# 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:Using radius: 8.0000 Alignment mode NUMB_ALIGNS: 57 Adding 852 constraints to all.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all.constraints maxweight: 1.0000 Optimizing... Probability sum: -230.9379, CN propb: -230.9379 weights: 0.2411 constraints: 246 # command:Found ConstraintSet # PrintContacts align.constraints_v3 Number of constraints in align.constraints 246 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_v3 Number of constraints in align.constraints.bonus 246 # command:Found ConstraintSet # PrintContacts rejected.constraints_v3 Number of constraints in rejected.constraints 606 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_v3 Number of constraints in rejected.constraints.bonus 606 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_v3 Number of constraints in noncontact.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_v3 Number of constraints in noncontact.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_v3 Number of constraints in all.constraints 852 # command: