# command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 1600 examples # computed average trans backbone unit before proline from 52 examples # trans (non-proline) backbone unit: # CA= -2.2097 1.0151 -0.0046 # O= -0.1488 2.2425 0.0020 # C= -0.6903 1.1357 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4580 -0.0000 -0.0000 # cis backbone unit: # CA= -0.1462 2.4515 0.0018 # O= -2.0272 0.9713 0.0022 # C= -0.8006 1.0755 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4659 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2063 1.0654 0.0002 # O= -0.1193 2.2442 0.0054 # C= -0.6842 1.1479 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4661 -0.0000 0.0000 # After reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz have 408 chains in training database # Count of chains,residues,atoms: 408,82795,639989 # 81291 residues have no bad marker # 565 residues lack atoms needed to compute omega # 313 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 1 # HAS_OXT 265 # TOO_MANY_ATOMS 0 # TOO_FEW_ATOMS 378 # HAS_UNKNOWN_ATOMS 0 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 139 # NON_PLANAR_PEPTIDE 424 # BAD_PEPTIDE 803 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-40pc-3157.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:# Prefix for input files set to # command:# Making conformation for sequence T0361 numbered 1 through 169 Created new target T0361 from T0361.a2m # command:CPU_time= 6.617 sec, elapsed time= 6.671 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f45B/T0361-1f45B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1f45B expands to /projects/compbio/data/pdb/1f45.pdb.gz 1f45B:# T0361 read from 1f45B/T0361-1f45B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f45B read from 1f45B/T0361-1f45B-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1f45B to template set # found chain 1f45B in template set Warning: unaligning (T0361)E103 because of BadResidue code BAD_PEPTIDE in next template residue (1f45B)R129 Warning: unaligning (T0361)T104 because of BadResidue code BAD_PEPTIDE at template residue (1f45B)R129 Warning: unaligning (T0361)G106 because of BadResidue code BAD_PEPTIDE in next template residue (1f45B)F132 Warning: unaligning (T0361)F107 because of BadResidue code BAD_PEPTIDE at template residue (1f45B)F132 Warning: unaligning (T0361)T123 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f45B)Y167 Warning: unaligning (T0361)A138 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f45B)Y167 T0361 80 :MDKWLYADIT 1f45B 101 :CLSSIYEDLK # choosing archetypes in rotamer library T0361 90 :HFSQYWHYLNEQD 1f45B 115 :EFKTMNAKLLMDP T0361 105 :P 1f45B 130 :Q T0361 108 :ADDITWDFISNVNSI 1f45B 133 :LDQNMLAVIDELMQA T0361 139 :DFAVWSEARF 1f45B 168 :KTKIKLCILL T0361 154 :TALTLAVTTTLK 1f45B 178 :HAFRIRAVTIDR Number of specific fragments extracted= 6 number of extra gaps= 2 total=6 Will force an alignment to be made, even if fragment is small Number of alignments=1 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f45B/T0361-1f45B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0361 read from 1f45B/T0361-1f45B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f45B read from 1f45B/T0361-1f45B-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1f45B in template set Warning: unaligning (T0361)E103 because of BadResidue code BAD_PEPTIDE in next template residue (1f45B)R129 Warning: unaligning (T0361)T104 because of BadResidue code BAD_PEPTIDE at template residue (1f45B)R129 Warning: unaligning (T0361)G106 because of BadResidue code BAD_PEPTIDE in next template residue (1f45B)F132 Warning: unaligning (T0361)F107 because of BadResidue code BAD_PEPTIDE at template residue (1f45B)F132 Warning: unaligning (T0361)T123 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f45B)Y167 Warning: unaligning (T0361)A138 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f45B)Y167 T0361 81 :DKWLYADIT 1f45B 102 :LSSIYEDLK T0361 90 :HFSQYWHYLNEQD 1f45B 115 :EFKTMNAKLLMDP T0361 105 :P 1f45B 130 :Q T0361 108 :ADDITWDFISNVNSI 1f45B 133 :LDQNMLAVIDELMQA T0361 139 :DFAVWSEARF 1f45B 168 :KTKIKLCILL T0361 154 :TALTLAVTTTLK 1f45B 178 :HAFRIRAVTIDR Number of specific fragments extracted= 6 number of extra gaps= 2 total=12 Will force an alignment to be made, even if fragment is small Number of alignments=2 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f45B/T0361-1f45B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0361 read from 1f45B/T0361-1f45B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1f45B read from 1f45B/T0361-1f45B-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1f45B in template set Warning: unaligning (T0361)E103 because of BadResidue code BAD_PEPTIDE in next template residue (1f45B)R129 Warning: unaligning (T0361)T104 because of BadResidue code BAD_PEPTIDE at template residue (1f45B)R129 Warning: unaligning (T0361)G106 because of BadResidue code BAD_PEPTIDE in next template residue (1f45B)F132 Warning: unaligning (T0361)F107 because of BadResidue code BAD_PEPTIDE at template residue (1f45B)F132 Warning: unaligning (T0361)A138 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f45B)Y167 T0361 79 :KMDKWLYADIT 1f45B 100 :LCLSSIYEDLK T0361 90 :HFSQYWHYLNEQD 1f45B 115 :EFKTMNAKLLMDP T0361 105 :P 1f45B 130 :Q T0361 108 :ADDITWDFISNVNSI 1f45B 133 :LDQNMLAVIDELMQA T0361 139 :DFAVWSEARFSG 1f45B 168 :KTKIKLCILLHA T0361 156 :LTLAVTTTLK 1f45B 180 :FRIRAVTIDR Number of specific fragments extracted= 6 number of extra gaps= 2 total=18 Will force an alignment to be made, even if fragment is small Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w33A/T0361-1w33A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1w33A expands to /projects/compbio/data/pdb/1w33.pdb.gz 1w33A:Skipped atom 676, because occupancy 0.35 <= existing 0.650 in 1w33A Skipped atom 678, because occupancy 0.350 <= existing 0.650 in 1w33A Skipped atom 680, because occupancy 0.350 <= existing 0.650 in 1w33A Skipped atom 682, because occupancy 0.350 <= existing 0.650 in 1w33A # T0361 read from 1w33A/T0361-1w33A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1w33A read from 1w33A/T0361-1w33A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1w33A to template set # found chain 1w33A in template set Warning: unaligning (T0361)N18 because of BadResidue code BAD_PEPTIDE at template residue (1w33A)T71 T0361 19 :LFSFMKTAHSILLQG 1w33A 72 :IASELKAIGKELEDQ T0361 34 :IRQFLPSL 1w33A 90 :ENIQIAKI T0361 57 :LLAQ 1w33A 104 :FLST T0361 62 :GPLDDID 1w33A 111 :GPYDLID T0361 69 :VALRLIYALGK 1w33A 124 :IKRTLYSSLDY T0361 81 :DK 1w33A 135 :KK T0361 86 :ADITHFSQYWHYLNEQDET 1w33A 137 :ENIEKLKEILEILKKNSEH T0361 109 :DDITWDFISN 1w33A 156 :YNIIGRLIYH T0361 119 :VNSITRNATLYDALK 1w33A 168 :WGIQFQIEQNLELIQ T0361 134 :AMKFADFAVWSEARFSGM 1w33A 187 :NLSQEESKSLLMQIKSNL T0361 152 :VKTALTLAVTTTLKE 1w33A 206 :IKQRLKKTLNETLKV Number of specific fragments extracted= 11 number of extra gaps= 1 total=29 Will force an alignment to be made, even if fragment is small Number of alignments=4 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w33A/T0361-1w33A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0361 read from 1w33A/T0361-1w33A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1w33A read from 1w33A/T0361-1w33A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1w33A in template set T0361 26 :AHSILLQG 1w33A 79 :IGKELEDQ T0361 34 :IRQFLPSL 1w33A 90 :ENIQIAKI T0361 42 :F 1w33A 102 :F T0361 43 :VDNDEEIVEY 1w33A 114 :DLIDEDIQMK T0361 69 :VALRLIYALGK 1w33A 124 :IKRTLYSSLDY T0361 81 :DK 1w33A 135 :KK T0361 86 :ADITHFSQYWHYLNEQDETPGFADDIT 1w33A 137 :ENIEKLKEILEILKKNSEHYNIIGRLI T0361 113 :WDFISNVNSITRNATL 1w33A 168 :WGIQFQIEQNLELIQN T0361 129 :YDALKAMKFADFAVWSEARFS 1w33A 185 :VENLSQEESKSLLMQIKSNLE T0361 150 :GMVKTALTLAVTTTLKE 1w33A 208 :QRLKKTLNETLKVYNQN Number of specific fragments extracted= 10 number of extra gaps= 0 total=39 Will force an alignment to be made, even if fragment is small Number of alignments=5 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w33A/T0361-1w33A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0361 read from 1w33A/T0361-1w33A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1w33A read from 1w33A/T0361-1w33A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1w33A in template set T0361 3 :TLTEDDVLEQLDA 1w33A 77 :KAIGKELEDQKKE T0361 34 :IRQFLPSLFVDND 1w33A 90 :ENIQIAKIAKEKF T0361 56 :PLLAQ 1w33A 103 :DFLST T0361 61 :SGPLDDIDVALRLIYALGKMDKWLYADITHFSQYWHYLNEQDETPG 1w33A 112 :PYDLIDEDIQMKIKRTLYSSLDYKKENIEKLKEILEILKKNSEHYN T0361 108 :ADDITWDFISNVNSITRNA 1w33A 163 :IYHISWGIQFQIEQNLELI T0361 129 :YDALKAMKFADFAVWSEARFSGM 1w33A 182 :QNGVENLSQEESKSLLMQIKSNL T0361 152 :VKTALTLAVTTTLKEL 1w33A 206 :IKQRLKKTLNETLKVY Number of specific fragments extracted= 7 number of extra gaps= 0 total=46 Will force an alignment to be made, even if fragment is small Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2grrB/T0361-2grrB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2grrB expands to /projects/compbio/data/pdb/2grr.pdb.gz 2grrB:# T0361 read from 2grrB/T0361-2grrB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2grrB read from 2grrB/T0361-2grrB-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2grrB to template set # found chain 2grrB in template set T0361 14 :DAQDNLFSFMKTAHSIL 2grrB 461 :TDTSDPEKVVSAFLKVS T0361 40 :SLF 2grrB 478 :SVF T0361 44 :DNDE 2grrB 481 :KDEA T0361 48 :EIVEYAVKPLLA 2grrB 488 :MAVQDAVDALMQ T0361 60 :QSGPLDDIDVALRLIYALGKMD 2grrB 503 :NSSSFNSNTFLTRLLVHMGLLK T0361 89 :THFSQYWHYLNEQDETPGFADDITWDFISN 2grrB 536 :YGPLMALNHMVQQDYFPKALAPLLLAFVTK T0361 129 :YDALKAMKFA 2grrB 567 :NSALESCSFA T0361 140 :FAVWSEARF 2grrB 577 :RHSLLQTLY Number of specific fragments extracted= 8 number of extra gaps= 0 total=54 Will force an alignment to be made, even if fragment is small Number of alignments=7 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2grrB/T0361-2grrB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0361 read from 2grrB/T0361-2grrB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2grrB read from 2grrB/T0361-2grrB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2grrB in template set T0361 15 :AQDNLFSFMKTAHSI 2grrB 462 :DTSDPEKVVSAFLKV T0361 39 :PSLF 2grrB 477 :SSVF T0361 44 :DNDE 2grrB 481 :KDEA T0361 48 :EIVEYAVKPLLA 2grrB 488 :MAVQDAVDALMQ T0361 60 :QSGPLDDIDVALRLIYALGKMD 2grrB 503 :NSSSFNSNTFLTRLLVHMGLLK T0361 88 :ITHFSQYWHYLNEQDETPGFADDITWDFISN 2grrB 535 :LYGPLMALNHMVQQDYFPKALAPLLLAFVTK T0361 129 :YDALKAMKFA 2grrB 567 :NSALESCSFA T0361 140 :FAVWSEARF 2grrB 577 :RHSLLQTLY Number of specific fragments extracted= 8 number of extra gaps= 0 total=62 Will force an alignment to be made, even if fragment is small Number of alignments=8 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2grrB/T0361-2grrB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0361 read from 2grrB/T0361-2grrB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2grrB read from 2grrB/T0361-2grrB-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2grrB in template set T0361 15 :AQDNLFSFMKTAHSI 2grrB 462 :DTSDPEKVVSAFLKV T0361 39 :PSLFVDNDE 2grrB 477 :SSVFKDEAT T0361 48 :EIVEYAVKPLLA 2grrB 488 :MAVQDAVDALMQ T0361 60 :QSGPLDDIDVALRLIYALGKM 2grrB 503 :NSSSFNSNTFLTRLLVHMGLL T0361 100 :EQDETPGFAD 2grrB 524 :KSEDKVKAIA T0361 111 :ITWDFISNVNSITRNATLYDALK 2grrB 534 :NLYGPLMALNHMVQQDYFPKALA T0361 138 :ADFAVWSE 2grrB 557 :PLLLAFVT T0361 146 :ARFSGMVKTALTLAVT 2grrB 570 :LESCSFARHSLLQTLY Number of specific fragments extracted= 8 number of extra gaps= 0 total=70 Will force an alignment to be made, even if fragment is small Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v4eA/T0361-1v4eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1v4eA expands to /projects/compbio/data/pdb/1v4e.pdb.gz 1v4eA:# T0361 read from 1v4eA/T0361-1v4eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v4eA read from 1v4eA/T0361-1v4eA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1v4eA to template set # found chain 1v4eA in template set T0361 8 :DVLEQLD 1v4eA 118 :HTVEEIG T0361 16 :QDNLFSFMKTAHSILLQGIRQFLPSLFVDNDEEIVEYAVKP 1v4eA 125 :NNKLRRAFLNVIGKMSEAELIEQLSRYKPITKEEYLRIVEG T0361 57 :LL 1v4eA 170 :LF T0361 68 :DVALRLIYAL 1v4eA 172 :GLALQLPALL T0361 78 :GKMDKWLYA 1v4eA 183 :GELGEDLYN T0361 87 :DITHFSQYWHYLNEQDETP 1v4eA 198 :TIYQMFDDIMDFAGMEKIG T0361 106 :GFAD 1v4eA 219 :GFLD T0361 115 :FISNVNSITRNATLYDALKAMKFADFAVWSEAR 1v4eA 229 :SFPLVTAMEKFPEARQMFENRDWSGLMSFMREK T0361 148 :FSGMVKTALTLAVTTTLKE 1v4eA 263 :ILKECEETLKVLVKNVIIE Number of specific fragments extracted= 9 number of extra gaps= 0 total=79 Will force an alignment to be made, even if fragment is small Number of alignments=10 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v4eA/T0361-1v4eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0361 read from 1v4eA/T0361-1v4eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v4eA read from 1v4eA/T0361-1v4eA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1v4eA in template set T0361 8 :DVLEQLD 1v4eA 118 :HTVEEIG T0361 16 :QDNLFSFMKTAHSILLQGIRQFLPSLFVDNDEEIVEYAVKP 1v4eA 125 :NNKLRRAFLNVIGKMSEAELIEQLSRYKPITKEEYLRIVEG T0361 57 :L 1v4eA 170 :L T0361 67 :IDVALRLIYAL 1v4eA 171 :FGLALQLPALL T0361 78 :GKMDKWLYADITHF 1v4eA 183 :GELGEDLYNLGVTI T0361 92 :SQYWHYLNEQDETP 1v4eA 203 :FDDIMDFAGMEKIG T0361 106 :GFAD 1v4eA 219 :GFLD T0361 115 :FISNVNSITRNATLYDALKAMKFADFAVWSEAR 1v4eA 229 :SFPLVTAMEKFPEARQMFENRDWSGLMSFMREK T0361 148 :FSGMVKTALTLAVTTTLKE 1v4eA 263 :ILKECEETLKVLVKNVIIE Number of specific fragments extracted= 9 number of extra gaps= 0 total=88 Will force an alignment to be made, even if fragment is small Number of alignments=11 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v4eA/T0361-1v4eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0361 read from 1v4eA/T0361-1v4eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1v4eA read from 1v4eA/T0361-1v4eA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1v4eA in template set T0361 21 :SFMKTAHSILLQG 1v4eA 111 :LVLVSAFHTVEEI T0361 34 :IRQFLPSLFVDND 1v4eA 128 :LRRAFLNVIGKMS T0361 48 :EIVEYAVK 1v4eA 141 :EAELIEQL T0361 59 :AQSGPLDDID 1v4eA 149 :SRYKPITKEE T0361 69 :VALRLIYAL 1v4eA 169 :ALFGLALQL T0361 78 :GKMDKWLYADITHF 1v4eA 183 :GELGEDLYNLGVTI T0361 92 :SQYWHYLNEQDETP 1v4eA 203 :FDDIMDFAGMEKIG T0361 106 :GFAD 1v4eA 219 :GFLD T0361 110 :DITWDFISNVNSITRNATLYDALKAMKFADFAVWSEAR 1v4eA 224 :KNGVASFPLVTAMEKFPEARQMFENRDWSGLMSFMREK T0361 148 :FSGMVKTALTLAVTTTLKE 1v4eA 263 :ILKECEETLKVLVKNVIIE Number of specific fragments extracted= 10 number of extra gaps= 0 total=98 Will force an alignment to be made, even if fragment is small Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t3wA/T0361-1t3wA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1t3wA expands to /projects/compbio/data/pdb/1t3w.pdb.gz 1t3wA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0361 read from 1t3wA/T0361-1t3wA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t3wA read from 1t3wA/T0361-1t3wA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1t3wA to template set # found chain 1t3wA in template set T0361 87 :DITHFSQYWHYLNEQDE 1t3wA 481 :GLGLFRELVNTCLSQPG T0361 107 :FADDITWDFISNVNSITRNATLYDALKAMKFADFAVWSEARFSGMVKTALTLAVTTTLKELT 1t3wA 498 :LTTGQLLEHYRGTNNAATLEKLSMWDDIADKNIAEQTFTDSLNHMFDSLLELRQEELIARER Number of specific fragments extracted= 2 number of extra gaps= 0 total=100 Will force an alignment to be made, even if fragment is small Number of alignments=13 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t3wA/T0361-1t3wA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0361 read from 1t3wA/T0361-1t3wA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t3wA read from 1t3wA/T0361-1t3wA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1t3wA in template set T0361 87 :DITHFSQYWHYLNEQD 1t3wA 481 :GLGLFRELVNTCLSQP T0361 106 :GFADDITWDFISNVNSITRNATLYDALKAMKFADFAVWSEARFSGMVKTALTLAVTTTLKEL 1t3wA 497 :GLTTGQLLEHYRGTNNAATLEKLSMWDDIADKNIAEQTFTDSLNHMFDSLLELRQEELIARE Number of specific fragments extracted= 2 number of extra gaps= 0 total=102 Will force an alignment to be made, even if fragment is small Number of alignments=14 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t3wA/T0361-1t3wA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0361 read from 1t3wA/T0361-1t3wA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t3wA read from 1t3wA/T0361-1t3wA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1t3wA in template set Warning: unaligning (T0361)D81 because of BadResidue code BAD_PEPTIDE in next template residue (1t3wA)E476 Warning: unaligning (T0361)K82 because of BadResidue code BAD_PEPTIDE at template residue (1t3wA)E476 T0361 48 :EIVEYAVKP 1t3wA 454 :LIGLLVQNP T0361 57 :LLAQSGPLDD 1t3wA 464 :LATLVPPLEN T0361 80 :M 1t3wA 474 :L T0361 83 :WLYADITHFSQYWHYLNEQDETP 1t3wA 477 :NKLPGLGLFRELVNTCLSQPGLT T0361 106 :GFADDITWDFISNVNSITRNATL 1t3wA 506 :HYRGTNNAATLEKLSMWDDIADK T0361 129 :YDALKAMKFADFAVWSEARFSGM 1t3wA 536 :TDSLNHMFDSLLELRQEELIARE T0361 153 :KTALTLAVTTTLKELTP 1t3wA 564 :SNEERLELWTLNQELAK Number of specific fragments extracted= 7 number of extra gaps= 1 total=109 Will force an alignment to be made, even if fragment is small Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3gcb/T0361-3gcb-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3gcb expands to /projects/compbio/data/pdb/3gcb.pdb.gz 3gcb:Warning: there is no chain 3gcb will retry with 3gcbA # T0361 read from 3gcb/T0361-3gcb-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3gcb read from 3gcb/T0361-3gcb-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3gcb to template set # found chain 3gcb in template set T0361 22 :FMKTAHSILLQGIRQFLPSLFVDNDEEIVEYAVKPLLAQSGP 3gcb 103 :FFYDKLEKANYFLDQIVSSADQDIDSRLVQYLLAAPTEDGGQ T0361 67 :IDVALRLIYALGKMDKWLYAD 3gcb 145 :YSMFLNLVKKYGLIPKDLYGD T0361 89 :THFSQYWHYLN 3gcb 175 :KWNSLLTTKLR T0361 114 :DFISNVNSITRNA 3gcb 186 :EFAETLRTALKER T0361 134 :AMKFADFAVWSEARFSGMVKTA 3gcb 199 :SADDSIIVTLREQMQREIFRLM T0361 157 :TL 3gcb 221 :SL Number of specific fragments extracted= 6 number of extra gaps= 0 total=115 Will force an alignment to be made, even if fragment is small Number of alignments=16 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3gcb/T0361-3gcb-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0361 read from 3gcb/T0361-3gcb-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3gcb read from 3gcb/T0361-3gcb-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3gcb in template set T0361 22 :FMKTAHSILLQGIRQFLPSLFVDNDEEIVEYAVK 3gcb 103 :FFYDKLEKANYFLDQIVSSADQDIDSRLVQYLLA T0361 59 :AQ 3gcb 140 :ED T0361 67 :IDVALRLIYALGKMDKWLYAD 3gcb 145 :YSMFLNLVKKYGLIPKDLYGD T0361 89 :THFSQYWHYL 3gcb 175 :KWNSLLTTKL T0361 113 :WDFISNVNSITRNA 3gcb 185 :REFAETLRTALKER T0361 134 :AMKFADFAVWSEARFSG 3gcb 199 :SADDSIIVTLREQMQRE T0361 160 :VTTTLKE 3gcb 216 :IFRLMSL Number of specific fragments extracted= 7 number of extra gaps= 0 total=122 Will force an alignment to be made, even if fragment is small Number of alignments=17 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3gcb/T0361-3gcb-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0361 read from 3gcb/T0361-3gcb-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3gcb read from 3gcb/T0361-3gcb-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3gcb in template set T0361 22 :FMKTAHSILLQGIRQFLPSLFVDNDEEIVEYAVKPLLAQSGP 3gcb 103 :FFYDKLEKANYFLDQIVSSADQDIDSRLVQYLLAAPTEDGGQ T0361 67 :IDVALRLIYALGKMDKWLYAD 3gcb 145 :YSMFLNLVKKYGLIPKDLYGD T0361 89 :THFSQYWHYLN 3gcb 175 :KWNSLLTTKLR T0361 114 :DFISNVNSITRNA 3gcb 186 :EFAETLRTALKER T0361 134 :AMKFADFAVWSEARFSGMVKT 3gcb 199 :SADDSIIVTLREQMQREIFRL T0361 156 :LTL 3gcb 220 :MSL Number of specific fragments extracted= 6 number of extra gaps= 0 total=128 Will force an alignment to be made, even if fragment is small Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1huxA/T0361-1huxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1huxA expands to /projects/compbio/data/pdb/1hux.pdb.gz 1huxA:# T0361 read from 1huxA/T0361-1huxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1huxA read from 1huxA/T0361-1huxA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1huxA to template set # found chain 1huxA in template set T0361 6 :EDDVLEQLDAQDNLFSFMKTAHSILLQGIRQFLPSLFVDND 1huxA 171 :ESEVISQLSKGTDKIDIIAGIHRSVASRVIGLANRVGIVKD T0361 62 :GPLDDID 1huxA 216 :GGVAQNY T0361 69 :VALRLIYAL 1huxA 224 :VRGALEEGL Number of specific fragments extracted= 3 number of extra gaps= 0 total=131 Will force an alignment to be made, even if fragment is small Number of alignments=19 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1huxA/T0361-1huxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0361 read from 1huxA/T0361-1huxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1huxA read from 1huxA/T0361-1huxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1huxA in template set T0361 6 :EDDVLEQLDAQDNLFSFMKTAHSILLQGIRQFLPSLFVDND 1huxA 171 :ESEVISQLSKGTDKIDIIAGIHRSVASRVIGLANRVGIVKD T0361 48 :EIVEYAVKPLLA 1huxA 222 :YGVRGALEEGLG Number of specific fragments extracted= 2 number of extra gaps= 0 total=133 Will force an alignment to be made, even if fragment is small Number of alignments=20 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1huxA/T0361-1huxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0361 read from 1huxA/T0361-1huxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1huxA read from 1huxA/T0361-1huxA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1huxA in template set T0361 5 :TEDDVLEQLDAQDNLFSFMKTAHSILLQGIRQFLPSL 1huxA 170 :AESEVISQLSKGTDKIDIIAGIHRSVASRVIGLANRV T0361 42 :FVDN 1huxA 208 :IVKD T0361 48 :EIVEYAVKPLLAQS 1huxA 222 :YGVRGALEEGLGVE T0361 62 :GPLDDID 1huxA 239 :SPLAQYN T0361 69 :VALRLIYAL 1huxA 247 :ALGAALYAY Number of specific fragments extracted= 5 number of extra gaps= 0 total=138 Will force an alignment to be made, even if fragment is small Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ll2A/T0361-1ll2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ll2A expands to /projects/compbio/data/pdb/1ll2.pdb.gz 1ll2A:# T0361 read from 1ll2A/T0361-1ll2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ll2A read from 1ll2A/T0361-1ll2A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ll2A to template set # found chain 1ll2A in template set Warning: unaligning (T0361)N18 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ll2A)T240 Warning: unaligning (T0361)S40 because last residue in template chain is (1ll2A)Q262 T0361 19 :LFSFMKTAHSILLQGIRQFLP 1ll2A 241 :HPQFLNVWWDIFTTSVVPLLQ Number of specific fragments extracted= 1 number of extra gaps= 0 total=139 Will force an alignment to be made, even if fragment is small Number of alignments=22 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ll2A/T0361-1ll2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0361 read from 1ll2A/T0361-1ll2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ll2A read from 1ll2A/T0361-1ll2A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ll2A in template set Warning: unaligning (T0361)N18 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ll2A)T240 Warning: unaligning (T0361)S40 because last residue in template chain is (1ll2A)Q262 T0361 19 :LFSFMKTAHSILLQGIRQFLP 1ll2A 241 :HPQFLNVWWDIFTTSVVPLLQ Number of specific fragments extracted= 1 number of extra gaps= 0 total=140 Will force an alignment to be made, even if fragment is small Number of alignments=23 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ll2A/T0361-1ll2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0361 read from 1ll2A/T0361-1ll2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ll2A read from 1ll2A/T0361-1ll2A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ll2A in template set Warning: unaligning (T0361)N18 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ll2A)T240 Warning: unaligning (T0361)S40 because last residue in template chain is (1ll2A)Q262 T0361 19 :LFSFMKTAHSILLQGIRQFLP 1ll2A 241 :HPQFLNVWWDIFTTSVVPLLQ Number of specific fragments extracted= 1 number of extra gaps= 0 total=141 Will force an alignment to be made, even if fragment is small Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1b3uA/T0361-1b3uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1b3uA expands to /projects/compbio/data/pdb/1b3u.pdb.gz 1b3uA:# T0361 read from 1b3uA/T0361-1b3uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1b3uA read from 1b3uA/T0361-1b3uA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1b3uA to template set # found chain 1b3uA in template set T0361 18 :NLF 1b3uA 456 :AIR T0361 24 :KTAHSILLQGIRQF 1b3uA 459 :EAATSNLKKLVEKF T0361 45 :NDEEIVEYAVKPLLAQSGPLD 1b3uA 473 :GKEWAHATIIPKVLAMSGDPN T0361 67 :IDVALRLIYALGKMDKWLYADITH 1b3uA 494 :YLHRMTTLFCINVLSEVCGQDITT T0361 92 :SQYWHYLNEQDETP 1b3uA 518 :KHMLPTVLRMAGDP T0361 106 :GFADDITWDFISNVNSITRNATLYDALKA 1b3uA 533 :ANVRFNVAKSLQKIGPILDNSTLQSEVKP T0361 139 :DF 1b3uA 562 :IL T0361 146 :ARFSGMVKTALTLAVTTTLKELT 1b3uA 564 :EKLTQDQDVDVKYFAQEALTVLS Number of specific fragments extracted= 8 number of extra gaps= 0 total=149 Will force an alignment to be made, even if fragment is small Number of alignments=25 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1b3uA/T0361-1b3uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0361 read from 1b3uA/T0361-1b3uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1b3uA read from 1b3uA/T0361-1b3uA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1b3uA in template set T0361 17 :DNLF 1b3uA 455 :YAIR T0361 24 :KTAHSILLQGIRQF 1b3uA 459 :EAATSNLKKLVEKF T0361 45 :NDEEIVEYAVKPLLAQSGPLDDID 1b3uA 473 :GKEWAHATIIPKVLAMSGDPNYLH T0361 70 :ALRLIYALGKMDKWLYADITH 1b3uA 497 :RMTTLFCINVLSEVCGQDITT T0361 92 :SQYWHYLNEQDETP 1b3uA 518 :KHMLPTVLRMAGDP T0361 108 :ADDITWDFISNVNSI 1b3uA 532 :VANVRFNVAKSLQKI T0361 126 :ATL 1b3uA 547 :GPI T0361 129 :YDALKA 1b3uA 552 :NSTLQS T0361 139 :DFAVWSEARFS 1b3uA 558 :EVKPILEKLTQ T0361 153 :KTALTLAVTTTLKELT 1b3uA 571 :DVDVKYFAQEALTVLS Number of specific fragments extracted= 10 number of extra gaps= 0 total=159 Will force an alignment to be made, even if fragment is small Number of alignments=26 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1b3uA/T0361-1b3uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0361 read from 1b3uA/T0361-1b3uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1b3uA read from 1b3uA/T0361-1b3uA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1b3uA in template set T0361 22 :FMKTAHSILLQGIRQF 1b3uA 457 :IREAATSNLKKLVEKF T0361 45 :NDEEIVEYAVKPLLAQSGPLDDIDV 1b3uA 473 :GKEWAHATIIPKVLAMSGDPNYLHR T0361 71 :LRLIYALGKMDKWLYADITH 1b3uA 498 :MTTLFCINVLSEVCGQDITT T0361 93 :QYWHYLNEQD 1b3uA 519 :HMLPTVLRMA T0361 106 :GFADDITWD 1b3uA 529 :GDPVANVRF T0361 117 :SNVNSITRNATLYDA 1b3uA 538 :NVAKSLQKIGPILDN T0361 138 :ADFA 1b3uA 553 :STLQ T0361 146 :ARFSGMVKTA 1b3uA 557 :SEVKPILEKL T0361 156 :LTLAVTTTLKEL 1b3uA 574 :VKYFAQEALTVL Number of specific fragments extracted= 9 number of extra gaps= 0 total=168 Will force an alignment to be made, even if fragment is small Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w7jA/T0361-1w7jA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1w7jA expands to /projects/compbio/data/pdb/1w7j.pdb.gz 1w7jA:Skipped atom 803, because occupancy 0.500 <= existing 0.500 in 1w7jA Skipped atom 805, because occupancy 0.500 <= existing 0.500 in 1w7jA Skipped atom 1256, because occupancy 0.500 <= existing 0.500 in 1w7jA Skipped atom 1258, because occupancy 0.500 <= existing 0.500 in 1w7jA Skipped atom 1260, because occupancy 0.500 <= existing 0.500 in 1w7jA Skipped atom 1571, because occupancy 0.500 <= existing 0.500 in 1w7jA Skipped atom 1573, because occupancy 0.500 <= existing 0.500 in 1w7jA Skipped atom 2802, because occupancy 0.500 <= existing 0.500 in 1w7jA Skipped atom 2804, because occupancy 0.500 <= existing 0.500 in 1w7jA Skipped atom 2806, because occupancy 0.500 <= existing 0.500 in 1w7jA Skipped atom 2808, because occupancy 0.500 <= existing 0.500 in 1w7jA Skipped atom 3233, because occupancy 0.500 <= existing 0.500 in 1w7jA Skipped atom 3235, because occupancy 0.500 <= existing 0.500 in 1w7jA Skipped atom 3237, because occupancy 0.500 <= existing 0.500 in 1w7jA Skipped atom 3239, because occupancy 0.500 <= existing 0.500 in 1w7jA Skipped atom 4044, because occupancy 0.500 <= existing 0.500 in 1w7jA Skipped atom 4046, because occupancy 0.500 <= existing 0.500 in 1w7jA Skipped atom 4048, because occupancy 0.500 <= existing 0.500 in 1w7jA Skipped atom 4050, because occupancy 0.500 <= existing 0.500 in 1w7jA Skipped atom 4373, because occupancy 0.500 <= existing 0.500 in 1w7jA Skipped atom 4375, because occupancy 0.500 <= existing 0.500 in 1w7jA Skipped atom 4377, because occupancy 0.500 <= existing 0.500 in 1w7jA Skipped atom 4379, because occupancy 0.500 <= existing 0.500 in 1w7jA Skipped atom 4595, because occupancy 0.500 <= existing 0.500 in 1w7jA Skipped atom 4597, because occupancy 0.500 <= existing 0.500 in 1w7jA # T0361 read from 1w7jA/T0361-1w7jA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1w7jA read from 1w7jA/T0361-1w7jA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1w7jA to template set # found chain 1w7jA in template set T0361 20 :FSFMKT 1w7jA 638 :HQFRNS T0361 27 :HSILLQGIRQ 1w7jA 644 :LHLLMETLNA T0361 42 :FVDN 1w7jA 671 :FTFD T0361 50 :VEYAVKP 1w7jA 675 :EKRAVQQ T0361 74 :IYALG 1w7jA 682 :LRACG T0361 84 :LYADITH 1w7jA 687 :VLETIRI T0361 91 :FSQYWHYLN 1w7jA 704 :YQEFFSRYR T0361 100 :EQDETPGFADDITWDFISNV 1w7jA 716 :KQKDVLSDRKQTCKNVLEKL T0361 121 :SITRNA 1w7jA 749 :IFFRAG T0361 128 :LYDAL 1w7jA 755 :QVAYL T0361 134 :AMKFADFAVWSEARFSGMVKTALTLAVTTTLK 1w7jA 760 :EKIRADKLRAACIRIQKTIRGWLMRKKYMRMR Number of specific fragments extracted= 11 number of extra gaps= 0 total=179 Will force an alignment to be made, even if fragment is small Number of alignments=28 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w7jA/T0361-1w7jA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0361 read from 1w7jA/T0361-1w7jA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1w7jA read from 1w7jA/T0361-1w7jA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1w7jA in template set T0361 19 :LFSFMKTAHS 1w7jA 637 :GHQFRNSLHL T0361 30 :LLQGIRQ 1w7jA 647 :LMETLNA T0361 44 :DNDEE 1w7jA 663 :KPNDF T0361 50 :VEYAVKPLL 1w7jA 675 :EKRAVQQLR T0361 76 :ALG 1w7jA 684 :ACG T0361 84 :LYADITH 1w7jA 687 :VLETIRI T0361 91 :FSQYWHYLNEQDETPGFAD 1w7jA 704 :YQEFFSRYRVLMKQKDVLS T0361 110 :DITWDFISNV 1w7jA 726 :QTCKNVLEKL T0361 134 :AMKFADFAVWSEARFSGMVKTALTLAVTTTLK 1w7jA 760 :EKIRADKLRAACIRIQKTIRGWLMRKKYMRMR Number of specific fragments extracted= 9 number of extra gaps= 0 total=188 Will force an alignment to be made, even if fragment is small Number of alignments=29 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w7jA/T0361-1w7jA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0361 read from 1w7jA/T0361-1w7jA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1w7jA read from 1w7jA/T0361-1w7jA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1w7jA in template set T0361 7 :DDVLEQLDAQ 1w7jA 645 :HLLMETLNAT T0361 18 :N 1w7jA 674 :D T0361 23 :MKTAHSIL 1w7jA 675 :EKRAVQQL T0361 31 :LQGIRQFLP 1w7jA 688 :LETIRISAA T0361 45 :NDEEIVEY 1w7jA 703 :TYQEFFSR T0361 54 :VKPLLAQSGPLDDID 1w7jA 711 :YRVLMKQKDVLSDRK T0361 89 :THFSQYWHYLNEQDETPGFADDITWDFISNVNSITRNA 1w7jA 726 :QTCKNVLEKLILDKDKYQFGKTKIFFRAGQVAYLEKIR T0361 138 :ADFAVWSEARFSGMVKTALTLAVTTTLK 1w7jA 764 :ADKLRAACIRIQKTIRGWLMRKKYMRMR Number of specific fragments extracted= 8 number of extra gaps= 0 total=196 Will force an alignment to be made, even if fragment is small Number of alignments=30 # command:CPU_time= 13.119 sec, elapsed time= 13.951 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 30 Adding 14196 constraints to all_contacts Done adding distance constraints # command:CPU_time= 13.155 sec, elapsed time= 13.992 sec. # command:Reading probabilities from T0361.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 3.880 Optimizing... Probability sum: -306.863, CN propb: -306.863 weights: 0.288 constraints: 302 # command:CPU_time= 25.995 sec, elapsed time= 26.864 sec. # command:Found ConstraintSet # PrintContacts log_align.constraints Number of constraints in align 302 # command:Found ConstraintSet # PrintContacts log_align_bonus.constraints Number of constraints in align.bonus 302 # command:Found ConstraintSet # PrintContacts log_rejected.constraints Number of constraints in rejected 1063 # command:Found ConstraintSet # PrintContacts log_rejected_bonus.constraints Number of constraints in rejected.bonus 1063 # command:Found ConstraintSet # PrintContacts log_noncontact.constraints Number of constraints in noncontact 11515 # command:Found ConstraintSet # PrintContacts log_noncontact_bonus.constraints Number of constraints in noncontact.bonus 11515 # command:CPU_time= 26.231 sec, elapsed time= 27.283 sec. # command: