parameters: 0.6 1.3 0.5 200 50 # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading dunbrack-2191.atoms # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 53157 examples # computed average trans backbone unit before proline from 2010 examples # computed average cis backbone unit from 97 examples # trans (non-proline) backbone unit: # CA= -2.2087 1.0126 -0.0030 # O= -0.1499 2.2440 0.0016 # C= -0.6889 1.1368 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4581 -0.0000 0.0000 # cis backbone unit: # CA= -0.1436 2.4534 -0.0002 # O= -2.0284 0.9742 0.0015 # C= -0.8018 1.0771 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4668 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2100 1.0631 -0.0014 # O= -0.1236 2.2458 0.0075 # C= -0.6872 1.1517 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4660 0.0000 0.0000 # After reading dunbrack-2191.atoms have 2191 chains in training database # Count of chains,residues,atoms: 2191,500310,3902258 # 493341 residues have no bad marker # 3226 residues lack atoms needed to compute omega # 1453 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 4 # HAS_OXT 1167 # TOO_MANY_ATOMS 1 # TOO_FEW_ATOMS 3052 # HAS_UNKNOWN_ATOMS 9 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 979 # NON_PLANAR_PEPTIDE 888 # BAD_PEPTIDE 2680 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-2191.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0361/ # command:# Making conformation for sequence T0361 numbered 1 through 169 Created new target T0361 from T0361.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0361/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0361//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0361/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0361//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0361/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0361/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0361/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ewqA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ewqA expands to /projects/compbio/data/pdb/1ewq.pdb.gz 1ewqA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0361 read from 1ewqA/merged-good-all-a2m # 1ewqA read from 1ewqA/merged-good-all-a2m # adding 1ewqA to template set # found chain 1ewqA in template set T0361 15 :AQDNLFSFMKTA 1ewqA 298 :DRGPLEARLDRV # choosing archetypes in rotamer library T0361 35 :RQFLP 1ewqA 310 :EGFVR T0361 46 :DEEIVEYAVK 1ewqA 315 :EGALREGVRR T0361 57 :LLAQ 1ewqA 325 :LLYR T0361 64 :LDDI 1ewqA 329 :LADL T0361 69 :VALRLIYALGKMD 1ewqA 333 :ERLATRLELGRAS T0361 82 :KWLYADITHFSQYWHYL 1ewqA 350 :GALRRSLQILPELRALL T0361 102 :DETPGFAD 1ewqA 367 :GEEVGLPD T0361 114 :DFISNVNSITRNATLYD 1ewqA 377 :PLKEELEAALVEDPPLK T0361 131 :ALKAMKFADFAVWSEARFSGM 1ewqA 399 :LIREGYDPDLDALRAAHREGV T0361 154 :TALTLAVTTTLKELTP 1ewqA 420 :AYFLELEERERERTGI Number of specific fragments extracted= 11 number of extra gaps= 0 total=11 Number of alignments=1 # 1ewqA read from 1ewqA/merged-good-all-a2m # found chain 1ewqA in template set T0361 16 :QDNLFSFM 1ewqA 299 :RGPLEARL T0361 28 :SILLQGIR 1ewqA 307 :DRVEGFVR T0361 46 :DEEIVEYAVKP 1ewqA 315 :EGALREGVRRL T0361 58 :LAQSGPL 1ewqA 326 :LYRLADL T0361 69 :VALRLIYALGKMD 1ewqA 333 :ERLATRLELGRAS T0361 82 :KWLYADITHFSQYWHYLNEQDETPGFA 1ewqA 350 :GALRRSLQILPELRALLGEEVGLPDLS T0361 114 :DFISNVNSITRNATLYD 1ewqA 377 :PLKEELEAALVEDPPLK T0361 131 :ALKAMKFADFAVWSEARFSGM 1ewqA 399 :LIREGYDPDLDALRAAHREGV T0361 154 :TALTLAVTTTLKELT 1ewqA 420 :AYFLELEERERERTG Number of specific fragments extracted= 9 number of extra gaps= 0 total=20 Number of alignments=2 # 1ewqA read from 1ewqA/merged-good-all-a2m # found chain 1ewqA in template set T0361 4 :LTEDDVLEQL 1ewqA 297 :LDRGPLEARL T0361 32 :QGIRQFLPS 1ewqA 307 :DRVEGFVRE T0361 43 :VDNDEEIVEY 1ewqA 316 :GALREGVRRL T0361 58 :LAQSGPLD 1ewqA 326 :LYRLADLE T0361 70 :ALRLIYALGKMD 1ewqA 334 :RLATRLELGRAS T0361 82 :KWLYADITHFSQYWHYL 1ewqA 350 :GALRRSLQILPELRALL T0361 102 :DETPGFAD 1ewqA 367 :GEEVGLPD T0361 112 :TWDFISNVNSI 1ewqA 375 :LSPLKEELEAA T0361 124 :RNATL 1ewqA 387 :VEDPP T0361 129 :YDALKAMKFADFAVWSEARFSGM 1ewqA 397 :GGLIREGYDPDLDALRAAHREGV T0361 154 :TALTLAVTTTLKELT 1ewqA 420 :AYFLELEERERERTG Number of specific fragments extracted= 11 number of extra gaps= 0 total=31 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rcwA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1rcwA expands to /projects/compbio/data/pdb/1rcw.pdb.gz 1rcwA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0361 read from 1rcwA/merged-good-all-a2m # 1rcwA read from 1rcwA/merged-good-all-a2m # adding 1rcwA to template set # found chain 1rcwA in template set Warning: unaligning (T0361)Q60 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rcwA)E82 T0361 6 :EDDVLEQLDAQ 1rcwA 23 :EHTFYVKWSKG T0361 17 :DNLFSFMK 1rcwA 38 :EQLQAYAK T0361 25 :TAHSILLQGIRQFLPSL 1rcwA 49 :LHIKAFPKYLSAIHSRC T0361 45 :NDEEIVEYAVKPLLA 1rcwA 66 :DDLEARKLLLDNLMD T0361 61 :SGPLDDIDVALRLIYALGK 1rcwA 83 :NGYPNHIDLWKQFVFALGV T0361 80 :MDKWLYADITHFSQYWH 1rcwA 111 :PSEAAKAKVATFMRWCT T0361 109 :DDITWDFISNVNSITRN 1rcwA 146 :PRIAREKIRGLTEYFGF T0361 133 :KAMKFADFAVWSEARFSGMVKT 1rcwA 163 :SNPEDYAYFTEHEEADVRHARE T0361 155 :ALTLAVTTTLKEL 1rcwA 199 :KVLEASQEVTQSL Number of specific fragments extracted= 9 number of extra gaps= 1 total=40 Number of alignments=4 # 1rcwA read from 1rcwA/merged-good-all-a2m # found chain 1rcwA in template set Warning: unaligning (T0361)Q60 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rcwA)E82 T0361 7 :DDVLEQLDAQ 1rcwA 24 :HTFYVKWSKG T0361 17 :DNLFSFMK 1rcwA 38 :EQLQAYAK T0361 25 :TAHSILLQGIRQFLPSL 1rcwA 49 :LHIKAFPKYLSAIHSRC T0361 45 :NDEEIVEYAVKPLLA 1rcwA 66 :DDLEARKLLLDNLMD T0361 61 :SGPLDDIDVALRLIYALGK 1rcwA 83 :NGYPNHIDLWKQFVFALGV T0361 81 :DKWLYADITHFSQY 1rcwA 112 :SEAAKAKVATFMRW T0361 108 :ADDITWDFISNVNSITRNATL 1rcwA 145 :IPRIAREKIRGLTEYFGFSNP T0361 129 :YDALKAMK 1rcwA 168 :YAYFTEHE T0361 137 :FADFAVWSEARFSGMV 1rcwA 178 :DVRHAREEKALIEMLL T0361 153 :KTALTLAVTTTLKEL 1rcwA 197 :ADKVLEASQEVTQSL Number of specific fragments extracted= 10 number of extra gaps= 1 total=50 Number of alignments=5 # 1rcwA read from 1rcwA/merged-good-all-a2m # found chain 1rcwA in template set Warning: unaligning (T0361)Q60 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rcwA)E82 T0361 8 :DVLEQLDAQD 1rcwA 25 :TFYVKWSKGE T0361 18 :NLFSFMK 1rcwA 39 :QLQAYAK T0361 25 :TAHSILLQGIRQFLPSL 1rcwA 49 :LHIKAFPKYLSAIHSRC T0361 45 :NDEEIVEYAVKPLLA 1rcwA 66 :DDLEARKLLLDNLMD T0361 61 :SGPLDDIDVALRLIYALGK 1rcwA 83 :NGYPNHIDLWKQFVFALGV T0361 80 :MDKWLYADITHFSQY 1rcwA 111 :PSEAAKAKVATFMRW T0361 95 :WHYLNEQ 1rcwA 153 :IRGLTEY T0361 105 :PGFADDITWDFISNVNSITRNATL 1rcwA 160 :FGFSNPEDYAYFTEHEEADVRHAR T0361 129 :YDALKAMKFADFAVWSEA 1rcwA 189 :IEMLLKDDADKVLEASQE T0361 156 :LTLAVTT 1rcwA 207 :VTQSLYG Number of specific fragments extracted= 10 number of extra gaps= 1 total=60 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v4eA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1v4eA expands to /projects/compbio/data/pdb/1v4e.pdb.gz 1v4eA:# T0361 read from 1v4eA/merged-good-all-a2m # 1v4eA read from 1v4eA/merged-good-all-a2m # adding 1v4eA to template set # found chain 1v4eA in template set T0361 8 :DVLEQLD 1v4eA 118 :HTVEEIG T0361 16 :QDNLFSFMKTAHSILLQGIRQFLPSLFVDNDEEIVEYAVKP 1v4eA 125 :NNKLRRAFLNVIGKMSEAELIEQLSRYKPITKEEYLRIVEG T0361 57 :L 1v4eA 170 :L T0361 67 :IDVALRLIYAL 1v4eA 171 :FGLALQLPALL T0361 78 :GKMDKWLYADITHF 1v4eA 183 :GELGEDLYNLGVTI T0361 92 :SQYWHYLNEQDETP 1v4eA 203 :FDDIMDFAGMEKIG T0361 106 :GFAD 1v4eA 219 :GFLD T0361 115 :FISNVNSITRNATLYDALKAMKFADFAVWSEAR 1v4eA 229 :SFPLVTAMEKFPEARQMFENRDWSGLMSFMREK T0361 148 :FSGMVKTALTLAVTTTLKE 1v4eA 263 :ILKECEETLKVLVKNVIIE Number of specific fragments extracted= 9 number of extra gaps= 0 total=69 Number of alignments=7 # 1v4eA read from 1v4eA/merged-good-all-a2m # found chain 1v4eA in template set T0361 8 :DVLEQLD 1v4eA 118 :HTVEEIG T0361 16 :QDNLFSFMKTAHSILLQGIRQFLPSLFVDNDEEIVEYAVKP 1v4eA 125 :NNKLRRAFLNVIGKMSEAELIEQLSRYKPITKEEYLRIVEG T0361 57 :LL 1v4eA 170 :LF T0361 68 :DVALRLIYAL 1v4eA 172 :GLALQLPALL T0361 78 :GKMDKWLYA 1v4eA 183 :GELGEDLYN T0361 87 :DITHFSQYWHYLNEQDETP 1v4eA 198 :TIYQMFDDIMDFAGMEKIG T0361 106 :GFAD 1v4eA 219 :GFLD T0361 115 :FISNVNSITRNATLYDALKAMKFADFAVWSEAR 1v4eA 229 :SFPLVTAMEKFPEARQMFENRDWSGLMSFMREK T0361 148 :FSGMVKTALTLAVTTTLKE 1v4eA 263 :ILKECEETLKVLVKNVIIE Number of specific fragments extracted= 9 number of extra gaps= 0 total=78 Number of alignments=8 # 1v4eA read from 1v4eA/merged-good-all-a2m # found chain 1v4eA in template set T0361 21 :SFMKTAHSILLQG 1v4eA 111 :LVLVSAFHTVEEI T0361 34 :IRQFLPSLFVDND 1v4eA 128 :LRRAFLNVIGKMS T0361 48 :EIVEYAVK 1v4eA 141 :EAELIEQL T0361 59 :AQSGPLDDID 1v4eA 149 :SRYKPITKEE T0361 69 :VALRLIYAL 1v4eA 169 :ALFGLALQL T0361 78 :GKMDKWLYADITHF 1v4eA 183 :GELGEDLYNLGVTI T0361 92 :SQYWHYLNEQDETP 1v4eA 203 :FDDIMDFAGMEKIG T0361 106 :GFAD 1v4eA 219 :GFLD T0361 110 :DITWDFISNVNSITRNATLYDALKAMKFADFAVWSEAR 1v4eA 224 :KNGVASFPLVTAMEKFPEARQMFENRDWSGLMSFMREK T0361 148 :FSGMVKTALTLAVTTTLKE 1v4eA 263 :ILKECEETLKVLVKNVIIE Number of specific fragments extracted= 10 number of extra gaps= 0 total=88 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ffkB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ffkB expands to /projects/compbio/data/pdb-ca-mod/1ffk.brk_ca_mod.gz 1ffkB:# T0361 read from 1ffkB/merged-good-all-a2m # 1ffkB read from 1ffkB/merged-good-all-a2m # adding 1ffkB to template set # found chain 1ffkB in template set Number of specific fragments extracted= 0 number of extra gaps= 0 total=88 # 1ffkB read from 1ffkB/merged-good-all-a2m # found chain 1ffkB in template set Number of specific fragments extracted= 0 number of extra gaps= 0 total=88 # 1ffkB read from 1ffkB/merged-good-all-a2m # found chain 1ffkB in template set Number of specific fragments extracted= 0 number of extra gaps= 0 total=88 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ahqA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2ahqA expands to /projects/compbio/data/pdb/2ahq.pdb.gz 2ahqA:# T0361 read from 2ahqA/merged-good-all-a2m # 2ahqA read from 2ahqA/merged-good-all-a2m # adding 2ahqA to template set # found chain 2ahqA in template set Warning: unaligning (T0361)T168 because last residue in template chain is (2ahqA)G67 T0361 83 :WLYAD 2ahqA 20 :ELMKL T0361 94 :YWHYLNEQDETPGFADDITWDFISN 2ahqA 25 :IKEIVENEDKRKPYSDQEIANILKE T0361 125 :NATLYD 2ahqA 52 :FKVARR T0361 159 :AVTTTLKEL 2ahqA 58 :TVAKYREML Number of specific fragments extracted= 4 number of extra gaps= 0 total=92 Number of alignments=10 # 2ahqA read from 2ahqA/merged-good-all-a2m # found chain 2ahqA in template set T0361 83 :WLYAD 2ahqA 20 :ELMKL T0361 94 :YWHYLNEQDETPGFADDITWDFISN 2ahqA 25 :IKEIVENEDKRKPYSDQEIANILKE T0361 134 :AMKFADFAVWSEA 2ahqA 53 :KVARRTVAKYREM Number of specific fragments extracted= 3 number of extra gaps= 0 total=95 Number of alignments=11 # 2ahqA read from 2ahqA/merged-good-all-a2m # found chain 2ahqA in template set T0361 84 :LY 2ahqA 21 :LM T0361 92 :SQYWHYLNEQDETPGFADDITWDFISN 2ahqA 23 :KLIKEIVENEDKRKPYSDQEIANILKE T0361 131 :ALKAMKFADFAVWSEA 2ahqA 50 :KGFKVARRTVAKYREM Number of specific fragments extracted= 3 number of extra gaps= 0 total=98 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qbqA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1qbqA expands to /projects/compbio/data/pdb/1qbq.pdb.gz 1qbqA:# T0361 read from 1qbqA/merged-good-all-a2m # 1qbqA read from 1qbqA/merged-good-all-a2m # adding 1qbqA to template set # found chain 1qbqA in template set T0361 8 :DVLEQLDAQDNLFSFMKTAHS 1qbqA 174 :VLVEWLKDPSQELEFIADILN T0361 29 :ILLQGIRQFLPSL 1qbqA 201 :HAWQHRQWVIQEF T0361 44 :DNDEEIVEY 1qbqA 214 :RLWDNELQY T0361 54 :VKPLLAQS 1qbqA 223 :VDQLLKED T0361 64 :LDDIDVALRLIYAL 1qbqA 231 :VRNNSVWNQRHFVI T0361 78 :GKMDKWLYA 1qbqA 249 :GYSDRAVLE T0361 87 :DITHFS 1qbqA 259 :EVQYTL T0361 96 :HYLNEQD 1qbqA 265 :EMIKLVP T0361 108 :ADDITWDFISNVNSITRNATLYDALK 1qbqA 272 :HNESAWNYLKGILQDRGLSRYPNLLN T0361 134 :AMKFADFAVWSEARFSGMV 1qbqA 305 :SHSSPYLIAFLVDIYEDML T0361 153 :KTALTLAVTTTLKEL 1qbqA 330 :KEDILNKALELCEIL Number of specific fragments extracted= 11 number of extra gaps= 0 total=109 Number of alignments=13 # 1qbqA read from 1qbqA/merged-good-all-a2m # found chain 1qbqA in template set T0361 8 :DVLEQLDAQDNLFSFMKTAHS 1qbqA 174 :VLVEWLKDPSQELEFIADILN T0361 29 :ILLQGIRQFLPSL 1qbqA 201 :HAWQHRQWVIQEF T0361 44 :DNDEEIVEY 1qbqA 214 :RLWDNELQY T0361 54 :VKPLLAQSGPLDD 1qbqA 223 :VDQLLKEDVRNNS T0361 67 :IDVALRLIYALGKM 1qbqA 237 :WNQRHFVISNTTGY T0361 81 :DKWLYA 1qbqA 252 :DRAVLE T0361 89 :THFSQYWHYLNEQD 1qbqA 258 :REVQYTLEMIKLVP T0361 108 :ADDITWDFISNVNSITRNATLYDALKAMKFAD 1qbqA 272 :HNESAWNYLKGILQDRGLSRYPNLLNQLLDLQ T0361 140 :FAVWSEARFSGMV 1qbqA 311 :LIAFLVDIYEDML T0361 153 :KTALTLAVTTTLKEL 1qbqA 330 :KEDILNKALELCEIL Number of specific fragments extracted= 10 number of extra gaps= 0 total=119 Number of alignments=14 # 1qbqA read from 1qbqA/merged-good-all-a2m # found chain 1qbqA in template set T0361 8 :DVLEQLDAQDNLFSFMKTAHS 1qbqA 174 :VLVEWLKDPSQELEFIADILN T0361 29 :ILLQGIRQFLPSL 1qbqA 201 :HAWQHRQWVIQEF T0361 42 :FVDNDEEIVEYAVKPLLA 1qbqA 215 :LWDNELQYVDQLLKEDVR T0361 64 :LDD 1qbqA 233 :NNS T0361 67 :IDVALRLIYALGKM 1qbqA 237 :WNQRHFVISNTTGY T0361 81 :DKWLYA 1qbqA 252 :DRAVLE T0361 89 :THFSQYWHYLNEQDE 1qbqA 258 :REVQYTLEMIKLVPH T0361 109 :DDITWDFISNV 1qbqA 273 :NESAWNYLKGI T0361 122 :ITRNATL 1qbqA 284 :LQDRGLS T0361 129 :YDALKAMKFADFAVWSEARFSGMV 1qbqA 300 :LDLQPSHSSPYLIAFLVDIYEDML T0361 153 :KTALTLAVTTTLKEL 1qbqA 330 :KEDILNKALELCEIL Number of specific fragments extracted= 11 number of extra gaps= 0 total=130 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gyqA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2gyqA expands to /projects/compbio/data/pdb/2gyq.pdb.gz 2gyqA:Skipped atom 26, because occupancy 0.4 <= existing 0.600 in 2gyqA Skipped atom 30, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 32, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 34, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 36, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 38, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 40, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 42, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 45, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 49, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 51, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 81, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 85, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 87, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 89, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 91, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 93, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 111, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 115, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 117, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 119, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 121, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 123, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 245, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 249, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 251, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 253, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 255, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 257, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 313, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 317, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 319, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 321, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 323, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 325, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 328, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 332, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 334, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 336, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 338, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 349, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 353, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 355, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 357, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 359, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 361, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 420, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 424, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 426, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 457, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 461, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 463, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 466, because occupancy 0.300 <= existing 0.700 in 2gyqA Skipped atom 470, because occupancy 0.300 <= existing 0.700 in 2gyqA Skipped atom 472, because occupancy 0.300 <= existing 0.700 in 2gyqA Skipped atom 474, because occupancy 0.300 <= existing 0.700 in 2gyqA Skipped atom 476, because occupancy 0.300 <= existing 0.700 in 2gyqA Skipped atom 478, because occupancy 0.300 <= existing 0.700 in 2gyqA Skipped atom 480, because occupancy 0.300 <= existing 0.700 in 2gyqA Skipped atom 500, because occupancy 0.300 <= existing 0.700 in 2gyqA Skipped atom 504, because occupancy 0.300 <= existing 0.700 in 2gyqA Skipped atom 506, because occupancy 0.300 <= existing 0.700 in 2gyqA Skipped atom 508, because occupancy 0.300 <= existing 0.700 in 2gyqA Skipped atom 510, because occupancy 0.300 <= existing 0.700 in 2gyqA Skipped atom 512, because occupancy 0.300 <= existing 0.700 in 2gyqA Skipped atom 522, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 526, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 528, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 530, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 532, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 534, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 546, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 550, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 552, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 554, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 556, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 558, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 632, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 636, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 638, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 640, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 642, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 644, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 677, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 681, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 683, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 685, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 687, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 689, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 787, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 791, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 793, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 795, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 797, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 799, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 807, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 811, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 813, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 815, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 817, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 820, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 824, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 826, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 828, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 830, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 832, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 881, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 885, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 887, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 889, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 891, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 893, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 990, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 994, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 996, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 998, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 1000, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 1002, because occupancy 0.500 <= existing 0.500 in 2gyqA Skipped atom 1132, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 1136, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 1138, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 1140, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 1142, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 1144, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 1268, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 1272, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 1274, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 1276, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 1278, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 1280, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 1326, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 1330, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 1332, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 1334, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 1336, because occupancy 0.400 <= existing 0.600 in 2gyqA Skipped atom 1338, because occupancy 0.400 <= existing 0.600 in 2gyqA # T0361 read from 2gyqA/merged-good-all-a2m # 2gyqA read from 2gyqA/merged-good-all-a2m # adding 2gyqA to template set # found chain 2gyqA in template set T0361 3 :TLTEDDVLEQ 2gyqA 9 :QTMEDLLLHG T0361 19 :LFSFMKTA 2gyqA 19 :LRDIYYAE T0361 28 :SILLQGIRQFLPSLF 2gyqA 27 :QQITKALPKMIEQAT T0361 46 :DEEIVEYAVKPL 2gyqA 42 :NRDLSQGLTSHL T0361 82 :KWLYADITHFSQYWHYLN 2gyqA 54 :EETQKQIERLDQVFKKLG T0361 102 :DETPGFADDITWDFISNVNSITRNATLYDALKA 2gyqA 72 :QKPSGVNCPAIDGLIKEADETAGEIADKTVLDA T0361 144 :SEARFSGMVKTALTLAVTTTLKE 2gyqA 105 :AIVANAQAVEHYEIARYGTLIAW Number of specific fragments extracted= 7 number of extra gaps= 0 total=137 Number of alignments=16 # 2gyqA read from 2gyqA/merged-good-all-a2m # found chain 2gyqA in template set T0361 3 :TLTEDDVLEQL 2gyqA 9 :QTMEDLLLHGL T0361 20 :FSFMKT 2gyqA 20 :RDIYYA T0361 27 :HSILLQGIRQFLPSLF 2gyqA 26 :EQQITKALPKMIEQAT T0361 46 :DEEIVEYAVKPL 2gyqA 42 :NRDLSQGLTSHL T0361 82 :KWLYADITHFSQYWHYLNEQDETPG 2gyqA 54 :EETQKQIERLDQVFKKLGQKPSGVN T0361 109 :DDITWDFISNVNSITRNATLYDALKAM 2gyqA 79 :CPAIDGLIKEADETAGEIADKTVLDAA T0361 136 :KFADFAVWSEARFSGMVKTA 2gyqA 109 :NAQAVEHYEIARYGTLIAWA T0361 156 :LTLAVTTTLKE 2gyqA 136 :IVRFLTTNLNE Number of specific fragments extracted= 8 number of extra gaps= 0 total=145 Number of alignments=17 # 2gyqA read from 2gyqA/merged-good-all-a2m # found chain 2gyqA in template set T0361 2 :ATLTEDDVLEQL 2gyqA 8 :IQTMEDLLLHGL T0361 20 :FSFMKTA 2gyqA 20 :RDIYYAE T0361 28 :SILLQGIRQFLPSL 2gyqA 27 :QQITKALPKMIEQA T0361 45 :NDEEIVE 2gyqA 41 :TNRDLSQ T0361 76 :ALGKMDKWLYADITHFSQYWHYLNEQDET 2gyqA 48 :GLTSHLEETQKQIERLDQVFKKLGQKPSG T0361 107 :FADDITWDFISNVNSITRNATLYDALKAM 2gyqA 77 :VNCPAIDGLIKEADETAGEIADKTVLDAA T0361 145 :EARFSGMVKTALTLAVTTTLKEL 2gyqA 106 :IVANAQAVEHYEIARYGTLIAWA Number of specific fragments extracted= 7 number of extra gaps= 0 total=152 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f45B/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1f45B expands to /projects/compbio/data/pdb/1f45.pdb.gz 1f45B:# T0361 read from 1f45B/merged-good-all-a2m # 1f45B read from 1f45B/merged-good-all-a2m # adding 1f45B to template set # found chain 1f45B in template set Warning: unaligning (T0361)E103 because of BadResidue code BAD_PEPTIDE in next template residue (1f45B)R129 Warning: unaligning (T0361)T104 because of BadResidue code BAD_PEPTIDE at template residue (1f45B)R129 Warning: unaligning (T0361)G106 because of BadResidue code BAD_PEPTIDE in next template residue (1f45B)F132 Warning: unaligning (T0361)F107 because of BadResidue code BAD_PEPTIDE at template residue (1f45B)F132 Warning: unaligning (T0361)T123 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f45B)Y167 Warning: unaligning (T0361)A138 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f45B)Y167 T0361 81 :DKWLYADIT 1f45B 102 :LSSIYEDLK T0361 90 :HFSQYWHYLNEQD 1f45B 115 :EFKTMNAKLLMDP T0361 105 :P 1f45B 130 :Q T0361 108 :ADDITWDFISNVNSI 1f45B 133 :LDQNMLAVIDELMQA T0361 139 :DFAVWSEARF 1f45B 168 :KTKIKLCILL T0361 154 :TALTLAVTTTLK 1f45B 178 :HAFRIRAVTIDR Number of specific fragments extracted= 6 number of extra gaps= 2 total=158 Number of alignments=19 # 1f45B read from 1f45B/merged-good-all-a2m # found chain 1f45B in template set Warning: unaligning (T0361)E103 because of BadResidue code BAD_PEPTIDE in next template residue (1f45B)R129 Warning: unaligning (T0361)T104 because of BadResidue code BAD_PEPTIDE at template residue (1f45B)R129 Warning: unaligning (T0361)G106 because of BadResidue code BAD_PEPTIDE in next template residue (1f45B)F132 Warning: unaligning (T0361)F107 because of BadResidue code BAD_PEPTIDE at template residue (1f45B)F132 Warning: unaligning (T0361)T123 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1f45B)Y167 Warning: unaligning (T0361)A138 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f45B)Y167 T0361 80 :MDKWLYADIT 1f45B 101 :CLSSIYEDLK T0361 90 :HFSQYWHYLNEQD 1f45B 115 :EFKTMNAKLLMDP T0361 105 :P 1f45B 130 :Q T0361 108 :ADDITWDFISNVNSI 1f45B 133 :LDQNMLAVIDELMQA T0361 139 :DFAVWSEARF 1f45B 168 :KTKIKLCILL T0361 154 :TALTLAVTTTLK 1f45B 178 :HAFRIRAVTIDR Number of specific fragments extracted= 6 number of extra gaps= 2 total=164 Number of alignments=20 # 1f45B read from 1f45B/merged-good-all-a2m # found chain 1f45B in template set Warning: unaligning (T0361)E103 because of BadResidue code BAD_PEPTIDE in next template residue (1f45B)R129 Warning: unaligning (T0361)T104 because of BadResidue code BAD_PEPTIDE at template residue (1f45B)R129 Warning: unaligning (T0361)G106 because of BadResidue code BAD_PEPTIDE in next template residue (1f45B)F132 Warning: unaligning (T0361)F107 because of BadResidue code BAD_PEPTIDE at template residue (1f45B)F132 Warning: unaligning (T0361)A138 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1f45B)Y167 T0361 79 :KMDKWLYADIT 1f45B 100 :LCLSSIYEDLK T0361 90 :HFSQYWHYLNEQD 1f45B 115 :EFKTMNAKLLMDP T0361 105 :P 1f45B 130 :Q T0361 108 :ADDITWDFISNVNSI 1f45B 133 :LDQNMLAVIDELMQA T0361 139 :DFAVWSEARFSG 1f45B 168 :KTKIKLCILLHA T0361 156 :LTLAVTTTLK 1f45B 180 :FRIRAVTIDR Number of specific fragments extracted= 6 number of extra gaps= 2 total=170 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ll2A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ll2A expands to /projects/compbio/data/pdb/1ll2.pdb.gz 1ll2A:# T0361 read from 1ll2A/merged-good-all-a2m # 1ll2A read from 1ll2A/merged-good-all-a2m # adding 1ll2A to template set # found chain 1ll2A in template set Warning: unaligning (T0361)N18 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ll2A)T240 Warning: unaligning (T0361)S40 because last residue in template chain is (1ll2A)Q262 T0361 19 :LFSFMKTAHSILLQGIRQFLP 1ll2A 241 :HPQFLNVWWDIFTTSVVPLLQ Number of specific fragments extracted= 1 number of extra gaps= 0 total=171 Number of alignments=22 # 1ll2A read from 1ll2A/merged-good-all-a2m # found chain 1ll2A in template set Warning: unaligning (T0361)N18 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ll2A)T240 Warning: unaligning (T0361)S40 because last residue in template chain is (1ll2A)Q262 T0361 19 :LFSFMKTAHSILLQGIRQFLP 1ll2A 241 :HPQFLNVWWDIFTTSVVPLLQ Number of specific fragments extracted= 1 number of extra gaps= 0 total=172 Number of alignments=23 # 1ll2A read from 1ll2A/merged-good-all-a2m # found chain 1ll2A in template set Warning: unaligning (T0361)N18 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ll2A)T240 Warning: unaligning (T0361)S40 because last residue in template chain is (1ll2A)Q262 T0361 19 :LFSFMKTAHSILLQGIRQFLP 1ll2A 241 :HPQFLNVWWDIFTTSVVPLLQ Number of specific fragments extracted= 1 number of extra gaps= 0 total=173 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2grrB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2grrB expands to /projects/compbio/data/pdb/2grr.pdb.gz 2grrB:# T0361 read from 2grrB/merged-good-all-a2m # 2grrB read from 2grrB/merged-good-all-a2m # adding 2grrB to template set # found chain 2grrB in template set T0361 15 :AQDNLFSFMKTAHSI 2grrB 462 :DTSDPEKVVSAFLKV T0361 39 :PSLF 2grrB 477 :SSVF T0361 44 :DNDE 2grrB 481 :KDEA T0361 48 :EIVEYAVKPLLA 2grrB 488 :MAVQDAVDALMQ T0361 60 :QSGPLDDIDVALRLIYALGKMD 2grrB 503 :NSSSFNSNTFLTRLLVHMGLLK T0361 88 :ITHFSQYWHYLNEQDETPGFADDITWDFISN 2grrB 535 :LYGPLMALNHMVQQDYFPKALAPLLLAFVTK T0361 129 :YDALKAMKFA 2grrB 567 :NSALESCSFA T0361 140 :FAVWSEARF 2grrB 577 :RHSLLQTLY Number of specific fragments extracted= 8 number of extra gaps= 0 total=181 Number of alignments=25 # 2grrB read from 2grrB/merged-good-all-a2m # found chain 2grrB in template set T0361 14 :DAQDNLFSFMKTAHSIL 2grrB 461 :TDTSDPEKVVSAFLKVS T0361 40 :SLF 2grrB 478 :SVF T0361 44 :DNDE 2grrB 481 :KDEA T0361 48 :EIVEYAVKPLLA 2grrB 488 :MAVQDAVDALMQ T0361 60 :QSGPLDDIDVALRLIYALGKMD 2grrB 503 :NSSSFNSNTFLTRLLVHMGLLK T0361 89 :THFSQYWHYLNEQDETPGFADDITWDFISN 2grrB 536 :YGPLMALNHMVQQDYFPKALAPLLLAFVTK T0361 129 :YDALKAMKFA 2grrB 567 :NSALESCSFA T0361 140 :FAVWSEARF 2grrB 577 :RHSLLQTLY Number of specific fragments extracted= 8 number of extra gaps= 0 total=189 Number of alignments=26 # 2grrB read from 2grrB/merged-good-all-a2m # found chain 2grrB in template set T0361 15 :AQDNLFSFMKTAHSI 2grrB 462 :DTSDPEKVVSAFLKV T0361 39 :PSLFVDNDE 2grrB 477 :SSVFKDEAT T0361 48 :EIVEYAVKPLLA 2grrB 488 :MAVQDAVDALMQ T0361 60 :QSGPLDDIDVALRLIYALGKM 2grrB 503 :NSSSFNSNTFLTRLLVHMGLL T0361 100 :EQDETPGFAD 2grrB 524 :KSEDKVKAIA T0361 111 :ITWDFISNVNSITRNATLYDALK 2grrB 534 :NLYGPLMALNHMVQQDYFPKALA T0361 138 :ADFAVWSE 2grrB 557 :PLLLAFVT T0361 146 :ARFSGMVKTALTLAVT 2grrB 570 :LESCSFARHSLLQTLY Number of specific fragments extracted= 8 number of extra gaps= 0 total=197 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3gcb/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 3gcb expands to /projects/compbio/data/pdb/3gcb.pdb.gz 3gcb:Warning: there is no chain 3gcb will retry with 3gcbA # T0361 read from 3gcb/merged-good-all-a2m # 3gcb read from 3gcb/merged-good-all-a2m # adding 3gcb to template set # found chain 3gcb in template set T0361 22 :FMKTAHSILLQGIRQFLPSLFVDNDEEIVEYAVK 3gcb 103 :FFYDKLEKANYFLDQIVSSADQDIDSRLVQYLLA T0361 59 :AQ 3gcb 140 :ED T0361 67 :IDVALRLIYALGKMDKWLYAD 3gcb 145 :YSMFLNLVKKYGLIPKDLYGD T0361 89 :THFSQYWHYL 3gcb 175 :KWNSLLTTKL T0361 113 :WDFISNVNSITRNA 3gcb 185 :REFAETLRTALKER T0361 134 :AMKFADFAVWSEARFSG 3gcb 199 :SADDSIIVTLREQMQRE T0361 160 :VTTTLKE 3gcb 216 :IFRLMSL Number of specific fragments extracted= 7 number of extra gaps= 0 total=204 Number of alignments=28 # 3gcb read from 3gcb/merged-good-all-a2m # found chain 3gcb in template set T0361 22 :FMKTAHSILLQGIRQFLPSLFVDNDEEIVEYAVKPLLAQSGP 3gcb 103 :FFYDKLEKANYFLDQIVSSADQDIDSRLVQYLLAAPTEDGGQ T0361 67 :IDVALRLIYALGKMDKWLYAD 3gcb 145 :YSMFLNLVKKYGLIPKDLYGD T0361 89 :THFSQYWHYLN 3gcb 175 :KWNSLLTTKLR T0361 114 :DFISNVNSITRNA 3gcb 186 :EFAETLRTALKER T0361 134 :AMKFADFAVWSEARFSGMVKTA 3gcb 199 :SADDSIIVTLREQMQREIFRLM T0361 157 :TL 3gcb 221 :SL Number of specific fragments extracted= 6 number of extra gaps= 0 total=210 Number of alignments=29 # 3gcb read from 3gcb/merged-good-all-a2m # found chain 3gcb in template set T0361 22 :FMKTAHSILLQGIRQFLPSLFVDNDEEIVEYAVKPLLAQSGP 3gcb 103 :FFYDKLEKANYFLDQIVSSADQDIDSRLVQYLLAAPTEDGGQ T0361 67 :IDVALRLIYALGKMDKWLYAD 3gcb 145 :YSMFLNLVKKYGLIPKDLYGD T0361 89 :THFSQYWHYLN 3gcb 175 :KWNSLLTTKLR T0361 114 :DFISNVNSITRNA 3gcb 186 :EFAETLRTALKER T0361 134 :AMKFADFAVWSEARFSGMVKT 3gcb 199 :SADDSIIVTLREQMQREIFRL T0361 156 :LTL 3gcb 220 :MSL Number of specific fragments extracted= 6 number of extra gaps= 0 total=216 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v7bA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1v7bA expands to /projects/compbio/data/pdb/1v7b.pdb.gz 1v7bA:# T0361 read from 1v7bA/merged-good-all-a2m # 1v7bA read from 1v7bA/merged-good-all-a2m # adding 1v7bA to template set # found chain 1v7bA in template set T0361 3 :TLTEDDVLEQLDAQ 1v7bA 35 :GLSKSGLIYHFPSR T0361 20 :FSFMKTAHSILLQGIRQFLPSLF 1v7bA 49 :HALLLGMHELLADDWDKELRDIT T0361 44 :DNDEEIVEYAVKPLLAQSGPLDD 1v7bA 72 :RDPEDPLERLRAVVVTLAENVSR T0361 69 :VALRLIYAL 1v7bA 95 :PELLLLIDA T0361 79 :KMDKWL 1v7bA 104 :PSHPDF T0361 88 :ITHFSQYWHYLNEQDETPG 1v7bA 110 :LNAWRTVNHQWIPDTDDLE T0361 109 :DDITWDFISNVNSITRNATLYDALKAMKFA 1v7bA 129 :NDAHKRAVYLVQLAADGLFVHDYIHDDVLS T0361 153 :KTALTLAVTTTLKELTP 1v7bA 159 :KSKRQAMLETILELIPS Number of specific fragments extracted= 8 number of extra gaps= 0 total=224 Number of alignments=31 # 1v7bA read from 1v7bA/merged-good-all-a2m # found chain 1v7bA in template set T0361 3 :TLTEDDVLEQLD 1v7bA 35 :GLSKSGLIYHFP T0361 18 :NLFSFMKTAHSILLQGIRQFLPSLF 1v7bA 47 :SRHALLLGMHELLADDWDKELRDIT T0361 44 :DNDE 1v7bA 72 :RDPE T0361 48 :EIVEYAVKPLL 1v7bA 79 :ERLRAVVVTLA T0361 65 :DDIDVALRLIYALGKMDK 1v7bA 90 :ENVSRPELLLLIDAPSHP T0361 86 :ADITHFSQYWHYLNEQDETPGFAD 1v7bA 108 :DFLNAWRTVNHQWIPDTDDLENDA T0361 110 :DITWDFISNVNSI 1v7bA 134 :RAVYLVQLAADGL T0361 127 :TLYDALKAMK 1v7bA 147 :FVHDYIHDDV T0361 151 :MVKTALTLAVTTTLKELTP 1v7bA 157 :LSKSKRQAMLETILELIPS Number of specific fragments extracted= 9 number of extra gaps= 0 total=233 Number of alignments=32 # 1v7bA read from 1v7bA/merged-good-all-a2m # found chain 1v7bA in template set T0361 3 :TLTEDDVLEQL 1v7bA 35 :GLSKSGLIYHF T0361 17 :DNLFSFMKTAHSILLQGIRQFLPSLFV 1v7bA 46 :PSRHALLLGMHELLADDWDKELRDITR T0361 44 :DNDEEIVEYAVKPLLAQSG 1v7bA 75 :EDPLERLRAVVVTLAENVS T0361 70 :ALRLIYAL 1v7bA 94 :RPELLLLI T0361 81 :DKWLYADI 1v7bA 102 :DAPSHPDF T0361 89 :THFSQYWHYLNEQDETPGFA 1v7bA 111 :NAWRTVNHQWIPDTDDLEND T0361 109 :DDITWDFISNVNSITRNATLYDAL 1v7bA 133 :KRAVYLVQLAADGLFVHDYIHDDV T0361 135 :MKFADFAVWSE 1v7bA 157 :LSKSKRQAMLE T0361 162 :TTLKELTP 1v7bA 168 :TILELIPS Number of specific fragments extracted= 9 number of extra gaps= 0 total=242 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w33A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1w33A expands to /projects/compbio/data/pdb/1w33.pdb.gz 1w33A:Skipped atom 676, because occupancy 0.350 <= existing 0.650 in 1w33A Skipped atom 678, because occupancy 0.350 <= existing 0.650 in 1w33A Skipped atom 680, because occupancy 0.350 <= existing 0.650 in 1w33A Skipped atom 682, because occupancy 0.350 <= existing 0.650 in 1w33A # T0361 read from 1w33A/merged-good-all-a2m # 1w33A read from 1w33A/merged-good-all-a2m # adding 1w33A to template set # found chain 1w33A in template set T0361 26 :AHSILLQG 1w33A 79 :IGKELEDQ T0361 34 :IRQFLPSL 1w33A 90 :ENIQIAKI T0361 42 :F 1w33A 102 :F T0361 43 :VDNDEEIVEY 1w33A 114 :DLIDEDIQMK T0361 69 :VALRLIYALGK 1w33A 124 :IKRTLYSSLDY T0361 81 :DK 1w33A 135 :KK T0361 86 :ADITHFSQYWHYLNEQDETPGFADDIT 1w33A 137 :ENIEKLKEILEILKKNSEHYNIIGRLI T0361 113 :WDFISNVNSITRNATL 1w33A 168 :WGIQFQIEQNLELIQN T0361 129 :YDALKAMKFADFAVWSEARFS 1w33A 185 :VENLSQEESKSLLMQIKSNLE T0361 150 :GMVKTALTLAVTTTLKE 1w33A 208 :QRLKKTLNETLKVYNQN Number of specific fragments extracted= 10 number of extra gaps= 0 total=252 Number of alignments=34 # 1w33A read from 1w33A/merged-good-all-a2m # found chain 1w33A in template set Warning: unaligning (T0361)N18 because of BadResidue code BAD_PEPTIDE at template residue (1w33A)T71 T0361 19 :LFSFMKTAHSILLQG 1w33A 72 :IASELKAIGKELEDQ T0361 34 :IRQFLPSL 1w33A 90 :ENIQIAKI T0361 57 :LLAQ 1w33A 104 :FLST T0361 62 :GPLDDID 1w33A 111 :GPYDLID T0361 69 :VALRLIYALGK 1w33A 124 :IKRTLYSSLDY T0361 81 :DK 1w33A 135 :KK T0361 86 :ADITHFSQYWHYLNEQDET 1w33A 137 :ENIEKLKEILEILKKNSEH T0361 109 :DDITWDFISN 1w33A 156 :YNIIGRLIYH T0361 119 :VNSITRNATLYDALK 1w33A 168 :WGIQFQIEQNLELIQ T0361 134 :AMKFADFAVWSEARFSGM 1w33A 187 :NLSQEESKSLLMQIKSNL T0361 152 :VKTALTLAVTTTLKE 1w33A 206 :IKQRLKKTLNETLKV Number of specific fragments extracted= 11 number of extra gaps= 1 total=263 Number of alignments=35 # 1w33A read from 1w33A/merged-good-all-a2m # found chain 1w33A in template set T0361 3 :TLTEDDVLEQLDA 1w33A 77 :KAIGKELEDQKKE T0361 34 :IRQFLPSLFVDND 1w33A 90 :ENIQIAKIAKEKF T0361 56 :PLLAQ 1w33A 103 :DFLST T0361 61 :SGPLDDIDVALRLIYALGKMDKWLYADITHFSQYWHYLNEQDETPG 1w33A 112 :PYDLIDEDIQMKIKRTLYSSLDYKKENIEKLKEILEILKKNSEHYN T0361 108 :ADDITWDFISNVNSITRNA 1w33A 163 :IYHISWGIQFQIEQNLELI T0361 129 :YDALKAMKFADFAVWSEARFSGM 1w33A 182 :QNGVENLSQEESKSLLMQIKSNL T0361 152 :VKTALTLAVTTTLKEL 1w33A 206 :IKQRLKKTLNETLKVY Number of specific fragments extracted= 7 number of extra gaps= 0 total=270 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1huxA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1huxA expands to /projects/compbio/data/pdb/1hux.pdb.gz 1huxA:# T0361 read from 1huxA/merged-good-all-a2m # 1huxA read from 1huxA/merged-good-all-a2m # adding 1huxA to template set # found chain 1huxA in template set T0361 6 :EDDVLEQLDAQDNLFSFMKTAHSILLQGIRQFLPSLFVDND 1huxA 171 :ESEVISQLSKGTDKIDIIAGIHRSVASRVIGLANRVGIVKD T0361 48 :EIVEYAVKPLLA 1huxA 222 :YGVRGALEEGLG Number of specific fragments extracted= 2 number of extra gaps= 0 total=272 Number of alignments=37 # 1huxA read from 1huxA/merged-good-all-a2m # found chain 1huxA in template set T0361 6 :EDDVLEQLDAQDNLFSFMKTAHSILLQGIRQFLPSLFVDND 1huxA 171 :ESEVISQLSKGTDKIDIIAGIHRSVASRVIGLANRVGIVKD T0361 62 :GPLDDID 1huxA 216 :GGVAQNY T0361 69 :VALRLIYAL 1huxA 224 :VRGALEEGL Number of specific fragments extracted= 3 number of extra gaps= 0 total=275 Number of alignments=38 # 1huxA read from 1huxA/merged-good-all-a2m # found chain 1huxA in template set T0361 5 :TEDDVLEQLDAQDNLFSFMKTAHSILLQGIRQFLPSL 1huxA 170 :AESEVISQLSKGTDKIDIIAGIHRSVASRVIGLANRV T0361 42 :FVDN 1huxA 208 :IVKD T0361 48 :EIVEYAVKPLLAQS 1huxA 222 :YGVRGALEEGLGVE T0361 62 :GPLDDID 1huxA 239 :SPLAQYN T0361 69 :VALRLIYAL 1huxA 247 :ALGAALYAY Number of specific fragments extracted= 5 number of extra gaps= 0 total=280 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jcrA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1jcrA expands to /projects/compbio/data/pdb/1jcr.pdb.gz 1jcrA:# T0361 read from 1jcrA/merged-good-all-a2m # 1jcrA read from 1jcrA/merged-good-all-a2m # adding 1jcrA to template set # found chain 1jcrA in template set T0361 8 :DVLEQLDAQDNLFSFMK 1jcrA 174 :VLVEWLKDPSQELEFIA T0361 25 :TAHSILLQGIRQF 1jcrA 201 :HAWQHRQWVIQEF T0361 44 :DNDEEIVEY 1jcrA 214 :RLWDNELQY T0361 54 :VKPLLAQS 1jcrA 223 :VDQLLKED T0361 64 :LDDIDVALRLIYAL 1jcrA 231 :VRNNSVWNQRHFVI T0361 78 :GKMDKWLYA 1jcrA 249 :GYSDRAVLE T0361 87 :DITHFSQYWHYLNE 1jcrA 259 :EVQYTLEMIKLVPH T0361 109 :DDITWDFISNVNSITRNATLYDALK 1jcrA 273 :NESAWNYLKGILQDRGLSRYPNLLN T0361 134 :AMKFADFAVWSEARFSGMV 1jcrA 305 :SHSSPYLIAFLVDIYEDML T0361 153 :KTALTLAVTTTLKEL 1jcrA 330 :KEDILNKALELCEIL Number of specific fragments extracted= 10 number of extra gaps= 0 total=290 Number of alignments=40 # 1jcrA read from 1jcrA/merged-good-all-a2m # found chain 1jcrA in template set T0361 8 :DVLEQLDAQDNLFSFMK 1jcrA 174 :VLVEWLKDPSQELEFIA T0361 25 :TAHSILLQGIRQF 1jcrA 201 :HAWQHRQWVIQEF T0361 44 :DNDEEIVEY 1jcrA 214 :RLWDNELQY T0361 54 :VKPLLAQSGPLDD 1jcrA 223 :VDQLLKEDVRNNS T0361 67 :IDVALRLIYAL 1jcrA 237 :WNQRHFVISNT T0361 78 :GKMDKWLY 1jcrA 249 :GYSDRAVL T0361 86 :ADITHFSQYWHYLNE 1jcrA 258 :REVQYTLEMIKLVPH T0361 109 :DDITWDFISNVNSITRNATLYDALKAMKFAD 1jcrA 273 :NESAWNYLKGILQDRGLSRYPNLLNQLLDLQ T0361 140 :FAVWSEARFSGMV 1jcrA 311 :LIAFLVDIYEDML T0361 153 :KTALTLAVTTTLKEL 1jcrA 330 :KEDILNKALELCEIL Number of specific fragments extracted= 10 number of extra gaps= 0 total=300 Number of alignments=41 # 1jcrA read from 1jcrA/merged-good-all-a2m # found chain 1jcrA in template set T0361 8 :DVLEQLDAQDNLFSFMKTAHS 1jcrA 174 :VLVEWLKDPSQELEFIADILN T0361 29 :ILLQGIRQFLPSL 1jcrA 201 :HAWQHRQWVIQEF T0361 42 :FVDNDEEIVEYAVKPLL 1jcrA 215 :LWDNELQYVDQLLKEDV T0361 65 :DDIDVALRLIYAL 1jcrA 232 :RNNSVWNQRHFVI T0361 78 :GKMDKWLYA 1jcrA 249 :GYSDRAVLE T0361 87 :DITHFSQYWHYLNE 1jcrA 259 :EVQYTLEMIKLVPH T0361 109 :DDITWDFISNV 1jcrA 273 :NESAWNYLKGI T0361 120 :NSITRNA 1jcrA 294 :NLLNQLL T0361 130 :DALKAMKFADFAVWSEARFSGMV 1jcrA 301 :DLQPSHSSPYLIAFLVDIYEDML T0361 153 :KTALTLAVTTTLKEL 1jcrA 330 :KEDILNKALELCEIL Number of specific fragments extracted= 10 number of extra gaps= 0 total=310 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1av6A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1av6A expands to /projects/compbio/data/pdb/1av6.pdb.gz 1av6A:# T0361 read from 1av6A/merged-good-all-a2m # 1av6A read from 1av6A/merged-good-all-a2m # adding 1av6A to template set # found chain 1av6A in template set T0361 102 :DETPGF 1av6A 216 :GENMRL T0361 108 :ADDITWDFISNVNSITRNATL 1av6A 225 :TKSDAVNYEKKMYYLNKIVRN T0361 130 :DALKAMKFAD 1av6A 246 :KVVVNFDYPN T0361 140 :FAVWSEARFS 1av6A 260 :YFHMYFMLRT T0361 150 :GMVKTALTLAVTTTLKEL 1av6A 277 :PTTKAKVLFLQQSIFRFL Number of specific fragments extracted= 5 number of extra gaps= 0 total=315 Number of alignments=43 # 1av6A read from 1av6A/merged-good-all-a2m # found chain 1av6A in template set T0361 81 :DKWLYADITHFSQYWHYL 1av6A 226 :KSDAVNYEKKMYYLNKIV T0361 99 :NEQD 1av6A 249 :VNFD T0361 103 :ETPGFADDITWDFISNVNSITRNAT 1av6A 254 :PNQEYDYFHMYFMLRTVYCNKTFPT T0361 152 :VKTALTLAVTTTLKELT 1av6A 279 :TKAKVLFLQQSIFRFLN Number of specific fragments extracted= 4 number of extra gaps= 0 total=319 Number of alignments=44 # 1av6A read from 1av6A/merged-good-all-a2m # found chain 1av6A in template set T0361 86 :ADITHFSQYWHYLNEQD 1av6A 227 :SDAVNYEKKMYYLNKIV T0361 103 :ETPGFADDITWDFI 1av6A 249 :VNFDYPNQEYDYFH T0361 119 :VNSITRNATLYDAL 1av6A 263 :MYFMLRTVYCNKTF T0361 138 :ADFAVWSEARFSGMVK 1av6A 277 :PTTKAKVLFLQQSIFR Number of specific fragments extracted= 4 number of extra gaps= 0 total=323 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yl3E/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/T0361/1yl3E/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0361/1yl3E/merged-good-all-a2m.gz for input Trying 1yl3E/merged-good-all-a2m Error: Couldn't open file 1yl3E/merged-good-all-a2m or 1yl3E/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f5nA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0361 read from 1f5nA/merged-good-all-a2m # 1f5nA read from 1f5nA/merged-good-all-a2m # found chain 1f5nA in training set T0361 6 :EDDVLEQLDA 1f5nA 381 :QKELAAQLEK T0361 18 :NLFSFMKTAHSILLQGIRQFLPSLF 1f5nA 391 :KRDDFCKQNQEASSDRCSGLLQVIF T0361 47 :EEIVEYA 1f5nA 416 :SPLEEEV T0361 74 :IYALGKMDKWLYADITHFSQYWHYLNEQDETPGFADDITWDFISN 1f5nA 423 :KAGIYSKPGGYRLFVQKLQDLKKKYYEEPRKGIQAEEILQTYLKS T0361 119 :VNSITR 1f5nA 472 :TDAILQ T0361 125 :NATL 1f5nA 481 :TLTE T0361 129 :YDALKAMK 1f5nA 491 :VERVKAES T0361 137 :FADFAVWSEARFSGMV 1f5nA 502 :SAKMLHEMQRKNEQMM T0361 153 :KTALTLAVTTTLKE 1f5nA 520 :KERSYQEHLKQLTE Number of specific fragments extracted= 9 number of extra gaps= 0 total=332 Number of alignments=46 # 1f5nA read from 1f5nA/merged-good-all-a2m # found chain 1f5nA in training set T0361 16 :QDNLFSFMKTAHSILLQGIRQFLPSLFVDNDEEIVEYAVKPLLA 1f5nA 347 :TESLQELLDLHRDSEREAIEVFIRSSFKDVDHLFQKELAAQLEK T0361 65 :DDI 1f5nA 405 :DRC T0361 68 :DVALRLIYALGKMDKWLYADITHFSQYWHYLNEQDETPGFADDITWDFISN 1f5nA 417 :PLEEEVKAGIYSKPGGYRLFVQKLQDLKKKYYEEPRKGIQAEEILQTYLKS T0361 119 :VNSITR 1f5nA 472 :TDAILQ T0361 125 :NATL 1f5nA 481 :TLTE T0361 129 :YDALKAMK 1f5nA 491 :VERVKAES T0361 137 :FADFAVWSEARFSGMV 1f5nA 502 :SAKMLHEMQRKNEQMM Number of specific fragments extracted= 7 number of extra gaps= 0 total=339 Number of alignments=47 # 1f5nA read from 1f5nA/merged-good-all-a2m # found chain 1f5nA in training set T0361 4 :LTEDDVLEQLDA 1f5nA 379 :LFQKELAAQLEK T0361 18 :NLFSFMKTAHSILLQGIRQFLPSLFVDNDEEI 1f5nA 391 :KRDDFCKQNQEASSDRCSGLLQVIFSPLEEEV T0361 54 :VKPLLAQSG 1f5nA 423 :KAGIYSKPG T0361 83 :WLYADITHFSQYWHYLNEQDETPGFADDITWDFISNVNSI 1f5nA 432 :GYRLFVQKLQDLKKKYYEEPRKGIQAEEILQTYLKSKESM T0361 123 :TRNATLYDALKAMKFADFAVWSEARFSGMV 1f5nA 473 :DAILQTDQTLTEKEKEIEVERVKAESAQAS T0361 154 :TALTLAVTTTLKE 1f5nA 503 :AKMLHEMQRKNEQ Number of specific fragments extracted= 6 number of extra gaps= 0 total=345 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1oxjA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0361 read from 1oxjA/merged-good-all-a2m # 1oxjA read from 1oxjA/merged-good-all-a2m # found chain 1oxjA in training set T0361 4 :LTEDDVLEQ 1oxjA 628 :ITEDFLQSV T0361 14 :DAQDNLFSFMKTAHSI 1oxjA 641 :GASHKLALCIDKLKER T0361 31 :LQGIRQFLPSLFVDNDE 1oxjA 657 :ANILNRVEQELLSGQME T0361 50 :VEYAVKPL 1oxjA 674 :LSTAVEEL T0361 58 :LAQSGPLDD 1oxjA 692 :LESPGPPEE T0361 68 :DVALRLI 1oxjA 701 :NIGLRFL T0361 86 :AD 1oxjA 708 :KV T0361 91 :FSQYWHYLNEQDET 1oxjA 710 :IDIVTNTLQQDPYA T0361 107 :FADDITWDFISN 1oxjA 724 :VQDDETLGVLMW T0361 119 :VNSITRNATLYDALKAMK 1oxjA 737 :LDRSIHNEAFMNHASQLK T0361 142 :VWSEAR 1oxjA 755 :DLKFKL T0361 149 :S 1oxjA 761 :S Number of specific fragments extracted= 12 number of extra gaps= 0 total=357 Number of alignments=49 # 1oxjA read from 1oxjA/merged-good-all-a2m # found chain 1oxjA in training set T0361 5 :TEDD 1oxjA 629 :TEDF T0361 10 :LEQLDAQDNLFSFMKTAHSILLQG 1oxjA 633 :LQSVGVTKGASHKLALCIDKLKER T0361 34 :IRQFLPSLFVDNDE 1oxjA 660 :LNRVEQELLSGQME T0361 50 :VEYAVKPL 1oxjA 674 :LSTAVEEL T0361 58 :LAQSGPLDD 1oxjA 692 :LESPGPPEE T0361 68 :DVALRLI 1oxjA 701 :NIGLRFL T0361 86 :AD 1oxjA 708 :KV T0361 91 :FSQYWHYLNEQDE 1oxjA 710 :IDIVTNTLQQDPY T0361 106 :GFADDITWDFISN 1oxjA 723 :AVQDDETLGVLMW T0361 119 :VNSITRNATLYDAL 1oxjA 737 :LDRSIHNEAFMNHA T0361 138 :ADFAVWSEARFS 1oxjA 751 :SQLKDLKFKLSK Number of specific fragments extracted= 11 number of extra gaps= 0 total=368 Number of alignments=50 # 1oxjA read from 1oxjA/merged-good-all-a2m # found chain 1oxjA in training set T0361 2 :ATLTEDDVLE 1oxjA 639 :TKGASHKLAL T0361 22 :FMKTAHSI 1oxjA 649 :CIDKLKER T0361 31 :LQGIRQFLPSLFVDNDE 1oxjA 657 :ANILNRVEQELLSGQME T0361 48 :EIVEYA 1oxjA 676 :TAVEEL T0361 54 :VKPLLAQSGPLDDIDVAL 1oxjA 689 :MKPLESPGPPEENIGLRF T0361 88 :ITHFSQYWHYLNEQDETPG 1oxjA 707 :LKVIDIVTNTLQQDPYAVQ T0361 109 :DDI 1oxjA 726 :DDE T0361 115 :FISNVNSITRNATLYDALKAM 1oxjA 729 :TLGVLMWILDRSIHNEAFMNH T0361 137 :FADFAVWSEARFS 1oxjA 750 :ASQLKDLKFKLSK Number of specific fragments extracted= 9 number of extra gaps= 0 total=377 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t3wA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1t3wA expands to /projects/compbio/data/pdb/1t3w.pdb.gz 1t3wA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0361 read from 1t3wA/merged-good-all-a2m # 1t3wA read from 1t3wA/merged-good-all-a2m # adding 1t3wA to template set # found chain 1t3wA in template set T0361 87 :DITHFSQYWHYLNEQD 1t3wA 481 :GLGLFRELVNTCLSQP T0361 106 :GFADDITWDFISNVNSITRNATLYDALKAMKFADFAVWSEARFSGMVKTALTLAVTTTLKEL 1t3wA 497 :GLTTGQLLEHYRGTNNAATLEKLSMWDDIADKNIAEQTFTDSLNHMFDSLLELRQEELIARE Number of specific fragments extracted= 2 number of extra gaps= 0 total=379 Number of alignments=52 # 1t3wA read from 1t3wA/merged-good-all-a2m # found chain 1t3wA in template set T0361 87 :DITHFSQYWHYLNEQDE 1t3wA 481 :GLGLFRELVNTCLSQPG T0361 107 :FADDITWDFISNVNSITRNATLYDALKAMKFADFAVWSEARFSGMVKTALTLAVTTTLKELT 1t3wA 498 :LTTGQLLEHYRGTNNAATLEKLSMWDDIADKNIAEQTFTDSLNHMFDSLLELRQEELIARER Number of specific fragments extracted= 2 number of extra gaps= 0 total=381 Number of alignments=53 # 1t3wA read from 1t3wA/merged-good-all-a2m # found chain 1t3wA in template set Warning: unaligning (T0361)D81 because of BadResidue code BAD_PEPTIDE in next template residue (1t3wA)E476 Warning: unaligning (T0361)K82 because of BadResidue code BAD_PEPTIDE at template residue (1t3wA)E476 T0361 48 :EIVEYAVKP 1t3wA 454 :LIGLLVQNP T0361 57 :LLAQSGPLDD 1t3wA 464 :LATLVPPLEN T0361 80 :M 1t3wA 474 :L T0361 83 :WLYADITHFSQYWHYLNEQDETP 1t3wA 477 :NKLPGLGLFRELVNTCLSQPGLT T0361 106 :GFADDITWDFISNVNSITRNATL 1t3wA 506 :HYRGTNNAATLEKLSMWDDIADK T0361 129 :YDALKAMKFADFAVWSEARFSGM 1t3wA 536 :TDSLNHMFDSLLELRQEELIARE T0361 153 :KTALTLAVTTTLKELTP 1t3wA 564 :SNEERLELWTLNQELAK Number of specific fragments extracted= 7 number of extra gaps= 1 total=388 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1b3uA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1b3uA expands to /projects/compbio/data/pdb/1b3u.pdb.gz 1b3uA:# T0361 read from 1b3uA/merged-good-all-a2m # 1b3uA read from 1b3uA/merged-good-all-a2m # adding 1b3uA to template set # found chain 1b3uA in template set T0361 17 :DNLF 1b3uA 455 :YAIR T0361 24 :KTAHSILLQGIRQF 1b3uA 459 :EAATSNLKKLVEKF T0361 45 :NDEEIVEYAVKPLLAQSGPLDDID 1b3uA 473 :GKEWAHATIIPKVLAMSGDPNYLH T0361 70 :ALRLIYALGKMDKWLYADITH 1b3uA 497 :RMTTLFCINVLSEVCGQDITT T0361 92 :SQYWHYLNEQDETP 1b3uA 518 :KHMLPTVLRMAGDP T0361 108 :ADDITWDFISNVNSI 1b3uA 532 :VANVRFNVAKSLQKI T0361 126 :ATL 1b3uA 547 :GPI T0361 129 :YDALKA 1b3uA 552 :NSTLQS T0361 139 :DFAVWSEARFS 1b3uA 558 :EVKPILEKLTQ T0361 153 :KTALTLAVTTTLKELT 1b3uA 571 :DVDVKYFAQEALTVLS Number of specific fragments extracted= 10 number of extra gaps= 0 total=398 Number of alignments=55 # 1b3uA read from 1b3uA/merged-good-all-a2m # found chain 1b3uA in template set T0361 18 :NLF 1b3uA 456 :AIR T0361 24 :KTAHSILLQGIRQF 1b3uA 459 :EAATSNLKKLVEKF T0361 45 :NDEEIVEYAVKPLLAQSGPLD 1b3uA 473 :GKEWAHATIIPKVLAMSGDPN T0361 67 :IDVALRLIYALGKMDKWLYADITH 1b3uA 494 :YLHRMTTLFCINVLSEVCGQDITT T0361 92 :SQYWHYLNEQDETP 1b3uA 518 :KHMLPTVLRMAGDP T0361 106 :GFADDITWDFISNVNSITRNATLYDALKA 1b3uA 533 :ANVRFNVAKSLQKIGPILDNSTLQSEVKP T0361 139 :DF 1b3uA 562 :IL T0361 146 :ARFSGMVKTALTLAVTTTLKELT 1b3uA 564 :EKLTQDQDVDVKYFAQEALTVLS Number of specific fragments extracted= 8 number of extra gaps= 0 total=406 Number of alignments=56 # 1b3uA read from 1b3uA/merged-good-all-a2m # found chain 1b3uA in template set T0361 22 :FMKTAHSILLQGIRQF 1b3uA 457 :IREAATSNLKKLVEKF T0361 45 :NDEEIVEYAVKPLLAQSGPLDDIDV 1b3uA 473 :GKEWAHATIIPKVLAMSGDPNYLHR T0361 71 :LRLIYALGKMDKWLYADITH 1b3uA 498 :MTTLFCINVLSEVCGQDITT T0361 93 :QYWHYLNEQD 1b3uA 519 :HMLPTVLRMA T0361 106 :GFADDITWD 1b3uA 529 :GDPVANVRF T0361 117 :SNVNSITRNATLYDA 1b3uA 538 :NVAKSLQKIGPILDN T0361 138 :ADFA 1b3uA 553 :STLQ T0361 146 :ARFSGMVKTA 1b3uA 557 :SEVKPILEKL T0361 156 :LTLAVTTTLKEL 1b3uA 574 :VKYFAQEALTVL Number of specific fragments extracted= 9 number of extra gaps= 0 total=415 Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1po5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0361 read from 1po5A/merged-good-all-a2m # 1po5A read from 1po5A/merged-good-all-a2m # found chain 1po5A in training set Warning: unaligning (T0361)P105 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1po5A)D189 Warning: unaligning (T0361)G106 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1po5A)D189 T0361 14 :DAQDNLFSFMKTAHS 1po5A 119 :ERWRALRRFSLATMR T0361 29 :ILLQGIR 1po5A 141 :SVEERIQ T0361 48 :EIVEYAVKPLLAQSGPLDD 1po5A 148 :EEARCLVEELRKSKGALLD T0361 67 :IDVALRLIYALG 1po5A 172 :HSITSNIICSIV T0361 101 :QDET 1po5A 184 :FGKR T0361 107 :FADDITWDFISNVNSITR 1po5A 190 :YKDPVFLRLLDLFFQSFS T0361 125 :NATLYDALK 1po5A 210 :SSFSSQVFE T0361 134 :AMKFADFAVWSEARFSGMVKTALTLAVTTTLKELT 1po5A 223 :FLKHFPGTHRQIYRNLQEINTFIGQSVEKHRATLD Number of specific fragments extracted= 8 number of extra gaps= 1 total=423 Number of alignments=58 # 1po5A read from 1po5A/merged-good-all-a2m # found chain 1po5A in training set Warning: unaligning (T0361)T3 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1po5A)F115 Warning: unaligning (T0361)T5 because of BadResidue code BAD_PEPTIDE in next template residue (1po5A)G118 Warning: unaligning (T0361)E6 because of BadResidue code BAD_PEPTIDE at template residue (1po5A)G118 Warning: unaligning (T0361)P105 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1po5A)D189 Warning: unaligning (T0361)G106 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1po5A)D189 T0361 4 :L 1po5A 116 :A T0361 7 :DD 1po5A 119 :ER T0361 16 :QDNLFSFMKTAHS 1po5A 121 :WRALRRFSLATMR T0361 29 :ILLQGIR 1po5A 141 :SVEERIQ T0361 48 :EIVEYAVKPLLAQSGPLDDI 1po5A 148 :EEARCLVEELRKSKGALLDN T0361 68 :DVALRLIYALG 1po5A 173 :SITSNIICSIV T0361 101 :QDET 1po5A 184 :FGKR T0361 107 :FADDITWDFISNVNSITR 1po5A 190 :YKDPVFLRLLDLFFQSFS T0361 125 :NATL 1po5A 213 :SSQV T0361 129 :YDALKAMKFA 1po5A 221 :SGFLKHFPGT T0361 142 :VWSEARFSGMVKTALTLAVTTTLKELT 1po5A 231 :HRQIYRNLQEINTFIGQSVEKHRATLD Number of specific fragments extracted= 11 number of extra gaps= 3 total=434 Number of alignments=59 # 1po5A read from 1po5A/merged-good-all-a2m # found chain 1po5A in training set Warning: unaligning (T0361)T3 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1po5A)F115 Warning: unaligning (T0361)T5 because of BadResidue code BAD_PEPTIDE in next template residue (1po5A)G118 Warning: unaligning (T0361)E6 because of BadResidue code BAD_PEPTIDE at template residue (1po5A)G118 Warning: unaligning (T0361)P105 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1po5A)D189 Warning: unaligning (T0361)G106 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1po5A)D189 T0361 4 :L 1po5A 116 :A T0361 7 :DDVLE 1po5A 119 :ERWRA T0361 19 :LFSFMKTAHS 1po5A 124 :LRRFSLATMR T0361 29 :ILLQGIR 1po5A 141 :SVEERIQ T0361 48 :EIVEYAVKPLLAQSGPLDD 1po5A 148 :EEARCLVEELRKSKGALLD T0361 67 :IDVALRLIYALGK 1po5A 172 :HSITSNIICSIVF T0361 102 :DET 1po5A 185 :GKR T0361 107 :FADDITWDFISNVNSITRNATL 1po5A 190 :YKDPVFLRLLDLFFQSFSLISS T0361 129 :YDALKAMKFADFAV 1po5A 213 :SSQVFELFSGFLKH T0361 143 :WSEARFSGMVKTALTLAVTTTLKELT 1po5A 232 :RQIYRNLQEINTFIGQSVEKHRATLD Number of specific fragments extracted= 10 number of extra gaps= 3 total=444 Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1htjF/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1htjF expands to /projects/compbio/data/pdb/1htj.pdb.gz 1htjF:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0361 read from 1htjF/merged-good-all-a2m # 1htjF read from 1htjF/merged-good-all-a2m # adding 1htjF to template set # found chain 1htjF in template set T0361 29 :ILLQGIRQFLPSLFVDNDEEIVEYAVKPLLAQSGPLD 1htjF 340 :LLFYLCAEVYQQASPKDSRSLGKDIWNIFLEKNAPLR T0361 78 :GKMDKWLYADIT 1htjF 377 :VKIPEMLQAEID T0361 90 :HFSQYWHYLN 1htjF 400 :VLCEAQEAAM T0361 110 :DITWDFISNVNSITRNATLYD 1htjF 410 :PEIQEQIHDYRTKRTLGLGSL T0361 131 :ALKAMKFAD 1htjF 435 :DLLDLDGDP T0361 146 :ARFSGM 1htjF 444 :LRERQV T0361 153 :KTALTLAVTTTLKEL 1htjF 450 :AEKQLAALGDILSAY Number of specific fragments extracted= 7 number of extra gaps= 0 total=451 Number of alignments=61 # 1htjF read from 1htjF/merged-good-all-a2m # found chain 1htjF in template set T0361 14 :DAQDNLFSFMKTAHSILL 1htjF 333 :SQADPSPLLFYLCAEVYQ T0361 40 :SLFVDNDEEIVEYAVKPLLAQSGPLD 1htjF 351 :QASPKDSRSLGKDIWNIFLEKNAPLR T0361 79 :KMDKWLYADIT 1htjF 378 :KIPEMLQAEID T0361 90 :HFSQYWHYLN 1htjF 400 :VLCEAQEAAM T0361 110 :DITWDFISNVNSITRNATL 1htjF 410 :PEIQEQIHDYRTKRTLGLG T0361 129 :YDALKAMKFAD 1htjF 433 :ENDLLDLDGDP T0361 146 :ARFSGMVKTALT 1htjF 444 :LRERQVAEKQLA T0361 159 :AVTTTLKELT 1htjF 456 :ALGDILSAYA Number of specific fragments extracted= 8 number of extra gaps= 0 total=459 Number of alignments=62 # 1htjF read from 1htjF/merged-good-all-a2m # found chain 1htjF in template set T0361 14 :DAQDNLF 1htjF 333 :SQADPSP T0361 29 :ILLQGIRQFLPSLFVDNDEEIVEYAVKPLLAQSGPLD 1htjF 340 :LLFYLCAEVYQQASPKDSRSLGKDIWNIFLEKNAPLR T0361 79 :KMDKWLYADIT 1htjF 378 :KIPEMLQAEID T0361 90 :HFSQYWHYLN 1htjF 400 :VLCEAQEAAM T0361 110 :DITWDFISNVNSITRNATL 1htjF 410 :PEIQEQIHDYRTKRTLGLG T0361 129 :YDALKAMKFADF 1htjF 433 :ENDLLDLDGDPL T0361 147 :RFSGMVKTAL 1htjF 445 :RERQVAEKQL T0361 158 :LAVTTTLKELT 1htjF 455 :AALGDILSAYA Number of specific fragments extracted= 8 number of extra gaps= 0 total=467 Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ow4A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0361 read from 1ow4A/merged-good-all-a2m # 1ow4A read from 1ow4A/merged-good-all-a2m # found chain 1ow4A in training set T0361 27 :HSILLQGIRQFLPSL 1ow4A 6 :KDAMGPLVRECMGSV T0361 44 :DNDEEIVEYAV 1ow4A 21 :SATEDDFKTVL T0361 60 :QSGPLDDIDVALRLIYAL 1ow4A 32 :NRNPLESRTAQCLLACAL T0361 78 :GKMD 1ow4A 53 :GLIS T0361 82 :KWLYADITHFS 1ow4A 65 :DDLMPVMNRLY T0361 93 :QYWHYLNEQDETPGFADDITWDFISNVN 1ow4A 88 :AVNDCANQVNGAYPDRCDLIKNFTDCVR Number of specific fragments extracted= 6 number of extra gaps= 0 total=473 Number of alignments=64 # 1ow4A read from 1ow4A/merged-good-all-a2m # found chain 1ow4A in training set T0361 27 :HSILLQGIRQFLPSL 1ow4A 6 :KDAMGPLVRECMGSV T0361 44 :DNDEEIVEYAV 1ow4A 21 :SATEDDFKTVL T0361 60 :QSGPLDDIDVALRLIYAL 1ow4A 32 :NRNPLESRTAQCLLACAL T0361 78 :GKMD 1ow4A 53 :GLIS T0361 82 :KWLYADITHFS 1ow4A 65 :DDLMPVMNRLY T0361 93 :QYWHYLNEQDETPGFADDITWDFISNV 1ow4A 88 :AVNDCANQVNGAYPDRCDLIKNFTDCV Number of specific fragments extracted= 6 number of extra gaps= 0 total=479 Number of alignments=65 # 1ow4A read from 1ow4A/merged-good-all-a2m # found chain 1ow4A in training set T0361 31 :LQGIRQFLPSLFVDN 1ow4A 6 :KDAMGPLVRECMGSV T0361 46 :DEEIVEYAV 1ow4A 23 :TEDDFKTVL T0361 60 :QSGPLDDIDVALRLIYALGKMD 1ow4A 32 :NRNPLESRTAQCLLACALDKVG T0361 101 :QDETPGFADDITWDFISNVN 1ow4A 56 :SPEGAIYTGDDLMPVMNRLY T0361 127 :TLYDALKAMKFADFAVWSEAR 1ow4A 76 :GFNDFKTVMKAKAVNDCANQV T0361 148 :FSGMVKTALTLAV 1ow4A 103 :RCDLIKNFTDCVR Number of specific fragments extracted= 6 number of extra gaps= 0 total=485 Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w7jA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1w7jA expands to /projects/compbio/data/pdb/1w7j.pdb.gz 1w7jA:Skipped atom 803, because occupancy 0.500 <= existing 0.500 in 1w7jA Skipped atom 805, because occupancy 0.500 <= existing 0.500 in 1w7jA Skipped atom 1256, because occupancy 0.500 <= existing 0.500 in 1w7jA Skipped atom 1258, because occupancy 0.500 <= existing 0.500 in 1w7jA Skipped atom 1260, because occupancy 0.500 <= existing 0.500 in 1w7jA Skipped atom 1571, because occupancy 0.500 <= existing 0.500 in 1w7jA Skipped atom 1573, because occupancy 0.500 <= existing 0.500 in 1w7jA Skipped atom 2802, because occupancy 0.500 <= existing 0.500 in 1w7jA Skipped atom 2804, because occupancy 0.500 <= existing 0.500 in 1w7jA Skipped atom 2806, because occupancy 0.500 <= existing 0.500 in 1w7jA Skipped atom 2808, because occupancy 0.500 <= existing 0.500 in 1w7jA Skipped atom 3233, because occupancy 0.500 <= existing 0.500 in 1w7jA Skipped atom 3235, because occupancy 0.500 <= existing 0.500 in 1w7jA Skipped atom 3237, because occupancy 0.500 <= existing 0.500 in 1w7jA Skipped atom 3239, because occupancy 0.500 <= existing 0.500 in 1w7jA Skipped atom 4044, because occupancy 0.500 <= existing 0.500 in 1w7jA Skipped atom 4046, because occupancy 0.500 <= existing 0.500 in 1w7jA Skipped atom 4048, because occupancy 0.500 <= existing 0.500 in 1w7jA Skipped atom 4050, because occupancy 0.500 <= existing 0.500 in 1w7jA Skipped atom 4373, because occupancy 0.500 <= existing 0.500 in 1w7jA Skipped atom 4375, because occupancy 0.500 <= existing 0.500 in 1w7jA Skipped atom 4377, because occupancy 0.500 <= existing 0.500 in 1w7jA Skipped atom 4379, because occupancy 0.500 <= existing 0.500 in 1w7jA Skipped atom 4595, because occupancy 0.500 <= existing 0.500 in 1w7jA Skipped atom 4597, because occupancy 0.500 <= existing 0.500 in 1w7jA # T0361 read from 1w7jA/merged-good-all-a2m # 1w7jA read from 1w7jA/merged-good-all-a2m # adding 1w7jA to template set # found chain 1w7jA in template set T0361 19 :LFSFMKTAHS 1w7jA 637 :GHQFRNSLHL T0361 30 :LLQGIRQ 1w7jA 647 :LMETLNA T0361 44 :DNDEE 1w7jA 663 :KPNDF T0361 50 :VEYAVKPLL 1w7jA 675 :EKRAVQQLR T0361 76 :ALG 1w7jA 684 :ACG T0361 84 :LYADITH 1w7jA 687 :VLETIRI T0361 91 :FSQYWHYLNEQDETPGFAD 1w7jA 704 :YQEFFSRYRVLMKQKDVLS T0361 110 :DITWDFISNV 1w7jA 726 :QTCKNVLEKL T0361 134 :AMKFADFAVWSEARFSGMVKTALTLAVTTTLK 1w7jA 760 :EKIRADKLRAACIRIQKTIRGWLMRKKYMRMR Number of specific fragments extracted= 9 number of extra gaps= 0 total=494 Number of alignments=67 # 1w7jA read from 1w7jA/merged-good-all-a2m # found chain 1w7jA in template set T0361 20 :FSFMKT 1w7jA 638 :HQFRNS T0361 27 :HSILLQGIRQ 1w7jA 644 :LHLLMETLNA T0361 42 :FVDN 1w7jA 671 :FTFD T0361 50 :VEYAVKP 1w7jA 675 :EKRAVQQ T0361 74 :IYALG 1w7jA 682 :LRACG T0361 84 :LYADITH 1w7jA 687 :VLETIRI T0361 91 :FSQYWHYLN 1w7jA 704 :YQEFFSRYR T0361 100 :EQDETPGFADDITWDFISNV 1w7jA 716 :KQKDVLSDRKQTCKNVLEKL T0361 121 :SITRNA 1w7jA 749 :IFFRAG T0361 128 :LYDAL 1w7jA 755 :QVAYL T0361 134 :AMKFADFAVWSEARFSGMVKTALTLAVTTTLK 1w7jA 760 :EKIRADKLRAACIRIQKTIRGWLMRKKYMRMR Number of specific fragments extracted= 11 number of extra gaps= 0 total=505 Number of alignments=68 # 1w7jA read from 1w7jA/merged-good-all-a2m # found chain 1w7jA in template set T0361 7 :DDVLEQLDAQ 1w7jA 645 :HLLMETLNAT T0361 18 :N 1w7jA 674 :D T0361 23 :MKTAHSIL 1w7jA 675 :EKRAVQQL T0361 31 :LQGIRQFLP 1w7jA 688 :LETIRISAA T0361 45 :NDEEIVEY 1w7jA 703 :TYQEFFSR T0361 54 :VKPLLAQSGPLDDID 1w7jA 711 :YRVLMKQKDVLSDRK T0361 89 :THFSQYWHYLNEQDETPGFADDITWDFISNVNSITRNA 1w7jA 726 :QTCKNVLEKLILDKDKYQFGKTKIFFRAGQVAYLEKIR T0361 138 :ADFAVWSEARFSGMVKTALTLAVTTTLK 1w7jA 764 :ADKLRAACIRIQKTIRGWLMRKKYMRMR Number of specific fragments extracted= 8 number of extra gaps= 0 total=513 Number of alignments=69 # command:# PrintAlignmentsContacts allconstraints.under Using radius: 8.0000 NUMB_ALIGNS: 69 Done printing distance constraints # command: