# 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/T0344/ # command:# Making conformation for sequence T0344 numbered 1 through 229 Created new target T0344 from T0344.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0344/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0344//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0344/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0344//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0344/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0344/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0344/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gvoA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1gvoA expands to /projects/compbio/data/pdb/1gvo.pdb.gz 1gvoA:# T0344 read from 1gvoA/merged-good-all-a2m # 1gvoA read from 1gvoA/merged-good-all-a2m # adding 1gvoA to template set # found chain 1gvoA in template set T0344 44 :YANPYDYDLTGR 1gvoA 237 :IGTFQNVDNGPN # choosing archetypes in rotamer library T0344 58 :IRDEVLLAIELARKVKPDVIHLDSTLG 1gvoA 249 :EEADALYLIEELAKRGIAYLHMSETDL Number of specific fragments extracted= 2 number of extra gaps= 0 total=2 Number of alignments=1 # 1gvoA read from 1gvoA/merged-good-all-a2m # found chain 1gvoA in template set T0344 48 :YDYD 1gvoA 241 :QNVD T0344 54 :GRQAIRDEVLLAIELARKVKPDVIHLDSTLG 1gvoA 245 :NGPNEEADALYLIEELAKRGIAYLHMSETDL Number of specific fragments extracted= 2 number of extra gaps= 0 total=4 Number of alignments=2 # 1gvoA read from 1gvoA/merged-good-all-a2m # found chain 1gvoA in template set T0344 12 :VLDET 1gvoA 133 :LRDEN T0344 37 :AKEVMVKYANPYDYDLTGRQAIRDEVLLAIELARKVKPDVIHLDSTLG 1gvoA 138 :GNAIRVDTTTPRALELDEIPGIVNDFRQAVANAREAGFDLVELHSAHG T0344 100 :GISDKGKEVWKELSKDLQPLARKFWEETN 1gvoA 198 :QRTDQYGGSVENRARLVLEVVDAVCNEWS T0344 129 :IEIVAIGKSSV 1gvoA 230 :IGIRVSPIGTF T0344 148 :AGIYSAKWGIENVEKEG 1gvoA 248 :NEEADALYLIEELAKRG T0344 165 :HLIIGLP 1gvoA 266 :AYLHMSE Number of specific fragments extracted= 6 number of extra gaps= 0 total=10 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1u0sY/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1u0sY expands to /projects/compbio/data/pdb/1u0s.pdb.gz 1u0sY:Skipped atom 825, because occupancy 0.5 <= existing 0.500 in 1u0sY Skipped atom 827, because occupancy 0.500 <= existing 0.500 in 1u0sY Skipped atom 829, because occupancy 0.500 <= existing 0.500 in 1u0sY Skipped atom 831, because occupancy 0.500 <= existing 0.500 in 1u0sY Skipped atom 833, because occupancy 0.500 <= existing 0.500 in 1u0sY Skipped atom 835, because occupancy 0.500 <= existing 0.500 in 1u0sY Skipped atom 837, because occupancy 0.500 <= existing 0.500 in 1u0sY Skipped atom 839, because occupancy 0.500 <= existing 0.500 in 1u0sY Skipped atom 841, because occupancy 0.500 <= existing 0.500 in 1u0sY Skipped atom 843, because occupancy 0.500 <= existing 0.500 in 1u0sY Skipped atom 845, because occupancy 0.500 <= existing 0.500 in 1u0sY # T0344 read from 1u0sY/merged-good-all-a2m # 1u0sY read from 1u0sY/merged-good-all-a2m # adding 1u0sY to template set # found chain 1u0sY in template set T0344 55 :RQAIRDEVLL 1u0sY 15 :RMMLKDIITK T0344 65 :AIELARKVKPDVIHLDSTLGG 1u0sY 39 :AVEKYKELKPDIVTMDITMPE T0344 96 :ID 1u0sY 60 :MN T0344 116 :LQPLARKFWE 1u0sY 62 :GIDAIKEIMK T0344 126 :ETNIEIVAIGKSSVP 1u0sY 73 :DPNAKIIVCSAMGQQ Number of specific fragments extracted= 5 number of extra gaps= 0 total=15 Number of alignments=4 # 1u0sY read from 1u0sY/merged-good-all-a2m # found chain 1u0sY in template set T0344 2 :RIVAADTGGA 1u0sY 4 :RVLIVDDAAF T0344 54 :GRQAIRDEVLL 1u0sY 14 :MRMMLKDIITK T0344 65 :AIELARKVKPDVIHLDSTLGGIE 1u0sY 39 :AVEKYKELKPDIVTMDITMPEMN T0344 116 :LQPLARKFWEE 1u0sY 62 :GIDAIKEIMKI T0344 127 :TNIEIVAIGKSSVPVRIAEIYA 1u0sY 74 :PNAKIIVCSAMGQQAMVIEAIK Number of specific fragments extracted= 5 number of extra gaps= 0 total=20 Number of alignments=5 # 1u0sY read from 1u0sY/merged-good-all-a2m # found chain 1u0sY in template set T0344 55 :RQAIRDEVLL 1u0sY 15 :RMMLKDIITK T0344 65 :AIELARKVKPDVIHLDSTLGGI 1u0sY 39 :AVEKYKELKPDIVTMDITMPEM T0344 115 :DLQPLARKFWE 1u0sY 61 :NGIDAIKEIMK T0344 126 :ETNIEIVAIGKSSVPV 1u0sY 73 :DPNAKIIVCSAMGQQA T0344 156 :GIENVEKEG 1u0sY 89 :MVIEAIKAG T0344 165 :HLIIGLP 1u0sY 99 :KDFIVKP Number of specific fragments extracted= 6 number of extra gaps= 0 total=26 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1tmy/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1tmy expands to /projects/compbio/data/pdb/1tmy.pdb.gz 1tmy:Warning: there is no chain 1tmy will retry with 1tmyA # T0344 read from 1tmy/merged-good-all-a2m # 1tmy read from 1tmy/merged-good-all-a2m # adding 1tmy to template set # found chain 1tmy in template set T0344 55 :RQAIRDEVLL 1tmy 15 :RMMLKDIITK T0344 65 :AIELARKVKPDVIHLDSTLGGIE 1tmy 39 :AVEKYKELKPDIVTMDITMPEMN T0344 116 :LQPLARKFWE 1tmy 62 :GIDAIKEIMK T0344 126 :ETNIEIVAIGKSSVPVRIAE 1tmy 73 :DPNAKIIVCSAMGQQAMVIE Number of specific fragments extracted= 4 number of extra gaps= 0 total=30 Number of alignments=7 # 1tmy read from 1tmy/merged-good-all-a2m # found chain 1tmy in template set T0344 55 :RQAIRDEVLL 1tmy 15 :RMMLKDIITK T0344 65 :AIELARKVKPDVIHLDSTLGGIE 1tmy 39 :AVEKYKELKPDIVTMDITMPEMN T0344 116 :LQPLARKFWEE 1tmy 62 :GIDAIKEIMKI T0344 127 :TNIEIVAIGKSSVPVRIAEIYAG 1tmy 74 :PNAKIIVCSAMGQQAMVIEAIKA Number of specific fragments extracted= 4 number of extra gaps= 0 total=34 Number of alignments=8 # 1tmy read from 1tmy/merged-good-all-a2m # found chain 1tmy in template set Warning: unaligning (T0344)I167 because of BadResidue code BAD_PEPTIDE in next template residue (1tmy)I102 Warning: unaligning (T0344)I168 because of BadResidue code BAD_PEPTIDE at template residue (1tmy)I102 T0344 55 :RQAIRDEVLL 1tmy 15 :RMMLKDIITK T0344 65 :AIELARKVKPDVIHLDSTLGGI 1tmy 39 :AVEKYKELKPDIVTMDITMPEM T0344 115 :DLQPLARKFWE 1tmy 61 :NGIDAIKEIMK T0344 126 :ETNIEIVAIGKSSVPV 1tmy 73 :DPNAKIIVCSAMGQQA T0344 156 :GIENVEKEG 1tmy 89 :MVIEAIKAG T0344 165 :HL 1tmy 99 :KD T0344 169 :GLP 1tmy 103 :VKP Number of specific fragments extracted= 7 number of extra gaps= 1 total=41 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1atr/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1atr expands to /projects/compbio/data/pdb/1atr.pdb.gz 1atr:Warning: there is no chain 1atr will retry with 1atrA # T0344 read from 1atr/merged-good-all-a2m # 1atr read from 1atr/merged-good-all-a2m # adding 1atr to template set # found chain 1atr in template set T0344 2 :RIVAADTGGAVL 1atr 194 :NVLIFDLGGGVF T0344 25 :TVAVLVEKPYR 1atr 206 :DVSILTIEDGI T0344 39 :EVMVKYANPY 1atr 218 :EVKSTAGDTH T0344 49 :DYDLTGRQAIRDEVLLAIELARKV 1atr 250 :KKDISENKRAVRRLRTACERAKRT T0344 79 :LDSTLGGIELRKLDEP 1atr 275 :SSSTQASIEIDSLYEG T0344 96 :IDALGISDKGK 1atr 291 :IDFYTSITRAR T0344 107 :EVWKELSKDLQPLARKFWEETNI 1atr 304 :ELNADLFRGTLDPVEKALRDAKL T0344 130 :EIVAIGKSS 1atr 333 :DIVLVGGST T0344 152 :SAKWGIENVEK 1atr 342 :RIPKIQKLLQD T0344 163 :EGH 1atr 355 :NGK Number of specific fragments extracted= 10 number of extra gaps= 0 total=51 Number of alignments=10 # 1atr read from 1atr/merged-good-all-a2m # found chain 1atr in template set T0344 37 :AKEVMVKYANPYD 1atr 98 :AGRPKVQVEYKGE T0344 50 :YDLTGRQAIRDEVLLAIELARK 1atr 112 :KSFYPEEVSSMVLTKMKEIAEA T0344 73 :KPDVIHLDSTLG 1atr 138 :TVTNAVVTVPAY T0344 91 :L 1atr 150 :F T0344 113 :SKDLQPLARKFWEETNIEIVAIGK 1atr 151 :NDSQRQATKDAGTIAGLNVLRIIN T0344 149 :GIYSAKWGIENVEKEGH 1atr 175 :EPTAAAIAYGLDKKVGA T0344 166 :LIIGL 1atr 196 :LIFDL T0344 171 :PRYMEV 1atr 202 :GGVFDV T0344 177 :NIKDGKIIGRSL 1atr 211 :TIEDGIFEVKST Number of specific fragments extracted= 9 number of extra gaps= 0 total=60 Number of alignments=11 # 1atr read from 1atr/merged-good-all-a2m # found chain 1atr in template set T0344 3 :IVAADTGGAVLD 1atr 195 :VLIFDLGGGVFD T0344 25 :TVAVLVEKPYRSAKEVMVKYANP 1atr 207 :VSILTIEDGIFEVKSTAGDTHLG T0344 49 :DYDLTGRQAIRDEVLLAIELARKVKPD 1atr 250 :KKDISENKRAVRRLRTACERAKRTLSS T0344 81 :STLGGIELRKLDEP 1atr 277 :STQASIEIDSLYEG T0344 95 :TIDA 1atr 298 :TRAR T0344 105 :GKEVWKELSKDLQPLARKFWEETNI 1atr 302 :FEELNADLFRGTLDPVEKALRDAKL T0344 130 :EIVAIGK 1atr 333 :DIVLVGG T0344 150 :IYSAKWGIENVEK 1atr 340 :STRIPKIQKLLQD T0344 163 :EGH 1atr 355 :NGK Number of specific fragments extracted= 9 number of extra gaps= 0 total=69 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ats/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ats expands to /projects/compbio/data/pdb/1ats.pdb.gz 1ats:Warning: there is no chain 1ats will retry with 1atsA # T0344 read from 1ats/merged-good-all-a2m # 1ats read from 1ats/merged-good-all-a2m # adding 1ats to template set # found chain 1ats in template set T0344 3 :IVAADTGGAV 1ats 195 :VLIFDLGGGE T0344 23 :I 1ats 205 :F T0344 25 :TVAVLVEKP 1ats 206 :DVSILTIED T0344 38 :KEVMVKYA 1ats 215 :GIFEVKST T0344 46 :NPY 1ats 225 :DTH T0344 49 :DYDLTGRQAIRDEVLLAIELARKV 1ats 250 :KKDISENKRAVRRLRTACERAKRT T0344 80 :DSTLGGIELRKLDEP 1ats 276 :SSTQASIEIDSLYEG T0344 96 :IDALGISDKG 1ats 291 :IDFYTSITRA T0344 106 :KEVWKELSKDLQPLARKFWEETNI 1ats 303 :EELNADLFRGTLDPVEKALRDAKL T0344 130 :EIVAIGKSS 1ats 333 :DIVLVGGST T0344 152 :SAKWGIENVEK 1ats 342 :RIPKIQKLLQD T0344 163 :EGH 1ats 355 :NGK Number of specific fragments extracted= 12 number of extra gaps= 0 total=81 Number of alignments=13 # 1ats read from 1ats/merged-good-all-a2m # found chain 1ats in template set T0344 3 :IVAADTGGAVL 1ats 195 :VLIFDLGGGEF T0344 24 :ATVAVLVEKPYRSAKEVMVKYA 1ats 206 :DVSILTIEDGIFEVKSTAGDTH T0344 49 :DYDLTGRQAIRDEVLLAIELARK 1ats 250 :KKDISENKRAVRRLRTACERAKR T0344 72 :VKPDVIHLDSTLGGIEL 1ats 277 :STQASIEIDSLYEGIDF T0344 89 :RKLDEPTID 1ats 295 :TSITRARFE T0344 107 :EVWKELSKDLQPLARKFWEETNI 1ats 304 :ELNADLFRGTLDPVEKALRDAKL T0344 130 :EIVAIGK 1ats 333 :DIVLVGG Number of specific fragments extracted= 7 number of extra gaps= 0 total=88 Number of alignments=14 # 1ats read from 1ats/merged-good-all-a2m # found chain 1ats in template set T0344 3 :IVAADTGGAV 1ats 195 :VLIFDLGGGE T0344 23 :IATVAVLVEKPYRSAKEVMVKYANP 1ats 205 :FDVSILTIEDGIFEVKSTAGDTHLG T0344 49 :DYDLTGRQAIRDEVLLAIELARKV 1ats 250 :KKDISENKRAVRRLRTACERAKRT T0344 73 :KPDVIHLDSTLGGIE 1ats 278 :TQASIEIDSLYEGID T0344 88 :LRKLDEPTID 1ats 294 :YTSITRARFE T0344 107 :EVWKELSKDLQPLARKFWEETNI 1ats 304 :ELNADLFRGTLDPVEKALRDAKL T0344 130 :EIVAIGK 1ats 333 :DIVLVGG T0344 150 :IYSAKWGIENVEK 1ats 340 :STRIPKIQKLLQD T0344 163 :EGH 1ats 355 :NGK Number of specific fragments extracted= 9 number of extra gaps= 0 total=97 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1l2tA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1l2tA expands to /projects/compbio/data/pdb/1l2t.pdb.gz 1l2tA:# T0344 read from 1l2tA/merged-good-all-a2m # 1l2tA read from 1l2tA/merged-good-all-a2m # adding 1l2tA to template set # found chain 1l2tA in template set T0344 51 :DLTGRQA 1l2tA 145 :QLSGGQQ T0344 60 :DEVLLAIELA 1l2tA 152 :QRVAIARALA T0344 72 :VKPDVIHLDSTLGGI 1l2tA 162 :NNPPIILADQPTGAL T0344 92 :DE 1l2tA 177 :DS T0344 111 :ELSKDLQPLARKFWEETNIEIVAIGKS 1l2tA 179 :KTGEKIMQLLKKLNEEDGKTVVVVTHD T0344 158 :ENVEKEGHLII 1l2tA 206 :INVARFGERII T0344 177 :NIKDGKIIGRS 1l2tA 217 :YLKDGEVEREE Number of specific fragments extracted= 7 number of extra gaps= 0 total=104 Number of alignments=16 # 1l2tA read from 1l2tA/merged-good-all-a2m # found chain 1l2tA in template set T0344 51 :DLTGRQ 1l2tA 145 :QLSGGQ T0344 59 :RDEVLLAIELA 1l2tA 151 :QQRVAIARALA T0344 72 :VKPDVIHLDSTLGG 1l2tA 162 :NNPPIILADQPTGA T0344 91 :LDEPTI 1l2tA 176 :LDSKTG T0344 114 :KDLQPLARKFWEETNIEIVAIGKS 1l2tA 182 :EKIMQLLKKLNEEDGKTVVVVTHD T0344 158 :ENVEKEGHLII 1l2tA 206 :INVARFGERII T0344 177 :NIKDGKIIGRS 1l2tA 217 :YLKDGEVEREE Number of specific fragments extracted= 7 number of extra gaps= 0 total=111 Number of alignments=17 # 1l2tA read from 1l2tA/merged-good-all-a2m # found chain 1l2tA in template set T0344 44 :YANPYDYDLTGRQA 1l2tA 138 :FANHKPNQLSGGQQ T0344 60 :DEVLLAIELA 1l2tA 152 :QRVAIARALA T0344 72 :VKPDVIHLDSTLGGIE 1l2tA 162 :NNPPIILADQPTGALD T0344 110 :KELSKDLQPLARKFWEETNIEIVAIGKS 1l2tA 178 :SKTGEKIMQLLKKLNEEDGKTVVVVTHD T0344 158 :ENVEKEGHLII 1l2tA 206 :INVARFGERII T0344 177 :NIKDGKIIGRS 1l2tA 217 :YLKDGEVEREE Number of specific fragments extracted= 6 number of extra gaps= 0 total=117 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hx1A/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/T0344/1hx1A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0344/1hx1A/merged-good-all-a2m.gz for input Trying 1hx1A/merged-good-all-a2m Error: Couldn't open file 1hx1A/merged-good-all-a2m or 1hx1A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1h61A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1h61A expands to /projects/compbio/data/pdb/1h61.pdb.gz 1h61A:# T0344 read from 1h61A/merged-good-all-a2m # 1h61A read from 1h61A/merged-good-all-a2m # adding 1h61A to template set # found chain 1h61A in template set T0344 32 :KPYRSAKEVMVKYANPYDYDLTGRQAIRDEVLLAIELARKVKPDVIHLDSTLG 1h61A 133 :LRDENGNAIRVDTTTPRALELDEIPGIVNDFRQAVANAREAGFDLVELHSAHG T0344 97 :DALGISDKGKEVWKELSKDLQPLARKFWEETN 1h61A 195 :SSNQRTDQYGGSVENRARLVLEVVDAVCNEWS T0344 129 :IEIVAIGKSSV 1h61A 230 :IGIRVSPIGTF T0344 148 :AGIYSAKWGIENVEKEGHLII 1h61A 248 :NEEADALYLIEELAKRGIAYL Number of specific fragments extracted= 4 number of extra gaps= 0 total=121 Number of alignments=19 # 1h61A read from 1h61A/merged-good-all-a2m # found chain 1h61A in template set T0344 7 :DTGGAVLDETFEP 1h61A 128 :NTRTSLRDENGNA T0344 40 :VMVKYANPYDYDLTGRQAIRDEVLLAIELARKVKPDVIHLDSTLG 1h61A 141 :IRVDTTTPRALELDEIPGIVNDFRQAVANAREAGFDLVELHSAHG T0344 97 :DALGISDKGKEVWKELSKDLQPLARKFWEETN 1h61A 195 :SSNQRTDQYGGSVENRARLVLEVVDAVCNEWS T0344 129 :IEIVAIGKSSV 1h61A 230 :IGIRVSPIGTF T0344 148 :AGIYSAKWGIENVEKEG 1h61A 248 :NEEADALYLIEELAKRG Number of specific fragments extracted= 5 number of extra gaps= 0 total=126 Number of alignments=20 # 1h61A read from 1h61A/merged-good-all-a2m # found chain 1h61A in template set T0344 11 :AVLDET 1h61A 132 :SLRDEN T0344 37 :AKEVMVKYANPYDYDLTGRQAIRDEVLLAIELARKVKPDVIHLDSTLG 1h61A 138 :GNAIRVDTTTPRALELDEIPGIVNDFRQAVANAREAGFDLVELHSAHG T0344 100 :GISDKGKEVWKELSKDLQPLARKFWEETN 1h61A 198 :QRTDQYGGSVENRARLVLEVVDAVCNEWS T0344 129 :IEIVAIGKSSV 1h61A 230 :IGIRVSPIGTF T0344 148 :AGIYSAKWGIENVEKEG 1h61A 248 :NEEADALYLIEELAKRG T0344 165 :HLIIGL 1h61A 266 :AYLHMS Number of specific fragments extracted= 6 number of extra gaps= 0 total=132 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bupA/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/T0344/2bupA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0344/2bupA/merged-good-all-a2m.gz for input Trying 2bupA/merged-good-all-a2m Error: Couldn't open file 2bupA/merged-good-all-a2m or 2bupA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hpm/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1hpm expands to /projects/compbio/data/pdb/1hpm.pdb.gz 1hpm:Warning: there is no chain 1hpm will retry with 1hpmA # T0344 read from 1hpm/merged-good-all-a2m # 1hpm read from 1hpm/merged-good-all-a2m # adding 1hpm to template set # found chain 1hpm in template set T0344 3 :IVAADTGGAV 1hpm 195 :VLIFDLGGGT T0344 23 :IATVAVLVEKPYRSAKEVMVK 1hpm 205 :FDVSILTIEDGIFEVKSTAGD T0344 47 :PY 1hpm 226 :TH T0344 49 :DYDLTGRQAIRDEVLLAIELARKV 1hpm 250 :KKDISENKRAVRRLRTACERAKRT T0344 79 :LDSTLGGIELRKLDEP 1hpm 275 :SSSTQASIEIDSLYEG T0344 96 :IDALGISDKG 1hpm 291 :IDFYTSITRA T0344 106 :KEVWKELSKDLQPLARKFWEETNI 1hpm 303 :EELNADLFRGTLDPVEKALRDAKL T0344 130 :EIVAIGKSS 1hpm 333 :DIVLVGGST T0344 152 :SAKWGIENVEK 1hpm 342 :RIPKIQKLLQD T0344 163 :EGH 1hpm 355 :NGK Number of specific fragments extracted= 10 number of extra gaps= 0 total=142 Number of alignments=22 # 1hpm read from 1hpm/merged-good-all-a2m # found chain 1hpm in template set T0344 3 :IVAADTGGAVL 1hpm 195 :VLIFDLGGGTF T0344 24 :ATVA 1hpm 206 :DVSI T0344 176 :VNIKDGKIIGRS 1hpm 210 :LTIEDGIFEVKS Number of specific fragments extracted= 3 number of extra gaps= 0 total=145 Number of alignments=23 # 1hpm read from 1hpm/merged-good-all-a2m # found chain 1hpm in template set T0344 3 :IVAADTGGAV 1hpm 195 :VLIFDLGGGT T0344 23 :IATVAVLVEKPYRSAKEVMVKYANP 1hpm 205 :FDVSILTIEDGIFEVKSTAGDTHLG T0344 49 :DYDLTGRQAIRDEVLLAIELARKVKPD 1hpm 250 :KKDISENKRAVRRLRTACERAKRTLSS T0344 77 :IHLDSTLGGIE 1hpm 282 :IEIDSLYEGID T0344 88 :LRKLDEPTID 1hpm 294 :YTSITRARFE T0344 107 :EVWKELSKDLQPLARKFWEETNI 1hpm 304 :ELNADLFRGTLDPVEKALRDAKL T0344 130 :EIVAIGK 1hpm 333 :DIVLVGG T0344 150 :IYSAKWGIENVEK 1hpm 340 :STRIPKIQKLLQD T0344 163 :EGH 1hpm 355 :NGK Number of specific fragments extracted= 9 number of extra gaps= 0 total=154 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fobA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0344 read from 1fobA/merged-good-all-a2m # 1fobA read from 1fobA/merged-good-all-a2m # found chain 1fobA in training set T0344 44 :YANPYDYDL 1fobA 49 :WVNPSDGSY T0344 58 :IRDEVLLAIELARKVKPDVIHL 1fobA 58 :DLDYNLELAKRVKAAGMSLYLD T0344 80 :DST 1fobA 83 :SDT T0344 90 :KLDEPTIDALG 1fobA 86 :WADPSDQTTPS T0344 101 :ISDKG 1fobA 98 :WSTTD T0344 106 :KEVWKELSKDLQPLARKFWEET 1fobA 104 :GTLKWQLYNYTLEVCNTFAEND T0344 128 :NIEIVAIG 1fobA 127 :DIEIISIG T0344 139 :VPVRIAEIYAGIYSAKWGIENVEKEG 1fobA 147 :ETSSYSNIGALLHSGAWGVKDSNLAT T0344 165 :HLIIGL 1fobA 175 :KIMIHL Number of specific fragments extracted= 9 number of extra gaps= 0 total=163 Number of alignments=25 # 1fobA read from 1fobA/merged-good-all-a2m # found chain 1fobA in training set T0344 45 :ANPYDYD 1fobA 50 :VNPSDGS T0344 57 :AIRDEVLLAIELARKVKPDVIHL 1fobA 57 :YDLDYNLELAKRVKAAGMSLYLD T0344 80 :DSTLG 1fobA 81 :HLSDT T0344 90 :KLDEPTIDA 1fobA 86 :WADPSDQTT T0344 99 :LGISDKG 1fobA 96 :SGWSTTD T0344 106 :KEVWKELSKDLQPLARKFWEET 1fobA 104 :GTLKWQLYNYTLEVCNTFAEND T0344 128 :NIEIVAIG 1fobA 127 :DIEIISIG T0344 137 :SSVPVRIAEIYAGIYSAKWGIENVEKEG 1fobA 145 :LGETSSYSNIGALLHSGAWGVKDSNLAT T0344 165 :HLIIGLP 1fobA 175 :KIMIHLD Number of specific fragments extracted= 9 number of extra gaps= 0 total=172 Number of alignments=26 # 1fobA read from 1fobA/merged-good-all-a2m # found chain 1fobA in training set T0344 44 :YANPYDYDLT 1fobA 49 :WVNPSDGSYD T0344 59 :RDEVLLAIELARKVKPDV 1fobA 59 :LDYNLELAKRVKAAGMSL T0344 77 :IHLDSTLGGIE 1fobA 78 :LDLHLSDTWAD T0344 90 :KLDEPTIDALGISDKG 1fobA 89 :PSDQTTPSGWSTTDLG T0344 107 :EVWKELSKDLQPLARKFWEET 1fobA 105 :TLKWQLYNYTLEVCNTFAEND T0344 128 :NIEIVAIG 1fobA 127 :DIEIISIG T0344 147 :YAGIYS 1fobA 151 :YSNIGA T0344 153 :AKWGIENVEK 1fobA 158 :LHSGAWGVKD T0344 165 :HLIIGLPR 1fobA 175 :KIMIHLDD Number of specific fragments extracted= 9 number of extra gaps= 0 total=181 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b99A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2b99A expands to /projects/compbio/data/pdb/2b99.pdb.gz 2b99A:# T0344 read from 2b99A/merged-good-all-a2m # 2b99A read from 2b99A/merged-good-all-a2m # adding 2b99A to template set # found chain 2b99A in template set T0344 3 :IVAADTGGA 2b99A 34 :IIRKTVPGI T0344 56 :QA 2b99A 43 :KD T0344 61 :EVLLAIELARKVKPDVIHLDSTLG 2b99A 45 :LPVACKKLLEEEGCDIVMALGMPG T0344 105 :GKEVWKELSKDLQPLARKFWEETNIEIVAIG 2b99A 69 :KAEKDKVCAHEASLGLMLAQLMTNKHIIEVF Number of specific fragments extracted= 4 number of extra gaps= 0 total=185 Number of alignments=28 # 2b99A read from 2b99A/merged-good-all-a2m # found chain 2b99A in template set T0344 39 :EVMVKYANPY 2b99A 33 :KIIRKTVPGI T0344 59 :RDEVLLAIELARKVKPDVIHLDSTL 2b99A 43 :KDLPVACKKLLEEEGCDIVMALGMP T0344 100 :G 2b99A 68 :G T0344 105 :GKEVWKELSKDLQPLARKFWEETNIEIVAI 2b99A 69 :KAEKDKVCAHEASLGLMLAQLMTNKHIIEV Number of specific fragments extracted= 4 number of extra gaps= 0 total=189 Number of alignments=29 # 2b99A read from 2b99A/merged-good-all-a2m # found chain 2b99A in template set T0344 1 :MRIVAADTGGA 2b99A 3 :KKVGIVDTTFA T0344 49 :DYDL 2b99A 14 :RVDM T0344 62 :VLLAIELARKVKPDVIHLDSTLGGI 2b99A 18 :ASIAIKKLKELSPNIKIIRKTVPGI T0344 114 :KDLQPLARKFWEETNIEIVAI 2b99A 43 :KDLPVACKKLLEEEGCDIVMA T0344 135 :GKSS 2b99A 68 :GKAE T0344 146 :IYAGIYSAKWGIENVEK 2b99A 73 :DKVCAHEASLGLMLAQL T0344 163 :EGHLIIGLP 2b99A 92 :NKHIIEVFV Number of specific fragments extracted= 7 number of extra gaps= 0 total=196 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kax/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/T0344/1kax/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0344/1kax/merged-good-all-a2m.gz for input Trying 1kax/merged-good-all-a2m Error: Couldn't open file 1kax/merged-good-all-a2m or 1kax/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kaz/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/T0344/1kaz/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0344/1kaz/merged-good-all-a2m.gz for input Trying 1kaz/merged-good-all-a2m Error: Couldn't open file 1kaz/merged-good-all-a2m or 1kaz/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ngc/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/T0344/1ngc/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0344/1ngc/merged-good-all-a2m.gz for input Trying 1ngc/merged-good-all-a2m Error: Couldn't open file 1ngc/merged-good-all-a2m or 1ngc/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ngd/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/T0344/1ngd/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0344/1ngd/merged-good-all-a2m.gz for input Trying 1ngd/merged-good-all-a2m Error: Couldn't open file 1ngd/merged-good-all-a2m or 1ngd/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nge/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/T0344/1nge/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0344/1nge/merged-good-all-a2m.gz for input Trying 1nge/merged-good-all-a2m Error: Couldn't open file 1nge/merged-good-all-a2m or 1nge/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z47A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1z47A expands to /projects/compbio/data/pdb/1z47.pdb.gz 1z47A:# T0344 read from 1z47A/merged-good-all-a2m # 1z47A read from 1z47A/merged-good-all-a2m # adding 1z47A to template set # found chain 1z47A in template set T0344 47 :PYDYDLTGRQ 1z47A 141 :RFPHELSGGQ T0344 61 :EVLLAIELARKVKPDVIHLDSTLGG 1z47A 151 :QQRVALARALAPRPQVLLFDEPFAA T0344 104 :KGKEVWKELS 1z47A 176 :IDTQIRRELR T0344 118 :PLARKFWEETNI 1z47A 186 :TFVRQVHDEMGV T0344 130 :EIVAIGKSSV 1z47A 215 :RVLVLHEGNV T0344 140 :PVRIAEIY 1z47A 227 :FGTPEEVY T0344 148 :AGIYSAKWGIENV 1z47A 238 :GTLFVASFIGESN T0344 161 :EKEGHLIIG 1z47A 256 :VQNGRIEVA T0344 173 :YMEVNIKDG 1z47A 265 :GAALPVDPA T0344 183 :IIGRSLDPREGGL 1z47A 289 :VELQPASEREAHA T0344 196 :YGSAEVSVPEGVKWEIY 1z47A 312 :YSACWIRTKDGEVWEVH Number of specific fragments extracted= 11 number of extra gaps= 0 total=207 Number of alignments=31 # 1z47A read from 1z47A/merged-good-all-a2m # found chain 1z47A in template set T0344 51 :DLTGRQ 1z47A 145 :ELSGGQ T0344 61 :EVLLAIELARKVKPDVIHLDSTLG 1z47A 151 :QQRVALARALAPRPQVLLFDEPFA T0344 103 :DKGKEVWKELS 1z47A 175 :AIDTQIRRELR T0344 118 :PLARKFWEETNI 1z47A 186 :TFVRQVHDEMGV T0344 130 :EIVAIGKSSV 1z47A 215 :RVLVLHEGNV T0344 140 :PVRIAEIYA 1z47A 227 :FGTPEEVYE T0344 149 :GIYSAKWGIE 1z47A 239 :TLFVASFIGE T0344 159 :NVEKEGHLIIG 1z47A 254 :RAVQNGRIEVA T0344 173 :YMEVNIKDG 1z47A 265 :GAALPVDPA T0344 183 :IIGRSLDPREGGL 1z47A 289 :VELQPASEREAHA T0344 196 :YGSAEVSVPEGVKWEIYPNPVA 1z47A 312 :YSACWIRTKDGEVWEVHVPSAD Number of specific fragments extracted= 11 number of extra gaps= 0 total=218 Number of alignments=32 # 1z47A read from 1z47A/merged-good-all-a2m # found chain 1z47A in template set T0344 44 :YANPYDYDLTGRQAI 1z47A 138 :YANRFPHELSGGQQQ T0344 63 :LLAIELARKVKPDVIHLDSTLGGIE 1z47A 153 :RVALARALAPRPQVLLFDEPFAAID T0344 110 :KELSKDLQPLARKFWEETNIEIVAIGK 1z47A 178 :TQIRRELRTFVRQVHDEMGVTSVFVTH T0344 152 :SAKWGIENV 1z47A 205 :DQEEALEVA T0344 164 :GHLIIGLPR 1z47A 214 :DRVLVLHEG T0344 173 :YMEVNIKDGKII 1z47A 251 :VWTRAVQNGRIE T0344 185 :G 1z47A 267 :A T0344 186 :RSLDPREG 1z47A 292 :QPASEREA T0344 194 :GLYGSAEVSVPEGVKWEIY 1z47A 310 :GSYSACWIRTKDGEVWEVH Number of specific fragments extracted= 9 number of extra gaps= 0 total=227 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ngf/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/T0344/1ngf/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0344/1ngf/merged-good-all-a2m.gz for input Trying 1ngf/merged-good-all-a2m Error: Couldn't open file 1ngf/merged-good-all-a2m or 1ngf/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ngg/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/T0344/1ngg/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0344/1ngg/merged-good-all-a2m.gz for input Trying 1ngg/merged-good-all-a2m Error: Couldn't open file 1ngg/merged-good-all-a2m or 1ngg/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ngh/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/T0344/1ngh/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0344/1ngh/merged-good-all-a2m.gz for input Trying 1ngh/merged-good-all-a2m Error: Couldn't open file 1ngh/merged-good-all-a2m or 1ngh/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mb3A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0344 read from 1mb3A/merged-good-all-a2m # 1mb3A read from 1mb3A/merged-good-all-a2m # found chain 1mb3A in training set Warning: unaligning (T0344)G135 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1mb3A)D90 Warning: unaligning (T0344)R142 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1mb3A)D90 T0344 57 :AIRDEVLL 1mb3A 17 :LFHDLLEA T0344 65 :AIELARKVKPDVIHLDSTLGGIE 1mb3A 38 :ALSIARENKPDLILMDIQLPEIS T0344 116 :LQPLARKFWEE 1mb3A 61 :GLEVTKWLKED T0344 127 :TNIEIVAI 1mb3A 75 :AHIPVVAV T0344 143 :IAEIYA 1mb3A 91 :EERIRE Number of specific fragments extracted= 5 number of extra gaps= 0 total=232 Number of alignments=34 # 1mb3A read from 1mb3A/merged-good-all-a2m # found chain 1mb3A in training set Warning: unaligning (T0344)G135 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1mb3A)D90 Warning: unaligning (T0344)R142 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1mb3A)D90 T0344 64 :LAIELARKVKPDVIHLDSTLGGIE 1mb3A 37 :SALSIARENKPDLILMDIQLPEIS T0344 116 :LQPLARKFWEE 1mb3A 61 :GLEVTKWLKED T0344 127 :TNIEIVAI 1mb3A 75 :AHIPVVAV T0344 143 :IAEIYAG 1mb3A 91 :EERIREG Number of specific fragments extracted= 4 number of extra gaps= 0 total=236 Number of alignments=35 # 1mb3A read from 1mb3A/merged-good-all-a2m # found chain 1mb3A in training set Warning: unaligning (T0344)G135 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1mb3A)D90 T0344 56 :QAIRDEVLL 1mb3A 16 :KLFHDLLEA T0344 65 :AIELARKVKPDVIHLDSTLGGIE 1mb3A 38 :ALSIARENKPDLILMDIQLPEIS T0344 116 :LQPLARKFWEETN 1mb3A 61 :GLEVTKWLKEDDD T0344 129 :IEIVAI 1mb3A 77 :IPVVAV Number of specific fragments extracted= 4 number of extra gaps= 0 total=240 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1srrA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1srrA expands to /projects/compbio/data/pdb/1srr.pdb.gz 1srrA:# T0344 read from 1srrA/merged-good-all-a2m # 1srrA read from 1srrA/merged-good-all-a2m # adding 1srrA to template set # found chain 1srrA in template set T0344 64 :LAIELARKVKPDVIHLDSTLGGIE 1srrA 38 :QALDIVTKERPDLVLLDMKIPGMD T0344 105 :GKEVWKEL 1srrA 62 :GIEILKRM T0344 124 :WE 1srrA 70 :KV T0344 126 :ETNIEIVAIGKSS 1srrA 73 :DENIRVIIMTAYG Number of specific fragments extracted= 4 number of extra gaps= 0 total=244 Number of alignments=37 # 1srrA read from 1srrA/merged-good-all-a2m # found chain 1srrA in template set T0344 62 :VLLAIELARKVKPDVIHLDSTLGGIE 1srrA 36 :GLQALDIVTKERPDLVLLDMKIPGMD T0344 116 :LQPLARKFWEE 1srrA 62 :GIEILKRMKVI T0344 127 :TNIEIVAIGKSSVPVRIAEIYA 1srrA 74 :ENIRVIIMTAYGELDMIQESKE Number of specific fragments extracted= 3 number of extra gaps= 0 total=247 Number of alignments=38 # 1srrA read from 1srrA/merged-good-all-a2m # found chain 1srrA in template set T0344 64 :LAIELARKVKPDVIHLDSTLGGIE 1srrA 38 :QALDIVTKERPDLVLLDMKIPGMD T0344 116 :LQPLARKFWE 1srrA 62 :GIEILKRMKV T0344 126 :ETNIEIVAIGKSSVP 1srrA 73 :DENIRVIIMTAYGEL T0344 155 :WGIENVEK 1srrA 88 :DMIQESKE Number of specific fragments extracted= 4 number of extra gaps= 0 total=251 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ba0/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/T0344/1ba0/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0344/1ba0/merged-good-all-a2m.gz for input Trying 1ba0/merged-good-all-a2m Error: Couldn't open file 1ba0/merged-good-all-a2m or 1ba0/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ba1/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ba1 expands to /projects/compbio/data/pdb/1ba1.pdb.gz 1ba1:Warning: there is no chain 1ba1 will retry with 1ba1A # T0344 read from 1ba1/merged-good-all-a2m # 1ba1 read from 1ba1/merged-good-all-a2m # adding 1ba1 to template set # found chain 1ba1 in template set T0344 3 :IVAADTGGAV 1ba1 195 :VLIFDLGGGT T0344 23 :IATVAVLVEKPYRSAKEVMV 1ba1 205 :FDVSILTIEDGIFEVKSTAG T0344 46 :NPY 1ba1 225 :DTH T0344 49 :DYDLTGRQAIRDEVLLAIELARKV 1ba1 250 :KKDISENKRAVRRLRTACERAKRT T0344 79 :LDSTLGGIELRKLDEP 1ba1 275 :SSSTQASIEIDSLYEG T0344 96 :IDALGISDKGK 1ba1 291 :IDFYTSITRAR T0344 107 :EVWKELSKDLQPLARKFWEETNI 1ba1 304 :ELNADLFRGTLDPVEKALRDAKL T0344 130 :EIVAIGKSS 1ba1 333 :DIVLVGGST T0344 149 :G 1ba1 342 :R T0344 153 :AKWGIENVEK 1ba1 343 :IPKIQKLLQD T0344 163 :EGH 1ba1 355 :NGK Number of specific fragments extracted= 11 number of extra gaps= 0 total=262 Number of alignments=40 # 1ba1 read from 1ba1/merged-good-all-a2m # found chain 1ba1 in template set T0344 3 :IVAADTGGAVL 1ba1 195 :VLIFDLGGGTF T0344 24 :ATVAV 1ba1 206 :DVSIL T0344 177 :NIKDGKIIGRSL 1ba1 211 :TIEDGIFEVKST Number of specific fragments extracted= 3 number of extra gaps= 0 total=265 Number of alignments=41 # 1ba1 read from 1ba1/merged-good-all-a2m # found chain 1ba1 in template set T0344 3 :IVAADTGGAV 1ba1 195 :VLIFDLGGGT T0344 23 :IATVAVLVEKPYRSAKEVMVKYANP 1ba1 205 :FDVSILTIEDGIFEVKSTAGDTHLG T0344 49 :DYDLTGRQAIRDEVLLAIELARKVKPD 1ba1 250 :KKDISENKRAVRRLRTACERAKRTLSS T0344 81 :STLGGIELRKLDEP 1ba1 277 :STQASIEIDSLYEG T0344 95 :TIDAL 1ba1 298 :TRARF T0344 106 :KEVWKELSKDLQPLARKFWEETNI 1ba1 303 :EELNADLFRGTLDPVEKALRDAKL T0344 130 :EIVAIGK 1ba1 333 :DIVLVGG T0344 150 :IYSAKWGIENVEK 1ba1 340 :STRIPKIQKLLQD T0344 163 :EGH 1ba1 355 :NGK Number of specific fragments extracted= 9 number of extra gaps= 0 total=274 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1c9kA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1c9kA expands to /projects/compbio/data/pdb/1c9k.pdb.gz 1c9kA:# T0344 read from 1c9kA/merged-good-all-a2m # 1c9kA read from 1c9kA/merged-good-all-a2m # adding 1c9kA to template set # found chain 1c9kA in template set Warning: unaligning (T0344)N46 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1c9kA)D98 T0344 47 :PYDYDLTG 1c9kA 99 :PEQWDYAA T0344 55 :RQAIRDEVLLAIELARKVKPDVIHLDSTLGG 1c9kA 108 :ERAIDDEIQILIAACQRCPAKVVLVTNEVGM T0344 100 :GISD 1c9kA 139 :GIVP T0344 105 :GKEVWKELSKDLQPLARKFWEETNIEIVAIGKSSVP 1c9kA 143 :ENRLARHFRDIAGRVNQRLAAAADEVWLVVSGIGVK Number of specific fragments extracted= 4 number of extra gaps= 0 total=278 Number of alignments=43 # 1c9kA read from 1c9kA/merged-good-all-a2m # found chain 1c9kA in template set Warning: unaligning (T0344)N46 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1c9kA)D98 T0344 47 :PYDYDLTG 1c9kA 99 :PEQWDYAA T0344 55 :RQAIRDEVLLAIELARKVKPDVIHLDSTLGG 1c9kA 108 :ERAIDDEIQILIAACQRCPAKVVLVTNEVGM T0344 89 :RKLDE 1c9kA 139 :GIVPE T0344 106 :KEVWKELSKDLQPLARKFWEETNIEIVAIGKSSVPV 1c9kA 144 :NRLARHFRDIAGRVNQRLAAAADEVWLVVSGIGVKI Number of specific fragments extracted= 4 number of extra gaps= 0 total=282 Number of alignments=44 # 1c9kA read from 1c9kA/merged-good-all-a2m # found chain 1c9kA in template set Warning: unaligning (T0344)N46 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1c9kA)D98 T0344 47 :PYDYDLTG 1c9kA 99 :PEQWDYAA T0344 55 :RQAIRDEVLLAIELARKVKPDVIHLDSTLGG 1c9kA 108 :ERAIDDEIQILIAACQRCPAKVVLVTNEVGM T0344 100 :GISD 1c9kA 139 :GIVP T0344 105 :GKEVWKELSKDLQPLARKFWEETNIEIVAIGKSSVP 1c9kA 143 :ENRLARHFRDIAGRVNQRLAAAADEVWLVVSGIGVK Number of specific fragments extracted= 4 number of extra gaps= 0 total=286 Number of alignments=45 # command:Using radius: 8.0000 Alignment mode NUMB_ALIGNS: 45 Adding 1413 constraints to all.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all.constraints maxweight: 1.0000 Optimizing... Probability sum: -498.4290, CN propb: -498.4290 weights: 0.2085 constraints: 570 # command:Found ConstraintSet # PrintContacts align.constraints_v3 Number of constraints in align.constraints 570 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_v3 Number of constraints in align.constraints.bonus 570 # command:Found ConstraintSet # PrintContacts rejected.constraints_v3 Number of constraints in rejected.constraints 843 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_v3 Number of constraints in rejected.constraints.bonus 843 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_v3 Number of constraints in noncontact.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_v3 Number of constraints in noncontact.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_v3 Number of constraints in all.constraints 1413 # command: