# 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/T0382/ # command:# Making conformation for sequence T0382 numbered 1 through 123 Created new target T0382 from T0382.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0382/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0382//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0382/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0382//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0382/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0382/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0382/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 2a9uA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2a9uA expands to /projects/compbio/data/pdb/2a9u.pdb.gz 2a9uA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0382 read from 2a9uA/merged-good-all-a2m # 2a9uA read from 2a9uA/merged-good-all-a2m # adding 2a9uA to template set # found chain 2a9uA in template set T0382 3 :KLDLHQMTTQDLVALFAKVTVEQDDALLGNQISRFNRLFGVMAEIADELKARDGD 2a9uA 25 :EVKPEKISTKSYVHSALKIFKTAEECRLDRDEERAYVLYMKYVTVYNLIKKRPDF # choosing archetypes in rotamer library T0382 58 :QRTALLSLFEYPNMQVRLQAAKLT 2a9uA 82 :QQDYFHSILGPGNIKKAVEEAERL T0382 82 :LAVAPVKAREQLEAIVSS 2a9uA 111 :LRYEEAEVRKKLEEKDRQ Number of specific fragments extracted= 3 number of extra gaps= 0 total=3 Number of alignments=1 # 2a9uA read from 2a9uA/merged-good-all-a2m # found chain 2a9uA in template set T0382 3 :KLDLHQMTTQDLVALFAKVTVEQDDALLGNQISRFNRLFGVMAEIADELKARDG 2a9uA 25 :EVKPEKISTKSYVHSALKIFKTAEECRLDRDEERAYVLYMKYVTVYNLIKKRPD T0382 58 :QRTALLSLFEYPNMQVRLQAAKLT 2a9uA 82 :QQDYFHSILGPGNIKKAVEEAERL T0382 82 :LAVAPVKAREQLEAIVS 2a9uA 111 :LRYEEAEVRKKLEEKDR Number of specific fragments extracted= 3 number of extra gaps= 0 total=6 Number of alignments=2 # 2a9uA read from 2a9uA/merged-good-all-a2m # found chain 2a9uA in template set T0382 3 :KLDLHQMTTQDLVALFAKVTVEQDDALLGNQISRFNRLFGVMAEIADELKARDG 2a9uA 25 :EVKPEKISTKSYVHSALKIFKTAEECRLDRDEERAYVLYMKYVTVYNLIKKRPD T0382 57 :DQRTALLSLFEYPNMQVRLQAAKLT 2a9uA 81 :QQQDYFHSILGPGNIKKAVEEAERL T0382 82 :LAVAPVKAREQLEAIVS 2a9uA 111 :LRYEEAEVRKKLEEKDR Number of specific fragments extracted= 3 number of extra gaps= 0 total=9 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1d1rA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1d1rA expands to /projects/compbio/data/pdb/1d1r.pdb.gz 1d1rA:# T0382 read from 1d1rA/merged-good-all-a2m # 1d1rA read from 1d1rA/merged-good-all-a2m # adding 1d1rA to template set # found chain 1d1rA in template set T0382 42 :GVMAEIADELKA 1d1rA 59 :AELTKLAAELKK T0382 55 :DGDQRTALLSLFE 1d1rA 86 :QGDKRDLLKSLLE Number of specific fragments extracted= 2 number of extra gaps= 0 total=11 Number of alignments=4 # 1d1rA read from 1d1rA/merged-good-all-a2m # found chain 1d1rA in template set T0382 42 :GVMAEIADELKAR 1d1rA 59 :AELTKLAAELKKK T0382 55 :DGDQRTALLSLFE 1d1rA 86 :QGDKRDLLKSLLE Number of specific fragments extracted= 2 number of extra gaps= 0 total=13 Number of alignments=5 # 1d1rA read from 1d1rA/merged-good-all-a2m # found chain 1d1rA in template set T0382 42 :GVMAEIADELKAR 1d1rA 59 :AELTKLAAELKKK T0382 55 :DGDQRTALLSLFE 1d1rA 86 :QGDKRDLLKSLLE Number of specific fragments extracted= 2 number of extra gaps= 0 total=15 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bvsB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1bvsB expands to /projects/compbio/data/pdb/1bvs.pdb.gz 1bvsB:# T0382 read from 1bvsB/merged-good-all-a2m # 1bvsB read from 1bvsB/merged-good-all-a2m # adding 1bvsB to template set # found chain 1bvsB in template set T0382 8 :QMTTQDLVALFA 1bvsB 79 :GVGPRLAMATLA T0382 23 :VEQDDALLGNQIS 1bvsB 95 :AALRQALADSDVA T0382 50 :ELKARDG 1bvsB 108 :SLTRVPG T0382 104 :QAGDAGMCLDLLDDG 1bvsB 116 :GRRGAERIVLELADK Number of specific fragments extracted= 4 number of extra gaps= 0 total=19 Number of alignments=7 # 1bvsB read from 1bvsB/merged-good-all-a2m # found chain 1bvsB in template set T0382 54 :RDGDQRTALLSLFEYPNMQVRL 1bvsB 63 :SDAENRDLFLALLSVSGVGPRL T0382 78 :AKLTLAVAP 1bvsB 85 :AMATLAVHD T0382 87 :VKAREQLE 1bvsB 95 :AALRQALA T0382 95 :AIVSSKWF 1bvsB 108 :SLTRVPGI T0382 104 :QAGDAGMCLDLLDDG 1bvsB 116 :GRRGAERIVLELADK Number of specific fragments extracted= 5 number of extra gaps= 0 total=24 Number of alignments=8 # 1bvsB read from 1bvsB/merged-good-all-a2m # found chain 1bvsB in template set T0382 54 :RDGDQRTALLSLFEYPNMQVRL 1bvsB 63 :SDAENRDLFLALLSVSGVGPRL T0382 78 :AKLTLAVAP 1bvsB 85 :AMATLAVHD T0382 87 :VKAREQLE 1bvsB 95 :AALRQALA T0382 95 :AIVS 1bvsB 108 :SLTR T0382 100 :KWFPQAGDAGMCLDLLDDGT 1bvsB 112 :VPGIGRRGAERIVLELADKV Number of specific fragments extracted= 5 number of extra gaps= 0 total=29 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lniA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0382 read from 1lniA/merged-good-all-a2m # 1lniA read from 1lniA/merged-good-all-a2m # found chain 1lniA in training set Warning: unaligning (T0382)K100 because of BadResidue code BAD_PEPTIDE in next template residue (1lniA)P27 Warning: unaligning (T0382)W101 because of BadResidue code BAD_PEPTIDE at template residue (1lniA)P27 Warning: unaligning (T0382)F102 because of BadResidue code BAD_PEPTIDE at template residue (1lniA)F28 T0382 85 :APVKAREQLEAIVSS 1lniA 11 :LPPEATDTLNLIASD T0382 103 :PQAG 1lniA 29 :PYSQ Number of specific fragments extracted= 2 number of extra gaps= 1 total=31 # 1lniA read from 1lniA/merged-good-all-a2m # found chain 1lniA in training set Warning: unaligning (T0382)K100 because of BadResidue code BAD_PEPTIDE in next template residue (1lniA)P27 Warning: unaligning (T0382)W101 because of BadResidue code BAD_PEPTIDE at template residue (1lniA)P27 Warning: unaligning (T0382)F102 because of BadResidue code BAD_PEPTIDE at template residue (1lniA)F28 T0382 85 :APVKAREQLEAIVSS 1lniA 11 :LPPEATDTLNLIASD T0382 103 :PQAG 1lniA 29 :PYSQ Number of specific fragments extracted= 2 number of extra gaps= 1 total=33 # 1lniA read from 1lniA/merged-good-all-a2m # found chain 1lniA in training set Warning: unaligning (T0382)K100 because of BadResidue code BAD_PEPTIDE in next template residue (1lniA)P27 Warning: unaligning (T0382)W101 because of BadResidue code BAD_PEPTIDE at template residue (1lniA)P27 Warning: unaligning (T0382)F102 because of BadResidue code BAD_PEPTIDE at template residue (1lniA)F28 T0382 85 :APVKAREQLEAIVSS 1lniA 11 :LPPEATDTLNLIASD T0382 103 :PQAGD 1lniA 29 :PYSQD Number of specific fragments extracted= 2 number of extra gaps= 1 total=35 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rgoA/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/T0382/1rgoA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0382/1rgoA/merged-good-all-a2m.gz for input Trying 1rgoA/merged-good-all-a2m Error: Couldn't open file 1rgoA/merged-good-all-a2m or 1rgoA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1e9xA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1e9xA expands to /projects/compbio/data/pdb/1e9x.pdb.gz 1e9xA:# T0382 read from 1e9xA/merged-good-all-a2m # 1e9xA read from 1e9xA/merged-good-all-a2m # adding 1e9xA to template set # found chain 1e9xA in template set T0382 9 :MT 1e9xA 161 :LD T0382 16 :ALFAKVTVEQDD 1e9xA 163 :GRFAKLYHELER T0382 30 :LGNQISRFNRLFGVMAEIADELKA 1e9xA 184 :PYLPIESFRRRDEARNGLVALVAD T0382 54 :RDGDQRTALLSLF 1e9xA 218 :TDKSDRDMLDVLI T0382 67 :EYPNMQVRLQAAKLTLA 1e9xA 240 :RFSADEITGMFISMMFA T0382 84 :V 1e9xA 272 :L T0382 85 :AP 1e9xA 274 :RH T0382 87 :VKAREQLEAIVSSKW 1e9xA 280 :AAVIDELDELYGDGR Number of specific fragments extracted= 8 number of extra gaps= 0 total=43 Number of alignments=10 # 1e9xA read from 1e9xA/merged-good-all-a2m # found chain 1e9xA in template set T0382 4 :LDLHQMTTQDLVALFAKVTVEQDDALLG 1e9xA 236 :TGTPRFSADEITGMFISMMFAGHHTSSG T0382 32 :NQISRFNRLFGVMAEI 1e9xA 267 :WTLIELMRHRDAYAAV T0382 90 :REQLEAIVSSKW 1e9xA 283 :IDELDELYGDGR Number of specific fragments extracted= 3 number of extra gaps= 0 total=46 Number of alignments=11 # 1e9xA read from 1e9xA/merged-good-all-a2m # found chain 1e9xA in template set T0382 2 :SKLDLHQMTTQDLVALFAKVTVEQDDALLG 1e9xA 234 :AETGTPRFSADEITGMFISMMFAGHHTSSG T0382 32 :NQISRFNRLFGVMAEIADELKARDGDQRTALLSLFE 1e9xA 267 :WTLIELMRHRDAYAAVIDELDELYGDGRSVSFHALR T0382 70 :NMQVRLQAAKLTLAVAP 1e9xA 303 :QIPQLENVLKETLRLHP Number of specific fragments extracted= 3 number of extra gaps= 0 total=49 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1favA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1favA expands to /projects/compbio/data/pdb/1fav.pdb.gz 1favA:# T0382 read from 1favA/merged-good-all-a2m # 1favA read from 1favA/merged-good-all-a2m # adding 1favA to template set # found chain 1favA in template set T0382 24 :EQDDALLGNQISRFNRLFGVMAEIADELKA 1favA 10 :LSKIYHIENEIARIKKLIGEARQLLSGIVQ T0382 58 :QRT 1favA 40 :QQN T0382 70 :NMQVRLQAAKLTLAVAPVKAREQLEAIVS 1favA 43 :NLLRAIEAQQHLLQLTVWGIKQLQARILA Number of specific fragments extracted= 3 number of extra gaps= 0 total=52 Number of alignments=13 # 1favA read from 1favA/merged-good-all-a2m # found chain 1favA in template set T0382 27 :DALLGNQISRFNRLFGVMAEIA 1favA 7 :EEILSKIYHIENEIARIKKLIG T0382 57 :DQRTALLSLFEYPNMQVRLQAAKLTLAVAPVKAREQLEAI 1favA 29 :EARQLLSGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQAR Number of specific fragments extracted= 2 number of extra gaps= 0 total=54 Number of alignments=14 # 1favA read from 1favA/merged-good-all-a2m # found chain 1favA in template set T0382 12 :QDLVALF 1favA 7 :EEILSKI T0382 19 :AKVTVEQDDALLGNQISRFNRLFGVMAEIADE 1favA 16 :IENEIARIKKLIGEARQLLSGIVQQQNNLLRA T0382 75 :LQAAKLTLAVAPVKAREQLEAIVS 1favA 48 :IEAQQHLLQLTVWGIKQLQARILA Number of specific fragments extracted= 3 number of extra gaps= 0 total=57 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hjp/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1hjp expands to /projects/compbio/data/pdb/1hjp.pdb.gz 1hjp:Warning: there is no chain 1hjp will retry with 1hjpA # T0382 read from 1hjp/merged-good-all-a2m # 1hjp read from 1hjp/merged-good-all-a2m # adding 1hjp to template set # found chain 1hjp in template set Warning: unaligning (T0382)Q72 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1hjp)D158 T0382 8 :QMTTQDLVALF 1hjp 92 :GMSAQQFVNAV T0382 30 :LGNQI 1hjp 103 :EREEV T0382 35 :SRFNRL 1hjp 119 :KTAERL T0382 44 :MAEIADELKARDGD 1hjp 125 :IVEMKDRFKGLHGD T0382 73 :VRLQAAKLTLA 1hjp 159 :AEQEAVAALVA T0382 84 :VAPVKAREQLE 1hjp 172 :YKPQEASRMVS T0382 100 :KWFPQAGDAGMCLDLL 1hjp 183 :KIARPDASSETLIREA Number of specific fragments extracted= 7 number of extra gaps= 0 total=64 Number of alignments=16 # 1hjp read from 1hjp/merged-good-all-a2m # found chain 1hjp in template set Warning: unaligning (T0382)Q72 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1hjp)D158 T0382 7 :HQMTTQDLVALFAKV 1hjp 79 :NGVGPKLALAILSGM T0382 22 :TVEQDDALLGNQI 1hjp 95 :AQQFVNAVEREEV T0382 35 :SRFNRL 1hjp 119 :KTAERL T0382 44 :MAEIADELKARDGD 1hjp 125 :IVEMKDRFKGLHGD T0382 73 :VRLQAAKLTLA 1hjp 159 :AEQEAVAALVA T0382 84 :VAPVKAREQLEA 1hjp 172 :YKPQEASRMVSK T0382 101 :WFPQAGDAGMCLDLL 1hjp 184 :IARPDASSETLIREA Number of specific fragments extracted= 7 number of extra gaps= 0 total=71 Number of alignments=17 # 1hjp read from 1hjp/merged-good-all-a2m # found chain 1hjp in template set Warning: unaligning (T0382)R59 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1hjp)D158 Warning: unaligning (T0382)Q72 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1hjp)D158 T0382 9 :MTTQDLVALF 1hjp 93 :MSAQQFVNAV T0382 28 :ALL 1hjp 109 :ALV T0382 35 :SRFNRLF 1hjp 119 :KTAERLI T0382 45 :AEIADELKARDGDQ 1hjp 126 :VEMKDRFKGLHGDL T0382 73 :VRLQAAKLTLA 1hjp 159 :AEQEAVAALVA T0382 84 :VAPVKAREQLEA 1hjp 172 :YKPQEASRMVSK T0382 101 :WFPQAGDAGMCLDLL 1hjp 184 :IARPDASSETLIREA Number of specific fragments extracted= 7 number of extra gaps= 0 total=78 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cuk/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1cuk expands to /projects/compbio/data/pdb/1cuk.pdb.gz 1cuk:Warning: there is no chain 1cuk will retry with 1cukA # T0382 read from 1cuk/merged-good-all-a2m # 1cuk read from 1cuk/merged-good-all-a2m # adding 1cuk to template set # found chain 1cuk in template set Warning: unaligning (T0382)G42 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1cuk)T120 Warning: unaligning (T0382)V43 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1cuk)T120 Warning: unaligning (T0382)N70 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cuk)T156 Warning: unaligning (T0382)Q92 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1cuk)V181 Warning: unaligning (T0382)L93 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1cuk)V181 Warning: unaligning (T0382)E94 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cuk)K183 Warning: unaligning (T0382)K100 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cuk)K183 Warning: unaligning (T0382)W101 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cuk)A185 Warning: unaligning (T0382)F102 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cuk)A185 Warning: unaligning (T0382)P103 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1cuk)R186 Warning: unaligning (T0382)Q104 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1cuk)P187 Warning: unaligning (T0382)A105 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE at template residue (1cuk)D188 Warning: unaligning (T0382)G106 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1cuk)A189 Warning: unaligning (T0382)D107 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1cuk)S191 Warning: unaligning (T0382)A108 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1cuk)S191 T0382 8 :QMTTQDLV 1cuk 92 :GMSAQQFV T0382 27 :DALLGNQISRFNRL 1cuk 100 :NAVEREEVGALVKL T0382 41 :F 1cuk 118 :K T0382 44 :MAEIADELKAR 1cuk 121 :AERLIVEMKDR T0382 55 :DGD 1cuk 136 :HGD T0382 71 :MQVRLQAAKLTLA 1cuk 157 :DDAEQEAVARLVA T0382 84 :VAPVKARE 1cuk 172 :YKPQEASR T0382 109 :GMCLDLL 1cuk 192 :ETLIREA Number of specific fragments extracted= 8 number of extra gaps= 2 total=86 Number of alignments=19 # 1cuk read from 1cuk/merged-good-all-a2m # found chain 1cuk in template set Warning: unaligning (T0382)G42 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1cuk)T120 Warning: unaligning (T0382)V43 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1cuk)T120 Warning: unaligning (T0382)N70 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cuk)T156 Warning: unaligning (T0382)Q92 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1cuk)V181 Warning: unaligning (T0382)L93 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1cuk)V181 Warning: unaligning (T0382)E94 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cuk)K183 Warning: unaligning (T0382)A95 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cuk)K183 Warning: unaligning (T0382)W101 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cuk)A185 Warning: unaligning (T0382)F102 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cuk)A185 Warning: unaligning (T0382)P103 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1cuk)R186 Warning: unaligning (T0382)Q104 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1cuk)P187 Warning: unaligning (T0382)A105 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE at template residue (1cuk)D188 Warning: unaligning (T0382)G106 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1cuk)A189 Warning: unaligning (T0382)D107 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1cuk)S191 Warning: unaligning (T0382)A108 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1cuk)S191 T0382 8 :QMTTQDLVALFAKV 1cuk 80 :GVGPKLALAILSGM T0382 22 :TVEQDDALLGNQISRFNRL 1cuk 95 :AQQFVNAVEREEVGALVKL T0382 41 :F 1cuk 118 :K T0382 44 :MAEIADELKAR 1cuk 121 :AERLIVEMKDR T0382 55 :DGD 1cuk 136 :HGD T0382 71 :MQVRLQAAKLTLA 1cuk 157 :DDAEQEAVARLVA T0382 84 :VAPVKARE 1cuk 172 :YKPQEASR T0382 109 :GMCLDLL 1cuk 192 :ETLIREA Number of specific fragments extracted= 8 number of extra gaps= 2 total=94 Number of alignments=20 # 1cuk read from 1cuk/merged-good-all-a2m # found chain 1cuk in template set Warning: unaligning (T0382)G42 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1cuk)T120 Warning: unaligning (T0382)V43 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1cuk)T120 Warning: unaligning (T0382)N70 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cuk)T156 Warning: unaligning (T0382)Q92 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1cuk)V181 Warning: unaligning (T0382)L93 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1cuk)V181 Warning: unaligning (T0382)E94 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cuk)K183 Warning: unaligning (T0382)A95 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cuk)K183 Warning: unaligning (T0382)W101 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cuk)A185 Warning: unaligning (T0382)F102 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cuk)A185 Warning: unaligning (T0382)P103 because of BadResidue code TOO_FEW_ATOMS+BAD_PEPTIDE at template residue (1cuk)R186 Warning: unaligning (T0382)Q104 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1cuk)P187 Warning: unaligning (T0382)A105 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE at template residue (1cuk)D188 Warning: unaligning (T0382)G106 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1cuk)A189 Warning: unaligning (T0382)D107 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1cuk)S191 Warning: unaligning (T0382)A108 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1cuk)S191 T0382 9 :MTTQDLVA 1cuk 93 :MSAQQFVN T0382 28 :ALLGNQISRFNRL 1cuk 101 :AVEREEVGALVKL T0382 41 :F 1cuk 118 :K T0382 44 :MAEIADELKAR 1cuk 121 :AERLIVEMKDR T0382 71 :MQVRLQAAKLTLA 1cuk 157 :DDAEQEAVARLVA T0382 84 :VAPVKARE 1cuk 172 :YKPQEASR T0382 109 :GMCLDLL 1cuk 192 :ETLIREA Number of specific fragments extracted= 7 number of extra gaps= 2 total=101 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gvhA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1gvhA expands to /projects/compbio/data/pdb/1gvh.pdb.gz 1gvhA:# T0382 read from 1gvhA/merged-good-all-a2m # 1gvhA read from 1gvhA/merged-good-all-a2m # adding 1gvhA to template set # found chain 1gvhA in template set T0382 11 :TQDLVALFAKVTVEQDD 1gvhA 54 :REALFNAIAAYASNIEN T0382 28 :ALLGNQISRFNRLF 1gvhA 73 :ALLPAVEKIAQKHT T0382 42 :GVMAEIADELK 1gvhA 93 :EQYNIVGEHLL T0382 60 :TALLSLFEY 1gvhA 104 :ATLDEMFSP T0382 69 :PNMQVRLQAAKLTLAVAPVKAREQLEAIVSSKWFPQA 1gvhA 115 :EVLDAWGKAYGVLANVFINREAEIYNENASKAGGWEG Number of specific fragments extracted= 5 number of extra gaps= 0 total=106 Number of alignments=22 # 1gvhA read from 1gvhA/merged-good-all-a2m # found chain 1gvhA in template set T0382 11 :TQDLVALFAKVTVEQDD 1gvhA 54 :REALFNAIAAYASNIEN T0382 28 :ALL 1gvhA 73 :ALL T0382 71 :MQVRLQAAKLTLAVAPVKAREQLEAIV 1gvhA 76 :PAVEKIAQKHTSFQIKPEQYNIVGEHL T0382 112 :LDLLD 1gvhA 103 :LATLD Number of specific fragments extracted= 4 number of extra gaps= 0 total=110 Number of alignments=23 # 1gvhA read from 1gvhA/merged-good-all-a2m # found chain 1gvhA in template set T0382 11 :TQDLVALFAKVT 1gvhA 54 :REALFNAIAAYA T0382 23 :VEQDDALLGNQISRFNRLFGVMAEIADELKARDGDQRTAL 1gvhA 81 :IAQKHTSFQIKPEQYNIVGEHLLATLDEMFSPGQEVLDAW T0382 75 :LQAAKLTLAVAPVKAREQLEAIVSSKWFPQA 1gvhA 121 :GKAYGVLANVFINREAEIYNENASKAGGWEG Number of specific fragments extracted= 3 number of extra gaps= 0 total=113 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ueyA/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/T0382/1ueyA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0382/1ueyA/merged-good-all-a2m.gz for input Trying 1ueyA/merged-good-all-a2m Error: Couldn't open file 1ueyA/merged-good-all-a2m or 1ueyA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gmpA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1gmpA expands to /projects/compbio/data/pdb/1gmp.pdb.gz 1gmpA:Skipped atom 39, because occupancy 0.5 <= existing 0.500 in 1gmpA Skipped atom 41, because occupancy 0.500 <= existing 0.500 in 1gmpA Skipped atom 293, because occupancy 0.500 <= existing 0.500 in 1gmpA Skipped atom 295, because occupancy 0.500 <= existing 0.500 in 1gmpA Skipped atom 297, because occupancy 0.500 <= existing 0.500 in 1gmpA Skipped atom 299, because occupancy 0.500 <= existing 0.500 in 1gmpA Skipped atom 301, because occupancy 0.500 <= existing 0.500 in 1gmpA Skipped atom 561, because occupancy 0.400 <= existing 0.600 in 1gmpA Skipped atom 595, because occupancy 0.500 <= existing 0.500 in 1gmpA Skipped atom 597, because occupancy 0.500 <= existing 0.500 in 1gmpA # T0382 read from 1gmpA/merged-good-all-a2m # 1gmpA read from 1gmpA/merged-good-all-a2m # adding 1gmpA to template set # found chain 1gmpA in template set T0382 85 :APVKAREQLEAIVSSKWFPQAG 1gmpA 11 :LPPEATDTLNLIASDGPFPYSQ T0382 116 :DDGTFK 1gmpA 33 :DGVVFQ Number of specific fragments extracted= 2 number of extra gaps= 0 total=115 Number of alignments=25 # 1gmpA read from 1gmpA/merged-good-all-a2m # found chain 1gmpA in template set T0382 85 :APVKAREQLEAIVSSKWFPQAG 1gmpA 11 :LPPEATDTLNLIASDGPFPYSQ T0382 116 :DDGTFK 1gmpA 33 :DGVVFQ Number of specific fragments extracted= 2 number of extra gaps= 0 total=117 Number of alignments=26 # 1gmpA read from 1gmpA/merged-good-all-a2m # found chain 1gmpA in template set T0382 85 :APVKAREQLEAIVSSKWFPQAGD 1gmpA 11 :LPPEATDTLNLIASDGPFPYSQD Number of specific fragments extracted= 1 number of extra gaps= 0 total=118 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1u13A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1u13A expands to /projects/compbio/data/pdb/1u13.pdb.gz 1u13A:# T0382 read from 1u13A/merged-good-all-a2m # 1u13A read from 1u13A/merged-good-all-a2m # adding 1u13A to template set # found chain 1u13A in template set T0382 2 :SKLDLHQMTTQDLVALFAKVTVEQDDALLG 1u13A 234 :AETGTPRFSADEITGMFISMMFAGHHTSSG T0382 32 :NQISRFNRLFGVMAEIADELKARDGD 1u13A 267 :WTLIELMRHRDAYAAVIDELDELYGD T0382 62 :LLSLFEYPNMQVR 1u13A 296 :VSFHALRQIPQLE T0382 76 :QAAKLTLAV 1u13A 309 :NVLKETLRL Number of specific fragments extracted= 4 number of extra gaps= 0 total=122 Number of alignments=28 # 1u13A read from 1u13A/merged-good-all-a2m # found chain 1u13A in template set T0382 2 :SKLDLHQMTTQDLVALFAKVTVEQDDALLG 1u13A 234 :AETGTPRFSADEITGMFISMMFAGHHTSSG T0382 32 :NQISRFNRLFGVMAEIADELKARDGDQRTALLSLF 1u13A 267 :WTLIELMRHRDAYAAVIDELDELYGDGRSVSFHAL T0382 68 :YPN 1u13A 302 :RQI T0382 72 :QVRLQAAKLTLAVA 1u13A 305 :PQLENVLKETLRLH Number of specific fragments extracted= 4 number of extra gaps= 0 total=126 Number of alignments=29 # 1u13A read from 1u13A/merged-good-all-a2m # found chain 1u13A in template set T0382 2 :SKLDLHQMTTQDLVALFAKVTVEQDD 1u13A 234 :AETGTPRFSADEITGMFISMMFAGHH T0382 28 :ALLGNQISRFNRLFGVMAEIADELKARDGDQRTALLSLFE 1u13A 263 :GTASWTLIELMRHRDAYAAVIDELDELYGDGRSVSFHALR T0382 70 :NMQVRLQAAKLTLAVAP 1u13A 303 :QIPQLENVLKETLRLHP Number of specific fragments extracted= 3 number of extra gaps= 0 total=129 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1h5zA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1h5zA expands to /projects/compbio/data/pdb/1h5z.pdb.gz 1h5zA:# T0382 read from 1h5zA/merged-good-all-a2m # 1h5zA read from 1h5zA/merged-good-all-a2m # adding 1h5zA to template set # found chain 1h5zA in template set T0382 2 :SKLDLHQMTTQDLVALFAKVTVEQDDALLG 1h5zA 234 :AETGTPRFSADEITGMFISMMFAGHHTSSG T0382 32 :NQISRFNRLFGVMAEIADELKARDGD 1h5zA 267 :WTLIELMRHRDAYAAVIDELDELYGD T0382 62 :LLSLFEYPNMQVR 1h5zA 296 :VSFHALRQIPQLE T0382 76 :QAAK 1h5zA 309 :NVLK Number of specific fragments extracted= 4 number of extra gaps= 0 total=133 Number of alignments=31 # 1h5zA read from 1h5zA/merged-good-all-a2m # found chain 1h5zA in template set T0382 3 :KLDLHQMTTQDLVALFAKVTVEQDDALLG 1h5zA 235 :ETGTPRFSADEITGMFISMMFAGHHTSSG T0382 32 :NQISRFNRLFGVMAEIADELKARDGDQRTALLSLFE 1h5zA 267 :WTLIELMRHRDAYAAVIDELDELYGDGRSVSFHALR T0382 69 :P 1h5zA 303 :Q T0382 71 :MQVRLQAAKLTLAV 1h5zA 304 :IPQLENVLKETLRL Number of specific fragments extracted= 4 number of extra gaps= 0 total=137 Number of alignments=32 # 1h5zA read from 1h5zA/merged-good-all-a2m # found chain 1h5zA in template set T0382 2 :SKLDLHQMTTQDLVALFAKVTVEQDD 1h5zA 234 :AETGTPRFSADEITGMFISMMFAGHH T0382 28 :ALLGNQISRFNRLFGVMAEIADELKARDGDQRTALLSLFE 1h5zA 263 :GTASWTLIELMRHRDAYAAVIDELDELYGDGRSVSFHALR T0382 70 :NMQVRLQAAKLTLAVAP 1h5zA 303 :QIPQLENVLKETLRLHP Number of specific fragments extracted= 3 number of extra gaps= 0 total=140 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1envA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1envA expands to /projects/compbio/data/pdb/1env.pdb.gz 1envA:# T0382 read from 1envA/merged-good-all-a2m # 1envA read from 1envA/merged-good-all-a2m # adding 1envA to template set # found chain 1envA in template set T0382 27 :DALLGNQISRFNRLFGVMAEI 1envA 7 :EEILSKIYHIENEIARIKKLI T0382 56 :GDQRTALLSLFEYPNMQVRLQAAKLT 1envA 28 :GEARQLLSGIVQQQNNLLRAIEAQQH T0382 82 :LAVAPVKAREQLEA 1envA 55 :LQLTVWGIKQLQAR Number of specific fragments extracted= 3 number of extra gaps= 0 total=143 Number of alignments=34 # 1envA read from 1envA/merged-good-all-a2m # found chain 1envA in template set T0382 27 :DALLGNQISRFNRLFGVMAEI 1envA 7 :EEILSKIYHIENEIARIKKLI T0382 56 :GDQRTALLSLFEYPNMQVRLQAAKLT 1envA 28 :GEARQLLSGIVQQQNNLLRAIEAQQH T0382 82 :LAVAPVKAREQ 1envA 55 :LQLTVWGIKQL Number of specific fragments extracted= 3 number of extra gaps= 0 total=146 Number of alignments=35 # 1envA read from 1envA/merged-good-all-a2m # found chain 1envA in template set Warning: unaligning (T0382)K52 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1envA)W117 Warning: unaligning (T0382)Y68 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1envA)W117 T0382 12 :QDLVALFAKVT 1envA 35 :SGIVQQQNNLL T0382 23 :VEQDDALLGNQISRFNRLFGVMAEIADEL 1envA 48 :IEAQQHLLQLTVWGIKQLQARILAVERYL T0382 69 :PNMQVRLQ 1envA 118 :MEWDREIN T0382 95 :AIVS 1envA 126 :NYTS Number of specific fragments extracted= 4 number of extra gaps= 0 total=150 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1oyzA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1oyzA expands to /projects/compbio/data/pdb/1oyz.pdb.gz 1oyzA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0382 read from 1oyzA/merged-good-all-a2m # 1oyzA read from 1oyzA/merged-good-all-a2m # adding 1oyzA to template set # found chain 1oyzA in template set T0382 48 :ADELKARDGD 1oyzA 17 :YNQCKKLNDD T0382 61 :ALLSLFEYPNMQVRLQAAKLTLAVAPVKAREQLEAIVSSKW 1oyzA 27 :ELFRLLDDHNSLKRISSARVLQLRGGQDAVRLAIEFCSDKN T0382 102 :FPQAGDAGMCLDLL 1oyzA 82 :KICKKCEDNVFNIL Number of specific fragments extracted= 3 number of extra gaps= 0 total=153 Number of alignments=37 # 1oyzA read from 1oyzA/merged-good-all-a2m # found chain 1oyzA in template set T0382 47 :IADELKARDGD 1oyzA 16 :LYNQCKKLNDD T0382 61 :ALLSLFEYPNMQVRLQAAKLTLAVAPVKAREQLEAIVSSKW 1oyzA 27 :ELFRLLDDHNSLKRISSARVLQLRGGQDAVRLAIEFCSDKN T0382 102 :FPQAGDAGMCLDLLD 1oyzA 82 :KICKKCEDNVFNILN Number of specific fragments extracted= 3 number of extra gaps= 0 total=156 Number of alignments=38 # 1oyzA read from 1oyzA/merged-good-all-a2m # found chain 1oyzA in template set T0382 11 :TQDLVALFAKVTVEQDDALLGNQISRFNRL 1oyzA 88 :EDNVFNILNNMALNDKSACVRATAIESTAQ T0382 41 :FGVMAEIADELKARDG 1oyzA 126 :SPKIVEQSQITAFDKS T0382 57 :DQRT 1oyzA 143 :NVRR T0382 61 :ALLSLFEYPNMQVRLQAAKLTL 1oyzA 163 :LLINLLKDPNGDVRNWAAFAIN T0382 83 :AVAPVKAREQLEAIVSSKW 1oyzA 187 :KYDNSDIRDCFVEMLQDKN Number of specific fragments extracted= 5 number of extra gaps= 0 total=161 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yn9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0382 read from 1yn9A/merged-good-all-a2m # 1yn9A read from 1yn9A/merged-good-all-a2m # found chain 1yn9A in training set T0382 3 :KLDLHQMTTQDLVAL 1yn9A 37 :TSEEDVWTAEQIVKQ T0382 33 :QISRFNR 1yn9A 69 :DGVHFLR T0382 42 :GVMAEIADELKA 1yn9A 94 :SIVQEFIDTVKE T0382 54 :RDGD 1yn9A 110 :CPGM T0382 66 :FEYPNMQVRLQAAKLTLAV 1yn9A 119 :CTHGINRTGYMVCRYLMHT T0382 85 :APVKAREQLEAIVSSKW 1yn9A 141 :APQEAIDRFEKARGHKI T0382 107 :DAGMCLDLL 1yn9A 158 :ERQNYVQDL Number of specific fragments extracted= 7 number of extra gaps= 0 total=168 Number of alignments=40 # 1yn9A read from 1yn9A/merged-good-all-a2m # found chain 1yn9A in training set T0382 3 :KLDLHQMTTQDLVAL 1yn9A 37 :TSEEDVWTAEQIVKQ T0382 33 :QISRFNRL 1yn9A 69 :DGVHFLRA T0382 41 :FGVMAEIADELKA 1yn9A 93 :ESIVQEFIDTVKE T0382 54 :RDGD 1yn9A 110 :CPGM T0382 66 :FEYPNMQVRLQAAKLTLAV 1yn9A 119 :CTHGINRTGYMVCRYLMHT T0382 85 :APVKAREQLEAIVSSKW 1yn9A 141 :APQEAIDRFEKARGHKI T0382 107 :DAGMCLDLL 1yn9A 158 :ERQNYVQDL Number of specific fragments extracted= 7 number of extra gaps= 0 total=175 Number of alignments=41 # 1yn9A read from 1yn9A/merged-good-all-a2m # found chain 1yn9A in training set T0382 3 :KLDLHQMTTQDLVAL 1yn9A 37 :TSEEDVWTAEQIVKQ T0382 23 :VEQDDA 1yn9A 71 :VHFLRA T0382 33 :QISRFNRLFGVMAEIADE 1yn9A 92 :PESIVQEFIDTVKEFTEK T0382 54 :RDG 1yn9A 110 :CPG T0382 67 :EYPNMQVRLQAAKLTLA 1yn9A 120 :THGINRTGYMVCRYLMH T0382 84 :VAPVKAREQLEAIVSSKWFP 1yn9A 140 :IAPQEAIDRFEKARGHKIER T0382 109 :GMCLDL 1yn9A 160 :QNYVQD Number of specific fragments extracted= 7 number of extra gaps= 0 total=182 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ea1A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ea1A expands to /projects/compbio/data/pdb/1ea1.pdb.gz 1ea1A:# T0382 read from 1ea1A/merged-good-all-a2m # 1ea1A read from 1ea1A/merged-good-all-a2m # adding 1ea1A to template set # found chain 1ea1A in template set T0382 8 :QMT 1ea1A 160 :QLD T0382 16 :ALFAKVTVEQDD 1ea1A 163 :GRFAKLYHELER T0382 28 :AL 1ea1A 180 :AY T0382 30 :LGNQISRFNRLFGVMAEIADELKAR 1ea1A 184 :PYLPIESFRRRDEARNGLVALVADI T0382 55 :DGDQRTALLSLF 1ea1A 219 :DKSDRDMLDVLI T0382 67 :EYPNMQVRLQ 1ea1A 240 :RFSADEITGM T0382 77 :AAKLTLAVAP 1ea1A 265 :ASWTLIELMR T0382 87 :VKAREQLEAIVSSKW 1ea1A 280 :AAVIDELDELYGDGR Number of specific fragments extracted= 8 number of extra gaps= 0 total=190 Number of alignments=43 # 1ea1A read from 1ea1A/merged-good-all-a2m # found chain 1ea1A in template set T0382 3 :KLDLHQMTTQDLVALFAKVTVEQ 1ea1A 235 :ETGTPRFSADEITGMFISMMFAG T0382 26 :DDALLGNQISRFNRLFGVMA 1ea1A 261 :SSGTASWTLIELMRHRDAYA T0382 88 :KAREQLEAIVSSK 1ea1A 281 :AVIDELDELYGDG Number of specific fragments extracted= 3 number of extra gaps= 0 total=193 Number of alignments=44 # 1ea1A read from 1ea1A/merged-good-all-a2m # found chain 1ea1A in template set T0382 2 :SKLDLHQMTTQDLVALFAKVTVE 1ea1A 234 :AETGTPRFSADEITGMFISMMFA T0382 25 :QDDALLGNQISRFNRLFGVMAEIADELKARDGDQRTA 1ea1A 260 :TSSGTASWTLIELMRHRDAYAAVIDELDELYGDGRSV T0382 63 :LSLFEYPNMQVR 1ea1A 297 :SFHALRQIPQLE T0382 76 :QAAKLTLAVAP 1ea1A 309 :NVLKETLRLHP Number of specific fragments extracted= 4 number of extra gaps= 0 total=197 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1xtcA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1xtcA expands to /projects/compbio/data/pdb/1xtc.pdb.gz 1xtcA:# T0382 read from 1xtcA/merged-good-all-a2m # 1xtcA read from 1xtcA/merged-good-all-a2m # adding 1xtcA to template set # found chain 1xtcA in template set Warning: unaligning (T0382)P86 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xtcA)D14 Warning: unaligning (T0382)V87 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xtcA)D14 Warning: unaligning (T0382)K88 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xtcA)E15 Warning: unaligning (T0382)A89 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xtcA)I16 Warning: unaligning (T0382)R90 because of BadResidue code BAD_PEPTIDE at template residue (1xtcA)K17 Warning: unaligning (T0382)E91 because of BadResidue code BAD_PEPTIDE at template residue (1xtcA)Q18 Warning: unaligning (T0382)Q92 because of BadResidue code BAD_PEPTIDE at template residue (1xtcA)S19 Number of specific fragments extracted= 0 number of extra gaps= 1 total=197 # 1xtcA read from 1xtcA/merged-good-all-a2m # found chain 1xtcA in template set Warning: unaligning (T0382)P86 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xtcA)D14 Warning: unaligning (T0382)V87 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xtcA)D14 Warning: unaligning (T0382)K88 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xtcA)E15 Warning: unaligning (T0382)A89 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xtcA)I16 Warning: unaligning (T0382)R90 because of BadResidue code BAD_PEPTIDE at template residue (1xtcA)K17 Warning: unaligning (T0382)E91 because of BadResidue code BAD_PEPTIDE at template residue (1xtcA)Q18 Warning: unaligning (T0382)Q92 because of BadResidue code BAD_PEPTIDE at template residue (1xtcA)S19 Number of specific fragments extracted= 0 number of extra gaps= 1 total=197 # 1xtcA read from 1xtcA/merged-good-all-a2m # found chain 1xtcA in template set Warning: unaligning (T0382)P86 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1xtcA)D14 Warning: unaligning (T0382)V87 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1xtcA)D14 Warning: unaligning (T0382)K88 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xtcA)E15 Warning: unaligning (T0382)A89 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1xtcA)I16 Warning: unaligning (T0382)R90 because of BadResidue code BAD_PEPTIDE at template residue (1xtcA)K17 Warning: unaligning (T0382)E91 because of BadResidue code BAD_PEPTIDE at template residue (1xtcA)Q18 Warning: unaligning (T0382)Q92 because of BadResidue code BAD_PEPTIDE at template residue (1xtcA)S19 T0382 85 :A 1xtcA 12 :P Number of specific fragments extracted= 1 number of extra gaps= 1 total=198 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ahc/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ahc expands to /projects/compbio/data/pdb/1ahc.pdb.gz 1ahc:Warning: there is no chain 1ahc will retry with 1ahcA # T0382 read from 1ahc/merged-good-all-a2m # 1ahc read from 1ahc/merged-good-all-a2m # adding 1ahc to template set # found chain 1ahc in template set T0382 49 :DELK 1ahc 130 :PALD T0382 60 :TALLSLFEYPNMQVRLQAAKLT 1ahc 134 :SAISTLLHYDSTAAAGALLVLI T0382 82 :LAVA 1ahc 161 :AARF T0382 90 :REQLEAIVSSKWFPQAGD 1ahc 165 :KYIEQQIQERAYRDEVPS T0382 108 :AGMCLDLL 1ahc 185 :TISLENSW Number of specific fragments extracted= 5 number of extra gaps= 0 total=203 Number of alignments=46 # 1ahc read from 1ahc/merged-good-all-a2m # found chain 1ahc in template set T0382 50 :EL 1ahc 131 :AL T0382 59 :RTALLSLFEYPNMQVRLQAAKLT 1ahc 133 :DSAISTLLHYDSTAAAGALLVLI T0382 82 :LAVAPVKAREQLEAIVSSKWFPQA 1ahc 160 :EAARFKYIEQQIQERAYRDEVPSL T0382 107 :DAGMCLDLL 1ahc 184 :ATISLENSW Number of specific fragments extracted= 4 number of extra gaps= 0 total=207 Number of alignments=47 # 1ahc read from 1ahc/merged-good-all-a2m # found chain 1ahc in template set T0382 58 :QRTALLSLFEYPN 1ahc 132 :LDSAISTLLHYDS T0382 75 :LQAAKLTLAV 1ahc 145 :TAAAGALLVL T0382 87 :VKAREQLEAIVSSKWFP 1ahc 165 :KYIEQQIQERAYRDEVP Number of specific fragments extracted= 3 number of extra gaps= 0 total=210 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i8vA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1i8vA expands to /projects/compbio/data/pdb/1i8v.pdb.gz 1i8vA:Skipped atom 39, because occupancy 0.500 <= existing 0.500 in 1i8vA Skipped atom 41, because occupancy 0.500 <= existing 0.500 in 1i8vA Skipped atom 250, because occupancy 0.400 <= existing 0.600 in 1i8vA Skipped atom 252, because occupancy 0.400 <= existing 0.600 in 1i8vA Skipped atom 306, because occupancy 0.400 <= existing 0.600 in 1i8vA Skipped atom 308, because occupancy 0.400 <= existing 0.600 in 1i8vA Skipped atom 310, because occupancy 0.400 <= existing 0.600 in 1i8vA Skipped atom 317, because occupancy 0.300 <= existing 0.700 in 1i8vA Skipped atom 418, because occupancy 0.500 <= existing 0.500 in 1i8vA Skipped atom 420, because occupancy 0.500 <= existing 0.500 in 1i8vA Skipped atom 422, because occupancy 0.500 <= existing 0.500 in 1i8vA Skipped atom 424, because occupancy 0.500 <= existing 0.500 in 1i8vA # T0382 read from 1i8vA/merged-good-all-a2m # 1i8vA read from 1i8vA/merged-good-all-a2m # adding 1i8vA to template set # found chain 1i8vA in template set T0382 85 :APVKAREQLEAIVSSKWFPQAG 1i8vA 11 :LPPEATDTLNLIASDGPFPYSQ T0382 116 :DDGTF 1i8vA 33 :DGVVF Number of specific fragments extracted= 2 number of extra gaps= 0 total=212 Number of alignments=49 # 1i8vA read from 1i8vA/merged-good-all-a2m # found chain 1i8vA in template set T0382 85 :APVKAREQLEAIVSSKWFPQAG 1i8vA 11 :LPPEATDTLNLIASDGPFPYSQ T0382 116 :DDGTFK 1i8vA 33 :DGVVFQ Number of specific fragments extracted= 2 number of extra gaps= 0 total=214 Number of alignments=50 # 1i8vA read from 1i8vA/merged-good-all-a2m # found chain 1i8vA in template set T0382 85 :APVKAREQLEAIVSSKWFPQAGD 1i8vA 11 :LPPEATDTLNLIASDGPFPYSQD Number of specific fragments extracted= 1 number of extra gaps= 0 total=215 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2a5dB/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/T0382/2a5dB/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0382/2a5dB/merged-good-all-a2m.gz for input Trying 2a5dB/merged-good-all-a2m Error: Couldn't open file 2a5dB/merged-good-all-a2m or 2a5dB/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1s5eA/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/T0382/1s5eA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0382/1s5eA/merged-good-all-a2m.gz for input Trying 1s5eA/merged-good-all-a2m Error: Couldn't open file 1s5eA/merged-good-all-a2m or 1s5eA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r6aA/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/T0382/1r6aA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0382/1r6aA/merged-good-all-a2m.gz for input Trying 1r6aA/merged-good-all-a2m Error: Couldn't open file 1r6aA/merged-good-all-a2m or 1r6aA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1x8vA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0382 read from 1x8vA/merged-good-all-a2m # 1x8vA read from 1x8vA/merged-good-all-a2m # found chain 1x8vA in training set Warning: unaligning (T0382)L6 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1x8vA)T238 T0382 7 :HQMTTQDLVALFAKVTVEQDDALLG 1x8vA 239 :PRFSADEITGMFISMMFAGHHTSSG T0382 32 :NQISRFNRLFGVMAEIADELKAR 1x8vA 267 :WTLIELMRHRDAYAAVIDELDEL T0382 97 :VSSKW 1x8vA 290 :YGDGR Number of specific fragments extracted= 3 number of extra gaps= 0 total=218 Number of alignments=52 # 1x8vA read from 1x8vA/merged-good-all-a2m # found chain 1x8vA in training set T0382 8 :QMTTQDLVALFAKVTVEQDDALLG 1x8vA 240 :RFSADEITGMFISMMFAGHHTSSG T0382 32 :NQISRFNRLFGVMAEIADELKARDGDQRTALLSLFE 1x8vA 267 :WTLIELMRHRDAYAAVIDELDELYGDGRSVSFHALR T0382 69 :PN 1x8vA 303 :QI T0382 72 :QVRLQAAKLTLAV 1x8vA 305 :PQLENVLKETLRL Number of specific fragments extracted= 4 number of extra gaps= 0 total=222 Number of alignments=53 # 1x8vA read from 1x8vA/merged-good-all-a2m # found chain 1x8vA in training set Warning: unaligning (T0382)L6 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1x8vA)T238 T0382 7 :HQMTTQDLVALFAKVTVEQDDALLG 1x8vA 239 :PRFSADEITGMFISMMFAGHHTSSG T0382 32 :NQISRFNRLFGVMAEIADELKARDGDQRTALLSLFE 1x8vA 267 :WTLIELMRHRDAYAAVIDELDELYGDGRSVSFHALR T0382 70 :NMQVRLQAAKLTLAVAP 1x8vA 303 :QIPQLENVLKETLRLHP Number of specific fragments extracted= 3 number of extra gaps= 0 total=225 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lrv/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1lrv expands to /projects/compbio/data/pdb/1lrv.pdb.gz 1lrv:Warning: there is no chain 1lrv will retry with 1lrvA # T0382 read from 1lrv/merged-good-all-a2m # 1lrv read from 1lrv/merged-good-all-a2m # adding 1lrv to template set # found chain 1lrv in template set T0382 2 :SKLDLHQMT 1lrv 171 :PEESLGLMT T0382 34 :I 1lrv 183 :E T0382 41 :FGVMAEIADE 1lrv 184 :PEVRRIVASR T0382 54 :RDGD 1lrv 194 :LRGD T0382 62 :LLSLFEYPNMQVRLQAAKL 1lrv 199 :LLELLHDPDWTVRLAAVEH T0382 85 :APVKAREQ 1lrv 218 :ASLEALRE Number of specific fragments extracted= 6 number of extra gaps= 0 total=231 Number of alignments=55 # 1lrv read from 1lrv/merged-good-all-a2m # found chain 1lrv in template set T0382 41 :FGVMAEIADE 1lrv 184 :PEVRRIVASR T0382 54 :RDGDQ 1lrv 194 :LRGDD T0382 62 :LLSLFEYPNMQVRLQAAKL 1lrv 199 :LLELLHDPDWTVRLAAVEH T0382 85 :APVKAREQ 1lrv 218 :ASLEALRE T0382 104 :QAGDAGMC 1lrv 229 :PDPEVRLA Number of specific fragments extracted= 5 number of extra gaps= 0 total=236 Number of alignments=56 # 1lrv read from 1lrv/merged-good-all-a2m # found chain 1lrv in template set T0382 2 :SKLDLHQM 1lrv 171 :PEESLGLM T0382 10 :TTQDLVALFAKV 1lrv 182 :PEPEVRRIVASR T0382 54 :RDGDQ 1lrv 194 :LRGDD T0382 62 :LLSLFEYPNMQVRLQAAKL 1lrv 199 :LLELLHDPDWTVRLAAVEH T0382 85 :APVKAREQ 1lrv 218 :ASLEALRE T0382 93 :LEAIVS 1lrv 233 :VRLAIA Number of specific fragments extracted= 6 number of extra gaps= 0 total=242 Number of alignments=57 # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0382//projects/compbio/experiments/protein-predict/casp7/T0382/align.constraints_v3.costfcn or /projects/compbio/experiments/protein-predict/casp7/T0382//projects/compbio/experiments/protein-predict/casp7/T0382/align.constraints_v3.costfcn.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/T0382/align.constraints_v3.costfcn # reading script from file /projects/compbio/experiments/protein-predict/casp7/T0382/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((T0382)F37.CB, (T0382)I47.CB) [> 4.0134 = 6.6890 < 8.6957] w=1.0000 to align # Constraint # added constraint: constraint((T0382)F37.CB, (T0382)A77.CB) [> 3.8447 = 6.4078 < 8.3301] w=0.9181 to align # Constraint # added constraint: constraint((T0382)A78.CB, (T0382)R90.CB) [> 3.5998 = 5.9997 < 7.7996] w=0.7703 to align # Constraint # added constraint: constraint((T0382)I47.CB, (T0382)V73.CB) [> 2.9515 = 4.9192 < 6.3950] w=0.7448 to align # Constraint # added constraint: constraint((T0382)E50.CB, (T0382)V73.CB) [> 3.0997 = 5.1661 < 6.7160] w=0.6833 to align # Constraint # added constraint: constraint((T0382)E50.CB, (T0382)Q72.CB) [> 3.8192 = 6.3654 < 8.2750] w=0.6833 to align # Constraint # added constraint: constraint((T0382)I47.CB, (T0382)A77.CB) [> 3.7122 = 6.1869 < 8.0430] w=0.6833 to align # Constraint # added constraint: constraint((T0382)R36.CB, (T0382)A77.CB) [> 3.8900 = 6.4833 < 8.4283] w=0.6833 to align # Constraint # added constraint: constraint((T0382)L51.CB, (T0382)R74.CB) [> 3.9706 = 6.6176 < 8.6029] w=0.6689 to align # Constraint # added constraint: constraint((T0382)N32.CB, (T0382)V84.CB) [> 4.5760 = 7.6266 < 9.9146] w=0.6132 to align # Constraint # added constraint: constraint((T0382)R36.CB, (T0382)L80.CB) [> 4.1821 = 6.9702 < 9.0613] w=0.6132 to align # Constraint # added constraint: constraint((T0382)R36.CB, (T0382)T81.CB) [> 2.9743 = 4.9573 < 6.4444] w=0.6132 to align # Constraint # added constraint: constraint((T0382)R36.CB, (T0382)V84.CB) [> 4.3474 = 7.2456 < 9.4193] w=0.6132 to align # Constraint # added constraint: constraint((T0382)I47.CB, (T0382)R74.CB) [> 2.9218 = 4.8696 < 6.3305] w=0.6063 to align # Constraint # added constraint: constraint((T0382)L51.CB, (T0382)L62.CB) [> 4.2833 = 7.1389 < 9.2806] w=0.6043 to align # Constraint # added constraint: constraint((T0382)A78.CB, (T0382)A89.CB) [> 2.7330 = 4.5551 < 5.9216] w=0.5811 to align # Constraint # added constraint: constraint((T0382)R74.CB, (T0382)C111.CB) [> 3.9573 = 6.5955 < 8.5742] w=0.5811 to align # Constraint # added constraint: constraint((T0382)L65.CB, (T0382)Q76.CB) [> 4.2357 = 7.0595 < 9.1773] w=0.5576 to align # Constraint # added constraint: constraint((T0382)L65.CB, (T0382)A77.CB) [> 2.9091 = 4.8485 < 6.3031] w=0.5562 to align # Constraint # added constraint: constraint((T0382)L62.CB, (T0382)L80.CB) [> 4.0285 = 6.7141 < 8.7283] w=0.5562 to align # Constraint # added constraint: constraint((T0382)F18.CB, (T0382)I47.CB) [> 3.3639 = 5.6065 < 7.2885] w=0.5546 to align # Constraint # added constraint: constraint((T0382)E50.CB, (T0382)M71.CB) [> 4.1613 = 6.9354 < 9.0160] w=0.5451 to align # Constraint # added constraint: constraint((T0382)E50.CB, (T0382)R74.CB) [> 4.0726 = 6.7877 < 8.8240] w=0.5410 to align # Constraint # added constraint: constraint((T0382)A78.CB, (T0382)L93.CB) [> 3.4199 = 5.6999 < 7.4098] w=0.5202 to align # Constraint # added constraint: constraint((T0382)T81.CB, (T0382)L93.CB) [> 4.2989 = 7.1649 < 9.3143] w=0.5187 to align # Constraint # added constraint: constraint((T0382)R54.CB, (T0382)L65.CB) [> 3.9952 = 6.6587 < 8.6563] w=0.5169 to align # Constraint # added constraint: constraint((T0382)F66.CB, (T0382)A78.CB) [> 3.7167 = 6.1945 < 8.0529] w=0.5009 to align # Constraint # added constraint: constraint((T0382)A48.CB, (T0382)R74.CB) [> 4.1374 = 6.8957 < 8.9644] w=0.4886 to align # Constraint # added constraint: constraint((T0382)R54.CB, (T0382)S64.CB) [> 3.4852 = 5.8087 < 7.5514] w=0.4787 to align # Constraint # added constraint: constraint((T0382)E46.CB, (T0382)V73.CB) [> 2.8281 = 4.7134 < 6.1275] w=0.4787 to align # Constraint # added constraint: constraint((T0382)R36.CB, (T0382)A85.CB) [> 4.6940 = 7.8234 < 10.1704] w=0.4675 to align # Constraint # added constraint: constraint((T0382)N32.CB, (T0382)A85.CB) [> 2.8056 = 4.6761 < 6.0789] w=0.4675 to align # Constraint # added constraint: constraint((T0382)R74.CB, (T0382)L93.CB) [> 3.2817 = 5.4696 < 7.1104] w=0.4587 to align # Constraint # added constraint: constraint((T0382)L62.CB, (T0382)A77.CB) [> 3.0072 = 5.0120 < 6.5156] w=0.4365 to align # Constraint # added constraint: constraint((T0382)Y68.CB, (T0382)A77.CB) [> 4.2426 = 7.0711 < 9.1924] w=0.4346 to align # Constraint # added constraint: constraint((T0382)F18.CB, (T0382)L51.CB) [> 4.4543 = 7.4238 < 9.6509] w=0.4270 to align # Constraint # added constraint: constraint((T0382)A28.CB, (T0382)F37.CB) [> 3.0104 = 5.0174 < 6.5226] w=0.4203 to align # Constraint # added constraint: constraint((T0382)W101.CB, (T0382)C111.CB) [> 3.9541 = 6.5902 < 8.5673] w=0.3956 to align # Constraint # added constraint: constraint((T0382)T81.CB, (T0382)Q92.CB) [> 3.8276 = 6.3794 < 8.2932] w=0.3956 to align # Constraint # added constraint: constraint((T0382)A77.CB, (T0382)L93.CB) [> 3.0376 = 5.0626 < 6.5814] w=0.3956 to align # Constraint # added constraint: constraint((T0382)R74.CB, (T0382)A108.CB) [> 4.3316 = 7.2193 < 9.3850] w=0.3916 to align # Constraint # added constraint: constraint((T0382)A77.CB, (T0382)A89.CB) [> 4.6801 = 7.8002 < 10.1402] w=0.3868 to align # Constraint # added constraint: constraint((T0382)V73.CB, (T0382)G109.CA) [> 4.6950 = 7.8250 < 10.1725] w=0.3797 to align # Constraint # added constraint: constraint((T0382)V73.CB, (T0382)C111.CB) [> 3.6908 = 6.1514 < 7.9968] w=0.3797 to align # Constraint # added constraint: constraint((T0382)Q76.CB, (T0382)G109.CA) [> 4.7267 = 7.8777 < 10.2411] w=0.3797 to align # Constraint # added constraint: constraint((T0382)A77.CB, (T0382)G109.CA) [> 3.9260 = 6.5434 < 8.5064] w=0.3797 to align # Constraint # added constraint: constraint((T0382)A77.CB, (T0382)C111.CB) [> 2.2642 = 3.7737 < 4.9058] w=0.3797 to align # Constraint # added constraint: constraint((T0382)L80.CB, (T0382)G109.CA) [> 4.5599 = 7.5998 < 9.8798] w=0.3797 to align # Constraint # added constraint: constraint((T0382)L80.CB, (T0382)L112.CB) [> 3.0234 = 5.0390 < 6.5507] w=0.3797 to align # Constraint # added constraint: constraint((T0382)T81.CB, (T0382)L112.CB) [> 3.8271 = 6.3786 < 8.2921] w=0.3797 to align # Constraint # added constraint: constraint((T0382)F66.CB, (T0382)A77.CB) [> 3.0468 = 5.0780 < 6.6014] w=0.3739 to align # Constraint # added constraint: constraint((T0382)L65.CB, (T0382)R74.CB) [> 4.0886 = 6.8143 < 8.8586] w=0.3739 to align # Constraint # added constraint: constraint((T0382)L63.CB, (T0382)A89.CB) [> 3.8604 = 6.4339 < 8.3641] w=0.3739 to align # Constraint # added constraint: constraint((T0382)L62.CB, (T0382)A89.CB) [> 4.3714 = 7.2857 < 9.4714] w=0.3739 to align # Constraint # added constraint: constraint((T0382)V15.CB, (T0382)L51.CB) [> 4.2074 = 7.0123 < 9.1160] w=0.3644 to align # Constraint # added constraint: constraint((T0382)F18.CB, (T0382)A48.CB) [> 3.6839 = 6.1398 < 7.9818] w=0.3644 to align # Constraint # added constraint: constraint((T0382)Q25.CB, (T0382)M44.CB) [> 3.7308 = 6.2180 < 8.0834] w=0.3624 to align # Constraint # added constraint: constraint((T0382)Q25.CB, (T0382)L40.CB) [> 2.5964 = 4.3273 < 5.6255] w=0.3624 to align # Constraint # added constraint: constraint((T0382)E24.CB, (T0382)L40.CB) [> 3.4453 = 5.7421 < 7.4648] w=0.3624 to align # Constraint # added constraint: constraint((T0382)V21.CB, (T0382)M44.CB) [> 3.4850 = 5.8083 < 7.5508] w=0.3624 to align # Constraint # added constraint: constraint((T0382)F18.CB, (T0382)M44.CB) [> 3.4585 = 5.7642 < 7.4934] w=0.3622 to align # Constraint # added constraint: constraint((T0382)E50.CB, (T0382)N70.CB) [> 3.8153 = 6.3589 < 8.2666] w=0.3427 to align # Constraint # added constraint: constraint((T0382)R54.CB, (T0382)M71.CB) [> 3.8983 = 6.4972 < 8.4463] w=0.3406 to align # Constraint # added constraint: constraint((T0382)L75.CB, (T0382)W101.CB) [> 4.1434 = 6.9056 < 8.9773] w=0.3264 to align # Constraint # added constraint: constraint((T0382)R74.CB, (T0382)W101.CB) [> 3.1067 = 5.1778 < 6.7312] w=0.3264 to align # Constraint # added constraint: constraint((T0382)M71.CB, (T0382)D107.CB) [> 3.8861 = 6.4769 < 8.4199] w=0.3243 to align # Constraint # added constraint: constraint((T0382)L93.CB, (T0382)L115.CB) [> 3.1270 = 5.2116 < 6.7751] w=0.3212 to align # Constraint # added constraint: constraint((T0382)A48.CB, (T0382)K79.CB) [> 3.8709 = 6.4516 < 8.3871] w=0.3200 to align # Constraint # added constraint: constraint((T0382)R54.CB, (T0382)L80.CB) [> 4.4229 = 7.3714 < 9.5829] w=0.3123 to align # Constraint # added constraint: constraint((T0382)A19.CB, (T0382)L65.CB) [> 4.3078 = 7.1796 < 9.3335] w=0.2979 to align # Constraint # added constraint: constraint((T0382)V15.CB, (T0382)L65.CB) [> 3.7627 = 6.2712 < 8.1526] w=0.2979 to align # Constraint # added constraint: constraint((T0382)L6.CB, (T0382)E50.CB) [> 3.6464 = 6.0774 < 7.9006] w=0.2979 to align # Constraint # added constraint: constraint((T0382)T22.CB, (T0382)R74.CB) [> 3.9867 = 6.6445 < 8.6378] w=0.2975 to align # Constraint # added constraint: constraint((T0382)Q25.CB, (T0382)A77.CB) [> 4.0622 = 6.7704 < 8.8015] w=0.2975 to align # Constraint # added constraint: constraint((T0382)A45.CB, (T0382)L75.CB) [> 3.4437 = 5.7394 < 7.4613] w=0.2975 to align # Constraint # added constraint: constraint((T0382)M71.CB, (T0382)W101.CB) [> 3.2515 = 5.4192 < 7.0450] w=0.2629 to align # Constraint # added constraint: constraint((T0382)K52.CB, (T0382)V84.CB) [> 4.6802 = 7.8003 < 10.1404] w=0.2573 to align # Constraint # added constraint: constraint((T0382)A48.CB, (T0382)L75.CB) [> 4.2627 = 7.1045 < 9.2359] w=0.2557 to align # Constraint # added constraint: constraint((T0382)F66.CB, (T0382)A89.CB) [> 3.8017 = 6.3362 < 8.2371] w=0.2508 to align # Constraint # added constraint: constraint((T0382)L29.CB, (T0382)I47.CB) [> 4.0098 = 6.6831 < 8.6880] w=0.2502 to align # Constraint # added constraint: constraint((T0382)L51.CB, (T0382)K79.CB) [> 4.0221 = 6.7035 < 8.7146] w=0.2446 to align # Constraint # added constraint: constraint((T0382)T22.CB, (T0382)N70.CB) [> 3.3927 = 5.6546 < 7.3509] w=0.2349 to align # Constraint # added constraint: constraint((T0382)T22.CB, (T0382)M44.CB) [> 3.2177 = 5.3628 < 6.9716] w=0.2349 to align # Constraint # added constraint: constraint((T0382)T22.CB, (T0382)F41.CB) [> 4.7595 = 7.9325 < 10.3123] w=0.2349 to align # Constraint # added constraint: constraint((T0382)T22.CB, (T0382)L40.CB) [> 4.5653 = 7.6088 < 9.8915] w=0.2349 to align # Constraint # added constraint: constraint((T0382)V21.CB, (T0382)L40.CB) [> 3.1508 = 5.2513 < 6.8267] w=0.2349 to align # Constraint # added constraint: constraint((T0382)A19.CB, (T0382)F66.CB) [> 4.3666 = 7.2777 < 9.4610] w=0.2349 to align # Constraint # added constraint: constraint((T0382)L17.CB, (T0382)I47.CB) [> 3.7772 = 6.2953 < 8.1839] w=0.2349 to align # Constraint # added constraint: constraint((T0382)V15.CB, (T0382)L62.CB) [> 3.6181 = 6.0301 < 7.8392] w=0.2349 to align # Constraint # added constraint: constraint((T0382)L14.CB, (T0382)L51.CB) [> 2.9068 = 4.8446 < 6.2980] w=0.2349 to align # Constraint # added constraint: constraint((T0382)L14.CB, (T0382)E50.CB) [> 4.2210 = 7.0350 < 9.1455] w=0.2349 to align # Constraint # added constraint: constraint((T0382)L14.CB, (T0382)I47.CB) [> 3.0906 = 5.1510 < 6.6963] w=0.2349 to align # Constraint # added constraint: constraint((T0382)T11.CB, (T0382)L62.CB) [> 4.3056 = 7.1759 < 9.3287] w=0.2349 to align # Constraint # added constraint: constraint((T0382)T11.CB, (T0382)G56.CA) [> 3.6695 = 6.1158 < 7.9506] w=0.2349 to align # Constraint # added constraint: constraint((T0382)T11.CB, (T0382)R54.CB) [> 3.2765 = 5.4608 < 7.0990] w=0.2349 to align # Constraint # added constraint: constraint((T0382)T11.CB, (T0382)L51.CB) [> 3.0929 = 5.1549 < 6.7013] w=0.2349 to align # Constraint # added constraint: constraint((T0382)K3.CB, (T0382)D13.CB) [> 4.7762 = 7.9603 < 10.3484] w=0.2349 to align # Constraint # added constraint: constraint((T0382)F41.CB, (T0382)T81.CB) [> 4.0735 = 6.7891 < 8.8259] w=0.2349 to align # Constraint # added constraint: constraint((T0382)N38.CB, (T0382)T81.CB) [> 2.3176 = 3.8626 < 5.0214] w=0.2349 to align # Constraint # added constraint: constraint((T0382)N38.CB, (T0382)A77.CB) [> 4.6484 = 7.7473 < 10.0715] w=0.2349 to align # Constraint # added constraint: constraint((T0382)F37.CB, (T0382)T81.CB) [> 3.5280 = 5.8800 < 7.6440] w=0.2349 to align # Constraint # added constraint: constraint((T0382)I34.CB, (T0382)A83.CB) [> 4.3939 = 7.3231 < 9.5201] w=0.2349 to align # Constraint # added constraint: constraint((T0382)Q25.CB, (T0382)R74.CB) [> 4.2485 = 7.0809 < 9.2051] w=0.2349 to align # Constraint # added constraint: constraint((T0382)Q25.CB, (T0382)R36.CB) [> 4.6972 = 7.8287 < 10.1773] w=0.2349 to align # Constraint # added constraint: constraint((T0382)I47.CB, (T0382)Q58.CB) [> 3.3420 = 5.5700 < 7.2410] w=0.2103 to align # Constraint # added constraint: constraint((T0382)I47.CB, (T0382)R59.CB) [> 3.9451 = 6.5752 < 8.5477] w=0.2103 to align # Constraint # added constraint: constraint((T0382)L40.CB, (T0382)A77.CB) [> 4.7666 = 7.9444 < 10.3277] w=0.2073 to align # Constraint # added constraint: constraint((T0382)L29.CB, (T0382)A78.CB) [> 4.6021 = 7.6702 < 9.9713] w=0.2045 to align # Constraint # added constraint: constraint((T0382)L29.CB, (T0382)T81.CB) [> 4.0535 = 6.7559 < 8.7826] w=0.2045 to align # Constraint # added constraint: constraint((T0382)R74.CB, (T0382)E94.CB) [> 4.3786 = 7.2977 < 9.4870] w=0.2014 to align # Constraint # added constraint: constraint((T0382)R74.CB, (T0382)V97.CB) [> 4.1774 = 6.9623 < 9.0509] w=0.2014 to align # Constraint # added constraint: constraint((T0382)L75.CB, (T0382)L114.CB) [> 4.4643 = 7.4405 < 9.6726] w=0.2014 to align # Constraint # added constraint: constraint((T0382)G31.CA, (T0382)A85.CB) [> 4.5957 = 7.6595 < 9.9574] w=0.2004 to align # Constraint # added constraint: constraint((T0382)L75.CB, (T0382)A108.CB) [> 3.9261 = 6.5436 < 8.5066] w=0.1973 to align # Constraint # added constraint: constraint((T0382)M71.CB, (T0382)A108.CB) [> 2.6911 = 4.4852 < 5.8308] w=0.1973 to align # Constraint # added constraint: constraint((T0382)P86.CB, (T0382)L115.CB) [> 3.1549 = 5.2582 < 6.8357] w=0.1950 to align # Constraint # added constraint: constraint((T0382)V73.CB, (T0382)G106.CA) [> 3.2970 = 5.4950 < 7.1435] w=0.1943 to align # Constraint # added constraint: constraint((T0382)V73.CB, (T0382)A108.CB) [> 2.5023 = 4.1705 < 5.4217] w=0.1943 to align # Constraint # added constraint: constraint((T0382)R74.CB, (T0382)Q104.CB) [> 4.6410 = 7.7349 < 10.0554] w=0.1943 to align # Constraint # added constraint: constraint((T0382)A77.CB, (T0382)F102.CB) [> 4.7618 = 7.9364 < 10.3173] w=0.1943 to align # Constraint # added constraint: constraint((T0382)A77.CB, (T0382)A108.CB) [> 2.7311 = 4.5518 < 5.9174] w=0.1943 to align # Constraint # added constraint: constraint((T0382)L80.CB, (T0382)A108.CB) [> 4.2290 = 7.0484 < 9.1629] w=0.1943 to align # Constraint # added constraint: constraint((T0382)Q92.CB, (T0382)L115.CB) [> 2.5291 = 4.2151 < 5.4796] w=0.1943 to align # Constraint # added constraint: constraint((T0382)L93.CB, (T0382)C111.CB) [> 3.3688 = 5.6146 < 7.2990] w=0.1943 to align # Constraint # added constraint: constraint((T0382)F102.CB, (T0382)C111.CB) [> 3.9044 = 6.5073 < 8.4595] w=0.1943 to align # Constraint # added constraint: constraint((T0382)V15.CB, (T0382)A28.CB) [> 3.8247 = 6.3745 < 8.2868] w=0.1907 to align # Constraint # added constraint: constraint((T0382)M9.CB, (T0382)F18.CB) [> 2.8380 = 4.7300 < 6.1490] w=0.1907 to align # Constraint # added constraint: constraint((T0382)I96.CB, (T0382)L112.CB) [> 4.5846 = 7.6411 < 9.9334] w=0.1896 to align # Constraint # added constraint: constraint((T0382)D57.CB, (T0382)P86.CB) [> 4.3347 = 7.2245 < 9.3919] w=0.1892 to align # Constraint # added constraint: constraint((T0382)L62.CB, (T0382)P86.CB) [> 4.4447 = 7.4078 < 9.6301] w=0.1892 to align # Constraint # added constraint: constraint((T0382)L63.CB, (T0382)A85.CB) [> 4.4072 = 7.3454 < 9.5490] w=0.1892 to align # Constraint # added constraint: constraint((T0382)T22.CB, (T0382)I47.CB) [> 3.9092 = 6.5153 < 8.4699] w=0.1891 to align # Constraint # added constraint: constraint((T0382)M9.CB, (T0382)A28.CB) [> 4.2783 = 7.1304 < 9.2696] w=0.1884 to align # Constraint # added constraint: constraint((T0382)M9.CB, (T0382)R36.CB) [> 4.3136 = 7.1893 < 9.3461] w=0.1884 to align # Constraint # added constraint: constraint((T0382)V15.CB, (T0382)L30.CB) [> 3.8428 = 6.4046 < 8.3260] w=0.1884 to align # Constraint # added constraint: constraint((T0382)V97.CB, (T0382)L114.CB) [> 3.4157 = 5.6928 < 7.4006] w=0.1857 to align # Constraint # added constraint: constraint((T0382)A28.CB, (T0382)A48.CB) [> 4.6605 = 7.7675 < 10.0977] w=0.1854 to align # Constraint # added constraint: constraint((T0382)L30.CB, (T0382)K52.CB) [> 3.9301 = 6.5502 < 8.5153] w=0.1854 to align # Constraint # added constraint: constraint((T0382)F37.CB, (T0382)A48.CB) [> 4.3643 = 7.2739 < 9.4561] w=0.1854 to align # Constraint # added constraint: constraint((T0382)L51.CB, (T0382)A77.CB) [> 3.5760 = 5.9599 < 7.7479] w=0.1853 to align # Constraint # added constraint: constraint((T0382)F66.CB, (T0382)I96.CB) [> 4.3626 = 7.2710 < 9.4522] w=0.1847 to align # Constraint # added constraint: constraint((T0382)L63.CB, (T0382)Q92.CB) [> 3.6605 = 6.1009 < 7.9311] w=0.1847 to align # Constraint # added constraint: constraint((T0382)E50.CB, (T0382)A61.CB) [> 3.6933 = 6.1555 < 8.0021] w=0.1841 to align # Constraint # added constraint: constraint((T0382)L51.CB, (T0382)T60.CB) [> 4.4198 = 7.3664 < 9.5763] w=0.1841 to align # Constraint # added constraint: constraint((T0382)L51.CB, (T0382)A61.CB) [> 3.2965 = 5.4942 < 7.1425] w=0.1841 to align # Constraint # added constraint: constraint((T0382)A61.CB, (T0382)L75.CB) [> 4.5888 = 7.6480 < 9.9424] w=0.1841 to align # Constraint # added constraint: constraint((T0382)A61.CB, (T0382)A77.CB) [> 4.2201 = 7.0335 < 9.1436] w=0.1841 to align # Constraint # added constraint: constraint((T0382)S64.CB, (T0382)Q76.CB) [> 2.6375 = 4.3959 < 5.7147] w=0.1823 to align # Constraint # added constraint: constraint((T0382)A61.CB, (T0382)K79.CB) [> 3.2931 = 5.4885 < 7.1350] w=0.1823 to align # Constraint # added constraint: constraint((T0382)L75.CB, (T0382)I96.CB) [> 3.6470 = 6.0783 < 7.9019] w=0.1355 to align # Constraint # added constraint: constraint((T0382)T10.CB, (T0382)R36.CB) [> 4.7262 = 7.8770 < 10.2401] w=0.1342 to align # Constraint # added constraint: constraint((T0382)T11.CB, (T0382)R36.CB) [> 2.3055 = 3.8425 < 4.9953] w=0.1342 to align # Constraint # added constraint: constraint((T0382)Q12.CB, (T0382)R36.CB) [> 3.6968 = 6.1613 < 8.0097] w=0.1342 to align # Constraint # added constraint: constraint((T0382)V15.CB, (T0382)R36.CB) [> 4.6542 = 7.7569 < 10.0840] w=0.1342 to align # Constraint # added constraint: constraint((T0382)L82.CB, (T0382)L115.CB) [> 4.5869 = 7.6449 < 9.9383] w=0.1342 to align # Constraint # added constraint: constraint((T0382)K79.CB, (T0382)L115.CB) [> 4.5206 = 7.5343 < 9.7947] w=0.1342 to align # Constraint # added constraint: constraint((T0382)A48.CB, (T0382)V84.CB) [> 4.5555 = 7.5925 < 9.8703] w=0.1342 to align # Constraint # added constraint: constraint((T0382)A48.CB, (T0382)A83.CB) [> 3.4118 = 5.6864 < 7.3923] w=0.1342 to align # Constraint # added constraint: constraint((T0382)R74.CB, (T0382)I96.CB) [> 3.9425 = 6.5709 < 8.5422] w=0.1339 to align # Constraint # added constraint: constraint((T0382)L75.CB, (T0382)P103.CB) [> 3.9088 = 6.5147 < 8.4691] w=0.1306 to align # Constraint # added constraint: constraint((T0382)A48.CB, (T0382)R59.CB) [> 3.5302 = 5.8837 < 7.6488] w=0.1281 to align # Constraint # added constraint: constraint((T0382)A48.CB, (T0382)Q58.CB) [> 4.3930 = 7.3216 < 9.5181] w=0.1281 to align # Constraint # added constraint: constraint((T0382)V21.CB, (T0382)E50.CB) [> 4.3987 = 7.3312 < 9.5305] w=0.1276 to align # Constraint # added constraint: constraint((T0382)T10.CB, (T0382)A19.CB) [> 4.7220 = 7.8700 < 10.2310] w=0.1276 to align # Constraint # added constraint: constraint((T0382)M9.CB, (T0382)E50.CB) [> 4.7301 = 7.8835 < 10.2486] w=0.1276 to align # Constraint # added constraint: constraint((T0382)Y68.CB, (T0382)L114.CB) [> 3.3970 = 5.6617 < 7.3601] w=0.1270 to align # Constraint # added constraint: constraint((T0382)Y68.CB, (T0382)M110.CB) [> 3.9031 = 6.5051 < 8.4567] w=0.1270 to align # Constraint # added constraint: constraint((T0382)S64.CB, (T0382)L115.CB) [> 3.6923 = 6.1539 < 8.0001] w=0.1270 to align # Constraint # added constraint: constraint((T0382)A61.CB, (T0382)L82.CB) [> 3.8995 = 6.4991 < 8.4488] w=0.1270 to align # Constraint # added constraint: constraint((T0382)Q58.CB, (T0382)P86.CB) [> 4.5233 = 7.5388 < 9.8004] w=0.1270 to align # Constraint # added constraint: constraint((T0382)V97.CB, (T0382)A108.CB) [> 2.7984 = 4.6640 < 6.0632] w=0.1270 to align # Constraint # added constraint: constraint((T0382)V97.CB, (T0382)D107.CB) [> 4.5063 = 7.5104 < 9.7636] w=0.1270 to align # Constraint # added constraint: constraint((T0382)L93.CB, (T0382)D116.CB) [> 3.2422 = 5.4037 < 7.0248] w=0.1270 to align # Constraint # added constraint: constraint((T0382)P69.CB, (T0382)M110.CB) [> 3.8414 = 6.4024 < 8.3231] w=0.1270 to align # Constraint # added constraint: constraint((T0382)A16.CB, (T0382)L30.CB) [> 3.5229 = 5.8715 < 7.6330] w=0.1266 to align # Constraint # added constraint: constraint((T0382)K3.CB, (T0382)R54.CB) [> 4.2491 = 7.0818 < 9.2064] w=0.1262 to align # Constraint # added constraint: constraint((T0382)L6.CB, (T0382)R54.CB) [> 3.2895 = 5.4824 < 7.1272] w=0.1262 to align # Constraint # added constraint: constraint((T0382)H7.CB, (T0382)R54.CB) [> 4.1039 = 6.8398 < 8.8917] w=0.1262 to align # Constraint # added constraint: constraint((T0382)A48.CB, (T0382)A77.CB) [> 2.7929 = 4.6548 < 6.0512] w=0.1262 to align # Constraint # added constraint: constraint((T0382)F18.CB, (T0382)A78.CB) [> 4.0952 = 6.8253 < 8.8730] w=0.1252 to align # Constraint # added constraint: constraint((T0382)L93.CB, (T0382)Q104.CB) [> 4.0180 = 6.6966 < 8.7056] w=0.1252 to align # Constraint # added constraint: constraint((T0382)M9.CB, (T0382)I47.CB) [> 3.5491 = 5.9152 < 7.6898] w=0.1249 to align # Constraint # added constraint: constraint((T0382)L14.CB, (T0382)A28.CB) [> 3.3960 = 5.6600 < 7.3580] w=0.1236 to align # Constraint # added constraint: constraint((T0382)L14.CB, (T0382)L29.CB) [> 3.9310 = 6.5517 < 8.5172] w=0.1236 to align # Constraint # added constraint: constraint((T0382)R54.CB, (T0382)A77.CB) [> 4.5308 = 7.5513 < 9.8167] w=0.1231 to align # Constraint # added constraint: constraint((T0382)V87.CB, (T0382)Q104.CB) [> 4.7413 = 7.9022 < 10.2729] w=0.1231 to align # Constraint # added constraint: constraint((T0382)R90.CB, (T0382)P103.CB) [> 3.2722 = 5.4537 < 7.0898] w=0.1231 to align # Constraint # added constraint: constraint((T0382)R90.CB, (T0382)D107.CB) [> 4.1278 = 6.8797 < 8.9436] w=0.1231 to align # Constraint # added constraint: constraint((T0382)A83.CB, (T0382)L93.CB) [> 3.8801 = 6.4668 < 8.4069] w=0.1215 to align # Constraint # added constraint: constraint((T0382)R54.CB, (T0382)E67.CB) [> 4.7712 = 7.9520 < 10.3376] w=0.0691 to align # Constraint # added constraint: constraint((T0382)Q12.CB, (T0382)A28.CB) [> 4.6645 = 7.7741 < 10.1064] w=0.0671 to align # Constraint # added constraint: constraint((T0382)P103.CB, (T0382)L112.CB) [> 4.0305 = 6.7175 < 8.7327] w=0.0671 to align # Constraint # added constraint: constraint((T0382)R74.CB, (T0382)P103.CB) [> 4.7700 = 7.9499 < 10.3349] w=0.0671 to align # Constraint # added constraint: constraint((T0382)F41.CB, (T0382)A83.CB) [> 3.4187 = 5.6978 < 7.4071] w=0.0671 to align # Constraint # added constraint: constraint((T0382)A48.CB, (T0382)T60.CB) [> 4.3006 = 7.1677 < 9.3180] w=0.0655 to align # Constraint # added constraint: constraint((T0382)E50.CB, (T0382)A77.CB) [> 3.4207 = 5.7012 < 7.4116] w=0.0655 to align # Constraint # added constraint: constraint((T0382)R59.CB, (T0382)Q72.CB) [> 3.7433 = 6.2388 < 8.1104] w=0.0655 to align # Constraint # added constraint: constraint((T0382)V43.CB, (T0382)K88.CB) [> 3.3755 = 5.6259 < 7.3137] w=0.0653 to align # Constraint # added constraint: constraint((T0382)H7.CB, (T0382)R36.CB) [> 4.7712 = 7.9520 < 10.3376] w=0.0648 to align # Constraint # added constraint: constraint((T0382)H7.CB, (T0382)R39.CB) [> 4.5016 = 7.5026 < 9.7534] w=0.0648 to align # Constraint # added constraint: constraint((T0382)Q8.CB, (T0382)R36.CB) [> 2.7446 = 4.5743 < 5.9466] w=0.0648 to align # Constraint # added constraint: constraint((T0382)L17.CB, (T0382)G31.CA) [> 4.0598 = 6.7664 < 8.7963] w=0.0648 to align # Constraint # added constraint: constraint((T0382)L29.CB, (T0382)M44.CB) [> 3.1993 = 5.3322 < 6.9319] w=0.0648 to align # Constraint # added constraint: constraint((T0382)D26.CB, (T0382)L51.CB) [> 4.1749 = 6.9582 < 9.0456] w=0.0648 to align # Constraint # added constraint: constraint((T0382)D26.CB, (T0382)I47.CB) [> 4.7964 = 7.9939 < 10.3921] w=0.0648 to align # Constraint # added constraint: constraint((T0382)I34.CB, (T0382)G109.CA) [> 3.5523 = 5.9205 < 7.6966] w=0.0635 to align # Constraint # added constraint: constraint((T0382)Q8.CB, (T0382)M110.CB) [> 4.3674 = 7.2789 < 9.4626] w=0.0635 to align # Constraint # added constraint: constraint((T0382)L93.CB, (T0382)T119.CB) [> 4.0803 = 6.8005 < 8.8406] w=0.0635 to align # Constraint # added constraint: constraint((T0382)V84.CB, (T0382)S99.CB) [> 3.1358 = 5.2264 < 6.7943] w=0.0635 to align # Constraint # added constraint: constraint((T0382)A83.CB, (T0382)K100.CB) [> 4.7730 = 7.9551 < 10.3416] w=0.0635 to align # Constraint # added constraint: constraint((T0382)L51.CB, (T0382)D107.CB) [> 4.7217 = 7.8695 < 10.2303] w=0.0635 to align # Constraint # added constraint: constraint((T0382)L51.CB, (T0382)A108.CB) [> 2.2179 = 3.6966 < 4.8055] w=0.0635 to align # Constraint # added constraint: constraint((T0382)L51.CB, (T0382)G109.CA) [> 4.5117 = 7.5195 < 9.7754] w=0.0635 to align # Constraint # added constraint: constraint((T0382)A61.CB, (T0382)T119.CB) [> 4.2804 = 7.1340 < 9.2742] w=0.0635 to align # Constraint # added constraint: constraint((T0382)T10.CB, (T0382)R54.CB) [> 4.5295 = 7.5492 < 9.8140] w=0.0631 to align # Constraint # added constraint: constraint((T0382)L6.CB, (T0382)I47.CB) [> 3.1449 = 5.2415 < 6.8139] w=0.0631 to align # Constraint # added constraint: constraint((T0382)L6.CB, (T0382)V21.CB) [> 3.4736 = 5.7893 < 7.5261] w=0.0631 to align # Constraint # added constraint: constraint((T0382)L75.CB, (T0382)L93.CB) [> 3.1204 = 5.2006 < 6.7608] w=0.0631 to align # Constraint # added constraint: constraint((T0382)R74.CB, (T0382)A105.CB) [> 4.3029 = 7.1715 < 9.3229] w=0.0631 to align # Constraint # added constraint: constraint((T0382)A19.CB, (T0382)R54.CB) [> 3.8551 = 6.4251 < 8.3527] w=0.0631 to align # Constraint # added constraint: constraint((T0382)A19.CB, (T0382)R74.CB) [> 4.7889 = 7.9815 < 10.3759] w=0.0631 to align # Constraint # added constraint: constraint((T0382)A19.CB, (T0382)A77.CB) [> 2.7929 = 4.6548 < 6.0512] w=0.0631 to align # Constraint # added constraint: constraint((T0382)K20.CB, (T0382)R54.CB) [> 4.7233 = 7.8722 < 10.2338] w=0.0631 to align # Constraint # added constraint: constraint((T0382)G31.CA, (T0382)A105.CB) [> 3.7963 = 6.3272 < 8.2254] w=0.0626 to align # Constraint # added constraint: constraint((T0382)V23.CB, (T0382)A77.CB) [> 4.0686 = 6.7810 < 8.8153] w=0.0626 to align # Constraint # added constraint: constraint((T0382)V23.CB, (T0382)A85.CB) [> 4.3195 = 7.1992 < 9.3590] w=0.0626 to align # Constraint # added constraint: constraint((T0382)A48.CB, (T0382)L82.CB) [> 3.8138 = 6.3563 < 8.2632] w=0.0626 to align # Constraint # added constraint: constraint((T0382)A95.CB, (T0382)D113.CB) [> 3.6166 = 6.0277 < 7.8360] w=0.0626 to align # Constraint # added constraint: constraint((T0382)I47.CB, (T0382)L82.CB) [> 4.7701 = 7.9501 < 10.3352] w=0.0626 to align # Constraint # added constraint: constraint((T0382)I47.CB, (T0382)L93.CB) [> 3.5691 = 5.9484 < 7.7329] w=0.0622 to align # Constraint # added constraint: constraint((T0382)L14.CB, (T0382)D27.CB) [> 4.3629 = 7.2715 < 9.4529] w=0.0618 to align # Constraint # added constraint: constraint((T0382)V23.CB, (T0382)I47.CB) [> 3.9707 = 6.6178 < 8.6032] w=0.0616 to align # Constraint # added constraint: constraint((T0382)L63.CB, (T0382)A77.CB) [> 4.6637 = 7.7728 < 10.1046] w=0.0616 to align # Constraint # added constraint: constraint((T0382)N38.CB, (T0382)I47.CB) [> 3.9345 = 6.5574 < 8.5247] w=0.0616 to align # Constraint # added constraint: constraint((T0382)L82.CB, (T0382)L93.CB) [> 2.4134 = 4.0223 < 5.2291] w=0.0608 to align # Constraint # added constraint: constraint((T0382)Q58.CB, (T0382)V84.CB) [> 4.1347 = 6.8911 < 8.9584] w=0.0608 to align # Constraint # added constraint: constraint((T0382)E50.CB, (T0382)P103.CB) [> 2.7664 = 4.6108 < 5.9940] w=0.0608 to align # Constraint # added constraint: constraint((T0382)E50.CB, (T0382)R59.CB) [> 4.2792 = 7.1319 < 9.2715] w=0.0608 to align # Constraint # added constraint: constraint((T0382)L82.CB, (T0382)A108.CB) [> 4.6482 = 7.7470 < 10.0711] w=0.0608 to align # Constraint # added constraint: constraint((T0382)L82.CB, (T0382)L112.CB) [> 3.1319 = 5.2198 < 6.7858] w=0.0608 to align # Constraint # added constraint: constraint((T0382)V84.CB, (T0382)C111.CB) [> 4.7355 = 7.8926 < 10.2603] w=0.0608 to align # Constraint # added constraint: constraint((T0382)V84.CB, (T0382)L112.CB) [> 4.7445 = 7.9076 < 10.2798] w=0.0608 to align # Constraint # added constraint: constraint((T0382)P86.CB, (T0382)L112.CB) [> 4.7778 = 7.9630 < 10.3519] w=0.0608 to align # Constraint # added constraint: constraint((T0382)G106.CA, (T0382)D117.CB) [> 4.1218 = 6.8697 < 8.9306] w=0.0501 to align # Constraint # added constraint: constraint((T0382)G106.CA, (T0382)D116.CB) [> 2.9533 = 4.9222 < 6.3988] w=0.0501 to align # Constraint # added constraint: constraint((T0382)F102.CB, (T0382)D117.CB) [> 3.8838 = 6.4730 < 8.4149] w=0.0501 to align # SetCost created cost = # ( 1.0000 * align ) # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0382/ # command:# reading script from file servers-clean.under # Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0382/decoys/ # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0382 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 T0382 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 T0382 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 # WARNING: incomplete conformation T0382 can't currently be optimized by undertaker # 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 T0382 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 # Found a chain break before 122 # copying to AlignedFragments data structure # 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 122 # 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 # Found a chain break before 122 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_RECOM_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS4.pdb.gz looking for model 1 # Found a chain break before 122 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_RECOM_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS5.pdb.gz looking for model 1 # Found a chain break before 122 # copying to AlignedFragments data structure # 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 T0382 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS2.pdb.gz looking for model 1 # Found a chain break before 122 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_TS2 # ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1 # Found a chain break before 107 # 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 68 # 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 50 # 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 107 # 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 111 # 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 107 # 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 119 # 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 88 # 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 60 # 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 114 # 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 113 # copying to AlignedFragments data structure # naming current conformation BayesHH_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS1.pdb.gz looking for model 1 # Found a chain break before 104 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS2.pdb.gz looking for model 1 # naming current conformation Bilab-ENABLE_TS2 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS3.pdb.gz looking for model 1 # Found a chain break before 122 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS3 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS4.pdb.gz looking for model 1 # Found a chain break before 122 # 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 122 # 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 117 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS1 # ReadConformPDB reading from PDB file servers/CIRCLE_TS2.pdb.gz looking for model 1 # Found a chain break before 121 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS2 # ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1 # Found a chain break before 121 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS3 # ReadConformPDB reading from PDB file servers/CIRCLE_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0382 can't currently be optimized by undertaker # 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 121 # 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 T0382 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 T0382 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 T0382 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: atoms too close: (T0382)Q72.C and (T0382)V73.N only 0.000 apart, marking (T0382)V73.N as missing WARNING: atoms too close: (T0382)V73.N and (T0382)V73.CA only 0.000 apart, marking (T0382)V73.CA as missing WARNING: atoms too close: (T0382)Q72.C and (T0382)V73.CA only 0.000 apart, marking (T0382)V73.CA as missing WARNING: atoms too close: (T0382)V73.CA and (T0382)V73.CB only 0.000 apart, marking (T0382)V73.CB as missing WARNING: atoms too close: (T0382)V73.N and (T0382)V73.CB only 0.000 apart, marking (T0382)V73.CB as missing WARNING: atoms too close: (T0382)Q72.C and (T0382)V73.CB only 0.000 apart, marking (T0382)V73.CB as missing WARNING: atoms too close: (T0382)V73.CB and (T0382)V73.CG1 only 0.000 apart, marking (T0382)V73.CG1 as missing WARNING: atoms too close: (T0382)V73.CA and (T0382)V73.CG1 only 0.000 apart, marking (T0382)V73.CG1 as missing WARNING: atoms too close: (T0382)V73.N and (T0382)V73.CG1 only 0.000 apart, marking (T0382)V73.CG1 as missing WARNING: atoms too close: (T0382)Q72.C and (T0382)V73.CG1 only 0.000 apart, marking (T0382)V73.CG1 as missing WARNING: atoms too close: (T0382)V73.CG1 and (T0382)V73.CG2 only 0.000 apart, marking (T0382)V73.CG2 as missing WARNING: atoms too close: (T0382)V73.CB and (T0382)V73.CG2 only 0.000 apart, marking (T0382)V73.CG2 as missing WARNING: atoms too close: (T0382)V73.CA and (T0382)V73.CG2 only 0.000 apart, marking (T0382)V73.CG2 as missing WARNING: atoms too close: (T0382)V73.N and (T0382)V73.CG2 only 0.000 apart, marking (T0382)V73.CG2 as missing WARNING: atoms too close: (T0382)Q72.C and (T0382)V73.CG2 only 0.000 apart, marking (T0382)V73.CG2 as missing WARNING: atoms too close: (T0382)V73.CG2 and (T0382)V73.O only 0.000 apart, marking (T0382)V73.O as missing WARNING: atoms too close: (T0382)V73.CG1 and (T0382)V73.O only 0.000 apart, marking (T0382)V73.O as missing WARNING: atoms too close: (T0382)V73.CB and (T0382)V73.O only 0.000 apart, marking (T0382)V73.O as missing WARNING: atoms too close: (T0382)V73.CA and (T0382)V73.O only 0.000 apart, marking (T0382)V73.O as missing WARNING: atoms too close: (T0382)V73.N and (T0382)V73.O only 0.000 apart, marking (T0382)V73.O as missing WARNING: atoms too close: (T0382)Q72.C and (T0382)V73.O only 0.000 apart, marking (T0382)V73.O as missing WARNING: atoms too close: (T0382)V73.O and (T0382)V73.C only 0.000 apart, marking (T0382)V73.C as missing WARNING: atoms too close: (T0382)V73.CG2 and (T0382)V73.C only 0.000 apart, marking (T0382)V73.C as missing WARNING: atoms too close: (T0382)V73.CG1 and (T0382)V73.C only 0.000 apart, marking (T0382)V73.C as missing WARNING: atoms too close: (T0382)V73.CB and (T0382)V73.C only 0.000 apart, marking (T0382)V73.C as missing WARNING: atoms too close: (T0382)V73.CA and (T0382)V73.C only 0.000 apart, marking (T0382)V73.C as missing WARNING: atoms too close: (T0382)V73.N and (T0382)V73.C only 0.000 apart, marking (T0382)V73.C as missing WARNING: atoms too close: (T0382)Q72.C and (T0382)V73.C only 0.000 apart, marking (T0382)V73.C as missing # WARNING: incomplete conformation T0382 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 # Found a chain break before 110 # copying to AlignedFragments data structure # naming current conformation CaspIta-FOX_TS5 # ReadConformPDB reading from PDB file servers/Distill_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0382 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 T0382 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 T0382 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 T0382 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 T0382 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 119 # 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 T0382 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 122 # 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 T0382 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 T0382 can't currently be optimized by undertaker # naming current conformation FAMSD_TS5 # ReadConformPDB reading from PDB file servers/FAMS_TS1.pdb.gz looking for model 1 # Found a chain break before 121 # 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 122 # 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 122 # 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 119 # copying to AlignedFragments data structure # naming current conformation FAMS_TS4 # ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1 # Found a chain break before 122 # copying to AlignedFragments data structure # naming current conformation FAMS_TS5 # ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1 # Found a chain break before 68 # 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 50 # 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 107 # 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 111 # 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 106 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS5 # ReadConformPDB reading from PDB file servers/FORTE1_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0382 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 T0382 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 T0382 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 Skipped atom 2, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 4, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 6, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 8, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 302, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 304, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 306, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 308, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz # WARNING: incomplete conformation T0382 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 T0382 can't currently be optimized by undertaker # naming current conformation FORTE1_AL5 # ReadConformPDB reading from PDB file servers/FORTE2_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0382 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 T0382 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 T0382 can't currently be optimized by undertaker # naming current conformation FORTE2_AL3 # ReadConformPDB reading from PDB file servers/FORTE2_AL4.pdb.gz looking for model 1 Skipped atom 2, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 4, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 6, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 8, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 302, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 304, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 306, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 308, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz # WARNING: incomplete conformation T0382 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 T0382 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 118 # 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 105 # 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 # 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 65 # 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 109 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS5 # ReadConformPDB reading from PDB file servers/FUGMOD_TS1.pdb.gz looking for model 1 # Found a chain break before 47 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS1 # ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1 # Found a chain break before 83 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS2 # ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1 # Found a chain break before 76 # 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 T0382 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 T0382 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 T0382 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 T0382 can't currently be optimized by undertaker # naming current conformation FUGUE_AL2 # ReadConformPDB reading from PDB file servers/FUGUE_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0382 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGUE_AL3 # ReadConformPDB reading from PDB file servers/FUGUE_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0382 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 T0382 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 120 # 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 121 # 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 121 # 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 118 # 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 117 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS5 # ReadConformPDB reading from PDB file servers/Frankenstein_TS1.pdb.gz looking for model 1 # Found a chain break before 63 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS1 # ReadConformPDB reading from PDB file servers/Frankenstein_TS2.pdb.gz looking for model 1 # Found a chain break before 85 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS2 # ReadConformPDB reading from PDB file servers/Frankenstein_TS3.pdb.gz looking for model 1 # Found a chain break before 76 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS3 # ReadConformPDB reading from PDB file servers/Frankenstein_TS4.pdb.gz looking for model 1 # Found a chain break before 77 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS4 # ReadConformPDB reading from PDB file servers/Frankenstein_TS5.pdb.gz looking for model 1 # Found a chain break before 121 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS5 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0382 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS1 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0382 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS2 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0382 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS3 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0382 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS4 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS5.pdb.gz looking for model 1 # naming current conformation GeneSilicoMetaServer_TS5 # ReadConformPDB reading from PDB file servers/HHpred1_TS1.pdb.gz looking for model 1 # Found a chain break before 86 # 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 86 # copying to AlignedFragments data structure # naming current conformation HHpred2_TS1 # ReadConformPDB reading from PDB file servers/HHpred3_TS1.pdb.gz looking for model 1 # naming current conformation HHpred3_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0382 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 T0382 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS2 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0382 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 T0382 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 T0382 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 T0382 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 T0382 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation LOOPP_TS2 # ReadConformPDB reading from PDB file servers/LOOPP_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0382 can't currently be optimized by undertaker # naming current conformation LOOPP_TS3 # ReadConformPDB reading from PDB file servers/LOOPP_TS4.pdb.gz looking for model 1 # Found a chain break before 103 # copying to AlignedFragments data structure # naming current conformation LOOPP_TS4 # ReadConformPDB reading from PDB file servers/LOOPP_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0382 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 T0382 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 # Found a chain break before 58 # copying to AlignedFragments data structure # 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 73 # 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 # 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 86 # 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 86 # 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 72 # 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 # naming current conformation Ma-OPUS-server_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS3.pdb.gz looking for model 1 # 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 38 # 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 # 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 105 # 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 119 # 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 122 # 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 120 # 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 122 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS5 # ReadConformPDB reading from PDB file servers/NN_PUT_lab_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0382 can't currently be optimized by undertaker # 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 99 # 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 84 # 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 104 # 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 87 # 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 104 # 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 # 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 # naming current conformation PROTINFO_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1 # Found a chain break before 113 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1 # Found a chain break before 121 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS5 # ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1 # naming current conformation Pcons6_TS1 # ReadConformPDB reading from PDB file servers/Pcons6_TS2.pdb.gz looking for model 1 # naming current conformation Pcons6_TS2 # ReadConformPDB reading from PDB file servers/Pcons6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0382 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 T0382 can't currently be optimized by undertaker # naming current conformation Pcons6_TS4 # ReadConformPDB reading from PDB file servers/Pcons6_TS5.pdb.gz looking for model 1 # Found a chain break before 66 # copying to AlignedFragments data structure # naming current conformation Pcons6_TS5 # ReadConformPDB reading from PDB file servers/Phyre-1_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0382 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 121 # 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 117 # 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 101 # 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 121 # 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 106 # 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 100 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS3 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0382 can't currently be optimized by undertaker # 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 T0382 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0382 can't currently be optimized by undertaker # 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 # 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 81 # 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 101 # 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 118 # 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 121 # 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 121 # 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 121 # 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 20 # 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 85 # 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 71 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR_TS2.pdb.gz looking for model 1 # Found a chain break before 85 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR_TS3.pdb.gz looking for model 1 # Found a chain break before 119 # 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 65 # 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 20 # 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 87 # 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 100 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS3 # ReadConformPDB reading from PDB file servers/ROBETTA_TS4.pdb.gz looking for model 1 # naming current conformation ROBETTA_TS4 # ReadConformPDB reading from PDB file servers/ROBETTA_TS5.pdb.gz looking for model 1 # Found a chain break before 100 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS5 # ReadConformPDB reading from PDB file servers/ROKKY_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0382 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS1 # ReadConformPDB reading from PDB file servers/ROKKY_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0382 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS2 # ReadConformPDB reading from PDB file servers/ROKKY_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0382 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS3 # ReadConformPDB reading from PDB file servers/ROKKY_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0382 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS4 # ReadConformPDB reading from PDB file servers/ROKKY_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0382 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS5 # ReadConformPDB reading from PDB file servers/SAM-T02_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0382 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 T0382 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 T0382 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 T0382 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL4 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS1.pdb.gz looking for model 1 # Found a chain break before 120 # 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 T0382 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 T0382 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 T0382 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 T0382 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 69 # copying to AlignedFragments data structure # naming current conformation SP3_TS1 # ReadConformPDB reading from PDB file servers/SP3_TS2.pdb.gz looking for model 1 # Found a chain break before 105 # copying to AlignedFragments data structure # naming current conformation SP3_TS2 # ReadConformPDB reading from PDB file servers/SP3_TS3.pdb.gz looking for model 1 # Found a chain break before 70 # copying to AlignedFragments data structure # naming current conformation SP3_TS3 # ReadConformPDB reading from PDB file servers/SP3_TS4.pdb.gz looking for model 1 # Found a chain break before 78 # 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 41 # 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 68 # 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 84 # copying to AlignedFragments data structure # naming current conformation SP4_TS2 # ReadConformPDB reading from PDB file servers/SP4_TS3.pdb.gz looking for model 1 # Found a chain break before 93 # copying to AlignedFragments data structure # naming current conformation SP4_TS3 # ReadConformPDB reading from PDB file servers/SP4_TS4.pdb.gz looking for model 1 # naming current conformation SP4_TS4 # ReadConformPDB reading from PDB file servers/SP4_TS5.pdb.gz looking for model 1 # Found a chain break before 72 # copying to AlignedFragments data structure # naming current conformation SP4_TS5 # ReadConformPDB reading from PDB file servers/SPARKS2_TS1.pdb.gz looking for model 1 # Found a chain break before 27 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS1 # ReadConformPDB reading from PDB file servers/SPARKS2_TS2.pdb.gz looking for model 1 # Found a chain break before 105 # 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 101 # 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 65 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS4 # ReadConformPDB reading from PDB file servers/SPARKS2_TS5.pdb.gz looking for model 1 # Found a chain break before 106 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0382 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0382 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 T0382 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 T0382 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 T0382 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 T0382 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 T0382 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 T0382 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 7, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL3.pdb.gz # WARNING: incomplete conformation T0382 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 T0382 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 T0382 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 115 # 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 121 # 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 107 # 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 121 # 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 121 # 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 122 # 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 T0382 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 T0382 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 T0382 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 T0382 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 T0382 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 T0382 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 101 # 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 51 # 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 50 # 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 # 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 86 # 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 117 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS2.pdb.gz looking for model 1 # Found a chain break before 120 # 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 WARNING: atoms too close: (T0382)P69.O and (T0382)N70.N only 0.000 apart, marking (T0382)N70.N as missing # WARNING: incomplete conformation T0382 can't currently be optimized by undertaker # 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: (T0382)L6.O and (T0382)H7.N only 0.000 apart, marking (T0382)H7.N as missing WARNING: atoms too close: (T0382)A108.O and (T0382)G109.N only 0.000 apart, marking (T0382)G109.N as missing WARNING: atoms too close: (T0382)L112.O and (T0382)D113.N only 0.000 apart, marking (T0382)D113.N as missing # WARNING: incomplete conformation T0382 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 WARNING: atoms too close: (T0382)D113.O and (T0382)L114.N only 0.000 apart, marking (T0382)L114.N as missing # WARNING: incomplete conformation T0382 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0382 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 # WARNING: incomplete conformation T0382 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0382 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 T0382 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 T0382 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 T0382 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 T0382 can't currently be optimized by undertaker # naming current conformation nFOLD_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0382 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation nFOLD_TS2 # ReadConformPDB reading from PDB file servers/nFOLD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0382 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation nFOLD_TS3 # ReadConformPDB reading from PDB file servers/nFOLD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0382 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 T0382 can't currently be optimized by undertaker # naming current conformation nFOLD_TS5 # ReadConformPDB reading from PDB file servers/panther2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0382 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 T0382 can't currently be optimized by undertaker # naming current conformation shub_TS1 # command:Using radius: 8.0000 Using models AND alignments for constraints model score 2.2702 model score 2.1806 model score 2.1861 model score 2.3480 model score 2.2161 model score 2.0916 model score 2.0908 model score 2.0908 model score 2.0908 model score 2.0908 model score 2.1193 model score 2.0908 model score 1.6253 model score 2.1281 model score 1.8546 model score 2.0436 model score 1.7331 model score 1.6253 model score 1.7474 model score 1.5628 model score 1.4308 model score 1.5224 model score 1.2693 model score 1.6467 model score 3.0261 model score 1.6066 model score 1.7029 model score 1.6974 model score 1.5279 model score 1.6493 model score 1.6715 model score 1.4909 model score 2.0296 model score 1.5296 model score 2.1478 model score 1.4868 model score 1.7257 model score 1.9206 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.8528 model score 1.7085 model score 1.5114 model score 1.9255 model score 1.7357 model score 1.7201 model score 1.5204 model score 1.8217 model score 1.5688 model score 1.5593 model score 2.1281 model score 1.8546 model score 2.0436 model score 1.7331 model score 1.7366 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 1.9100 model score 2.1659 model score 2.0948 model score 1.9875 model score 2.3631 model score 2.6401 model score 2.1003 model score 1.6741 model score 2.5619 model score 1.9056 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.5141 model score 1.9159 model score 1.3470 model score 1.6857 model score 1.9984 model score 1.8096 model score 1.7283 model score 1.6246 model score 2.0797 model score 1.9165 model score 1.1415 model score 1.2939 model score 1.5996 model score 1.8847 model score 1.9516 model score 1.2036 model score 1.2036 model score 1.3850 model score 1.4710 model score 1.7736 model score 1.3239 model score 1.3669 model score 1.5125 model score 1.5871 model score 1.6155 model score 1.9541 model score 1.5600 model score 1.9060 model score 1.2771 model score 1.6680 model score 1.5700 model score 2.0758 model score 2.1557 model score 1.9383 model score 1.5239 model score 1.6612 model score 1.3767 model score 1.0758 model score 1.6109 model score 1.5061 model score 1.5411 model score 0.9236 model score 1.3158 model score 1.8254 model score 1.9669 model score 1.6802 model score 1.8652 model score 1.6668 model score 1.8665 model score 1.7009 model score 1.5992 model score 1.6102 model score 1.5839 model score 1.6143 model score 1.5554 model score 1.5607 model score 1.6225 model score 1.5839 model score 2.0796 model score 2.0063 model score 1.2251 model score 1.3907 model score 2.1656 model score 2.0760 model score 2.0703 model score 2.0798 model score 1.3149 model score 1.8763 model score 1.5501 model score 1.8909 model score 1.8033 model score 1.5430 model score 1.2522 model score 1.6709 model score 1.3994 model score 1.8150 model score 1.9071 model score 1.8700 model score 1.6129 model score 1.4171 model score 1.5258 model score 1.1778 model score 1.2791 model score 1.2552 model score 1.7091 model score 1.4837 model score 1.1794 model score 1.2317 model score 1.1939 model score 1.6740 model score 1.4583 model score 1.8697 model score 1.2251 model score 1.9903 model score 1.3907 model score 1.6709 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 1.3841 model score 1.2206 model score 1.0961 model score 1.3415 model score 1.2944 model score 1.9614 model score 1.6841 model score 1.8330 model score 1.6475 model score 2.0820 model score 1.3973 model score 1.1908 model score 1.8521 model score 1.9964 model score 1.8794 model score 2.0182 model score 1.6841 model score 2.1064 model score 2.0568 model score 2.0750 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 2.1283 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.0782 model score 1.1084 model score 1.0143 model score 0.9361 model score 1.5100 model score 1.9420 model score 1.9238 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.7284 model score 2.1926 model score 2.2914 model score 1.6812 model score 2.1945 model score 2.0776 model score 2.1194 model score 1.9075 model score 2.0639 model score 1.8121 model score 1.3036 model score 1.6585 model score 1.5604 model score 1.6957 model score 1.3021 model score 1.7590 model score 1.1760 model score 1.6753 model score 1.7259 model score 1.7276 model score 1.9669 model score 1.9669 model score 1.9719 model score 1.9511 model score 2.0631 model score 1.4478 model score 1.2865 model score 1.8398 USE_META, weight: 0.4236 cost: 2.2702 min: 0.9236 max: 3.0261 USE_META, weight: 0.4619 cost: 2.1806 min: 0.9236 max: 3.0261 USE_META, weight: 0.4596 cost: 2.1861 min: 0.9236 max: 3.0261 USE_META, weight: 0.3903 cost: 2.3480 min: 0.9236 max: 3.0261 USE_META, weight: 0.4467 cost: 2.2161 min: 0.9236 max: 3.0261 USE_META, weight: 0.5000 cost: 2.0916 min: 0.9236 max: 3.0261 USE_META, weight: 0.5004 cost: 2.0908 min: 0.9236 max: 3.0261 USE_META, weight: 0.5004 cost: 2.0908 min: 0.9236 max: 3.0261 USE_META, weight: 0.5004 cost: 2.0908 min: 0.9236 max: 3.0261 USE_META, weight: 0.5004 cost: 2.0908 min: 0.9236 max: 3.0261 USE_META, weight: 0.4882 cost: 2.1193 min: 0.9236 max: 3.0261 USE_META, weight: 0.5004 cost: 2.0908 min: 0.9236 max: 3.0261 USE_META, weight: 0.6996 cost: 1.6253 min: 0.9236 max: 3.0261 USE_META, weight: 0.4844 cost: 2.1281 min: 0.9236 max: 3.0261 USE_META, weight: 0.6015 cost: 1.8546 min: 0.9236 max: 3.0261 USE_META, weight: 0.5206 cost: 2.0436 min: 0.9236 max: 3.0261 USE_META, weight: 0.6535 cost: 1.7331 min: 0.9236 max: 3.0261 USE_META, weight: 0.6996 cost: 1.6253 min: 0.9236 max: 3.0261 USE_META, weight: 0.6474 cost: 1.7474 min: 0.9236 max: 3.0261 USE_META, weight: 0.7264 cost: 1.5628 min: 0.9236 max: 3.0261 USE_META, weight: 0.7829 cost: 1.4308 min: 0.9236 max: 3.0261 USE_META, weight: 0.7437 cost: 1.5224 min: 0.9236 max: 3.0261 USE_META, weight: 0.8520 cost: 1.2693 min: 0.9236 max: 3.0261 USE_META, weight: 0.6905 cost: 1.6467 min: 0.9236 max: 3.0261 USE_META, weight: 0.1000 cost: 3.0261 min: 0.9236 max: 3.0261 USE_META, weight: 0.7076 cost: 1.6066 min: 0.9236 max: 3.0261 USE_META, weight: 0.6664 cost: 1.7029 min: 0.9236 max: 3.0261 USE_META, weight: 0.6688 cost: 1.6974 min: 0.9236 max: 3.0261 USE_META, weight: 0.7413 cost: 1.5279 min: 0.9236 max: 3.0261 USE_META, weight: 0.6893 cost: 1.6493 min: 0.9236 max: 3.0261 USE_META, weight: 0.6798 cost: 1.6715 min: 0.9236 max: 3.0261 USE_META, weight: 0.7572 cost: 1.4909 min: 0.9236 max: 3.0261 USE_META, weight: 0.5266 cost: 2.0296 min: 0.9236 max: 3.0261 USE_META, weight: 0.7406 cost: 1.5296 min: 0.9236 max: 3.0261 USE_META, weight: 0.4760 cost: 2.1478 min: 0.9236 max: 3.0261 USE_META, weight: 0.7589 cost: 1.4868 min: 0.9236 max: 3.0261 USE_META, weight: 0.6566 cost: 1.7257 min: 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USE_META, weight: 0.8380 cost: 1.3021 min: 0.9236 max: 3.0261 USE_META, weight: 0.6424 cost: 1.7590 min: 0.9236 max: 3.0261 USE_META, weight: 0.8919 cost: 1.1760 min: 0.9236 max: 3.0261 USE_META, weight: 0.6782 cost: 1.6753 min: 0.9236 max: 3.0261 USE_META, weight: 0.6566 cost: 1.7259 min: 0.9236 max: 3.0261 USE_META, weight: 0.6558 cost: 1.7276 min: 0.9236 max: 3.0261 USE_META, weight: 0.5534 cost: 1.9669 min: 0.9236 max: 3.0261 USE_META, weight: 0.5534 cost: 1.9669 min: 0.9236 max: 3.0261 USE_META, weight: 0.5513 cost: 1.9719 min: 0.9236 max: 3.0261 USE_META, weight: 0.5602 cost: 1.9511 min: 0.9236 max: 3.0261 USE_META, weight: 0.5122 cost: 2.0631 min: 0.9236 max: 3.0261 USE_META, weight: 0.7756 cost: 1.4478 min: 0.9236 max: 3.0261 USE_META, weight: 0.8447 cost: 1.2865 min: 0.9236 max: 3.0261 USE_META, weight: 0.6078 cost: 1.8398 min: 0.9236 max: 3.0261 USE_EVALUE, weight: 1.0000 eval: 0.5143 min: 0.5143 max: 51.5000 USE_EVALUE, weight: 1.0000 eval: 0.5143 min: 0.5143 max: 51.5000 USE_EVALUE, weight: 1.0000 eval: 0.5143 min: 0.5143 max: 51.5000 USE_EVALUE, weight: 0.7615 eval: 14.0230 min: 0.5143 max: 51.5000 USE_EVALUE, weight: 0.7615 eval: 14.0230 min: 0.5143 max: 51.5000 USE_EVALUE, weight: 0.7615 eval: 14.0230 min: 0.5143 max: 51.5000 USE_EVALUE, weight: 0.8109 eval: 11.2280 min: 0.5143 max: 51.5000 USE_EVALUE, weight: 0.8109 eval: 11.2280 min: 0.5143 max: 51.5000 USE_EVALUE, weight: 0.8109 eval: 11.2280 min: 0.5143 max: 51.5000 USE_EVALUE, weight: 0.7950 eval: 12.1250 min: 0.5143 max: 51.5000 USE_EVALUE, weight: 0.7950 eval: 12.1250 min: 0.5143 max: 51.5000 USE_EVALUE, weight: 0.7950 eval: 12.1250 min: 0.5143 max: 51.5000 USE_EVALUE, weight: 0.8366 eval: 9.7691 min: 0.5143 max: 51.5000 USE_EVALUE, weight: 0.8366 eval: 9.7691 min: 0.5143 max: 51.5000 USE_EVALUE, weight: 0.8366 eval: 9.7691 min: 0.5143 max: 51.5000 USE_EVALUE, weight: 0.8271 eval: 10.3070 min: 0.5143 max: 51.5000 USE_EVALUE, weight: 0.8271 eval: 10.3070 min: 0.5143 max: 51.5000 USE_EVALUE, weight: 0.8271 eval: 10.3070 min: 0.5143 max: 51.5000 USE_EVALUE, weight: 0.7896 eval: 12.4340 min: 0.5143 max: 51.5000 USE_EVALUE, weight: 0.7896 eval: 12.4340 min: 0.5143 max: 51.5000 USE_EVALUE, weight: 0.7896 eval: 12.4340 min: 0.5143 max: 51.5000 USE_EVALUE, weight: 0.7999 eval: 11.8500 min: 0.5143 max: 51.5000 USE_EVALUE, weight: 0.7999 eval: 11.8500 min: 0.5143 max: 51.5000 USE_EVALUE, weight: 0.7999 eval: 11.8500 min: 0.5143 max: 51.5000 USE_EVALUE, weight: 0.2200 eval: 44.7000 min: 0.5143 max: 51.5000 USE_EVALUE, weight: 0.2200 eval: 44.7000 min: 0.5143 max: 51.5000 USE_EVALUE, weight: 0.2200 eval: 44.7000 min: 0.5143 max: 51.5000 USE_EVALUE, weight: 0.8825 eval: 7.1687 min: 0.5143 max: 51.5000 USE_EVALUE, weight: 0.8825 eval: 7.1687 min: 0.5143 max: 51.5000 USE_EVALUE, weight: 0.8825 eval: 7.1687 min: 0.5143 max: 51.5000 USE_EVALUE, weight: 0.8954 eval: 6.4406 min: 0.5143 max: 51.5000 USE_EVALUE, weight: 0.8954 eval: 6.4406 min: 0.5143 max: 51.5000 USE_EVALUE, weight: 0.8954 eval: 6.4406 min: 0.5143 max: 51.5000 USE_EVALUE, weight: 0.9245 eval: 4.7900 min: 0.5143 max: 51.5000 USE_EVALUE, weight: 0.9245 eval: 4.7900 min: 0.5143 max: 51.5000 USE_EVALUE, weight: 0.9245 eval: 4.7900 min: 0.5143 max: 51.5000 USE_EVALUE, weight: 0.7863 eval: 12.6230 min: 0.5143 max: 51.5000 USE_EVALUE, weight: 0.7863 eval: 12.6230 min: 0.5143 max: 51.5000 USE_EVALUE, weight: 0.7863 eval: 12.6230 min: 0.5143 max: 51.5000 USE_EVALUE, weight: 0.8574 eval: 8.5950 min: 0.5143 max: 51.5000 USE_EVALUE, weight: 0.8574 eval: 8.5950 min: 0.5143 max: 51.5000 USE_EVALUE, weight: 0.8574 eval: 8.5950 min: 0.5143 max: 51.5000 USE_EVALUE, weight: 0.8347 eval: 9.8779 min: 0.5143 max: 51.5000 USE_EVALUE, weight: 0.8347 eval: 9.8779 min: 0.5143 max: 51.5000 USE_EVALUE, weight: 0.8347 eval: 9.8779 min: 0.5143 max: 51.5000 USE_EVALUE, weight: 0.7761 eval: 13.2000 min: 0.5143 max: 51.5000 USE_EVALUE, weight: 0.7761 eval: 13.2000 min: 0.5143 max: 51.5000 USE_EVALUE, weight: 0.7761 eval: 13.2000 min: 0.5143 max: 51.5000 USE_EVALUE, weight: 0.1000 eval: 51.5000 min: 0.5143 max: 51.5000 USE_EVALUE, weight: 0.1000 eval: 51.5000 min: 0.5143 max: 51.5000 USE_EVALUE, weight: 0.1000 eval: 51.5000 min: 0.5143 max: 51.5000 USE_EVALUE, weight: 0.8821 eval: 7.1928 min: 0.5143 max: 51.5000 USE_EVALUE, weight: 0.8821 eval: 7.1928 min: 0.5143 max: 51.5000 USE_EVALUE, weight: 0.8821 eval: 7.1928 min: 0.5143 max: 51.5000 USE_EVALUE, weight: 0.8057 eval: 11.5200 min: 0.5143 max: 51.5000 USE_EVALUE, weight: 0.8057 eval: 11.5200 min: 0.5143 max: 51.5000 USE_EVALUE, weight: 0.8057 eval: 11.5200 min: 0.5143 max: 51.5000 Number of contacts in models: 259 Number of contacts in alignments: 57 NUMB_ALIGNS: 57 Adding 5557 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: -236.4124, CN propb: -236.4124 weights: 0.2466 constraints: 314 # command:Found ConstraintSet # PrintContacts align.constraints_meta03 Number of constraints in align3.constraints 314 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_meta03 Number of constraints in align3.constraints.bonus 314 # command:Found ConstraintSet # PrintContacts rejected.constraints_meta03 Number of constraints in rejected3.constraints 5243 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_meta03 Number of constraints in rejected3.constraints.bonus 5243 # 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 5557 # command: