint((T0324)T104.CB, (T0324)A130.CB) [> 4.2054 = 7.0090 < 9.1117] w=0.6083 to align # Constraint # added constraint: constraint((T0324)M7.CB, (T0324)V175.CB) [> 4.3797 = 7.2994 < 9.4892] w=0.6081 to align # Constraint # added constraint: constraint((T0324)P138.CB, (T0324)S165.CB) [> 3.2769 = 5.4615 < 7.0999] w=0.6062 to align # Constraint # added constraint: constraint((T0324)I160.CB, (T0324)F177.CB) [> 4.5597 = 7.5995 < 9.8793] w=0.6061 to align # Constraint # added constraint: constraint((T0324)L100.CB, (T0324)A125.CB) [> 3.3650 = 5.6083 < 7.2908] w=0.6058 to align # Constraint # added constraint: constraint((T0324)R99.CB, (T0324)A125.CB) [> 3.1191 = 5.1984 < 6.7579] w=0.6058 to align # Constraint # added constraint: constraint((T0324)I87.CB, (T0324)P200.CB) [> 3.3232 = 5.5387 < 7.2003] w=0.6037 to align # Constraint # added constraint: constraint((T0324)L144.CB, (T0324)A173.CB) [> 3.8991 = 6.4985 < 8.4481] w=0.6025 to align # Constraint # added constraint: constraint((T0324)G101.CA, (T0324)I128.CB) [> 4.2775 = 7.1291 < 9.2678] w=0.6011 to align # Constraint # added constraint: constraint((T0324)F177.CB, (T0324)A194.CB) [> 3.1940 = 5.3233 < 6.9203] w=0.6010 to align # Constraint # added constraint: constraint((T0324)L90.CB, (T0324)I203.CB) [> 3.6753 = 6.1255 < 7.9631] w=0.5990 to align # Constraint # added constraint: constraint((T0324)F159.CB, (T0324)T169.CB) [> 3.5186 = 5.8643 < 7.6236] w=0.5990 to align # Constraint # added constraint: constraint((T0324)V181.CB, (T0324)F197.CB) [> 4.1482 = 6.9136 < 8.9877] w=0.5939 to align # Constraint # added constraint: constraint((T0324)P138.CB, (T0324)T169.CB) [> 2.7474 = 4.5789 < 5.9526] w=0.5920 to align # Constraint # added constraint: constraint((T0324)D9.CB, (T0324)I102.CB) [> 4.4921 = 7.4868 < 9.7328] w=0.5863 to align # Constraint # added constraint: constraint((T0324)L90.CB, (T0324)L204.CB) [> 3.6685 = 6.1142 < 7.9485] w=0.5823 to align # Constraint # added constraint: constraint((T0324)S105.CB, (T0324)A130.CB) [> 3.3951 = 5.6585 < 7.3561] w=0.5798 to align # Constraint # added constraint: constraint((T0324)G161.CA, (T0324)F177.CB) [> 4.5258 = 7.5430 < 9.8058] w=0.5797 to align # Constraint # added constraint: constraint((T0324)F177.CB, (T0324)H195.CB) [> 4.2881 = 7.1469 < 9.2910] w=0.5776 to align # Constraint # added constraint: constraint((T0324)F91.CB, (T0324)F120.CB) [> 3.9578 = 6.5964 < 8.5753] w=0.5772 to align # Constraint # added constraint: constraint((T0324)I10.CB, (T0324)Q106.CB) [> 3.8656 = 6.4427 < 8.3755] w=0.5771 to align # Constraint # added constraint: constraint((T0324)G86.CA, (T0324)P200.CB) [> 3.1258 = 5.2097 < 6.7726] w=0.5752 to align # Constraint # added constraint: constraint((T0324)Y84.CB, (T0324)P200.CB) [> 3.7049 = 6.1749 < 8.0273] w=0.5681 to align # Constraint # added constraint: constraint((T0324)Y3.CB, (T0324)D176.CB) [> 4.0238 = 6.7064 < 8.7183] w=0.5635 to align # Constraint # added constraint: constraint((T0324)V126.CB, (T0324)V150.CB) [> 3.7843 = 6.3071 < 8.1992] w=0.5563 to align # Constraint # added constraint: constraint((T0324)K137.CB, (T0324)S165.CB) [> 3.2567 = 5.4278 < 7.0562] w=0.5563 to align # Constraint # added constraint: constraint((T0324)D139.CB, (T0324)T169.CB) [> 3.9216 = 6.5359 < 8.4967] w=0.5563 to align # Constraint # added constraint: constraint((T0324)T104.CB, (T0324)T127.CB) [> 4.4793 = 7.4655 < 9.7052] w=0.5509 to align # Constraint # added constraint: constraint((T0324)E167.CB, (T0324)G178.CA) [> 4.2012 = 7.0021 < 9.1027] w=0.5493 to align # Constraint # added constraint: constraint((T0324)V126.CB, (T0324)K149.CB) [> 3.3159 = 5.5265 < 7.1845] w=0.5492 to align # Constraint # added constraint: constraint((T0324)I128.CB, (T0324)T145.CB) [> 3.4886 = 5.8143 < 7.5586] w=0.5420 to align # Constraint # added constraint: constraint((T0324)F177.CB, (T0324)V193.CB) [> 3.0126 = 5.0210 < 6.5273] w=0.5419 to align # Constraint # added constraint: constraint((T0324)D11.CB, (T0324)S105.CB) [> 4.3473 = 7.2455 < 9.4191] w=0.5414 to align # Constraint # added constraint: constraint((T0324)V103.CB, (T0324)F159.CB) [> 4.4913 = 7.4855 < 9.7312] w=0.5370 to align # Constraint # added constraint: constraint((T0324)G12.CA, (T0324)Y84.CB) [> 4.3167 = 7.1945 < 9.3528] w=0.5365 to align # Constraint # added constraint: constraint((T0324)T133.CB, (T0324)P142.CB) [> 3.5489 = 5.9148 < 7.6892] w=0.5349 to align # Constraint # added constraint: constraint((T0324)G101.CA, (T0324)A146.CB) [> 3.8543 = 6.4239 < 8.3511] w=0.5345 to align # Constraint # added constraint: constraint((T0324)L100.CB, (T0324)R123.CB) [> 3.6920 = 6.1533 < 7.9993] w=0.5240 to align # Constraint # added constraint: constraint((T0324)R108.CB, (T0324)S129.CB) [> 3.0093 = 5.0155 < 6.5201] w=0.5084 to align # Constraint # added constraint: constraint((T0324)D176.CB, (T0324)A194.CB) [> 3.2474 = 5.4124 < 7.0361] w=0.5062 to align # Constraint # added constraint: constraint((T0324)Q106.CB, (T0324)S129.CB) [> 3.6414 = 6.0689 < 7.8896] w=0.4993 to align # Constraint # added constraint: constraint((T0324)T88.CB, (T0324)F120.CB) [> 3.9870 = 6.6450 < 8.6385] w=0.4989 to align # Constraint # added constraint: constraint((T0324)H195.CB, (T0324)L206.CB) [> 3.4519 = 5.7531 < 7.4791] w=0.4920 to align # Constraint # added constraint: constraint((T0324)D162.CB, (T0324)W182.CB) [> 3.4131 = 5.6885 < 7.3951] w=0.4870 to align # Constraint # added constraint: constraint((T0324)V103.CB, (T0324)K137.CB) [> 4.1920 = 6.9866 < 9.0826] w=0.4849 to align # Constraint # added constraint: constraint((T0324)F159.CB, (T0324)A173.CB) [> 3.3733 = 5.6222 < 7.3089] w=0.4847 to align # Constraint # added constraint: constraint((T0324)L158.CB, (T0324)F207.CB) [> 4.0376 = 6.7293 < 8.7481] w=0.4765 to align # Constraint # added constraint: constraint((T0324)W182.CB, (T0324)K199.CB) [> 3.8642 = 6.4404 < 8.3725] w=0.4755 to align # Constraint # added constraint: constraint((T0324)G178.CA, (T0324)L206.CB) [> 4.2331 = 7.0551 < 9.1717] w=0.4753 to align # Constraint # added constraint: constraint((T0324)I128.CB, (T0324)K149.CB) [> 3.9392 = 6.5652 < 8.5348] w=0.4707 to align # Constraint # added constraint: constraint((T0324)A130.CB, (T0324)P142.CB) [> 3.7389 = 6.2314 < 8.1009] w=0.4707 to align # Constraint # added constraint: constraint((T0324)A5.CB, (T0324)L147.CB) [> 4.0012 = 6.6686 < 8.6692] w=0.4706 to align # Constraint # added constraint: constraint((T0324)Q155.CB, (T0324)V175.CB) [> 4.2946 = 7.1576 < 9.3049] w=0.4703 to align # Constraint # added constraint: constraint((T0324)A180.CB, (T0324)P200.CB) [> 3.9188 = 6.5314 < 8.4908] w=0.4682 to align # Constraint # added constraint: constraint((T0324)L111.CB, (T0324)T127.CB) [> 3.5032 = 5.8387 < 7.5902] w=0.4657 to align # Constraint # added constraint: constraint((T0324)F91.CB, (T0324)R123.CB) [> 2.8255 = 4.7092 < 6.1219] w=0.4588 to align # Constraint # added constraint: constraint((T0324)E112.CB, (T0324)T127.CB) [> 3.9950 = 6.6584 < 8.6559] w=0.4586 to align # Constraint # added constraint: constraint((T0324)L14.CB, (T0324)F120.CB) [> 4.2179 = 7.0299 < 9.1389] w=0.4565 to align # Constraint # added constraint: constraint((T0324)G86.CA, (T0324)K199.CB) [> 4.0448 = 6.7413 < 8.7637] w=0.4564 to align # Constraint # added constraint: constraint((T0324)L90.CB, (T0324)L201.CB) [> 3.6673 = 6.1121 < 7.9457] w=0.4564 to align # Constraint # added constraint: constraint((T0324)R107.CB, (T0324)S129.CB) [> 3.6223 = 6.0372 < 7.8484] w=0.4564 to align # Constraint # added constraint: constraint((T0324)L111.CB, (T0324)S129.CB) [> 3.5735 = 5.9558 < 7.7425] w=0.4514 to align # Constraint # added constraint: constraint((T0324)E167.CB, (T0324)V193.CB) [> 3.2624 = 5.4373 < 7.0685] w=0.4494 to align # Constraint # added constraint: constraint((T0324)A146.CB, (T0324)A157.CB) [> 4.3874 = 7.3124 < 9.5061] w=0.4493 to align # Constraint # added constraint: constraint((T0324)Q93.CB, (T0324)L204.CB) [> 3.3036 = 5.5060 < 7.1578] w=0.4492 to align # Constraint # added constraint: constraint((T0324)G161.CA, (T0324)A170.CB) [> 4.4364 = 7.3939 < 9.6121] w=0.4492 to align # Constraint # added constraint: constraint((T0324)L83.CB, (T0324)F120.CB) [> 3.7720 = 6.2867 < 8.1727] w=0.4490 to align # Constraint # added constraint: constraint((T0324)T15.CB, (T0324)G114.CA) [> 4.4075 = 7.3459 < 9.5497] w=0.4434 to align # Constraint # added constraint: constraint((T0324)A157.CB, (T0324)A173.CB) [> 3.6811 = 6.1352 < 7.9758] w=0.4419 to align # Constraint # added constraint: constraint((T0324)Q155.CB, (T0324)D176.CB) [> 4.2914 = 7.1523 < 9.2980] w=0.4419 to align # Constraint # added constraint: constraint((T0324)T88.CB, (T0324)Y118.CB) [> 4.0563 = 6.7605 < 8.7886] w=0.4366 to align # Constraint # added constraint: constraint((T0324)I128.CB, (T0324)P142.CB) [> 3.4282 = 5.7137 < 7.4279] w=0.4351 to align # Constraint # added constraint: constraint((T0324)F91.CB, (T0324)M124.CB) [> 4.4529 = 7.4215 < 9.6479] w=0.4347 to align # Constraint # added constraint: constraint((T0324)M7.CB, (T0324)L100.CB) [> 4.6514 = 7.7523 < 10.0779] w=0.4336 to align # Constraint # added constraint: constraint((T0324)G12.CA, (T0324)A180.CB) [> 4.3339 = 7.2231 < 9.3900] w=0.4300 to align # Constraint # added constraint: constraint((T0324)L100.CB, (T0324)V126.CB) [> 4.4889 = 7.4815 < 9.7259] w=0.4286 to align # Constraint # added constraint: constraint((T0324)P138.CB, (T0324)D166.CB) [> 3.9609 = 6.6015 < 8.5820] w=0.4279 to align # Constraint # added constraint: constraint((T0324)Y78.CB, (T0324)E110.CB) [> 3.8202 = 6.3670 < 8.2771] w=0.4264 to align # Constraint # added constraint: constraint((T0324)M115.CB, (T0324)T127.CB) [> 4.1012 = 6.8353 < 8.8859] w=0.4229 to align # Constraint # added constraint: constraint((T0324)R99.CB, (T0324)V126.CB) [> 4.5105 = 7.5174 < 9.7727] w=0.4208 to align # Constraint # added constraint: constraint((T0324)I87.CB, (T0324)F120.CB) [> 4.2144 = 7.0240 < 9.1312] w=0.4205 to align # Constraint # added constraint: constraint((T0324)P138.CB, (T0324)A172.CB) [> 4.0104 = 6.6840 < 8.6892] w=0.4137 to align # Constraint # added constraint: constraint((T0324)D162.CB, (T0324)G183.CA) [> 3.6410 = 6.0683 < 7.8888] w=0.4136 to align # Constraint # added constraint: constraint((T0324)M115.CB, (T0324)M124.CB) [> 4.0311 = 6.7186 < 8.7341] w=0.4128 to align # Constraint # added constraint: constraint((T0324)D9.CB, (T0324)F159.CB) [> 4.5380 = 7.5633 < 9.8322] w=0.4085 to align # Constraint # added constraint: constraint((T0324)T13.CB, (T0324)D166.CB) [> 4.6348 = 7.7247 < 10.0421] w=0.4062 to align # Constraint # added constraint: constraint((T0324)P95.CB, (T0324)R123.CB) [> 3.7787 = 6.2978 < 8.1871] w=0.3963 to align # Constraint # added constraint: constraint((T0324)R108.CB, (T0324)D131.CB) [> 3.4678 = 5.7796 < 7.5135] w=0.3923 to align # Constraint # added constraint: constraint((T0324)F197.CB, (T0324)L206.CB) [> 3.8280 = 6.3800 < 8.2940] w=0.3923 to align # Constraint # added constraint: constraint((T0324)S17.CB, (T0324)I81.CB) [> 3.5763 = 5.9606 < 7.7488] w=0.3918 to align # Constraint # added constraint: constraint((T0324)V126.CB, (T0324)A146.CB) [> 3.7336 = 6.2226 < 8.0894] w=0.3887 to align # Constraint # added constraint: constraint((T0324)D176.CB, (T0324)H195.CB) [> 4.4864 = 7.4773 < 9.7205] w=0.3871 to align # Constraint # added constraint: constraint((T0324)Q171.CB, (T0324)K192.CB) [> 3.7927 = 6.3211 < 8.2175] w=0.3852 to align # Constraint # added constraint: constraint((T0324)G12.CA, (T0324)S163.CB) [> 4.5150 = 7.5250 < 9.7825] w=0.3852 to align # Constraint # added constraint: constraint((T0324)L14.CB, (T0324)Y118.CB) [> 4.3305 = 7.2175 < 9.3828] w=0.3811 to align # Constraint # added constraint: constraint((T0324)Y3.CB, (T0324)F207.CB) [> 3.5919 = 5.9864 < 7.7824] w=0.3780 to align # Constraint # added constraint: constraint((T0324)I160.CB, (T0324)P200.CB) [> 4.4444 = 7.4073 < 9.6295] w=0.3730 to align # Constraint # added constraint: constraint((T0324)D162.CB, (T0324)M184.CB) [> 3.5048 = 5.8414 < 7.5938] w=0.3729 to align # Constraint # added constraint: constraint((T0324)S105.CB, (T0324)S129.CB) [> 4.5401 = 7.5669 < 9.8369] w=0.3693 to align # Constraint # added constraint: constraint((T0324)D162.CB, (T0324)D185.CB) [> 3.2517 = 5.4195 < 7.0453] w=0.3658 to align # Constraint # added constraint: constraint((T0324)F8.CB, (T0324)F159.CB) [> 4.5629 = 7.6048 < 9.8863] w=0.3653 to align # Constraint # added constraint: constraint((T0324)T13.CB, (T0324)P200.CB) [> 4.2071 = 7.0119 < 9.1154] w=0.3565 to align # Constraint # added constraint: constraint((T0324)L144.CB, (T0324)P154.CB) [> 4.0780 = 6.7967 < 8.8357] w=0.3564 to align # Constraint # added constraint: constraint((T0324)V164.CB, (T0324)L179.CB) [> 3.9276 = 6.5460 < 8.5097] w=0.3516 to align # Constraint # added constraint: constraint((T0324)L14.CB, (T0324)P200.CB) [> 4.3447 = 7.2413 < 9.4136] w=0.3494 to align # Constraint # added constraint: constraint((T0324)L6.CB, (T0324)F207.CB) [> 4.3414 = 7.2357 < 9.4064] w=0.3494 to align # Constraint # added constraint: constraint((T0324)V28.CB, (T0324)F66.CB) [> 3.3860 = 5.6433 < 7.3363] w=0.3422 to align # Constraint # added constraint: constraint((T0324)L94.CB, (T0324)L204.CB) [> 3.9316 = 6.5526 < 8.5184] w=0.3373 to align # Constraint # added constraint: constraint((T0324)I10.CB, (T0324)M115.CB) [> 4.4970 = 7.4950 < 9.7435] w=0.3361 to align # Constraint # added constraint: constraint((T0324)L6.CB, (T0324)I203.CB) [> 4.4102 = 7.3503 < 9.5553] w=0.3352 to align # Constraint # added constraint: constraint((T0324)G178.CA, (T0324)I203.CB) [> 4.4565 = 7.4275 < 9.6558] w=0.3348 to align # Constraint # added constraint: constraint((T0324)V24.CB, (T0324)V73.CB) [> 3.0016 = 5.0026 < 6.5034] w=0.3276 to align # Constraint # added constraint: constraint((T0324)V103.CB, (T0324)T169.CB) [> 4.1461 = 6.9102 < 8.9832] w=0.3208 to align # Constraint # added constraint: constraint((T0324)A170.CB, (T0324)V193.CB) [> 4.0231 = 6.7052 < 8.7168] w=0.3208 to align # Constraint # added constraint: constraint((T0324)D166.CB, (T0324)F177.CB) [> 4.3440 = 7.2400 < 9.4121] w=0.3138 to align # Constraint # added constraint: constraint((T0324)L94.CB, (T0324)F207.CB) [> 4.3033 = 7.1722 < 9.3239] w=0.3137 to align # Constraint # added constraint: constraint((T0324)V164.CB, (T0324)H190.CB) [> 3.9182 = 6.5304 < 8.4895] w=0.3087 to align # Constraint # added constraint: constraint((T0324)S163.CB, (T0324)D185.CB) [> 3.7929 = 6.3215 < 8.2180] w=0.3066 to align # Constraint # added constraint: constraint((T0324)T13.CB, (T0324)I87.CB) [> 4.2417 = 7.0695 < 9.1903] w=0.3016 to align # Constraint # added constraint: constraint((T0324)I81.CB, (T0324)S117.CB) [> 3.6653 = 6.1088 < 7.9414] w=0.2996 to align # Constraint # added constraint: constraint((T0324)A157.CB, (T0324)N174.CB) [> 3.5802 = 5.9670 < 7.7571] w=0.2994 to align # Constraint # added constraint: constraint((T0324)V28.CB, (T0324)V73.CB) [> 3.8547 = 6.4246 < 8.3519] w=0.2979 to align # Constraint # added constraint: constraint((T0324)F8.CB, (T0324)M124.CB) [> 4.4272 = 7.3787 < 9.5923] w=0.2960 to align # Constraint # added constraint: constraint((T0324)V24.CB, (T0324)Y70.CB) [> 3.3496 = 5.5827 < 7.2575] w=0.2924 to align # Constraint # added constraint: constraint((T0324)L94.CB, (T0324)I203.CB) [> 4.3326 = 7.2210 < 9.3873] w=0.2853 to align # Constraint # added constraint: constraint((T0324)V28.CB, (T0324)Y70.CB) [> 3.3250 = 5.5416 < 7.2041] w=0.2853 to align # Constraint # added constraint: constraint((T0324)L14.CB, (T0324)F91.CB) [> 4.4700 = 7.4500 < 9.6850] w=0.2802 to align # Constraint # added constraint: constraint((T0324)A20.CB, (T0324)H77.CB) [> 3.1351 = 5.2251 < 6.7926] w=0.2795 to align # Constraint # added constraint: constraint((T0324)T31.CB, (T0324)Q69.CB) [> 3.7881 = 6.3135 < 8.2076] w=0.2781 to align # Constraint # added constraint: constraint((T0324)V24.CB, (T0324)H77.CB) [> 3.5766 = 5.9610 < 7.7493] w=0.2719 to align # Constraint # added constraint: constraint((T0324)I87.CB, (T0324)Y118.CB) [> 4.2182 = 7.0303 < 9.1394] w=0.2705 to align # Constraint # added constraint: constraint((T0324)V24.CB, (T0324)M74.CB) [> 2.9957 = 4.9928 < 6.4906] w=0.2699 to align # Constraint # added constraint: constraint((T0324)L29.CB, (T0324)L56.CB) [> 3.7778 = 6.2964 < 8.1853] w=0.2698 to align # Constraint # added constraint: constraint((T0324)V103.CB, (T0324)S129.CB) [> 4.2716 = 7.1193 < 9.2551] w=0.2694 to align # Constraint # added constraint: constraint((T0324)G12.CA, (T0324)W182.CB) [> 3.6479 = 6.0799 < 7.9039] w=0.2660 to align # Constraint # added constraint: constraint((T0324)L98.CB, (T0324)F207.CB) [> 4.3203 = 7.2006 < 9.3607] w=0.2639 to align # Constraint # added constraint: constraint((T0324)Y32.CB, (T0324)F66.CB) [> 4.1376 = 6.8960 < 8.9648] w=0.2639 to align # Constraint # added constraint: constraint((T0324)V164.CB, (T0324)P186.CB) [> 4.0147 = 6.6911 < 8.6985] w=0.2638 to align # Constraint # added constraint: constraint((T0324)M25.CB, (T0324)Y70.CB) [> 4.0082 = 6.6803 < 8.6844] w=0.2635 to align # Constraint # added constraint: constraint((T0324)Q106.CB, (T0324)A130.CB) [> 3.8379 = 6.3965 < 8.3154] w=0.2627 to align # Constraint # added constraint: constraint((T0324)M7.CB, (T0324)A170.CB) [> 4.5390 = 7.5651 < 9.8346] w=0.2568 to align # Constraint # added constraint: constraint((T0324)L14.CB, (T0324)M115.CB) [> 4.5433 = 7.5721 < 9.8437] w=0.2552 to align # Constraint # added constraint: constraint((T0324)A20.CB, (T0324)Q80.CB) [> 3.1935 = 5.3225 < 6.9193] w=0.2510 to align # Constraint # added constraint: constraint((T0324)Q4.CB, (T0324)E97.CB) [> 4.3439 = 7.2397 < 9.4117] w=0.2510 to align # Constraint # added constraint: constraint((T0324)M25.CB, (T0324)L56.CB) [> 3.7712 = 6.2853 < 8.1709] w=0.2502 to align # Constraint # added constraint: constraint((T0324)L83.CB, (T0324)P119.CB) [> 3.9348 = 6.5581 < 8.5255] w=0.2497 to align # Constraint # added constraint: constraint((T0324)K137.CB, (T0324)S163.CB) [> 4.5381 = 7.5636 < 9.8326] w=0.2460 to align # Constraint # added constraint: constraint((T0324)T15.CB, (T0324)I87.CB) [> 4.5433 = 7.5722 < 9.8438] w=0.2446 to align # Constraint # added constraint: constraint((T0324)L83.CB, (T0324)G114.CA) [> 4.3629 = 7.2714 < 9.4529] w=0.2435 to align # Constraint # added constraint: constraint((T0324)G12.CA, (T0324)G183.CA) [> 2.9853 = 4.9755 < 6.4681] w=0.2425 to align # Constraint # added constraint: constraint((T0324)F177.CB, (T0324)K192.CB) [> 3.9829 = 6.6381 < 8.6295] w=0.2423 to align # Constraint # added constraint: constraint((T0324)R107.CB, (T0324)A130.CB) [> 3.6999 = 6.1665 < 8.0165] w=0.2413 to align # Constraint # added constraint: constraint((T0324)L179.CB, (T0324)A194.CB) [> 3.6845 = 6.1408 < 7.9830] w=0.2374 to align # Constraint # added constraint: constraint((T0324)F8.CB, (T0324)F91.CB) [> 4.1986 = 6.9977 < 9.0970] w=0.2374 to align # Constraint # added constraint: constraint((T0324)T22.CB, (T0324)A41.CB) [> 3.1050 = 5.1750 < 6.7276] w=0.2354 to align # Constraint # added constraint: constraint((T0324)Q4.CB, (T0324)A153.CB) [> 4.5764 = 7.6273 < 9.9154] w=0.2354 to align # Constraint # added constraint: constraint((T0324)L147.CB, (T0324)N156.CB) [> 4.5936 = 7.6560 < 9.9528] w=0.2352 to align # Constraint # added constraint: constraint((T0324)M7.CB, (T0324)T169.CB) [> 3.7605 = 6.2674 < 8.1477] w=0.2352 to align # Constraint # added constraint: constraint((T0324)F159.CB, (T0324)A172.CB) [> 4.3872 = 7.3121 < 9.5057] w=0.2349 to align # Constraint # added constraint: constraint((T0324)V103.CB, (T0324)A130.CB) [> 4.5238 = 7.5397 < 9.8017] w=0.2338 to align # Constraint # added constraint: constraint((T0324)D11.CB, (T0324)S163.CB) [> 4.5270 = 7.5450 < 9.8084] w=0.2315 to align # Constraint # added constraint: constraint((T0324)S105.CB, (T0324)D131.CB) [> 4.2452 = 7.0753 < 9.1979] w=0.2304 to align # Constraint # added constraint: constraint((T0324)T22.CB, (T0324)Q42.CB) [> 3.6314 = 6.0524 < 7.8681] w=0.2283 to align # Constraint # added constraint: constraint((T0324)S105.CB, (T0324)P142.CB) [> 4.4119 = 7.3532 < 9.5592] w=0.2283 to align # Constraint # added constraint: constraint((T0324)T13.CB, (T0324)W182.CB) [> 3.7598 = 6.2664 < 8.1463] w=0.2282 to align # Constraint # added constraint: constraint((T0324)I10.CB, (T0324)V103.CB) [> 4.5379 = 7.5632 < 9.8322] w=0.2280 to align # Constraint # added constraint: constraint((T0324)M7.CB, (T0324)A173.CB) [> 4.1306 = 6.8843 < 8.9496] w=0.2279 to align # Constraint # added constraint: constraint((T0324)Y21.CB, (T0324)M74.CB) [> 3.8981 = 6.4967 < 8.4458] w=0.2278 to align # Constraint # added constraint: constraint((T0324)W182.CB, (T0324)P200.CB) [> 4.0083 = 6.6805 < 8.6847] w=0.2270 to align # Constraint # added constraint: constraint((T0324)I102.CB, (T0324)S129.CB) [> 4.4583 = 7.4306 < 9.6597] w=0.2210 to align # Constraint # added constraint: constraint((T0324)L158.CB, (T0324)N174.CB) [> 4.1063 = 6.8438 < 8.8970] w=0.2209 to align # Constraint # added constraint: constraint((T0324)N156.CB, (T0324)N174.CB) [> 3.5806 = 5.9676 < 7.7579] w=0.2209 to align # Constraint # added constraint: constraint((T0324)Y78.CB, (T0324)G114.CA) [> 3.8625 = 6.4375 < 8.3688] w=0.2160 to align # Constraint # added constraint: constraint((T0324)V103.CB, (T0324)T127.CB) [> 4.3150 = 7.1917 < 9.3492] w=0.2157 to align # Constraint # added constraint: constraint((T0324)T23.CB, (T0324)H77.CB) [> 3.6374 = 6.0624 < 7.8811] w=0.2128 to align # Constraint # added constraint: constraint((T0324)M74.CB, (T0324)E110.CB) [> 4.1267 = 6.8778 < 8.9412] w=0.2068 to align # Constraint # added constraint: constraint((T0324)V181.CB, (T0324)H190.CB) [> 3.4545 = 5.7575 < 7.4847] w=0.1997 to align # Constraint # added constraint: constraint((T0324)T44.CB, (T0324)L56.CB) [> 3.7912 = 6.3187 < 8.2143] w=0.1996 to align # Constraint # added constraint: constraint((T0324)I10.CB, (T0324)G114.CA) [> 4.5973 = 7.6621 < 9.9608] w=0.1995 to align # Constraint # added constraint: constraint((T0324)I102.CB, (T0324)A146.CB) [> 4.1936 = 6.9893 < 9.0861] w=0.1926 to align # Constraint # added constraint: constraint((T0324)A5.CB, (T0324)A125.CB) [> 4.6889 = 7.8148 < 10.1593] w=0.1926 to align # Constraint # added constraint: constraint((T0324)T2.CB, (T0324)N156.CB) [> 3.8840 = 6.4734 < 8.4154] w=0.1924 to align # Constraint # added constraint: constraint((T0324)D11.CB, (T0324)I81.CB) [> 4.0325 = 6.7208 < 8.7370] w=0.1912 to align # Constraint # added constraint: constraint((T0324)V164.CB, (T0324)V193.CB) [> 4.3906 = 7.3177 < 9.5130] w=0.1855 to align # Constraint # added constraint: constraint((T0324)W182.CB, (T0324)F197.CB) [> 3.7897 = 6.3161 < 8.2109] w=0.1854 to align # Constraint # added constraint: constraint((T0324)W182.CB, (T0324)R196.CB) [> 4.1795 = 6.9659 < 9.0556] w=0.1853 to align # Constraint # added constraint: constraint((T0324)S17.CB, (T0324)E82.CB) [> 4.0580 = 6.7633 < 8.7923] w=0.1852 to align # Constraint # added constraint: constraint((T0324)M7.CB, (T0324)I128.CB) [> 4.6891 = 7.8152 < 10.1598] w=0.1819 to align # Constraint # added constraint: constraint((T0324)I102.CB, (T0324)F120.CB) [> 3.6685 = 6.1142 < 7.9485] w=0.1795 to align # Constraint # added constraint: constraint((T0324)P95.CB, (T0324)A125.CB) [> 4.4420 = 7.4033 < 9.6243] w=0.1783 to align # Constraint # added constraint: constraint((T0324)G161.CA, (T0324)W182.CB) [> 3.8291 = 6.3819 < 8.2964] w=0.1782 to align # Constraint # added constraint: constraint((T0324)G161.CA, (T0324)V181.CB) [> 3.6146 = 6.0243 < 7.8316] w=0.1782 to align # Constraint # added constraint: constraint((T0324)E50.CB, (T0324)Q67.CB) [> 3.3566 = 5.5944 < 7.2727] w=0.1726 to align # Constraint # added constraint: constraint((T0324)L158.CB, (T0324)A170.CB) [> 4.6477 = 7.7463 < 10.0701] w=0.1712 to align # Constraint # added constraint: constraint((T0324)F159.CB, (T0324)L179.CB) [> 3.5880 = 5.9801 < 7.7741] w=0.1710 to align # Constraint # added constraint: constraint((T0324)M53.CB, (T0324)F66.CB) [> 3.2445 = 5.4075 < 7.0297] w=0.1654 to align # Constraint # added constraint: constraint((T0324)L158.CB, (T0324)L179.CB) [> 4.2927 = 7.1544 < 9.3007] w=0.1640 to align # Constraint # added constraint: constraint((T0324)A180.CB, (T0324)H195.CB) [> 3.6321 = 6.0534 < 7.8695] w=0.1639 to align # Constraint # added constraint: constraint((T0324)I102.CB, (T0324)M122.CB) [> 4.0270 = 6.7116 < 8.7251] w=0.1639 to align # Constraint # added constraint: constraint((T0324)T54.CB, (T0324)F63.CB) [> 3.5791 = 5.9651 < 7.7547] w=0.1629 to align # Constraint # added constraint: constraint((T0324)D9.CB, (T0324)S105.CB) [> 4.6295 = 7.7159 < 10.0307] w=0.1601 to align # Constraint # added constraint: constraint((T0324)G183.CA, (T0324)Q198.CB) [> 3.8195 = 6.3658 < 8.2755] w=0.1569 to align # Constraint # added constraint: constraint((T0324)S163.CB, (T0324)P186.CB) [> 3.9559 = 6.5931 < 8.5711] w=0.1568 to align # Constraint # added constraint: constraint((T0324)L179.CB, (T0324)K192.CB) [> 4.2764 = 7.1274 < 9.2656] w=0.1567 to align # Constraint # added constraint: constraint((T0324)L100.CB, (T0324)F120.CB) [> 3.2371 = 5.3951 < 7.0136] w=0.1567 to align # Constraint # added constraint: constraint((T0324)N16.CB, (T0324)G183.CA) [> 4.1326 = 6.8876 < 8.9539] w=0.1546 to align # Constraint # added constraint: constraint((T0324)I102.CB, (T0324)R123.CB) [> 2.9467 = 4.9112 < 6.3846] w=0.1517 to align # Constraint # added constraint: constraint((T0324)P46.CB, (T0324)V164.CB) [> 4.2613 = 7.1021 < 9.2327] w=0.1498 to align # Constraint # added constraint: constraint((T0324)Q4.CB, (T0324)V150.CB) [> 4.5836 = 7.6394 < 9.9312] w=0.1498 to align # Constraint # added constraint: constraint((T0324)Y32.CB, (T0324)E62.CB) [> 4.2059 = 7.0098 < 9.1127] w=0.1497 to align # Constraint # added constraint: constraint((T0324)L100.CB, (T0324)M122.CB) [> 4.0929 = 6.8214 < 8.8679] w=0.1493 to align # Constraint # added constraint: constraint((T0324)L100.CB, (T0324)M121.CB) [> 3.4689 = 5.7815 < 7.5160] w=0.1484 to align # Constraint # added constraint: constraint((T0324)G101.CA, (T0324)R123.CB) [> 3.8258 = 6.3763 < 8.2893] w=0.1438 to align # Constraint # added constraint: constraint((T0324)Y21.CB, (T0324)F45.CB) [> 4.0266 = 6.7110 < 8.7242] w=0.1427 to align # Constraint # added constraint: constraint((T0324)L111.CB, (T0324)A130.CB) [> 3.8233 = 6.3722 < 8.2838] w=0.1426 to align # Constraint # added constraint: constraint((T0324)R99.CB, (T0324)N151.CB) [> 4.4578 = 7.4297 < 9.6586] w=0.1426 to align # Constraint # added constraint: constraint((T0324)S17.CB, (T0324)R26.CB) [> 4.1414 = 6.9023 < 8.9730] w=0.1425 to align # Constraint # added constraint: constraint((T0324)G101.CA, (T0324)F120.CB) [> 3.3235 = 5.5392 < 7.2010] w=0.1424 to align # Constraint # added constraint: constraint((T0324)G12.CA, (T0324)V181.CB) [> 4.3718 = 7.2864 < 9.4723] w=0.1391 to align # Constraint # added constraint: constraint((T0324)T15.CB, (T0324)V24.CB) [> 4.2976 = 7.1627 < 9.3115] w=0.1360 to align # Constraint # added constraint: constraint((T0324)E50.CB, (T0324)F63.CB) [> 4.0342 = 6.7237 < 8.7408] w=0.1355 to align # Constraint # added constraint: constraint((T0324)Y32.CB, (T0324)I58.CB) [> 3.7511 = 6.2519 < 8.1275] w=0.1355 to align # Constraint # added constraint: constraint((T0324)S163.CB, (T0324)G183.CA) [> 4.3724 = 7.2874 < 9.4736] w=0.1354 to align # Constraint # added constraint: constraint((T0324)T104.CB, (T0324)V126.CB) [> 4.5007 = 7.5012 < 9.7516] w=0.1349 to align # Constraint # added constraint: constraint((T0324)D11.CB, (T0324)Y21.CB) [> 4.1492 = 6.9153 < 8.9898] w=0.1344 to align # Constraint # added constraint: constraint((T0324)Y21.CB, (T0324)H77.CB) [> 4.1430 = 6.9050 < 8.9765] w=0.1286 to align # Constraint # added constraint: constraint((T0324)T13.CB, (T0324)G183.CA) [> 4.1206 = 6.8677 < 8.9280] w=0.1284 to align # Constraint # added constraint: constraint((T0324)I160.CB, (T0324)A170.CB) [> 4.7404 = 7.9006 < 10.2708] w=0.1284 to align # Constraint # added constraint: constraint((T0324)Y78.CB, (T0324)S117.CB) [> 4.0197 = 6.6995 < 8.7093] w=0.1284 to align # Constraint # added constraint: constraint((T0324)N156.CB, (T0324)V175.CB) [> 4.6842 = 7.8070 < 10.1491] w=0.1284 to align # Constraint # added constraint: constraint((T0324)L111.CB, (T0324)I128.CB) [> 4.1371 = 6.8951 < 8.9636] w=0.1283 to align # Constraint # added constraint: constraint((T0324)N156.CB, (T0324)D176.CB) [> 3.8748 = 6.4580 < 8.3953] w=0.1283 to align # Constraint # added constraint: constraint((T0324)Y32.CB, (T0324)H65.CB) [> 4.2429 = 7.0715 < 9.1929] w=0.1283 to align # Constraint # added constraint: constraint((T0324)I160.CB, (T0324)V181.CB) [> 4.2454 = 7.0757 < 9.1984] w=0.1283 to align # Constraint # added constraint: constraint((T0324)G101.CA, (T0324)M122.CB) [> 2.7098 = 4.5163 < 5.8712] w=0.1282 to align # Constraint # added constraint: constraint((T0324)S17.CB, (T0324)E27.CB) [> 3.3256 = 5.5426 < 7.2054] w=0.1270 to align # Constraint # added constraint: constraint((T0324)D11.CB, (T0324)Y78.CB) [> 4.4391 = 7.3984 < 9.6180] w=0.1234 to align # Constraint # added constraint: constraint((T0324)D9.CB, (T0324)A180.CB) [> 4.3897 = 7.3161 < 9.5110] w=0.1232 to align # Constraint # added constraint: constraint((T0324)M53.CB, (T0324)Q67.CB) [> 3.4022 = 5.6703 < 7.3714] w=0.1226 to align # Constraint # added constraint: constraint((T0324)Q18.CB, (T0324)M184.CB) [> 4.2226 = 7.0376 < 9.1489] w=0.1226 to align # Constraint # added constraint: constraint((T0324)T15.CB, (T0324)Q80.CB) [> 4.1311 = 6.8852 < 8.9508] w=0.1213 to align # Constraint # added constraint: constraint((T0324)M1.CB, (T0324)N156.CB) [> 3.8049 = 6.3415 < 8.2439] w=0.1213 to align # Constraint # added constraint: constraint((T0324)A180.CB, (T0324)V193.CB) [> 3.0783 = 5.1306 < 6.6697] w=0.1212 to align # Constraint # added constraint: constraint((T0324)T13.CB, (T0324)V181.CB) [> 3.8265 = 6.3774 < 8.2906] w=0.1211 to align # Constraint # added constraint: constraint((T0324)D11.CB, (T0324)V24.CB) [> 3.4235 = 5.7059 < 7.4176] w=0.1211 to align # Constraint # added constraint: constraint((T0324)Q106.CB, (T0324)V126.CB) [> 3.7113 = 6.1856 < 8.0412] w=0.1211 to align # Constraint # added constraint: constraint((T0324)S105.CB, (T0324)V126.CB) [> 4.0044 = 6.6740 < 8.6762] w=0.1211 to align # Constraint # added constraint: constraint((T0324)T13.CB, (T0324)M184.CB) [> 4.3960 = 7.3267 < 9.5247] w=0.1189 to align # Constraint # added constraint: constraint((T0324)F177.CB, (T0324)R196.CB) [> 4.2349 = 7.0582 < 9.1757] w=0.1141 to align # Constraint # added constraint: constraint((T0324)F159.CB, (T0324)A180.CB) [> 4.1444 = 6.9074 < 8.9796] w=0.1140 to align # Constraint # added constraint: constraint((T0324)T104.CB, (T0324)M124.CB) [> 4.3034 = 7.1724 < 9.3241] w=0.1139 to align # Constraint # added constraint: constraint((T0324)D11.CB, (T0324)M25.CB) [> 4.3156 = 7.1927 < 9.3505] w=0.1128 to align # Constraint # added constraint: constraint((T0324)S17.CB, (T0324)Y78.CB) [> 4.2271 = 7.0452 < 9.1587] w=0.1091 to align # Constraint # added constraint: constraint((T0324)I10.CB, (T0324)Y118.CB) [> 4.4941 = 7.4902 < 9.7372] w=0.1081 to align # Constraint # added constraint: constraint((T0324)Y21.CB, (T0324)Y70.CB) [> 3.8927 = 6.4878 < 8.4342] w=0.1076 to align # Constraint # added constraint: constraint((T0324)A130.CB, (T0324)L141.CB) [> 4.4582 = 7.4303 < 9.6594] w=0.1070 to align # Constraint # added constraint: constraint((T0324)T13.CB, (T0324)S163.CB) [> 4.3629 = 7.2714 < 9.4528] w=0.1070 to align # Constraint # added constraint: constraint((T0324)M124.CB, (T0324)P142.CB) [> 3.4709 = 5.7848 < 7.5202] w=0.1068 to align # Constraint # added constraint: constraint((T0324)S105.CB, (T0324)S163.CB) [> 4.5903 = 7.6505 < 9.9457] w=0.1068 to align # Constraint # added constraint: constraint((T0324)L94.CB, (T0324)R123.CB) [> 4.3338 = 7.2230 < 9.3899] w=0.1066 to align # Constraint # added constraint: constraint((T0324)L90.CB, (T0324)F207.CB) [> 3.3099 = 5.5165 < 7.1715] w=0.1058 to align # Constraint # added constraint: constraint((T0324)A130.CB, (T0324)D139.CB) [> 4.5806 = 7.6344 < 9.9247] w=0.0999 to align # Constraint # added constraint: constraint((T0324)N16.CB, (T0324)M184.CB) [> 3.7213 = 6.2022 < 8.0628] w=0.0999 to align # Constraint # added constraint: constraint((T0324)F8.CB, (T0324)P200.CB) [> 4.2562 = 7.0937 < 9.2218] w=0.0999 to align # Constraint # added constraint: constraint((T0324)L6.CB, (T0324)V28.CB) [> 3.6505 = 6.0841 < 7.9094] w=0.0999 to align # Constraint # added constraint: constraint((T0324)T104.CB, (T0324)A125.CB) [> 2.6899 = 4.4831 < 5.8281] w=0.0925 to align # Constraint # added constraint: constraint((T0324)R99.CB, (T0324)M121.CB) [> 2.8976 = 4.8293 < 6.2781] w=0.0925 to align # Constraint # added constraint: constraint((T0324)M47.CB, (T0324)S163.CB) [> 2.9550 = 4.9250 < 6.4025] w=0.0870 to align # Constraint # added constraint: constraint((T0324)L29.CB, (T0324)M53.CB) [> 3.9817 = 6.6361 < 8.6270] w=0.0856 to align # Constraint # added constraint: constraint((T0324)Q4.CB, (T0324)Q155.CB) [> 3.5252 = 5.8754 < 7.6380] w=0.0856 to align # Constraint # added constraint: constraint((T0324)I160.CB, (T0324)W182.CB) [> 4.1437 = 6.9061 < 8.9780] w=0.0856 to align # Constraint # added constraint: constraint((T0324)T13.CB, (T0324)F197.CB) [> 3.0692 = 5.1154 < 6.6500] w=0.0856 to align # Constraint # added constraint: constraint((T0324)S105.CB, (T0324)D132.CB) [> 3.8476 = 6.4126 < 8.3364] w=0.0856 to align # Constraint # added constraint: constraint((T0324)M25.CB, (T0324)G57.CA) [> 3.7422 = 6.2370 < 8.1081] w=0.0855 to align # Constraint # added constraint: constraint((T0324)V28.CB, (T0324)H65.CB) [> 3.8679 = 6.4466 < 8.3805] w=0.0855 to align # Constraint # added constraint: constraint((T0324)S163.CB, (T0324)W182.CB) [> 4.2589 = 7.0981 < 9.2276] w=0.0855 to align # Constraint # added constraint: constraint((T0324)V181.CB, (T0324)H195.CB) [> 4.2234 = 7.0390 < 9.1507] w=0.0855 to align # Constraint # added constraint: constraint((T0324)M25.CB, (T0324)Q42.CB) [> 3.4495 = 5.7491 < 7.4738] w=0.0785 to align # Constraint # added constraint: constraint((T0324)L29.CB, (T0324)F66.CB) [> 4.4468 = 7.4114 < 9.6348] w=0.0784 to align # Constraint # added constraint: constraint((T0324)A180.CB, (T0324)D202.CB) [> 4.3345 = 7.2241 < 9.3913] w=0.0783 to align # Constraint # added constraint: constraint((T0324)A60.CB, (T0324)A130.CB) [> 3.0999 = 5.1665 < 6.7164] w=0.0780 to align # Constraint # added constraint: constraint((T0324)Q18.CB, (T0324)D162.CB) [> 3.8421 = 6.4035 < 8.3245] w=0.0761 to align # Constraint # added constraint: constraint((T0324)S105.CB, (T0324)T133.CB) [> 3.7373 = 6.2288 < 8.0975] w=0.0734 to align # Constraint # added constraint: constraint((T0324)L14.CB, (T0324)M25.CB) [> 4.1012 = 6.8354 < 8.8860] w=0.0713 to align # Constraint # added constraint: constraint((T0324)Y3.CB, (T0324)N174.CB) [> 4.2734 = 7.1224 < 9.2591] w=0.0713 to align # Constraint # added constraint: constraint((T0324)V181.CB, (T0324)V193.CB) [> 2.2863 = 3.8105 < 4.9536] w=0.0713 to align # Constraint # added constraint: constraint((T0324)M25.CB, (T0324)E50.CB) [> 3.8977 = 6.4961 < 8.4449] w=0.0713 to align # Constraint # added constraint: constraint((T0324)A157.CB, (T0324)F177.CB) [> 4.3077 = 7.1795 < 9.3333] w=0.0712 to align # Constraint # added constraint: constraint((T0324)L14.CB, (T0324)M124.CB) [> 4.6813 = 7.8022 < 10.1429] w=0.0642 to align # Constraint # added constraint: constraint((T0324)F8.CB, (T0324)M25.CB) [> 4.6505 = 7.7509 < 10.0762] w=0.0642 to align # Constraint # added constraint: constraint((T0324)G161.CA, (T0324)V193.CB) [> 4.7362 = 7.8937 < 10.2619] w=0.0642 to align # Constraint # added constraint: constraint((T0324)V103.CB, (T0324)D132.CB) [> 4.1510 = 6.9184 < 8.9939] w=0.0642 to align # Constraint # added constraint: constraint((T0324)L100.CB, (T0324)T127.CB) [> 4.2381 = 7.0634 < 9.1825] w=0.0642 to align # Constraint # added constraint: constraint((T0324)Y3.CB, (T0324)V150.CB) [> 4.0160 = 6.6933 < 8.7012] w=0.0640 to align # Constraint # added constraint: constraint((T0324)Q4.CB, (T0324)L94.CB) [> 4.5335 = 7.5559 < 9.8227] w=0.0640 to align # Constraint # added constraint: constraint((T0324)L14.CB, (T0324)I160.CB) [> 4.4860 = 7.4766 < 9.7196] w=0.0638 to align # Constraint # added constraint: constraint((T0324)Y21.CB, (T0324)V73.CB) [> 3.8738 = 6.4564 < 8.3933] w=0.0577 to align # Constraint # added constraint: constraint((T0324)V28.CB, (T0324)A41.CB) [> 3.5739 = 5.9565 < 7.7435] w=0.0571 to align # Constraint # added constraint: constraint((T0324)V181.CB, (T0324)P200.CB) [> 3.5629 = 5.9381 < 7.7195] w=0.0569 to align # Constraint # added constraint: constraint((T0324)Q93.CB, (T0324)P200.CB) [> 3.1962 = 5.3269 < 6.9250] w=0.0499 to align # Constraint # added constraint: constraint((T0324)V28.CB, (T0324)G57.CA) [> 4.0879 = 6.8131 < 8.8570] w=0.0499 to align # Constraint # added constraint: constraint((T0324)V28.CB, (T0324)F45.CB) [> 2.9609 = 4.9349 < 6.4154] w=0.0499 to align # Constraint # added constraint: constraint((T0324)Y3.CB, (T0324)Q155.CB) [> 4.5671 = 7.6119 < 9.8954] w=0.0499 to align # Constraint # added constraint: constraint((T0324)L111.CB, (T0324)D131.CB) [> 4.4054 = 7.3424 < 9.5451] w=0.0499 to align # Constraint # added constraint: constraint((T0324)M25.CB, (T0324)F66.CB) [> 4.1071 = 6.8452 < 8.8987] w=0.0499 to align # Constraint # added constraint: constraint((T0324)T2.CB, (T0324)V152.CB) [> 4.6899 = 7.8165 < 10.1614] w=0.0498 to align # Constraint # added constraint: constraint((T0324)F63.CB, (T0324)I128.CB) [> 4.0597 = 6.7661 < 8.7959] w=0.0498 to align # Constraint # added constraint: constraint((T0324)D11.CB, (T0324)G183.CA) [> 4.6861 = 7.8102 < 10.1532] w=0.0428 to align # Constraint # added constraint: constraint((T0324)F45.CB, (T0324)S105.CB) [> 4.4997 = 7.4996 < 9.7494] w=0.0428 to align # Constraint # added constraint: constraint((T0324)L158.CB, (T0324)H195.CB) [> 4.0525 = 6.7542 < 8.7805] w=0.0428 to align # Constraint # added constraint: constraint((T0324)M47.CB, (T0324)D162.CB) [> 4.4822 = 7.4702 < 9.7113] w=0.0428 to align # Constraint # added constraint: constraint((T0324)V164.CB, (T0324)V181.CB) [> 4.5856 = 7.6427 < 9.9355] w=0.0428 to align # Constraint # added constraint: constraint((T0324)I10.CB, (T0324)T127.CB) [> 4.6568 = 7.7613 < 10.0897] w=0.0428 to align # Constraint # added constraint: constraint((T0324)S163.CB, (T0324)V181.CB) [> 4.1072 = 6.8453 < 8.8989] w=0.0428 to align # Constraint # added constraint: constraint((T0324)D162.CB, (T0324)P200.CB) [> 4.1996 = 6.9994 < 9.0992] w=0.0428 to align # Constraint # added constraint: constraint((T0324)T127.CB, (T0324)V150.CB) [> 4.1087 = 6.8478 < 8.9021] w=0.0428 to align # Constraint # added constraint: constraint((T0324)T2.CB, (T0324)Q155.CB) [> 4.0676 = 6.7794 < 8.8132] w=0.0428 to align # Constraint # added constraint: constraint((T0324)V28.CB, (T0324)I58.CB) [> 4.2017 = 7.0028 < 9.1036] w=0.0427 to align # Constraint # added constraint: constraint((T0324)D11.CB, (T0324)F45.CB) [> 4.6149 = 7.6915 < 9.9989] w=0.0357 to align # Constraint # added constraint: constraint((T0324)D11.CB, (T0324)M47.CB) [> 4.5919 = 7.6532 < 9.9492] w=0.0357 to align # Constraint # added constraint: constraint((T0324)M1.CB, (T0324)L98.CB) [> 4.5957 = 7.6595 < 9.9573] w=0.0357 to align # Constraint # added constraint: constraint((T0324)V181.CB, (T0324)K192.CB) [> 4.4754 = 7.4590 < 9.6967] w=0.0357 to align # Constraint # added constraint: constraint((T0324)S163.CB, (T0324)L179.CB) [> 3.5478 = 5.9130 < 7.6869] w=0.0356 to align # Constraint # added constraint: constraint((T0324)N156.CB, (T0324)F177.CB) [> 4.3582 = 7.2636 < 9.4427] w=0.0355 to align # Constraint # added constraint: constraint((T0324)A49.CB, (T0324)A60.CB) [> 4.6564 = 7.7606 < 10.0888] w=0.0285 to align # Constraint # added constraint: constraint((T0324)M25.CB, (T0324)P200.CB) [> 4.1083 = 6.8472 < 8.9014] w=0.0285 to align # Constraint # added constraint: constraint((T0324)G161.CA, (T0324)H195.CB) [> 4.0539 = 6.7565 < 8.7835] w=0.0284 to align # Constraint # added constraint: constraint((T0324)F36.CB, (T0324)M53.CB) [> 3.9820 = 6.6367 < 8.6277] w=0.0228 to align # Constraint # added constraint: constraint((T0324)Q42.CB, (T0324)G183.CA) [> 4.1610 = 6.9350 < 9.0155] w=0.0214 to align # Constraint # added constraint: constraint((T0324)I10.CB, (T0324)F120.CB) [> 4.2390 = 7.0651 < 9.1846] w=0.0214 to align # Constraint # added constraint: constraint((T0324)A49.CB, (T0324)I58.CB) [> 4.1157 = 6.8595 < 8.9174] w=0.0214 to align # Constraint # added constraint: constraint((T0324)S105.CB, (T0324)T127.CB) [> 4.3999 = 7.3332 < 9.5331] w=0.0214 to align # Constraint # added constraint: constraint((T0324)V28.CB, (T0324)I81.CB) [> 4.7154 = 7.8590 < 10.2167] w=0.0214 to align # Constraint # added constraint: constraint((T0324)F8.CB, (T0324)F36.CB) [> 3.7962 = 6.3269 < 8.2250] w=0.0214 to align # Constraint # added constraint: constraint((T0324)M25.CB, (T0324)S105.CB) [> 4.4089 = 7.3481 < 9.5526] w=0.0214 to align # Constraint # added constraint: constraint((T0324)A5.CB, (T0324)M121.CB) [> 4.5358 = 7.5596 < 9.8275] w=0.0214 to align # Constraint # added constraint: constraint((T0324)M7.CB, (T0324)T127.CB) [> 4.1678 = 6.9463 < 9.0302] w=0.0214 to align # Constraint # added constraint: constraint((T0324)M74.CB, (T0324)I128.CB) [> 4.3706 = 7.2843 < 9.4695] w=0.0213 to align # Constraint # added constraint: constraint((T0324)D11.CB, (T0324)G161.CA) [> 4.1586 = 6.9310 < 9.0103] w=0.0213 to align # Constraint # added constraint: constraint((T0324)V150.CB, (T0324)V175.CB) [> 4.7339 = 7.8899 < 10.2568] w=0.0210 to align # Constraint # added constraint: constraint((T0324)F8.CB, (T0324)A180.CB) [> 4.4451 = 7.4085 < 9.6310] w=0.0180 to align # Constraint # added constraint: constraint((T0324)L29.CB, (T0324)P46.CB) [> 3.7649 = 6.2749 < 8.1574] w=0.0143 to align # Constraint # added constraint: constraint((T0324)V28.CB, (T0324)P200.CB) [> 3.3268 = 5.5446 < 7.2080] w=0.0143 to align # Constraint # added constraint: constraint((T0324)S163.CB, (T0324)A180.CB) [> 4.4918 = 7.4863 < 9.7323] w=0.0143 to align # Constraint # added constraint: constraint((T0324)M25.CB, (T0324)L100.CB) [> 3.0633 = 5.1055 < 6.6371] w=0.0143 to align # Constraint # added constraint: constraint((T0324)V28.CB, (T0324)L98.CB) [> 2.6512 = 4.4187 < 5.7444] w=0.0143 to align # Constraint # added constraint: constraint((T0324)V28.CB, (T0324)L100.CB) [> 3.3983 = 5.6639 < 7.3631] w=0.0143 to align # Constraint # added constraint: constraint((T0324)M7.CB, (T0324)A172.CB) [> 3.1363 = 5.2272 < 6.7953] w=0.0140 to align # Constraint # added constraint: constraint((T0324)M1.CB, (T0324)L206.CB) [> 3.4914 = 5.8190 < 7.5647] w=0.0071 to align # Constraint # added constraint: constraint((T0324)V103.CB, (T0324)G161.CA) [> 4.7616 = 7.9360 < 10.3168] w=0.0071 to align # Constraint # added constraint: constraint((T0324)G12.CA, (T0324)M25.CB) [> 4.7758 = 7.9597 < 10.3476] w=0.0060 to align # SetCost created cost = # ( 1.0000 * align ) # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0324/ # command:# reading script from file servers-clean.under # Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0324/decoys/ # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS3.pdb.gz looking for model 1 # Found a chain break before 200 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS4.pdb.gz looking for model 1 # Found a chain break before 183 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS5.pdb.gz looking for model 1 # Found a chain break before 183 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS3.pdb.gz looking for model 1 # Found a chain break before 205 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_RECOM_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS4.pdb.gz looking for model 1 # Found a chain break before 205 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS5 # ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS1 # ReadConformPDB reading from PDB file servers/3Dpro_TS2.pdb.gz looking for model 1 # Found a chain break before 190 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS2 # ReadConformPDB reading from PDB file servers/3Dpro_TS3.pdb.gz looking for model 1 # Found a chain break before 138 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS3 # ReadConformPDB reading from PDB file servers/3Dpro_TS4.pdb.gz looking for model 1 # Found a chain break before 152 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS4 # ReadConformPDB reading from PDB file servers/3Dpro_TS5.pdb.gz looking for model 1 # Found a chain break before 197 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS5 # ReadConformPDB reading from PDB file servers/ABIpro_TS1.pdb.gz looking for model 1 # Found a chain break before 203 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS1 # ReadConformPDB reading from PDB file servers/ABIpro_TS2.pdb.gz looking for model 1 # Found a chain break before 150 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS2 # ReadConformPDB reading from PDB file servers/ABIpro_TS3.pdb.gz looking for model 1 # Found a chain break before 197 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS3 # ReadConformPDB reading from PDB file servers/ABIpro_TS4.pdb.gz looking for model 1 # Found a chain break before 175 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS4 # ReadConformPDB reading from PDB file servers/ABIpro_TS5.pdb.gz looking for model 1 # Found a chain break before 195 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS5 # ReadConformPDB reading from PDB file servers/BayesHH_TS1.pdb.gz looking for model 1 # Found a chain break before 106 # copying to AlignedFragments data structure # naming current conformation BayesHH_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS1.pdb.gz looking for model 1 # Found a chain break before 139 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS2.pdb.gz looking for model 1 # Found a chain break before 136 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS2 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS3.pdb.gz looking for model 1 # Found a chain break before 136 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS3 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS4.pdb.gz looking for model 1 # Found a chain break before 207 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS4 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS5.pdb.gz looking for model 1 # Found a chain break before 207 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS5 # ReadConformPDB reading from PDB file servers/CIRCLE_TS1.pdb.gz looking for model 1 # Found a chain break before 199 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS1 # ReadConformPDB reading from PDB file servers/CIRCLE_TS2.pdb.gz looking for model 1 # Found a chain break before 199 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS2 # ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1 # Found a chain break before 196 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS3 # ReadConformPDB reading from PDB file servers/CIRCLE_TS4.pdb.gz looking for model 1 # Found a chain break before 201 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS4 # ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1 # Found a chain break before 185 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS5 # ReadConformPDB reading from PDB file servers/CPHmodels_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # naming current conformation CPHmodels_TS1 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS1 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS2 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS3 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS4.pdb.gz looking for model 1 # Found a chain break before 196 # copying to AlignedFragments data structure # naming current conformation CaspIta-FOX_TS4 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS5 # ReadConformPDB reading from PDB file servers/Distill_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # naming current conformation Distill_TS1 # ReadConformPDB reading from PDB file servers/Distill_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # naming current conformation Distill_TS2 # ReadConformPDB reading from PDB file servers/Distill_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # naming current conformation Distill_TS3 # ReadConformPDB reading from PDB file servers/Distill_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # naming current conformation Distill_TS4 # ReadConformPDB reading from PDB file servers/Distill_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # naming current conformation Distill_TS5 # ReadConformPDB reading from PDB file servers/FAMSD_TS1.pdb.gz looking for model 1 # Found a chain break before 201 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS1 # ReadConformPDB reading from PDB file servers/FAMSD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FAMSD_TS2 # ReadConformPDB reading from PDB file servers/FAMSD_TS3.pdb.gz looking for model 1 # Found a chain break before 199 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS3 # ReadConformPDB reading from PDB file servers/FAMSD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FAMSD_TS4 # ReadConformPDB reading from PDB file servers/FAMSD_TS5.pdb.gz looking for model 1 # Found a chain break before 196 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS5 # ReadConformPDB reading from PDB file servers/FAMS_TS1.pdb.gz looking for model 1 # Found a chain break before 199 # copying to AlignedFragments data structure # naming current conformation FAMS_TS1 # ReadConformPDB reading from PDB file servers/FAMS_TS2.pdb.gz looking for model 1 # Found a chain break before 199 # copying to AlignedFragments data structure # naming current conformation FAMS_TS2 # ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1 # Found a chain break before 201 # copying to AlignedFragments data structure # naming current conformation FAMS_TS3 # ReadConformPDB reading from PDB file servers/FAMS_TS4.pdb.gz looking for model 1 # Found a chain break before 201 # copying to AlignedFragments data structure # naming current conformation FAMS_TS4 # ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1 # Found a chain break before 196 # copying to AlignedFragments data structure # naming current conformation FAMS_TS5 # ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1 # Found a chain break before 186 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS1 # ReadConformPDB reading from PDB file servers/FOLDpro_TS2.pdb.gz looking for model 1 # Found a chain break before 186 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS2 # ReadConformPDB reading from PDB file servers/FOLDpro_TS3.pdb.gz looking for model 1 # Found a chain break before 132 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS3 # ReadConformPDB reading from PDB file servers/FOLDpro_TS4.pdb.gz looking for model 1 # Found a chain break before 205 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS4 # ReadConformPDB reading from PDB file servers/FOLDpro_TS5.pdb.gz looking for model 1 # Found a chain break before 192 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS5 # ReadConformPDB reading from PDB file servers/FORTE1_AL1.pdb.gz looking for model 1 Skipped atom 15, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 300, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL1 # ReadConformPDB reading from PDB file servers/FORTE1_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL2 # ReadConformPDB reading from PDB file servers/FORTE1_AL3.pdb.gz looking for model 1 Skipped atom 38, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 40, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 42, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 44, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 102, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 104, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 106, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 108, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 206, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 208, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 210, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 212, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 242, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 244, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 246, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 248, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 482, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 484, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 486, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 488, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL3 # ReadConformPDB reading from PDB file servers/FORTE1_AL4.pdb.gz looking for model 1 Skipped atom 786, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 788, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 790, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 792, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 794, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 796, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 798, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 800, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 802, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 804, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 806, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 808, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 810, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 812, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 814, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 816, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 818, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 820, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 822, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 824, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 826, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 828, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 830, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 832, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL4 # ReadConformPDB reading from PDB file servers/FORTE1_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL5 # ReadConformPDB reading from PDB file servers/FORTE2_AL1.pdb.gz looking for model 1 Skipped atom 15, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 300, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE2_AL1 # ReadConformPDB reading from PDB file servers/FORTE2_AL2.pdb.gz looking for model 1 Skipped atom 38, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 40, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 42, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 44, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 102, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 104, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 106, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 108, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 206, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 208, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 210, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 212, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 242, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 244, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 246, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 248, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 482, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 484, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 486, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 488, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE2_AL2 # ReadConformPDB reading from PDB file servers/FORTE2_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE2_AL3 # ReadConformPDB reading from PDB file servers/FORTE2_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE2_AL4 # ReadConformPDB reading from PDB file servers/FORTE2_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # naming current conformation FORTE2_AL5 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS1.pdb.gz looking for model 1 # Found a chain break before 194 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS1 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS2.pdb.gz looking for model 1 # Found a chain break before 171 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS2 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS3.pdb.gz looking for model 1 # Found a chain break before 168 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS3 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS4.pdb.gz looking for model 1 # Found a chain break before 168 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS4 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS5.pdb.gz looking for model 1 # Found a chain break before 194 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS5 # ReadConformPDB reading from PDB file servers/FUGMOD_TS1.pdb.gz looking for model 1 # naming current conformation FUGMOD_TS1 # ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS2 # ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS3 # ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS4 # ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS5 # ReadConformPDB reading from PDB file servers/FUGUE_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGUE_AL1 # ReadConformPDB reading from PDB file servers/FUGUE_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # naming current conformation FUGUE_AL2 # ReadConformPDB reading from PDB file servers/FUGUE_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # naming current conformation FUGUE_AL3 # ReadConformPDB reading from PDB file servers/FUGUE_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGUE_AL4 # ReadConformPDB reading from PDB file servers/FUGUE_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # naming current conformation FUGUE_AL5 # ReadConformPDB reading from PDB file servers/FUNCTION_TS1.pdb.gz looking for model 1 # Found a chain break before 195 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS1 # ReadConformPDB reading from PDB file servers/FUNCTION_TS2.pdb.gz looking for model 1 # Found a chain break before 199 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS2 # ReadConformPDB reading from PDB file servers/FUNCTION_TS3.pdb.gz looking for model 1 # Found a chain break before 192 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS3 # ReadConformPDB reading from PDB file servers/FUNCTION_TS4.pdb.gz looking for model 1 # Found a chain break before 199 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS4 # ReadConformPDB reading from PDB file servers/FUNCTION_TS5.pdb.gz looking for model 1 # Found a chain break before 196 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS5 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1 # Found a chain break before 45 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS1 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS2.pdb.gz looking for model 1 # Found a chain break before 136 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS2 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS3 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS4.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS4 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS5.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS5 # ReadConformPDB reading from PDB file servers/HHpred1_TS1.pdb.gz looking for model 1 # Found a chain break before 142 # copying to AlignedFragments data structure # naming current conformation HHpred1_TS1 # ReadConformPDB reading from PDB file servers/HHpred2_TS1.pdb.gz looking for model 1 # naming current conformation HHpred2_TS1 # ReadConformPDB reading from PDB file servers/HHpred3_TS1.pdb.gz looking for model 1 # Found a chain break before 59 # copying to AlignedFragments data structure # naming current conformation HHpred3_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Huber-Torda-Server_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS2 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Huber-Torda-Server_TS3 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS4 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS5 # ReadConformPDB reading from PDB file servers/LOOPP_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # naming current conformation LOOPP_TS1 # ReadConformPDB reading from PDB file servers/LOOPP_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation LOOPP_TS2 # ReadConformPDB reading from PDB file servers/LOOPP_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation LOOPP_TS3 # ReadConformPDB reading from PDB file servers/LOOPP_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # naming current conformation LOOPP_TS4 # ReadConformPDB reading from PDB file servers/LOOPP_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation LOOPP_TS5 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS1.pdb.gz looking for model 1 # Found a chain break before 182 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS2.pdb.gz looking for model 1 # Found a chain break before 95 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS3.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS4.pdb.gz looking for model 1 # Found a chain break before 150 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS5.pdb.gz looking for model 1 # Found a chain break before 139 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS5 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS1.pdb.gz looking for model 1 # Found a chain break before 117 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS2.pdb.gz looking for model 1 # Found a chain break before 95 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS3.pdb.gz looking for model 1 # Found a chain break before 150 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS4.pdb.gz looking for model 1 # Found a chain break before 133 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS5.pdb.gz looking for model 1 # Found a chain break before 142 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS5 # ReadConformPDB reading from PDB file servers/MetaTasser_TS1.pdb.gz looking for model 1 # Found a chain break before 196 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS1 # ReadConformPDB reading from PDB file servers/MetaTasser_TS2.pdb.gz looking for model 1 # Found a chain break before 201 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS2 # ReadConformPDB reading from PDB file servers/MetaTasser_TS3.pdb.gz looking for model 1 # Found a chain break before 196 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS3 # ReadConformPDB reading from PDB file servers/MetaTasser_TS4.pdb.gz looking for model 1 # Found a chain break before 207 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS4 # ReadConformPDB reading from PDB file servers/MetaTasser_TS5.pdb.gz looking for model 1 # Found a chain break before 201 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS5 # ReadConformPDB reading from PDB file servers/NN_PUT_lab_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # naming current conformation NN_PUT_lab_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS1.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS2.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS3.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS4.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS5.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO_TS1.pdb.gz looking for model 1 # Found a chain break before 193 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1 # Found a chain break before 173 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1 # Found a chain break before 185 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1 # naming current conformation PROTINFO_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1 # naming current conformation PROTINFO_TS5 # ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Pcons6_TS1 # ReadConformPDB reading from PDB file servers/Pcons6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Pcons6_TS2 # ReadConformPDB reading from PDB file servers/Pcons6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Pcons6_TS3 # ReadConformPDB reading from PDB file servers/Pcons6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # naming current conformation Pcons6_TS4 # ReadConformPDB reading from PDB file servers/Pcons6_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Pcons6_TS5 # ReadConformPDB reading from PDB file servers/Phyre-1_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-1_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS1.pdb.gz looking for model 1 # Found a chain break before 183 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS2.pdb.gz looking for model 1 # Found a chain break before 207 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS2 # ReadConformPDB reading from PDB file servers/Phyre-2_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS3 # ReadConformPDB reading from PDB file servers/Phyre-2_TS4.pdb.gz looking for model 1 # Found a chain break before 207 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS4 # ReadConformPDB reading from PDB file servers/Phyre-2_TS5.pdb.gz looking for model 1 # Found a chain break before 207 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS5 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS1 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1 # Found a chain break before 138 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS2 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1 # Found a chain break before 189 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS3 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1 # Found a chain break before 192 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS4 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS2.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS3.pdb.gz looking for model 1 # Found a chain break before 139 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS5.pdb.gz looking for model 1 # Found a chain break before 133 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS5 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS1.pdb.gz looking for model 1 # Found a chain break before 133 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS1 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS2.pdb.gz looking for model 1 # Found a chain break before 190 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS2 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS3.pdb.gz looking for model 1 # Found a chain break before 2 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS3 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS4.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS4 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS5.pdb.gz looking for model 1 # Found a chain break before 199 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR_TS1.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR_TS2.pdb.gz looking for model 1 # Found a chain break before 157 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR_TS3.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR_TS4.pdb.gz looking for model 1 # Found a chain break before 201 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR_TS5.pdb.gz looking for model 1 # Found a chain break before 189 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS5 # ReadConformPDB reading from PDB file servers/ROBETTA_TS1.pdb.gz looking for model 1 # Found a chain break before 192 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS1 # ReadConformPDB reading from PDB file servers/ROBETTA_TS2.pdb.gz looking for model 1 # Found a chain break before 190 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS2 # ReadConformPDB reading from PDB file servers/ROBETTA_TS3.pdb.gz looking for model 1 # Found a chain break before 189 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS3 # ReadConformPDB reading from PDB file servers/ROBETTA_TS4.pdb.gz looking for model 1 # Found a chain break before 138 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS4 # ReadConformPDB reading from PDB file servers/ROBETTA_TS5.pdb.gz looking for model 1 # Found a chain break before 138 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS5 # ReadConformPDB reading from PDB file servers/ROKKY_TS1.pdb.gz looking for model 1 # Found a chain break before 139 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS1 # ReadConformPDB reading from PDB file servers/ROKKY_TS2.pdb.gz looking for model 1 # Found a chain break before 174 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS2 # ReadConformPDB reading from PDB file servers/ROKKY_TS3.pdb.gz looking for model 1 # Found a chain break before 113 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS3 # ReadConformPDB reading from PDB file servers/ROKKY_TS4.pdb.gz looking for model 1 # Found a chain break before 125 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS4 # ReadConformPDB reading from PDB file servers/ROKKY_TS5.pdb.gz looking for model 1 # Found a chain break before 104 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS5 # ReadConformPDB reading from PDB file servers/SAM-T02_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation SAM-T02_AL1 # ReadConformPDB reading from PDB file servers/SAM-T02_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL2 # ReadConformPDB reading from PDB file servers/SAM-T02_AL3.pdb.gz looking for model 1 Skipped atom 294, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 296, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 298, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 300, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 346, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 348, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 350, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 352, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 366, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 368, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 370, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 372, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 374, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 376, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 378, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 380, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 654, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 656, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 658, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 660, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation SAM-T02_AL3 # ReadConformPDB reading from PDB file servers/SAM-T02_AL4.pdb.gz looking for model 1 Skipped atom 30, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 32, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 34, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 36, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 94, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 96, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 98, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 100, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 202, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 204, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 206, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 208, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 470, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 472, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 474, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 476, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL4 # ReadConformPDB reading from PDB file servers/SAM-T02_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation SAM-T02_AL5 # ReadConformPDB reading from PDB file servers/SAM-T99_AL1.pdb.gz looking for model 1 Skipped atom 186, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 188, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 190, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 192, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 194, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 196, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 198, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 200, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 262, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 264, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 266, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 268, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL1 # ReadConformPDB reading from PDB file servers/SAM-T99_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation SAM-T99_AL2 # ReadConformPDB reading from PDB file servers/SAM-T99_AL3.pdb.gz looking for model 1 Skipped atom 22, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 24, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 26, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 28, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 86, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 88, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 90, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 92, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 194, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 196, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 198, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 200, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 230, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 232, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 234, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 236, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 466, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 468, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 470, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 472, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL3 # ReadConformPDB reading from PDB file servers/SAM-T99_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation SAM-T99_AL4 # ReadConformPDB reading from PDB file servers/SAM-T99_AL5.pdb.gz looking for model 1 Skipped atom 106, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL5.pdb.gz Skipped atom 108, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL5.pdb.gz Skipped atom 110, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL5.pdb.gz Skipped atom 112, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL5.pdb.gz Skipped atom 118, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL5.pdb.gz Skipped atom 120, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL5.pdb.gz Skipped atom 122, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL5.pdb.gz Skipped atom 124, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL5.pdb.gz Skipped atom 142, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL5.pdb.gz Skipped atom 144, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL5.pdb.gz Skipped atom 146, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL5.pdb.gz Skipped atom 148, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL5.pdb.gz Skipped atom 346, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL5.pdb.gz Skipped atom 348, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL5.pdb.gz Skipped atom 350, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL5.pdb.gz Skipped atom 352, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL5.pdb.gz Skipped atom 394, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL5.pdb.gz Skipped atom 396, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL5.pdb.gz Skipped atom 398, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL5.pdb.gz Skipped atom 400, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL5.pdb.gz Skipped atom 550, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL5.pdb.gz Skipped atom 552, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL5.pdb.gz Skipped atom 554, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL5.pdb.gz Skipped atom 556, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL5.pdb.gz # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation SAM-T99_AL5 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS1.pdb.gz looking for model 1 # Found a chain break before 198 # copying to AlignedFragments data structure # naming current conformation SAM_T06_server_TS1 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS2 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS3 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS4 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS5 # ReadConformPDB reading from PDB file servers/SP3_TS1.pdb.gz looking for model 1 # Found a chain break before 95 # copying to AlignedFragments data structure # naming current conformation SP3_TS1 # ReadConformPDB reading from PDB file servers/SP3_TS2.pdb.gz looking for model 1 # Found a chain break before 139 # copying to AlignedFragments data structure # naming current conformation SP3_TS2 # ReadConformPDB reading from PDB file servers/SP3_TS3.pdb.gz looking for model 1 # Found a chain break before 157 # copying to AlignedFragments data structure # naming current conformation SP3_TS3 # ReadConformPDB reading from PDB file servers/SP3_TS4.pdb.gz looking for model 1 # Found a chain break before 117 # copying to AlignedFragments data structure # naming current conformation SP3_TS4 # ReadConformPDB reading from PDB file servers/SP3_TS5.pdb.gz looking for model 1 # Found a chain break before 180 # copying to AlignedFragments data structure # naming current conformation SP3_TS5 # ReadConformPDB reading from PDB file servers/SP4_TS1.pdb.gz looking for model 1 # Found a chain break before 139 # copying to AlignedFragments data structure # naming current conformation SP4_TS1 # ReadConformPDB reading from PDB file servers/SP4_TS2.pdb.gz looking for model 1 # Found a chain break before 185 # copying to AlignedFragments data structure # naming current conformation SP4_TS2 # ReadConformPDB reading from PDB file servers/SP4_TS3.pdb.gz looking for model 1 # Found a chain break before 122 # copying to AlignedFragments data structure # naming current conformation SP4_TS3 # ReadConformPDB reading from PDB file servers/SP4_TS4.pdb.gz looking for model 1 # Found a chain break before 117 # copying to AlignedFragments data structure # naming current conformation SP4_TS4 # ReadConformPDB reading from PDB file servers/SP4_TS5.pdb.gz looking for model 1 # Found a chain break before 182 # copying to AlignedFragments data structure # naming current conformation SP4_TS5 # ReadConformPDB reading from PDB file servers/SPARKS2_TS1.pdb.gz looking for model 1 # Found a chain break before 139 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS1 # ReadConformPDB reading from PDB file servers/SPARKS2_TS2.pdb.gz looking for model 1 # Found a chain break before 95 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS2 # ReadConformPDB reading from PDB file servers/SPARKS2_TS3.pdb.gz looking for model 1 # Found a chain break before 157 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS3 # ReadConformPDB reading from PDB file servers/SPARKS2_TS4.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS4 # ReadConformPDB reading from PDB file servers/SPARKS2_TS5.pdb.gz looking for model 1 # Found a chain break before 190 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation UNI-EID_bnmx_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation UNI-EID_bnmx_TS2 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS3 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS4 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_expm_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation UNI-EID_expm_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation UNI-EID_sfst_AL1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL2.pdb.gz looking for model 1 Skipped atom 34, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 36, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 38, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 40, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 98, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 100, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 102, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 104, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 202, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 204, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 206, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 208, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 474, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 476, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 478, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 480, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL2 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL3 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL4 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL5.pdb.gz looking for model 1 Skipped atom 302, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL5.pdb.gz Skipped atom 304, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL5.pdb.gz Skipped atom 306, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL5.pdb.gz Skipped atom 308, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL5.pdb.gz Skipped atom 350, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL5.pdb.gz Skipped atom 352, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL5.pdb.gz Skipped atom 354, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL5.pdb.gz Skipped atom 356, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL5.pdb.gz Skipped atom 370, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL5.pdb.gz Skipped atom 372, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL5.pdb.gz Skipped atom 374, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL5.pdb.gz Skipped atom 376, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL5.pdb.gz Skipped atom 378, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL5.pdb.gz Skipped atom 380, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL5.pdb.gz Skipped atom 382, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL5.pdb.gz Skipped atom 384, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL5.pdb.gz Skipped atom 658, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL5.pdb.gz Skipped atom 660, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL5.pdb.gz Skipped atom 662, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL5.pdb.gz Skipped atom 664, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL5.pdb.gz # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation UNI-EID_sfst_AL5 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS1.pdb.gz looking for model 1 # Found a chain break before 184 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS1 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS2.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS2 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS3.pdb.gz looking for model 1 # Found a chain break before 190 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS3 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS4.pdb.gz looking for model 1 # Found a chain break before 194 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS4 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS5.pdb.gz looking for model 1 # Found a chain break before 181 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS5 # ReadConformPDB reading from PDB file servers/beautshot_TS1.pdb.gz looking for model 1 # Found a chain break before 207 # copying to AlignedFragments data structure # naming current conformation beautshot_TS1 # ReadConformPDB reading from PDB file servers/beautshotbase_TS1.pdb.gz looking for model 1 # Found a chain break before 195 # copying to AlignedFragments data structure # naming current conformation beautshotbase_TS1 # ReadConformPDB reading from PDB file servers/forecast-s_AL1.pdb.gz looking for model 1 Skipped atom 63, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 64, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 97, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 606, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 611, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 732, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation forecast-s_AL1 # ReadConformPDB reading from PDB file servers/forecast-s_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # naming current conformation forecast-s_AL2 # ReadConformPDB reading from PDB file servers/forecast-s_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # naming current conformation forecast-s_AL3 # ReadConformPDB reading from PDB file servers/forecast-s_AL4.pdb.gz looking for model 1 Skipped atom 62, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 64, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 66, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 68, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 82, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 84, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 86, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 88, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 210, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 212, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 214, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 216, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 774, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 776, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 778, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz Skipped atom 780, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL4.pdb.gz # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # naming current conformation forecast-s_AL4 # ReadConformPDB reading from PDB file servers/forecast-s_AL5.pdb.gz looking for model 1 Skipped atom 38, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL5.pdb.gz Skipped atom 40, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL5.pdb.gz Skipped atom 42, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL5.pdb.gz Skipped atom 44, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL5.pdb.gz Skipped atom 242, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL5.pdb.gz Skipped atom 244, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL5.pdb.gz Skipped atom 246, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL5.pdb.gz Skipped atom 248, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL5.pdb.gz Skipped atom 262, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL5.pdb.gz Skipped atom 264, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL5.pdb.gz Skipped atom 266, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL5.pdb.gz Skipped atom 268, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL5.pdb.gz Skipped atom 530, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL5.pdb.gz Skipped atom 532, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL5.pdb.gz Skipped atom 534, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL5.pdb.gz Skipped atom 536, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL5.pdb.gz Skipped atom 642, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL5.pdb.gz Skipped atom 644, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL5.pdb.gz Skipped atom 646, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL5.pdb.gz Skipped atom 648, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL5.pdb.gz # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # naming current conformation forecast-s_AL5 # ReadConformPDB reading from PDB file servers/gtg_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # naming current conformation gtg_AL4 # ReadConformPDB reading from PDB file servers/gtg_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # naming current conformation gtg_AL5 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1 # Found a chain break before 129 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS2.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS3.pdb.gz looking for model 1 # Found a chain break before 187 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS4.pdb.gz looking for model 1 # Found a chain break before 191 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS5.pdb.gz looking for model 1 # Found a chain break before 45 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS1.pdb.gz looking for model 1 WARNING: atoms too close: (T0324)T104.O and (T0324)S105.N only 0.000 apart, marking (T0324)S105.N as missing # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS2.pdb.gz looking for model 1 # Found a chain break before 205 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS3.pdb.gz looking for model 1 WARNING: atoms too close: (T0324)S129.O and (T0324)A130.N only 0.000 apart, marking (T0324)A130.N as missing # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS4.pdb.gz looking for model 1 WARNING: atoms too close: (T0324)A180.O and (T0324)V181.N only 0.000 apart, marking (T0324)V181.N as missing # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS5.pdb.gz looking for model 1 WARNING: atoms too close: (T0324)T133.O and (T0324)P134.N only 0.000 apart, marking (T0324)P134.N as missing # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv_TS1.pdb.gz looking for model 1 # Found a chain break before 191 # copying to AlignedFragments data structure # naming current conformation karypis.srv_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv_TS4.pdb.gz looking for model 1 # Found a chain break before 191 # copying to AlignedFragments data structure # naming current conformation karypis.srv_TS4 # ReadConformPDB reading from PDB file servers/keasar-server_TS1.pdb.gz looking for model 1 # Found a chain break before 181 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS1 # ReadConformPDB reading from PDB file servers/keasar-server_TS2.pdb.gz looking for model 1 # Found a chain break before 192 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS2 # ReadConformPDB reading from PDB file servers/keasar-server_TS3.pdb.gz looking for model 1 # Found a chain break before 175 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS3 # ReadConformPDB reading from PDB file servers/keasar-server_TS4.pdb.gz looking for model 1 # Found a chain break before 190 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS4 # ReadConformPDB reading from PDB file servers/keasar-server_TS5.pdb.gz looking for model 1 # Found a chain break before 194 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS5 # ReadConformPDB reading from PDB file servers/mGen-3D_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation mGen-3D_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation nFOLD_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation nFOLD_TS2 # ReadConformPDB reading from PDB file servers/nFOLD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation nFOLD_TS3 # ReadConformPDB reading from PDB file servers/nFOLD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation nFOLD_TS4 # ReadConformPDB reading from PDB file servers/nFOLD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation nFOLD_TS5 # ReadConformPDB reading from PDB file servers/panther2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0324 can't currently be optimized by undertaker # naming current conformation panther2_TS1 # ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1 # Found a chain break before 203 # copying to AlignedFragments data structure # naming current conformation shub_TS1 # command:Using radius: 8.0000 Using models AND alignments for constraints model score -0.3171 model score -0.4615 model score -0.2970 model score -0.4833 model score -0.4217 model score -0.4736 model score -0.4399 model score -0.5011 model score -0.4999 model score -0.4754 model score -0.0509 model score -0.4245 model score 0.1338 model score -0.5022 model score -0.4813 model score -0.6406 model score 1.1472 model score 1.2778 model score 1.3951 model score 1.6322 model score 1.7393 model score 1.8339 model score 1.6802 model score 1.7854 model score 1.9204 model score -0.4195 model score -0.5545 model score -0.5288 model score -0.5544 model score -0.2001 model score -0.1853 model score -0.5094 model score -0.5333 model score -0.4677 model score -0.4778 model score -0.3614 model score 0.1357 model score -0.0436 model score 0.0944 model score 0.4319 model score -0.4745 model score -0.0617 model score 1.2596 model score 1.2599 model score 1.2615 model score 1.2636 model score 1.2609 model score -0.4778 model score -0.5433 model score -0.5198 model score -0.5366 model score -0.4677 model score -0.5128 model score -0.5333 model score -0.4778 model score -0.4778 model score -0.4677 model score -0.6206 model score 1.1801 model score 1.0630 model score 1.0460 model score 1.1005 model score 1.2664 model score 1.2597 model score 1.2592 model score 1.2594 model score 1.2562 model score 1.2664 model score 1.2592 model score 1.2597 model score 1.2562 model score 1.2592 model score 2.1488 model score 2.0649 model score 2.3311 model score 2.3336 model score 2.5086 model score -0.5172 model score -0.1932 model score -0.0682 model score -0.0570 model score -0.0488 model score 1.2562 model score 1.2584 model score 1.2564 model score 1.2551 model score 1.2587 model score -0.4647 model score -0.3336 model score -0.5480 model score -0.3629 model score -0.4284 model score -0.5063 model score -0.5069 model score -0.4209 model score -0.5001 model score -0.3888 model score -0.5315 model score -0.3977 model score -0.3862 model score -0.4190 model score 0.0486 model score -0.4367 model score 0.1985 model score -0.1704 model score 0.1192 model score -0.0477 model score -0.1656 model score 0.0965 model score -0.1803 model score -0.4707 model score -0.5636 model score -0.4897 model score -0.5036 model score -0.5552 model score -0.3765 model score -0.5636 model score -0.5036 model score -0.4809 model score -0.5609 model score -0.5650 model score -0.3366 model score -0.2135 model score -0.4220 model score -0.5074 model score 0.1192 model score -0.5218 model score -0.5236 model score -0.5226 model score -0.4394 model score -0.4472 model score -0.3976 model score -0.3986 model score -0.4347 model score -0.4530 model score -0.5225 model score -0.5233 model score -0.5440 model score -0.5765 model score -0.3734 model score -0.3928 model score 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model score -0.3438 model score -0.5461 model score 0.0128 model score -0.3654 model score -0.2791 model score -0.5461 model score -0.3649 model score 0.0114 model score -0.3654 model score -0.4000 model score -0.5453 model score -0.3438 model score -0.1112 model score -0.3694 model score -0.3413 model score 1.2562 model score 1.2592 model score 1.2597 model score 1.2584 model score 1.2584 model score -0.5473 model score 1.2562 model score 1.2592 model score 1.2597 model score 1.2584 model score 1.2567 model score -0.6016 model score -0.6068 model score -0.3695 model score -0.3929 model score -0.3367 model score -0.5455 model score -0.5125 model score 1.2565 model score 1.2667 model score 1.2568 model score 1.2667 model score 1.2688 model score 1.2674 model score 1.2709 model score -0.5446 model score -0.5531 model score -0.5442 model score -0.2869 model score -0.5528 model score 1.9872 model score 2.4044 model score 2.3216 model score 1.9057 model score 2.0127 model score -0.2868 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USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0011 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0011 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0011 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0011 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0011 USE_EVALUE, weight: 0.9967 eval: 0.0000 min: 0.0000 max: 0.0011 USE_EVALUE, weight: 0.9967 eval: 0.0000 min: 0.0000 max: 0.0011 USE_EVALUE, weight: 0.9967 eval: 0.0000 min: 0.0000 max: 0.0011 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0011 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0011 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0011 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0011 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0011 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0011 USE_EVALUE, weight: 0.1001 eval: 0.0011 min: 0.0000 max: 0.0011 USE_EVALUE, weight: 0.1001 eval: 0.0011 min: 0.0000 max: 0.0011 USE_EVALUE, weight: 0.1001 eval: 0.0011 min: 0.0000 max: 0.0011 Number of contacts in models: 259 Number of contacts in alignments: 144 NUMB_ALIGNS: 144 Adding 7096 constraints to all3.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all3.constraints maxweight: 1.0000 Optimizing... Probability sum: -344.2204, CN propb: -344.2204 weights: 0.3896 constraints: 570 # command:Found ConstraintSet # PrintContacts align.constraints_meta03 Number of constraints in align3.constraints 570 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_meta03 Number of constraints in align3.constraints.bonus 570 # command:Found ConstraintSet # PrintContacts rejected.constraints_meta03 Number of constraints in rejected3.constraints 6526 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_meta03 Number of constraints in rejected3.constraints.bonus 6526 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_meta03 Number of constraints in noncontact3.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_meta03 Number of constraints in noncontact3.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_meta03 Number of constraints in all3.constraints 7096 # command: