# 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:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0361//projects/compbio/experiments/protein-predict/casp7/T0361/align.constraints_v3.costfcn or /projects/compbio/experiments/protein-predict/casp7/T0361//projects/compbio/experiments/protein-predict/casp7/T0361/align.constraints_v3.costfcn.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/T0361/align.constraints_v3.costfcn # reading script from file /projects/compbio/experiments/protein-predict/casp7/T0361/align.constraints_v3.costfcn # future Constraint commands -> align # future HelixConstraint commands -> align # future StrandConstraint commands -> align # future SheetConstraint commands -> align # future Hbond commands -> align # future SSbond commands -> align # Constraint # added constraint: constraint((T0361)L98.CB, (T0361)T112.CB) [> 3.7854 = 6.3090 < 8.2017] w=1.0000 to align # Constraint # added constraint: constraint((T0361)Y97.CB, (T0361)F115.CB) [> 3.7851 = 6.3085 < 8.2011] w=0.9526 to align # Constraint # added constraint: constraint((T0361)L98.CB, (T0361)F115.CB) [> 3.6047 = 6.0079 < 7.8102] w=0.9283 to align # Constraint # added constraint: constraint((T0361)F91.CB, (T0361)I116.CB) [> 3.8703 = 6.4505 < 8.3857] w=0.9193 to align # Constraint # added constraint: constraint((T0361)F37.CB, (T0361)A53.CB) [> 3.5743 = 5.9571 < 7.7443] w=0.9007 to align # Constraint # added constraint: constraint((T0361)W95.CB, (T0361)T112.CB) [> 3.9739 = 6.6232 < 8.6101] w=0.8540 to align # Constraint # added constraint: constraint((T0361)F91.CB, (T0361)T112.CB) [> 3.6200 = 6.0333 < 7.8433] w=0.8392 to align # Constraint # added constraint: constraint((T0361)I88.CB, (T0361)V119.CB) [> 3.7738 = 6.2896 < 8.1765] w=0.8294 to align # Constraint # added constraint: constraint((T0361)L58.CB, (T0361)Y94.CB) [> 3.9954 = 6.6590 < 8.6567] w=0.8124 to align # Constraint # added constraint: constraint((T0361)V119.CB, (T0361)T163.CB) [> 3.8556 = 6.4260 < 8.3538] w=0.7779 to align # Constraint # added constraint: constraint((T0361)F148.CB, (T0361)T157.CB) [> 3.9521 = 6.5869 < 8.5630] w=0.7733 to align # Constraint # added constraint: constraint((T0361)R147.CB, (T0361)L156.CB) [> 3.5334 = 5.8890 < 7.6557] w=0.7520 to align # Constraint # added constraint: constraint((T0361)A126.CB, (T0361)F140.CB) [> 3.6767 = 6.1279 < 7.9663] w=0.7351 to align # Constraint # added constraint: constraint((T0361)Y85.CB, (T0361)N120.CB) [> 3.9186 = 6.5311 < 8.4904] w=0.7252 to align # Constraint # added constraint: constraint((T0361)W95.CB, (T0361)I116.CB) [> 4.2217 = 7.0361 < 9.1469] w=0.7230 to align # Constraint # added constraint: constraint((T0361)L98.CB, (T0361)F107.CB) [> 3.7005 = 6.1675 < 8.0178] w=0.7230 to align # Constraint # added constraint: constraint((T0361)V54.CB, (T0361)I116.CB) [> 4.0360 = 6.7266 < 8.7446] w=0.7063 to align # Constraint # added constraint: constraint((T0361)T112.CB, (T0361)L156.CB) [> 3.5236 = 5.8727 < 7.6344] w=0.6954 to align # Constraint # added constraint: constraint((T0361)L77.CB, (T0361)F91.CB) [> 3.8057 = 6.3428 < 8.2456] w=0.6898 to align # Constraint # added constraint: constraint((T0361)D87.CB, (T0361)T163.CB) [> 4.3801 = 7.3002 < 9.4902] w=0.6858 to align # Constraint # added constraint: constraint((T0361)W95.CB, (T0361)W113.CB) [> 4.0907 = 6.8179 < 8.8632] w=0.6768 to align # Constraint # added constraint: constraint((T0361)W95.CB, (T0361)D109.CB) [> 4.1138 = 6.8563 < 8.9132] w=0.6756 to align # Constraint # added constraint: constraint((T0361)D109.CB, (T0361)R147.CB) [> 4.2179 = 7.0299 < 9.1388] w=0.6734 to align # Constraint # added constraint: constraint((T0361)T89.CB, (T0361)N120.CB) [> 4.3976 = 7.3294 < 9.5282] w=0.6703 to align # Constraint # added constraint: constraint((T0361)L84.CB, (T0361)V119.CB) [> 4.3715 = 7.2858 < 9.4715] w=0.6703 to align # Constraint # added constraint: constraint((T0361)L98.CB, (T0361)I116.CB) [> 4.0489 = 6.7481 < 8.7725] w=0.6619 to align # Constraint # added constraint: constraint((T0361)Y94.CB, (T0361)T163.CB) [> 3.7882 = 6.3137 < 8.2078] w=0.6443 to align # Constraint # added constraint: constraint((T0361)I34.CB, (T0361)A53.CB) [> 3.8538 = 6.4230 < 8.3499] w=0.6349 to align # Constraint # added constraint: constraint((T0361)V54.CB, (T0361)Y94.CB) [> 3.7893 = 6.3155 < 8.2102] w=0.6298 to align # Constraint # added constraint: constraint((T0361)I122.CB, (T0361)W143.CB) [> 3.6839 = 6.1398 < 7.9817] w=0.6290 to align # Constraint # added constraint: constraint((T0361)L98.CB, (T0361)D109.CB) [> 4.3902 = 7.3170 < 9.5122] w=0.6286 to align # Constraint # added constraint: constraint((T0361)A26.CB, (T0361)F91.CB) [> 4.6122 = 7.6869 < 9.9930] w=0.6212 to align # Constraint # added constraint: constraint((T0361)T112.CB, (T0361)V160.CB) [> 4.1861 = 6.9769 < 9.0700] w=0.6212 to align # Constraint # added constraint: constraint((T0361)G78.CA, (T0361)D87.CB) [> 3.8252 = 6.3753 < 8.2879] w=0.6180 to align # Constraint # added constraint: constraint((T0361)L58.CB, (T0361)A70.CB) [> 3.3001 = 5.5001 < 7.1501] w=0.6170 to align # Constraint # added constraint: constraint((T0361)L41.CB, (T0361)V50.CB) [> 3.8386 = 6.3977 < 8.3170] w=0.6089 to align # Constraint # added constraint: constraint((T0361)Y94.CB, (T0361)I116.CB) [> 3.3122 = 5.5202 < 7.1763] w=0.6040 to align # Constraint # added constraint: constraint((T0361)L84.CB, (T0361)Y94.CB) [> 4.0706 = 6.7844 < 8.8197] w=0.6021 to align # Constraint # added constraint: constraint((T0361)S40.CB, (T0361)A53.CB) [> 4.3724 = 7.2874 < 9.4736] w=0.6017 to align # Constraint # added constraint: constraint((T0361)V9.CB, (T0361)F22.CB) [> 3.9507 = 6.5844 < 8.5598] w=0.5962 to align # Constraint # added constraint: constraint((T0361)L77.CB, (T0361)I88.CB) [> 3.6516 = 6.0860 < 7.9118] w=0.5912 to align # Constraint # added constraint: constraint((T0361)D109.CB, (T0361)S144.CB) [> 3.7884 = 6.3140 < 8.2082] w=0.5868 to align # Constraint # added constraint: constraint((T0361)Y94.CB, (T0361)W143.CB) [> 3.9179 = 6.5298 < 8.4887] w=0.5868 to align # Constraint # added constraint: constraint((T0361)D109.CB, (T0361)F148.CB) [> 3.7566 = 6.2611 < 8.1394] w=0.5848 to align # Constraint # added constraint: constraint((T0361)K24.CB, (T0361)A76.CB) [> 4.5327 = 7.5545 < 9.8209] w=0.5789 to align # Constraint # added constraint: constraint((T0361)F91.CB, (T0361)T163.CB) [> 4.4029 = 7.3382 < 9.5397] w=0.5754 to align # Constraint # added constraint: constraint((T0361)L128.CB, (T0361)R147.CB) [> 4.1077 = 6.8461 < 8.9000] w=0.5718 to align # Constraint # added constraint: constraint((T0361)F37.CB, (T0361)I49.CB) [> 4.2443 = 7.0739 < 9.1961] w=0.5712 to align # Constraint # added constraint: constraint((T0361)L58.CB, (T0361)L73.CB) [> 3.9324 = 6.5540 < 8.5203] w=0.5614 to align # Constraint # added constraint: constraint((T0361)A26.CB, (T0361)L57.CB) [> 3.6848 = 6.1413 < 7.9837] w=0.5547 to align # Constraint # added constraint: constraint((T0361)Y94.CB, (T0361)F140.CB) [> 4.2337 = 7.0562 < 9.1731] w=0.5507 to align # Constraint # added constraint: constraint((T0361)A131.CB, (T0361)F140.CB) [> 3.1436 = 5.2393 < 6.8111] w=0.5480 to align # Constraint # added constraint: constraint((T0361)L128.CB, (T0361)W143.CB) [> 3.5170 = 5.8617 < 7.6202] w=0.5444 to align # Constraint # added constraint: constraint((T0361)L30.CB, (T0361)L57.CB) [> 4.0570 = 6.7617 < 8.7902] w=0.5442 to align # Constraint # added constraint: constraint((T0361)S92.CB, (T0361)W113.CB) [> 4.3184 = 7.1974 < 9.3566] w=0.5410 to align # Constraint # added constraint: constraint((T0361)S40.CB, (T0361)I49.CB) [> 3.7286 = 6.2144 < 8.0787] w=0.5391 to align # Constraint # added constraint: constraint((T0361)L98.CB, (T0361)A108.CB) [> 4.4162 = 7.3604 < 9.5685] w=0.5292 to align # Constraint # added constraint: constraint((T0361)I34.CB, (T0361)Y75.CB) [> 3.5420 = 5.9033 < 7.6743] w=0.5169 to align # Constraint # added constraint: constraint((T0361)D87.CB, (T0361)A159.CB) [> 3.5973 = 5.9955 < 7.7941] w=0.5124 to align # Constraint # added constraint: constraint((T0361)L58.CB, (T0361)L98.CB) [> 3.4824 = 5.8040 < 7.5452] w=0.5050 to align # Constraint # added constraint: constraint((T0361)F148.CB, (T0361)V160.CB) [> 2.9718 = 4.9530 < 6.4389] w=0.5033 to align # Constraint # added constraint: constraint((T0361)L38.CB, (T0361)V50.CB) [> 3.6840 = 6.1400 < 7.9820] w=0.4987 to align # Constraint # added constraint: constraint((T0361)M23.CB, (T0361)V69.CB) [> 3.8833 = 6.4722 < 8.4138] w=0.4890 to align # Constraint # added constraint: constraint((T0361)F22.CB, (T0361)V69.CB) [> 3.6292 = 6.0486 < 7.8632] w=0.4890 to align # Constraint # added constraint: constraint((T0361)S92.CB, (T0361)I116.CB) [> 4.5994 = 7.6657 < 9.9654] w=0.4886 to align # Constraint # added constraint: constraint((T0361)I29.CB, (T0361)L57.CB) [> 4.1866 = 6.9776 < 9.0709] w=0.4845 to align # Constraint # added constraint: constraint((T0361)A26.CB, (T0361)L58.CB) [> 3.8454 = 6.4091 < 8.3318] w=0.4845 to align # Constraint # added constraint: constraint((T0361)I122.CB, (T0361)L132.CB) [> 3.5740 = 5.9567 < 7.7437] w=0.4840 to align # Constraint # added constraint: constraint((T0361)A26.CB, (T0361)Y94.CB) [> 4.3893 = 7.3155 < 9.5102] w=0.4803 to align # Constraint # added constraint: constraint((T0361)F37.CB, (T0361)K79.CB) [> 3.3013 = 5.5021 < 7.1528] w=0.4786 to align # Constraint # added constraint: constraint((T0361)Q36.CB, (T0361)A53.CB) [> 3.3078 = 5.5129 < 7.1668] w=0.4764 to align # Constraint # added constraint: constraint((T0361)H90.CB, (T0361)R147.CB) [> 3.4315 = 5.7192 < 7.4350] w=0.4763 to align # Constraint # added constraint: constraint((T0361)F91.CB, (T0361)R147.CB) [> 4.3675 = 7.2792 < 9.4629] w=0.4763 to align # Constraint # added constraint: constraint((T0361)Y94.CB, (T0361)R147.CB) [> 4.1067 = 6.8446 < 8.8979] w=0.4763 to align # Constraint # added constraint: constraint((T0361)L98.CB, (T0361)F140.CB) [> 4.0038 = 6.6730 < 8.6749] w=0.4763 to align # Constraint # added constraint: constraint((T0361)T112.CB, (T0361)T157.CB) [> 4.6540 = 7.7566 < 10.0836] w=0.4763 to align # Constraint # added constraint: constraint((T0361)F115.CB, (T0361)V160.CB) [> 4.1921 = 6.9868 < 9.0828] w=0.4763 to align # Constraint # added constraint: constraint((T0361)I116.CB, (T0361)R147.CB) [> 4.0849 = 6.8082 < 8.8507] w=0.4574 to align # Constraint # added constraint: constraint((T0361)L13.CB, (T0361)F22.CB) [> 3.6296 = 6.0494 < 7.8642] w=0.4574 to align # Constraint # added constraint: constraint((T0361)I49.CB, (T0361)V69.CB) [> 3.7576 = 6.2627 < 8.1416] w=0.4567 to align # Constraint # added constraint: constraint((T0361)M23.CB, (T0361)L73.CB) [> 3.3638 = 5.6063 < 7.2882] w=0.4566 to align # Constraint # added constraint: constraint((T0361)I34.CB, (T0361)I49.CB) [> 3.4114 = 5.6856 < 7.3913] w=0.4426 to align # Constraint # added constraint: constraint((T0361)F37.CB, (T0361)G78.CA) [> 4.7175 = 7.8625 < 10.2213] w=0.4403 to align # Constraint # added constraint: constraint((T0361)L38.CB, (T0361)L71.CB) [> 4.3030 = 7.1717 < 9.3232] w=0.4403 to align # Constraint # added constraint: constraint((T0361)L38.CB, (T0361)I74.CB) [> 3.4361 = 5.7269 < 7.4450] w=0.4403 to align # Constraint # added constraint: constraint((T0361)L41.CB, (T0361)I74.CB) [> 4.0930 = 6.8217 < 8.8682] w=0.4403 to align # Constraint # added constraint: constraint((T0361)L41.CB, (T0361)I88.CB) [> 4.4181 = 7.3636 < 9.5727] w=0.4403 to align # Constraint # added constraint: constraint((T0361)A76.CB, (T0361)K153.CB) [> 3.7293 = 6.2156 < 8.0802] w=0.4403 to align # Constraint # added constraint: constraint((T0361)A76.CB, (T0361)L156.CB) [> 3.2505 = 5.4174 < 7.0427] w=0.4403 to align # Constraint # added constraint: constraint((T0361)L77.CB, (T0361)V160.CB) [> 4.4226 = 7.3710 < 9.5824] w=0.4403 to align # Constraint # added constraint: constraint((T0361)H90.CB, (T0361)L164.CB) [> 3.7449 = 6.2415 < 8.1139] w=0.4403 to align # Constraint # added constraint: constraint((T0361)F91.CB, (T0361)V160.CB) [> 4.4485 = 7.4141 < 9.6383] w=0.4403 to align # Constraint # added constraint: constraint((T0361)L10.CB, (T0361)L19.CB) [> 3.9141 = 6.5236 < 8.4806] w=0.4403 to align # Constraint # added constraint: constraint((T0361)A131.CB, (T0361)W143.CB) [> 3.5970 = 5.9949 < 7.7934] w=0.4367 to align # Constraint # added constraint: constraint((T0361)H27.CB, (T0361)F91.CB) [> 3.4864 = 5.8107 < 7.5539] w=0.4359 to align # Constraint # added constraint: constraint((T0361)N118.CB, (T0361)R147.CB) [> 4.1670 = 6.9449 < 9.0284] w=0.4299 to align # Constraint # added constraint: constraint((T0361)L19.CB, (T0361)L64.CB) [> 3.6864 = 6.1441 < 7.9873] w=0.4271 to align # Constraint # added constraint: constraint((T0361)I116.CB, (T0361)V152.CB) [> 3.2728 = 5.4546 < 7.0910] w=0.4209 to align # Constraint # added constraint: constraint((T0361)L73.CB, (T0361)F91.CB) [> 3.9987 = 6.6645 < 8.6638] w=0.4188 to align # Constraint # added constraint: constraint((T0361)L58.CB, (T0361)I74.CB) [> 3.9302 = 6.5504 < 8.5155] w=0.4188 to align # Constraint # added constraint: constraint((T0361)I74.CB, (T0361)T112.CB) [> 4.1124 = 6.8541 < 8.9103] w=0.4184 to align # Constraint # added constraint: constraint((T0361)L38.CB, (T0361)A53.CB) [> 3.4301 = 5.7169 < 7.4319] w=0.4151 to align # Constraint # added constraint: constraint((T0361)V50.CB, (T0361)Q93.CB) [> 4.2884 = 7.1473 < 9.2915] w=0.4142 to align # Constraint # added constraint: constraint((T0361)M80.CB, (T0361)Y94.CB) [> 3.6319 = 6.0532 < 7.8691] w=0.4140 to align # Constraint # added constraint: constraint((T0361)V54.CB, (T0361)I88.CB) [> 4.3113 = 7.1854 < 9.3411] w=0.4140 to align # Constraint # added constraint: constraint((T0361)L73.CB, (T0361)I116.CB) [> 4.5378 = 7.5631 < 9.8320] w=0.4063 to align # Constraint # added constraint: constraint((T0361)K79.CB, (T0361)I88.CB) [> 4.2673 = 7.1122 < 9.2458] w=0.3981 to align # Constraint # added constraint: constraint((T0361)L41.CB, (T0361)A70.CB) [> 4.3982 = 7.3304 < 9.5295] w=0.3902 to align # Constraint # added constraint: constraint((T0361)I74.CB, (T0361)I88.CB) [> 3.6806 = 6.1344 < 7.9747] w=0.3902 to align # Constraint # added constraint: constraint((T0361)L71.CB, (T0361)L84.CB) [> 3.0851 = 5.1419 < 6.6845] w=0.3873 to align # Constraint # added constraint: constraint((T0361)L30.CB, (T0361)Y94.CB) [> 3.2741 = 5.4569 < 7.0940] w=0.3817 to align # Constraint # added constraint: constraint((T0361)L57.CB, (T0361)V69.CB) [> 3.4617 = 5.7695 < 7.5004] w=0.3808 to align # Constraint # added constraint: constraint((T0361)I34.CB, (T0361)P56.CB) [> 3.9977 = 6.6629 < 8.6617] w=0.3768 to align # Constraint # added constraint: constraint((T0361)S28.CB, (T0361)R72.CB) [> 4.2667 = 7.1112 < 9.2445] w=0.3725 to align # Constraint # added constraint: constraint((T0361)A126.CB, (T0361)M135.CB) [> 4.4952 = 7.4920 < 9.7396] w=0.3678 to align # Constraint # added constraint: constraint((T0361)D46.CB, (T0361)Y85.CB) [> 3.2949 = 5.4916 < 7.1390] w=0.3638 to align # Constraint # added constraint: constraint((T0361)I34.CB, (T0361)L73.CB) [> 3.9034 = 6.5057 < 8.4575] w=0.3622 to align # Constraint # added constraint: constraint((T0361)I29.CB, (T0361)L41.CB) [> 3.9724 = 6.6207 < 8.6069] w=0.3614 to align # Constraint # added constraint: constraint((T0361)F22.CB, (T0361)L57.CB) [> 4.1266 = 6.8777 < 8.9410] w=0.3614 to align # Constraint # added constraint: constraint((T0361)Y52.CB, (T0361)V69.CB) [> 3.4677 = 5.7796 < 7.5134] w=0.3600 to align # Constraint # added constraint: constraint((T0361)Y52.CB, (T0361)R72.CB) [> 4.5397 = 7.5662 < 9.8360] w=0.3600 to align # Constraint # added constraint: constraint((T0361)Y75.CB, (T0361)L84.CB) [> 3.4513 = 5.7522 < 7.4778] w=0.3569 to align # Constraint # added constraint: constraint((T0361)L38.CB, (T0361)A70.CB) [> 3.4663 = 5.7771 < 7.5102] w=0.3562 to align # Constraint # added constraint: constraint((T0361)I34.CB, (T0361)L71.CB) [> 3.2679 = 5.4465 < 7.0804] w=0.3562 to align # Constraint # added constraint: constraint((T0361)W113.CB, (T0361)L156.CB) [> 3.0738 = 5.1230 < 6.6599] w=0.3555 to align # Constraint # added constraint: constraint((T0361)A108.CB, (T0361)F137.CB) [> 3.5075 = 5.8459 < 7.5997] w=0.3536 to align # Constraint # added constraint: constraint((T0361)L128.CB, (T0361)F140.CB) [> 3.8165 = 6.3609 < 8.2691] w=0.3526 to align # Constraint # added constraint: constraint((T0361)H27.CB, (T0361)L73.CB) [> 4.4416 = 7.4026 < 9.6235] w=0.3480 to align # Constraint # added constraint: constraint((T0361)A26.CB, (T0361)L73.CB) [> 4.0935 = 6.8224 < 8.8692] w=0.3480 to align # Constraint # added constraint: constraint((T0361)M23.CB, (T0361)A76.CB) [> 3.4850 = 5.8083 < 7.5508] w=0.3480 to align # Constraint # added constraint: constraint((T0361)A70.CB, (T0361)T112.CB) [> 3.9350 = 6.5583 < 8.5258] w=0.3478 to align # Constraint # added constraint: constraint((T0361)Y85.CB, (T0361)V119.CB) [> 3.1536 = 5.2560 < 6.8328] w=0.3464 to align # Constraint # added constraint: constraint((T0361)L98.CB, (T0361)I111.CB) [> 4.1006 = 6.8343 < 8.8846] w=0.3437 to align # Constraint # added constraint: constraint((T0361)A70.CB, (T0361)I111.CB) [> 3.2727 = 5.4545 < 7.0909] w=0.3436 to align # Constraint # added constraint: constraint((T0361)L30.CB, (T0361)V50.CB) [> 3.5045 = 5.8408 < 7.5931] w=0.3430 to align # Constraint # added constraint: constraint((T0361)D139.CB, (T0361)F148.CB) [> 3.5204 = 5.8673 < 7.6275] w=0.3417 to align # Constraint # added constraint: constraint((T0361)L71.CB, (T0361)I116.CB) [> 3.9799 = 6.6332 < 8.6231] w=0.3412 to align # Constraint # added constraint: constraint((T0361)S121.CB, (T0361)S144.CB) [> 3.2461 = 5.4102 < 7.0332] w=0.3376 to align # Constraint # added constraint: constraint((T0361)L30.CB, (T0361)M151.CB) [> 3.3185 = 5.5308 < 7.1901] w=0.3356 to align # Constraint # added constraint: constraint((T0361)L41.CB, (T0361)K79.CB) [> 3.6829 = 6.1381 < 7.9795] w=0.3318 to align # Constraint # added constraint: constraint((T0361)R72.CB, (T0361)F115.CB) [> 4.0311 = 6.7185 < 8.7340] w=0.3297 to align # Constraint # added constraint: constraint((T0361)I34.CB, (T0361)V54.CB) [> 3.8837 = 6.4729 < 8.4147] w=0.3260 to align # Constraint # added constraint: constraint((T0361)L30.CB, (T0361)A53.CB) [> 4.1382 = 6.8970 < 8.9660] w=0.3210 to align # Constraint # added constraint: constraint((T0361)E11.CB, (T0361)F20.CB) [> 3.5950 = 5.9917 < 7.7893] w=0.3204 to align # Constraint # added constraint: constraint((T0361)L10.CB, (T0361)F20.CB) [> 3.0701 = 5.1168 < 6.6518] w=0.3204 to align # Constraint # added constraint: constraint((T0361)S149.CB, (T0361)V160.CB) [> 3.8411 = 6.4018 < 8.3223] w=0.3190 to align # Constraint # added constraint: constraint((T0361)L10.CB, (T0361)M23.CB) [> 3.2653 = 5.4421 < 7.0747] w=0.3186 to align # Constraint # added constraint: constraint((T0361)E145.CB, (T0361)T154.CB) [> 3.9892 = 6.6486 < 8.6432] w=0.3175 to align # Constraint # added constraint: constraint((T0361)F37.CB, (T0361)D46.CB) [> 3.5724 = 5.9541 < 7.7403] w=0.3173 to align # Constraint # added constraint: constraint((T0361)Q12.CB, (T0361)F22.CB) [> 3.2500 = 5.4167 < 7.0417] w=0.3167 to align # Constraint # added constraint: constraint((T0361)S121.CB, (T0361)R147.CB) [> 4.1757 = 6.9595 < 9.0473] w=0.3132 to align # Constraint # added constraint: constraint((T0361)F140.CB, (T0361)L167.CB) [> 4.1911 = 6.9851 < 9.0806] w=0.3127 to align # Constraint # added constraint: constraint((T0361)L31.CB, (T0361)P56.CB) [> 4.5057 = 7.5095 < 9.7623] w=0.3101 to align # Constraint # added constraint: constraint((T0361)L38.CB, (T0361)P56.CB) [> 4.0358 = 6.7263 < 8.7442] w=0.3037 to align # Constraint # added constraint: constraint((T0361)Y97.CB, (T0361)F107.CB) [> 4.1022 = 6.8371 < 8.8882] w=0.3030 to align # Constraint # added constraint: constraint((T0361)I67.CB, (T0361)A108.CB) [> 4.2371 = 7.0618 < 9.1804] w=0.3003 to align # Constraint # added constraint: constraint((T0361)I49.CB, (T0361)Y97.CB) [> 3.8886 = 6.4810 < 8.4253] w=0.2986 to align # Constraint # added constraint: constraint((T0361)I49.CB, (T0361)L98.CB) [> 4.0404 = 6.7340 < 8.7542] w=0.2986 to align # Constraint # added constraint: constraint((T0361)F91.CB, (T0361)A159.CB) [> 4.6967 = 7.8279 < 10.1762] w=0.2958 to align # Constraint # added constraint: constraint((T0361)Q16.CB, (T0361)L64.CB) [> 4.1547 = 6.9245 < 9.0018] w=0.2958 to align # Constraint # added constraint: constraint((T0361)L19.CB, (T0361)D68.CB) [> 2.6164 = 4.3607 < 5.6689] w=0.2958 to align # Constraint # added constraint: constraint((T0361)L19.CB, (T0361)V69.CB) [> 2.6567 = 4.4278 < 5.7561] w=0.2958 to align # Constraint # added constraint: constraint((T0361)L19.CB, (T0361)R72.CB) [> 3.4348 = 5.7247 < 7.4421] w=0.2958 to align # Constraint # added constraint: constraint((T0361)M23.CB, (T0361)R72.CB) [> 2.8445 = 4.7408 < 6.1631] w=0.2958 to align # Constraint # added constraint: constraint((T0361)A26.CB, (T0361)V54.CB) [> 3.9145 = 6.5242 < 8.4815] w=0.2958 to align # Constraint # added constraint: constraint((T0361)H27.CB, (T0361)A76.CB) [> 3.5643 = 5.9405 < 7.7227] w=0.2958 to align # Constraint # added constraint: constraint((T0361)I29.CB, (T0361)V50.CB) [> 3.4761 = 5.7935 < 7.5315] w=0.2958 to align # Constraint # added constraint: constraint((T0361)L30.CB, (T0361)A76.CB) [> 4.1748 = 6.9581 < 9.0455] w=0.2936 to align # Constraint # added constraint: constraint((T0361)F37.CB, (T0361)I74.CB) [> 4.1535 = 6.9225 < 8.9992] w=0.2936 to align # Constraint # added constraint: constraint((T0361)A59.CB, (T0361)A70.CB) [> 4.3450 = 7.2417 < 9.4142] w=0.2936 to align # Constraint # added constraint: constraint((T0361)V69.CB, (T0361)I116.CB) [> 4.0103 = 6.6838 < 8.6889] w=0.2936 to align # Constraint # added constraint: constraint((T0361)Y75.CB, (T0361)K153.CB) [> 4.4550 = 7.4250 < 9.6525] w=0.2936 to align # Constraint # added constraint: constraint((T0361)D87.CB, (T0361)L164.CB) [> 3.5021 = 5.8368 < 7.5879] w=0.2936 to align # Constraint # added constraint: constraint((T0361)F91.CB, (T0361)L164.CB) [> 4.4319 = 7.3864 < 9.6024] w=0.2936 to align # Constraint # added constraint: constraint((T0361)Y94.CB, (T0361)V152.CB) [> 4.7891 = 7.9819 < 10.3764] w=0.2899 to align # Constraint # added constraint: constraint((T0361)Y94.CB, (T0361)N118.CB) [> 4.6277 = 7.7129 < 10.0267] w=0.2899 to align # Constraint # added constraint: constraint((T0361)S92.CB, (T0361)L156.CB) [> 3.6848 = 6.1413 < 7.9837] w=0.2899 to align # Constraint # added constraint: constraint((T0361)T127.CB, (T0361)W143.CB) [> 4.1925 = 6.9876 < 9.0838] w=0.2899 to align # Constraint # added constraint: constraint((T0361)S121.CB, (T0361)F140.CB) [> 4.4988 = 7.4981 < 9.7475] w=0.2899 to align # Constraint # added constraint: constraint((T0361)F107.CB, (T0361)F137.CB) [> 4.7812 = 7.9686 < 10.3592] w=0.2899 to align # Constraint # added constraint: constraint((T0361)F107.CB, (T0361)M135.CB) [> 4.5517 = 7.5862 < 9.8621] w=0.2899 to align # Constraint # added constraint: constraint((T0361)R35.CB, (T0361)Y94.CB) [> 3.0034 = 5.0056 < 6.5073] w=0.2882 to align # Constraint # added constraint: constraint((T0361)P39.CB, (T0361)V50.CB) [> 4.0799 = 6.7997 < 8.8397] w=0.2840 to align # Constraint # added constraint: constraint((T0361)I34.CB, (T0361)R147.CB) [> 3.5541 = 5.9235 < 7.7005] w=0.2832 to align # Constraint # added constraint: constraint((T0361)I34.CB, (T0361)I116.CB) [> 4.7878 = 7.9797 < 10.3736] w=0.2832 to align # Constraint # added constraint: constraint((T0361)I34.CB, (T0361)L98.CB) [> 4.5726 = 7.6211 < 9.9074] w=0.2832 to align # Constraint # added constraint: constraint((T0361)G33.CA, (T0361)L98.CB) [> 4.2210 = 7.0351 < 9.1456] w=0.2832 to align # Constraint # added constraint: constraint((T0361)T25.CB, (T0361)L73.CB) [> 3.4650 = 5.7750 < 7.5076] w=0.2832 to align # Constraint # added constraint: constraint((T0361)T25.CB, (T0361)V69.CB) [> 4.2087 = 7.0144 < 9.1188] w=0.2832 to align # Constraint # added constraint: constraint((T0361)F22.CB, (T0361)Q60.CB) [> 4.5634 = 7.6056 < 9.8872] w=0.2832 to align # Constraint # added constraint: constraint((T0361)I122.CB, (T0361)D139.CB) [> 3.8132 = 6.3553 < 8.2619] w=0.2832 to align # Constraint # added constraint: constraint((T0361)L41.CB, (T0361)T123.CB) [> 2.5798 = 4.2997 < 5.5896] w=0.2832 to align # Constraint # added constraint: constraint((T0361)F91.CB, (T0361)L156.CB) [> 3.9943 = 6.6572 < 8.6543] w=0.2796 to align # Constraint # added constraint: constraint((T0361)I34.CB, (T0361)M80.CB) [> 4.1357 = 6.8929 < 8.9607] w=0.2715 to align # Constraint # added constraint: constraint((T0361)D66.CB, (T0361)A108.CB) [> 3.4707 = 5.7845 < 7.5199] w=0.2695 to align # Constraint # added constraint: constraint((T0361)I116.CB, (T0361)L128.CB) [> 3.9269 = 6.5449 < 8.5084] w=0.2669 to align # Constraint # added constraint: constraint((T0361)I34.CB, (T0361)E48.CB) [> 4.2720 = 7.1199 < 9.2559] w=0.2647 to align # Constraint # added constraint: constraint((T0361)V54.CB, (T0361)L98.CB) [> 3.7092 = 6.1821 < 8.0367] w=0.2641 to align # Constraint # added constraint: constraint((T0361)M135.CB, (T0361)R147.CB) [> 3.6162 = 6.0270 < 7.8351] w=0.2639 to align # Constraint # added constraint: constraint((T0361)I34.CB, (T0361)N45.CB) [> 3.4962 = 5.8270 < 7.5752] w=0.2637 to align # Constraint # added constraint: constraint((T0361)F42.CB, (T0361)Y94.CB) [> 3.5826 = 5.9710 < 7.7623] w=0.2588 to align # Constraint # added constraint: constraint((T0361)G33.CA, (T0361)Y52.CB) [> 4.4206 = 7.3677 < 9.5779] w=0.2559 to align # Constraint # added constraint: constraint((T0361)G33.CA, (T0361)P56.CB) [> 2.9639 = 4.9398 < 6.4217] w=0.2559 to align # Constraint # added constraint: constraint((T0361)L71.CB, (T0361)F91.CB) [> 3.7909 = 6.3182 < 8.2136] w=0.2559 to align # Constraint # added constraint: constraint((T0361)Y129.CB, (T0361)F140.CB) [> 4.1436 = 6.9060 < 8.9778] w=0.2553 to align # Constraint # added constraint: constraint((T0361)I49.CB, (T0361)Y94.CB) [> 3.7249 = 6.2081 < 8.0706] w=0.2538 to align # Constraint # added constraint: constraint((T0361)L41.CB, (T0361)Y94.CB) [> 3.7936 = 6.3226 < 8.2194] w=0.2495 to align # Constraint # added constraint: constraint((T0361)N125.CB, (T0361)G150.CA) [> 3.9415 = 6.5692 < 8.5400] w=0.2483 to align # Constraint # added constraint: constraint((T0361)A141.CB, (T0361)L167.CB) [> 3.3183 = 5.5305 < 7.1896] w=0.2480 to align # Constraint # added constraint: constraint((T0361)A141.CB, (T0361)T163.CB) [> 3.6525 = 6.0875 < 7.9138] w=0.2480 to align # Constraint # added constraint: constraint((T0361)H90.CB, (T0361)A159.CB) [> 4.1130 = 6.8551 < 8.9116] w=0.2456 to align # Constraint # added constraint: constraint((T0361)L77.CB, (T0361)A108.CB) [> 4.4275 = 7.3791 < 9.5928] w=0.2454 to align # Constraint # added constraint: constraint((T0361)N120.CB, (T0361)A159.CB) [> 3.5435 = 5.9058 < 7.6775] w=0.2433 to align # Constraint # added constraint: constraint((T0361)D66.CB, (T0361)A131.CB) [> 4.2779 = 7.1298 < 9.2687] w=0.2393 to align # Constraint # added constraint: constraint((T0361)Y94.CB, (T0361)A159.CB) [> 3.6791 = 6.1318 < 7.9713] w=0.2353 to align # Constraint # added constraint: constraint((T0361)L31.CB, (T0361)V69.CB) [> 3.8984 = 6.4974 < 8.4466] w=0.2302 to align # Constraint # added constraint: constraint((T0361)D66.CB, (T0361)P105.CB) [> 2.9918 = 4.9863 < 6.4822] w=0.2280 to align # Constraint # added constraint: constraint((T0361)I74.CB, (T0361)I111.CB) [> 3.8793 = 6.4655 < 8.4051] w=0.2213 to align # Constraint # added constraint: constraint((T0361)D66.CB, (T0361)I111.CB) [> 3.9973 = 6.6622 < 8.6608] w=0.2188 to align # Constraint # added constraint: constraint((T0361)Q36.CB, (T0361)N45.CB) [> 4.5486 = 7.5810 < 9.8554] w=0.2170 to align # Constraint # added constraint: constraint((T0361)L13.CB, (T0361)I34.CB) [> 3.6281 = 6.0469 < 7.8610] w=0.2115 to align # Constraint # added constraint: constraint((T0361)I116.CB, (T0361)A155.CB) [> 4.5147 = 7.5244 < 9.7818] w=0.2063 to align # Constraint # added constraint: constraint((T0361)R147.CB, (T0361)A159.CB) [> 3.5386 = 5.8977 < 7.6670] w=0.2034 to align # Constraint # added constraint: constraint((T0361)H27.CB, (T0361)I67.CB) [> 3.9317 = 6.5528 < 8.5186] w=0.1979 to align # Constraint # added constraint: constraint((T0361)G78.CA, (T0361)Y129.CB) [> 4.4420 = 7.4034 < 9.6244] w=0.1972 to align # Constraint # added constraint: constraint((T0361)N118.CB, (T0361)Y129.CB) [> 3.7055 = 6.1758 < 8.0285] w=0.1972 to align # Constraint # added constraint: constraint((T0361)M80.CB, (T0361)L98.CB) [> 4.7419 = 7.9032 < 10.2741] w=0.1970 to align # Constraint # added constraint: constraint((T0361)A138.CB, (T0361)R147.CB) [> 2.5185 = 4.1975 < 5.4567] w=0.1970 to align # Constraint # added constraint: constraint((T0361)F137.CB, (T0361)R147.CB) [> 4.6602 = 7.7670 < 10.0971] w=0.1970 to align # Constraint # added constraint: constraint((T0361)A131.CB, (T0361)A155.CB) [> 3.8781 = 6.4634 < 8.4024] w=0.1970 to align # Constraint # added constraint: constraint((T0361)V43.CB, (T0361)K133.CB) [> 4.6201 = 7.7001 < 10.0101] w=0.1933 to align # Constraint # added constraint: constraint((T0361)F42.CB, (T0361)F107.CB) [> 4.7032 = 7.8387 < 10.1903] w=0.1933 to align # Constraint # added constraint: constraint((T0361)D44.CB, (T0361)Y129.CB) [> 2.9423 = 4.9039 < 6.3751] w=0.1933 to align # Constraint # added constraint: constraint((T0361)Y94.CB, (T0361)M151.CB) [> 4.1220 = 6.8700 < 8.9310] w=0.1888 to align # Constraint # added constraint: constraint((T0361)L98.CB, (T0361)M151.CB) [> 4.5127 = 7.5211 < 9.7774] w=0.1888 to align # Constraint # added constraint: constraint((T0361)L98.CB, (T0361)R147.CB) [> 4.2873 = 7.1455 < 9.2891] w=0.1879 to align # Constraint # added constraint: constraint((T0361)Y94.CB, (T0361)L167.CB) [> 3.3763 = 5.6271 < 7.3152] w=0.1840 to align # Constraint # added constraint: constraint((T0361)I67.CB, (T0361)I111.CB) [> 2.6612 = 4.4353 < 5.7659] w=0.1831 to align # Constraint # added constraint: constraint((T0361)F148.CB, (T0361)T161.CB) [> 3.6335 = 6.0558 < 7.8726] w=0.1829 to align # Constraint # added constraint: constraint((T0361)G62.CA, (T0361)L71.CB) [> 3.9950 = 6.6584 < 8.6559] w=0.1817 to align # Constraint # added constraint: constraint((T0361)W113.CB, (T0361)K153.CB) [> 4.4761 = 7.4601 < 9.6981] w=0.1800 to align # Constraint # added constraint: constraint((T0361)H27.CB, (T0361)Y52.CB) [> 4.5586 = 7.5976 < 9.8769] w=0.1788 to align # Constraint # added constraint: constraint((T0361)W113.CB, (T0361)A155.CB) [> 3.4697 = 5.7828 < 7.5177] w=0.1755 to align # Constraint # added constraint: constraint((T0361)V54.CB, (T0361)F91.CB) [> 4.5998 = 7.6663 < 9.9662] w=0.1636 to align # Constraint # added constraint: constraint((T0361)I67.CB, (T0361)F91.CB) [> 3.3471 = 5.5785 < 7.2521] w=0.1636 to align # Constraint # added constraint: constraint((T0361)Y75.CB, (T0361)Y85.CB) [> 3.4762 = 5.7937 < 7.5319] w=0.1636 to align # Constraint # added constraint: constraint((T0361)V9.CB, (T0361)M151.CB) [> 4.1146 = 6.8576 < 8.9149] w=0.1630 to align # Constraint # added constraint: constraint((T0361)M23.CB, (T0361)L77.CB) [> 3.7133 = 6.1889 < 8.0455] w=0.1608 to align # Constraint # added constraint: constraint((T0361)I34.CB, (T0361)Y94.CB) [> 3.2344 = 5.3907 < 7.0079] w=0.1569 to align # Constraint # added constraint: constraint((T0361)L13.CB, (T0361)T25.CB) [> 3.6639 = 6.1065 < 7.9384] w=0.1569 to align # Constraint # added constraint: constraint((T0361)N118.CB, (T0361)E166.CB) [> 3.8969 = 6.4948 < 8.4433] w=0.1569 to align # Constraint # added constraint: constraint((T0361)I67.CB, (T0361)D114.CB) [> 4.5377 = 7.5629 < 9.8318] w=0.1523 to align # Constraint # added constraint: constraint((T0361)V142.CB, (T0361)L167.CB) [> 3.8688 = 6.4480 < 8.3824] w=0.1523 to align # Constraint # added constraint: constraint((T0361)Y75.CB, (T0361)F91.CB) [> 4.4399 = 7.3999 < 9.6198] w=0.1489 to align # Constraint # added constraint: constraint((T0361)I122.CB, (T0361)M151.CB) [> 4.3819 = 7.3032 < 9.4941] w=0.1480 to align # Constraint # added constraint: constraint((T0361)L13.CB, (T0361)Y75.CB) [> 4.7180 = 7.8634 < 10.2224] w=0.1468 to align # Constraint # added constraint: constraint((T0361)V9.CB, (T0361)R147.CB) [> 4.1573 = 6.9289 < 9.0075] w=0.1468 to align # Constraint # added constraint: constraint((T0361)V9.CB, (T0361)I122.CB) [> 4.4082 = 7.3470 < 9.5511] w=0.1468 to align # Constraint # added constraint: constraint((T0361)V9.CB, (T0361)V119.CB) [> 3.7168 = 6.1946 < 8.0530] w=0.1468 to align # Constraint # added constraint: constraint((T0361)E6.CB, (T0361)R147.CB) [> 4.7193 = 7.8656 < 10.2252] w=0.1468 to align # Constraint # added constraint: constraint((T0361)E6.CB, (T0361)I122.CB) [> 4.6097 = 7.6829 < 9.9878] w=0.1468 to align # Constraint # added constraint: constraint((T0361)T5.CB, (T0361)R147.CB) [> 3.2592 = 5.4320 < 7.0616] w=0.1468 to align # Constraint # added constraint: constraint((T0361)T3.CB, (T0361)L132.CB) [> 3.7009 = 6.1682 < 8.0187] w=0.1468 to align # Constraint # added constraint: constraint((T0361)A15.CB, (T0361)I34.CB) [> 3.1336 = 5.2226 < 6.7894] w=0.1468 to align # Constraint # added constraint: constraint((T0361)D14.CB, (T0361)I34.CB) [> 4.4872 = 7.4787 < 9.7223] w=0.1468 to align # Constraint # added constraint: constraint((T0361)M80.CB, (T0361)T161.CB) [> 4.6648 = 7.7747 < 10.1071] w=0.1468 to align # Constraint # added constraint: constraint((T0361)S121.CB, (T0361)L156.CB) [> 4.2913 = 7.1522 < 9.2978] w=0.1468 to align # Constraint # added constraint: constraint((T0361)S121.CB, (T0361)K153.CB) [> 3.6926 = 6.1544 < 8.0007] w=0.1468 to align # Constraint # added constraint: constraint((T0361)Y75.CB, (T0361)T157.CB) [> 4.3743 = 7.2905 < 9.4776] w=0.1468 to align # Constraint # added constraint: constraint((T0361)R72.CB, (T0361)V152.CB) [> 3.8204 = 6.3673 < 8.2775] w=0.1468 to align # Constraint # added constraint: constraint((T0361)G78.CA, (T0361)S121.CB) [> 3.3741 = 5.6236 < 7.3106] w=0.1447 to align # Constraint # added constraint: constraint((T0361)E145.CB, (T0361)T157.CB) [> 3.7077 = 6.1796 < 8.0334] w=0.1348 to align # Constraint # added constraint: constraint((T0361)A131.CB, (T0361)T154.CB) [> 3.2009 = 5.3348 < 6.9353] w=0.1313 to align # Constraint # added constraint: constraint((T0361)Y94.CB, (T0361)P105.CB) [> 4.7853 = 7.9756 < 10.3682] w=0.1294 to align # Constraint # added constraint: constraint((T0361)I116.CB, (T0361)L167.CB) [> 4.4648 = 7.4413 < 9.6737] w=0.1246 to align # Constraint # added constraint: constraint((T0361)V43.CB, (T0361)L77.CB) [> 3.0736 = 5.1227 < 6.6596] w=0.1168 to align # Constraint # added constraint: constraint((T0361)N45.CB, (T0361)D68.CB) [> 3.1839 = 5.3064 < 6.8983] w=0.1148 to align # Constraint # added constraint: constraint((T0361)Y52.CB, (T0361)D65.CB) [> 4.5753 = 7.6255 < 9.9132] w=0.1148 to align # Constraint # added constraint: constraint((T0361)G106.CA, (T0361)A155.CB) [> 4.5784 = 7.6307 < 9.9198] w=0.1106 to align # Constraint # added constraint: constraint((T0361)G33.CA, (T0361)F91.CB) [> 3.7516 = 6.2527 < 8.1285] w=0.1085 to align # Constraint # added constraint: constraint((T0361)T123.CB, (T0361)L158.CB) [> 4.3271 = 7.2119 < 9.3755] w=0.1077 to align # Constraint # added constraint: constraint((T0361)S121.CB, (T0361)L158.CB) [> 4.4656 = 7.4427 < 9.6756] w=0.1077 to align # Constraint # added constraint: constraint((T0361)S121.CB, (T0361)A155.CB) [> 3.6960 = 6.1601 < 8.0081] w=0.1077 to align # Constraint # added constraint: constraint((T0361)A138.CB, (T0361)T157.CB) [> 4.6896 = 7.8160 < 10.1608] w=0.1077 to align # Constraint # added constraint: constraint((T0361)L132.CB, (T0361)V142.CB) [> 2.7373 = 4.5622 < 5.9309] w=0.1077 to align # Constraint # added constraint: constraint((T0361)T127.CB, (T0361)A155.CB) [> 4.3135 = 7.1891 < 9.3459] w=0.1077 to align # Constraint # added constraint: constraint((T0361)T127.CB, (T0361)T154.CB) [> 2.7266 = 4.5443 < 5.9076] w=0.1077 to align # Constraint # added constraint: constraint((T0361)T127.CB, (T0361)V152.CB) [> 3.2294 = 5.3823 < 6.9970] w=0.1077 to align # Constraint # added constraint: constraint((T0361)N125.CB, (T0361)L158.CB) [> 3.9059 = 6.5098 < 8.4628] w=0.1077 to align # Constraint # added constraint: constraint((T0361)N125.CB, (T0361)A138.CB) [> 4.0630 = 6.7716 < 8.8031] w=0.1031 to align # Constraint # added constraint: constraint((T0361)D110.CB, (T0361)D139.CB) [> 3.6978 = 6.1631 < 8.0120] w=0.1015 to align # Constraint # added constraint: constraint((T0361)A141.CB, (T0361)T161.CB) [> 4.7724 = 7.9540 < 10.3402] w=0.0986 to align # Constraint # added constraint: constraint((T0361)Y75.CB, (T0361)P105.CB) [> 3.4261 = 5.7101 < 7.4232] w=0.0986 to align # Constraint # added constraint: constraint((T0361)E48.CB, (T0361)F91.CB) [> 3.5198 = 5.8663 < 7.6262] w=0.0957 to align # Constraint # added constraint: constraint((T0361)L64.CB, (T0361)M80.CB) [> 2.9984 = 4.9973 < 6.4965] w=0.0957 to align # Constraint # added constraint: constraint((T0361)V9.CB, (T0361)L19.CB) [> 3.4989 = 5.8314 < 7.5809] w=0.0947 to align # Constraint # added constraint: constraint((T0361)V9.CB, (T0361)F20.CB) [> 3.8724 = 6.4541 < 8.3903] w=0.0785 to align # Constraint # added constraint: constraint((T0361)I67.CB, (T0361)F115.CB) [> 2.9653 = 4.9421 < 6.4247] w=0.0782 to align # Constraint # added constraint: constraint((T0361)P63.CB, (T0361)I116.CB) [> 4.6443 = 7.7405 < 10.0626] w=0.0766 to align # Constraint # added constraint: constraint((T0361)V152.CB, (T0361)T163.CB) [> 3.2313 = 5.3855 < 7.0011] w=0.0723 to align # Constraint # added constraint: constraint((T0361)D110.CB, (T0361)L158.CB) [> 4.3389 = 7.2316 < 9.4010] w=0.0723 to align # Constraint # added constraint: constraint((T0361)I116.CB, (T0361)D139.CB) [> 4.2915 = 7.1524 < 9.2982] w=0.0723 to align # Constraint # added constraint: constraint((T0361)Y94.CB, (T0361)T162.CB) [> 4.4804 = 7.4673 < 9.7075] w=0.0723 to align # Constraint # added constraint: constraint((T0361)E47.CB, (T0361)I67.CB) [> 4.1392 = 6.8987 < 8.9684] w=0.0670 to align # Constraint # added constraint: constraint((T0361)S21.CB, (T0361)L98.CB) [> 4.5443 = 7.5738 < 9.8460] w=0.0657 to align # Constraint # added constraint: constraint((T0361)F91.CB, (T0361)P105.CB) [> 4.6274 = 7.7123 < 10.0260] w=0.0647 to align # Constraint # added constraint: constraint((T0361)I34.CB, (T0361)I67.CB) [> 4.3381 = 7.2301 < 9.3992] w=0.0626 to align # Constraint # added constraint: constraint((T0361)K55.CB, (T0361)D68.CB) [> 3.9794 = 6.6323 < 8.6220] w=0.0626 to align # Constraint # added constraint: constraint((T0361)F42.CB, (T0361)L98.CB) [> 4.7387 = 7.8978 < 10.2672] w=0.0616 to align # Constraint # added constraint: constraint((T0361)F42.CB, (T0361)E51.CB) [> 3.5010 = 5.8351 < 7.5856] w=0.0523 to align # Constraint # added constraint: constraint((T0361)V142.CB, (T0361)T162.CB) [> 3.8344 = 6.3907 < 8.3079] w=0.0523 to align # Constraint # added constraint: constraint((T0361)A138.CB, (T0361)T154.CB) [> 3.1049 = 5.1748 < 6.7272] w=0.0523 to align # Constraint # added constraint: constraint((T0361)P63.CB, (T0361)F137.CB) [> 3.8747 = 6.4578 < 8.3951] w=0.0523 to align # Constraint # added constraint: constraint((T0361)L71.CB, (T0361)L128.CB) [> 4.0176 = 6.6960 < 8.7048] w=0.0523 to align # Constraint # added constraint: constraint((T0361)I67.CB, (T0361)D130.CB) [> 4.6244 = 7.7073 < 10.0196] w=0.0523 to align # Constraint # added constraint: constraint((T0361)I67.CB, (T0361)L128.CB) [> 3.4172 = 5.6953 < 7.4039] w=0.0523 to align # Constraint # added constraint: constraint((T0361)I67.CB, (T0361)T127.CB) [> 3.2164 = 5.3606 < 6.9688] w=0.0523 to align # Constraint # added constraint: constraint((T0361)V43.CB, (T0361)A76.CB) [> 4.0634 = 6.7723 < 8.8039] w=0.0508 to align # Constraint # added constraint: constraint((T0361)L10.CB, (T0361)L98.CB) [> 3.8439 = 6.4064 < 8.3284] w=0.0486 to align # Constraint # added constraint: constraint((T0361)L64.CB, (T0361)V152.CB) [> 4.2680 = 7.1133 < 9.2473] w=0.0383 to align # Constraint # added constraint: constraint((T0361)L71.CB, (T0361)V152.CB) [> 4.7978 = 7.9964 < 10.3953] w=0.0383 to align # Constraint # added constraint: constraint((T0361)R147.CB, (T0361)L158.CB) [> 3.7260 = 6.2100 < 8.0730] w=0.0383 to align # Constraint # added constraint: constraint((T0361)Y129.CB, (T0361)T161.CB) [> 3.4737 = 5.7895 < 7.5264] w=0.0372 to align # Constraint # added constraint: constraint((T0361)K55.CB, (T0361)T154.CB) [> 4.0796 = 6.7994 < 8.8392] w=0.0362 to align # Constraint # added constraint: constraint((T0361)D7.CB, (T0361)L167.CB) [> 4.7598 = 7.9330 < 10.3129] w=0.0362 to align # Constraint # added constraint: constraint((T0361)V9.CB, (T0361)N18.CB) [> 4.7976 = 7.9959 < 10.3947] w=0.0362 to align # Constraint # added constraint: constraint((T0361)I116.CB, (T0361)A138.CB) [> 3.2709 = 5.4514 < 7.0869] w=0.0362 to align # Constraint # added constraint: constraint((T0361)I116.CB, (T0361)V142.CB) [> 4.2175 = 7.0292 < 9.1379] w=0.0362 to align # Constraint # added constraint: constraint((T0361)I67.CB, (T0361)I116.CB) [> 3.7997 = 6.3328 < 8.2327] w=0.0318 to align # Constraint # added constraint: constraint((T0361)I116.CB, (T0361)M151.CB) [> 3.5997 = 5.9995 < 7.7993] w=0.0308 to align # SetCost created cost = # ( 1.0000 * align ) # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0361/ # command:# reading script from file servers-clean.under # Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0361/decoys/ # ReadConformPDB reading from PDB file ROBETTA_deNovo1.repack.pdb.gz looking for model 1 # ReadConformPDB reading from PDB file ROBETTA_deNovo10.repack.pdb.gz looking for model 1 # ReadConformPDB reading from PDB file ROBETTA_deNovo2.repack.pdb.gz looking for model 1 # Found a chain break before 136 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file ROBETTA_deNovo3.repack.pdb.gz looking for model 1 # Found a chain break before 116 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file ROBETTA_deNovo4.repack.pdb.gz looking for model 1 # ReadConformPDB reading from PDB file ROBETTA_deNovo5.repack.pdb.gz looking for model 1 # ReadConformPDB reading from PDB file ROBETTA_deNovo6.repack.pdb.gz looking for model 1 # ReadConformPDB reading from PDB file ROBETTA_deNovo7.repack.pdb.gz looking for model 1 # ReadConformPDB reading from PDB file ROBETTA_deNovo8.repack.pdb.gz looking for model 1 # ReadConformPDB reading from PDB file ROBETTA_deNovo9.repack.pdb.gz looking for model 1 # ReadConformPDB reading from PDB file ROBETTA_parent1.repack.pdb.gz looking for model 1 # Found a chain break before 150 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file ROBETTA_parent2.repack.pdb.gz looking for model 1 # Found a chain break before 152 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file ROBETTA_parent3.repack.pdb.gz looking for model 1 # Found a chain break before 146 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file ROBETTA_parent4.repack.pdb.gz looking for model 1 # Found a chain break before 146 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file ROBETTA_parent5.repack.pdb.gz looking for model 1 # Found a chain break before 149 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS4.pdb.gz looking for model 1 # Found a chain break before 154 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS2.pdb.gz looking for model 1 # Found a chain break before 154 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_RECOM_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS5 # ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1 # Found a chain break before 153 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS1 # ReadConformPDB reading from PDB file servers/3Dpro_TS2.pdb.gz looking for model 1 # Found a chain break before 141 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS2 # ReadConformPDB reading from PDB file servers/3Dpro_TS3.pdb.gz looking for model 1 # Found a chain break before 125 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS3 # ReadConformPDB reading from PDB file servers/3Dpro_TS4.pdb.gz looking for model 1 # Found a chain break before 4 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS4 # ReadConformPDB reading from PDB file servers/3Dpro_TS5.pdb.gz looking for model 1 # Found a chain break before 115 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS5 # ReadConformPDB reading from PDB file servers/ABIpro_TS1.pdb.gz looking for model 1 # Found a chain break before 153 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS1 # ReadConformPDB reading from PDB file servers/ABIpro_TS2.pdb.gz looking for model 1 # Found a chain break before 125 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS2 # ReadConformPDB reading from PDB file servers/ABIpro_TS3.pdb.gz looking for model 1 # Found a chain break before 159 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS3 # ReadConformPDB reading from PDB file servers/ABIpro_TS4.pdb.gz looking for model 1 # Found a chain break before 109 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS4 # ReadConformPDB reading from PDB file servers/ABIpro_TS5.pdb.gz looking for model 1 # Found a chain break before 151 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS5 # ReadConformPDB reading from PDB file servers/BayesHH_TS1.pdb.gz looking for model 1 # Found a chain break before 155 # copying to AlignedFragments data structure # naming current conformation BayesHH_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS1.pdb.gz looking for model 1 # naming current conformation Bilab-ENABLE_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS2.pdb.gz looking for model 1 # Found a chain break before 168 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS2 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS3.pdb.gz looking for model 1 # naming current conformation Bilab-ENABLE_TS3 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS4.pdb.gz looking for model 1 # Found a chain break before 120 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS4 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS5.pdb.gz looking for model 1 # Found a chain break before 168 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS5 # ReadConformPDB reading from PDB file servers/CIRCLE_TS1.pdb.gz looking for model 1 # Found a chain break before 161 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS1 # ReadConformPDB reading from PDB file servers/CIRCLE_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS2 # ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1 # Found a chain break before 168 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS3 # ReadConformPDB reading from PDB file servers/CIRCLE_TS4.pdb.gz looking for model 1 # Found a chain break before 168 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS4 # ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1 # Found a chain break before 168 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS5 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS1 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS2 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS3 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS4 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS5 # ReadConformPDB reading from PDB file servers/Distill_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation Distill_TS1 # ReadConformPDB reading from PDB file servers/Distill_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation Distill_TS2 # ReadConformPDB reading from PDB file servers/Distill_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation Distill_TS3 # ReadConformPDB reading from PDB file servers/Distill_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation Distill_TS4 # ReadConformPDB reading from PDB file servers/Distill_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation Distill_TS5 # ReadConformPDB reading from PDB file servers/FAMSD_TS1.pdb.gz looking for model 1 # Found a chain break before 161 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS1 # ReadConformPDB reading from PDB file servers/FAMSD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation FAMSD_TS2 # ReadConformPDB reading from PDB file servers/FAMSD_TS3.pdb.gz looking for model 1 # Found a chain break before 168 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS3 # ReadConformPDB reading from PDB file servers/FAMSD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation FAMSD_TS4 # ReadConformPDB reading from PDB file servers/FAMSD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FAMSD_TS5 # ReadConformPDB reading from PDB file servers/FAMS_TS1.pdb.gz looking for model 1 # Found a chain break before 168 # copying to AlignedFragments data structure # naming current conformation FAMS_TS1 # ReadConformPDB reading from PDB file servers/FAMS_TS2.pdb.gz looking for model 1 # Found a chain break before 168 # copying to AlignedFragments data structure # naming current conformation FAMS_TS2 # ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1 # Found a chain break before 161 # copying to AlignedFragments data structure # naming current conformation FAMS_TS3 # ReadConformPDB reading from PDB file servers/FAMS_TS4.pdb.gz looking for model 1 # Found a chain break before 161 # copying to AlignedFragments data structure # naming current conformation FAMS_TS4 # ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation FAMS_TS5 # ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1 # Found a chain break before 161 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS1 # ReadConformPDB reading from PDB file servers/FOLDpro_TS2.pdb.gz looking for model 1 # Found a chain break before 101 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS2 # ReadConformPDB reading from PDB file servers/FOLDpro_TS3.pdb.gz looking for model 1 # Found a chain break before 80 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS3 # ReadConformPDB reading from PDB file servers/FOLDpro_TS4.pdb.gz looking for model 1 # Found a chain break before 134 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS4 # ReadConformPDB reading from PDB file servers/FOLDpro_TS5.pdb.gz looking for model 1 # Found a chain break before 120 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS5 # ReadConformPDB reading from PDB file servers/FORTE1_AL1.pdb.gz looking for model 1 Skipped atom 223, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation FORTE1_AL1 # ReadConformPDB reading from PDB file servers/FORTE1_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation FORTE1_AL2 # ReadConformPDB reading from PDB file servers/FORTE1_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation FORTE1_AL3 # ReadConformPDB reading from PDB file servers/FORTE1_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation FORTE1_AL4 # ReadConformPDB reading from PDB file servers/FORTE1_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL5 # ReadConformPDB reading from PDB file servers/FORTE2_AL1.pdb.gz looking for model 1 Skipped atom 223, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation FORTE2_AL1 # ReadConformPDB reading from PDB file servers/FORTE2_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation FORTE2_AL2 # ReadConformPDB reading from PDB file servers/FORTE2_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE2_AL3 # ReadConformPDB reading from PDB file servers/FORTE2_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation FORTE2_AL4 # ReadConformPDB reading from PDB file servers/FORTE2_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation FORTE2_AL5 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS1.pdb.gz looking for model 1 # Found a chain break before 138 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS1 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS2.pdb.gz looking for model 1 # Found a chain break before 109 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS2 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS3.pdb.gz looking for model 1 # Found a chain break before 139 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS3 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS4.pdb.gz looking for model 1 # Found a chain break before 100 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS4 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS5.pdb.gz looking for model 1 # Found a chain break before 150 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS5 # ReadConformPDB reading from PDB file servers/FUGMOD_TS1.pdb.gz looking for model 1 # naming current conformation FUGMOD_TS1 # ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1 # Found a chain break before 95 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS2 # ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS3 # ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS4 # ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS5 # ReadConformPDB reading from PDB file servers/FUGUE_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGUE_AL1 # ReadConformPDB reading from PDB file servers/FUGUE_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGUE_AL2 # ReadConformPDB reading from PDB file servers/FUGUE_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation FUGUE_AL3 # ReadConformPDB reading from PDB file servers/FUGUE_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation FUGUE_AL4 # ReadConformPDB reading from PDB file servers/FUGUE_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation FUGUE_AL5 # ReadConformPDB reading from PDB file servers/FUNCTION_TS1.pdb.gz looking for model 1 # Found a chain break before 168 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS1 # ReadConformPDB reading from PDB file servers/FUNCTION_TS2.pdb.gz looking for model 1 # Found a chain break before 168 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS2 # ReadConformPDB reading from PDB file servers/FUNCTION_TS3.pdb.gz looking for model 1 # Found a chain break before 168 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS3 # ReadConformPDB reading from PDB file servers/FUNCTION_TS4.pdb.gz looking for model 1 # Found a chain break before 168 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS4 # ReadConformPDB reading from PDB file servers/FUNCTION_TS5.pdb.gz looking for model 1 # Found a chain break before 168 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS5 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS1 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS2.pdb.gz looking for model 1 # Found a chain break before 76 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS2 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1 # Found a chain break before 63 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS3 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS4.pdb.gz looking for model 1 # Found a chain break before 95 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS4 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS5.pdb.gz looking for model 1 # naming current conformation GeneSilicoMetaServer_TS5 # ReadConformPDB reading from PDB file servers/HHpred1_TS1.pdb.gz looking for model 1 # Found a chain break before 43 # copying to AlignedFragments data structure # naming current conformation HHpred1_TS1 # ReadConformPDB reading from PDB file servers/HHpred2_TS1.pdb.gz looking for model 1 # Found a chain break before 123 # copying to AlignedFragments data structure # naming current conformation HHpred2_TS1 # ReadConformPDB reading from PDB file servers/HHpred3_TS1.pdb.gz looking for model 1 # Found a chain break before 63 # copying to AlignedFragments data structure # naming current conformation HHpred3_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Huber-Torda-Server_TS2 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS3 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS4 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS5 # ReadConformPDB reading from PDB file servers/LOOPP_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation LOOPP_TS1 # ReadConformPDB reading from PDB file servers/LOOPP_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation LOOPP_TS2 # ReadConformPDB reading from PDB file servers/LOOPP_TS3.pdb.gz looking for model 1 # naming current conformation LOOPP_TS3 # ReadConformPDB reading from PDB file servers/LOOPP_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation LOOPP_TS4 # ReadConformPDB reading from PDB file servers/LOOPP_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation LOOPP_TS5 # ReadConformPDB reading from PDB file servers/MIG_FROST_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation MIG_FROST_AL1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS1.pdb.gz looking for model 1 # naming current conformation Ma-OPUS-server2_TS1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS2.pdb.gz looking for model 1 # Found a chain break before 14 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS3.pdb.gz looking for model 1 # Found a chain break before 136 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS4.pdb.gz looking for model 1 # Found a chain break before 125 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS5.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS5 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS1.pdb.gz looking for model 1 # Found a chain break before 156 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS2.pdb.gz looking for model 1 # Found a chain break before 121 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS3.pdb.gz looking for model 1 # Found a chain break before 119 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS4.pdb.gz looking for model 1 # Found a chain break before 104 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS5.pdb.gz looking for model 1 # Found a chain break before 56 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS5 # ReadConformPDB reading from PDB file servers/MetaTasser_TS1.pdb.gz looking for model 1 # Found a chain break before 155 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS1 # ReadConformPDB reading from PDB file servers/MetaTasser_TS2.pdb.gz looking for model 1 # Found a chain break before 167 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS2 # ReadConformPDB reading from PDB file servers/MetaTasser_TS3.pdb.gz looking for model 1 # Found a chain break before 167 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS3 # ReadConformPDB reading from PDB file servers/MetaTasser_TS4.pdb.gz looking for model 1 # Found a chain break before 168 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS4 # ReadConformPDB reading from PDB file servers/MetaTasser_TS5.pdb.gz looking for model 1 # Found a chain break before 165 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS5 # ReadConformPDB reading from PDB file servers/NN_PUT_lab_TS1.pdb.gz looking for model 1 # naming current conformation NN_PUT_lab_TS1 # ReadConformPDB reading from PDB file servers/POMYSL_TS1.pdb.gz looking for model 1 # Found a chain break before 94 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS1 # ReadConformPDB reading from PDB file servers/POMYSL_TS2.pdb.gz looking for model 1 # Found a chain break before 135 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS2 # ReadConformPDB reading from PDB file servers/POMYSL_TS3.pdb.gz looking for model 1 # Found a chain break before 135 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS3 # ReadConformPDB reading from PDB file servers/POMYSL_TS4.pdb.gz looking for model 1 # Found a chain break before 117 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS4 # ReadConformPDB reading from PDB file servers/POMYSL_TS5.pdb.gz looking for model 1 # Found a chain break before 136 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS1.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS2.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS3.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS4.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS5.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO_TS1.pdb.gz looking for model 1 # Found a chain break before 127 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1 # naming current conformation PROTINFO_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1 # Found a chain break before 121 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1 # naming current conformation PROTINFO_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1 # Found a chain break before 84 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS5 # ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation Pcons6_TS1 # ReadConformPDB reading from PDB file servers/Pcons6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation Pcons6_TS2 # ReadConformPDB reading from PDB file servers/Pcons6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation Pcons6_TS3 # ReadConformPDB reading from PDB file servers/Pcons6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation Pcons6_TS4 # ReadConformPDB reading from PDB file servers/Pcons6_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation Pcons6_TS5 # ReadConformPDB reading from PDB file servers/Phyre-1_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation Phyre-1_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS1.pdb.gz looking for model 1 # Found a chain break before 125 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS2.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS2 # ReadConformPDB reading from PDB file servers/Phyre-2_TS3.pdb.gz looking for model 1 # Found a chain break before 126 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS3 # ReadConformPDB reading from PDB file servers/Phyre-2_TS4.pdb.gz looking for model 1 # Found a chain break before 93 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS4 # ReadConformPDB reading from PDB file servers/Phyre-2_TS5.pdb.gz looking for model 1 # Found a chain break before 125 # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS5 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS1.pdb.gz looking for model 1 # naming current conformation Pmodeller6_TS1 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1 # naming current conformation Pmodeller6_TS2 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1 # Found a chain break before 127 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS3 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1 # Found a chain break before 146 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS4 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS1.pdb.gz looking for model 1 # Found a chain break before 164 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS2.pdb.gz looking for model 1 # Found a chain break before 146 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS3.pdb.gz looking for model 1 # Found a chain break before 125 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS4.pdb.gz looking for model 1 # Found a chain break before 119 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS5.pdb.gz looking for model 1 # Found a chain break before 98 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS5 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS1.pdb.gz looking for model 1 # Found a chain break before 168 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS1 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS2.pdb.gz looking for model 1 # Found a chain break before 159 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS2 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS3.pdb.gz looking for model 1 # Found a chain break before 116 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS3 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS4.pdb.gz looking for model 1 # Found a chain break before 60 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS4 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS5.pdb.gz looking for model 1 # Found a chain break before 62 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR_TS1.pdb.gz looking for model 1 # Found a chain break before 81 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR_TS2.pdb.gz looking for model 1 # naming current conformation RAPTOR_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR_TS3.pdb.gz looking for model 1 # Found a chain break before 167 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR_TS4.pdb.gz looking for model 1 # Found a chain break before 142 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR_TS5.pdb.gz looking for model 1 # Found a chain break before 42 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS5 # ReadConformPDB reading from PDB file servers/ROBETTA_TS1.pdb.gz looking for model 1 # Found a chain break before 150 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS1 # ReadConformPDB reading from PDB file servers/ROBETTA_TS2.pdb.gz looking for model 1 # naming current conformation ROBETTA_TS2 # ReadConformPDB reading from PDB file servers/ROBETTA_TS3.pdb.gz looking for model 1 # Found a chain break before 152 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS3 # ReadConformPDB reading from PDB file servers/ROBETTA_TS4.pdb.gz looking for model 1 # Found a chain break before 136 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS4 # ReadConformPDB reading from PDB file servers/ROBETTA_TS5.pdb.gz looking for model 1 # Found a chain break before 146 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS5 # ReadConformPDB reading from PDB file servers/ROKKY_TS1.pdb.gz looking for model 1 # Found a chain break before 81 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS1 # ReadConformPDB reading from PDB file servers/ROKKY_TS2.pdb.gz looking for model 1 # Found a chain break before 93 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS2 # ReadConformPDB reading from PDB file servers/SAM-T02_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL1 # ReadConformPDB reading from PDB file servers/SAM-T02_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL2 # ReadConformPDB reading from PDB file servers/SAM-T02_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL3 # ReadConformPDB reading from PDB file servers/SAM-T02_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL4 # ReadConformPDB reading from PDB file servers/SAM-T02_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL5 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS1.pdb.gz looking for model 1 # Found a chain break before 137 # copying to AlignedFragments data structure # naming current conformation SAM_T06_server_TS1 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS2 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS3 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS4 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS5 # ReadConformPDB reading from PDB file servers/SP3_TS1.pdb.gz looking for model 1 # Found a chain break before 100 # copying to AlignedFragments data structure # naming current conformation SP3_TS1 # ReadConformPDB reading from PDB file servers/SP3_TS2.pdb.gz looking for model 1 # naming current conformation SP3_TS2 # ReadConformPDB reading from PDB file servers/SP3_TS3.pdb.gz looking for model 1 # naming current conformation SP3_TS3 # ReadConformPDB reading from PDB file servers/SP3_TS4.pdb.gz looking for model 1 # Found a chain break before 142 # copying to AlignedFragments data structure # naming current conformation SP3_TS4 # ReadConformPDB reading from PDB file servers/SP3_TS5.pdb.gz looking for model 1 # Found a chain break before 149 # copying to AlignedFragments data structure # naming current conformation SP3_TS5 # ReadConformPDB reading from PDB file servers/SP4_TS1.pdb.gz looking for model 1 # Found a chain break before 100 # copying to AlignedFragments data structure # naming current conformation SP4_TS1 # ReadConformPDB reading from PDB file servers/SP4_TS2.pdb.gz looking for model 1 # Found a chain break before 63 # copying to AlignedFragments data structure # naming current conformation SP4_TS2 # ReadConformPDB reading from PDB file servers/SP4_TS3.pdb.gz looking for model 1 # naming current conformation SP4_TS3 # ReadConformPDB reading from PDB file servers/SP4_TS4.pdb.gz looking for model 1 # Found a chain break before 107 # copying to AlignedFragments data structure # naming current conformation SP4_TS4 # ReadConformPDB reading from PDB file servers/SP4_TS5.pdb.gz looking for model 1 # naming current conformation SP4_TS5 # ReadConformPDB reading from PDB file servers/SPARKS2_TS1.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS1 # ReadConformPDB reading from PDB file servers/SPARKS2_TS2.pdb.gz looking for model 1 # Found a chain break before 59 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS2 # ReadConformPDB reading from PDB file servers/SPARKS2_TS3.pdb.gz looking for model 1 # Found a chain break before 131 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS3 # ReadConformPDB reading from PDB file servers/SPARKS2_TS4.pdb.gz looking for model 1 # Found a chain break before 87 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS4 # ReadConformPDB reading from PDB file servers/SPARKS2_TS5.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation UNI-EID_bnmx_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS2 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS3 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS4 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_expm_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation UNI-EID_expm_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL2 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL3.pdb.gz looking for model 1 Skipped atom 51, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 56, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 97, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 142, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 167, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 336, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 421, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 478, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz Skipped atom 487, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL3 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL4 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL5 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS1.pdb.gz looking for model 1 # Found a chain break before 162 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS1 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS2.pdb.gz looking for model 1 # Found a chain break before 147 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS2 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS3.pdb.gz looking for model 1 # Found a chain break before 140 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS3 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS4.pdb.gz looking for model 1 # Found a chain break before 153 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS4 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS5.pdb.gz looking for model 1 # Found a chain break before 167 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS5 # ReadConformPDB reading from PDB file servers/beautshot_TS1.pdb.gz looking for model 1 # Found a chain break before 168 # copying to AlignedFragments data structure # naming current conformation beautshot_TS1 # ReadConformPDB reading from PDB file servers/beautshotbase_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation beautshotbase_TS1 # ReadConformPDB reading from PDB file servers/forecast-s_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation forecast-s_AL1 # ReadConformPDB reading from PDB file servers/forecast-s_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation forecast-s_AL2 # ReadConformPDB reading from PDB file servers/forecast-s_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation forecast-s_AL3 # ReadConformPDB reading from PDB file servers/forecast-s_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation forecast-s_AL4 # ReadConformPDB reading from PDB file servers/forecast-s_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation forecast-s_AL5 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1 # Found a chain break before 136 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS2.pdb.gz looking for model 1 # Found a chain break before 128 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS3.pdb.gz looking for model 1 # Found a chain break before 53 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS4.pdb.gz looking for model 1 # Found a chain break before 146 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS5.pdb.gz looking for model 1 # Found a chain break before 18 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS1.pdb.gz looking for model 1 # Found a chain break before 167 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS2.pdb.gz looking for model 1 WARNING: atoms too close: (T0361)Q12.O and (T0361)L13.N only 0.000 apart, marking (T0361)L13.N as missing WARNING: atoms too close: (T0361)I29.O and (T0361)L30.N only 0.000 apart, marking (T0361)L30.N as missing WARNING: atoms too close: (T0361)D102.O and (T0361)E103.N only 0.000 apart, marking (T0361)E103.N as missing # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS3.pdb.gz looking for model 1 # Found a chain break before 168 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS4.pdb.gz looking for model 1 WARNING: atoms too close: (T0361)A126.O and (T0361)T127.N only 0.000 apart, marking (T0361)T127.N as missing # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS5.pdb.gz looking for model 1 # Found a chain break before 168 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv_TS2.pdb.gz looking for model 1 # Found a chain break before 58 # copying to AlignedFragments data structure # naming current conformation karypis.srv_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS5 # ReadConformPDB reading from PDB file servers/keasar-server_TS1.pdb.gz looking for model 1 # naming current conformation keasar-server_TS1 # ReadConformPDB reading from PDB file servers/keasar-server_TS2.pdb.gz looking for model 1 # naming current conformation keasar-server_TS2 # ReadConformPDB reading from PDB file servers/keasar-server_TS3.pdb.gz looking for model 1 # naming current conformation keasar-server_TS3 # ReadConformPDB reading from PDB file servers/keasar-server_TS4.pdb.gz looking for model 1 # naming current conformation keasar-server_TS4 # ReadConformPDB reading from PDB file servers/keasar-server_TS5.pdb.gz looking for model 1 # naming current conformation keasar-server_TS5 # ReadConformPDB reading from PDB file servers/mGen-3D_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation mGen-3D_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation nFOLD_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation nFOLD_TS2 # ReadConformPDB reading from PDB file servers/nFOLD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation nFOLD_TS3 # ReadConformPDB reading from PDB file servers/nFOLD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation nFOLD_TS4 # ReadConformPDB reading from PDB file servers/nFOLD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation nFOLD_TS5 # ReadConformPDB reading from PDB file servers/panther2_TS1.pdb.gz looking for model 1 WARNING: atoms too close: (T0361)P63.N and (T0361)L64.N only 0.000 apart, marking (T0361)L64.N as missing WARNING: atoms too close: (T0361)P63.CA and (T0361)L64.CA only 0.000 apart, marking (T0361)L64.CA as missing WARNING: atoms too close: (T0361)P63.CB and (T0361)L64.CB only 0.000 apart, marking (T0361)L64.CB as missing WARNING: atoms too close: (T0361)P63.O and (T0361)L64.O only 0.000 apart, marking (T0361)L64.O as missing WARNING: atoms too close: (T0361)P63.C and (T0361)L64.C only 0.000 apart, marking (T0361)L64.C as missing WARNING: atoms too close: (T0361)L64.N and (T0361)D65.N only 0.000 apart, marking (T0361)L64.N as missing WARNING: atoms too close: (T0361)P63.N and (T0361)D65.N only 0.000 apart, marking (T0361)D65.N as missing WARNING: atoms too close: (T0361)L64.CA and (T0361)D65.CA only 0.000 apart, marking (T0361)D65.CA as missing WARNING: atoms too close: (T0361)P63.CA and (T0361)D65.CA only 0.000 apart, marking (T0361)D65.CA as missing WARNING: atoms too close: (T0361)L64.CB and (T0361)D65.CB only 0.000 apart, marking (T0361)D65.CB as missing WARNING: atoms too close: (T0361)P63.CB and (T0361)D65.CB only 0.000 apart, marking (T0361)D65.CB as missing WARNING: atoms too close: (T0361)L64.O and (T0361)D65.O only 0.000 apart, marking (T0361)D65.O as missing WARNING: atoms too close: (T0361)P63.O and (T0361)D65.O only 0.000 apart, marking (T0361)D65.O as missing WARNING: atoms too close: (T0361)L64.C and (T0361)D65.C only 0.000 apart, marking (T0361)D65.C as missing WARNING: atoms too close: (T0361)P63.C and (T0361)D65.C only 0.000 apart, marking (T0361)D65.C as missing WARNING: atoms too close: (T0361)D65.N and (T0361)D66.N only 0.000 apart, marking (T0361)D65.N as missing WARNING: atoms too close: (T0361)L64.N and (T0361)D66.N only 0.000 apart, marking (T0361)L64.N as missing WARNING: atoms too close: (T0361)P63.N and (T0361)D66.N only 0.000 apart, marking (T0361)D66.N as missing WARNING: atoms too close: (T0361)D65.CA and (T0361)D66.CA only 0.000 apart, marking (T0361)D66.CA as missing WARNING: atoms too close: (T0361)L64.CA and (T0361)D66.CA only 0.000 apart, marking (T0361)D66.CA as missing WARNING: atoms too close: (T0361)P63.CA and (T0361)D66.CA only 0.000 apart, marking (T0361)D66.CA as missing WARNING: atoms too close: (T0361)D65.CB and (T0361)D66.CB only 0.000 apart, marking (T0361)D66.CB as missing WARNING: atoms too close: (T0361)L64.CB and (T0361)D66.CB only 0.000 apart, marking (T0361)D66.CB as missing WARNING: atoms too close: (T0361)P63.CB and (T0361)D66.CB only 0.000 apart, marking (T0361)D66.CB as missing WARNING: atoms too close: (T0361)D65.O and (T0361)D66.O only 0.000 apart, marking (T0361)D66.O as missing WARNING: atoms too close: (T0361)L64.O and (T0361)D66.O only 0.000 apart, marking (T0361)D66.O as missing WARNING: atoms too close: (T0361)P63.O and (T0361)D66.O only 0.000 apart, marking (T0361)D66.O as missing WARNING: atoms too close: (T0361)D65.C and (T0361)D66.C only 0.000 apart, marking (T0361)D66.C as missing WARNING: atoms too close: (T0361)L64.C and (T0361)D66.C only 0.000 apart, marking (T0361)D66.C as missing WARNING: atoms too close: (T0361)P63.C and (T0361)D66.C only 0.000 apart, marking (T0361)D66.C as missing WARNING: atoms too close: (T0361)D66.N and (T0361)I67.N only 0.000 apart, marking (T0361)D66.N as missing WARNING: atoms too close: (T0361)D65.N and (T0361)I67.N only 0.000 apart, marking (T0361)D65.N as missing WARNING: atoms too close: (T0361)L64.N and (T0361)I67.N only 0.000 apart, marking (T0361)L64.N as missing WARNING: atoms too close: (T0361)P63.N and (T0361)I67.N only 0.000 apart, marking (T0361)I67.N as missing WARNING: atoms too close: (T0361)D66.CA and (T0361)I67.CA only 0.000 apart, marking (T0361)I67.CA as missing WARNING: atoms too close: (T0361)D65.CA and (T0361)I67.CA only 0.000 apart, marking (T0361)I67.CA as missing WARNING: atoms too close: (T0361)L64.CA and (T0361)I67.CA only 0.000 apart, marking (T0361)I67.CA as missing WARNING: atoms too close: (T0361)P63.CA and (T0361)I67.CA only 0.000 apart, marking (T0361)I67.CA as missing WARNING: atoms too close: (T0361)D66.CB and (T0361)I67.CB only 0.000 apart, marking (T0361)I67.CB as missing WARNING: atoms too close: (T0361)D65.CB and (T0361)I67.CB only 0.000 apart, marking (T0361)I67.CB as missing WARNING: atoms too close: (T0361)L64.CB and (T0361)I67.CB only 0.000 apart, marking (T0361)I67.CB as missing WARNING: atoms too close: (T0361)P63.CB and (T0361)I67.CB only 0.000 apart, marking (T0361)I67.CB as missing WARNING: atoms too close: (T0361)D66.O and (T0361)I67.O only 0.000 apart, marking (T0361)I67.O as missing WARNING: atoms too close: (T0361)D65.O and (T0361)I67.O only 0.000 apart, marking (T0361)I67.O as missing WARNING: atoms too close: (T0361)L64.O and (T0361)I67.O only 0.000 apart, marking (T0361)I67.O as missing WARNING: atoms too close: (T0361)P63.O and (T0361)I67.O only 0.000 apart, marking (T0361)I67.O as missing WARNING: atoms too close: (T0361)D66.C and (T0361)I67.C only 0.000 apart, marking (T0361)I67.C as missing WARNING: atoms too close: (T0361)D65.C and (T0361)I67.C only 0.000 apart, marking (T0361)I67.C as missing WARNING: atoms too close: (T0361)L64.C and (T0361)I67.C only 0.000 apart, marking (T0361)I67.C as missing WARNING: atoms too close: (T0361)P63.C and (T0361)I67.C only 0.000 apart, marking (T0361)I67.C as missing # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # naming current conformation panther2_TS1 # ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0361 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation shub_TS1 # command:Using radius: 8.0000 Using models AND alignments for constraints model score 1.8949 model score 1.8685 model score 1.7097 model score 1.5580 model score 1.4798 model score 1.5385 model score 1.8146 model score 1.6794 model score 1.7753 model score 1.7976 model score 1.8492 model score 1.9235 model score 1.6561 model score 1.6839 model score 1.6879 model score 1.7819 model score 1.9788 model score 1.8545 model score 2.0034 model score 1.9980 model score 1.8997 model score 1.9890 model score 1.9932 model score 2.0944 model score 2.0787 model score 1.7289 model score 1.9384 model score 1.7201 model score 2.2952 model score 1.9600 model score 1.3656 model score 1.9948 model score 1.3768 model score 2.0532 model score 1.8730 model score 1.3656 model score 1.3768 model score 1.4148 model score 1.4596 model score 1.4523 model score 1.5796 model score 1.3789 model score 1.8802 model score 1.6782 model score 1.9770 model score 1.9118 model score 2.0141 model score 1.5803 model score 2.0241 model score 1.6751 model score 2.2670 model score 1.5790 model score 2.0320 model score 1.5531 model score 2.0041 model score 2.0584 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 2.0129 model score 1.8357 model score 1.8427 model score 1.8489 model score 1.9104 model score 1.6672 model score 2.0241 model score 2.0141 model score 2.0129 model score 1.8357 model score 2.0850 model score 1.8305 model score 2.0542 model score 2.2128 model score 1.5559 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 2.1299 model score 1.9483 model score 2.0283 model score 2.1062 model score 2.1274 model score 1.9231 model score 1.6898 model score 2.0179 model score 2.0404 model score 1.2825 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 2.0646 model score 1.9892 model score 1.8339 model score 2.0042 model score 1.8588 model score 2.2650 model score 1.3847 model score 1.8133 model score 1.6909 model score 1.9145 model score 1.4995 model score 1.6673 model score 2.2405 model score 1.6285 model score 1.7155 model score 1.5100 model score 1.4056 model score 1.5275 model score 1.6713 model score 1.5592 model score 1.7213 model score 1.5904 model score 1.8398 model score 1.2771 model score 1.4504 model score 1.5606 model score 1.4777 model score 1.6825 model score 1.3091 model score 1.3446 model score 1.4448 model score 1.4445 model score 1.5127 model score 1.5060 model score 1.4217 model score 1.3993 model score 1.4397 model score 1.5836 model score 1.5007 model score 1.8902 model score 1.8863 model score 2.0684 model score 1.7651 model score 1.8247 model score 2.1504 model score 2.0638 model score 2.0052 model score 2.1118 model score 2.0208 model score 1.9575 model score 1.9922 model score 2.0220 model score 1.9428 model score 2.0084 model score 2.0062 model score 1.9681 model score 2.0080 model score 2.0047 model score 1.9183 model score 1.9221 model score 1.4387 model score 1.8818 model score 1.7664 model score 1.7857 model score 1.9151 model score 1.8048 model score 1.8949 model score 1.4798 model score 1.6326 model score 1.6561 model score 2.2730 model score 1.6827 model score 1.3948 model score 2.2625 model score 1.6321 model score 1.9302 model score 1.6620 model score 1.7024 model score 1.6853 model score 1.6813 model score 1.6758 model score 1.6082 model score 1.6831 model score 2.4000 model score 1.6596 model score 1.6884 model score 1.8492 model score 1.8949 model score 1.9235 model score 1.7097 model score 1.6561 model score 2.0627 model score 1.9163 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.7653 model score 0.9674 model score 1.1809 model score 1.2449 model score 1.6341 model score 1.8593 model score 1.6936 model score 1.8489 model score 1.6689 model score 2.0210 model score 1.6685 model score 1.6946 model score 1.8499 model score 1.6542 model score 1.6672 model score 1.8902 model score 1.8537 model score 2.2164 model score 1.8647 model score 2.0988 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.1600 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.4279 model score 1.3863 model score 1.3186 model score 1.3876 model score 1.4267 model score 1.6654 model score 1.4905 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.6268 model score 1.6706 model score 1.7132 model score 1.7488 model score 1.7178 model score 2.2577 model score 2.0920 model score 1.9854 model score 2.1882 model score 2.3165 model score 1.5466 model score 1.8346 model score 1.6536 model score 1.5930 model score 1.8874 model score 2.0659 model score 1.9759 model score 1.9661 model score 1.9845 model score 1.9248 model score 1.4532 model score 1.8821 model score 1.9746 model score 2.0995 model score 1.8589 model score 1.8694 model score 1.4449 model score 1.5517 USE_META, weight: 0.4173 cost: 1.8949 min: 0.9674 max: 2.4000 USE_META, weight: 0.4339 cost: 1.8685 min: 0.9674 max: 2.4000 USE_META, weight: 0.5336 cost: 1.7097 min: 0.9674 max: 2.4000 USE_META, weight: 0.6290 cost: 1.5580 min: 0.9674 max: 2.4000 USE_META, weight: 0.6781 cost: 1.4798 min: 0.9674 max: 2.4000 USE_META, weight: 0.6413 cost: 1.5385 min: 0.9674 max: 2.4000 USE_META, weight: 0.4678 cost: 1.8146 min: 0.9674 max: 2.4000 USE_META, weight: 0.5527 cost: 1.6794 min: 0.9674 max: 2.4000 USE_META, weight: 0.4925 cost: 1.7753 min: 0.9674 max: 2.4000 USE_META, weight: 0.4784 cost: 1.7976 min: 0.9674 max: 2.4000 USE_META, weight: 0.4460 cost: 1.8492 min: 0.9674 max: 2.4000 USE_META, weight: 0.3994 cost: 1.9235 min: 0.9674 max: 2.4000 USE_META, weight: 0.5674 cost: 1.6561 min: 0.9674 max: 2.4000 USE_META, weight: 0.5499 cost: 1.6839 min: 0.9674 max: 2.4000 USE_META, weight: 0.5473 cost: 1.6879 min: 0.9674 max: 2.4000 USE_META, weight: 0.4883 cost: 1.7819 min: 0.9674 max: 2.4000 USE_META, weight: 0.3646 cost: 1.9788 min: 0.9674 max: 2.4000 USE_META, weight: 0.4427 cost: 1.8545 min: 0.9674 max: 2.4000 USE_META, weight: 0.3492 cost: 2.0034 min: 0.9674 max: 2.4000 USE_META, weight: 0.3525 cost: 1.9980 min: 0.9674 max: 2.4000 USE_META, weight: 0.4143 cost: 1.8997 min: 0.9674 max: 2.4000 USE_META, weight: 0.3582 cost: 1.9890 min: 0.9674 max: 2.4000 USE_META, weight: 0.3556 cost: 1.9932 min: 0.9674 max: 2.4000 USE_META, weight: 0.2920 cost: 2.0944 min: 0.9674 max: 2.4000 USE_META, weight: 0.3018 cost: 2.0787 min: 0.9674 max: 2.4000 USE_META, weight: 0.5216 cost: 1.7289 min: 0.9674 max: 2.4000 USE_META, weight: 0.3900 cost: 1.9384 min: 0.9674 max: 2.4000 USE_META, weight: 0.5271 cost: 1.7201 min: 0.9674 max: 2.4000 USE_META, weight: 0.1658 cost: 2.2952 min: 0.9674 max: 2.4000 USE_META, weight: 0.3764 cost: 1.9600 min: 0.9674 max: 2.4000 USE_META, weight: 0.7499 cost: 1.3656 min: 0.9674 max: 2.4000 USE_META, weight: 0.3546 cost: 1.9948 min: 0.9674 max: 2.4000 USE_META, weight: 0.7428 cost: 1.3768 min: 0.9674 max: 2.4000 USE_META, weight: 0.3179 cost: 2.0532 min: 0.9674 max: 2.4000 USE_META, weight: 0.4311 cost: 1.8730 min: 0.9674 max: 2.4000 USE_META, weight: 0.7499 cost: 1.3656 min: 0.9674 max: 2.4000 USE_META, weight: 0.7428 cost: 1.3768 min: 0.9674 max: 2.4000 USE_META, weight: 0.7190 cost: 1.4148 min: 0.9674 max: 2.4000 USE_META, weight: 0.6908 cost: 1.4596 min: 0.9674 max: 2.4000 USE_META, weight: 0.6954 cost: 1.4523 min: 0.9674 max: 2.4000 USE_META, weight: 0.6154 cost: 1.5796 min: 0.9674 max: 2.4000 USE_META, weight: 0.7415 cost: 1.3789 min: 0.9674 max: 2.4000 USE_META, weight: 0.4265 cost: 1.8802 min: 0.9674 max: 2.4000 USE_META, weight: 0.5535 cost: 1.6782 min: 0.9674 max: 2.4000 USE_META, weight: 0.3658 cost: 1.9770 min: 0.9674 max: 2.4000 USE_META, weight: 0.4067 cost: 1.9118 min: 0.9674 max: 2.4000 USE_META, weight: 0.3424 cost: 2.0141 min: 0.9674 max: 2.4000 USE_META, weight: 0.6150 cost: 1.5803 min: 0.9674 max: 2.4000 USE_META, weight: 0.3362 cost: 2.0241 min: 0.9674 max: 2.4000 USE_META, weight: 0.5554 cost: 1.6751 min: 0.9674 max: 2.4000 USE_META, weight: 0.1836 cost: 2.2670 min: 0.9674 max: 2.4000 USE_META, weight: 0.6158 cost: 1.5790 min: 0.9674 max: 2.4000 USE_META, weight: 0.3312 cost: 2.0320 min: 0.9674 max: 2.4000 USE_META, weight: 0.6321 cost: 1.5531 min: 0.9674 max: 2.4000 USE_META, weight: 0.3487 cost: 2.0041 min: 0.9674 max: 2.4000 USE_META, weight: 0.3146 cost: 2.0584 min: 0.9674 max: 2.4000 USE_META, weight: 0.8055 cost: 1.2771 min: 0.9674 max: 2.4000 USE_META, weight: 0.8055 cost: 1.2771 min: 0.9674 max: 2.4000 USE_META, weight: 0.8055 cost: 1.2771 min: 0.9674 max: 2.4000 USE_META, weight: 0.8055 cost: 1.2771 min: 0.9674 max: 2.4000 USE_META, weight: 0.8055 cost: 1.2771 min: 0.9674 max: 2.4000 USE_META, weight: 0.3432 cost: 2.0129 min: 0.9674 max: 2.4000 USE_META, weight: 0.4545 cost: 1.8357 min: 0.9674 max: 2.4000 USE_META, weight: 0.4501 cost: 1.8427 min: 0.9674 max: 2.4000 USE_META, weight: 0.4462 cost: 1.8489 min: 0.9674 max: 2.4000 USE_META, weight: 0.4076 cost: 1.9104 min: 0.9674 max: 2.4000 USE_META, weight: 0.5604 cost: 1.6672 min: 0.9674 max: 2.4000 USE_META, weight: 0.3362 cost: 2.0241 min: 0.9674 max: 2.4000 USE_META, weight: 0.3424 cost: 2.0141 min: 0.9674 max: 2.4000 USE_META, weight: 0.3432 cost: 2.0129 min: 0.9674 max: 2.4000 USE_META, weight: 0.4545 cost: 1.8357 min: 0.9674 max: 2.4000 USE_META, weight: 0.2979 cost: 2.0850 min: 0.9674 max: 2.4000 USE_META, weight: 0.4578 cost: 1.8305 min: 0.9674 max: 2.4000 USE_META, weight: 0.3173 cost: 2.0542 min: 0.9674 max: 2.4000 USE_META, weight: 0.2176 cost: 2.2128 min: 0.9674 max: 2.4000 USE_META, weight: 0.6303 cost: 1.5559 min: 0.9674 max: 2.4000 USE_META, weight: 0.8055 cost: 1.2771 min: 0.9674 max: 2.4000 USE_META, weight: 0.8055 cost: 1.2771 min: 0.9674 max: 2.4000 USE_META, weight: 0.8055 cost: 1.2771 min: 0.9674 max: 2.4000 USE_META, weight: 0.8055 cost: 1.2771 min: 0.9674 max: 2.4000 USE_META, weight: 0.8055 cost: 1.2771 min: 0.9674 max: 2.4000 USE_META, weight: 0.8055 cost: 1.2771 min: 0.9674 max: 2.4000 USE_META, weight: 0.8055 cost: 1.2771 min: 0.9674 max: 2.4000 USE_META, weight: 0.8055 cost: 1.2771 min: 0.9674 max: 2.4000 USE_META, weight: 0.8055 cost: 1.2771 min: 0.9674 max: 2.4000 USE_META, weight: 0.8055 cost: 1.2771 min: 0.9674 max: 2.4000 USE_META, weight: 0.2697 cost: 2.1299 min: 0.9674 max: 2.4000 USE_META, weight: 0.3838 cost: 1.9483 min: 0.9674 max: 2.4000 USE_META, weight: 0.3335 cost: 2.0283 min: 0.9674 max: 2.4000 USE_META, weight: 0.2846 cost: 2.1062 min: 0.9674 max: 2.4000 USE_META, weight: 0.2713 cost: 2.1274 min: 0.9674 max: 2.4000 USE_META, weight: 0.3996 cost: 1.9231 min: 0.9674 max: 2.4000 USE_META, weight: 0.5462 cost: 1.6898 min: 0.9674 max: 2.4000 USE_META, weight: 0.3401 cost: 2.0179 min: 0.9674 max: 2.4000 USE_META, weight: 0.3259 cost: 2.0404 min: 0.9674 max: 2.4000 USE_META, weight: 0.8021 cost: 1.2825 min: 0.9674 max: 2.4000 USE_META, weight: 0.8055 cost: 1.2771 min: 0.9674 max: 2.4000 USE_META, weight: 0.8055 cost: 1.2771 min: 0.9674 max: 2.4000 USE_META, weight: 0.8055 cost: 1.2771 min: 0.9674 max: 2.4000 USE_META, weight: 0.8055 cost: 1.2771 min: 0.9674 max: 2.4000 USE_META, weight: 0.8055 cost: 1.2771 min: 0.9674 max: 2.4000 USE_META, weight: 0.3107 cost: 2.0646 min: 0.9674 max: 2.4000 USE_META, weight: 0.3581 cost: 1.9892 min: 0.9674 max: 2.4000 USE_META, weight: 0.4556 cost: 1.8339 min: 0.9674 max: 2.4000 USE_META, weight: 0.3486 cost: 2.0042 min: 0.9674 max: 2.4000 USE_META, weight: 0.4400 cost: 1.8588 min: 0.9674 max: 2.4000 USE_META, weight: 0.1848 cost: 2.2650 min: 0.9674 max: 2.4000 USE_META, weight: 0.7378 cost: 1.3847 min: 0.9674 max: 2.4000 USE_META, weight: 0.4686 cost: 1.8133 min: 0.9674 max: 2.4000 USE_META, weight: 0.5455 cost: 1.6909 min: 0.9674 max: 2.4000 USE_META, weight: 0.4050 cost: 1.9145 min: 0.9674 max: 2.4000 USE_META, weight: 0.6657 cost: 1.4995 min: 0.9674 max: 2.4000 USE_META, weight: 0.5603 cost: 1.6673 min: 0.9674 max: 2.4000 USE_META, weight: 0.2002 cost: 2.2405 min: 0.9674 max: 2.4000 USE_META, weight: 0.5847 cost: 1.6285 min: 0.9674 max: 2.4000 USE_META, weight: 0.5300 cost: 1.7155 min: 0.9674 max: 2.4000 USE_META, weight: 0.6591 cost: 1.5100 min: 0.9674 max: 2.4000 USE_META, weight: 0.7247 cost: 1.4056 min: 0.9674 max: 2.4000 USE_META, weight: 0.6482 cost: 1.5275 min: 0.9674 max: 2.4000 USE_META, weight: 0.5578 cost: 1.6713 min: 0.9674 max: 2.4000 USE_META, weight: 0.6282 cost: 1.5592 min: 0.9674 max: 2.4000 USE_META, weight: 0.5264 cost: 1.7213 min: 0.9674 max: 2.4000 USE_META, weight: 0.6087 cost: 1.5904 min: 0.9674 max: 2.4000 USE_META, weight: 0.4519 cost: 1.8398 min: 0.9674 max: 2.4000 USE_META, weight: 0.8055 cost: 1.2771 min: 0.9674 max: 2.4000 USE_META, weight: 0.6966 cost: 1.4504 min: 0.9674 max: 2.4000 USE_META, weight: 0.6273 cost: 1.5606 min: 0.9674 max: 2.4000 USE_META, weight: 0.6794 cost: 1.4777 min: 0.9674 max: 2.4000 USE_META, weight: 0.5507 cost: 1.6825 min: 0.9674 max: 2.4000 USE_META, weight: 0.7853 cost: 1.3091 min: 0.9674 max: 2.4000 USE_META, weight: 0.7630 cost: 1.3446 min: 0.9674 max: 2.4000 USE_META, weight: 0.7001 cost: 1.4448 min: 0.9674 max: 2.4000 USE_META, weight: 0.7003 cost: 1.4445 min: 0.9674 max: 2.4000 USE_META, weight: 0.6575 cost: 1.5127 min: 0.9674 max: 2.4000 USE_META, weight: 0.6617 cost: 1.5060 min: 0.9674 max: 2.4000 USE_META, weight: 0.7146 cost: 1.4217 min: 0.9674 max: 2.4000 USE_META, weight: 0.7287 cost: 1.3993 min: 0.9674 max: 2.4000 USE_META, weight: 0.7033 cost: 1.4397 min: 0.9674 max: 2.4000 USE_META, weight: 0.6129 cost: 1.5836 min: 0.9674 max: 2.4000 USE_META, weight: 0.6650 cost: 1.5007 min: 0.9674 max: 2.4000 USE_META, weight: 0.4203 cost: 1.8902 min: 0.9674 max: 2.4000 USE_META, weight: 0.4227 cost: 1.8863 min: 0.9674 max: 2.4000 USE_META, weight: 0.3083 cost: 2.0684 min: 0.9674 max: 2.4000 USE_META, weight: 0.4988 cost: 1.7651 min: 0.9674 max: 2.4000 USE_META, weight: 0.4614 cost: 1.8247 min: 0.9674 max: 2.4000 USE_META, weight: 0.2568 cost: 2.1504 min: 0.9674 max: 2.4000 USE_META, weight: 0.3112 cost: 2.0638 min: 0.9674 max: 2.4000 USE_META, weight: 0.3480 cost: 2.0052 min: 0.9674 max: 2.4000 USE_META, weight: 0.2810 cost: 2.1118 min: 0.9674 max: 2.4000 USE_META, weight: 0.3382 cost: 2.0208 min: 0.9674 max: 2.4000 USE_META, weight: 0.3780 cost: 1.9575 min: 0.9674 max: 2.4000 USE_META, weight: 0.3562 cost: 1.9922 min: 0.9674 max: 2.4000 USE_META, weight: 0.3375 cost: 2.0220 min: 0.9674 max: 2.4000 USE_META, weight: 0.3873 cost: 1.9428 min: 0.9674 max: 2.4000 USE_META, weight: 0.3460 cost: 2.0084 min: 0.9674 max: 2.4000 USE_META, weight: 0.3474 cost: 2.0062 min: 0.9674 max: 2.4000 USE_META, weight: 0.3713 cost: 1.9681 min: 0.9674 max: 2.4000 USE_META, weight: 0.3463 cost: 2.0080 min: 0.9674 max: 2.4000 USE_META, weight: 0.3483 cost: 2.0047 min: 0.9674 max: 2.4000 USE_META, weight: 0.4026 cost: 1.9183 min: 0.9674 max: 2.4000 USE_META, weight: 0.4002 cost: 1.9221 min: 0.9674 max: 2.4000 USE_META, weight: 0.7039 cost: 1.4387 min: 0.9674 max: 2.4000 USE_META, weight: 0.4255 cost: 1.8818 min: 0.9674 max: 2.4000 USE_META, weight: 0.4980 cost: 1.7664 min: 0.9674 max: 2.4000 USE_META, weight: 0.4860 cost: 1.7857 min: 0.9674 max: 2.4000 USE_META, weight: 0.4046 cost: 1.9151 min: 0.9674 max: 2.4000 USE_META, weight: 0.4739 cost: 1.8048 min: 0.9674 max: 2.4000 USE_META, weight: 0.4173 cost: 1.8949 min: 0.9674 max: 2.4000 USE_META, weight: 0.6781 cost: 1.4798 min: 0.9674 max: 2.4000 USE_META, weight: 0.5821 cost: 1.6326 min: 0.9674 max: 2.4000 USE_META, weight: 0.5674 cost: 1.6561 min: 0.9674 max: 2.4000 USE_META, weight: 0.1798 cost: 2.2730 min: 0.9674 max: 2.4000 USE_META, weight: 0.5506 cost: 1.6827 min: 0.9674 max: 2.4000 USE_META, weight: 0.7315 cost: 1.3948 min: 0.9674 max: 2.4000 USE_META, weight: 0.1864 cost: 2.2625 min: 0.9674 max: 2.4000 USE_META, weight: 0.5824 cost: 1.6321 min: 0.9674 max: 2.4000 USE_META, weight: 0.3951 cost: 1.9302 min: 0.9674 max: 2.4000 USE_META, weight: 0.5636 cost: 1.6620 min: 0.9674 max: 2.4000 USE_META, weight: 0.5382 cost: 1.7024 min: 0.9674 max: 2.4000 USE_META, weight: 0.5490 cost: 1.6853 min: 0.9674 max: 2.4000 USE_META, weight: 0.5515 cost: 1.6813 min: 0.9674 max: 2.4000 USE_META, weight: 0.5550 cost: 1.6758 min: 0.9674 max: 2.4000 USE_META, weight: 0.5974 cost: 1.6082 min: 0.9674 max: 2.4000 USE_META, weight: 0.5504 cost: 1.6831 min: 0.9674 max: 2.4000 USE_META, weight: 0.1000 cost: 2.4000 min: 0.9674 max: 2.4000 USE_META, weight: 0.5652 cost: 1.6596 min: 0.9674 max: 2.4000 USE_META, weight: 0.5471 cost: 1.6884 min: 0.9674 max: 2.4000 USE_META, weight: 0.4460 cost: 1.8492 min: 0.9674 max: 2.4000 USE_META, weight: 0.4173 cost: 1.8949 min: 0.9674 max: 2.4000 USE_META, weight: 0.3994 cost: 1.9235 min: 0.9674 max: 2.4000 USE_META, weight: 0.5336 cost: 1.7097 min: 0.9674 max: 2.4000 USE_META, weight: 0.5674 cost: 1.6561 min: 0.9674 max: 2.4000 USE_META, weight: 0.3119 cost: 2.0627 min: 0.9674 max: 2.4000 USE_META, weight: 0.4039 cost: 1.9163 min: 0.9674 max: 2.4000 USE_META, weight: 0.8055 cost: 1.2771 min: 0.9674 max: 2.4000 USE_META, weight: 0.8055 cost: 1.2771 min: 0.9674 max: 2.4000 USE_META, weight: 0.8055 cost: 1.2771 min: 0.9674 max: 2.4000 USE_META, weight: 0.8055 cost: 1.2771 min: 0.9674 max: 2.4000 USE_META, weight: 0.8055 cost: 1.2771 min: 0.9674 max: 2.4000 USE_META, weight: 0.4988 cost: 1.7653 min: 0.9674 max: 2.4000 USE_META, weight: 1.0000 cost: 0.9674 min: 0.9674 max: 2.4000 USE_META, weight: 0.8659 cost: 1.1809 min: 0.9674 max: 2.4000 USE_META, weight: 0.8257 cost: 1.2449 min: 0.9674 max: 2.4000 USE_META, weight: 0.5812 cost: 1.6341 min: 0.9674 max: 2.4000 USE_META, weight: 0.4397 cost: 1.8593 min: 0.9674 max: 2.4000 USE_META, weight: 0.5438 cost: 1.6936 min: 0.9674 max: 2.4000 USE_META, weight: 0.4462 cost: 1.8489 min: 0.9674 max: 2.4000 USE_META, weight: 0.5593 cost: 1.6689 min: 0.9674 max: 2.4000 USE_META, weight: 0.3381 cost: 2.0210 min: 0.9674 max: 2.4000 USE_META, weight: 0.5595 cost: 1.6685 min: 0.9674 max: 2.4000 USE_META, weight: 0.5431 cost: 1.6946 min: 0.9674 max: 2.4000 USE_META, weight: 0.4456 cost: 1.8499 min: 0.9674 max: 2.4000 USE_META, weight: 0.5686 cost: 1.6542 min: 0.9674 max: 2.4000 USE_META, weight: 0.5604 cost: 1.6672 min: 0.9674 max: 2.4000 USE_META, weight: 0.4203 cost: 1.8902 min: 0.9674 max: 2.4000 USE_META, weight: 0.4432 cost: 1.8537 min: 0.9674 max: 2.4000 USE_META, weight: 0.2153 cost: 2.2164 min: 0.9674 max: 2.4000 USE_META, weight: 0.4363 cost: 1.8647 min: 0.9674 max: 2.4000 USE_META, weight: 0.2892 cost: 2.0988 min: 0.9674 max: 2.4000 USE_META, weight: 0.8055 cost: 1.2771 min: 0.9674 max: 2.4000 USE_META, weight: 0.8055 cost: 1.2771 min: 0.9674 max: 2.4000 USE_META, weight: 0.8055 cost: 1.2771 min: 0.9674 max: 2.4000 USE_META, weight: 0.8055 cost: 1.2771 min: 0.9674 max: 2.4000 USE_META, weight: 0.8055 cost: 1.2771 min: 0.9674 max: 2.4000 USE_META, weight: 0.8791 cost: 1.1600 min: 0.9674 max: 2.4000 USE_META, weight: 0.8055 cost: 1.2771 min: 0.9674 max: 2.4000 USE_META, weight: 0.8055 cost: 1.2771 min: 0.9674 max: 2.4000 USE_META, weight: 0.8055 cost: 1.2771 min: 0.9674 max: 2.4000 USE_META, weight: 0.8055 cost: 1.2771 min: 0.9674 max: 2.4000 USE_META, weight: 0.8055 cost: 1.2771 min: 0.9674 max: 2.4000 USE_META, weight: 0.7107 cost: 1.4279 min: 0.9674 max: 2.4000 USE_META, weight: 0.7369 cost: 1.3863 min: 0.9674 max: 2.4000 USE_META, weight: 0.7794 cost: 1.3186 min: 0.9674 max: 2.4000 USE_META, weight: 0.7360 cost: 1.3876 min: 0.9674 max: 2.4000 USE_META, weight: 0.7115 cost: 1.4267 min: 0.9674 max: 2.4000 USE_META, weight: 0.5615 cost: 1.6654 min: 0.9674 max: 2.4000 USE_META, weight: 0.6714 cost: 1.4905 min: 0.9674 max: 2.4000 USE_META, weight: 0.8055 cost: 1.2771 min: 0.9674 max: 2.4000 USE_META, weight: 0.8055 cost: 1.2771 min: 0.9674 max: 2.4000 USE_META, weight: 0.8055 cost: 1.2771 min: 0.9674 max: 2.4000 USE_META, weight: 0.8055 cost: 1.2771 min: 0.9674 max: 2.4000 USE_META, weight: 0.8055 cost: 1.2771 min: 0.9674 max: 2.4000 USE_META, weight: 0.5857 cost: 1.6268 min: 0.9674 max: 2.4000 USE_META, weight: 0.5582 cost: 1.6706 min: 0.9674 max: 2.4000 USE_META, weight: 0.5315 cost: 1.7132 min: 0.9674 max: 2.4000 USE_META, weight: 0.5091 cost: 1.7488 min: 0.9674 max: 2.4000 USE_META, weight: 0.5286 cost: 1.7178 min: 0.9674 max: 2.4000 USE_META, weight: 0.1894 cost: 2.2577 min: 0.9674 max: 2.4000 USE_META, weight: 0.2935 cost: 2.0920 min: 0.9674 max: 2.4000 USE_META, weight: 0.3605 cost: 1.9854 min: 0.9674 max: 2.4000 USE_META, weight: 0.2331 cost: 2.1882 min: 0.9674 max: 2.4000 USE_META, weight: 0.1524 cost: 2.3165 min: 0.9674 max: 2.4000 USE_META, weight: 0.6361 cost: 1.5466 min: 0.9674 max: 2.4000 USE_META, weight: 0.4552 cost: 1.8346 min: 0.9674 max: 2.4000 USE_META, weight: 0.5689 cost: 1.6536 min: 0.9674 max: 2.4000 USE_META, weight: 0.6070 cost: 1.5930 min: 0.9674 max: 2.4000 USE_META, weight: 0.4220 cost: 1.8874 min: 0.9674 max: 2.4000 USE_META, weight: 0.3099 cost: 2.0659 min: 0.9674 max: 2.4000 USE_META, weight: 0.3664 cost: 1.9759 min: 0.9674 max: 2.4000 USE_META, weight: 0.3726 cost: 1.9661 min: 0.9674 max: 2.4000 USE_META, weight: 0.3610 cost: 1.9845 min: 0.9674 max: 2.4000 USE_META, weight: 0.3986 cost: 1.9248 min: 0.9674 max: 2.4000 USE_META, weight: 0.6948 cost: 1.4532 min: 0.9674 max: 2.4000 USE_META, weight: 0.4254 cost: 1.8821 min: 0.9674 max: 2.4000 USE_META, weight: 0.3673 cost: 1.9746 min: 0.9674 max: 2.4000 USE_META, weight: 0.2888 cost: 2.0995 min: 0.9674 max: 2.4000 USE_META, weight: 0.4400 cost: 1.8589 min: 0.9674 max: 2.4000 USE_META, weight: 0.4334 cost: 1.8694 min: 0.9674 max: 2.4000 USE_META, weight: 0.7000 cost: 1.4449 min: 0.9674 max: 2.4000 USE_META, weight: 0.6330 cost: 1.5517 min: 0.9674 max: 2.4000 USE_EVALUE, weight: 0.4074 eval: 22.0070 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.4074 eval: 22.0070 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.4074 eval: 22.0070 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.2278 eval: 27.5160 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.2278 eval: 27.5160 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.2278 eval: 27.5160 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.6087 eval: 15.8320 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.6087 eval: 15.8320 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.6087 eval: 15.8320 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.2343 eval: 27.3180 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.2343 eval: 27.3180 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.2343 eval: 27.3180 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.1729 eval: 29.2000 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.1729 eval: 29.2000 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.1729 eval: 29.2000 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.1020 eval: 31.3770 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.1020 eval: 31.3770 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.1020 eval: 31.3770 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 1.0000 eval: 3.8306 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 1.0000 eval: 3.8306 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 1.0000 eval: 3.8306 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.4994 eval: 19.1870 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.4994 eval: 19.1870 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.4994 eval: 19.1870 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.6210 eval: 15.4570 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.6210 eval: 15.4570 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.6210 eval: 15.4570 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.5945 eval: 16.2680 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.5945 eval: 16.2680 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.5945 eval: 16.2680 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.3294 eval: 24.4010 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.3294 eval: 24.4010 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.3294 eval: 24.4010 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.9245 eval: 6.1455 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.9245 eval: 6.1455 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.9245 eval: 6.1455 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.5630 eval: 17.2340 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.5630 eval: 17.2340 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.5630 eval: 17.2340 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.1468 eval: 30.0000 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.1468 eval: 30.0000 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.1468 eval: 30.0000 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.6782 eval: 13.7000 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.6782 eval: 13.7000 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.6782 eval: 13.7000 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.1942 eval: 28.5490 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.1942 eval: 28.5490 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.1942 eval: 28.5490 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.3945 eval: 22.4030 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.3945 eval: 22.4030 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.3945 eval: 22.4030 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.6028 eval: 16.0150 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.6028 eval: 16.0150 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.6028 eval: 16.0150 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.4557 eval: 20.5260 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.4557 eval: 20.5260 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.4557 eval: 20.5260 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.1000 eval: 31.4370 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.1000 eval: 31.4370 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.1000 eval: 31.4370 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.4135 eval: 21.8200 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.4135 eval: 21.8200 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.4135 eval: 21.8200 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.2411 eval: 27.1080 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.2411 eval: 27.1080 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.2411 eval: 27.1080 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.4218 eval: 21.5670 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.4218 eval: 21.5670 min: 3.8306 max: 31.4370 USE_EVALUE, weight: 0.4218 eval: 21.5670 min: 3.8306 max: 31.4370 Number of contacts in models: 270 Number of contacts in alignments: 69 NUMB_ALIGNS: 69 Adding 10491 constraints to all3.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all3.constraints maxweight: 1.0000 Optimizing... Probability sum: -328.4476, CN propb: -328.4476 weights: 0.2931 constraints: 471 # command:Found ConstraintSet # PrintContacts align.constraints_meta03 Number of constraints in align3.constraints 471 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_meta03 Number of constraints in align3.constraints.bonus 471 # command:Found ConstraintSet # PrintContacts rejected.constraints_meta03 Number of constraints in rejected3.constraints 10020 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_meta03 Number of constraints in rejected3.constraints.bonus 10020 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_meta03 Number of constraints in noncontact3.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_meta03 Number of constraints in noncontact3.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_meta03 Number of constraints in all3.constraints 10491 # command: