# 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/T0297/ # command:# Making conformation for sequence T0297 numbered 1 through 211 Created new target T0297 from T0297.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0297/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0297//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0297/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0297//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0297/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0297/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0297/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yzfA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1yzfA expands to /projects/compbio/data/pdb/1yzf.pdb.gz 1yzfA:# T0297 read from 1yzfA/merged-good-all-a2m # 1yzfA read from 1yzfA/merged-good-all-a2m # adding 1yzfA to template set # found chain 1yzfA in template set T0297 32 :PNILFIGDSIVEYYP 1yzfA 2 :RKIVLFGDSITAGYL # choosing archetypes in rotamer library T0297 47 :LQELFGT 1yzfA 24 :LVDLVKR T0297 54 :SKTIVNRGIRGYQTGLLLENLDAHLYGGAVDKIFLLIGTNDIGKD 1yzfA 39 :EVAVINAGMPGDTTEDGLKRLNKEVLIEKPDEVVIFFGANDASLD T0297 99 :VPVNEALNNLEAIIQSV 1yzfA 86 :ITVATFRENLETMIHEI T0297 121 :LTE 1yzfA 103 :GSE T0297 124 :IKLLSIL 1yzfA 107 :VILITPP T0297 131 :PVNEREEYQ 1yzfA 116 :DSGRRPERP T0297 147 :NEKIQNWNQAYQELASAY 1yzfA 125 :QTRIKELVKVAQEVGAAH T0297 166 :QVEFVPVFDCLTDQAGQ 1yzfA 143 :NLPVIDLYKAMTVYPGT T0297 184 :KKEYTTDGLHLSIAGYQALSKSLKDYLY 1yzfA 160 :DEFLQADGLHFSQVGYELLGALIVREIK Number of specific fragments extracted= 10 number of extra gaps= 0 total=10 Number of alignments=1 # 1yzfA read from 1yzfA/merged-good-all-a2m # found chain 1yzfA in template set T0297 32 :PNILFIGDSIVEYYPLQELFGT 1yzfA 2 :RKIVLFGDSITAGYLDEAVSPV T0297 54 :SKTIVNRGIRGYQTGLLLENLDAHLYGGAVDKIFLLIGTNDIGKD 1yzfA 39 :EVAVINAGMPGDTTEDGLKRLNKEVLIEKPDEVVIFFGANDASLD T0297 99 :VPVNEALNNLEAIIQSV 1yzfA 86 :ITVATFRENLETMIHEI T0297 121 :LTE 1yzfA 103 :GSE T0297 124 :IKLLSI 1yzfA 107 :VILITP T0297 130 :LPVNEREEY 1yzfA 115 :ADSGRRPER T0297 146 :SNEKIQNWNQAYQELASAY 1yzfA 124 :PQTRIKELVKVAQEVGAAH T0297 166 :QVEFVPVFDCLTDQAGQ 1yzfA 143 :NLPVIDLYKAMTVYPGT T0297 184 :KKEYTTDGLHLSIAGYQALSKSLKDYLY 1yzfA 160 :DEFLQADGLHFSQVGYELLGALIVREIK Number of specific fragments extracted= 9 number of extra gaps= 0 total=19 Number of alignments=2 # 1yzfA read from 1yzfA/merged-good-all-a2m # found chain 1yzfA in template set T0297 32 :PNILFIGDSIVEYYPLQELFGT 1yzfA 2 :RKIVLFGDSITAGYLDEAVSPV T0297 54 :SKTIVNRGIRGYQTGLLLENLDAHLYGGAVDKIFLLIGTNDIG 1yzfA 39 :EVAVINAGMPGDTTEDGLKRLNKEVLIEKPDEVVIFFGANDAS T0297 97 :KDVPVNEALNNLEAIIQSV 1yzfA 84 :RNITVATFRENLETMIHEI T0297 119 :YPLTEIKLLSILPVNERE 1yzfA 104 :SEKVILITPPYADSGRRP T0297 144 :IRSNEKIQNWNQAYQELASAY 1yzfA 122 :ERPQTRIKELVKVAQEVGAAH T0297 166 :QVEFVPVFDCLTDQAGQ 1yzfA 143 :NLPVIDLYKAMTVYPGT T0297 184 :KKEYTTDGLHLSIAGYQALSKSLKDYL 1yzfA 160 :DEFLQADGLHFSQVGYELLGALIVREI Number of specific fragments extracted= 7 number of extra gaps= 0 total=26 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j00A/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/T0297/1j00A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0297/1j00A/merged-good-all-a2m.gz for input Trying 1j00A/merged-good-all-a2m Error: Couldn't open file 1j00A/merged-good-all-a2m or 1j00A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1esc/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1esc expands to /projects/compbio/data/pdb/1esc.pdb.gz 1esc:Warning: there is no chain 1esc will retry with 1escA # T0297 read from 1esc/merged-good-all-a2m # 1esc read from 1esc/merged-good-all-a2m # adding 1esc to template set # found chain 1esc in template set Warning: unaligning (T0297)V30 because first residue in template chain is (1esc)D4 Warning: unaligning (T0297)G38 because of BadResidue code BAD_PEPTIDE in next template residue (1esc)D13 Warning: unaligning (T0297)D39 because of BadResidue code BAD_PEPTIDE at template residue (1esc)D13 Warning: unaligning (T0297)Q140 because of BadResidue code BAD_PEPTIDE at template residue (1esc)Q214 Warning: unaligning (T0297)A141 because of BadResidue code BAD_PEPTIDE at template residue (1esc)D215 Warning: unaligning (T0297)Q151 because of BadResidue code BAD_PEPTIDE in next template residue (1esc)R226 Warning: unaligning (T0297)N152 because of BadResidue code BAD_PEPTIDE at template residue (1esc)R226 T0297 31 :EPNILFI 1esc 5 :PVPTVFF T0297 40 :SIVEYYP 1esc 14 :SYTANFG T0297 47 :LQELFGT 1esc 45 :ATRSLAD T0297 54 :SKTIVNRG 1esc 53 :GITLDVQA T0297 62 :IRGYQTGL 1esc 64 :CGGALIHH T0297 70 :LLENL 1esc 88 :QQDAL T0297 79 :YG 1esc 93 :KQ T0297 82 :AVDKIFLLIGTNDIGKD 1esc 95 :DTQLTVGSLGGNTLGFN T0297 101 :VNEALNNLEAIIQSVARDYPLTEIKLLSILPVN 1esc 158 :FERVGAELEELLDRIGYFAPDAKRVLVGYPRLV T0297 142 :VYIRSNEKI 1esc 216 :ALPVLDQIQ T0297 153 :WNQAYQELASAY 1esc 227 :LNDAMKKAAADG T0297 166 :QVEFVPVFDCLTDQAGQ 1esc 239 :GADFVDLYAGTGANTAC T0297 183 :LKKEYT 1esc 275 :GTKIPW T0297 191 :GLHLSIAGYQALSKSLKDYL 1esc 281 :YAHPNDKGRDIQAKQVADKI Number of specific fragments extracted= 14 number of extra gaps= 3 total=40 Number of alignments=4 # 1esc read from 1esc/merged-good-all-a2m # found chain 1esc in template set Warning: unaligning (T0297)V30 because first residue in template chain is (1esc)D4 Warning: unaligning (T0297)G38 because of BadResidue code BAD_PEPTIDE in next template residue (1esc)D13 Warning: unaligning (T0297)D39 because of BadResidue code BAD_PEPTIDE at template residue (1esc)D13 Warning: unaligning (T0297)T53 because of BadResidue code BAD_PEPTIDE in next template residue (1esc)D28 Warning: unaligning (T0297)Q139 because of BadResidue code BAD_PEPTIDE in next template residue (1esc)Q214 Warning: unaligning (T0297)Q140 because of BadResidue code BAD_PEPTIDE at template residue (1esc)Q214 Warning: unaligning (T0297)A141 because of BadResidue code BAD_PEPTIDE at template residue (1esc)D215 Warning: unaligning (T0297)Q151 because of BadResidue code BAD_PEPTIDE in next template residue (1esc)R226 Warning: unaligning (T0297)N152 because of BadResidue code BAD_PEPTIDE at template residue (1esc)R226 T0297 31 :EPNILFI 1esc 5 :PVPTVFF T0297 40 :SIVEYYPLQELFG 1esc 14 :SYTANFGIAPVTN T0297 54 :SKTIVNR 1esc 53 :GITLDVQ T0297 61 :GIRGYQTGLL 1esc 63 :SCGGALIHHF T0297 75 :DAHL 1esc 89 :QDAL T0297 80 :GGAVDKIFLLIGTNDIGKD 1esc 93 :KQDTQLTVGSLGGNTLGFN T0297 99 :VPVNEALNNLEAIIQSVARDYPLTEIKLLSILPVN 1esc 156 :DQFERVGAELEELLDRIGYFAPDAKRVLVGYPRLV T0297 135 :REEY 1esc 192 :EDTT T0297 142 :VYIRSNEKI 1esc 216 :ALPVLDQIQ T0297 153 :WNQAYQELASAY 1esc 227 :LNDAMKKAAADG T0297 166 :QVEFVPVFDCLTDQAGQLKK 1esc 239 :GADFVDLYAGTGANTACDGA T0297 186 :EYT 1esc 279 :PWY T0297 192 :LHLSIAGYQALSKSLKDYL 1esc 282 :AHPNDKGRDIQAKQVADKI Number of specific fragments extracted= 13 number of extra gaps= 4 total=53 Number of alignments=5 # 1esc read from 1esc/merged-good-all-a2m # found chain 1esc in template set Warning: unaligning (T0297)V30 because first residue in template chain is (1esc)D4 Warning: unaligning (T0297)G38 because of BadResidue code BAD_PEPTIDE in next template residue (1esc)D13 Warning: unaligning (T0297)D39 because of BadResidue code BAD_PEPTIDE at template residue (1esc)D13 Warning: unaligning (T0297)Q151 because of BadResidue code BAD_PEPTIDE in next template residue (1esc)R226 Warning: unaligning (T0297)N152 because of BadResidue code BAD_PEPTIDE at template residue (1esc)R226 T0297 31 :EPNILFI 1esc 5 :PVPTVFF T0297 40 :SIVEYYP 1esc 14 :SYTANFG T0297 49 :ELFGT 1esc 29 :SERGW T0297 54 :SKTIVNRG 1esc 53 :GITLDVQA T0297 62 :IRGYQT 1esc 64 :CGGALI T0297 75 :DAHLYG 1esc 89 :QDALKQ T0297 82 :AVDKIFLLIGTNDIG 1esc 95 :DTQLTVGSLGGNTLG T0297 102 :NEALNNLEAIIQSVARDYPLTEIKLLSILPVNEREE 1esc 159 :ERVGAELEELLDRIGYFAPDAKRVLVGYPRLVPEDT T0297 143 :YIRSNEKI 1esc 217 :LPVLDQIQ T0297 153 :WNQAYQELASAY 1esc 227 :LNDAMKKAAADG T0297 166 :QVEFVPVFDCLTDQAGQ 1esc 239 :GADFVDLYAGTGANTAC T0297 183 :LKKEYTTDGLHLSIAGYQALSKSLKDYL 1esc 273 :LLGTKIPWYAHPNDKGRDIQAKQVADKI Number of specific fragments extracted= 12 number of extra gaps= 2 total=65 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vbuA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vbuA expands to /projects/compbio/data/pdb/1vbu.pdb.gz 1vbuA:# T0297 read from 1vbuA/merged-good-all-a2m # 1vbuA read from 1vbuA/merged-good-all-a2m # adding 1vbuA to template set # found chain 1vbuA in template set Warning: unaligning (T0297)D39 because of BadResidue code BAD_PEPTIDE in next template residue (1vbuA)T599 Warning: unaligning (T0297)S40 because of BadResidue code BAD_PEPTIDE at template residue (1vbuA)T599 T0297 35 :LFIG 1vbuA 594 :IVHG T0297 41 :IVEYYP 1vbuA 600 :LVWHNQ T0297 47 :LQELFGT 1vbuA 660 :WYKTIGP T0297 54 :SKTIVNRG 1vbuA 682 :DAILIYND T0297 62 :IRGYQTGLLLENLDAHLYGG 1vbuA 694 :EINAKSNFVYNMIKELKEKG T0297 82 :AVDKIFLLIGTN 1vbuA 715 :PVDGIGFQMHID T0297 96 :GKDVPVNEALNN 1vbuA 727 :YRGLNYDSFRRN T0297 112 :IQSVARD 1vbuA 739 :LERFAKL T0297 121 :LTEIKLLSI 1vbuA 746 :GLQIYITEM T0297 130 :LPVNERE 1vbuA 758 :IPLSGSE T0297 147 :NEKIQNWNQAYQELAS 1vbuA 765 :EYYLKKQAEVCAKIFD T0297 163 :AYMQVEFVPVFD 1vbuA 784 :DNPAVKAIQFWG T0297 176 :LTDQAGQ 1vbuA 796 :FTDKYSW T0297 183 :LKKEYTTDGLHLSI 1vbuA 811 :GKALLFDENYNPKP T0297 198 :GYQALSKSLKDYL 1vbuA 825 :CYYAIKEVLEKKI Number of specific fragments extracted= 15 number of extra gaps= 1 total=80 Number of alignments=7 # 1vbuA read from 1vbuA/merged-good-all-a2m # found chain 1vbuA in template set T0297 31 :EPNILFI 1vbuA 527 :NIYIGFA T0297 43 :EYYPLQELFGT 1vbuA 534 :AINNFWSLSDA T0297 54 :SKTIV 1vbuA 682 :DAILI T0297 71 :LENLDAHLYGGAV 1vbuA 703 :YNMIKELKEKGVP T0297 84 :DKIFLLIGTN 1vbuA 717 :DGIGFQMHID T0297 96 :GKDVPVNEALN 1vbuA 727 :YRGLNYDSFRR T0297 111 :IIQSVARD 1vbuA 738 :NLERFAKL T0297 121 :LTEIKLLSI 1vbuA 746 :GLQIYITEM T0297 130 :LPVNEREEY 1vbuA 758 :IPLSGSEEY T0297 149 :KIQNWNQAYQELAS 1vbuA 767 :YLKKQAEVCAKIFD T0297 163 :AYMQVEFVPVFDCLTDQAGQLKK 1vbuA 784 :DNPAVKAIQFWGFTDKYSWVPGF T0297 186 :EYTTDGLHLSI 1vbuA 814 :LLFDENYNPKP T0297 198 :GYQALSKSLKDYL 1vbuA 825 :CYYAIKEVLEKKI Number of specific fragments extracted= 13 number of extra gaps= 0 total=93 Number of alignments=8 # 1vbuA read from 1vbuA/merged-good-all-a2m # found chain 1vbuA in template set Warning: unaligning (T0297)D39 because of BadResidue code BAD_PEPTIDE in next template residue (1vbuA)T599 Warning: unaligning (T0297)S40 because of BadResidue code BAD_PEPTIDE at template residue (1vbuA)T599 T0297 36 :FIG 1vbuA 595 :VHG T0297 41 :IVEYYPLQELFGT 1vbuA 600 :LVWHNQLPGWITG T0297 54 :SKTIVNRGIRGYQT 1vbuA 682 :DAILIYNDYSIEEI T0297 68 :GLLLENLDAHLYG 1vbuA 700 :NFVYNMIKELKEK T0297 81 :GAVDKIFLLIGTN 1vbuA 714 :VPVDGIGFQMHID T0297 96 :GKDVPVNEALNNLEAI 1vbuA 727 :YRGLNYDSFRRNLERF T0297 116 :ARD 1vbuA 743 :AKL T0297 121 :LTEIKL 1vbuA 746 :GLQIYI T0297 127 :LSILPVNERE 1vbuA 755 :DVRIPLSGSE T0297 147 :NEKIQNWNQAYQELAS 1vbuA 765 :EYYLKKQAEVCAKIFD T0297 163 :AYMQVEFVPVFDC 1vbuA 784 :DNPAVKAIQFWGF T0297 183 :LKKEYTTDGLHLS 1vbuA 811 :GKALLFDENYNPK T0297 197 :AGYQALSKSLKDYL 1vbuA 824 :PCYYAIKEVLEKKI Number of specific fragments extracted= 13 number of extra gaps= 1 total=106 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1udc/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1udc expands to /projects/compbio/data/pdb/1udc.pdb.gz 1udc:Warning: there is no chain 1udc will retry with 1udcA # T0297 read from 1udc/merged-good-all-a2m # 1udc read from 1udc/merged-good-all-a2m # adding 1udc to template set # found chain 1udc in template set Warning: unaligning (T0297)P32 because first residue in template chain is (1udc)M1 T0297 33 :NILFIGDSIV 1udc 2 :RVLVTGGSGY T0297 47 :LQELFGTSKTIVNRGIRGYQTGLLLENLDAHLYGG 1udc 17 :CVQLLQNGHDVIILDNLCNSKRSVLPVIERLGGKH T0297 82 :AVDKIFLLIGTN 1udc 73 :AIDTVIHFAGLK T0297 98 :D 1udc 85 :A T0297 99 :VPVNEALNNL 1udc 91 :QKPLEYYDNN T0297 109 :EAIIQSVARD 1udc 105 :LRLISAMRAA T0297 121 :LTE 1udc 115 :NVK T0297 124 :IKLLSILPVN 1udc 119 :FIFSSSATVY T0297 134 :EREEYQQAVYIRS 1udc 141 :PTGTPQSPYGKSK T0297 151 :QNWNQAYQELASAYMQVEFV 1udc 154 :LMVEQILTDLQKAQPDWSIA T0297 171 :PVFDCLTDQAGQ 1udc 176 :RYFNPVGAHPSG T0297 183 :LKKEYTTDG 1udc 219 :GNDYPTEDG T0297 192 :LHLS 1udc 234 :IHVM T0297 196 :IAGYQALSKSLK 1udc 240 :ADGHVVAMEKLA Number of specific fragments extracted= 14 number of extra gaps= 0 total=120 Number of alignments=10 # 1udc read from 1udc/merged-good-all-a2m # found chain 1udc in template set Warning: unaligning (T0297)P32 because first residue in template chain is (1udc)M1 T0297 33 :NILFIGDS 1udc 2 :RVLVTGGS T0297 53 :T 1udc 10 :G T0297 54 :SKTIVNR 1udc 24 :GHDVIIL T0297 61 :GIRGYQTGLL 1udc 34 :CNSKRSVLPV T0297 71 :LENLDAHLYGGAVDKIFLLIGTN 1udc 62 :EALMTEILHDHAIDTVIHFAGLK T0297 98 :D 1udc 85 :A T0297 99 :VPVNEALNNL 1udc 91 :QKPLEYYDNN T0297 109 :EAIIQSVARD 1udc 105 :LRLISAMRAA T0297 121 :LTE 1udc 115 :NVK T0297 124 :IKLLSILPVN 1udc 119 :FIFSSSATVY T0297 139 :QQA 1udc 146 :QSP T0297 146 :SNEKIQNWNQAYQELASAYMQVEFV 1udc 149 :YGKSKLMVEQILTDLQKAQPDWSIA T0297 171 :PVF 1udc 179 :NPV T0297 176 :LTDQAGQLK 1udc 186 :SGDMGEDPQ T0297 186 :EYTTDG 1udc 222 :YPTEDG T0297 192 :LHLS 1udc 234 :IHVM T0297 196 :IAGYQALSKSLK 1udc 240 :ADGHVVAMEKLA Number of specific fragments extracted= 17 number of extra gaps= 0 total=137 Number of alignments=11 # 1udc read from 1udc/merged-good-all-a2m # found chain 1udc in template set Warning: unaligning (T0297)P32 because first residue in template chain is (1udc)M1 T0297 33 :NILFIGDS 1udc 2 :RVLVTGGS T0297 53 :T 1udc 10 :G T0297 54 :SKTIVNRGIRGYQTGLLLENLDAHLYG 1udc 24 :GHDVIILDNLCNSKRSVLPVIERLGGK T0297 81 :GAVDKIFLLIGTNDIG 1udc 72 :HAIDTVIHFAGLKAVG T0297 101 :VNEALNNLEAIIQSVARDYPLTEIKLLSILPVNEREE 1udc 97 :YDNNVNGTLRLISAMRAANVKNFIFSSSATVYGDQPK T0297 143 :YIRSNEKIQNWNQAYQELASAYMQVEFVPV 1udc 146 :QSPYGKSKLMVEQILTDLQKAQPDWSIALL Number of specific fragments extracted= 6 number of extra gaps= 0 total=143 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ivnA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ivnA expands to /projects/compbio/data/pdb/1ivn.pdb.gz 1ivnA:# T0297 read from 1ivnA/merged-good-all-a2m # 1ivnA read from 1ivnA/merged-good-all-a2m # adding 1ivnA to template set # found chain 1ivnA in template set T0297 32 :PNILFIGDSIVEYYP 1ivnA 2 :DTLLILGDSLSAGYR T0297 47 :LQELFGT 1ivnA 23 :WPALLND T0297 54 :SKTIVNRGIRGYQTGLLLENLDAHLYGGAVDKIFLLIGTNDIGKDVPVNEALNNLEAIIQSVARD 1ivnA 34 :KTSVVNASISGDTSQQGLARLPALLKQHQPRWVLVELGGNDGLRGFQPQQTEQTLRQILQDVKAA T0297 121 :LTEIKLLSI 1ivnA 99 :NAEPLLMQI T0297 130 :LPVNEREEYQ 1ivnA 109 :LPANYGRRYN T0297 151 :QNWNQAYQELASAY 1ivnA 119 :EAFSAIYPKLAKEF T0297 166 :QVEFVPV 1ivnA 133 :DVPLLPF T0297 176 :LTDQAGQLKKEYTTDGLHLSIAGYQALSKSLKDYL 1ivnA 140 :FMEEVYLKPQWMQDDGIHPNRDAQPFIADWMAKQL Number of specific fragments extracted= 8 number of extra gaps= 0 total=151 Number of alignments=13 # 1ivnA read from 1ivnA/merged-good-all-a2m # found chain 1ivnA in template set Warning: unaligning (T0297)E31 because first residue in template chain is (1ivnA)A1 T0297 32 :PNILFIGDSIVEYYPLQELFGT 1ivnA 2 :DTLLILGDSLSAGYRMSASAAW T0297 54 :SKTIVNRGIRGYQTGLLLENLDAHLYGGAVDKIFLLIGTNDIGKDVPVNEALNNLEAIIQSVARD 1ivnA 34 :KTSVVNASISGDTSQQGLARLPALLKQHQPRWVLVELGGNDGLRGFQPQQTEQTLRQILQDVKAA T0297 121 :LTEIKLLSI 1ivnA 99 :NAEPLLMQI T0297 130 :LPVNEREEYQ 1ivnA 109 :LPANYGRRYN T0297 151 :QNWNQAYQELASAY 1ivnA 119 :EAFSAIYPKLAKEF T0297 166 :QVEFVPV 1ivnA 133 :DVPLLPF T0297 176 :LTDQAGQLKKEYTTDGLHLSIAGYQALSKSLKDYL 1ivnA 140 :FMEEVYLKPQWMQDDGIHPNRDAQPFIADWMAKQL Number of specific fragments extracted= 7 number of extra gaps= 0 total=158 Number of alignments=14 # 1ivnA read from 1ivnA/merged-good-all-a2m # found chain 1ivnA in template set Warning: unaligning (T0297)E31 because first residue in template chain is (1ivnA)A1 T0297 32 :PNILFIGDSIVEYYPLQELFGT 1ivnA 2 :DTLLILGDSLSAGYRMSASAAW T0297 54 :SKTIVNRGIRGYQTGLLLENLDAHLYGGAVDKIFLLIGTNDIGKDVPVNEALNNLEAIIQSVARDYPLTEIKLLSILPVNER 1ivnA 34 :KTSVVNASISGDTSQQGLARLPALLKQHQPRWVLVELGGNDGLRGFQPQQTEQTLRQILQDVKAANAEPLLMQIRLPANYGR T0297 148 :EKIQNWNQAYQELASAY 1ivnA 116 :RYNEAFSAIYPKLAKEF T0297 166 :QVEFV 1ivnA 133 :DVPLL T0297 174 :DCLTDQAGQLKKEYTTDGLHLSIAGYQALSKSLKDYL 1ivnA 138 :PFFMEEVYLKPQWMQDDGIHPNRDAQPFIADWMAKQL Number of specific fragments extracted= 5 number of extra gaps= 0 total=163 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fxwF/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/T0297/1fxwF/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0297/1fxwF/merged-good-all-a2m.gz for input Trying 1fxwF/merged-good-all-a2m Error: Couldn't open file 1fxwF/merged-good-all-a2m or 1fxwF/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bwp/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/T0297/1bwp/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0297/1bwp/merged-good-all-a2m.gz for input Trying 1bwp/merged-good-all-a2m Error: Couldn't open file 1bwp/merged-good-all-a2m or 1bwp/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bwq/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/T0297/1bwq/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0297/1bwq/merged-good-all-a2m.gz for input Trying 1bwq/merged-good-all-a2m Error: Couldn't open file 1bwq/merged-good-all-a2m or 1bwq/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bwr/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/T0297/1bwr/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0297/1bwr/merged-good-all-a2m.gz for input Trying 1bwr/merged-good-all-a2m Error: Couldn't open file 1bwr/merged-good-all-a2m or 1bwr/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1es9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0297 read from 1es9A/merged-good-all-a2m # 1es9A read from 1es9A/merged-good-all-a2m # found chain 1es9A in training set Warning: unaligning (T0297)P46 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1es9A)Q54 Warning: unaligning (T0297)L47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1es9A)W58 Warning: unaligning (T0297)E49 because of BadResidue code BAD_PEPTIDE in next template residue (1es9A)L61 Warning: unaligning (T0297)L50 because of BadResidue code BAD_PEPTIDE at template residue (1es9A)L61 Warning: unaligning (T0297)F51 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1es9A)F62 Warning: unaligning (T0297)A76 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1es9A)G87 Warning: unaligning (T0297)D178 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1es9A)S181 Warning: unaligning (T0297)Q179 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1es9A)S181 T0297 6 :LENWLLKEQEKIQTK 1es9A 6 :NPASKPTPVQDVQGD T0297 31 :EPNILFIGDSIVEYY 1es9A 38 :EPEVVFIGDSLVQLM T0297 48 :Q 1es9A 59 :R T0297 52 :G 1es9A 63 :S T0297 54 :SKTIVNRGIRGYQTGLLLENLD 1es9A 64 :PLHALNFGIGGDSTQHVLWRLE T0297 77 :HLYGGAVDKIFLLIGTND 1es9A 88 :ELEHIRPKIVVVWVGTNN T0297 97 :KDVPVNEALNNLEAIIQSVARDYPLTEIKLLSILPVNEREEYQ 1es9A 106 :HGHTAEQVTGGIKAIVQLVNERQPQARVVVLGLLPRGQHPNPL T0297 147 :NEKIQNWNQAYQELASAYMQVEFVPVFDCLT 1es9A 149 :REKNRRVNELVRAALAGHPRAHFLDADPGFV T0297 180 :AGQLKKEYTTDGLHLSIAGYQALSKSLKDYLY 1es9A 182 :DGTISHHDMYDYLHLSRLGYTPVCRALHSLLL Number of specific fragments extracted= 9 number of extra gaps= 5 total=172 Number of alignments=16 # 1es9A read from 1es9A/merged-good-all-a2m # found chain 1es9A in training set Warning: unaligning (T0297)P46 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1es9A)W58 Warning: unaligning (T0297)L47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1es9A)W58 Warning: unaligning (T0297)E49 because of BadResidue code BAD_PEPTIDE in next template residue (1es9A)L61 Warning: unaligning (T0297)L50 because of BadResidue code BAD_PEPTIDE at template residue (1es9A)L61 Warning: unaligning (T0297)F51 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1es9A)F62 Warning: unaligning (T0297)A76 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1es9A)G87 Warning: unaligning (T0297)D178 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1es9A)S181 Warning: unaligning (T0297)Q179 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1es9A)S181 T0297 6 :LENWLLKEQEKIQTKYRHLNHISVVEPNILFIGDSIVEYY 1es9A 13 :PVQDVQGDGKWMSLHHRFVADSKDKEPEVVFIGDSLVQLM T0297 48 :Q 1es9A 59 :R T0297 52 :G 1es9A 63 :S T0297 54 :SKTIVNRGIRGYQTGLLLENLD 1es9A 64 :PLHALNFGIGGDSTQHVLWRLE T0297 77 :HLYGGAVDKIFLLIGTND 1es9A 88 :ELEHIRPKIVVVWVGTNN T0297 97 :KDVPVNEALNNLEAIIQSVARDYPLTEIKLLSILPVNEREEY 1es9A 106 :HGHTAEQVTGGIKAIVQLVNERQPQARVVVLGLLPRGQHPNP T0297 146 :SNEKIQNWNQAYQELASAYMQVEFVPVFDCLT 1es9A 148 :LREKNRRVNELVRAALAGHPRAHFLDADPGFV T0297 180 :AGQLKKEYTTDGLHLSIAGYQALSKSLKDYLY 1es9A 182 :DGTISHHDMYDYLHLSRLGYTPVCRALHSLLL Number of specific fragments extracted= 8 number of extra gaps= 4 total=180 Number of alignments=17 # 1es9A read from 1es9A/merged-good-all-a2m # found chain 1es9A in training set Warning: unaligning (T0297)P46 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1es9A)Q54 Warning: unaligning (T0297)L47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1es9A)W58 Warning: unaligning (T0297)Q48 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1es9A)W58 Warning: unaligning (T0297)L50 because of BadResidue code BAD_PEPTIDE in next template residue (1es9A)L61 Warning: unaligning (T0297)F51 because of BadResidue code BAD_PEPTIDE at template residue (1es9A)L61 Warning: unaligning (T0297)G52 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1es9A)F62 Warning: unaligning (T0297)D75 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1es9A)G87 Warning: unaligning (T0297)A76 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1es9A)G87 Warning: unaligning (T0297)D178 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1es9A)S181 Warning: unaligning (T0297)Q179 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1es9A)S181 T0297 3 :VQLLENWLLKEQEKIQTKYRHLNHISVVEPNILFIGDSIVEYY 1es9A 10 :KPTPVQDVQGDGKWMSLHHRFVADSKDKEPEVVFIGDSLVQLM T0297 49 :E 1es9A 59 :R T0297 53 :TSKTIVNRGIRGYQTGLLLENL 1es9A 63 :SPLHALNFGIGGDSTQHVLWRL T0297 77 :HLYGGAVDKIFLLIGTNDI 1es9A 88 :ELEHIRPKIVVVWVGTNNH T0297 98 :DVPVNEALNNLEAIIQSVARDYPLTEIKLLSILPVNER 1es9A 107 :GHTAEQVTGGIKAIVQLVNERQPQARVVVLGLLPRGQH T0297 143 :YIRSNEKIQNWNQAYQELASAYMQVEFVPVFDCLT 1es9A 145 :PNPLREKNRRVNELVRAALAGHPRAHFLDADPGFV T0297 180 :AGQLKKEYTTDGLHLSIAGYQALSKSLKDYL 1es9A 182 :DGTISHHDMYDYLHLSRLGYTPVCRALHSLL Number of specific fragments extracted= 7 number of extra gaps= 5 total=187 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1deoA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1deoA expands to /projects/compbio/data/pdb/1deo.pdb.gz 1deoA:# T0297 read from 1deoA/merged-good-all-a2m # 1deoA read from 1deoA/merged-good-all-a2m # adding 1deoA to template set # found chain 1deoA in template set Warning: unaligning (T0297)P32 because first residue in template chain is (1deoA)T1 T0297 33 :NILFIGDSIVEYYP 1deoA 2 :TVYLAGDSTMAKNG T0297 47 :LQELFGT 1deoA 23 :WGEYLAS T0297 54 :SKTIVNRGIRGYQTGLLLE 1deoA 32 :SATVVNDAVAGRSARSYTR T0297 73 :NLDAHLYGGA 1deoA 53 :RFENIADVVT T0297 83 :VDKIFLLIGTNDIGKD 1deoA 64 :GDYVIVEFGHNDGGSL T0297 99 :VPVNEA 1deoA 108 :LTFPAY T0297 108 :LEAIIQSVARD 1deoA 114 :LENAAKLFTAK T0297 121 :LTEIKLLSILPV 1deoA 125 :GAKVILSSQTPN T0297 135 :REEYQQAVYIRS 1deoA 137 :NPWETGTFVNSP T0297 151 :QNWNQAYQELASAY 1deoA 149 :TRFVEYAELAAEVA T0297 166 :QVEFVPVFDCLTDQAGQ 1deoA 163 :GVEYVDHWSYVDSIYET T0297 183 :LKKEYTTDGLHLSIAGYQALSKSLKDYL 1deoA 185 :VNSYFPIDHTHTSPAGAEVVAEAFLKAV Number of specific fragments extracted= 12 number of extra gaps= 0 total=199 Number of alignments=19 # 1deoA read from 1deoA/merged-good-all-a2m # found chain 1deoA in template set Warning: unaligning (T0297)P32 because first residue in template chain is (1deoA)T1 T0297 33 :NILFIGDSIVE 1deoA 2 :TVYLAGDSTMA T0297 44 :YYPLQELFGT 1deoA 20 :TNGWGEYLAS T0297 54 :SKTIVNRGIRGYQTGLL 1deoA 32 :SATVVNDAVAGRSARSY T0297 71 :LENLDAHLYGGAV 1deoA 51 :EGRFENIADVVTA T0297 84 :DKIFLLIGTNDIGKD 1deoA 65 :DYVIVEFGHNDGGSL T0297 99 :VPVNEA 1deoA 108 :LTFPAY T0297 108 :LEAIIQSVARD 1deoA 114 :LENAAKLFTAK T0297 121 :LTEIKLLSILPVNEREEY 1deoA 125 :GAKVILSSQTPNNPWETG T0297 139 :Q 1deoA 148 :P T0297 151 :QNWNQAYQELASAY 1deoA 149 :TRFVEYAELAAEVA T0297 166 :QVEFVPVFDCLTDQAGQLKK 1deoA 163 :GVEYVDHWSYVDSIYETLGN T0297 186 :EYTTDGLHLSIAGYQALSKSLKDYL 1deoA 188 :YFPIDHTHTSPAGAEVVAEAFLKAV Number of specific fragments extracted= 12 number of extra gaps= 0 total=211 Number of alignments=20 # 1deoA read from 1deoA/merged-good-all-a2m # found chain 1deoA in template set Warning: unaligning (T0297)P32 because first residue in template chain is (1deoA)T1 T0297 33 :NILFIGDSIVE 1deoA 2 :TVYLAGDSTMA T0297 44 :YYPLQELFGT 1deoA 19 :GTNGWGEYLA T0297 54 :SKTIVNRGIRGYQT 1deoA 32 :SATVVNDAVAGRSA T0297 68 :GLLLENLDAHLYGG 1deoA 51 :EGRFENIADVVTAG T0297 84 :DKIFLLIGTNDIG 1deoA 65 :DYVIVEFGHNDGG T0297 103 :EALNNLEAIIQSVARD 1deoA 109 :TFPAYLENAAKLFTAK T0297 121 :LTEIKLLSILPVNERE 1deoA 125 :GAKVILSSQTPNNPWE T0297 139 :QQAVYIRSN 1deoA 141 :TGTFVNSPT T0297 152 :NWNQAYQELASAY 1deoA 150 :RFVEYAELAAEVA T0297 166 :QVEFVPVFDCLTDQAGQ 1deoA 163 :GVEYVDHWSYVDSIYET T0297 183 :LKKEYTTDGLHLSIAGYQALSKSLK 1deoA 185 :VNSYFPIDHTHTSPAGAEVVAEAFL Number of specific fragments extracted= 11 number of extra gaps= 0 total=222 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2apjA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2apjA expands to /projects/compbio/data/pdb/2apj.pdb.gz 2apjA:Bad short name: CI2 for alphabet: pdb_atoms Bad short name: CJ for alphabet: pdb_atoms Bad short name: CI1 for alphabet: pdb_atoms Bad short name: CH1 for alphabet: pdb_atoms Skipped atom 275, because occupancy 0.35 <= existing 0.650 in 2apjA Skipped atom 277, because occupancy 0.350 <= existing 0.650 in 2apjA Skipped atom 279, because occupancy 0.350 <= existing 0.650 in 2apjA Skipped atom 547, because occupancy 0.350 <= existing 0.650 in 2apjA Skipped atom 549, because occupancy 0.350 <= existing 0.650 in 2apjA Skipped atom 551, because occupancy 0.350 <= existing 0.650 in 2apjA Skipped atom 734, because occupancy 0.350 <= existing 0.650 in 2apjA Skipped atom 736, because occupancy 0.350 <= existing 0.650 in 2apjA Skipped atom 738, because occupancy 0.350 <= existing 0.650 in 2apjA Skipped atom 1623, because occupancy 0.350 <= existing 0.650 in 2apjA Skipped atom 1625, because occupancy 0.350 <= existing 0.650 in 2apjA Skipped atom 1627, because occupancy 0.350 <= existing 0.650 in 2apjA Skipped atom 1825, because occupancy 0.350 <= existing 0.650 in 2apjA Skipped atom 1827, because occupancy 0.350 <= existing 0.650 in 2apjA # T0297 read from 2apjA/merged-good-all-a2m # 2apjA read from 2apjA/merged-good-all-a2m # adding 2apjA to template set # found chain 2apjA in template set Warning: unaligning (T0297)S28 because first residue in template chain is (2apjA)S17 Warning: unaligning (T0297)D39 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2apjA)N32 Warning: unaligning (T0297)I41 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2apjA)N32 Warning: unaligning (T0297)V42 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2apjA)M33 T0297 29 :VVEPN 2apjA 18 :PIPPN T0297 34 :ILFIG 2apjA 25 :FILSG T0297 43 :EYYP 2apjA 34 :AGRG T0297 47 :LQELFGT 2apjA 102 :VKNRLET T0297 54 :SK 2apjA 110 :SA T0297 56 :TIVNRGIRGYQTGL 2apjA 114 :GLVPCASGGTAIKE T0297 70 :LLENLDAHLYGG 2apjA 138 :MVKRTEESRKCG T0297 82 :AVDKIFLLIGTNDIGKDVPVNEALNNLEAIIQSVARD 2apjA 151 :EIKAVLWYQGESDVLDIHDAESYGNNMDRLIKNLRHD T0297 119 :YPLTEIKLLSILP 2apjA 190 :LPSLPIIQVAIAS T0297 135 :REEYQ 2apjA 203 :GGGYI T0297 151 :QNWNQAYQE 2apjA 208 :DKVREAQLG T0297 164 :YM 2apjA 217 :LK T0297 166 :QVEFVPVFDC 2apjA 221 :NVVCVDAKGL T0297 187 :YTTDGLHLSIAGYQALSKSLKDY 2apjA 232 :LKSDNLHLTTEAQVQLGLSLAQA Number of specific fragments extracted= 14 number of extra gaps= 0 total=236 Number of alignments=22 # 2apjA read from 2apjA/merged-good-all-a2m # found chain 2apjA in template set Warning: unaligning (T0297)S28 because first residue in template chain is (2apjA)S17 Warning: unaligning (T0297)D39 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2apjA)N32 Warning: unaligning (T0297)I41 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2apjA)N32 Warning: unaligning (T0297)V42 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2apjA)M33 T0297 29 :VVEP 2apjA 18 :PIPP T0297 33 :NIL 2apjA 23 :QIF T0297 36 :FIG 2apjA 27 :LSG T0297 43 :EYYP 2apjA 34 :AGRG T0297 47 :LQELFG 2apjA 42 :DHHNNR T0297 54 :SK 2apjA 111 :AV T0297 56 :TIVNRGIRGYQTGLL 2apjA 114 :GLVPCASGGTAIKEW T0297 71 :LENLDAHLY 2apjA 139 :VKRTEESRK T0297 80 :GGAVDKIFLLIGTNDIGKDVPVNEALNNLEAIIQSVARD 2apjA 149 :GGEIKAVLWYQGESDVLDIHDAESYGNNMDRLIKNLRHD T0297 119 :YPLTEIKLLSILP 2apjA 190 :LPSLPIIQVAIAS T0297 135 :REEY 2apjA 203 :GGGY T0297 154 :NQAYQELASAYM 2apjA 207 :IDKVREAQLGLK T0297 166 :QVEFVPVFDC 2apjA 221 :NVVCVDAKGL T0297 186 :EYTTDGLHLSIAGYQALSKSLKDYL 2apjA 231 :PLKSDNLHLTTEAQVQLGLSLAQAY Number of specific fragments extracted= 14 number of extra gaps= 0 total=250 Number of alignments=23 # 2apjA read from 2apjA/merged-good-all-a2m # found chain 2apjA in template set Warning: unaligning (T0297)S28 because first residue in template chain is (2apjA)S17 Warning: unaligning (T0297)D39 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2apjA)N32 Warning: unaligning (T0297)I41 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2apjA)N32 Warning: unaligning (T0297)V42 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2apjA)M33 T0297 29 :VVEPNILFI 2apjA 18 :PIPPNQIFI T0297 38 :G 2apjA 29 :G T0297 43 :EYYP 2apjA 34 :AGRG T0297 54 :SKTIVNRGIRGYQT 2apjA 111 :AVIGLVPCASGGTA T0297 68 :GLLLENLDAHLYG 2apjA 136 :ERMVKRTEESRKC T0297 81 :GAVDKIFLLIGTNDIGKDVPVNEALNNLEAIIQSVAR 2apjA 150 :GEIKAVLWYQGESDVLDIHDAESYGNNMDRLIKNLRH T0297 118 :DYPLTEIKLLSILPVNER 2apjA 189 :NLPSLPIIQVAIASGGGY T0297 150 :IQNWNQAYQE 2apjA 207 :IDKVREAQLG T0297 164 :YMQVEFVPVFDCLTD 2apjA 219 :LSNVVCVDAKGLPLK T0297 189 :TDGLHLSIAGYQALSKSLKDY 2apjA 234 :SDNLHLTTEAQVQLGLSLAQA Number of specific fragments extracted= 10 number of extra gaps= 0 total=260 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1k7cA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0297 read from 1k7cA/merged-good-all-a2m # 1k7cA read from 1k7cA/merged-good-all-a2m # found chain 1k7cA in training set Warning: unaligning (T0297)P32 because first residue in template chain is (1k7cA)T1 Warning: unaligning (T0297)P131 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1k7cA)N136 Warning: unaligning (T0297)V132 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1k7cA)N136 T0297 33 :NILFIGDSIVEYYP 1k7cA 2 :TVYLAGDSTMAKNG T0297 47 :LQELFGT 1k7cA 23 :WGEYLAS T0297 54 :SKTIVNRGIRGYQTGLLLE 1k7cA 32 :SATVVNDAVAGRSARSYTR T0297 73 :NLDAHLYGGA 1k7cA 53 :RFENIADVVT T0297 83 :VDKIFLLIGTNDIGKD 1k7cA 64 :GDYVIVEFGHNDGGSL T0297 104 :ALNNLEAIIQSVARD 1k7cA 110 :FPAYLENAAKLFTAK T0297 121 :LTEIKLLSIL 1k7cA 125 :GAKVILSSQT T0297 135 :REEYQQAVYIRS 1k7cA 137 :NPWETGTFVNSP T0297 151 :QNWNQAYQELASAY 1k7cA 149 :TRFVEYAELAAEVA T0297 166 :QVEFVPVFDCLTDQAGQ 1k7cA 163 :GVEYVDHWSYVDSIYET T0297 183 :LKKEYTTDGLHLSIAGYQALSKSLKDYL 1k7cA 185 :VNSYFPIDHTHTSPAGAEVVAEAFLKAV Number of specific fragments extracted= 11 number of extra gaps= 1 total=271 Number of alignments=25 # 1k7cA read from 1k7cA/merged-good-all-a2m # found chain 1k7cA in training set Warning: unaligning (T0297)P32 because first residue in template chain is (1k7cA)T1 Warning: unaligning (T0297)P131 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1k7cA)N136 Warning: unaligning (T0297)V132 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1k7cA)N136 T0297 33 :NILFIGDSIVE 1k7cA 2 :TVYLAGDSTMA T0297 44 :YYPLQELFGT 1k7cA 20 :TNGWGEYLAS T0297 54 :SKTIVNRGIRGYQTGLL 1k7cA 32 :SATVVNDAVAGRSARSY T0297 71 :LENLDAHLYGGAV 1k7cA 51 :EGRFENIADVVTA T0297 84 :DKIFLLIGTNDIGKD 1k7cA 65 :DYVIVEFGHNDGGSL T0297 99 :VPVNEA 1k7cA 108 :LTFPAY T0297 108 :LEAIIQSVARD 1k7cA 114 :LENAAKLFTAK T0297 121 :LTEIKLLSIL 1k7cA 125 :GAKVILSSQT T0297 133 :NEREEY 1k7cA 137 :NPWETG T0297 139 :Q 1k7cA 148 :P T0297 151 :QNWNQAYQELASAY 1k7cA 149 :TRFVEYAELAAEVA T0297 166 :QVEFVPVFDCLTDQAGQLKK 1k7cA 163 :GVEYVDHWSYVDSIYETLGN T0297 186 :EYTTDGLHLSIAGYQALSKSLKDYL 1k7cA 188 :YFPIDHTHTSPAGAEVVAEAFLKAV Number of specific fragments extracted= 13 number of extra gaps= 1 total=284 Number of alignments=26 # 1k7cA read from 1k7cA/merged-good-all-a2m # found chain 1k7cA in training set Warning: unaligning (T0297)P32 because first residue in template chain is (1k7cA)T1 Warning: unaligning (T0297)P131 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1k7cA)N136 Warning: unaligning (T0297)V132 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1k7cA)N136 T0297 33 :NILFIGDSIVEYYPLQELFGT 1k7cA 2 :TVYLAGDSTMAKNGGGSGTNG T0297 54 :SKTIVNRGIRGYQT 1k7cA 32 :SATVVNDAVAGRSA T0297 68 :GLLLENLDAHLYGG 1k7cA 51 :EGRFENIADVVTAG T0297 84 :DKIFLLIGTNDIG 1k7cA 65 :DYVIVEFGHNDGG T0297 103 :EALNNLEAIIQSVARD 1k7cA 109 :TFPAYLENAAKLFTAK T0297 121 :LTEIKLLSIL 1k7cA 125 :GAKVILSSQT T0297 133 :NER 1k7cA 137 :NPW T0297 139 :QQAVYIRSNEKIQNWNQAYQELA 1k7cA 140 :ETGTFVNSPTRFVEYAELAAEVA T0297 166 :QVEFVPVFDCLTDQAGQ 1k7cA 163 :GVEYVDHWSYVDSIYET T0297 183 :LKKEYTTDGLHLSIAGYQALSKSLK 1k7cA 185 :VNSYFPIDHTHTSPAGAEVVAEAFL Number of specific fragments extracted= 10 number of extra gaps= 1 total=294 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vjgA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vjgA expands to /projects/compbio/data/pdb/1vjg.pdb.gz 1vjgA:Skipped atom 37, because occupancy 0.350 <= existing 0.650 in 1vjgA Skipped atom 39, because occupancy 0.350 <= existing 0.650 in 1vjgA Skipped atom 41, because occupancy 0.350 <= existing 0.650 in 1vjgA Skipped atom 43, because occupancy 0.350 <= existing 0.650 in 1vjgA Skipped atom 418, because occupancy 0.400 <= existing 0.600 in 1vjgA Skipped atom 422, because occupancy 0.400 <= existing 0.600 in 1vjgA Skipped atom 424, because occupancy 0.400 <= existing 0.600 in 1vjgA Skipped atom 490, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 494, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 496, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 498, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 500, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 502, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 521, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 525, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 527, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 557, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 561, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 563, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 565, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 567, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 569, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 571, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 878, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 882, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 884, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 886, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 888, because occupancy 0.500 <= existing 0.500 in 1vjgA Skipped atom 890, because occupancy 0.500 <= existing 0.500 in 1vjgA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0297 read from 1vjgA/merged-good-all-a2m # 1vjgA read from 1vjgA/merged-good-all-a2m # adding 1vjgA to template set # found chain 1vjgA in template set Warning: unaligning (T0297)S28 because first residue in template chain is (1vjgA)S5 Warning: unaligning (T0297)V29 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vjgA)K6 Warning: unaligning (T0297)Y119 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1vjgA)P119 Warning: unaligning (T0297)P120 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1vjgA)P119 T0297 30 :VEPNILFIGDSIVEYYP 1vjgA 7 :TQIRICFVGDSFVNGTG T0297 47 :LQELFGT 1vjgA 30 :WTGRVCV T0297 54 :SKTIVNRGIRGYQTGLLLENLDAHLYGG 1vjgA 44 :DVTYYNLGIRRDTSSDIAKRWLQEVSLR T0297 82 :A 1vjgA 75 :E T0297 83 :VDKIFLLIGTNDIGKD 1vjgA 77 :NSLVVFSFGLNDTTLE T0297 99 :VPVNEALNNLEAIIQSVARD 1vjgA 98 :VSIAETIKNTREILTQAKKL T0297 124 :IKLLSILPVN 1vjgA 120 :VLMISPAPYI T0297 136 :EEYQQAV 1vjgA 130 :EQQDPGR T0297 147 :NEKIQNWNQAYQELASAY 1vjgA 137 :RRRTIDLSQQLALVCQDL T0297 166 :QVEFVPVFDCLTDQAGQLKKEYTTDGLHLSIAGYQALSKSLKD 1vjgA 155 :DVPYLDVFPLLEKPSVWLHEAKANDGVHPQAGGYTEFARIVEN Number of specific fragments extracted= 10 number of extra gaps= 1 total=304 Number of alignments=28 # 1vjgA read from 1vjgA/merged-good-all-a2m # found chain 1vjgA in template set Warning: unaligning (T0297)S28 because first residue in template chain is (1vjgA)S5 Warning: unaligning (T0297)V29 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vjgA)K6 Warning: unaligning (T0297)Y119 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1vjgA)P119 Warning: unaligning (T0297)P120 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1vjgA)P119 T0297 30 :VEPNILFIGDSIVEYYPLQELFGT 1vjgA 7 :TQIRICFVGDSFVNGTGDPECLGW T0297 54 :SKTIVNRGIRGYQTGLLLENLDAHLY 1vjgA 44 :DVTYYNLGIRRDTSSDIAKRWLQEVS T0297 80 :GGAVDKIFLLIGTNDIGKD 1vjgA 74 :KEYNSLVVFSFGLNDTTLE T0297 99 :VPVNEALNNLEAIIQSVARD 1vjgA 98 :VSIAETIKNTREILTQAKKL T0297 124 :IKLLSILPVNEREEY 1vjgA 120 :VLMISPAPYIEQQDP T0297 140 :Q 1vjgA 135 :G T0297 146 :SNEKIQNWNQAYQELASAY 1vjgA 136 :RRRRTIDLSQQLALVCQDL T0297 166 :QVEFVPVFDCLTDQAGQLKKEYTTDGLHLSIAGYQALSKSLKD 1vjgA 155 :DVPYLDVFPLLEKPSVWLHEAKANDGVHPQAGGYTEFARIVEN Number of specific fragments extracted= 8 number of extra gaps= 1 total=312 Number of alignments=29 # 1vjgA read from 1vjgA/merged-good-all-a2m # found chain 1vjgA in template set Warning: unaligning (T0297)S28 because first residue in template chain is (1vjgA)S5 Warning: unaligning (T0297)V29 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1vjgA)K6 Warning: unaligning (T0297)Y119 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (1vjgA)P119 Warning: unaligning (T0297)P120 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (1vjgA)P119 T0297 30 :VEPNILFIGDSIVEYYPLQELFGT 1vjgA 7 :TQIRICFVGDSFVNGTGDPECLGW T0297 54 :SKTIVNRGIRGYQTGLLLENLDAHLYG 1vjgA 44 :DVTYYNLGIRRDTSSDIAKRWLQEVSL T0297 81 :GAVDKIFLLIGTNDIG 1vjgA 75 :EYNSLVVFSFGLNDTT T0297 97 :KDVPVNEALNNLEAIIQSVARD 1vjgA 96 :PRVSIAETIKNTREILTQAKKL T0297 124 :IKLLSILPVNERE 1vjgA 120 :VLMISPAPYIEQQ T0297 143 :YIRSNEKIQNWNQAYQELASAY 1vjgA 133 :DPGRRRRTIDLSQQLALVCQDL T0297 166 :QVEFVPVFDCLTDQAGQLKKEYTTDGLHLSIAGYQALSKSLK 1vjgA 155 :DVPYLDVFPLLEKPSVWLHEAKANDGVHPQAGGYTEFARIVE Number of specific fragments extracted= 7 number of extra gaps= 1 total=319 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qw9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0297 read from 1qw9A/merged-good-all-a2m # 1qw9A read from 1qw9A/merged-good-all-a2m # found chain 1qw9A in training set Warning: unaligning (T0297)G38 because of BadResidue code BAD_PEPTIDE in next template residue (1qw9A)G73 Warning: unaligning (T0297)D39 because of BadResidue code BAD_PEPTIDE at template residue (1qw9A)G73 Warning: unaligning (T0297)D94 because of BadResidue code BAD_PEPTIDE in next template residue (1qw9A)M176 Warning: unaligning (T0297)I95 because of BadResidue code BAD_PEPTIDE at template residue (1qw9A)M176 Warning: unaligning (T0297)P171 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1qw9A)V297 Warning: unaligning (T0297)V172 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1qw9A)V297 T0297 23 :HLNHISVV 1qw9A 15 :KIAEIDKR T0297 31 :EPNILFI 1qw9A 64 :QVPIIRY T0297 40 :SIVEYYPLQELFGT 1qw9A 74 :NFVSGYNWEDGVGP T0297 54 :SKTIVNRG 1qw9A 120 :GAEVNMAV T0297 62 :IRGYQTGLLLENLDAHLYGG 1qw9A 129 :LGTRGIDAARNLVEYCNHPS T0297 82 :AVDKIFL 1qw9A 166 :KIKTWCL T0297 92 :TN 1qw9A 173 :GN T0297 96 :GKD 1qw9A 177 :DGP T0297 99 :VPVNEALNNLEAIIQSVARDYPLTEIKLLSILPVN 1qw9A 185 :KTAVEYGRIACEAAKVMKWVDPTIELVVCGSSNRN T0297 135 :REEYQQA 1qw9A 250 :RDNDTAN T0297 142 :VYIRSNEKIQNWNQAYQELASAYM 1qw9A 260 :LSLEMDDFIRSVVAIADYVKAKKR T0297 166 :QVEFV 1qw9A 287 :TIHLS T0297 173 :FDCLTDQAGQ 1qw9A 298 :WYHSNEADKL Number of specific fragments extracted= 13 number of extra gaps= 3 total=332 Number of alignments=31 # 1qw9A read from 1qw9A/merged-good-all-a2m # found chain 1qw9A in training set Warning: unaligning (T0297)G38 because of BadResidue code BAD_PEPTIDE in next template residue (1qw9A)G73 Warning: unaligning (T0297)D39 because of BadResidue code BAD_PEPTIDE at template residue (1qw9A)G73 Warning: unaligning (T0297)D94 because of BadResidue code BAD_PEPTIDE in next template residue (1qw9A)M176 Warning: unaligning (T0297)I95 because of BadResidue code BAD_PEPTIDE at template residue (1qw9A)M176 Warning: unaligning (T0297)P171 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1qw9A)V297 Warning: unaligning (T0297)V172 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1qw9A)V297 T0297 31 :EPNILFI 1qw9A 64 :QVPIIRY T0297 40 :SIVEYYPLQELFGT 1qw9A 74 :NFVSGYNWEDGVGP T0297 54 :SKTIVNRGIRGYQTGLL 1qw9A 120 :GAEVNMAVNLGTRGIDA T0297 74 :LDAHLY 1qw9A 137 :ARNLVE T0297 80 :GGAVDKIFL 1qw9A 164 :PHKIKTWCL T0297 92 :TN 1qw9A 173 :GN T0297 96 :GKD 1qw9A 177 :DGP T0297 99 :VPVNEALNNLEAIIQSVARDYPLTEIKLLSILPVN 1qw9A 185 :KTAVEYGRIACEAAKVMKWVDPTIELVVCGSSNRN T0297 134 :EREEYQQAV 1qw9A 249 :NRDNDTANY T0297 143 :YIRSNEKIQNWNQAYQELASAYM 1qw9A 261 :SLEMDDFIRSVVAIADYVKAKKR T0297 166 :QVEFV 1qw9A 287 :TIHLS T0297 173 :FDCLTDQAGQLKK 1qw9A 298 :WYHSNEADKLIEP Number of specific fragments extracted= 12 number of extra gaps= 3 total=344 Number of alignments=32 # 1qw9A read from 1qw9A/merged-good-all-a2m # found chain 1qw9A in training set Warning: unaligning (T0297)G38 because of BadResidue code BAD_PEPTIDE in next template residue (1qw9A)G73 Warning: unaligning (T0297)D39 because of BadResidue code BAD_PEPTIDE at template residue (1qw9A)G73 Warning: unaligning (T0297)D94 because of BadResidue code BAD_PEPTIDE in next template residue (1qw9A)M176 Warning: unaligning (T0297)I95 because of BadResidue code BAD_PEPTIDE at template residue (1qw9A)M176 T0297 18 :QTKYRHLNH 1qw9A 57 :IELVKELQV T0297 32 :PNILFI 1qw9A 66 :PIIRYP T0297 40 :SIVEYYPLQELFGT 1qw9A 74 :NFVSGYNWEDGVGP T0297 54 :SKTIVNRGIRGYQ 1qw9A 120 :GAEVNMAVNLGTR T0297 67 :TGLLLENL 1qw9A 137 :ARNLVEYC T0297 81 :GAVDKIFL 1qw9A 165 :HKIKTWCL T0297 92 :TN 1qw9A 173 :GN T0297 96 :G 1qw9A 177 :D T0297 97 :KDVPVNEALNNLEAIIQSVARDYPLTEIKLLSILPVNERE 1qw9A 183 :GHKTAVEYGRIACEAAKVMKWVDPTIELVVCGSSNRNMPT T0297 139 :QQAV 1qw9A 223 :FAEW T0297 143 :YIRSNEKIQNWNQAYQEL 1qw9A 261 :SLEMDDFIRSVVAIADYV Number of specific fragments extracted= 11 number of extra gaps= 2 total=355 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jrlA/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/T0297/1jrlA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0297/1jrlA/merged-good-all-a2m.gz for input Trying 1jrlA/merged-good-all-a2m Error: Couldn't open file 1jrlA/merged-good-all-a2m or 1jrlA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hdoA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0297 read from 1hdoA/merged-good-all-a2m # 1hdoA read from 1hdoA/merged-good-all-a2m # found chain 1hdoA in training set Warning: unaligning (T0297)Y138 because of BadResidue code BAD_PEPTIDE in next template residue (1hdoA)V121 Warning: unaligning (T0297)Q139 because of BadResidue code BAD_PEPTIDE at template residue (1hdoA)V121 Warning: unaligning (T0297)M165 because of BadResidue code BAD_PEPTIDE in next template residue (1hdoA)G143 Warning: unaligning (T0297)Q166 because of BadResidue code BAD_PEPTIDE at template residue (1hdoA)G143 T0297 32 :PNILFIG 1hdoA 4 :KKIAIFG T0297 43 :EYYP 1hdoA 11 :ATGQ T0297 47 :LQELFGT 1hdoA 36 :DSSRLPS T0297 70 :LLENLDAHLYGG 1hdoA 57 :QAADVDKTVAGQ T0297 84 :DKIFLLIGTNDIGKDVP 1hdoA 69 :DAVIVLLGTRNDLSPTT T0297 103 :EALNNLEAIIQSVARD 1hdoA 86 :VMSEGARNIVAAMKAH T0297 121 :LTE 1hdoA 102 :GVD T0297 124 :IKLLSILPVNEREE 1hdoA 106 :VVACTSAFLLWDPT T0297 140 :QAVYIRSNEKIQNWNQAYQE 1hdoA 122 :PPRLQAVTDDHIRMHKVLRE T0297 167 :VEFVPVF 1hdoA 144 :LKYVAVM T0297 174 :DCLTDQAGQLKKEYTTDG 1hdoA 152 :PHIGDQPLTGAYTVTLDG Number of specific fragments extracted= 11 number of extra gaps= 2 total=366 Number of alignments=34 # 1hdoA read from 1hdoA/merged-good-all-a2m # found chain 1hdoA in training set Warning: unaligning (T0297)Y138 because of BadResidue code BAD_PEPTIDE in next template residue (1hdoA)V121 Warning: unaligning (T0297)Q139 because of BadResidue code BAD_PEPTIDE at template residue (1hdoA)V121 Warning: unaligning (T0297)Y164 because of BadResidue code BAD_PEPTIDE in next template residue (1hdoA)G143 Warning: unaligning (T0297)Q166 because of BadResidue code BAD_PEPTIDE at template residue (1hdoA)G143 T0297 31 :EPNILFIGD 1hdoA 3 :VKKIAIFGA T0297 52 :GT 1hdoA 12 :TG T0297 54 :SKTIVNRGIRGYQT 1hdoA 27 :GYEVTVLVRDSSRL T0297 71 :LENLDAHLYG 1hdoA 58 :AADVDKTVAG T0297 83 :VDKIFLLIGTNDIGKDVP 1hdoA 68 :QDAVIVLLGTRNDLSPTT T0297 103 :EALNNLEAIIQSVARD 1hdoA 86 :VMSEGARNIVAAMKAH T0297 121 :LTE 1hdoA 102 :GVD T0297 124 :IKLLSILPVNEREE 1hdoA 106 :VVACTSAFLLWDPT T0297 140 :QAVYIRSNEKIQNWNQAYQE 1hdoA 122 :PPRLQAVTDDHIRMHKVLRE T0297 167 :VEFVPVF 1hdoA 144 :LKYVAVM Number of specific fragments extracted= 10 number of extra gaps= 2 total=376 Number of alignments=35 # 1hdoA read from 1hdoA/merged-good-all-a2m # found chain 1hdoA in training set Warning: unaligning (T0297)Y138 because of BadResidue code BAD_PEPTIDE in next template residue (1hdoA)V121 Warning: unaligning (T0297)Q139 because of BadResidue code BAD_PEPTIDE at template residue (1hdoA)V121 Warning: unaligning (T0297)L160 because of BadResidue code BAD_PEPTIDE in next template residue (1hdoA)G143 Warning: unaligning (T0297)Q166 because of BadResidue code BAD_PEPTIDE at template residue (1hdoA)G143 T0297 32 :PNILFIG 1hdoA 4 :KKIAIFG T0297 51 :FGT 1hdoA 11 :ATG T0297 54 :SKTIVNRGIRGYQT 1hdoA 27 :GYEVTVLVRDSSRL T0297 68 :GLLLENL 1hdoA 59 :ADVDKTV T0297 79 :Y 1hdoA 66 :A T0297 82 :AVDKIFLLIGTNDIGKDVP 1hdoA 67 :GQDAVIVLLGTRNDLSPTT T0297 103 :EALNNLEAIIQSVARDYPL 1hdoA 86 :VMSEGARNIVAAMKAHGVD T0297 123 :EIKLLSILPVNEREE 1hdoA 105 :KVVACTSAFLLWDPT T0297 140 :QAVYIRSNEKIQNWNQAYQE 1hdoA 122 :PPRLQAVTDDHIRMHKVLRE T0297 167 :VEFVPVFDC 1hdoA 144 :LKYVAVMPP Number of specific fragments extracted= 10 number of extra gaps= 2 total=386 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bn7A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1bn7A expands to /projects/compbio/data/pdb/1bn7.pdb.gz 1bn7A:Skipped atom 520, because occupancy 0.120 <= existing 1.000 in 1bn7A Skipped atom 608, because occupancy 0.300 <= existing 0.560 in 1bn7A Skipped atom 610, because occupancy 0.310 <= existing 0.650 in 1bn7A Skipped atom 612, because occupancy 0.400 <= existing 0.460 in 1bn7A Skipped atom 614, because occupancy 0.420 <= existing 0.550 in 1bn7A Skipped atom 616, because occupancy 0.260 <= existing 0.270 in 1bn7A Skipped atom 983, because occupancy 0.280 <= existing 0.360 in 1bn7A Skipped atom 985, because occupancy 0.150 <= existing 0.180 in 1bn7A Skipped atom 987, because occupancy 0.120 <= existing 0.350 in 1bn7A Skipped atom 989, because occupancy 0.170 <= existing 0.200 in 1bn7A Skipped atom 1049, because occupancy 0.400 <= existing 0.450 in 1bn7A Skipped atom 1199, because occupancy 0.440 <= existing 0.750 in 1bn7A Skipped atom 1201, because occupancy 0.380 <= existing 0.880 in 1bn7A Skipped atom 1203, because occupancy 0.270 <= existing 0.860 in 1bn7A Skipped atom 1205, because occupancy 0.380 <= existing 1.000 in 1bn7A Skipped atom 1207, because occupancy 0.100 <= existing 0.740 in 1bn7A Skipped atom 1209, because occupancy 0.340 <= existing 0.950 in 1bn7A Skipped atom 1211, because occupancy 0.320 <= existing 0.870 in 1bn7A Skipped atom 1323, because occupancy 0.430 <= existing 0.540 in 1bn7A Skipped atom 2103, because occupancy 0.540 <= existing 0.590 in 1bn7A Skipped atom 2105, because occupancy 0.510 <= existing 0.630 in 1bn7A Skipped atom 2107, because occupancy 0.180 <= existing 0.480 in 1bn7A Skipped atom 2109, because occupancy 0.290 <= existing 0.400 in 1bn7A # T0297 read from 1bn7A/merged-good-all-a2m # 1bn7A read from 1bn7A/merged-good-all-a2m # adding 1bn7A to template set # found chain 1bn7A in template set T0297 9 :WLLKEQEKIQT 1bn7A 16 :GTGFPFDPHYV T0297 20 :KYRHLN 1bn7A 29 :LGERMH T0297 26 :HISVVEPNILFIGDSIVEYYP 1bn7A 38 :VGPRDGTPVLFLHGNPTSSYL T0297 47 :LQELFGT 1bn7A 63 :IPHVAPS T0297 54 :SKT 1bn7A 87 :DLD T0297 65 :YQTGLLLENLDAHLYGG 1bn7A 90 :YFFDDHVRYLDAFIEAL T0297 82 :AVDKIFLLIGTNDIGKD 1bn7A 133 :RVKGIACMEFIRPIPTW T0297 99 :VPVNEALNNLEAIIQSVARD 1bn7A 224 :GEPANIVALVEAYMNWLHQS T0297 121 :LTEIKLLSILPVNERE 1bn7A 244 :PVPKLLFWGTPGVLIP T0297 154 :NQAYQELASAYMQVEFVPVFDC 1bn7A 260 :PAEAARLAESLPNCKTVDIGPG T0297 184 :KKEYTTDG 1bn7A 282 :LHYLQEDN T0297 199 :YQALSKSLKDYL 1bn7A 290 :PDLIGSEIARWL Number of specific fragments extracted= 12 number of extra gaps= 0 total=398 Number of alignments=37 # 1bn7A read from 1bn7A/merged-good-all-a2m # found chain 1bn7A in template set T0297 26 :HISVVEPNILFIGD 1bn7A 38 :VGPRDGTPVLFLHG T0297 47 :LQELFGT 1bn7A 55 :SSYLWRN T0297 54 :SKT 1bn7A 87 :DLD T0297 65 :YQTGLLLENLDAHLY 1bn7A 90 :YFFDDHVRYLDAFIE T0297 80 :GGAVDKIFLLIGTN 1bn7A 131 :PERVKGIACMEFIR T0297 99 :VPVNEALNNLEAIIQSVARD 1bn7A 224 :GEPANIVALVEAYMNWLHQS T0297 121 :LTEIKLLSILPVNERE 1bn7A 244 :PVPKLLFWGTPGVLIP T0297 154 :NQAYQELASAYMQVEFVPVFD 1bn7A 260 :PAEAARLAESLPNCKTVDIGP T0297 186 :EYTTDG 1bn7A 284 :YLQEDN T0297 199 :YQALSKSLKDYL 1bn7A 290 :PDLIGSEIARWL Number of specific fragments extracted= 10 number of extra gaps= 0 total=408 Number of alignments=38 # 1bn7A read from 1bn7A/merged-good-all-a2m # found chain 1bn7A in template set T0297 28 :SVVEPNILFIGDSIVEYYPLQEL 1bn7A 40 :PRDGTPVLFLHGNPTSSYLWRNI T0297 54 :SKTIVNRGIRGYQT 1bn7A 69 :SHRCIAPDLIGMGK T0297 68 :GLLLENLDAHLYGGAVDKIFLLIGTNDIG 1bn7A 93 :DDHVRYLDAFIEALGLEEVVLVIHDWGSA T0297 97 :KDVP 1bn7A 223 :AGEP T0297 102 :NEALNNLEAIIQSVAR 1bn7A 227 :ANIVALVEAYMNWLHQ T0297 119 :YPLTEIKLLSILPVNER 1bn7A 243 :SPVPKLLFWGTPGVLIP T0297 154 :NQAYQELASAYMQVEFVPVFDCL 1bn7A 260 :PAEAARLAESLPNCKTVDIGPGL T0297 185 :KEYTTDG 1bn7A 283 :HYLQEDN T0297 199 :YQALSKSLKDYL 1bn7A 290 :PDLIGSEIARWL Number of specific fragments extracted= 9 number of extra gaps= 0 total=417 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zmbA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zmbA expands to /projects/compbio/data/pdb/1zmb.pdb.gz 1zmbA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0297 read from 1zmbA/merged-good-all-a2m # 1zmbA read from 1zmbA/merged-good-all-a2m # adding 1zmbA to template set # found chain 1zmbA in template set T0297 33 :NILFIGDSIVEYYP 1zmbA 4 :SFLMLGQSNMAGRG T0297 47 :LQELFGTSK 1zmbA 64 :WSQKNQEDI T0297 56 :TIVNRGIRGYQTGL 1zmbA 74 :GLIPCAEGGSSIDE T0297 70 :LLENLDAHLYGGAVDKIFLLIGTNDIGKD 1zmbA 98 :ALTEAKFAMESSELTGILWHQGESDSLNG T0297 102 :NEALNNLEAIIQSVARD 1zmbA 129 :KVYYKKLLLIIEALRKE T0297 119 :YPLTEIKLLSILPVNEREEYQQAVYI 1zmbA 148 :VPDIPIIIGGLGDFLGKERFGKGCTE T0297 150 :IQNWNQAYQELASAYMQVEFVPV 1zmbA 174 :YNFINKELQKFAFEQDNCYFVTA T0297 184 :KKE 1zmbA 197 :SGL T0297 187 :YTTDGLHLSIAGYQALSKSLK 1zmbA 201 :CNPDGIHIDAISQRKFGLRYF Number of specific fragments extracted= 9 number of extra gaps= 0 total=426 Number of alignments=40 # 1zmbA read from 1zmbA/merged-good-all-a2m # found chain 1zmbA in template set T0297 33 :NILFIGDSIVEYYPLQELFGT 1zmbA 4 :SFLMLGQSNMAGRGFINEVPM T0297 54 :SK 1zmbA 71 :DI T0297 56 :TIVNRGIRGYQTGLL 1zmbA 74 :GLIPCAEGGSSIDEW T0297 71 :LENLDAHLYGGAVDKIFLLIGTNDIGKD 1zmbA 99 :LTEAKFAMESSELTGILWHQGESDSLNG T0297 102 :NEALNNLEAIIQSVARDY 1zmbA 129 :KVYYKKLLLIIEALRKEL T0297 120 :PLTEIKLLSILPVNEREEYQQAVYIR 1zmbA 149 :PDIPIIIGGLGDFLGKERFGKGCTEY T0297 151 :QNWNQAYQELASAYMQVEFVPVFDCL 1zmbA 175 :NFINKELQKFAFEQDNCYFVTASGLT T0297 187 :YTTDGLHLSIAGYQALSKSLK 1zmbA 201 :CNPDGIHIDAISQRKFGLRYF Number of specific fragments extracted= 8 number of extra gaps= 0 total=434 Number of alignments=41 # 1zmbA read from 1zmbA/merged-good-all-a2m # found chain 1zmbA in template set T0297 33 :NILFIGDSIVEYYPLQELFGT 1zmbA 4 :SFLMLGQSNMAGRGFINEVPM T0297 54 :SKTIVNRGIRGYQT 1zmbA 72 :IIGLIPCAEGGSSI T0297 68 :GLLLENLDAHLYGGAVDKIFLLIGTNDIG 1zmbA 96 :RHALTEAKFAMESSELTGILWHQGESDSL T0297 98 :DVPVNEALNNLEAIIQSVAR 1zmbA 125 :NGNYKVYYKKLLLIIEALRK T0297 118 :DYPLTEIKLLSILPVNEREEYQQAVY 1zmbA 147 :NVPDIPIIIGGLGDFLGKERFGKGCT T0297 149 :KIQNWNQAYQELASAYMQVEFVPVFDCL 1zmbA 173 :EYNFINKELQKFAFEQDNCYFVTASGLT T0297 187 :YTTDGLHLSIAGYQALS 1zmbA 201 :CNPDGIHIDAISQRKFG Number of specific fragments extracted= 7 number of extra gaps= 0 total=441 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wab/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wab expands to /projects/compbio/data/pdb/1wab.pdb.gz 1wab:Warning: there is no chain 1wab will retry with 1wabA # T0297 read from 1wab/merged-good-all-a2m # 1wab read from 1wab/merged-good-all-a2m # adding 1wab to template set # found chain 1wab in template set Warning: unaligning (T0297)L6 because of BadResidue code BAD_PEPTIDE at template residue (1wab)N6 Warning: unaligning (T0297)L47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1wab)W58 Warning: unaligning (T0297)L50 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1wab)F62 Warning: unaligning (T0297)F51 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1wab)F62 T0297 7 :ENWLLKEQEKIQTK 1wab 7 :PASKPTPVQDVQGD T0297 31 :EPNILFIGDSIVEYYP 1wab 38 :EPEVVFIGDSLVQLMH T0297 48 :QE 1wab 59 :RE T0297 52 :G 1wab 63 :S T0297 54 :SKTIVNRGIRGYQTGLLLENLDA 1wab 64 :PLHALNFGIGGDSTQHVLWRLEN T0297 77 :HLYGGAVDKIFLLIGTND 1wab 88 :ELEHIRPKIVVVWVGTNN T0297 97 :KDVPVNEALNNLEAIIQSVARDYPLTEIKLLSILPVNEREEYQ 1wab 106 :HGHTAEQVTGGIKAIVQLVNERQPQARVVVLGLLPRGQHPNPL T0297 147 :NEKIQNWNQAYQELASAYMQVEFVPVFDCLTDQAGQLKKEYTTDGLHLSIAGYQALSKSLKDYLY 1wab 149 :REKNRRVNELVRAALAGHPRAHFLDADPGFVHSDGTISHHDMYDYLHLSRLGYTPVCRALHSLLL Number of specific fragments extracted= 8 number of extra gaps= 3 total=449 Number of alignments=43 # 1wab read from 1wab/merged-good-all-a2m # found chain 1wab in template set Warning: unaligning (T0297)P46 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1wab)W58 Warning: unaligning (T0297)L47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1wab)W58 Warning: unaligning (T0297)L50 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1wab)F62 Warning: unaligning (T0297)F51 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1wab)F62 T0297 5 :LLENWLLKEQEKIQTKYRHLNHISVVEPNILFIGDSIVEYY 1wab 12 :TPVQDVQGDGRWMSLHHRFVADSKDKEPEVVFIGDSLVQLM T0297 48 :QE 1wab 59 :RE T0297 52 :G 1wab 63 :S T0297 54 :SKTIVNRGIRGYQTGLLLENLDA 1wab 64 :PLHALNFGIGGDSTQHVLWRLEN T0297 77 :HLYGGAVDKIFLLIGTND 1wab 88 :ELEHIRPKIVVVWVGTNN T0297 97 :KDVPVNEALNNLEAIIQSVARDYPLTEIKLLSILPVNEREEY 1wab 106 :HGHTAEQVTGGIKAIVQLVNERQPQARVVVLGLLPRGQHPNP T0297 146 :SNEKIQNWNQAYQELASAYMQVEFVPVFDCLTDQAGQLKKEYTTDGLHLSIAGYQALSKSLKDYLY 1wab 148 :LREKNRRVNELVRAALAGHPRAHFLDADPGFVHSDGTISHHDMYDYLHLSRLGYTPVCRALHSLLL Number of specific fragments extracted= 7 number of extra gaps= 2 total=456 Number of alignments=44 # 1wab read from 1wab/merged-good-all-a2m # found chain 1wab in template set Warning: unaligning (T0297)L47 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1wab)W58 Warning: unaligning (T0297)Q48 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1wab)W58 Warning: unaligning (T0297)F51 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1wab)F62 Warning: unaligning (T0297)G52 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1wab)F62 T0297 3 :VQLLENWLLKEQEKIQTKYRHLNHISVVEPNILFIGDSIVEYYP 1wab 10 :KPTPVQDVQGDGRWMSLHHRFVADSKDKEPEVVFIGDSLVQLMH T0297 49 :EL 1wab 59 :RE T0297 53 :TSKTIVNRGIRGYQTGLLLENL 1wab 63 :SPLHALNFGIGGDSTQHVLWRL T0297 75 :DAHLYGGAVDKIFLLIGTNDI 1wab 86 :NGELEHIRPKIVVVWVGTNNH T0297 98 :DVPVNEALNNLEAIIQSVARDYPLTEIKLLSILPVNER 1wab 107 :GHTAEQVTGGIKAIVQLVNERQPQARVVVLGLLPRGQH T0297 143 :YIRSNEKIQNWNQAYQELASAYMQVEFVPVFDCLTDQAGQLKKEYTTDGLHLSIAGYQALSKSLKDYL 1wab 145 :PNPLREKNRRVNELVRAALAGHPRAHFLDADPGFVHSDGTISHHDMYDYLHLSRLGYTPVCRALHSLL Number of specific fragments extracted= 6 number of extra gaps= 2 total=462 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mh1/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0297 read from 1mh1/merged-good-all-a2m # 1mh1 read from 1mh1/merged-good-all-a2m # found chain 1mh1 in training set T0297 28 :SVVEPNILFIGDS 1mh1 2A:SPQAIKCVVVGDG T0297 44 :YYP 1mh1 13 :AVG T0297 47 :LQEL 1mh1 24 :TTNA T0297 54 :SKTIVNRGIRGYQT 1mh1 47 :DGKPVNLGLWDTAG T0297 75 :DAHLYGG 1mh1 61 :QEDYDRL T0297 82 :AVDKIFLLIGTN 1mh1 74 :QTDVSLICFSLV T0297 100 :PVNE 1mh1 86 :SPAS T0297 105 :LNNLEA 1mh1 90 :FENVRA T0297 111 :IIQSVARDYPLTEIKLLSI 1mh1 97 :WYPEVRHHCPNTPIILVGT T0297 135 :REEYQQA 1mh1 116 :KLDLRDD T0297 147 :NEKIQNWNQ 1mh1 123 :KDTIEKLKE T0297 156 :AYQELASAY 1mh1 141 :QGLAMAKEI T0297 166 :QVEFVPVFDCLTDQ 1mh1 150 :GAVKYLECSALTQR T0297 198 :GYQALSKSLKDYLY 1mh1 164 :GLKTVFDEAIRAVL Number of specific fragments extracted= 14 number of extra gaps= 0 total=476 Number of alignments=46 # 1mh1 read from 1mh1/merged-good-all-a2m # found chain 1mh1 in training set T0297 28 :SVVEPNILFIGD 1mh1 2A:SPQAIKCVVVGD T0297 54 :SKTIVNRGIRGYQTGLL 1mh1 47 :DGKPVNLGLWDTAGQED T0297 71 :LENLDAH 1mh1 65 :DRLRPLS T0297 80 :GGAVDKIFLLIGTN 1mh1 72 :YPQTDVSLICFSLV T0297 100 :PVNEA 1mh1 86 :SPASF T0297 106 :NNLEA 1mh1 91 :ENVRA T0297 111 :IIQSVARDYPLTEIKLLSIL 1mh1 97 :WYPEVRHHCPNTPIILVGTK T0297 135 :REEY 1mh1 117 :LDLR T0297 139 :QQAVYIRSNE 1mh1 122 :DKDTIEKLKE T0297 155 :QAYQELASAYMQVEFVPV 1mh1 140 :PQGLAMAKEIGAVKYLEC T0297 174 :DCLTDQA 1mh1 158 :SALTQRG T0297 199 :YQALSKSLKDYL 1mh1 165 :LKTVFDEAIRAV Number of specific fragments extracted= 12 number of extra gaps= 0 total=488 Number of alignments=47 # 1mh1 read from 1mh1/merged-good-all-a2m # found chain 1mh1 in training set T0297 28 :SVVEPNILFIGD 1mh1 2A:SPQAIKCVVVGD T0297 52 :GT 1mh1 12 :GA T0297 54 :SKTIVNRGIRGY 1mh1 50 :PVNLGLWDTAGQ T0297 76 :AHLYG 1mh1 62 :EDYDR T0297 81 :GAVDKIFLLIG 1mh1 73 :PQTDVSLICFS T0297 98 :DVPVNEA 1mh1 84 :LVSPASF T0297 106 :NNLEA 1mh1 91 :ENVRA T0297 111 :IIQSVARDYPLTEIKLLSIL 1mh1 97 :WYPEVRHHCPNTPIILVGTK T0297 143 :YIRSNEKIQNWNQ 1mh1 119 :LRDDKDTIEKLKE T0297 156 :AYQELASAY 1mh1 141 :QGLAMAKEI T0297 166 :QVEFVPVFDCLTDQ 1mh1 150 :GAVKYLECSALTQR T0297 198 :GYQALSKSLKD 1mh1 164 :GLKTVFDEAIR Number of specific fragments extracted= 12 number of extra gaps= 0 total=500 Number of alignments=48 # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0297//projects/compbio/experiments/protein-predict/casp7/T0297/align.constraints_v3.costfcn or /projects/compbio/experiments/protein-predict/casp7/T0297//projects/compbio/experiments/protein-predict/casp7/T0297/align.constraints_v3.costfcn.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/T0297/align.constraints_v3.costfcn # reading script from file /projects/compbio/experiments/protein-predict/casp7/T0297/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((T0297)K125.CB, (T0297)V170.CB) [> 3.7168 = 6.1947 < 8.0531] w=1.0000 to align # Constraint # added constraint: constraint((T0297)L88.CB, (T0297)K125.CB) [> 4.2135 = 7.0226 < 9.1293] w=0.9998 to align # Constraint # added constraint: constraint((T0297)F87.CB, (T0297)K125.CB) [> 2.8874 = 4.8123 < 6.2559] w=0.9976 to align # Constraint # added constraint: constraint((T0297)L88.CB, (T0297)L126.CB) [> 3.0702 = 5.1171 < 6.6522] w=0.9546 to align # Constraint # added constraint: constraint((T0297)I86.CB, (T0297)I124.CB) [> 3.2076 = 5.3460 < 6.9498] w=0.9546 to align # Constraint # added constraint: constraint((T0297)L126.CB, (T0297)V170.CB) [> 4.1210 = 6.8684 < 8.9289] w=0.9531 to align # Constraint # added constraint: constraint((T0297)L126.CB, (T0297)F169.CB) [> 3.4755 = 5.7925 < 7.5303] w=0.9531 to align # Constraint # added constraint: constraint((T0297)I124.CB, (T0297)V167.CB) [> 2.9729 = 4.9549 < 6.4414] w=0.9531 to align # Constraint # added constraint: constraint((T0297)I86.CB, (T0297)K125.CB) [> 4.3209 = 7.2015 < 9.3619] w=0.9523 to align # Constraint # added constraint: constraint((T0297)K85.CB, (T0297)K125.CB) [> 3.8941 = 6.4902 < 8.4373] w=0.9523 to align # Constraint # added constraint: constraint((T0297)I86.CB, (T0297)V115.CB) [> 3.3577 = 5.5961 < 7.2750] w=0.9323 to align # Constraint # added constraint: constraint((T0297)L88.CB, (T0297)I124.CB) [> 3.8440 = 6.4066 < 8.3286] w=0.9320 to align # Constraint # added constraint: constraint((T0297)I112.CB, (T0297)I124.CB) [> 3.5277 = 5.8795 < 7.6434] w=0.9300 to align # Constraint # added constraint: constraint((T0297)L88.CB, (T0297)L127.CB) [> 4.1068 = 6.8446 < 8.8980] w=0.9298 to align # Constraint # added constraint: constraint((T0297)S128.CB, (T0297)V172.CB) [> 3.3818 = 5.6362 < 7.3271] w=0.9057 to align # Constraint # added constraint: constraint((T0297)K85.CB, (T0297)I124.CB) [> 4.4023 = 7.3372 < 9.5384] w=0.8868 to align # Constraint # added constraint: constraint((T0297)L89.CB, (T0297)L127.CB) [> 2.6448 = 4.4079 < 5.7303] w=0.8855 to align # Constraint # added constraint: constraint((T0297)L127.CB, (T0297)V172.CB) [> 3.3658 = 5.6097 < 7.2925] w=0.8854 to align # Constraint # added constraint: constraint((T0297)V115.CB, (T0297)I124.CB) [> 3.5268 = 5.8780 < 7.6414] w=0.8848 to align # Constraint # added constraint: constraint((T0297)S128.CB, (T0297)P171.CB) [> 3.0897 = 5.1496 < 6.6944] w=0.8831 to align # Constraint # added constraint: constraint((T0297)F36.CB, (T0297)F87.CB) [> 3.0304 = 5.0506 < 6.5658] w=0.8649 to align # Constraint # added constraint: constraint((T0297)I86.CB, (T0297)T122.CB) [> 3.4404 = 5.7341 < 7.4543] w=0.8642 to align # Constraint # added constraint: constraint((T0297)K85.CB, (T0297)T122.CB) [> 3.8692 = 6.4487 < 8.3833] w=0.8642 to align # Constraint # added constraint: constraint((T0297)L35.CB, (T0297)F87.CB) [> 4.3063 = 7.1772 < 9.3304] w=0.8425 to align # Constraint # added constraint: constraint((T0297)Y157.CB, (T0297)F169.CB) [> 3.7013 = 6.1689 < 8.0195] w=0.8422 to align # Constraint # added constraint: constraint((T0297)I34.CB, (T0297)I57.CB) [> 3.1937 = 5.3228 < 6.9197] w=0.8422 to align # Constraint # added constraint: constraint((T0297)L126.CB, (T0297)Y157.CB) [> 3.5427 = 5.9045 < 7.6758] w=0.8404 to align # Constraint # added constraint: constraint((T0297)I86.CB, (T0297)E123.CB) [> 4.3792 = 7.2987 < 9.4883] w=0.8371 to align # Constraint # added constraint: constraint((T0297)K85.CB, (T0297)E123.CB) [> 2.7271 = 4.5452 < 5.9088] w=0.8371 to align # Constraint # added constraint: constraint((T0297)K125.CB, (T0297)E168.CB) [> 3.1441 = 5.2401 < 6.8122] w=0.8356 to align # Constraint # added constraint: constraint((T0297)I34.CB, (T0297)D84.CB) [> 3.9944 = 6.6573 < 8.6545] w=0.8203 to align # Constraint # added constraint: constraint((T0297)I37.CB, (T0297)I86.CB) [> 3.8076 = 6.3460 < 8.2498] w=0.8203 to align # Constraint # added constraint: constraint((T0297)I37.CB, (T0297)F87.CB) [> 4.2084 = 7.0140 < 9.1182] w=0.8203 to align # Constraint # added constraint: constraint((T0297)I37.CB, (T0297)L88.CB) [> 3.0535 = 5.0891 < 6.6159] w=0.8202 to align # Constraint # added constraint: constraint((T0297)L35.CB, (T0297)I86.CB) [> 2.8368 = 4.7280 < 6.1463] w=0.8202 to align # Constraint # added constraint: constraint((T0297)I34.CB, (T0297)K85.CB) [> 2.8471 = 4.7451 < 6.1687] w=0.8197 to align # Constraint # added constraint: constraint((T0297)I34.CB, (T0297)V58.CB) [> 4.1666 = 6.9444 < 9.0277] w=0.8196 to align # Constraint # added constraint: constraint((T0297)L35.CB, (T0297)K85.CB) [> 4.4147 = 7.3579 < 9.5652] w=0.7977 to align # Constraint # added constraint: constraint((T0297)I34.CB, (T0297)I86.CB) [> 4.2859 = 7.1431 < 9.2861] w=0.7976 to align # Constraint # added constraint: constraint((T0297)I34.CB, (T0297)F87.CB) [> 3.8579 = 6.4298 < 8.3587] w=0.7976 to align # Constraint # added constraint: constraint((T0297)F36.CB, (T0297)N59.CB) [> 3.2735 = 5.4558 < 7.0926] w=0.7975 to align # Constraint # added constraint: constraint((T0297)F87.CB, (T0297)L127.CB) [> 3.8479 = 6.4131 < 8.3370] w=0.7942 to align # Constraint # added constraint: constraint((T0297)I112.CB, (T0297)V167.CB) [> 3.7253 = 6.2088 < 8.0715] w=0.7911 to align # Constraint # added constraint: constraint((T0297)L126.CB, (T0297)V167.CB) [> 3.7349 = 6.2248 < 8.0922] w=0.7907 to align # Constraint # added constraint: constraint((T0297)D84.CB, (T0297)E123.CB) [> 4.0859 = 6.8098 < 8.8527] w=0.7896 to align # Constraint # added constraint: constraint((T0297)N33.CB, (T0297)D84.CB) [> 3.1194 = 5.1990 < 6.7587] w=0.7751 to align # Constraint # added constraint: constraint((T0297)G38.CA, (T0297)I90.CB) [> 3.1561 = 5.2601 < 6.8382] w=0.7749 to align # Constraint # added constraint: constraint((T0297)E123.CB, (T0297)E168.CB) [> 3.9225 = 6.5374 < 8.4986] w=0.7748 to align # Constraint # added constraint: constraint((T0297)F87.CB, (T0297)I124.CB) [> 4.6810 = 7.8017 < 10.1422] w=0.7737 to align # Constraint # added constraint: constraint((T0297)I124.CB, (T0297)E168.CB) [> 4.1892 = 6.9820 < 9.0766] w=0.7724 to align # Constraint # added constraint: constraint((T0297)T92.CB, (T0297)I129.CB) [> 3.4624 = 5.7707 < 7.5019] w=0.7683 to align # Constraint # added constraint: constraint((T0297)S128.CB, (T0297)F173.CB) [> 3.3717 = 5.6195 < 7.3053] w=0.7681 to align # Constraint # added constraint: constraint((T0297)L127.CB, (T0297)V170.CB) [> 3.0554 = 5.0924 < 6.6201] w=0.7680 to align # Constraint # added constraint: constraint((T0297)L108.CB, (T0297)L126.CB) [> 4.0169 = 6.6948 < 8.7033] w=0.7674 to align # Constraint # added constraint: constraint((T0297)Q158.CB, (T0297)F169.CB) [> 3.2098 = 5.3497 < 6.9546] w=0.7527 to align # Constraint # added constraint: constraint((T0297)G38.CA, (T0297)L88.CB) [> 3.9444 = 6.5740 < 8.5462] w=0.7524 to align # Constraint # added constraint: constraint((T0297)G38.CA, (T0297)L89.CB) [> 3.0701 = 5.1168 < 6.6519] w=0.7524 to align # Constraint # added constraint: constraint((T0297)F36.CB, (T0297)V58.CB) [> 4.0068 = 6.6779 < 8.6813] w=0.7518 to align # Constraint # added constraint: constraint((T0297)F36.CB, (T0297)I57.CB) [> 3.9443 = 6.5739 < 8.5461] w=0.7518 to align # Constraint # added constraint: constraint((T0297)L35.CB, (T0297)V58.CB) [> 3.0621 = 5.1034 < 6.6344] w=0.7518 to align # Constraint # added constraint: constraint((T0297)I34.CB, (T0297)T56.CB) [> 4.0642 = 6.7737 < 8.8058] w=0.7518 to align # Constraint # added constraint: constraint((T0297)D84.CB, (T0297)T122.CB) [> 3.7343 = 6.2238 < 8.0910] w=0.7511 to align # Constraint # added constraint: constraint((T0297)S128.CB, (T0297)N154.CB) [> 3.0176 = 5.0294 < 6.5382] w=0.7503 to align # Constraint # added constraint: constraint((T0297)S128.CB, (T0297)V170.CB) [> 4.1092 = 6.8487 < 8.9033] w=0.7455 to align # Constraint # added constraint: constraint((T0297)E43.CB, (T0297)I62.CB) [> 3.6150 = 6.0250 < 7.8324] w=0.7452 to align # Constraint # added constraint: constraint((T0297)E43.CB, (T0297)R63.CB) [> 3.4234 = 5.7056 < 7.4173] w=0.7452 to align # Constraint # added constraint: constraint((T0297)L35.CB, (T0297)R60.CB) [> 3.6694 = 6.1157 < 7.9504] w=0.7298 to align # Constraint # added constraint: constraint((T0297)I37.CB, (T0297)L89.CB) [> 4.3744 = 7.2906 < 9.4778] w=0.7297 to align # Constraint # added constraint: constraint((T0297)I37.CB, (T0297)R60.CB) [> 3.2718 = 5.4529 < 7.0888] w=0.7292 to align # Constraint # added constraint: constraint((T0297)N33.CB, (T0297)T56.CB) [> 2.8372 = 4.7287 < 6.1474] w=0.7292 to align # Constraint # added constraint: constraint((T0297)G91.CA, (T0297)A104.CB) [> 3.7922 = 6.3203 < 8.2164] w=0.7254 to align # Constraint # added constraint: constraint((T0297)F87.CB, (T0297)L126.CB) [> 4.6323 = 7.7205 < 10.0367] w=0.7249 to align # Constraint # added constraint: constraint((T0297)I112.CB, (T0297)Y164.CB) [> 3.2771 = 5.4619 < 7.1004] w=0.7230 to align # Constraint # added constraint: constraint((T0297)S128.CB, (T0297)Y157.CB) [> 3.3797 = 5.6328 < 7.3226] w=0.7229 to align # Constraint # added constraint: constraint((T0297)T67.CB, (T0297)N107.CB) [> 2.5830 = 4.3049 < 5.5964] w=0.7226 to align # Constraint # added constraint: constraint((T0297)N33.CB, (T0297)K55.CB) [> 3.9675 = 6.6125 < 8.5963] w=0.7066 to align # Constraint # added constraint: constraint((T0297)T67.CB, (T0297)A104.CB) [> 3.4055 = 5.6758 < 7.3786] w=0.7007 to align # Constraint # added constraint: constraint((T0297)S128.CB, (T0297)F169.CB) [> 4.1239 = 6.8731 < 8.9350] w=0.7006 to align # Constraint # added constraint: constraint((T0297)L126.CB, (T0297)E168.CB) [> 4.3255 = 7.2092 < 9.3719] w=0.7006 to align # Constraint # added constraint: constraint((T0297)V172.CB, (T0297)L202.CB) [> 3.7916 = 6.3193 < 8.2151] w=0.7005 to align # Constraint # added constraint: constraint((T0297)L126.CB, (T0297)A161.CB) [> 3.2885 = 5.4809 < 7.1252] w=0.7003 to align # Constraint # added constraint: constraint((T0297)G91.CA, (T0297)I129.CB) [> 3.1451 = 5.2419 < 6.8144] w=0.7003 to align # Constraint # added constraint: constraint((T0297)K125.CB, (T0297)V167.CB) [> 4.2007 = 7.0011 < 9.1015] w=0.7000 to align # Constraint # added constraint: constraint((T0297)F36.CB, (T0297)I86.CB) [> 4.5609 = 7.6016 < 9.8820] w=0.6846 to align # Constraint # added constraint: constraint((T0297)F36.CB, (T0297)R60.CB) [> 3.8820 = 6.4700 < 8.4110] w=0.6841 to align # Constraint # added constraint: constraint((T0297)L88.CB, (T0297)I111.CB) [> 3.5543 = 5.9239 < 7.7011] w=0.6837 to align # Constraint # added constraint: constraint((T0297)G38.CA, (T0297)G61.CA) [> 2.9269 = 4.8783 < 6.3417] w=0.6826 to align # Constraint # added constraint: constraint((T0297)V83.CB, (T0297)T122.CB) [> 3.6323 = 6.0539 < 7.8700] w=0.6812 to align # Constraint # added constraint: constraint((T0297)L105.CB, (T0297)A156.CB) [> 2.9655 = 4.9425 < 6.4252] w=0.6803 to align # Constraint # added constraint: constraint((T0297)T67.CB, (T0297)D94.CB) [> 3.2711 = 5.4519 < 7.0874] w=0.6783 to align # Constraint # added constraint: constraint((T0297)Q66.CB, (T0297)N93.CB) [> 2.8228 = 4.7046 < 6.1160] w=0.6783 to align # Constraint # added constraint: constraint((T0297)Y65.CB, (T0297)N93.CB) [> 3.7892 = 6.3154 < 8.2100] w=0.6783 to align # Constraint # added constraint: constraint((T0297)I129.CB, (T0297)N154.CB) [> 3.6671 = 6.1119 < 7.9455] w=0.6782 to align # Constraint # added constraint: constraint((T0297)F36.CB, (T0297)G61.CA) [> 3.8035 = 6.3391 < 8.2408] w=0.6782 to align # Constraint # added constraint: constraint((T0297)E109.CB, (T0297)L160.CB) [> 3.5958 = 5.9929 < 7.7908] w=0.6779 to align # Constraint # added constraint: constraint((T0297)L108.CB, (T0297)L160.CB) [> 3.3417 = 5.5695 < 7.2404] w=0.6779 to align # Constraint # added constraint: constraint((T0297)T67.CB, (T0297)I111.CB) [> 4.0570 = 6.7617 < 8.7902] w=0.6774 to align # Constraint # added constraint: constraint((T0297)E123.CB, (T0297)V167.CB) [> 4.3329 = 7.2215 < 9.3880] w=0.6621 to align # Constraint # added constraint: constraint((T0297)I34.CB, (T0297)K55.CB) [> 3.3369 = 5.5615 < 7.2299] w=0.6614 to align # Constraint # added constraint: constraint((T0297)L108.CB, (T0297)Y157.CB) [> 3.7718 = 6.2863 < 8.1722] w=0.6578 to align # Constraint # added constraint: constraint((T0297)A104.CB, (T0297)W153.CB) [> 3.4405 = 5.7341 < 7.4543] w=0.6578 to align # Constraint # added constraint: constraint((T0297)L89.CB, (T0297)L126.CB) [> 4.3274 = 7.2123 < 9.3760] w=0.6576 to align # Constraint # added constraint: constraint((T0297)T67.CB, (T0297)L108.CB) [> 3.6729 = 6.1215 < 7.9580] w=0.6557 to align # Constraint # added constraint: constraint((T0297)Q66.CB, (T0297)D94.CB) [> 3.0499 = 5.0832 < 6.6081] w=0.6557 to align # Constraint # added constraint: constraint((T0297)Q66.CB, (T0297)G91.CA) [> 4.2676 = 7.1127 < 9.2465] w=0.6557 to align # Constraint # added constraint: constraint((T0297)G64.CA, (T0297)N93.CB) [> 3.0181 = 5.0302 < 6.5393] w=0.6557 to align # Constraint # added constraint: constraint((T0297)I37.CB, (T0297)L70.CB) [> 3.7351 = 6.2251 < 8.0927] w=0.6557 to align # Constraint # added constraint: constraint((T0297)E43.CB, (T0297)G61.CA) [> 2.6535 = 4.4226 < 5.7494] w=0.6556 to align # Constraint # added constraint: constraint((T0297)G38.CA, (T0297)I62.CB) [> 4.1841 = 6.9735 < 9.0656] w=0.6555 to align # Constraint # added constraint: constraint((T0297)F36.CB, (T0297)L89.CB) [> 4.2935 = 7.1558 < 9.3026] w=0.6393 to align # Constraint # added constraint: constraint((T0297)K125.CB, (T0297)F169.CB) [> 4.2453 = 7.0754 < 9.1980] w=0.6388 to align # Constraint # added constraint: constraint((T0297)I37.CB, (T0297)G61.CA) [> 3.6336 = 6.0560 < 7.8729] w=0.6376 to align # Constraint # added constraint: constraint((T0297)L127.CB, (T0297)P171.CB) [> 4.3072 = 7.1786 < 9.3322] w=0.6347 to align # Constraint # added constraint: constraint((T0297)Q66.CB, (T0297)I90.CB) [> 4.3004 = 7.1674 < 9.3176] w=0.6331 to align # Constraint # added constraint: constraint((T0297)G38.CA, (T0297)Y65.CB) [> 3.8337 = 6.3895 < 8.3063] w=0.6328 to align # Constraint # added constraint: constraint((T0297)D39.CB, (T0297)G91.CA) [> 4.2088 = 7.0146 < 9.1190] w=0.6326 to align # Constraint # added constraint: constraint((T0297)V42.CB, (T0297)G61.CA) [> 2.8976 = 4.8293 < 6.2782] w=0.6322 to align # Constraint # added constraint: constraint((T0297)S40.CB, (T0297)R63.CB) [> 2.4542 = 4.0904 < 5.3175] w=0.6173 to align # Constraint # added constraint: constraint((T0297)I37.CB, (T0297)I90.CB) [> 4.2470 = 7.0784 < 9.2019] w=0.6170 to align # Constraint # added constraint: constraint((T0297)N33.CB, (T0297)V83.CB) [> 3.2572 = 5.4287 < 7.0573] w=0.6167 to align # Constraint # added constraint: constraint((T0297)L35.CB, (T0297)V83.CB) [> 3.1018 = 5.1697 < 6.7205] w=0.6167 to align # Constraint # added constraint: constraint((T0297)I41.CB, (T0297)L89.CB) [> 3.7372 = 6.2287 < 8.0973] w=0.6127 to align # Constraint # added constraint: constraint((T0297)S40.CB, (T0297)G64.CA) [> 3.4533 = 5.7554 < 7.4821] w=0.6127 to align # Constraint # added constraint: constraint((T0297)L130.CB, (T0297)F173.CB) [> 3.6802 = 6.1337 < 7.9738] w=0.6124 to align # Constraint # added constraint: constraint((T0297)L88.CB, (T0297)L108.CB) [> 3.8447 = 6.4078 < 8.3301] w=0.6114 to align # Constraint # added constraint: constraint((T0297)S40.CB, (T0297)H193.CB) [> 3.6915 = 6.1525 < 7.9983] w=0.6105 to align # Constraint # added constraint: constraint((T0297)I41.CB, (T0297)T92.CB) [> 3.8749 = 6.4582 < 8.3957] w=0.6105 to align # Constraint # added constraint: constraint((T0297)I41.CB, (T0297)H193.CB) [> 4.2440 = 7.0733 < 9.1953] w=0.6105 to align # Constraint # added constraint: constraint((T0297)V42.CB, (T0297)L89.CB) [> 3.1391 = 5.2318 < 6.8014] w=0.6105 to align # Constraint # added constraint: constraint((T0297)I129.CB, (T0297)W153.CB) [> 3.5619 = 5.9365 < 7.7175] w=0.6105 to align # Constraint # added constraint: constraint((T0297)D94.CB, (T0297)A104.CB) [> 2.9242 = 4.8738 < 6.3359] w=0.6105 to align # Constraint # added constraint: constraint((T0297)R60.CB, (T0297)N73.CB) [> 3.9130 = 6.5217 < 8.4782] w=0.6104 to align # Constraint # added constraint: constraint((T0297)D39.CB, (T0297)I90.CB) [> 3.4717 = 5.7862 < 7.5221] w=0.6101 to align # Constraint # added constraint: constraint((T0297)L88.CB, (T0297)I112.CB) [> 4.2757 = 7.1262 < 9.2640] w=0.6092 to align # Constraint # added constraint: constraint((T0297)V170.CB, (T0297)L206.CB) [> 3.7955 = 6.3258 < 8.2235] w=0.5924 to align # Constraint # added constraint: constraint((T0297)N154.CB, (T0297)P171.CB) [> 3.9219 = 6.5365 < 8.4974] w=0.5900 to align # Constraint # added constraint: constraint((T0297)L35.CB, (T0297)H77.CB) [> 3.9194 = 6.5324 < 8.4921] w=0.5899 to align # Constraint # added constraint: constraint((T0297)L78.CB, (T0297)V115.CB) [> 4.0285 = 6.7141 < 8.7283] w=0.5898 to align # Constraint # added constraint: constraint((T0297)E43.CB, (T0297)N59.CB) [> 3.9824 = 6.6374 < 8.6286] w=0.5879 to align # Constraint # added constraint: constraint((T0297)L105.CB, (T0297)L160.CB) [> 3.6785 = 6.1308 < 7.9700] w=0.5877 to align # Constraint # added constraint: constraint((T0297)I37.CB, (T0297)L74.CB) [> 3.9926 = 6.6543 < 8.6506] w=0.5874 to align # Constraint # added constraint: constraint((T0297)L127.CB, (T0297)F169.CB) [> 4.5033 = 7.5054 < 9.7571] w=0.5874 to align # Constraint # added constraint: constraint((T0297)P32.CB, (T0297)T56.CB) [> 3.7274 = 6.2124 < 8.0761] w=0.5873 to align # Constraint # added constraint: constraint((T0297)I90.CB, (T0297)I129.CB) [> 4.2267 = 7.0445 < 9.1578] w=0.5871 to align # Constraint # added constraint: constraint((T0297)G38.CA, (T0297)R60.CB) [> 4.3947 = 7.3245 < 9.5219] w=0.5720 to align # Constraint # added constraint: constraint((T0297)D39.CB, (T0297)L89.CB) [> 4.3249 = 7.2081 < 9.3705] w=0.5716 to align # Constraint # added constraint: constraint((T0297)N33.CB, (T0297)A82.CB) [> 3.8853 = 6.4755 < 8.4181] w=0.5716 to align # Constraint # added constraint: constraint((T0297)L35.CB, (T0297)I57.CB) [> 4.3413 = 7.2355 < 9.4061] w=0.5711 to align # Constraint # added constraint: constraint((T0297)D39.CB, (T0297)G61.CA) [> 3.9603 = 6.6005 < 8.5806] w=0.5697 to align # Constraint # added constraint: constraint((T0297)L130.CB, (T0297)V172.CB) [> 3.4976 = 5.8294 < 7.5782] w=0.5675 to align # Constraint # added constraint: constraint((T0297)I129.CB, (T0297)V172.CB) [> 3.8758 = 6.4597 < 8.3976] w=0.5670 to align # Constraint # added constraint: constraint((T0297)I129.CB, (T0297)F173.CB) [> 3.6098 = 6.0164 < 7.8213] w=0.5667 to align # Constraint # added constraint: constraint((T0297)G91.CA, (T0297)W153.CB) [> 3.4624 = 5.7707 < 7.5019] w=0.5652 to align # Constraint # added constraint: constraint((T0297)L127.CB, (T0297)L206.CB) [> 4.1957 = 6.9928 < 9.0906] w=0.5652 to align # Constraint # added constraint: constraint((T0297)D39.CB, (T0297)N93.CB) [> 3.3434 = 5.5723 < 7.2440] w=0.5651 to align # Constraint # added constraint: constraint((T0297)D39.CB, (T0297)T92.CB) [> 3.4910 = 5.8183 < 7.5638] w=0.5651 to align # Constraint # added constraint: constraint((T0297)D39.CB, (T0297)G64.CA) [> 3.2559 = 5.4265 < 7.0545] w=0.5651 to align # Constraint # added constraint: constraint((T0297)I112.CB, (T0297)L126.CB) [> 4.2636 = 7.1060 < 9.2378] w=0.5644 to align # Constraint # added constraint: constraint((T0297)D75.CB, (T0297)S114.CB) [> 3.7760 = 6.2933 < 8.1813] w=0.5445 to align # Constraint # added constraint: constraint((T0297)L74.CB, (T0297)I111.CB) [> 3.6164 = 6.0273 < 7.8355] w=0.5444 to align # Constraint # added constraint: constraint((T0297)L78.CB, (T0297)D118.CB) [> 3.2549 = 5.4249 < 7.0524] w=0.5440 to align # Constraint # added constraint: constraint((T0297)D39.CB, (T0297)Y65.CB) [> 2.9552 = 4.9254 < 6.4030] w=0.5426 to align # Constraint # added constraint: constraint((T0297)D39.CB, (T0297)R63.CB) [> 3.9757 = 6.6262 < 8.6140] w=0.5426 to align # Constraint # added constraint: constraint((T0297)D39.CB, (T0297)I62.CB) [> 4.1103 = 6.8505 < 8.9057] w=0.5426 to align # Constraint # added constraint: constraint((T0297)I41.CB, (T0297)L194.CB) [> 3.9900 = 6.6501 < 8.6451] w=0.5426 to align # Constraint # added constraint: constraint((T0297)V101.CB, (T0297)A156.CB) [> 3.6797 = 6.1328 < 7.9726] w=0.5426 to align # Constraint # added constraint: constraint((T0297)I37.CB, (T0297)H77.CB) [> 4.2569 = 7.0948 < 9.2232] w=0.5426 to align # Constraint # added constraint: constraint((T0297)L130.CB, (T0297)L176.CB) [> 3.6408 = 6.0680 < 7.8885] w=0.5423 to align # Constraint # added constraint: constraint((T0297)V170.CB, (T0297)S205.CB) [> 3.4503 = 5.7505 < 7.4756] w=0.5422 to align # Constraint # added constraint: constraint((T0297)I90.CB, (T0297)L108.CB) [> 4.0419 = 6.7365 < 8.7574] w=0.5422 to align # Constraint # added constraint: constraint((T0297)R60.CB, (T0297)H77.CB) [> 3.3377 = 5.5629 < 7.2317] w=0.5222 to align # Constraint # added constraint: constraint((T0297)L74.CB, (T0297)V115.CB) [> 4.1946 = 6.9910 < 9.0882] w=0.5215 to align # Constraint # added constraint: constraint((T0297)V101.CB, (T0297)W153.CB) [> 3.4214 = 5.7023 < 7.4130] w=0.5200 to align # Constraint # added constraint: constraint((T0297)E186.CB, (T0297)S195.CB) [> 3.6203 = 6.0339 < 7.8440] w=0.5198 to align # Constraint # added constraint: constraint((T0297)N33.CB, (T0297)I57.CB) [> 4.4224 = 7.3707 < 9.5820] w=0.5196 to align # Constraint # added constraint: constraint((T0297)K125.CB, (T0297)L206.CB) [> 4.0015 = 6.6691 < 8.6699] w=0.5014 to align # Constraint # added constraint: constraint((T0297)L74.CB, (T0297)S114.CB) [> 3.4743 = 5.7905 < 7.5277] w=0.4989 to align # Constraint # added constraint: constraint((T0297)L70.CB, (T0297)I90.CB) [> 3.6412 = 6.0687 < 7.8893] w=0.4974 to align # Constraint # added constraint: constraint((T0297)V170.CB, (T0297)Y209.CB) [> 3.1573 = 5.2622 < 6.8409] w=0.4974 to align # Constraint # added constraint: constraint((T0297)L130.CB, (T0297)L194.CB) [> 4.2607 = 7.1012 < 9.2316] w=0.4974 to align # Constraint # added constraint: constraint((T0297)A104.CB, (T0297)A156.CB) [> 3.5412 = 5.9020 < 7.6726] w=0.4972 to align # Constraint # added constraint: constraint((T0297)L89.CB, (T0297)I129.CB) [> 4.0926 = 6.8211 < 8.8674] w=0.4969 to align # Constraint # added constraint: constraint((T0297)F87.CB, (T0297)L206.CB) [> 3.7488 = 6.2480 < 8.1223] w=0.4968 to align # Constraint # added constraint: constraint((T0297)V42.CB, (T0297)N59.CB) [> 4.0609 = 6.7682 < 8.7986] w=0.4748 to align # Constraint # added constraint: constraint((T0297)D39.CB, (T0297)Q66.CB) [> 4.5738 = 7.6229 < 9.9098] w=0.4748 to align # Constraint # added constraint: constraint((T0297)V172.CB, (T0297)S205.CB) [> 3.5022 = 5.8370 < 7.5881] w=0.4748 to align # Constraint # added constraint: constraint((T0297)G38.CA, (T0297)L70.CB) [> 3.6545 = 6.0908 < 7.9180] w=0.4748 to align # Constraint # added constraint: constraint((T0297)P46.CB, (T0297)H193.CB) [> 3.5134 = 5.8557 < 7.6124] w=0.4748 to align # Constraint # added constraint: constraint((T0297)T92.CB, (T0297)L130.CB) [> 4.1253 = 6.8755 < 8.9382] w=0.4747 to align # Constraint # added constraint: constraint((T0297)E109.CB, (T0297)Y164.CB) [> 3.7221 = 6.2035 < 8.0645] w=0.4744 to align # Constraint # added constraint: constraint((T0297)I124.CB, (T0297)Y164.CB) [> 4.1687 = 6.9479 < 9.0322] w=0.4740 to align # Constraint # added constraint: constraint((T0297)P32.CB, (T0297)K55.CB) [> 3.3808 = 5.6347 < 7.3251] w=0.4736 to align # Constraint # added constraint: constraint((T0297)A116.CB, (T0297)Y164.CB) [> 4.0860 = 6.8100 < 8.8530] w=0.4584 to align # Constraint # added constraint: constraint((T0297)N33.CB, (T0297)G81.CA) [> 3.7996 = 6.3327 < 8.2325] w=0.4564 to align # Constraint # added constraint: constraint((T0297)E186.CB, (T0297)G198.CA) [> 3.1398 = 5.2330 < 6.8029] w=0.4522 to align # Constraint # added constraint: constraint((T0297)P46.CB, (T0297)L194.CB) [> 3.9603 = 6.6005 < 8.5806] w=0.4522 to align # Constraint # added constraint: constraint((T0297)P131.CB, (T0297)F173.CB) [> 3.7383 = 6.2305 < 8.0996] w=0.4521 to align # Constraint # added constraint: constraint((T0297)L70.CB, (T0297)I111.CB) [> 3.6611 = 6.1018 < 7.9324] w=0.4519 to align # Constraint # added constraint: constraint((T0297)T122.CB, (T0297)Q166.CB) [> 4.2583 = 7.0972 < 9.2263] w=0.4516 to align # Constraint # added constraint: constraint((T0297)E168.CB, (T0297)Y209.CB) [> 3.6863 = 6.1438 < 7.9869] w=0.4516 to align # Constraint # added constraint: constraint((T0297)P32.CB, (T0297)D84.CB) [> 3.3845 = 5.6409 < 7.3332] w=0.4515 to align # Constraint # added constraint: constraint((T0297)E123.CB, (T0297)Q166.CB) [> 3.3499 = 5.5832 < 7.2581] w=0.4334 to align # Constraint # added constraint: constraint((T0297)V132.CB, (T0297)I150.CB) [> 4.0259 = 6.7099 < 8.7229] w=0.4317 to align # Constraint # added constraint: constraint((T0297)D94.CB, (T0297)W153.CB) [> 3.7399 = 6.2332 < 8.1032] w=0.4296 to align # Constraint # added constraint: constraint((T0297)S40.CB, (T0297)T92.CB) [> 4.4245 = 7.3742 < 9.5864] w=0.4295 to align # Constraint # added constraint: constraint((T0297)L89.CB, (T0297)S128.CB) [> 4.1258 = 6.8764 < 8.9393] w=0.4289 to align # Constraint # added constraint: constraint((T0297)I90.CB, (T0297)N107.CB) [> 4.3151 = 7.1919 < 9.3495] w=0.4133 to align # Constraint # added constraint: constraint((T0297)I37.CB, (T0297)I111.CB) [> 4.1967 = 6.9945 < 9.0928] w=0.4133 to align # Constraint # added constraint: constraint((T0297)V101.CB, (T0297)N152.CB) [> 2.8767 = 4.7945 < 6.2328] w=0.4092 to align # Constraint # added constraint: constraint((T0297)Y157.CB, (T0297)P171.CB) [> 4.4710 = 7.4517 < 9.6871] w=0.4087 to align # Constraint # added constraint: constraint((T0297)D94.CB, (T0297)E103.CB) [> 4.4405 = 7.4008 < 9.6210] w=0.4070 to align # Constraint # added constraint: constraint((T0297)L130.CB, (T0297)L202.CB) [> 4.1552 = 6.9253 < 9.0029] w=0.4070 to align # Constraint # added constraint: constraint((T0297)S40.CB, (T0297)I62.CB) [> 4.6661 = 7.7768 < 10.1099] w=0.4070 to align # Constraint # added constraint: constraint((T0297)L176.CB, (T0297)G198.CA) [> 4.4204 = 7.3674 < 9.5776] w=0.4070 to align # Constraint # added constraint: constraint((T0297)G91.CA, (T0297)Y157.CB) [> 4.5943 = 7.6572 < 9.9543] w=0.4070 to align # Constraint # added constraint: constraint((T0297)D94.CB, (T0297)N107.CB) [> 4.2576 = 7.0960 < 9.2249] w=0.4070 to align # Constraint # added constraint: constraint((T0297)L88.CB, (T0297)V115.CB) [> 4.4263 = 7.3771 < 9.5903] w=0.4066 to align # Constraint # added constraint: constraint((T0297)K125.CB, (T0297)Y209.CB) [> 3.5899 = 5.9832 < 7.7781] w=0.4065 to align # Constraint # added constraint: constraint((T0297)V42.CB, (T0297)F87.CB) [> 4.5587 = 7.5978 < 9.8771] w=0.4061 to align # Constraint # added constraint: constraint((T0297)F87.CB, (T0297)L210.CB) [> 4.4992 = 7.4987 < 9.7483] w=0.3843 to align # Constraint # added constraint: constraint((T0297)L127.CB, (T0297)Y157.CB) [> 4.1820 = 6.9700 < 9.0610] w=0.3843 to align # Constraint # added constraint: constraint((T0297)K85.CB, (T0297)L210.CB) [> 3.8375 = 6.3958 < 8.3146] w=0.3839 to align # Constraint # added constraint: constraint((T0297)D84.CB, (T0297)L121.CB) [> 4.2631 = 7.1051 < 9.2366] w=0.3835 to align # Constraint # added constraint: constraint((T0297)V132.CB, (T0297)L192.CB) [> 3.3328 = 5.5547 < 7.2211] w=0.3618 to align # Constraint # added constraint: constraint((T0297)Y45.CB, (T0297)H193.CB) [> 2.4577 = 4.0962 < 5.3251] w=0.3618 to align # Constraint # added constraint: constraint((T0297)P131.CB, (T0297)L176.CB) [> 3.1639 = 5.2731 < 6.8551] w=0.3617 to align # Constraint # added constraint: constraint((T0297)E31.CB, (T0297)T56.CB) [> 4.0927 = 6.8212 < 8.8676] w=0.3615 to align # Constraint # added constraint: constraint((T0297)P32.CB, (T0297)K85.CB) [> 4.1336 = 6.8893 < 8.9562] w=0.3613 to align # Constraint # added constraint: constraint((T0297)A82.CB, (T0297)L121.CB) [> 4.1438 = 6.9063 < 8.9782] w=0.3609 to align # Constraint # added constraint: constraint((T0297)I90.CB, (T0297)L127.CB) [> 4.5977 = 7.6628 < 9.9617] w=0.3608 to align # Constraint # added constraint: constraint((T0297)F36.CB, (T0297)L88.CB) [> 4.5100 = 7.5167 < 9.7717] w=0.3458 to align # Constraint # added constraint: constraint((T0297)I90.CB, (T0297)I111.CB) [> 4.2779 = 7.1299 < 9.2688] w=0.3456 to align # Constraint # added constraint: constraint((T0297)P131.CB, (T0297)N147.CB) [> 3.6166 = 6.0276 < 7.8359] w=0.3436 to align # Constraint # added constraint: constraint((T0297)C175.CB, (T0297)S205.CB) [> 3.1976 = 5.3294 < 6.9282] w=0.3392 to align # Constraint # added constraint: constraint((T0297)L176.CB, (T0297)A201.CB) [> 4.2404 = 7.0673 < 9.1876] w=0.3392 to align # Constraint # added constraint: constraint((T0297)V172.CB, (T0297)L206.CB) [> 3.5843 = 5.9738 < 7.7659] w=0.3392 to align # Constraint # added constraint: constraint((T0297)Y45.CB, (T0297)R63.CB) [> 3.8971 = 6.4951 < 8.4437] w=0.3392 to align # Constraint # added constraint: constraint((T0297)Y45.CB, (T0297)Y199.CB) [> 3.8018 = 6.3363 < 8.2372] w=0.3392 to align # Constraint # added constraint: constraint((T0297)Y45.CB, (T0297)L194.CB) [> 4.2859 = 7.1432 < 9.2862] w=0.3391 to align # Constraint # added constraint: constraint((T0297)I129.CB, (T0297)Y157.CB) [> 4.2747 = 7.1245 < 9.2618] w=0.3391 to align # Constraint # added constraint: constraint((T0297)A116.CB, (T0297)V167.CB) [> 4.1669 = 6.9448 < 9.0283] w=0.3390 to align # Constraint # added constraint: constraint((T0297)L105.CB, (T0297)Y157.CB) [> 3.9170 = 6.5284 < 8.4869] w=0.3390 to align # Constraint # added constraint: constraint((T0297)I34.CB, (T0297)L210.CB) [> 3.9987 = 6.6645 < 8.6638] w=0.3388 to align # Constraint # added constraint: constraint((T0297)V42.CB, (T0297)R60.CB) [> 4.2024 = 7.0040 < 9.1052] w=0.3383 to align # Constraint # added constraint: constraint((T0297)Y44.CB, (T0297)L194.CB) [> 4.0111 = 6.6852 < 8.6907] w=0.3165 to align # Constraint # added constraint: constraint((T0297)Y44.CB, (T0297)H193.CB) [> 3.6069 = 6.0114 < 7.8149] w=0.3165 to align # Constraint # added constraint: constraint((T0297)K125.CB, (T0297)L210.CB) [> 4.2846 = 7.1409 < 9.2832] w=0.3165 to align # Constraint # added constraint: constraint((T0297)P46.CB, (T0297)S195.CB) [> 3.7060 = 6.1767 < 8.0297] w=0.3165 to align # Constraint # added constraint: constraint((T0297)N133.CB, (T0297)G191.CA) [> 3.5006 = 5.8343 < 7.5845] w=0.3165 to align # Constraint # added constraint: constraint((T0297)I90.CB, (T0297)A104.CB) [> 3.8221 = 6.3701 < 8.2811] w=0.3162 to align # Constraint # added constraint: constraint((T0297)I86.CB, (T0297)Y119.CB) [> 3.8657 = 6.4428 < 8.3756] w=0.3162 to align # Constraint # added constraint: constraint((T0297)L127.CB, (T0297)L202.CB) [> 3.8668 = 6.4447 < 8.3781] w=0.3160 to align # Constraint # added constraint: constraint((T0297)L47.CB, (T0297)Y199.CB) [> 3.3241 = 5.5402 < 7.2022] w=0.2939 to align # Constraint # added constraint: constraint((T0297)N133.CB, (T0297)L192.CB) [> 4.5600 = 7.6001 < 9.8801] w=0.2939 to align # Constraint # added constraint: constraint((T0297)L35.CB, (T0297)G81.CA) [> 3.9797 = 6.6329 < 8.6227] w=0.2939 to align # Constraint # added constraint: constraint((T0297)Y44.CB, (T0297)R63.CB) [> 4.4222 = 7.3703 < 9.5814] w=0.2936 to align # Constraint # added constraint: constraint((T0297)S40.CB, (T0297)N93.CB) [> 4.2343 = 7.0572 < 9.1744] w=0.2929 to align # Constraint # added constraint: constraint((T0297)S40.CB, (T0297)G61.CA) [> 4.4578 = 7.4297 < 9.6586] w=0.2758 to align # Constraint # added constraint: constraint((T0297)N133.CB, (T0297)N147.CB) [> 3.7812 = 6.3020 < 8.1926] w=0.2736 to align # Constraint # added constraint: constraint((T0297)R60.CB, (T0297)L74.CB) [> 4.3684 = 7.2806 < 9.4648] w=0.2734 to align # Constraint # added constraint: constraint((T0297)S40.CB, (T0297)L192.CB) [> 4.4877 = 7.4794 < 9.7233] w=0.2713 to align # Constraint # added constraint: constraint((T0297)I41.CB, (T0297)L202.CB) [> 4.4901 = 7.4835 < 9.7286] w=0.2713 to align # Constraint # added constraint: constraint((T0297)L176.CB, (T0297)L202.CB) [> 3.5052 = 5.8420 < 7.5946] w=0.2713 to align # Constraint # added constraint: constraint((T0297)L176.CB, (T0297)S205.CB) [> 3.3316 = 5.5526 < 7.2184] w=0.2713 to align # Constraint # added constraint: constraint((T0297)D39.CB, (T0297)L70.CB) [> 4.5150 = 7.5250 < 9.7824] w=0.2713 to align # Constraint # added constraint: constraint((T0297)V42.CB, (T0297)I90.CB) [> 4.5005 = 7.5008 < 9.7510] w=0.2713 to align # Constraint # added constraint: constraint((T0297)I41.CB, (T0297)L127.CB) [> 4.6212 = 7.7019 < 10.0125] w=0.2713 to align # Constraint # added constraint: constraint((T0297)V132.CB, (T0297)G191.CA) [> 3.5447 = 5.9078 < 7.6802] w=0.2713 to align # Constraint # added constraint: constraint((T0297)I41.CB, (T0297)I129.CB) [> 4.3372 = 7.2287 < 9.3973] w=0.2713 to align # Constraint # added constraint: constraint((T0297)I95.CB, (T0297)I129.CB) [> 4.0588 = 6.7647 < 8.7941] w=0.2713 to align # Constraint # added constraint: constraint((T0297)T67.CB, (T0297)N93.CB) [> 4.3927 = 7.3211 < 9.5175] w=0.2713 to align # Constraint # added constraint: constraint((T0297)Y187.CB, (T0297)G198.CA) [> 3.3611 = 5.6018 < 7.2823] w=0.2711 to align # Constraint # added constraint: constraint((T0297)V132.CB, (T0297)L183.CB) [> 4.3632 = 7.2720 < 9.4536] w=0.2711 to align # Constraint # added constraint: constraint((T0297)V132.CB, (T0297)S146.CB) [> 3.6058 = 6.0097 < 7.8126] w=0.2510 to align # Constraint # added constraint: constraint((T0297)V101.CB, (T0297)K149.CB) [> 3.6455 = 6.0759 < 7.8987] w=0.2510 to align # Constraint # added constraint: constraint((T0297)L50.CB, (T0297)S203.CB) [> 2.8296 = 4.7160 < 6.1308] w=0.2508 to align # Constraint # added constraint: constraint((T0297)N133.CB, (T0297)L183.CB) [> 4.0778 = 6.7963 < 8.8352] w=0.2487 to align # Constraint # added constraint: constraint((T0297)Y45.CB, (T0297)T188.CB) [> 4.0362 = 6.7270 < 8.7451] w=0.2487 to align # Constraint # added constraint: constraint((T0297)P32.CB, (T0297)I57.CB) [> 3.2848 = 5.4747 < 7.1171] w=0.2486 to align # Constraint # added constraint: constraint((T0297)P131.CB, (T0297)L183.CB) [> 3.8500 = 6.4167 < 8.3417] w=0.2486 to align # Constraint # added constraint: constraint((T0297)T67.CB, (T0297)A110.CB) [> 4.3078 = 7.1797 < 9.3336] w=0.2483 to align # Constraint # added constraint: constraint((T0297)L74.CB, (T0297)I86.CB) [> 4.1789 = 6.9648 < 9.0542] w=0.2481 to align # Constraint # added constraint: constraint((T0297)L78.CB, (T0297)Y119.CB) [> 3.3291 = 5.5486 < 7.2132] w=0.2481 to align # Constraint # added constraint: constraint((T0297)L71.CB, (T0297)V115.CB) [> 4.2356 = 7.0594 < 9.1772] w=0.2480 to align # Constraint # added constraint: constraint((T0297)V170.CB, (T0297)L202.CB) [> 4.2994 = 7.1656 < 9.3153] w=0.2302 to align # Constraint # added constraint: constraint((T0297)L78.CB, (T0297)T122.CB) [> 3.8238 = 6.3730 < 8.2849] w=0.2277 to align # Constraint # added constraint: constraint((T0297)I95.CB, (T0297)K149.CB) [> 3.6147 = 6.0246 < 7.8319] w=0.2261 to align # Constraint # added constraint: constraint((T0297)T92.CB, (T0297)V132.CB) [> 3.7129 = 6.1883 < 8.0447] w=0.2261 to align # Constraint # added constraint: constraint((T0297)I95.CB, (T0297)I150.CB) [> 3.0805 = 5.1341 < 6.6744] w=0.2261 to align # Constraint # added constraint: constraint((T0297)P46.CB, (T0297)I196.CB) [> 2.8101 = 4.6835 < 6.0886] w=0.2261 to align # Constraint # added constraint: constraint((T0297)E134.CB, (T0297)G191.CA) [> 3.4104 = 5.6840 < 7.3892] w=0.2261 to align # Constraint # added constraint: constraint((T0297)G64.CA, (T0297)T92.CB) [> 4.4005 = 7.3342 < 9.5344] w=0.2255 to align # Constraint # added constraint: constraint((T0297)L50.CB, (T0297)Y199.CB) [> 3.5143 = 5.8571 < 7.6143] w=0.2056 to align # Constraint # added constraint: constraint((T0297)P131.CB, (T0297)A180.CB) [> 4.0042 = 6.6736 < 8.6757] w=0.2035 to align # Constraint # added constraint: constraint((T0297)E49.CB, (T0297)N59.CB) [> 3.7637 = 6.2729 < 8.1548] w=0.2035 to align # Constraint # added constraint: constraint((T0297)F87.CB, (T0297)V170.CB) [> 4.6497 = 7.7495 < 10.0744] w=0.2035 to align # Constraint # added constraint: constraint((T0297)G68.CA, (T0297)D94.CB) [> 4.5717 = 7.6195 < 9.9053] w=0.2035 to align # Constraint # added constraint: constraint((T0297)I150.CB, (T0297)F173.CB) [> 4.1400 = 6.8999 < 8.9699] w=0.2035 to align # Constraint # added constraint: constraint((T0297)N133.CB, (T0297)S146.CB) [> 3.7187 = 6.1978 < 8.0572] w=0.2035 to align # Constraint # added constraint: constraint((T0297)E31.CB, (T0297)G81.CA) [> 3.9594 = 6.5990 < 8.5787] w=0.2035 to align # Constraint # added constraint: constraint((T0297)L47.CB, (T0297)S203.CB) [> 2.9141 = 4.8569 < 6.3140] w=0.2034 to align # Constraint # added constraint: constraint((T0297)L127.CB, (T0297)F173.CB) [> 4.0837 = 6.8061 < 8.8480] w=0.2029 to align # Constraint # added constraint: constraint((T0297)F51.CB, (T0297)S203.CB) [> 3.0466 = 5.0777 < 6.6010] w=0.1809 to align # Constraint # added constraint: constraint((T0297)L47.CB, (T0297)L202.CB) [> 2.9073 = 4.8455 < 6.2991] w=0.1809 to align # Constraint # added constraint: constraint((T0297)Q48.CB, (T0297)I57.CB) [> 3.8953 = 6.4921 < 8.4398] w=0.1809 to align # Constraint # added constraint: constraint((T0297)Q48.CB, (T0297)N59.CB) [> 2.8187 = 4.6978 < 6.1071] w=0.1809 to align # Constraint # added constraint: constraint((T0297)F51.CB, (T0297)K207.CB) [> 4.1005 = 6.8342 < 8.8845] w=0.1809 to align # Constraint # added constraint: constraint((T0297)E134.CB, (T0297)L183.CB) [> 3.7576 = 6.2627 < 8.1415] w=0.1809 to align # Constraint # added constraint: constraint((T0297)F51.CB, (T0297)Y199.CB) [> 4.1423 = 6.9039 < 8.9750] w=0.1809 to align # Constraint # added constraint: constraint((T0297)R135.CB, (T0297)G191.CA) [> 3.6734 = 6.1224 < 7.9591] w=0.1809 to align # Constraint # added constraint: constraint((T0297)P131.CB, (T0297)L192.CB) [> 3.8928 = 6.4879 < 8.4343] w=0.1809 to align # Constraint # added constraint: constraint((T0297)P32.CB, (T0297)S54.CB) [> 4.5080 = 7.5133 < 9.7673] w=0.1808 to align # Constraint # added constraint: constraint((T0297)C175.CB, (T0297)Y187.CB) [> 3.6716 = 6.1194 < 7.9552] w=0.1805 to align # Constraint # added constraint: constraint((T0297)G96.CA, (T0297)V142.CB) [> 4.0033 = 6.6722 < 8.6738] w=0.1805 to align # Constraint # added constraint: constraint((T0297)G38.CA, (T0297)G91.CA) [> 4.3299 = 7.2166 < 9.3815] w=0.1648 to align # Constraint # added constraint: constraint((T0297)T92.CB, (T0297)S146.CB) [> 4.1592 = 6.9321 < 9.0117] w=0.1627 to align # Constraint # added constraint: constraint((T0297)L50.CB, (T0297)Q200.CB) [> 3.3615 = 5.6026 < 7.2833] w=0.1605 to align # Constraint # added constraint: constraint((T0297)N133.CB, (T0297)Y143.CB) [> 4.0096 = 6.6827 < 8.6875] w=0.1605 to align # Constraint # added constraint: constraint((T0297)G96.CA, (T0297)S146.CB) [> 3.9454 = 6.5756 < 8.5483] w=0.1604 to align # Constraint # added constraint: constraint((T0297)S40.CB, (T0297)Y65.CB) [> 4.6112 = 7.6853 < 9.9909] w=0.1604 to align # Constraint # added constraint: constraint((T0297)L47.CB, (T0297)L194.CB) [> 4.3698 = 7.2830 < 9.4679] w=0.1583 to align # Constraint # added constraint: constraint((T0297)L47.CB, (T0297)L206.CB) [> 3.8162 = 6.3603 < 8.2684] w=0.1583 to align # Constraint # added constraint: constraint((T0297)N133.CB, (T0297)E186.CB) [> 4.5445 = 7.5743 < 9.8465] w=0.1583 to align # Constraint # added constraint: constraint((T0297)N133.CB, (T0297)Y187.CB) [> 3.4100 = 5.6833 < 7.3883] w=0.1583 to align # Constraint # added constraint: constraint((T0297)V170.CB, (T0297)L210.CB) [> 4.1571 = 6.9285 < 9.0071] w=0.1583 to align # Constraint # added constraint: constraint((T0297)L47.CB, (T0297)I196.CB) [> 3.4576 = 5.7627 < 7.4915] w=0.1583 to align # Constraint # added constraint: constraint((T0297)R135.CB, (T0297)L192.CB) [> 3.9845 = 6.6408 < 8.6331] w=0.1583 to align # Constraint # added constraint: constraint((T0297)L130.CB, (T0297)Y187.CB) [> 3.8855 = 6.4758 < 8.4185] w=0.1583 to align # Constraint # added constraint: constraint((T0297)G96.CA, (T0297)Y143.CB) [> 4.1682 = 6.9471 < 9.0312] w=0.1582 to align # Constraint # added constraint: constraint((T0297)Y44.CB, (T0297)N59.CB) [> 3.7138 = 6.1897 < 8.0466] w=0.1582 to align # Constraint # added constraint: constraint((T0297)I95.CB, (T0297)E134.CB) [> 4.2361 = 7.0602 < 9.1783] w=0.1582 to align # Constraint # added constraint: constraint((T0297)A180.CB, (T0297)A201.CB) [> 3.7317 = 6.2196 < 8.0855] w=0.1582 to align # Constraint # added constraint: constraint((T0297)L121.CB, (T0297)M165.CB) [> 4.2511 = 7.0851 < 9.2107] w=0.1579 to align # Constraint # added constraint: constraint((T0297)L35.CB, (T0297)Y119.CB) [> 4.4454 = 7.4089 < 9.6316] w=0.1579 to align # Constraint # added constraint: constraint((T0297)G91.CA, (T0297)S128.CB) [> 3.9292 = 6.5486 < 8.5132] w=0.1577 to align # Constraint # added constraint: constraint((T0297)I90.CB, (T0297)S128.CB) [> 3.9732 = 6.6219 < 8.6085] w=0.1575 to align # Constraint # added constraint: constraint((T0297)I124.CB, (T0297)V170.CB) [> 4.2657 = 7.1095 < 9.2424] w=0.1422 to align # Constraint # added constraint: constraint((T0297)I124.CB, (T0297)F169.CB) [> 3.3711 = 5.6186 < 7.3041] w=0.1422 to align # Constraint # added constraint: constraint((T0297)V172.CB, (T0297)L194.CB) [> 4.3715 = 7.2858 < 9.4716] w=0.1379 to align # Constraint # added constraint: constraint((T0297)T122.CB, (T0297)V167.CB) [> 3.6374 = 6.0623 < 7.8811] w=0.1379 to align # Constraint # added constraint: constraint((T0297)G91.CA, (T0297)E103.CB) [> 3.6218 = 6.0363 < 7.8472] w=0.1375 to align # Constraint # added constraint: constraint((T0297)K125.CB, (T0297)P171.CB) [> 4.2578 = 7.0963 < 9.2251] w=0.1374 to align # Constraint # added constraint: constraint((T0297)P171.CB, (T0297)Y209.CB) [> 4.0448 = 6.7414 < 8.7638] w=0.1357 to align # Constraint # added constraint: constraint((T0297)Q179.CB, (T0297)K204.CB) [> 4.6709 = 7.7848 < 10.1203] w=0.1357 to align # Constraint # added constraint: constraint((T0297)L89.CB, (T0297)L130.CB) [> 4.5626 = 7.6044 < 9.8857] w=0.1357 to align # Constraint # added constraint: constraint((T0297)I41.CB, (T0297)L192.CB) [> 4.0885 = 6.8141 < 8.8584] w=0.1357 to align # Constraint # added constraint: constraint((T0297)T188.CB, (T0297)G198.CA) [> 4.3127 = 7.1878 < 9.3441] w=0.1357 to align # Constraint # added constraint: constraint((T0297)Y187.CB, (T0297)A197.CB) [> 3.5730 = 5.9550 < 7.7414] w=0.1357 to align # Constraint # added constraint: constraint((T0297)D174.CB, (T0297)S205.CB) [> 4.5045 = 7.5075 < 9.7597] w=0.1357 to align # Constraint # added constraint: constraint((T0297)V132.CB, (T0297)T188.CB) [> 4.6946 = 7.8242 < 10.1715] w=0.1357 to align # Constraint # added constraint: constraint((T0297)Y45.CB, (T0297)N59.CB) [> 4.0891 = 6.8151 < 8.8596] w=0.1357 to align # Constraint # added constraint: constraint((T0297)F36.CB, (T0297)Y45.CB) [> 4.4240 = 7.3734 < 9.5854] w=0.1357 to align # Constraint # added constraint: constraint((T0297)P131.CB, (T0297)G191.CA) [> 3.1987 = 5.3311 < 6.9304] w=0.1357 to align # Constraint # added constraint: constraint((T0297)L127.CB, (T0297)S205.CB) [> 4.5416 = 7.5693 < 9.8401] w=0.1354 to align # Constraint # added constraint: constraint((T0297)I57.CB, (T0297)K85.CB) [> 4.2656 = 7.1094 < 9.2422] w=0.1354 to align # Constraint # added constraint: constraint((T0297)V30.CB, (T0297)V58.CB) [> 3.5832 = 5.9720 < 7.7635] w=0.1354 to align # Constraint # added constraint: constraint((T0297)I34.CB, (T0297)R60.CB) [> 3.7835 = 6.3059 < 8.1977] w=0.1353 to align # Constraint # added constraint: constraint((T0297)E31.CB, (T0297)V58.CB) [> 3.3299 = 5.5498 < 7.2147] w=0.1353 to align # Constraint # added constraint: constraint((T0297)T188.CB, (T0297)Y199.CB) [> 3.7585 = 6.2642 < 8.1435] w=0.1351 to align # Constraint # added constraint: constraint((T0297)A116.CB, (T0297)M165.CB) [> 4.5701 = 7.6169 < 9.9019] w=0.1351 to align # Constraint # added constraint: constraint((T0297)K125.CB, (T0297)S205.CB) [> 3.9642 = 6.6070 < 8.5891] w=0.1351 to align # Constraint # added constraint: constraint((T0297)I34.CB, (T0297)L206.CB) [> 3.8827 = 6.4712 < 8.4125] w=0.1350 to align # Constraint # added constraint: constraint((T0297)T92.CB, (T0297)L127.CB) [> 3.7984 = 6.3306 < 8.2298] w=0.1347 to align # Constraint # added constraint: constraint((T0297)G61.CA, (T0297)L88.CB) [> 4.2096 = 7.0160 < 9.1207] w=0.1346 to align # Constraint # added constraint: constraint((T0297)T56.CB, (T0297)D84.CB) [> 3.4283 = 5.7138 < 7.4279] w=0.1345 to align # Constraint # added constraint: constraint((T0297)I57.CB, (T0297)V83.CB) [> 3.6543 = 6.0905 < 7.9177] w=0.1345 to align # Constraint # added constraint: constraint((T0297)V58.CB, (T0297)I86.CB) [> 3.8435 = 6.4058 < 8.3275] w=0.1345 to align # Constraint # added constraint: constraint((T0297)G96.CA, (T0297)L130.CB) [> 3.4634 = 5.7723 < 7.5039] w=0.1345 to align # Constraint # added constraint: constraint((T0297)I37.CB, (T0297)N59.CB) [> 3.8942 = 6.4904 < 8.4375] w=0.1188 to align # Constraint # added constraint: constraint((T0297)C175.CB, (T0297)L194.CB) [> 3.2662 = 5.4437 < 7.0768] w=0.1153 to align # Constraint # added constraint: constraint((T0297)I129.CB, (T0297)P171.CB) [> 4.3128 = 7.1880 < 9.3443] w=0.1148 to align # Constraint # added constraint: constraint((T0297)L89.CB, (T0297)Y157.CB) [> 4.4830 = 7.4716 < 9.7131] w=0.1131 to align # Constraint # added constraint: constraint((T0297)I90.CB, (T0297)Y157.CB) [> 4.3466 = 7.2443 < 9.4176] w=0.1131 to align # Constraint # added constraint: constraint((T0297)L35.CB, (T0297)T122.CB) [> 4.5888 = 7.6480 < 9.9425] w=0.1131 to align # Constraint # added constraint: constraint((T0297)L47.CB, (T0297)H193.CB) [> 3.6582 = 6.0970 < 7.9261] w=0.1131 to align # Constraint # added constraint: constraint((T0297)L69.CB, (T0297)N93.CB) [> 4.5249 = 7.5415 < 9.8039] w=0.1131 to align # Constraint # added constraint: constraint((T0297)Y138.CB, (T0297)G191.CA) [> 3.4168 = 5.6947 < 7.4031] w=0.1131 to align # Constraint # added constraint: constraint((T0297)C175.CB, (T0297)G198.CA) [> 2.8115 = 4.6858 < 6.0915] w=0.1130 to align # Constraint # added constraint: constraint((T0297)C175.CB, (T0297)S195.CB) [> 4.6845 = 7.8074 < 10.1497] w=0.1130 to align # Constraint # added constraint: constraint((T0297)L24.CB, (T0297)H77.CB) [> 3.5533 = 5.9222 < 7.6989] w=0.1129 to align # Constraint # added constraint: constraint((T0297)P131.CB, (T0297)K184.CB) [> 3.9566 = 6.5944 < 8.5727] w=0.1129 to align # Constraint # added constraint: constraint((T0297)L47.CB, (T0297)T188.CB) [> 3.9509 = 6.5848 < 8.5603] w=0.1129 to align # Constraint # added constraint: constraint((T0297)G80.CA, (T0297)T122.CB) [> 4.1281 = 6.8801 < 8.9442] w=0.1129 to align # Constraint # added constraint: constraint((T0297)E123.CB, (T0297)L210.CB) [> 4.1237 = 6.8728 < 8.9347] w=0.1128 to align # Constraint # added constraint: constraint((T0297)A161.CB, (T0297)V170.CB) [> 3.3539 = 5.5899 < 7.2668] w=0.1126 to align # Constraint # added constraint: constraint((T0297)Y157.CB, (T0297)V167.CB) [> 3.6709 = 6.1181 < 7.9535] w=0.1124 to align # Constraint # added constraint: constraint((T0297)G61.CA, (T0297)F87.CB) [> 3.8827 = 6.4711 < 8.4125] w=0.1120 to align # Constraint # added constraint: constraint((T0297)I112.CB, (T0297)Y157.CB) [> 4.1743 = 6.9571 < 9.0443] w=0.0971 to align # Constraint # added constraint: constraint((T0297)L160.CB, (T0297)F169.CB) [> 4.5683 = 7.6138 < 9.8979] w=0.0968 to align # Constraint # added constraint: constraint((T0297)T53.CB, (T0297)L206.CB) [> 3.7788 = 6.2980 < 8.1874] w=0.0904 to align # Constraint # added constraint: constraint((T0297)I95.CB, (T0297)L130.CB) [> 4.1544 = 6.9240 < 9.0012] w=0.0904 to align # Constraint # added constraint: constraint((T0297)L47.CB, (T0297)L130.CB) [> 4.3223 = 7.2038 < 9.3649] w=0.0904 to align # Constraint # added constraint: constraint((T0297)S28.CB, (T0297)Y79.CB) [> 3.9717 = 6.6195 < 8.6054] w=0.0904 to align # Constraint # added constraint: constraint((T0297)I27.CB, (T0297)Y79.CB) [> 3.2926 = 5.4878 < 7.1341] w=0.0904 to align # Constraint # added constraint: constraint((T0297)I27.CB, (T0297)L78.CB) [> 4.1024 = 6.8373 < 8.8885] w=0.0904 to align # Constraint # added constraint: constraint((T0297)I27.CB, (T0297)V58.CB) [> 4.2510 = 7.0850 < 9.2106] w=0.0904 to align # Constraint # added constraint: constraint((T0297)H26.CB, (T0297)R60.CB) [> 4.6619 = 7.7698 < 10.1008] w=0.0904 to align # Constraint # added constraint: constraint((T0297)H26.CB, (T0297)V58.CB) [> 3.4029 = 5.6715 < 7.3729] w=0.0904 to align # Constraint # added constraint: constraint((T0297)L24.CB, (T0297)Y79.CB) [> 4.2475 = 7.0791 < 9.2029] w=0.0904 to align # Constraint # added constraint: constraint((T0297)L6.CB, (T0297)K20.CB) [> 4.6282 = 7.7137 < 10.0278] w=0.0904 to align # Constraint # added constraint: constraint((T0297)L6.CB, (T0297)L69.CB) [> 4.1337 = 6.8895 < 8.9564] w=0.0904 to align # Constraint # added constraint: constraint((T0297)E7.CB, (T0297)Y65.CB) [> 4.1826 = 6.9709 < 9.0622] w=0.0904 to align # Constraint # added constraint: constraint((T0297)K20.CB, (T0297)I62.CB) [> 4.6666 = 7.7777 < 10.1110] w=0.0904 to align # Constraint # added constraint: constraint((T0297)H23.CB, (T0297)V58.CB) [> 4.4103 = 7.3504 < 9.5555] w=0.0904 to align # Constraint # added constraint: constraint((T0297)H23.CB, (T0297)R60.CB) [> 2.7473 = 4.5789 < 5.9526] w=0.0904 to align # Constraint # added constraint: constraint((T0297)L47.CB, (T0297)S195.CB) [> 4.0781 = 6.7969 < 8.8359] w=0.0904 to align # Constraint # added constraint: constraint((T0297)I95.CB, (T0297)V142.CB) [> 2.5033 = 4.1722 < 5.4239] w=0.0904 to align # Constraint # added constraint: constraint((T0297)I95.CB, (T0297)N133.CB) [> 3.7063 = 6.1772 < 8.0303] w=0.0904 to align # Constraint # added constraint: constraint((T0297)G96.CA, (T0297)Y138.CB) [> 3.3254 = 5.5423 < 7.2050] w=0.0904 to align # Constraint # added constraint: constraint((T0297)I95.CB, (T0297)Y138.CB) [> 3.1242 = 5.2070 < 6.7691] w=0.0904 to align # Constraint # added constraint: constraint((T0297)T92.CB, (T0297)N133.CB) [> 4.1685 = 6.9474 < 9.0317] w=0.0903 to align # Constraint # added constraint: constraint((T0297)V30.CB, (T0297)S54.CB) [> 4.1363 = 6.8939 < 8.9620] w=0.0903 to align # Constraint # added constraint: constraint((T0297)I34.CB, (T0297)G61.CA) [> 4.2068 = 7.0113 < 9.1147] w=0.0902 to align # Constraint # added constraint: constraint((T0297)P171.CB, (T0297)S205.CB) [> 3.8485 = 6.4142 < 8.3385] w=0.0902 to align # Constraint # added constraint: constraint((T0297)T92.CB, (T0297)S128.CB) [> 2.9898 = 4.9831 < 6.4780] w=0.0901 to align # Constraint # added constraint: constraint((T0297)N93.CB, (T0297)L130.CB) [> 3.9438 = 6.5730 < 8.5449] w=0.0901 to align # Constraint # added constraint: constraint((T0297)E123.CB, (T0297)L206.CB) [> 4.6346 = 7.7243 < 10.0415] w=0.0901 to align # Constraint # added constraint: constraint((T0297)V30.CB, (T0297)T56.CB) [> 3.9649 = 6.6082 < 8.5907] w=0.0900 to align # Constraint # added constraint: constraint((T0297)L47.CB, (T0297)G61.CA) [> 4.4170 = 7.3617 < 9.5702] w=0.0896 to align # Constraint # added constraint: constraint((T0297)E43.CB, (T0297)G64.CA) [> 3.1869 = 5.3115 < 6.9049] w=0.0895 to align # Constraint # added constraint: constraint((T0297)G96.CA, (T0297)I129.CB) [> 4.0763 = 6.7937 < 8.8319] w=0.0895 to align # Constraint # added constraint: constraint((T0297)G38.CA, (T0297)N59.CB) [> 4.5343 = 7.5572 < 9.8244] w=0.0744 to align # Constraint # added constraint: constraint((T0297)K85.CB, (T0297)K207.CB) [> 4.5670 = 7.6117 < 9.8952] w=0.0720 to align # Constraint # added constraint: constraint((T0297)I34.CB, (T0297)S203.CB) [> 4.6823 = 7.8038 < 10.1449] w=0.0720 to align # Constraint # added constraint: constraint((T0297)S128.CB, (T0297)S146.CB) [> 4.6714 = 7.7856 < 10.1213] w=0.0701 to align # Constraint # added constraint: constraint((T0297)P131.CB, (T0297)Y143.CB) [> 4.1734 = 6.9557 < 9.0424] w=0.0700 to align # Constraint # added constraint: constraint((T0297)K125.CB, (T0297)Y157.CB) [> 4.3126 = 7.1877 < 9.3440] w=0.0700 to align # Constraint # added constraint: constraint((T0297)F36.CB, (T0297)L47.CB) [> 3.6428 = 6.0714 < 7.8927] w=0.0699 to align # Constraint # added constraint: constraint((T0297)L130.CB, (T0297)G198.CA) [> 3.8501 = 6.4168 < 8.3418] w=0.0678 to align # Constraint # added constraint: constraint((T0297)Y44.CB, (T0297)S195.CB) [> 3.9972 = 6.6621 < 8.6607] w=0.0678 to align # Constraint # added constraint: constraint((T0297)L47.CB, (T0297)G198.CA) [> 4.7166 = 7.8611 < 10.2194] w=0.0678 to align # Constraint # added constraint: constraint((T0297)F36.CB, (T0297)L206.CB) [> 4.5506 = 7.5843 < 9.8596] w=0.0678 to align # Constraint # added constraint: constraint((T0297)E134.CB, (T0297)D190.CB) [> 3.8177 = 6.3629 < 8.2718] w=0.0678 to align # Constraint # added constraint: constraint((T0297)L130.CB, (T0297)L192.CB) [> 3.3811 = 5.6351 < 7.3256] w=0.0678 to align # Constraint # added constraint: constraint((T0297)G38.CA, (T0297)F87.CB) [> 4.7009 = 7.8348 < 10.1852] w=0.0678 to align # Constraint # added constraint: constraint((T0297)V42.CB, (T0297)T53.CB) [> 3.9637 = 6.6062 < 8.5881] w=0.0678 to align # Constraint # added constraint: constraint((T0297)L47.CB, (T0297)D190.CB) [> 4.5275 = 7.5459 < 9.8097] w=0.0678 to align # Constraint # added constraint: constraint((T0297)V142.CB, (T0297)L192.CB) [> 4.3930 = 7.3217 < 9.5181] w=0.0678 to align # Constraint # added constraint: constraint((T0297)L47.CB, (T0297)K207.CB) [> 3.0178 = 5.0296 < 6.5385] w=0.0678 to align # Constraint # added constraint: constraint((T0297)P131.CB, (T0297)L194.CB) [> 4.6238 = 7.7064 < 10.0183] w=0.0678 to align # Constraint # added constraint: constraint((T0297)P131.CB, (T0297)H193.CB) [> 4.2366 = 7.0611 < 9.1794] w=0.0678 to align # Constraint # added constraint: constraint((T0297)T92.CB, (T0297)P131.CB) [> 3.4267 = 5.7112 < 7.4246] w=0.0678 to align # Constraint # added constraint: constraint((T0297)L130.CB, (T0297)G191.CA) [> 3.5347 = 5.8912 < 7.6585] w=0.0678 to align # Constraint # added constraint: constraint((T0297)G91.CA, (T0297)L127.CB) [> 2.9702 = 4.9504 < 6.4355] w=0.0678 to align # Constraint # added constraint: constraint((T0297)L35.CB, (T0297)G61.CA) [> 3.6303 = 6.0505 < 7.8656] w=0.0677 to align # Constraint # added constraint: constraint((T0297)D98.CB, (T0297)I144.CB) [> 3.9261 = 6.5435 < 8.5065] w=0.0677 to align # Constraint # added constraint: constraint((T0297)V29.CB, (T0297)K55.CB) [> 4.2747 = 7.1246 < 9.2619] w=0.0677 to align # Constraint # added constraint: constraint((T0297)D178.CB, (T0297)T189.CB) [> 3.7114 = 6.1857 < 8.0414] w=0.0677 to align # Constraint # added constraint: constraint((T0297)T177.CB, (T0297)D190.CB) [> 3.9470 = 6.5784 < 8.5519] w=0.0677 to align # Constraint # added constraint: constraint((T0297)I129.CB, (T0297)Y187.CB) [> 3.6397 = 6.0661 < 7.8860] w=0.0676 to align # Constraint # added constraint: constraint((T0297)K85.CB, (T0297)E168.CB) [> 4.5942 = 7.6571 < 9.9542] w=0.0676 to align # Constraint # added constraint: constraint((T0297)I57.CB, (T0297)D84.CB) [> 2.8595 = 4.7659 < 6.1957] w=0.0676 to align # Constraint # added constraint: constraint((T0297)I37.CB, (T0297)P171.CB) [> 4.1640 = 6.9400 < 9.0220] w=0.0676 to align # Constraint # added constraint: constraint((T0297)Y187.CB, (T0297)Y199.CB) [> 2.6866 = 4.4777 < 5.8210] w=0.0676 to align # Constraint # added constraint: constraint((T0297)S162.CB, (T0297)S205.CB) [> 3.2330 = 5.3883 < 7.0047] w=0.0676 to align # Constraint # added constraint: constraint((T0297)A161.CB, (T0297)L206.CB) [> 4.1592 = 6.9321 < 9.0117] w=0.0676 to align # Constraint # added constraint: constraint((T0297)A161.CB, (T0297)S205.CB) [> 2.8205 = 4.7007 < 6.1110] w=0.0676 to align # Constraint # added constraint: constraint((T0297)I150.CB, (T0297)S195.CB) [> 3.7200 = 6.2000 < 8.0599] w=0.0676 to align # Constraint # added constraint: constraint((T0297)G91.CA, (T0297)L130.CB) [> 3.4402 = 5.7337 < 7.4538] w=0.0676 to align # Constraint # added constraint: constraint((T0297)V172.CB, (T0297)D190.CB) [> 4.0081 = 6.6802 < 8.6843] w=0.0675 to align # Constraint # added constraint: constraint((T0297)F173.CB, (T0297)D190.CB) [> 4.6995 = 7.8324 < 10.1822] w=0.0675 to align # Constraint # added constraint: constraint((T0297)D174.CB, (T0297)D190.CB) [> 3.5338 = 5.8897 < 7.6566] w=0.0675 to align # Constraint # added constraint: constraint((T0297)D39.CB, (T0297)P100.CB) [> 4.5383 = 7.5638 < 9.8330] w=0.0675 to align # Constraint # added constraint: constraint((T0297)F36.CB, (T0297)I62.CB) [> 4.0167 = 6.6946 < 8.7029] w=0.0675 to align # Constraint # added constraint: constraint((T0297)K85.CB, (T0297)L206.CB) [> 3.0404 = 5.0673 < 6.5874] w=0.0675 to align # Constraint # added constraint: constraint((T0297)G91.CA, (T0297)P100.CB) [> 3.0776 = 5.1293 < 6.6681] w=0.0675 to align # Constraint # added constraint: constraint((T0297)E168.CB, (T0297)S205.CB) [> 4.1097 = 6.8495 < 8.9043] w=0.0675 to align # Constraint # added constraint: constraint((T0297)L47.CB, (T0297)I62.CB) [> 4.3572 = 7.2620 < 9.4406] w=0.0671 to align # Constraint # added constraint: constraint((T0297)I41.CB, (T0297)N93.CB) [> 4.7868 = 7.9781 < 10.3715] w=0.0669 to align # Constraint # added constraint: constraint((T0297)V42.CB, (T0297)N93.CB) [> 3.2035 = 5.3391 < 6.9408] w=0.0669 to align # Constraint # added constraint: constraint((T0297)E43.CB, (T0297)T92.CB) [> 3.3856 = 5.6426 < 7.3354] w=0.0669 to align # Constraint # added constraint: constraint((T0297)I62.CB, (T0297)T92.CB) [> 2.8305 = 4.7174 < 6.1326] w=0.0669 to align # Constraint # added constraint: constraint((T0297)R63.CB, (T0297)T92.CB) [> 2.7265 = 4.5442 < 5.9074] w=0.0669 to align # Constraint # added constraint: constraint((T0297)R63.CB, (T0297)V99.CB) [> 4.5720 = 7.6200 < 9.9060] w=0.0669 to align # Constraint # added constraint: constraint((T0297)L88.CB, (T0297)E123.CB) [> 3.9396 = 6.5660 < 8.5358] w=0.0475 to align # Constraint # added constraint: constraint((T0297)T92.CB, (T0297)R145.CB) [> 4.4374 = 7.3956 < 9.6143] w=0.0475 to align # Constraint # added constraint: constraint((T0297)I95.CB, (T0297)I144.CB) [> 3.0906 = 5.1511 < 6.6964] w=0.0475 to align # Constraint # added constraint: constraint((T0297)V83.CB, (T0297)P120.CB) [> 3.1084 = 5.1806 < 6.7348] w=0.0474 to align # Constraint # added constraint: constraint((T0297)L50.CB, (T0297)R63.CB) [> 4.0262 = 6.7104 < 8.7235] w=0.0452 to align # Constraint # added constraint: constraint((T0297)Y44.CB, (T0297)T189.CB) [> 4.1779 = 6.9631 < 9.0520] w=0.0452 to align # Constraint # added constraint: constraint((T0297)L10.CB, (T0297)G68.CA) [> 4.1115 = 6.8525 < 8.9083] w=0.0452 to align # Constraint # added constraint: constraint((T0297)L11.CB, (T0297)G68.CA) [> 3.2994 = 5.4990 < 7.1487] w=0.0452 to align # Constraint # added constraint: constraint((T0297)L11.CB, (T0297)L69.CB) [> 4.7604 = 7.9340 < 10.3141] w=0.0452 to align # Constraint # added constraint: constraint((T0297)L11.CB, (T0297)L71.CB) [> 2.5221 = 4.2036 < 5.4646] w=0.0452 to align # Constraint # added constraint: constraint((T0297)E7.CB, (T0297)G64.CA) [> 4.7066 = 7.8444 < 10.1977] w=0.0452 to align # Constraint # added constraint: constraint((T0297)L89.CB, (T0297)K125.CB) [> 2.4561 = 4.0935 < 5.3215] w=0.0452 to align # Constraint # added constraint: constraint((T0297)V3.CB, (T0297)G68.CA) [> 4.0630 = 6.7717 < 8.8032] w=0.0452 to align # Constraint # added constraint: constraint((T0297)W9.CB, (T0297)L71.CB) [> 4.0943 = 6.8239 < 8.8710] w=0.0452 to align # Constraint # added constraint: constraint((T0297)W9.CB, (T0297)T67.CB) [> 4.1697 = 6.9495 < 9.0344] w=0.0452 to align # Constraint # added constraint: constraint((T0297)L130.CB, (T0297)R145.CB) [> 3.7308 = 6.2181 < 8.0835] w=0.0452 to align # Constraint # added constraint: constraint((T0297)K97.CB, (T0297)I144.CB) [> 4.5545 = 7.5908 < 9.8680] w=0.0452 to align # Constraint # added constraint: constraint((T0297)I62.CB, (T0297)L89.CB) [> 3.5856 = 5.9760 < 7.7688] w=0.0451 to align # Constraint # added constraint: constraint((T0297)F87.CB, (T0297)S128.CB) [> 4.7460 = 7.9099 < 10.2829] w=0.0451 to align # Constraint # added constraint: constraint((T0297)I37.CB, (T0297)F169.CB) [> 4.7521 = 7.9202 < 10.2963] w=0.0451 to align # Constraint # added constraint: constraint((T0297)I37.CB, (T0297)K125.CB) [> 4.7453 = 7.9088 < 10.2815] w=0.0451 to align # Constraint # added constraint: constraint((T0297)D98.CB, (T0297)S128.CB) [> 3.4804 = 5.8008 < 7.5410] w=0.0450 to align # Constraint # added constraint: constraint((T0297)I90.CB, (T0297)N133.CB) [> 4.1036 = 6.8393 < 8.8911] w=0.0450 to align # Constraint # added constraint: constraint((T0297)L89.CB, (T0297)T188.CB) [> 4.5778 = 7.6297 < 9.9185] w=0.0450 to align # Constraint # added constraint: constraint((T0297)G38.CA, (T0297)L47.CB) [> 4.3783 = 7.2972 < 9.4864] w=0.0450 to align # Constraint # added constraint: constraint((T0297)C175.CB, (T0297)D190.CB) [> 2.6830 = 4.4717 < 5.8132] w=0.0450 to align # Constraint # added constraint: constraint((T0297)I129.CB, (T0297)D190.CB) [> 3.9709 = 6.6182 < 8.6036] w=0.0450 to align # Constraint # added constraint: constraint((T0297)V29.CB, (T0297)T56.CB) [> 3.3234 = 5.5389 < 7.2006] w=0.0450 to align # Constraint # added constraint: constraint((T0297)I37.CB, (T0297)I62.CB) [> 4.1320 = 6.8867 < 8.9528] w=0.0450 to align # Constraint # added constraint: constraint((T0297)N33.CB, (T0297)R63.CB) [> 4.2189 = 7.0315 < 9.1409] w=0.0450 to align # Constraint # added constraint: constraint((T0297)L35.CB, (T0297)R63.CB) [> 3.1455 = 5.2424 < 6.8151] w=0.0450 to align # Constraint # added constraint: constraint((T0297)L35.CB, (T0297)G64.CA) [> 4.2401 = 7.0668 < 9.1868] w=0.0450 to align # Constraint # added constraint: constraint((T0297)L35.CB, (T0297)Y65.CB) [> 3.9949 = 6.6581 < 8.6556] w=0.0450 to align # Constraint # added constraint: constraint((T0297)F36.CB, (T0297)G64.CA) [> 2.9445 = 4.9075 < 6.3797] w=0.0450 to align # Constraint # added constraint: constraint((T0297)F36.CB, (T0297)Y65.CB) [> 3.8018 = 6.3363 < 8.2373] w=0.0450 to align # Constraint # added constraint: constraint((T0297)V29.CB, (T0297)N59.CB) [> 2.5212 = 4.2019 < 5.4625] w=0.0450 to align # Constraint # added constraint: constraint((T0297)F169.CB, (T0297)S205.CB) [> 2.9445 = 4.9075 < 6.3797] w=0.0450 to align # Constraint # added constraint: constraint((T0297)T92.CB, (T0297)Y157.CB) [> 4.6610 = 7.7684 < 10.0989] w=0.0450 to align # Constraint # added constraint: constraint((T0297)L88.CB, (T0297)V167.CB) [> 4.4915 = 7.4858 < 9.7315] w=0.0450 to align # Constraint # added constraint: constraint((T0297)I150.CB, (T0297)F169.CB) [> 3.8854 = 6.4757 < 8.4184] w=0.0446 to align # Constraint # added constraint: constraint((T0297)Y157.CB, (T0297)E168.CB) [> 4.6871 = 7.8119 < 10.1554] w=0.0446 to align # Constraint # added constraint: constraint((T0297)G38.CA, (T0297)Q66.CB) [> 4.2321 = 7.0536 < 9.1696] w=0.0271 to align # Constraint # added constraint: constraint((T0297)T177.CB, (T0297)H193.CB) [> 4.0549 = 6.7581 < 8.7856] w=0.0249 to align # Constraint # added constraint: constraint((T0297)L47.CB, (T0297)L192.CB) [> 3.8153 = 6.3589 < 8.2666] w=0.0226 to align # Constraint # added constraint: constraint((T0297)L6.CB, (T0297)V99.CB) [> 4.6849 = 7.8082 < 10.1507] w=0.0226 to align # Constraint # added constraint: constraint((T0297)V3.CB, (T0297)L71.CB) [> 4.7811 = 7.9685 < 10.3591] w=0.0226 to align # Constraint # added constraint: constraint((T0297)S128.CB, (T0297)L194.CB) [> 4.4705 = 7.4509 < 9.6861] w=0.0226 to align # Constraint # added constraint: constraint((T0297)I37.CB, (T0297)K85.CB) [> 4.3842 = 7.3069 < 9.4990] w=0.0226 to align # Constraint # added constraint: constraint((T0297)F36.CB, (T0297)K85.CB) [> 3.2688 = 5.4480 < 7.0824] w=0.0226 to align # Constraint # added constraint: constraint((T0297)N133.CB, (T0297)D190.CB) [> 3.8342 = 6.3903 < 8.3073] w=0.0226 to align # Constraint # added constraint: constraint((T0297)I37.CB, (T0297)S128.CB) [> 4.1352 = 6.8920 < 8.9596] w=0.0225 to align # Constraint # added constraint: constraint((T0297)I37.CB, (T0297)L127.CB) [> 4.4805 = 7.4676 < 9.7079] w=0.0225 to align # Constraint # added constraint: constraint((T0297)I34.CB, (T0297)P171.CB) [> 4.3112 = 7.1853 < 9.3408] w=0.0225 to align # Constraint # added constraint: constraint((T0297)L35.CB, (T0297)P171.CB) [> 2.3016 = 3.8360 < 4.9868] w=0.0225 to align # Constraint # added constraint: constraint((T0297)F36.CB, (T0297)P171.CB) [> 3.5702 = 5.9504 < 7.7355] w=0.0225 to align # Constraint # added constraint: constraint((T0297)I150.CB, (T0297)A197.CB) [> 2.9131 = 4.8551 < 6.3117] w=0.0225 to align # Constraint # added constraint: constraint((T0297)Q179.CB, (T0297)G191.CA) [> 3.9543 = 6.5904 < 8.5676] w=0.0225 to align # Constraint # added constraint: constraint((T0297)G38.CA, (T0297)T92.CB) [> 4.5118 = 7.5196 < 9.7754] w=0.0225 to align # Constraint # added constraint: constraint((T0297)I37.CB, (T0297)G91.CA) [> 4.0618 = 6.7696 < 8.8005] w=0.0225 to align # Constraint # added constraint: constraint((T0297)F36.CB, (T0297)I90.CB) [> 4.6430 = 7.7383 < 10.0598] w=0.0225 to align # Constraint # added constraint: constraint((T0297)L35.CB, (T0297)L89.CB) [> 4.1732 = 6.9553 < 9.0418] w=0.0225 to align # Constraint # added constraint: constraint((T0297)L35.CB, (T0297)L88.CB) [> 3.3832 = 5.6386 < 7.3302] w=0.0225 to align # Constraint # added constraint: constraint((T0297)I34.CB, (T0297)L89.CB) [> 3.5542 = 5.9237 < 7.7008] w=0.0225 to align # Constraint # added constraint: constraint((T0297)I34.CB, (T0297)L88.CB) [> 4.7052 = 7.8421 < 10.1947] w=0.0225 to align # Constraint # added constraint: constraint((T0297)L24.CB, (T0297)N73.CB) [> 4.1446 = 6.9077 < 8.9800] w=0.0225 to align # Constraint # added constraint: constraint((T0297)L126.CB, (T0297)S205.CB) [> 4.4800 = 7.4667 < 9.7067] w=0.0225 to align # Constraint # added constraint: constraint((T0297)S128.CB, (T0297)D190.CB) [> 4.0620 = 6.7699 < 8.8009] w=0.0225 to align # Constraint # added constraint: constraint((T0297)P131.CB, (T0297)Y157.CB) [> 4.6198 = 7.6996 < 10.0095] w=0.0225 to align # Constraint # added constraint: constraint((T0297)L47.CB, (T0297)L89.CB) [> 4.6057 = 7.6761 < 9.9790] w=0.0225 to align # Constraint # added constraint: constraint((T0297)L89.CB, (T0297)L206.CB) [> 3.8672 = 6.4453 < 8.3789] w=0.0225 to align # Constraint # added constraint: constraint((T0297)P32.CB, (T0297)Y211.CB) [> 4.6407 = 7.7345 < 10.0548] w=0.0225 to align # Constraint # added constraint: constraint((T0297)T92.CB, (T0297)P171.CB) [> 3.9836 = 6.6393 < 8.6311] w=0.0225 to align # Constraint # added constraint: constraint((T0297)L130.CB, (T0297)Y143.CB) [> 2.8174 = 4.6957 < 6.1044] w=0.0225 to align # Constraint # added constraint: constraint((T0297)I37.CB, (T0297)L47.CB) [> 4.7382 = 7.8971 < 10.2662] w=0.0223 to align # Constraint # added constraint: constraint((T0297)Y21.CB, (T0297)K55.CB) [> 4.5459 = 7.5765 < 9.8494] w=0.0223 to align # Constraint # added constraint: constraint((T0297)K85.CB, (T0297)S203.CB) [> 3.4258 = 5.7097 < 7.4226] w=0.0045 to align # Constraint # added constraint: constraint((T0297)F87.CB, (T0297)S203.CB) [> 3.7267 = 6.2112 < 8.0746] w=0.0045 to align # Constraint # added constraint: constraint((T0297)L130.CB, (T0297)P171.CB) [> 3.9703 = 6.6172 < 8.6024] w=0.0045 to align # Constraint # added constraint: constraint((T0297)I129.CB, (T0297)Y143.CB) [> 4.2109 = 7.0181 < 9.1235] w=0.0023 to align # Constraint # added constraint: constraint((T0297)N133.CB, (T0297)P171.CB) [> 4.7914 = 7.9857 < 10.3814] w=0.0023 to align # Constraint # added constraint: constraint((T0297)P171.CB, (T0297)L192.CB) [> 4.0591 = 6.7652 < 8.7948] w=0.0023 to align # SetCost created cost = # ( 1.0000 * align ) # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0297/ # command:# reading script from file servers-clean.under # Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0297/decoys/ # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0297 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 # Found a chain break before 145 # copying to AlignedFragments data structure # 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 166 # 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 188 # 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 166 # 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 T0297 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 T0297 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 # WARNING: incomplete conformation T0297 can't currently be optimized by undertaker # 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 T0297 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 T0297 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 T0297 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 # Found a chain break before 171 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0297 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 # WARNING: incomplete conformation T0297 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0297 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 157 # 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 157 # 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 205 # 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 134 # 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 195 # 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 176 # 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 200 # 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 182 # 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 178 # 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 194 # 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 164 # 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 59 # 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 145 # 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 178 # 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 178 # 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 178 # 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 183 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS1 # ReadConformPDB reading from PDB file servers/CIRCLE_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0297 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS2 # ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0297 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS3 # ReadConformPDB reading from PDB file servers/CIRCLE_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0297 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS4 # ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0297 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS5 # ReadConformPDB reading from PDB file servers/CPHmodels_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0297 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 # Found a chain break before 182 # copying to AlignedFragments data structure # naming current conformation CaspIta-FOX_TS1 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS2.pdb.gz looking for model 1 # Found a chain break before 172 # copying to AlignedFragments data structure # naming current conformation CaspIta-FOX_TS2 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0297 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 # WARNING: incomplete conformation T0297 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS4 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0297 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 T0297 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 T0297 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 T0297 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 T0297 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 T0297 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 210 # 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 T0297 can't currently be optimized by undertaker # naming current conformation FAMSD_TS2 # ReadConformPDB reading from PDB file servers/FAMSD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0297 can't currently be optimized by undertaker # naming current conformation FAMSD_TS3 # ReadConformPDB reading from PDB file servers/FAMSD_TS4.pdb.gz looking for model 1 # Found a chain break before 170 # 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 210 # 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 188 # copying to AlignedFragments data structure # naming current conformation FAMS_TS1 # ReadConformPDB reading from PDB file servers/FAMS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0297 can't currently be optimized by undertaker # naming current conformation FAMS_TS2 # ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0297 can't currently be optimized by undertaker # naming current conformation FAMS_TS3 # ReadConformPDB reading from PDB file servers/FAMS_TS4.pdb.gz looking for model 1 # Found a chain break before 183 # copying to AlignedFragments data structure # naming current conformation FAMS_TS4 # ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0297 can't currently be optimized by undertaker # naming current conformation FAMS_TS5 # ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1 # Found a chain break before 165 # 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 157 # 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 186 # 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 159 # 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 97 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS5 # ReadConformPDB reading from PDB file servers/FORTE1_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0297 can't currently be optimized by undertaker # naming current conformation FORTE1_AL1 # ReadConformPDB reading from PDB file servers/FORTE1_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0297 can't currently be optimized by undertaker # naming current conformation FORTE1_AL2 # ReadConformPDB reading from PDB file servers/FORTE1_AL3.pdb.gz looking for model 1 Skipped atom 163, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 196, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 209, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz Skipped atom 350, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL3.pdb.gz # WARNING: incomplete conformation T0297 can't currently be optimized by undertaker # naming current conformation FORTE1_AL3 # ReadConformPDB reading from PDB file servers/FORTE1_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0297 can't currently be optimized by undertaker # naming current conformation FORTE1_AL4 # ReadConformPDB reading from PDB file servers/FORTE1_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0297 can't currently be optimized by undertaker # naming current conformation FORTE1_AL5 # ReadConformPDB reading from PDB file servers/FORTE2_AL1.pdb.gz looking for model 1 Skipped atom 163, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 196, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 209, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 350, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz # WARNING: incomplete conformation T0297 can't currently be optimized by undertaker # naming current conformation FORTE2_AL1 # ReadConformPDB reading from PDB file servers/FORTE2_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0297 can't currently be optimized by undertaker # naming current conformation FORTE2_AL2 # ReadConformPDB reading from PDB file servers/FORTE2_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0297 can't currently be optimized by undertaker # naming current conformation FORTE2_AL3 # ReadConformPDB reading from PDB file servers/FORTE2_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0297 can't currently be optimized by undertaker # naming current conformation FORTE2_AL4 # ReadConformPDB reading from PDB file servers/FORTE2_AL5.pdb.gz looking for model 1 Skipped atom 282, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 284, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 286, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 288, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 330, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 332, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 334, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 336, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 362, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 364, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 366, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 368, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 446, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 448, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 450, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 452, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 546, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 548, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 550, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 552, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 722, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 724, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 726, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz Skipped atom 728, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz # WARNING: incomplete conformation T0297 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 195 # 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 198 # 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 163 # 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 191 # 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 210 # 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 # Found a chain break before 94 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS1 # ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1 # Found a chain break before 143 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS2 # ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1 # Found a chain break before 59 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS3 # ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0297 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS4 # ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0297 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 T0297 can't currently be optimized by undertaker # naming current conformation FUGUE_AL1 # ReadConformPDB reading from PDB file servers/FUGUE_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0297 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 T0297 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 T0297 can't currently be optimized by undertaker # naming current conformation FUGUE_AL4 # ReadConformPDB reading from PDB file servers/FUGUE_AL5.pdb.gz looking for model 1 Skipped atom 163, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL5.pdb.gz Skipped atom 196, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL5.pdb.gz Skipped atom 209, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL5.pdb.gz Skipped atom 350, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL5.pdb.gz # WARNING: incomplete conformation T0297 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 178 # 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 208 # 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 206 # 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 209 # 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 210 # 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 152 # 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 59 # 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 81 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS3 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0297 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS4 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0297 can't currently be optimized by undertaker # 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 132 # copying to AlignedFragments data structure # naming current conformation HHpred1_TS1 # ReadConformPDB reading from PDB file servers/HHpred2_TS1.pdb.gz looking for model 1 # Found a chain break before 59 # copying to AlignedFragments data structure # naming current conformation HHpred2_TS1 # ReadConformPDB reading from PDB file servers/HHpred3_TS1.pdb.gz looking for model 1 # Found a chain break before 162 # 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 T0297 can't currently be optimized by undertaker # 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 T0297 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 T0297 can't currently be optimized by undertaker # 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 T0297 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 T0297 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 T0297 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 T0297 can't currently be optimized by undertaker # naming current conformation LOOPP_TS2 # ReadConformPDB reading from PDB file servers/LOOPP_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0297 can't currently be optimized by undertaker # naming current conformation LOOPP_TS3 # ReadConformPDB reading from PDB file servers/LOOPP_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0297 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 T0297 can't currently be optimized by undertaker # naming current conformation LOOPP_TS5 # ReadConformPDB reading from PDB file servers/MIG_FROST_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0297 can't currently be optimized by undertaker # naming current conformation MIG_FROST_AL1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS1.pdb.gz looking for model 1 # Found a chain break before 171 # 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 94 # 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 178 # 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 52 # 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 168 # 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 190 # 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 194 # 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 194 # 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 192 # 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 195 # 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 T0297 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 # WARNING: incomplete conformation T0297 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1 # Found a chain break before 188 # 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 144 # 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 T0297 can't currently be optimized by undertaker # naming current conformation Pcons6_TS1 # ReadConformPDB reading from PDB file servers/Pcons6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0297 can't currently be optimized by undertaker # naming current conformation Pcons6_TS2 # ReadConformPDB reading from PDB file servers/Pcons6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0297 can't currently be optimized by undertaker # naming current conformation Pcons6_TS3 # ReadConformPDB reading from PDB file servers/Pcons6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0297 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 # Found a chain break before 180 # 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 T0297 can't currently be optimized by undertaker # naming current conformation Phyre-1_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0297 can't currently be optimized by undertaker # 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 # WARNING: incomplete conformation T0297 can't currently be optimized by undertaker # 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 # Found a chain break before 178 # 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 # WARNING: incomplete conformation T0297 can't currently be optimized by undertaker # 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 204 # 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 T0297 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS1 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0297 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS2 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0297 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS3 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0297 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS4 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0297 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS1.pdb.gz looking for model 1 # Found a chain break before 59 # 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 143 # 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 142 # 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 # Found a chain break before 142 # 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 94 # 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 95 # 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 188 # 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 94 # 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 31 # 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 186 # 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 78 # 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 94 # 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 42 # 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 114 # 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 96 # 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 178 # 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 172 # 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 178 # 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 178 # 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 178 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS5 # ReadConformPDB reading from PDB file servers/ROKKY_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0297 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS1 # ReadConformPDB reading from PDB file servers/ROKKY_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0297 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS2 # ReadConformPDB reading from PDB file servers/SAM-T02_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0297 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL1 # ReadConformPDB reading from PDB file servers/SAM-T02_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0297 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 163, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 196, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 209, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz Skipped atom 342, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL3.pdb.gz # WARNING: incomplete conformation T0297 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL3 # ReadConformPDB reading from PDB file servers/SAM-T02_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0297 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 T0297 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL5 # ReadConformPDB reading from PDB file servers/SAM-T99_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0297 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 T0297 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL2 # ReadConformPDB reading from PDB file servers/SAM-T99_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0297 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 T0297 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL4 # ReadConformPDB reading from PDB file servers/SAM-T99_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0297 can't currently be optimized by undertaker # 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 192 # 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 T0297 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 T0297 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 T0297 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 T0297 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 59 # 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 123 # 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 52 # 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 178 # 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 55 # 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 143 # 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 124 # 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 147 # 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 178 # 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 134 # 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 59 # 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 176 # 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 123 # 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 178 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS4 # ReadConformPDB reading from PDB file servers/SPARKS2_TS5.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0297 can't currently be optimized by undertaker # 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 T0297 can't currently be optimized by undertaker # 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 T0297 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 T0297 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 T0297 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 T0297 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 T0297 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0297 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 T0297 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 T0297 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 # WARNING: incomplete conformation T0297 can't currently be optimized by undertaker # 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 175 # 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 143 # 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 173 # 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 195 # 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 184 # 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 195 # 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 199 # 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 163, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 196, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 209, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz Skipped atom 362, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL1.pdb.gz # WARNING: incomplete conformation T0297 can't currently be optimized by undertaker # naming current conformation forecast-s_AL1 # ReadConformPDB reading from PDB file servers/forecast-s_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0297 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 T0297 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 # WARNING: incomplete conformation T0297 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 # WARNING: incomplete conformation T0297 can't currently be optimized by undertaker # naming current conformation forecast-s_AL5 # ReadConformPDB reading from PDB file servers/gtg_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0297 can't currently be optimized by undertaker # naming current conformation gtg_AL1 # ReadConformPDB reading from PDB file servers/gtg_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0297 can't currently be optimized by undertaker # naming current conformation gtg_AL2 # ReadConformPDB reading from PDB file servers/gtg_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0297 can't currently be optimized by undertaker # naming current conformation gtg_AL3 # ReadConformPDB reading from PDB file servers/gtg_AL4.pdb.gz looking for model 1 Skipped atom 303, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 423, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 425, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 427, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 429, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 512, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 637, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz # WARNING: incomplete conformation T0297 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 T0297 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 147 # 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 59 # 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 98 # 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 95 # 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 162 # 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: (T0297)S40.O and (T0297)I41.N only 0.000 apart, marking (T0297)I41.N as missing # WARNING: incomplete conformation T0297 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 208 # 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 # Found a chain break before 208 # 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 # Found a chain break before 208 # 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: (T0297)A163.O and (T0297)Y164.N only 0.000 apart, marking (T0297)Y164.N as missing # WARNING: incomplete conformation T0297 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 # WARNING: incomplete conformation T0297 can't currently be optimized by undertaker # 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 T0297 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 T0297 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0297 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0297 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS5 # ReadConformPDB reading from PDB file servers/keasar-server_TS1.pdb.gz looking for model 1 # Found a chain break before 169 # 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 137 # 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 172 # 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 136 # 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 145 # 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 T0297 can't currently be optimized by undertaker # naming current conformation mGen-3D_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0297 can't currently be optimized by undertaker # naming current conformation nFOLD_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS2.pdb.gz looking for model 1 WARNING: atom 1 has residue number 1 < previous residue 211 in servers/nFOLD_TS2.pdb.gz # WARNING: incomplete conformation T0297 can't currently be optimized by undertaker # naming current conformation nFOLD_TS2 # ReadConformPDB reading from PDB file servers/nFOLD_TS3.pdb.gz looking for model 1 WARNING: atom 1 has residue number 1 < previous residue 211 in servers/nFOLD_TS3.pdb.gz # WARNING: incomplete conformation T0297 can't currently be optimized by undertaker # naming current conformation nFOLD_TS3 # ReadConformPDB reading from PDB file servers/nFOLD_TS4.pdb.gz looking for model 1 WARNING: atom 1 has residue number 1 < previous residue 211 in servers/nFOLD_TS4.pdb.gz # WARNING: incomplete conformation T0297 can't currently be optimized by undertaker # naming current conformation nFOLD_TS4 # ReadConformPDB reading from PDB file servers/nFOLD_TS5.pdb.gz looking for model 1 WARNING: atom 1 has residue number 1 < previous residue 211 in servers/nFOLD_TS5.pdb.gz # WARNING: incomplete conformation T0297 can't currently be optimized by undertaker # naming current conformation nFOLD_TS5 # ReadConformPDB reading from PDB file servers/panther2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0297 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 # WARNING: incomplete conformation T0297 can't currently be optimized by undertaker # naming current conformation shub_TS1 # command:Using radius: 8.0000 Using models AND alignments for constraints model score -0.2579 model score -0.2747 model score -0.4235 model score -0.4063 model score -0.4022 model score -0.3853 model score -0.4205 model score -0.3223 model score -0.2923 model score -0.3057 model score -0.2263 model score -0.2514 model score -0.0736 model score -0.2193 model score -0.2410 model score -0.3356 model score -0.3592 model score -0.3553 model score -0.0081 model score 1.0025 model score 1.2433 model score 1.2493 model score 1.4372 model score 1.4919 model score 1.1185 model score -0.4131 model score -0.4700 model score -0.3934 model score 1.7198 model score 1.7177 model score 1.7179 model score -0.3644 model score -0.3770 model score -0.3409 model score -0.3726 model score -0.2714 model score -0.0221 model score -0.4087 model score -0.3254 model score -0.3863 model score -0.1783 model score -0.2434 model score 1.2722 model score 1.2729 model score 1.2698 model score 1.2686 model score 1.2682 model score -0.3849 model score -0.3451 model score -0.3573 model score -0.4187 model score -0.4227 model score -0.0839 model score -0.3749 model score -0.3409 model score -0.3644 model score -0.3726 model score -0.3675 model score -0.3311 model score -0.5099 model score -0.0795 model score -0.2442 model score 1.2680 model score 1.2688 model score 1.2682 model score 1.2683 model score 1.2687 model score 1.2682 model score 1.2683 model score 1.2687 model score 1.2690 model score 1.2771 model score 2.5209 model score 2.5828 model score 2.3477 model score 2.4677 model score 2.0961 model score -0.4153 model score -0.4405 model score -0.4164 model score -0.0929 model score -0.2549 model score 1.2680 model score 1.2678 model score 1.2679 model score 1.2686 model score 1.2682 model score -0.4046 model score -0.3947 model score -0.3130 model score -0.2010 model score -0.1291 model score -0.4117 model score -0.4464 model score -0.4404 model score -0.2253 model score -0.3266 model score -0.4550 model score -0.4155 model score -0.4364 model score -0.3612 model score 0.2550 model score -0.3839 model score 0.8610 model score 1.0570 model score -0.1256 model score -0.0810 model score -0.0796 model score -0.0874 model score -0.0697 model score 1.2777 model score -0.4257 model score -0.3138 model score -0.3437 model score -0.2982 model score 1.6983 model score -0.4365 model score -0.3808 model score -0.4313 model score -0.4360 model score -0.4175 model score 1.2680 model score -0.4174 model score -0.4293 model score -0.4274 model score -0.4129 model score -0.4298 model score -0.3582 model score -0.3547 model score -0.4175 model score -0.4293 model score -0.4372 model score -0.4203 model score -0.4175 model score -0.4139 model score -0.4015 model score -0.4177 model score -0.4131 model score -0.3995 model score -0.4019 model score -0.4381 model score -0.4019 model score -0.3733 model score -0.1523 model score -0.3170 model score -0.2908 model score -0.2925 model score -0.4183 model score -0.4552 model score -0.4553 model score -0.4223 model score -0.4321 model score -0.4181 model score -0.3596 model score -0.3765 model score -0.3398 model score -0.1307 model score 0.7562 model score -0.4303 model score -0.3645 model score -0.3213 model score -0.4208 model score -0.3574 model score -0.4540 model score -0.3523 model score -0.3861 model score -0.4223 model score -0.3492 model score 1.2682 model score 1.2683 model score 1.2680 model score 1.2683 model score 1.2682 model score 1.2686 model score 1.2678 model score 1.2680 model score 1.2679 model score 1.2677 model score 1.2680 model score 1.2678 model score -0.4004 model score -0.1265 model score 0.0156 model score -0.3141 model score -0.2236 model score -0.4552 model score -0.4097 model score -0.3367 model score -0.2534 model score -0.2644 model score -0.4445 model score -0.3770 model score -0.3096 model score -0.2391 model score -0.2827 model score -0.4504 model score -0.3368 model score -0.4097 model score -0.2534 model score -0.2879 model score 1.2679 model score 1.2678 model score 1.2675 model score 1.2677 model score 1.2683 model score -0.4115 model score 1.2679 model score 1.2678 model score 1.2675 model score 1.2677 model score 1.2683 model score -0.4149 model score -0.4269 model score -0.3948 model score -0.4019 model score -0.4301 model score -0.4153 model score -0.4479 model score 1.2682 model score 1.2690 model score 1.2688 model score 1.2680 model score 1.2687 model score 1.2675 model score 1.2686 model score 1.2683 model score 1.2682 model score 1.2690 model score -0.4232 model score -0.4171 model score -0.4140 model score -0.3869 model score -0.4137 model score 2.0982 model score 2.5463 model score 2.3123 model score 2.1376 model score 2.1335 model score -0.4200 model score -0.4069 model score -0.3621 model score -0.3031 model score 1.6891 model score -0.1703 model score -0.3530 model score -0.3760 model score -0.3645 model score -0.2568 model score -0.4581 model score -0.4302 model score -0.3958 model score -0.3204 model score -0.3345 model score -0.2711 model score -0.2988 model score -0.3694 USE_META, weight: 0.9267 cost: -0.2579 min: -0.5099 max: 2.5828 USE_META, weight: 0.9315 cost: -0.2747 min: -0.5099 max: 2.5828 USE_META, weight: 0.9749 cost: -0.4235 min: -0.5099 max: 2.5828 USE_META, weight: 0.9698 cost: -0.4063 min: -0.5099 max: 2.5828 USE_META, weight: 0.9686 cost: -0.4022 min: -0.5099 max: 2.5828 USE_META, weight: 0.9637 cost: -0.3853 min: -0.5099 max: 2.5828 USE_META, weight: 0.9740 cost: -0.4205 min: -0.5099 max: 2.5828 USE_META, weight: 0.9454 cost: -0.3223 min: -0.5099 max: 2.5828 USE_META, weight: 0.9367 cost: -0.2923 min: -0.5099 max: 2.5828 USE_META, weight: 0.9406 cost: -0.3057 min: -0.5099 max: 2.5828 USE_META, weight: 0.9175 cost: -0.2263 min: -0.5099 max: 2.5828 USE_META, weight: 0.9248 cost: -0.2514 min: -0.5099 max: 2.5828 USE_META, weight: 0.8730 cost: -0.0736 min: -0.5099 max: 2.5828 USE_META, weight: 0.9154 cost: -0.2193 min: -0.5099 max: 2.5828 USE_META, weight: 0.9217 cost: -0.2410 min: -0.5099 max: 2.5828 USE_META, weight: 0.9493 cost: -0.3356 min: -0.5099 max: 2.5828 USE_META, weight: 0.9561 cost: -0.3592 min: -0.5099 max: 2.5828 USE_META, weight: 0.9550 cost: -0.3553 min: -0.5099 max: 2.5828 USE_META, weight: 0.8540 cost: -0.0081 min: -0.5099 max: 2.5828 USE_META, weight: 0.5599 cost: 1.0025 min: -0.5099 max: 2.5828 USE_META, weight: 0.4898 cost: 1.2433 min: -0.5099 max: 2.5828 USE_META, weight: 0.4881 cost: 1.2493 min: -0.5099 max: 2.5828 USE_META, weight: 0.4334 cost: 1.4372 min: -0.5099 max: 2.5828 USE_META, weight: 0.4175 cost: 1.4919 min: -0.5099 max: 2.5828 USE_META, weight: 0.5261 cost: 1.1185 min: -0.5099 max: 2.5828 USE_META, weight: 0.9718 cost: -0.4131 min: -0.5099 max: 2.5828 USE_META, weight: 0.9884 cost: -0.4700 min: -0.5099 max: 2.5828 USE_META, weight: 0.9661 cost: -0.3934 min: -0.5099 max: 2.5828 USE_META, weight: 0.3511 cost: 1.7198 min: -0.5099 max: 2.5828 USE_META, weight: 0.3517 cost: 1.7177 min: -0.5099 max: 2.5828 USE_META, weight: 0.3517 cost: 1.7179 min: -0.5099 max: 2.5828 USE_META, weight: 0.9577 cost: -0.3644 min: -0.5099 max: 2.5828 USE_META, weight: 0.9613 cost: -0.3770 min: 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38.0000 min: 0.0000 max: 38.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 38.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 38.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 38.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 38.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 38.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 38.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 38.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 38.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 38.0000 USE_EVALUE, weight: 0.9999 eval: 0.0059 min: 0.0000 max: 38.0000 USE_EVALUE, weight: 0.9999 eval: 0.0059 min: 0.0000 max: 38.0000 USE_EVALUE, weight: 0.9999 eval: 0.0059 min: 0.0000 max: 38.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 38.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 38.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 38.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 38.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 38.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 38.0000 USE_EVALUE, weight: 0.9869 eval: 0.5545 min: 0.0000 max: 38.0000 USE_EVALUE, weight: 0.9869 eval: 0.5545 min: 0.0000 max: 38.0000 USE_EVALUE, weight: 0.9869 eval: 0.5545 min: 0.0000 max: 38.0000 USE_EVALUE, weight: 0.9984 eval: 0.0661 min: 0.0000 max: 38.0000 USE_EVALUE, weight: 0.9984 eval: 0.0661 min: 0.0000 max: 38.0000 USE_EVALUE, weight: 0.9984 eval: 0.0661 min: 0.0000 max: 38.0000 USE_EVALUE, weight: 0.9952 eval: 0.2026 min: 0.0000 max: 38.0000 USE_EVALUE, weight: 0.9952 eval: 0.2026 min: 0.0000 max: 38.0000 USE_EVALUE, weight: 0.9952 eval: 0.2026 min: 0.0000 max: 38.0000 USE_EVALUE, weight: 1.0000 eval: 0.0005 min: 0.0000 max: 38.0000 USE_EVALUE, weight: 1.0000 eval: 0.0005 min: 0.0000 max: 38.0000 USE_EVALUE, weight: 1.0000 eval: 0.0005 min: 0.0000 max: 38.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 38.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 38.0000 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 38.0000 USE_EVALUE, weight: 0.9946 eval: 0.2275 min: 0.0000 max: 38.0000 USE_EVALUE, weight: 0.9946 eval: 0.2275 min: 0.0000 max: 38.0000 USE_EVALUE, weight: 0.9946 eval: 0.2275 min: 0.0000 max: 38.0000 Number of contacts in models: 256 Number of contacts in alignments: 48 NUMB_ALIGNS: 48 Adding 7115 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: -366.9246, CN propb: -366.9246 weights: 0.3456 constraints: 687 # command:Found ConstraintSet # PrintContacts align.constraints_meta03 Number of constraints in align3.constraints 687 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_meta03 Number of constraints in align3.constraints.bonus 687 # command:Found ConstraintSet # PrintContacts rejected.constraints_meta03 Number of constraints in rejected3.constraints 6428 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_meta03 Number of constraints in rejected3.constraints.bonus 6428 # 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 7115 # command: