# 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/T0330/ # command:# Making conformation for sequence T0330 numbered 1 through 233 Created new target T0330 from T0330.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0330/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0330//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0330/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0330//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0330/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0330/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0330/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1j97A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1j97A expands to /projects/compbio/data/pdb/1j97.pdb.gz 1j97A:Bad short name: BE for alphabet: pdb_atoms Bad short name: F1 for alphabet: pdb_atoms Bad short name: F2 for alphabet: pdb_atoms Bad short name: F3 for alphabet: pdb_atoms # T0330 read from 1j97A/merged-good-all-a2m # 1j97A read from 1j97A/merged-good-all-a2m # adding 1j97A to template set # found chain 1j97A in template set Warning: unaligning (T0330)F8 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1j97A)F12 Warning: unaligning (T0330)I10 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1j97A)F12 T0330 2 :SRTLVL 1j97A 4 :KKKLIL # choosing archetypes in rotamer library T0330 11 :DGTLLKVES 1j97A 13 :DSTLVNNET T0330 25 :LADAL 1j97A 22 :IDEIA T0330 31 :EVYGT 1j97A 27 :REAGV T0330 46 :GKMDGAIIYEVLSNV 1j97A 46 :KLNFEQSLRKRVSLL T0330 61 :GLERAEI 1j97A 62 :DLPIEKV T0330 72 :DKA 1j97A 69 :EKA T0330 86 :A 1j97A 72 :I T0330 89 :EDITLLEGVRELLDALSSRS 1j97A 73 :KRITPTEGAEETIKELKNRG T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFA 1j97A 93 :YVVAVVSGGFDIAVNKIKEKLGLDYAFANRLIV T0330 143 :DDALDRNELPHIALERARRM 1j97A 136 :GEVLKENAKGEILEKIAKIE T0330 166 :NYSPSQIVIIGDTEHDIRCARELD 1j97A 156 :GINLEDTVAVGDGANDISMFKKAG T0330 191 :RSIAVAT 1j97A 180 :LKIAFCA T0330 202 :MEELARH 1j97A 187 :KPILKEK T0330 210 :PGTLF 1j97A 194 :ADICI T0330 215 :KNFAETD 1j97A 201 :RDLREIL Number of specific fragments extracted= 16 number of extra gaps= 0 total=16 Number of alignments=1 # 1j97A read from 1j97A/merged-good-all-a2m # found chain 1j97A in template set Warning: unaligning (T0330)F8 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1j97A)F12 Warning: unaligning (T0330)I10 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1j97A)F12 T0330 2 :SRTLVL 1j97A 4 :KKKLIL T0330 11 :DGTLLKVES 1j97A 13 :DSTLVNNET T0330 25 :LADALIEVY 1j97A 22 :IDEIAREAG T0330 49 :DGAIIYEVLSNVGLERAEIADKFDKAKETY 1j97A 31 :VEEEVKKITKEAMEGKLNFEQSLRKRVSLL T0330 79 :IALFRE 1j97A 65 :IEKVEK T0330 87 :RREDITLLEGVRELLDALSSRS 1j97A 71 :AIKRITPTEGAEETIKELKNRG T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHYF 1j97A 93 :YVVAVVSGGFDIAVNKIKEKLGLDYAF T0330 137 :PFGAFADDALDR 1j97A 131 :TGDVEGEVLKEN T0330 149 :N 1j97A 144 :K T0330 152 :PHIALERARRM 1j97A 145 :GEILEKIAKIE T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIA 1j97A 156 :GINLEDTVAVGDGANDISMFKKAGLKIAF T0330 200 :FTMEELARH 1j97A 185 :CAKPILKEK T0330 210 :PGTLF 1j97A 194 :ADICI T0330 215 :KNFAETD 1j97A 201 :RDLREIL Number of specific fragments extracted= 14 number of extra gaps= 0 total=30 Number of alignments=2 # 1j97A read from 1j97A/merged-good-all-a2m # found chain 1j97A in template set Warning: unaligning (T0330)F8 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1j97A)F12 Warning: unaligning (T0330)I10 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1j97A)F12 T0330 2 :SRTLVL 1j97A 4 :KKKLIL T0330 11 :DGTLLKVESM 1j97A 13 :DSTLVNNETI T0330 26 :ADALIEVYGTEGSTGSHDFS 1j97A 23 :DEIAREAGVEEEVKKITKEA T0330 46 :GKMDGAIIYEVLSNVG 1j97A 45 :GKLNFEQSLRKRVSLL T0330 65 :AEIA 1j97A 61 :KDLP T0330 72 :DKAKETYIA 1j97A 65 :IEKVEKAIK T0330 90 :DITLLEGVRELLDALSS 1j97A 74 :RITPTEGAEETIKELKN T0330 108 :SDVLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADD 1j97A 91 :RGYVVAVVSGGFDIAVNKIKEKLGLDYAFANRLIVKD T0330 145 :ALDRNELPHIALERARR 1j97A 138 :VLKENAKGEILEKIAKI T0330 165 :ANYSPSQIVIIGDTEHDIRCARELDARSI 1j97A 155 :EGINLEDTVAVGDGANDISMFKKAGLKIA T0330 195 :V 1j97A 184 :F T0330 200 :FTMEELAR 1j97A 185 :CAKPILKE T0330 209 :KPGTLFKN 1j97A 193 :KADICIEK Number of specific fragments extracted= 13 number of extra gaps= 0 total=43 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2c4nA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2c4nA expands to /projects/compbio/data/pdb/2c4n.pdb.gz 2c4nA:# T0330 read from 2c4nA/merged-good-all-a2m # 2c4nA read from 2c4nA/merged-good-all-a2m # adding 2c4nA to template set # found chain 2c4nA in template set Warning: unaligning (T0330)L15 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c4nA)H16 Warning: unaligning (T0330)K16 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2c4nA)H16 T0330 1 :MSRTLVLFDIDGTL 2c4nA 1 :MTIKNVICDIDGVL T0330 17 :VESMNRRVLADAL 2c4nA 20 :AVPGAAEFLHGIM T0330 32 :VYGT 2c4nA 33 :DKGL T0330 47 :K 2c4nA 46 :S T0330 62 :LER 2c4nA 47 :QTG T0330 72 :DKAKETYIA 2c4nA 50 :QDLANRFAT T0330 89 :EDITLLE 2c4nA 59 :AGVDVPD T0330 96 :GVRELLDALSSRSDVLLGLLTGN 2c4nA 71 :SAMATADFLRRQEGKKAYVVGEG T0330 122 :SGRHKLKLPGID 2c4nA 94 :ALIHELYKAGFT T0330 136 :FPFGAFADDAL 2c4nA 111 :PDFVIVGETRS T0330 147 :DRNELPHIALERARRM 2c4nA 174 :VGKPSPWIIRAALNKM T0330 166 :NYSPSQIVIIGDTE 2c4nA 190 :QAHSEETVIVGDNL T0330 180 :HDIRCARELDARSIAVATGNFTMEEL 2c4nA 205 :TDILAGFQAGLETILVLSGVSSLDDI T0330 207 :RHKPGTLFKNFAET 2c4nA 234 :PFRPSWIYPSVAEI Number of specific fragments extracted= 14 number of extra gaps= 1 total=57 Number of alignments=4 # 2c4nA read from 2c4nA/merged-good-all-a2m # found chain 2c4nA in template set Warning: unaligning (T0330)L15 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c4nA)H16 Warning: unaligning (T0330)K16 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2c4nA)H16 T0330 1 :MSRTLVLFDIDGTL 2c4nA 1 :MTIKNVICDIDGVL T0330 17 :VESMNRRV 2c4nA 17 :DNVAVPGA T0330 26 :ADALIEVYGTEGSTGSHDFSGKMDGAIIYEVLSNVGLER 2c4nA 25 :AEFLHGIMDKGLPLVLLTNYPSQTGQDLANRFATAGVDV T0330 87 :RREDITLL 2c4nA 64 :PDSVFYTS T0330 97 :VRELLDALSSRSDVLLGLL 2c4nA 72 :AMATADFLRRQEGKKAYVV T0330 119 :FEASGRHKLKLPGID 2c4nA 91 :GEGALIHELYKAGFT T0330 136 :F 2c4nA 106 :I T0330 137 :PFGAFADDALD 2c4nA 112 :DFVIVGETRSY T0330 148 :RNELPHIALERARRM 2c4nA 175 :GKPSPWIIRAALNKM T0330 166 :NYSPSQIVIIGDTE 2c4nA 190 :QAHSEETVIVGDNL T0330 180 :HDIRCARELDARSIAVATGNFTMEELARHK 2c4nA 205 :TDILAGFQAGLETILVLSGVSSLDDIDSMP T0330 210 :PGTLFKNFAET 2c4nA 237 :PSWIYPSVAEI Number of specific fragments extracted= 12 number of extra gaps= 1 total=69 Number of alignments=5 # 2c4nA read from 2c4nA/merged-good-all-a2m # found chain 2c4nA in template set Warning: unaligning (T0330)L15 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2c4nA)H16 Warning: unaligning (T0330)K16 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2c4nA)H16 T0330 1 :MSRTLVLFDIDGTL 2c4nA 1 :MTIKNVICDIDGVL T0330 90 :DITLLEGVRELLDALSS 2c4nA 17 :DNVAVPGAAEFLHGIMD T0330 108 :SDVLLGLLTGNF 2c4nA 34 :KGLPLVLLTNYP T0330 120 :EASGRHKLKLPGI 2c4nA 49 :GQDLANRFATAGV T0330 133 :DHYFP 2c4nA 65 :DSVFY T0330 138 :FGAFADD 2c4nA 113 :FVIVGET T0330 147 :DRNELPHIALERARR 2c4nA 174 :VGKPSPWIIRAALNK T0330 165 :ANYSPSQIVIIGDTE 2c4nA 189 :MQAHSEETVIVGDNL T0330 180 :HDIRCARELDARSIAVATGNFTMEE 2c4nA 205 :TDILAGFQAGLETILVLSGVSSLDD T0330 208 :HKPGTLFKNFAE 2c4nA 235 :FRPSWIYPSVAE Number of specific fragments extracted= 10 number of extra gaps= 1 total=79 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gfhA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2gfhA expands to /projects/compbio/data/pdb/2gfh.pdb.gz 2gfhA:Skipped atom 62, because occupancy 0.5 <= existing 0.500 in 2gfhA Skipped atom 66, because occupancy 0.500 <= existing 0.500 in 2gfhA Skipped atom 68, because occupancy 0.500 <= existing 0.500 in 2gfhA Skipped atom 70, because occupancy 0.500 <= existing 0.500 in 2gfhA Skipped atom 72, because occupancy 0.500 <= existing 0.500 in 2gfhA Skipped atom 74, because occupancy 0.500 <= existing 0.500 in 2gfhA Skipped atom 76, because occupancy 0.500 <= existing 0.500 in 2gfhA Skipped atom 78, because occupancy 0.500 <= existing 0.500 in 2gfhA Skipped atom 789, because occupancy 0.500 <= existing 0.500 in 2gfhA Skipped atom 793, because occupancy 0.500 <= existing 0.500 in 2gfhA Skipped atom 795, because occupancy 0.500 <= existing 0.500 in 2gfhA # T0330 read from 2gfhA/merged-good-all-a2m # 2gfhA read from 2gfhA/merged-good-all-a2m # adding 2gfhA to template set # found chain 2gfhA in template set Warning: unaligning (T0330)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gfhA)D12 Warning: unaligning (T0330)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gfhA)D12 Warning: unaligning (T0330)S38 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2gfhA)C67 Warning: unaligning (T0330)D43 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2gfhA)C67 T0330 2 :SRTLVL 2gfhA 5 :RVRAVF T0330 10 :IDGTLLKVESMNRRVLADAL 2gfhA 13 :LDNTLIDTAGASRRGMLEVI T0330 31 :EVY 2gfhA 33 :KLL T0330 34 :GT 2gfhA 38 :KY T0330 36 :EG 2gfhA 60 :CF T0330 44 :FSGKMDGAIIYEVLSNVGLERA 2gfhA 68 :ITDVRTSHWEEAIQETKGGADN T0330 72 :DKAKETYIALFRERAR 2gfhA 90 :RKLAEECYFLWKSTRL T0330 89 :EDITLLEGVRELLDALSSR 2gfhA 106 :QHMILADDVKAMLTELRKE T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARRM 2gfhA 125 :VRLLLLTNGDRQTQREKIEACACQSYFDAIVIGGEQKEEKPAPSIFYHCCDLL T0330 166 :NYSPSQIVIIGDTE 2gfhA 178 :GVQPGDCVMVGDTL T0330 180 :HDIRCARELDA 2gfhA 193 :TDIQGGLNAGL T0330 191 :RSIAVATGNFT 2gfhA 205 :ATVWINKSGRV T0330 207 :RHKPGTLFKNFAETDEVLASILTP 2gfhA 220 :SPMPHYMVSSVLELPALLQSIDCK Number of specific fragments extracted= 13 number of extra gaps= 1 total=92 Number of alignments=7 # 2gfhA read from 2gfhA/merged-good-all-a2m # found chain 2gfhA in template set Warning: unaligning (T0330)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gfhA)D12 Warning: unaligning (T0330)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gfhA)D12 T0330 2 :SRTLVL 2gfhA 5 :RVRAVF T0330 10 :IDGTLLKVESMNRRVLADALIEVYGTEGSTGSHDF 2gfhA 13 :LDNTLIDTAGASRRGMLEVIKLLQSKYHYKEEAEI T0330 49 :DGAIIYEVLSNVG 2gfhA 48 :ICDKVQVKLSKEC T0330 62 :LERAEIADKFDKAKETYIALFRER 2gfhA 84 :KGGADNRKLAEECYFLWKSTRLQH T0330 91 :ITLLEGVRELLDALSSR 2gfhA 108 :MILADDVKAMLTELRKE T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARRM 2gfhA 125 :VRLLLLTNGDRQTQREKIEACACQSYFDAIVIGGEQKEEKPAPSIFYHCCDLL T0330 166 :NYSPSQIVIIGDTE 2gfhA 178 :GVQPGDCVMVGDTL T0330 180 :HDIRCARELDAR 2gfhA 193 :TDIQGGLNAGLK T0330 192 :SIAVATG 2gfhA 206 :TVWINKS T0330 199 :NFT 2gfhA 220 :SPM T0330 210 :PGTLFKNFAETDEVLASILTP 2gfhA 223 :PHYMVSSVLELPALLQSIDCK Number of specific fragments extracted= 11 number of extra gaps= 1 total=103 Number of alignments=8 # 2gfhA read from 2gfhA/merged-good-all-a2m # found chain 2gfhA in template set Warning: unaligning (T0330)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2gfhA)D12 Warning: unaligning (T0330)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2gfhA)D12 T0330 2 :SRTLVL 2gfhA 5 :RVRAVF T0330 10 :IDGTLLKVESMNRRVLADALIEV 2gfhA 13 :LDNTLIDTAGASRRGMLEVIKLL T0330 37 :GSTGSHDFS 2gfhA 40 :HYKEEAEII T0330 46 :GKMDGAIIYEVLSNVGL 2gfhA 69 :TDVRTSHWEEAIQETKG T0330 68 :ADKFDKAKETYIALFRERARR 2gfhA 86 :GADNRKLAEECYFLWKSTRLQ T0330 90 :DITLLEGVRELLDALSS 2gfhA 107 :HMILADDVKAMLTELRK T0330 109 :DVLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARR 2gfhA 124 :EVRLLLLTNGDRQTQREKIEACACQSYFDAIVIGGEQKEEKPAPSIFYHCCDL T0330 165 :ANYSPSQIVIIGDTE 2gfhA 177 :LGVQPGDCVMVGDTL T0330 180 :HDIRCARELDARSIAVATGNFT 2gfhA 193 :TDIQGGLNAGLKATVWINKSGR T0330 208 :HKPGTLFKNFAETDEVLASILT 2gfhA 221 :PMPHYMVSSVLELPALLQSIDC Number of specific fragments extracted= 10 number of extra gaps= 1 total=113 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wr8A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0330 read from 1wr8A/merged-good-all-a2m # 1wr8A read from 1wr8A/merged-good-all-a2m # found chain 1wr8A in training set Warning: unaligning (T0330)S2 because first residue in template chain is (1wr8A)K2 T0330 3 :RTLVLFDIDGTLLK 1wr8A 3 :IKAISIDIDGTITY T0330 89 :EDITLLEGVRELLDALSSRS 1wr8A 17 :PNRMIHEKALEAIRRAESLG T0330 110 :VLLGLLTGNFEASGRHKLKLPGID 1wr8A 37 :IPIMLVTGNTVQFAEAASILIGTS T0330 138 :FGAFADDAL 1wr8A 61 :GPVVAEDGG T0330 147 :DRNELPHIALERARRM 1wr8A 150 :PWINKGSGIEKASEFL T0330 166 :NYSPSQIVIIGDTEHDIRCARELD 1wr8A 166 :GIKPKEVAHVGDGENDLDAFKVVG T0330 191 :RSIAV 1wr8A 190 :YKVAV T0330 198 :GNFT 1wr8A 195 :AQAP T0330 203 :EELARH 1wr8A 199 :KILKEN T0330 210 :PGTLFKN 1wr8A 205 :ADYVTKK T0330 217 :FAETDEVLAS 1wr8A 217 :GAEAIYHILE Number of specific fragments extracted= 11 number of extra gaps= 0 total=124 Number of alignments=10 # 1wr8A read from 1wr8A/merged-good-all-a2m # found chain 1wr8A in training set Warning: unaligning (T0330)S2 because first residue in template chain is (1wr8A)K2 T0330 3 :RTLVLFDIDGTL 1wr8A 3 :IKAISIDIDGTI T0330 87 :RREDITLLEGVRELLDALSSRS 1wr8A 15 :TYPNRMIHEKALEAIRRAESLG T0330 110 :VLLGLLTGNF 1wr8A 37 :IPIMLVTGNT T0330 120 :EASGRHKLKLPGID 1wr8A 122 :VETVREIINELNLN T0330 136 :F 1wr8A 136 :L T0330 138 :FGAFADD 1wr8A 137 :VAVDSGF T0330 148 :RNELPHIALERARRM 1wr8A 151 :WINKGSGIEKASEFL T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIA 1wr8A 166 :GIKPKEVAHVGDGENDLDAFKVVGYKVAV T0330 199 :NFTMEELARH 1wr8A 195 :AQAPKILKEN T0330 210 :PGTLFKN 1wr8A 205 :ADYVTKK T0330 217 :FAETDEVLASIL 1wr8A 217 :GAEAIYHILEKF Number of specific fragments extracted= 11 number of extra gaps= 0 total=135 Number of alignments=11 # 1wr8A read from 1wr8A/merged-good-all-a2m # found chain 1wr8A in training set Warning: unaligning (T0330)S2 because first residue in template chain is (1wr8A)K2 T0330 3 :RTLVLFDIDGTLL 1wr8A 3 :IKAISIDIDGTIT T0330 88 :REDITLLEGVRELLDALSS 1wr8A 16 :YPNRMIHEKALEAIRRAES T0330 108 :SDVLLGLLTGNFEASGRHKLKLPGIDHYFP 1wr8A 35 :LGIPIMLVTGNTVQFAEAASILIGTSGPVV T0330 145 :ALDRNELPHIALERARR 1wr8A 148 :KKPWINKGSGIEKASEF T0330 165 :ANYSPSQIVIIGDTEHDIRCARELDARSI 1wr8A 165 :LGIKPKEVAHVGDGENDLDAFKVVGYKVA T0330 197 :TGNF 1wr8A 194 :VAQA T0330 202 :MEELAR 1wr8A 198 :PKILKE T0330 209 :KPGTLFKN 1wr8A 204 :NADYVTKK T0330 217 :FAETDEVLAS 1wr8A 214 :GEGGAEAIYH Number of specific fragments extracted= 9 number of extra gaps= 0 total=144 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qyiA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1qyiA expands to /projects/compbio/data/pdb/1qyi.pdb.gz 1qyiA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0330 read from 1qyiA/merged-good-all-a2m # 1qyiA read from 1qyiA/merged-good-all-a2m # adding 1qyiA to template set # found chain 1qyiA in template set T0330 1 :M 1qyiA 1 :M T0330 4 :TLVLFDIDGTLLKVESMN 1qyiA 2 :KKILFDVDGVFLSEERCF T0330 22 :RRVLADALI 1qyiA 23 :ALTVYELLM T0330 31 :EVYGTEGSTGSHDFSGKMDGAIIYE 1qyiA 34 :CYLGLHSHIDWETLTDNDIQDIRNR T0330 56 :VLSNVGLERAEIADKF 1qyiA 136 :FLDNVKVGKNNIYAAL T0330 79 :IALFRERARREDITL 1qyiA 152 :EEFATTELHVSDATL T0330 94 :LEGVRELLDALSSRS 1qyiA 217 :VDEVKVLLNDLKGAG T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHYF 1qyiA 232 :FELGIATGRPYTETVVPFENLGLLPYF T0330 137 :PFGAFADDAL 1qyiA 261 :DFIATASDVL T0330 148 :RNELPHIALERAR 1qyiA 283 :GKPNPFSYIAALY T0330 166 :NYSPSQ 1qyiA 296 :GNNRDK T0330 172 :IVIIGDTEHDIRCARELDARSIAVATGNFT 1qyiA 318 :VFIVGDSLADLLSAQKIGATFIGTLTGLKG T0330 202 :MEELARHKPGTLFKNFAETDEVL 1qyiA 351 :AGELEAHHADYVINHLGELRGVL Number of specific fragments extracted= 13 number of extra gaps= 0 total=157 Number of alignments=13 # 1qyiA read from 1qyiA/merged-good-all-a2m # found chain 1qyiA in template set T0330 1 :M 1qyiA 1 :M T0330 4 :TLVLFDIDGTLLKVESMNR 1qyiA 2 :KKILFDVDGVFLSEERCFD T0330 23 :RVLADALI 1qyiA 24 :LTVYELLM T0330 31 :EVYGTEGSTGSHDF 1qyiA 34 :CYLGLHSHIDWETL T0330 49 :DGAIIYEVLSNVG 1qyiA 48 :TDNDIQDIRNRIF T0330 62 :LERAEIADKFDKAKETY 1qyiA 142 :VGKNNIYAALEEFATTE T0330 79 :IALFRERA 1qyiA 188 :SKLYEDVE T0330 87 :RREDITLLEGVRELLDALSSRS 1qyiA 210 :QEIILRPVDEVKVLLNDLKGAG T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHYF 1qyiA 232 :FELGIATGRPYTETVVPFENLGLLPYF T0330 137 :PFGAFADDALD 1qyiA 261 :DFIATASDVLE T0330 148 :RNELPHIALERARRMT 1qyiA 283 :GKPNPFSYIAALYGNN T0330 164 :GANYSPSQIVIIGDTEHDIRCARELDARSIAVATGNFT 1qyiA 310 :DNIVNKDDVFIVGDSLADLLSAQKIGATFIGTLTGLKG T0330 202 :MEELARHKPGTLFKNFAETDEVL 1qyiA 351 :AGELEAHHADYVINHLGELRGVL Number of specific fragments extracted= 13 number of extra gaps= 0 total=170 Number of alignments=14 # 1qyiA read from 1qyiA/merged-good-all-a2m # found chain 1qyiA in template set T0330 4 :TLVLFDIDGTLLKVESM 1qyiA 2 :KKILFDVDGVFLSEERC T0330 22 :RRVLADALIEV 1qyiA 19 :FDVSALTVYEL T0330 34 :GT 1qyiA 44 :WE T0330 41 :SHDFSGKMDGAI 1qyiA 89 :LIDILKKLSHDE T0330 53 :IYEVLSNV 1qyiA 147 :IYAALEEF T0330 61 :GLERAEIADKFDKAKETYIALFRERA 1qyiA 163 :DATLFSLKGALWTLAQEVYQEWYLGS T0330 87 :R 1qyiA 195 :E T0330 91 :ITLLEGVRELLDALSS 1qyiA 214 :LRPVDEVKVLLNDLKG T0330 108 :SDVLLGLLTGNFEASGRHKLKLPGIDHYF 1qyiA 230 :AGFELGIATGRPYTETVVPFENLGLLPYF T0330 137 :PFGAFADD 1qyiA 261 :DFIATASD T0330 145 :ALDRNELPHIALERARR 1qyiA 278 :QARPLGKPNPFSYIAAL T0330 165 :ANYSPSQ 1qyiA 295 :YGNNRDK T0330 172 :IVIIGDTEHDIRCARELDARSIAVATGNFT 1qyiA 318 :VFIVGDSLADLLSAQKIGATFIGTLTGLKG T0330 202 :MEELARHKPGTLFKNFAETDEVL 1qyiA 351 :AGELEAHHADYVINHLGELRGVL Number of specific fragments extracted= 14 number of extra gaps= 0 total=184 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rqlA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1rqlA expands to /projects/compbio/data/pdb/1rql.pdb.gz 1rqlA:# T0330 read from 1rqlA/merged-good-all-a2m # 1rqlA read from 1rqlA/merged-good-all-a2m # adding 1rqlA to template set # found chain 1rqlA in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1rqlA)K5 Warning: unaligning (T0330)T229 because last residue in template chain is (1rqlA)K261 T0330 3 :RTLVLFDIDGTLLKVE 1rqlA 6 :IEAVIFDWAGTTVDYG T0330 19 :SMNRRVLADAL 1rqlA 23 :FAPLEVFMEIF T0330 31 :EVYGTEGSTGS 1rqlA 34 :HKRGVAITAEE T0330 42 :HDFSGKMDGAIIYE 1rqlA 46 :RKPMGLLKIDHVRA T0330 56 :VLSNVG 1rqlA 70 :WNRVFR T0330 62 :LERAEIA 1rqlA 77 :LPTEADI T0330 72 :DKAKETYIALFRERAR 1rqlA 84 :QEMYEEFEEILFAILP T0330 89 :EDITLLEGVRELLDALSSRS 1rqlA 100 :RYASPINAVKEVIASLRERG T0330 110 :VLLGLLTGNFEASGRHKLKLP 1rqlA 120 :IKIGSTTGYTREMMDIVAKEA T0330 131 :GID 1rqlA 144 :GYK T0330 136 :FPFGAFADDALDRNELPHIALERARRM 1rqlA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMEL T0330 166 :NY 1rqlA 174 :GV T0330 168 :SPSQIVIIGDTEHDIRCARELDARSIAVATG 1rqlA 177 :PMNHMIKVGDTVSDMKEGRNAGMWTVGVILG T0330 199 :NFTMEE 1rqlA 212 :GLTEEE T0330 205 :LARHKPGTLFKNFAETDEVLASIL 1rqlA 237 :FVENGAHFTIETMQELESVMEHIE Number of specific fragments extracted= 15 number of extra gaps= 0 total=199 Number of alignments=16 # 1rqlA read from 1rqlA/merged-good-all-a2m # found chain 1rqlA in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1rqlA)K5 Warning: unaligning (T0330)T229 because last residue in template chain is (1rqlA)K261 T0330 3 :RTLVLFDIDGTLLKVE 1rqlA 6 :IEAVIFDWAGTTVDYG T0330 19 :SMNRRVLADALIEVYGTEGSTGSHDFSGKM 1rqlA 23 :FAPLEVFMEIFHKRGVAITAEEARKPMGLL T0330 49 :DGAIIYEVLSNVG 1rqlA 62 :EMPRIASEWNRVF T0330 62 :LER 1rqlA 78 :PTE T0330 69 :DKFDKAKETYIALFRER 1rqlA 81 :ADIQEMYEEFEEILFAI T0330 87 :RREDITLLEGVRELLDALSSRS 1rqlA 98 :LPRYASPINAVKEVIASLRERG T0330 110 :VLLGLLTGNFEASGRHKLKLP 1rqlA 120 :IKIGSTTGYTREMMDIVAKEA T0330 131 :GID 1rqlA 144 :GYK T0330 136 :FPFGAFADDALDRNELPHIALERARRM 1rqlA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMEL T0330 166 :NY 1rqlA 174 :GV T0330 168 :SPSQIVIIGDTEHDIRCARELDARSIAVATG 1rqlA 177 :PMNHMIKVGDTVSDMKEGRNAGMWTVGVILG T0330 199 :NFTMEELARHK 1rqlA 220 :NMDSVELREKI T0330 210 :PGTLFKNFAETDEVLASIL 1rqlA 242 :AHFTIETMQELESVMEHIE Number of specific fragments extracted= 13 number of extra gaps= 0 total=212 Number of alignments=17 # 1rqlA read from 1rqlA/merged-good-all-a2m # found chain 1rqlA in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1rqlA)K5 Warning: unaligning (T0330)T229 because last residue in template chain is (1rqlA)K261 T0330 3 :RTLVLFDIDGTLLKVE 1rqlA 6 :IEAVIFDWAGTTVDYG T0330 20 :MNRRVLADALIEVYGTEGSTGSHDFSGKMDGAI 1rqlA 24 :APLEVFMEIFHKRGVAITAEEARKPMGLLKIDH T0330 53 :IYEVLSNVG 1rqlA 66 :IASEWNRVF T0330 64 :RAEIADKFDKAKETYIALFRERARREDITLLEGVRELLDALSS 1rqlA 75 :RQLPTEADIQEMYEEFEEILFAILPRYASPINAVKEVIASLRE T0330 108 :SDVLLGLLTGNFEASGRHKLKLPGIDHYF 1rqlA 118 :RGIKIGSTTGYTREMMDIVAKEAALQGYK T0330 137 :PFGAFADDALDRNELPHIALERARR 1rqlA 148 :DFLVTPDDVPAGRPYPWMCYKNAME T0330 165 :ANY 1rqlA 173 :LGV T0330 168 :SPSQIVIIGDTEHDIRCARELDARSIAVATGNF 1rqlA 177 :PMNHMIKVGDTVSDMKEGRNAGMWTVGVILGSS T0330 201 :TMEE 1rqlA 214 :TEEE T0330 205 :LARHKPGTLFKNFAETDEVLASIL 1rqlA 237 :FVENGAHFTIETMQELESVMEHIE Number of specific fragments extracted= 10 number of extra gaps= 0 total=222 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ek1A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ek1A expands to /projects/compbio/data/pdb/1ek1.pdb.gz 1ek1A:# T0330 read from 1ek1A/merged-good-all-a2m # 1ek1A read from 1ek1A/merged-good-all-a2m # adding 1ek1A to template set # found chain 1ek1A in template set Warning: unaligning (T0330)T4 because first residue in template chain is (1ek1A)R4 Warning: unaligning (T0330)E18 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ek1A)G48 Warning: unaligning (T0330)F44 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ek1A)Q90 Warning: unaligning (T0330)R87 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ek1A)Q90 T0330 5 :LVLFDIDGTLLK 1ek1A 5 :VAAFDLDGVLAL T0330 17 :V 1ek1A 18 :S T0330 36 :EGSTGS 1ek1A 57 :KITFSQ T0330 42 :HD 1ek1A 64 :VP T0330 88 :REDITLLEGVRELLDALSSRS 1ek1A 96 :MAARSINRPMLQAAIALKKKG T0330 110 :VLLGLLTG 1ek1A 117 :FTTCIVTN T0330 118 :NFEASGRHKLKL 1ek1A 131 :DKRDSLAQMMCE T0330 132 :IDHYFPFGAFADDALDRNELPHIALERARRM 1ek1A 143 :LSQHFDFLIESCQVGMIKPEPQIYNFLLDTL T0330 166 :NYSPSQIVIIGDTEHDIRCARELDAR 1ek1A 174 :KAKPNEVVFLDDFGSNLKPARDMGMV Number of specific fragments extracted= 9 number of extra gaps= 0 total=231 Number of alignments=19 # 1ek1A read from 1ek1A/merged-good-all-a2m # found chain 1ek1A in template set Warning: unaligning (T0330)T4 because first residue in template chain is (1ek1A)R4 Warning: unaligning (T0330)N21 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ek1A)G48 T0330 5 :LVLFDIDGTLLK 1ek1A 5 :VAAFDLDGVLAL T0330 19 :SM 1ek1A 17 :PS T0330 87 :RREDITLLEGVRELLDALSSRS 1ek1A 95 :AMAARSINRPMLQAAIALKKKG T0330 110 :VLLGLLTGNF 1ek1A 117 :FTTCIVTNNW T0330 120 :EASGRHKLKL 1ek1A 133 :RDSLAQMMCE T0330 132 :IDHYFPFGAFADDALDRNELPHIALERARRM 1ek1A 143 :LSQHFDFLIESCQVGMIKPEPQIYNFLLDTL T0330 166 :NYSPSQIVIIGDTEHDIRCARELDAR 1ek1A 174 :KAKPNEVVFLDDFGSNLKPARDMGMV Number of specific fragments extracted= 7 number of extra gaps= 0 total=238 Number of alignments=20 # 1ek1A read from 1ek1A/merged-good-all-a2m # found chain 1ek1A in template set Warning: unaligning (T0330)T4 because first residue in template chain is (1ek1A)R4 Warning: unaligning (T0330)T39 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1ek1A)G48 Warning: unaligning (T0330)K70 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1ek1A)Q90 T0330 5 :LVLFDIDGTLL 1ek1A 5 :VAAFDLDGVLA T0330 40 :GSHDFS 1ek1A 49 :PTEQLM T0330 59 :NVGLERAEIAD 1ek1A 55 :KGKITFSQWVP T0330 87 :RREDITLLEGVRELLDALSS 1ek1A 95 :AMAARSINRPMLQAAIALKK T0330 108 :SDVLLGLLTGNF 1ek1A 115 :KGFTTCIVTNNW T0330 120 :EASGRHKLKLP 1ek1A 133 :RDSLAQMMCEL T0330 133 :DHYFPFGAFADDALDRNELPHIALERARR 1ek1A 144 :SQHFDFLIESCQVGMIKPEPQIYNFLLDT T0330 165 :ANYSPSQIVIIGDTEHDIRCARELDA 1ek1A 173 :LKAKPNEVVFLDDFGSNLKPARDMGM Number of specific fragments extracted= 8 number of extra gaps= 0 total=246 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nnlA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0330 read from 1nnlA/merged-good-all-a2m # 1nnlA read from 1nnlA/merged-good-all-a2m # found chain 1nnlA in training set Warning: unaligning (T0330)G37 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1nnlA)P57 Warning: unaligning (T0330)M48 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1nnlA)P57 T0330 4 :TLVLFDIDGTLLKVES 1nnlA 15 :DAVCFDVDSTVIREEG T0330 25 :LADAL 1nnlA 31 :IDELA T0330 31 :EVYGTE 1nnlA 36 :KICGVE T0330 49 :DGAIIYEVLSNVGLERA 1nnlA 58 :FKAALTERLALIQPSRE T0330 81 :LFRERARREDITLLEGVRELLDALSSRS 1nnlA 75 :QVQRLIAEQPPHLTPGIRELVSRLQERN T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFA 1nnlA 103 :VQVFLISGGFRSIVEHVASKLNIPATNVFANRL T0330 147 :DRNELPHIALERARRM 1nnlA 154 :ESGGKGKVIKLLKEKF T0330 168 :SPSQIVIIGDTEHDIRC 1nnlA 170 :HFKKIIMIGDGATDMEA T0330 189 :DA 1nnlA 189 :PA T0330 191 :RSIAV 1nnlA 192 :AFIGF T0330 197 :TGNFTMEELARH 1nnlA 197 :GGNVIRQQVKDN T0330 210 :PGTLFKNFAET 1nnlA 209 :AKWYITDFVEL Number of specific fragments extracted= 12 number of extra gaps= 0 total=258 Number of alignments=22 # 1nnlA read from 1nnlA/merged-good-all-a2m # found chain 1nnlA in training set Warning: unaligning (T0330)I53 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1nnlA)P57 Warning: unaligning (T0330)E66 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1nnlA)P57 T0330 4 :TLVLFDIDGTLLKVES 1nnlA 15 :DAVCFDVDSTVIREEG T0330 25 :LADALIEVY 1nnlA 31 :IDELAKICG T0330 49 :DGAI 1nnlA 40 :VEDA T0330 67 :IADKFDKAKETY 1nnlA 58 :FKAALTERLALI T0330 79 :IALFRERARREDITLLEGVRELLDALSSRS 1nnlA 73 :REQVQRLIAEQPPHLTPGIRELVSRLQERN T0330 110 :VLLGLLTGNFEASGRHKLKLPGID 1nnlA 103 :VQVFLISGGFRSIVEHVASKLNIP T0330 134 :HYFPFGAFADDALD 1nnlA 129 :NVFANRLKFYFNGE T0330 148 :RN 1nnlA 157 :GK T0330 152 :PHIALERARRM 1nnlA 159 :GKVIKLLKEKF T0330 168 :SPSQIVIIGDTEHDIRCA 1nnlA 170 :HFKKIIMIGDGATDMEAC T0330 189 :DARSIAVATGNFTMEELARH 1nnlA 189 :PADAFIGFGGNVIRQQVKDN T0330 210 :PGTLFKNFAET 1nnlA 209 :AKWYITDFVEL Number of specific fragments extracted= 12 number of extra gaps= 0 total=270 Number of alignments=23 # 1nnlA read from 1nnlA/merged-good-all-a2m # found chain 1nnlA in training set Warning: unaligning (T0330)A51 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1nnlA)P57 Warning: unaligning (T0330)E66 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1nnlA)P57 T0330 4 :TLVLFDIDGTLLKVESM 1nnlA 15 :DAVCFDVDSTVIREEGI T0330 39 :TGSHDFSGKMDG 1nnlA 32 :DELAKICGVEDA T0330 67 :IADKFDKAKETY 1nnlA 58 :FKAALTERLALI T0330 79 :IALFRERARREDITLLEGVRELLDALSS 1nnlA 73 :REQVQRLIAEQPPHLTPGIRELVSRLQE T0330 108 :SDVLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFAD 1nnlA 101 :RNVQVFLISGGFRSIVEHVASKLNIPATNVFANRLK T0330 145 :ALDRNELPHIALERARR 1nnlA 152 :TAESGGKGKVIKLLKEK T0330 165 :ANY 1nnlA 169 :FHF T0330 170 :SQIVIIGDTEHDIRC 1nnlA 172 :KKIIMIGDGATDMEA T0330 189 :DARSIAVATGNFTMEELAR 1nnlA 189 :PADAFIGFGGNVIRQQVKD T0330 209 :KPGTLFKNFAET 1nnlA 208 :NAKWYITDFVEL Number of specific fragments extracted= 10 number of extra gaps= 0 total=280 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zd3A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zd3A expands to /projects/compbio/data/pdb/1zd3.pdb.gz 1zd3A:# T0330 read from 1zd3A/merged-good-all-a2m # 1zd3A read from 1zd3A/merged-good-all-a2m # adding 1zd3A to template set # found chain 1zd3A in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1zd3A)T2 T0330 3 :RTLVLFDIDGTLL 1zd3A 3 :LRAAVFDLDGVLA T0330 17 :VESMNRRV 1zd3A 19 :VFGVLGRT T0330 29 :L 1zd3A 27 :E T0330 31 :EVYGTEG 1zd3A 28 :EALALPR T0330 51 :AIIYE 1zd3A 35 :GLLND T0330 56 :VLSNVGLER 1zd3A 52 :RLMKGEITL T0330 72 :DKAKETYIALFRERARREDITL 1zd3A 61 :SQWIPLMEENCRKCSETAKVCL T0330 94 :LEGVRELLDALSSRS 1zd3A 102 :NRPMLQAALMLRKKG T0330 110 :VLLGLLTG 1zd3A 117 :FTTAILTN T0330 118 :NFEASGRHKLKLPG 1zd3A 131 :AERDGLAQLMCELK T0330 134 :HYFPFGAFADDALDRNELPHIALERARRM 1zd3A 145 :MHFDFLIESCQVGMVKPEPQIYKFLLDTL T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSI 1zd3A 174 :KASPSEVVFLDDIGANLKPARDLGMVTI T0330 213 :LFKNFAETDEVLASILTPK 1zd3A 202 :LVQDTDTALKELEKVTGIQ Number of specific fragments extracted= 13 number of extra gaps= 0 total=293 Number of alignments=25 # 1zd3A read from 1zd3A/merged-good-all-a2m # found chain 1zd3A in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1zd3A)T2 T0330 3 :RTLVLFDIDGTLLKVE 1zd3A 3 :LRAAVFDLDGVLALPA T0330 21 :NRRVLADALIEVYGTEGSTGSHDFSG 1zd3A 19 :VFGVLGRTEEALALPRGLLNDAFQKG T0330 49 :DGAIIYEVLSNVGLERAEIADKFDKAKETY 1zd3A 45 :GPEGATTRLMKGEITLSQWIPLMEENCRKC T0330 79 :IALFRE 1zd3A 89 :KEIFDK T0330 87 :RREDITLLEGVRELLDALSSRS 1zd3A 95 :AISARKINRPMLQAALMLRKKG T0330 110 :VLLGLLTGNF 1zd3A 117 :FTTAILTNTW T0330 120 :EASGRHKLKLPGID 1zd3A 133 :RDGLAQLMCELKMH T0330 136 :FPFGAFADDALDRNELPHIALERARRM 1zd3A 147 :FDFLIESCQVGMVKPEPQIYKFLLDTL T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIA 1zd3A 174 :KASPSEVVFLDDIGANLKPARDLGMVTIL T0330 214 :FKNFAETDEVLASILTPK 1zd3A 203 :VQDTDTALKELEKVTGIQ Number of specific fragments extracted= 10 number of extra gaps= 0 total=303 Number of alignments=26 # 1zd3A read from 1zd3A/merged-good-all-a2m # found chain 1zd3A in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1zd3A)T2 T0330 3 :RTLVLFDIDGTLL 1zd3A 3 :LRAAVFDLDGVLA T0330 16 :KVESMNRRV 1zd3A 18 :AVFGVLGRT T0330 29 :LIEVYGTEGSTG 1zd3A 27 :EEALALPRGLLN T0330 41 :SHDFSGKMDGAIIYEVLSNV 1zd3A 51 :TRLMKGEITLSQWIPLMEEN T0330 71 :FDKAKETY 1zd3A 71 :CRKCSETA T0330 79 :IALFRERAR 1zd3A 89 :KEIFDKAIS T0330 90 :DITLLEGVRELLDALSS 1zd3A 98 :ARKINRPMLQAALMLRK T0330 108 :SDVLLGLLTGNF 1zd3A 115 :KGFTTAILTNTW T0330 120 :EASGRHKLKLPG 1zd3A 133 :RDGLAQLMCELK T0330 134 :HYFPFGAFADDALDRNELPHIALERARR 1zd3A 145 :MHFDFLIESCQVGMVKPEPQIYKFLLDT T0330 165 :ANYSPSQIVIIGDTEHDIRCARELDARSI 1zd3A 173 :LKASPSEVVFLDDIGANLKPARDLGMVTI T0330 213 :LFKNFAETDEVLASIL 1zd3A 202 :LVQDTDTALKELEKVT Number of specific fragments extracted= 12 number of extra gaps= 0 total=315 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1l7mA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0330 read from 1l7mA/merged-good-all-a2m # 1l7mA read from 1l7mA/merged-good-all-a2m # found chain 1l7mA in training set T0330 2 :SRTLVLFDIDGTLLKVES 1l7mA 4 :KKKLILFDFDSTLVNNET T0330 25 :LADAL 1l7mA 22 :IDEIA T0330 31 :EVYGT 1l7mA 27 :REAGV T0330 46 :GKMDGAIIYEVLSNV 1l7mA 46 :KLNFEQSLRKRVSLL T0330 61 :GLERAEI 1l7mA 62 :DLPIEKV T0330 72 :DKA 1l7mA 69 :EKA T0330 86 :A 1l7mA 72 :I T0330 89 :EDITLLEGVRELLDALSSRS 1l7mA 73 :KRITPTEGAEETIKELKNRG T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFA 1l7mA 93 :YVVAVVSGGFDIAVNKIKEKLGLDYAFANRLIV T0330 143 :DDALDRNELPHIALERARRM 1l7mA 136 :GEVLKENAKGEILEKIAKIE T0330 166 :NYSPSQIVIIGDTEHDIRCARELD 1l7mA 156 :GINLEDTVAVGDGANDISMFKKAG T0330 191 :RSIAVAT 1l7mA 180 :LKIAFCA T0330 202 :MEELARH 1l7mA 187 :KPILKEK T0330 210 :PGTLFK 1l7mA 194 :ADICIE T0330 216 :NFAETD 1l7mA 202 :DLREIL Number of specific fragments extracted= 15 number of extra gaps= 0 total=330 Number of alignments=28 # 1l7mA read from 1l7mA/merged-good-all-a2m # found chain 1l7mA in training set T0330 2 :SRTLVLFDIDGTLLKVES 1l7mA 4 :KKKLILFDFDSTLVNNET T0330 25 :LADALIEVY 1l7mA 22 :IDEIAREAG T0330 49 :DGAIIYEVLSNVGLERAEIADKFDKAKETY 1l7mA 31 :VEEEVKKITKEAMEGKLNFEQSLRKRVSLL T0330 79 :IALFRE 1l7mA 65 :IEKVEK T0330 87 :RREDITLLEGVRELLDALSSRS 1l7mA 71 :AIKRITPTEGAEETIKELKNRG T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHYF 1l7mA 93 :YVVAVVSGGFDIAVNKIKEKLGLDYAF T0330 137 :PFGAFADDAL 1l7mA 131 :TGDVEGEVLK T0330 147 :DRN 1l7mA 142 :NAK T0330 152 :PHIALERARRM 1l7mA 145 :GEILEKIAKIE T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIA 1l7mA 156 :GINLEDTVAVGDGANDISMFKKAGLKIAF T0330 200 :FTMEELARH 1l7mA 185 :CAKPILKEK T0330 210 :PGTLF 1l7mA 194 :ADICI T0330 215 :KNFAETD 1l7mA 201 :RDLREIL Number of specific fragments extracted= 13 number of extra gaps= 0 total=343 Number of alignments=29 # 1l7mA read from 1l7mA/merged-good-all-a2m # found chain 1l7mA in training set T0330 2 :SRTLVLFDIDGTLLKVES 1l7mA 4 :KKKLILFDFDSTLVNNET T0330 25 :LADALIEVYGTEGSTGSHDFS 1l7mA 22 :IDEIAREAGVEEEVKKITKEA T0330 46 :GKMDGAIIYEVLSNVGL 1l7mA 45 :GKLNFEQSLRKRVSLLK T0330 66 :EIA 1l7mA 62 :DLP T0330 72 :DKAKETYIA 1l7mA 65 :IEKVEKAIK T0330 90 :DITLLEGVRELLDALSS 1l7mA 74 :RITPTEGAEETIKELKN T0330 108 :SDVLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADD 1l7mA 91 :RGYVVAVVSGGFDIAVNKIKEKLGLDYAFANRLIVKD T0330 145 :ALDRNELPHIALERARR 1l7mA 138 :VLKENAKGEILEKIAKI T0330 165 :ANYSPSQIVIIGDTEHDIRCARELDARSIA 1l7mA 155 :EGINLEDTVAVGDGANDISMFKKAGLKIAF T0330 200 :FTMEELAR 1l7mA 185 :CAKPILKE T0330 209 :KPGTLFKN 1l7mA 193 :KADICIEK Number of specific fragments extracted= 11 number of extra gaps= 0 total=354 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cqzA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1cqzA expands to /projects/compbio/data/pdb/1cqz.pdb.gz 1cqzA:# T0330 read from 1cqzA/merged-good-all-a2m # 1cqzA read from 1cqzA/merged-good-all-a2m # adding 1cqzA to template set # found chain 1cqzA in template set Warning: unaligning (T0330)T4 because first residue in template chain is (1cqzA)R4 Warning: unaligning (T0330)E18 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cqzA)G48 Warning: unaligning (T0330)E36 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cqzA)G48 Warning: unaligning (T0330)D49 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cqzA)Q90 T0330 5 :LVLFDIDGTLLK 1cqzA 5 :VAAFDLDGVLAL T0330 37 :GSTGS 1cqzA 49 :PTEQL T0330 42 :HDFSGKM 1cqzA 56 :GKITFSQ T0330 84 :ERA 1cqzA 94 :QAM T0330 89 :EDITLLEGVRELLDALSSRS 1cqzA 97 :AARSINRPMLQAAIALKKKG T0330 110 :VLLGLLTG 1cqzA 117 :FTTCIVTN T0330 118 :NFEASGRHKLKL 1cqzA 131 :DKRDSLAQMMCE T0330 132 :IDHYFPFGAFADDALDRNELPHIALERARRM 1cqzA 143 :LSQHFDFLIESCQVGMIKPEPQIYNFLLDTL T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAVA 1cqzA 174 :KAKPNEVVFLDDFGSNLKPARDMGMVTILVH T0330 215 :KNFAETDEVLASILTPKHS 1cqzA 205 :NTASALRELEKVTGTQFPE Number of specific fragments extracted= 10 number of extra gaps= 0 total=364 Number of alignments=31 # 1cqzA read from 1cqzA/merged-good-all-a2m # found chain 1cqzA in template set Warning: unaligning (T0330)T4 because first residue in template chain is (1cqzA)R4 Warning: unaligning (T0330)S19 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cqzA)G48 Warning: unaligning (T0330)E36 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cqzA)G48 Warning: unaligning (T0330)I52 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1cqzA)Q90 T0330 5 :LVLFDIDGTLLKVE 1cqzA 5 :VAAFDLDGVLALPS T0330 37 :GSTGSHDFSGK 1cqzA 49 :PTEQLMKGKIT T0330 49 :DGA 1cqzA 60 :FSQ T0330 87 :RREDITLLEGVRELLDALSSRS 1cqzA 95 :AMAARSINRPMLQAAIALKKKG T0330 110 :VLLGLLTGNF 1cqzA 117 :FTTCIVTNNW T0330 120 :EASGRHKLKL 1cqzA 133 :RDSLAQMMCE T0330 132 :IDHYFPFGAFADDALDRNELPHIALERARRM 1cqzA 143 :LSQHFDFLIESCQVGMIKPEPQIYNFLLDTL T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAVA 1cqzA 174 :KAKPNEVVFLDDFGSNLKPARDMGMVTILVH T0330 215 :KNFAETDEVLASILTPKH 1cqzA 205 :NTASALRELEKVTGTQFP Number of specific fragments extracted= 9 number of extra gaps= 0 total=373 Number of alignments=32 # 1cqzA read from 1cqzA/merged-good-all-a2m # found chain 1cqzA in template set Warning: unaligning (T0330)T4 because first residue in template chain is (1cqzA)R4 Warning: unaligning (T0330)A65 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1cqzA)Q90 T0330 5 :LVLFDIDGTLL 1cqzA 5 :VAAFDLDGVLA T0330 66 :EIADKFD 1cqzA 91 :IFSQAMA T0330 90 :DITLLEGVRELLDALSS 1cqzA 98 :ARSINRPMLQAAIALKK T0330 108 :SDVLLGLLTGNF 1cqzA 115 :KGFTTCIVTNNW T0330 120 :EASGRHKLKL 1cqzA 133 :RDSLAQMMCE T0330 132 :IDHYFPFGAFADDALDRNELPHIALERARR 1cqzA 143 :LSQHFDFLIESCQVGMIKPEPQIYNFLLDT T0330 165 :ANYSPSQIVIIGDTEHDIRCARELDARSI 1cqzA 173 :LKAKPNEVVFLDDFGSNLKPARDMGMVTI T0330 212 :TLFKNFAETDEVLASILTPKH 1cqzA 202 :LVHNTASALRELEKVTGTQFP Number of specific fragments extracted= 8 number of extra gaps= 0 total=381 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wviA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1wviA expands to /projects/compbio/data/pdb/1wvi.pdb.gz 1wviA:# T0330 read from 1wviA/merged-good-all-a2m # 1wviA read from 1wviA/merged-good-all-a2m # adding 1wviA to template set # found chain 1wviA in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1wviA)T1002 T0330 3 :RTLVLFDIDGTLLK 1wviA 1003 :YKGYLIDLDGTIYK T0330 17 :VESMNRRVLADAL 1wviA 1020 :RIPAGEDFVKRLQ T0330 31 :EV 1wviA 1033 :ER T0330 34 :GT 1wviA 1035 :QL T0330 46 :GKMDGAIIYE 1wviA 1045 :TTRTPEMVQE T0330 56 :VLSNVGLERAE 1wviA 1056 :LATSFNIKTPL T0330 72 :D 1wviA 1067 :E T0330 74 :AKET 1wviA 1072 :ATLA T0330 97 :VRELLDA 1wviA 1076 :TIDYMND T0330 105 :SSRS 1wviA 1083 :MKRG T0330 110 :VLLGLLTG 1wviA 1087 :KTAYVIGE T0330 121 :ASGRHKLKLPGID 1wviA 1095 :TGLKKAVAEAGYR T0330 134 :HYFPFGAFADDAL 1wviA 1111 :ENPAYVVVGLDTN T0330 147 :DRNELPHIALERARRM 1wviA 1179 :IGKPEAVIMNKALDRL T0330 166 :NYSPSQIVIIGDTE 1wviA 1195 :GVKRHEAIMVGDNY T0330 180 :HDIRCARELDARSIAVATGNFTMEELARHK 1wviA 1210 :TDITAGIKNDIATLLVTTGFTKPEEVPALP T0330 210 :PGTLFKNFAE 1wviA 1242 :PDFVLSSLAE Number of specific fragments extracted= 17 number of extra gaps= 0 total=398 Number of alignments=34 # 1wviA read from 1wviA/merged-good-all-a2m # found chain 1wviA in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1wviA)T1002 T0330 3 :RTLVLFDIDGTLLKVESMNRRV 1wviA 1003 :YKGYLIDLDGTIYKGKDRIPAG T0330 26 :ADALIEVYGTEGSTGSHDFSGKMDGAIIYEVLSNVG 1wviA 1025 :EDFVKRLQERQLPYILVTNNTTRTPEMVQEMLATSF T0330 62 :LERAE 1wviA 1064 :TPLET T0330 74 :AKETYIALFRERARREDITLL 1wviA 1072 :ATLATIDYMNDMKRGKTAYVI T0330 95 :EGVRELL 1wviA 1095 :TGLKKAV T0330 105 :SSRS 1wviA 1102 :AEAG T0330 109 :DVLLGLLTGNF 1wviA 1112 :NPAYVVVGLDT T0330 120 :EASGRHKLKLP 1wviA 1129 :LTLATLAIQKG T0330 136 :FPFGAFADDAL 1wviA 1140 :AVFIGTNPDLN T0330 148 :RNELPHIALERARRM 1wviA 1180 :GKPEAVIMNKALDRL T0330 166 :NYSPSQIVIIGDTE 1wviA 1195 :GVKRHEAIMVGDNY T0330 180 :HDIRCARELDARSIAVATGNFTMEELARHK 1wviA 1210 :TDITAGIKNDIATLLVTTGFTKPEEVPALP T0330 210 :PGTLFKNFAE 1wviA 1242 :PDFVLSSLAE Number of specific fragments extracted= 13 number of extra gaps= 0 total=411 Number of alignments=35 # 1wviA read from 1wviA/merged-good-all-a2m # found chain 1wviA in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1wviA)T1002 T0330 3 :RTLVLFDIDGTLL 1wviA 1003 :YKGYLIDLDGTIY T0330 92 :TLLEGVRELLDALSS 1wviA 1019 :DRIPAGEDFVKRLQE T0330 108 :SDVLLGLLTGNF 1wviA 1034 :RQLPYILVTNNT T0330 120 :EASGRHKLKL 1wviA 1049 :PEMVQEMLAT T0330 130 :PGI 1wviA 1060 :FNI T0330 133 :DHYFP 1wviA 1066 :LETIY T0330 138 :FGAFADD 1wviA 1116 :VVVGLDT T0330 148 :RNELPHIALERARR 1wviA 1180 :GKPEAVIMNKALDR T0330 165 :ANYSPSQIVIIGDTE 1wviA 1194 :LGVKRHEAIMVGDNY T0330 180 :HDIRCARELDARSIAVATGNFTMEELAR 1wviA 1210 :TDITAGIKNDIATLLVTTGFTKPEEVPA T0330 208 :HKPGTLFKNFAE 1wviA 1240 :IQPDFVLSSLAE Number of specific fragments extracted= 11 number of extra gaps= 0 total=422 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zjjA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zjjA expands to /projects/compbio/data/pdb/1zjj.pdb.gz 1zjjA:# T0330 read from 1zjjA/merged-good-all-a2m # 1zjjA read from 1zjjA/merged-good-all-a2m # adding 1zjjA to template set # found chain 1zjjA in template set T0330 4 :TLVLFDIDGTLLK 1zjjA 2 :VAIIFDMDGVLYR T0330 90 :DITLLEGVRELLDALSSRS 1zjjA 15 :GNRAIPGVRELIEFLKERG T0330 110 :VLLGLLTG 1zjjA 34 :IPFAFLTN T0330 118 :NFEASGRHKLKLPGIDHYFPFGAFADDAL 1zjjA 45 :KTPEMYREKLLKMGIDVSSSIIITSGLAT T0330 148 :RNELPHIALERARRMTGA 1zjjA 186 :GKPNEPMYEVVREMFPGE T0330 171 :QIVIIGDTE 1zjjA 204 :ELWMVGDRL T0330 180 :HDIRCARELDARSIAVATGNFTMEELAR 1zjjA 214 :TDIAFAKKFGMKAIMVLTGVSSLEDIKK T0330 208 :HKPGTLFKNFAETD 1zjjA 244 :YKPDLVLPSVYELI Number of specific fragments extracted= 8 number of extra gaps= 0 total=430 Number of alignments=37 # 1zjjA read from 1zjjA/merged-good-all-a2m # found chain 1zjjA in template set T0330 1 :M 1zjjA 1 :M T0330 4 :TLVLFDIDGTLLKVES 1zjjA 2 :VAIIFDMDGVLYRGNR T0330 93 :LLEGVRELLDALSSRS 1zjjA 18 :AIPGVRELIEFLKERG T0330 110 :VLLGLLTGNF 1zjjA 34 :IPFAFLTNNS T0330 120 :EASGRHKLKLPGID 1zjjA 47 :PEMYREKLLKMGID T0330 136 :F 1zjjA 61 :V T0330 137 :PFGAFADDALD 1zjjA 64 :SIIITSGLATR T0330 148 :RNE 1zjjA 186 :GKP T0330 152 :PHIALERARRMTG 1zjjA 189 :NEPMYEVVREMFP T0330 166 :NY 1zjjA 202 :GE T0330 171 :QIVIIGDTE 1zjjA 204 :ELWMVGDRL T0330 180 :HDIRCARELDARSIAVATGNFTMEELARHK 1zjjA 214 :TDIAFAKKFGMKAIMVLTGVSSLEDIKKSE T0330 210 :PGTLFKNFAETD 1zjjA 246 :PDLVLPSVYELI Number of specific fragments extracted= 13 number of extra gaps= 0 total=443 Number of alignments=38 # 1zjjA read from 1zjjA/merged-good-all-a2m # found chain 1zjjA in template set T0330 4 :TLVLFDIDGTLLK 1zjjA 2 :VAIIFDMDGVLYR T0330 90 :DITLLEGVRELLDALSS 1zjjA 15 :GNRAIPGVRELIEFLKE T0330 108 :SDVLLGLLTGNF 1zjjA 32 :RGIPFAFLTNNS T0330 120 :EASGRHKLKLPGID 1zjjA 47 :PEMYREKLLKMGID T0330 134 :HYFP 1zjjA 64 :SIII T0330 138 :FGAFADD 1zjjA 122 :VVVGLDP T0330 149 :NE 1zjjA 187 :KP T0330 152 :PHIALERARRM 1zjjA 189 :NEPMYEVVREM T0330 167 :YSPSQIVIIGDTE 1zjjA 200 :FPGEELWMVGDRL T0330 180 :HDIRCARELDARSIAVATGNFTMEELAR 1zjjA 214 :TDIAFAKKFGMKAIMVLTGVSSLEDIKK T0330 208 :HKPGTLFKNFAET 1zjjA 244 :YKPDLVLPSVYEL Number of specific fragments extracted= 11 number of extra gaps= 0 total=454 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2go7A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2go7A expands to /projects/compbio/data/pdb/2go7.pdb.gz 2go7A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0330 read from 2go7A/merged-good-all-a2m # 2go7A read from 2go7A/merged-good-all-a2m # adding 2go7A to template set # found chain 2go7A in template set Warning: unaligning (T0330)R3 because first residue in template chain is (2go7A)K3 Warning: unaligning (T0330)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2go7A)D9 Warning: unaligning (T0330)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2go7A)D9 Warning: unaligning (T0330)L114 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2go7A)Y106 Warning: unaligning (T0330)L115 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2go7A)Y106 T0330 4 :TLVL 2go7A 4 :TAFI T0330 10 :IDGTLLKVESMNRRVLADAL 2go7A 10 :LDGTLLDSYEAILSGIEETF T0330 31 :EVYGTEGSTGS 2go7A 30 :AQFSIPYDKEK T0330 42 :HDFS 2go7A 42 :REFI T0330 46 :GKMDGAIIYEVLSNVGLER 2go7A 47 :KYSVQDLLVRVAEDRNLDV T0330 72 :DKAKETYIALFRERA 2go7A 66 :EVLNQVRAQSLAEKN T0330 89 :EDITLLEGVRELLDALSSRS 2go7A 81 :AQVVLMPGAREVLAWADESG T0330 110 :VLLG 2go7A 101 :IQQF T0330 116 :TG 2go7A 107 :TH T0330 119 :FEASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARRM 2go7A 109 :KGNNAFTILKDLGVESYFTEILTSQSGFVRKPSPEAATYLLDKY T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAVA 2go7A 153 :QLNSDNTYYIGDRTLDVEFAQNSGIQSINFL T0330 199 :NFTME 2go7A 184 :ESTYE T0330 210 :PGTLFKNFAETDEV 2go7A 189 :GNHRIQALADISRI Number of specific fragments extracted= 13 number of extra gaps= 2 total=467 Number of alignments=40 # 2go7A read from 2go7A/merged-good-all-a2m # found chain 2go7A in template set Warning: unaligning (T0330)R3 because first residue in template chain is (2go7A)K3 Warning: unaligning (T0330)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2go7A)D9 Warning: unaligning (T0330)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2go7A)D9 Warning: unaligning (T0330)L114 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2go7A)Y106 Warning: unaligning (T0330)L115 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2go7A)Y106 T0330 4 :TLVL 2go7A 4 :TAFI T0330 10 :IDGTLLKVESMNRRVLADALIEVYGTEGSTGSHDFSGKMDGAIIYEVL 2go7A 10 :LDGTLLDSYEAILSGIEETFAQFSIPYDKEKVREFIFKYSVQDLLVRV T0330 58 :SNVGLERAE 2go7A 59 :EDRNLDVEV T0330 74 :AKETYIALFRE 2go7A 68 :LNQVRAQSLAE T0330 87 :RREDITLLEGVRELLDALSSRS 2go7A 79 :KNAQVVLMPGAREVLAWADESG T0330 110 :VLLG 2go7A 101 :IQQF T0330 116 :TGNFE 2go7A 107 :THKGN T0330 122 :SGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARRM 2go7A 112 :NAFTILKDLGVESYFTEILTSQSGFVRKPSPEAATYLLDKY T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAVATGNF 2go7A 153 :QLNSDNTYYIGDRTLDVEFAQNSGIQSINFLESTY T0330 209 :KPGTLFKNFAETD 2go7A 188 :EGNHRIQALADIS T0330 226 :SILTP 2go7A 201 :RIFET Number of specific fragments extracted= 11 number of extra gaps= 2 total=478 Number of alignments=41 # 2go7A read from 2go7A/merged-good-all-a2m # found chain 2go7A in template set Warning: unaligning (T0330)R3 because first residue in template chain is (2go7A)K3 Warning: unaligning (T0330)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2go7A)D9 Warning: unaligning (T0330)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2go7A)D9 Warning: unaligning (T0330)L114 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2go7A)Y106 Warning: unaligning (T0330)L115 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2go7A)Y106 T0330 4 :TLVL 2go7A 4 :TAFI T0330 10 :IDGTLLKVESMNRRVLADALIEVYGTEGSTGSHDFSGKMDGAIIYEVLSNVGLER 2go7A 10 :LDGTLLDSYEAILSGIEETFAQFSIPYDKEKVREFIFKYSVQDLLVRVAEDRNLD T0330 68 :ADKFDKAKETYI 2go7A 65 :VEVLNQVRAQSL T0330 85 :RARREDITLLEGVRELLDALSS 2go7A 77 :AEKNAQVVLMPGAREVLAWADE T0330 108 :SDVLLG 2go7A 99 :SGIQQF T0330 116 :TGN 2go7A 107 :THK T0330 120 :EASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARR 2go7A 110 :GNNAFTILKDLGVESYFTEILTSQSGFVRKPSPEAATYLLDK T0330 165 :ANYSPSQIVIIGDTEHDIRCARELDARSIA 2go7A 152 :YQLNSDNTYYIGDRTLDVEFAQNSGIQSIN T0330 197 :TGNFTM 2go7A 182 :FLESTY T0330 209 :KPGTLFKNFAETDEV 2go7A 188 :EGNHRIQALADISRI Number of specific fragments extracted= 10 number of extra gaps= 2 total=488 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nrwA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0330 read from 1nrwA/merged-good-all-a2m # 1nrwA read from 1nrwA/merged-good-all-a2m # found chain 1nrwA in training set Warning: unaligning (T0330)R3 because first residue in template chain is (1nrwA)M1 Warning: unaligning (T0330)L228 because last residue in template chain is (1nrwA)L285 T0330 4 :TLVLFDIDGTLLK 1nrwA 2 :KLIAIDLDGTLLN T0330 17 :VESMNRRVLADAL 1nrwA 19 :VSLENENALRQAQ T0330 31 :EV 1nrwA 32 :RD T0330 34 :GT 1nrwA 34 :GI T0330 38 :STGSHDFSGK 1nrwA 71 :DPEGRLYHHE T0330 48 :MDGAIIYE 1nrwA 86 :RAYDILSW T0330 56 :VLSNV 1nrwA 125 :RFRSA T0330 61 :GLERAEIADKFDKAKET 1nrwA 132 :EADLSVLKQAAEVQYSQ T0330 89 :EDITLLE 1nrwA 149 :SGFAYIN T0330 104 :LSSRSD 1nrwA 160 :LFEADE T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADDA 1nrwA 169 :FYNILGFSFFKEKLEAGWKRYEHAEDLTLVSSAEHN T0330 147 :DRNELPHIALERARRM 1nrwA 210 :RKASKGQALKRLAKQL T0330 166 :NYSPSQIVIIGDTEHDIRCARELD 1nrwA 226 :NIPLEETAAVGDSLNDKSMLEAAG T0330 191 :RSIAV 1nrwA 250 :KGVAM T0330 199 :NFTMEELARH 1nrwA 255 :GNAREDIKSI T0330 210 :PGTLFKNFAE 1nrwA 265 :ADAVTLTNDE T0330 220 :TDEVLASI 1nrwA 277 :VAHMMKHL Number of specific fragments extracted= 17 number of extra gaps= 0 total=505 Number of alignments=43 # 1nrwA read from 1nrwA/merged-good-all-a2m # found chain 1nrwA in training set Warning: unaligning (T0330)R3 because first residue in template chain is (1nrwA)M1 T0330 4 :TLVLFDIDGTLLKVE 1nrwA 2 :KLIAIDLDGTLLNSK T0330 91 :ITLLEGVRELLDALSSRS 1nrwA 17 :HQVSLENENALRQAQRDG T0330 110 :VLLGLLTGNFEASGRHKLKLPGID 1nrwA 35 :IEVVVSTGRAHFDVMSIFEPLGIK T0330 137 :PFGAFA 1nrwA 59 :TWVISA T0330 144 :DAL 1nrwA 65 :NGA T0330 148 :RN 1nrwA 213 :SK T0330 152 :PHIALERARRM 1nrwA 215 :GQALKRLAKQL T0330 166 :NYSPSQIVIIGDTEHDIRCARELD 1nrwA 226 :NIPLEETAAVGDSLNDKSMLEAAG T0330 191 :RSIAV 1nrwA 250 :KGVAM T0330 199 :NFTMEELARH 1nrwA 255 :GNAREDIKSI T0330 210 :PGTLFKNFAE 1nrwA 265 :ADAVTLTNDE T0330 220 :TDEVLASI 1nrwA 277 :VAHMMKHL Number of specific fragments extracted= 12 number of extra gaps= 0 total=517 Number of alignments=44 # 1nrwA read from 1nrwA/merged-good-all-a2m # found chain 1nrwA in training set Warning: unaligning (T0330)R3 because first residue in template chain is (1nrwA)M1 T0330 4 :TLVLFDIDGTLLKV 1nrwA 2 :KLIAIDLDGTLLNS T0330 90 :DITLLEGVRELLDALSS 1nrwA 16 :KHQVSLENENALRQAQR T0330 108 :SDVLLGLLTGNFEASGRHKLKLPGIDHYF 1nrwA 33 :DGIEVVVSTGRAHFDVMSIFEPLGIKTWV T0330 138 :FGAFADD 1nrwA 196 :TLVSSAE T0330 147 :DRNELPHIALERARR 1nrwA 210 :RKASKGQALKRLAKQ T0330 165 :ANYSPSQIVIIGDTEHDIRCARELD 1nrwA 225 :LNIPLEETAAVGDSLNDKSMLEAAG T0330 191 :R 1nrwA 250 :K T0330 194 :AVATGNFT 1nrwA 251 :GVAMGNAR T0330 203 :EELARH 1nrwA 259 :EDIKSI T0330 210 :PGTLFKNFAE 1nrwA 265 :ADAVTLTNDE Number of specific fragments extracted= 10 number of extra gaps= 0 total=527 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rdfA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1rdfA expands to /projects/compbio/data/pdb/1rdf.pdb.gz 1rdfA:# T0330 read from 1rdfA/merged-good-all-a2m # 1rdfA read from 1rdfA/merged-good-all-a2m # adding 1rdfA to template set # found chain 1rdfA in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1rdfA)K5 Warning: unaligning (T0330)S168 because of BadResidue code BAD_PEPTIDE at template residue (1rdfA)P177 T0330 3 :RTLVLFDIDGTLLK 1rdfA 6 :IEAVIFDWAGTTVD T0330 19 :SMNRRVLADAL 1rdfA 23 :FAPLEVFMEIF T0330 31 :EVYGTEGSTGS 1rdfA 34 :HKRGVAITAEE T0330 42 :HDFSGK 1rdfA 46 :RKPMPL T0330 48 :MDGAIIYEVLSNVG 1rdfA 62 :EMPRIASEWNRVFR T0330 62 :LERAEI 1rdfA 78 :PTEADI T0330 72 :DKAKETYIALFRERAR 1rdfA 84 :QEMYEEFEEILFAILP T0330 89 :EDITLLEGVRELLDALSSRS 1rdfA 100 :RYASPINAVKEVIASLRERG T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHY 1rdfA 120 :IKIGSTTGYTREMMDIVAKEAALQGY T0330 136 :FPFGAFADDALDRNELPHIALERARRM 1rdfA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMEL T0330 166 :NY 1rdfA 174 :GV T0330 169 :PSQIVIIGDTEHDIRCARELDARSIAVAT 1rdfA 178 :MNHMIKVGDTVSDMKEGRNAGMWTVGVIL T0330 199 :NFTMEE 1rdfA 212 :GLTEEE T0330 205 :LARHKPGTLFKNFAETDEVLASILT 1rdfA 237 :FVENGAHFTIETMQELESVMEHIEK Number of specific fragments extracted= 14 number of extra gaps= 1 total=541 Number of alignments=46 # 1rdfA read from 1rdfA/merged-good-all-a2m # found chain 1rdfA in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1rdfA)K5 Warning: unaligning (T0330)S168 because of BadResidue code BAD_PEPTIDE at template residue (1rdfA)P177 T0330 3 :RTLVLFDIDGTLLKVE 1rdfA 6 :IEAVIFDWAGTTVDYG T0330 19 :SMNRRVLADALIEVYGTEG 1rdfA 23 :FAPLEVFMEIFHKRGVAIT T0330 38 :STGSHDFSGKMDGAIIYEVLSNVG 1rdfA 51 :LLKIDHVRALTEMPRIASEWNRVF T0330 62 :LER 1rdfA 78 :PTE T0330 69 :DKFDKAKETYIALFRER 1rdfA 81 :ADIQEMYEEFEEILFAI T0330 87 :RREDITLLEGVRELLDALSSRS 1rdfA 98 :LPRYASPINAVKEVIASLRERG T0330 110 :VLLGLLTGNFEASGRHKLKLP 1rdfA 120 :IKIGSTTGYTREMMDIVAKEA T0330 131 :GID 1rdfA 144 :GYK T0330 136 :FPFGAFADDALDRNELPHIALERARRM 1rdfA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMEL T0330 166 :NY 1rdfA 174 :GV T0330 169 :PSQIVIIGDTEHDIRCARELDARSIAVATG 1rdfA 178 :MNHMIKVGDTVSDMKEGRNAGMWTVGVILG T0330 199 :NFTMEELARHK 1rdfA 220 :NMDSVELREKI T0330 210 :PGTLFKNFAET 1rdfA 242 :AHFTIETMQEL T0330 221 :DEVLASILTP 1rdfA 256 :MEHIEKQELI Number of specific fragments extracted= 14 number of extra gaps= 1 total=555 Number of alignments=47 # 1rdfA read from 1rdfA/merged-good-all-a2m # found chain 1rdfA in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1rdfA)K5 Warning: unaligning (T0330)S168 because of BadResidue code BAD_PEPTIDE at template residue (1rdfA)P177 T0330 3 :RTLVLFDIDGTLLK 1rdfA 6 :IEAVIFDWAGTTVD T0330 20 :MNRRVLADALIEVYGTEGSTGSHDFS 1rdfA 24 :APLEVFMEIFHKRGVAITAEEARKPM T0330 46 :GKMDGAIIYEVLSNVG 1rdfA 59 :ALTEMPRIASEWNRVF T0330 64 :RAEIADKFDKAKETYIALFRERARREDITLLEGVRELLDALSS 1rdfA 75 :RQLPTEADIQEMYEEFEEILFAILPRYASPINAVKEVIASLRE T0330 108 :SDVLLGLLTGNFEASGRHKLKLPGIDHYF 1rdfA 118 :RGIKIGSTTGYTREMMDIVAKEAALQGYK T0330 137 :PFGAFADDALDRNELPHIALERARR 1rdfA 148 :DFLVTPDDVPAGRPYPWMCYKNAME T0330 165 :ANY 1rdfA 173 :LGV T0330 169 :PSQIVIIGDTEHDIRCARELDARSIAVATGNF 1rdfA 178 :MNHMIKVGDTVSDMKEGRNAGMWTVGVILGSS T0330 201 :TMEE 1rdfA 214 :TEEE T0330 205 :LARHKPGTLFKNFAETDEVLASILTPKH 1rdfA 237 :FVENGAHFTIETMQELESVMEHIEKQEL Number of specific fragments extracted= 10 number of extra gaps= 1 total=565 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fdrA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fdrA expands to /projects/compbio/data/pdb/2fdr.pdb.gz 2fdrA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 600, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 602, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 604, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 606, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 608, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 610, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 612, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 614, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 616, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 618, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 620, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 709, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 711, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 713, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 715, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 717, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 719, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 721, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 723, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 725, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 751, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 753, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 755, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 757, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 759, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 761, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 763, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 765, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 767, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 769, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 771, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 773, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 775, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 777, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 779, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 781, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 783, because occupancy 0.500 <= existing 0.500 in 2fdrA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1330, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 1332, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 1334, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 1336, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 1338, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 1340, because occupancy 0.500 <= existing 0.500 in 2fdrA Skipped atom 1342, because occupancy 0.500 <= existing 0.500 in 2fdrA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0330 read from 2fdrA/merged-good-all-a2m # 2fdrA read from 2fdrA/merged-good-all-a2m # adding 2fdrA to template set # found chain 2fdrA in template set Warning: unaligning (T0330)S2 because first residue in template chain is (2fdrA)G3 Warning: unaligning (T0330)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fdrA)D10 Warning: unaligning (T0330)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fdrA)D10 Warning: unaligning (T0330)T229 because last residue in template chain is (2fdrA)E224 T0330 3 :RTLVL 2fdrA 4 :FDLII T0330 10 :IDGTLLKVESMNRRVLADAL 2fdrA 11 :CDGVLVDSEIIAAQVESRLL T0330 31 :EVYGTEGSTGS 2fdrA 31 :TEAGYPISVEE T0330 42 :HDFSGKMDGAIIYEVLSNVGLERA 2fdrA 44 :ERFAGMTWKNILLQVESEASIPLS T0330 72 :DKAKETYIALFRERAR 2fdrA 68 :ASLLDKSEKLLDMRLE T0330 89 :EDITLLEGVRELLDAL 2fdrA 84 :RDVKIIDGVKFALSRL T0330 109 :DVLLGLLTGNFEASGRHKLKLPGIDHYF 2fdrA 100 :TTPRCICSNSSSHRLDMMLTKVGLKPYF T0330 137 :PFGAFADDALD 2fdrA 129 :PHIYSAKDLGA T0330 148 :RNELPHIALERARRM 2fdrA 142 :VKPKPDIFLHGAAQF T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAVATGNFT 2fdrA 157 :GVSPDRVVVVEDSVHGIHGARAAGMRVIGFTGASHT T0330 202 :MEELARHKPGTLFKNFAETDEVLASIL 2fdrA 197 :ADRLTDAGAETVISRMQDLPAVIAAMA Number of specific fragments extracted= 11 number of extra gaps= 1 total=576 Number of alignments=49 # 2fdrA read from 2fdrA/merged-good-all-a2m # found chain 2fdrA in template set Warning: unaligning (T0330)S2 because first residue in template chain is (2fdrA)G3 Warning: unaligning (T0330)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fdrA)D10 Warning: unaligning (T0330)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fdrA)D10 Warning: unaligning (T0330)T229 because last residue in template chain is (2fdrA)E224 T0330 3 :RTLVL 2fdrA 4 :FDLII T0330 10 :IDGTLLKVESMNRRVLADALIEVYGTEGSTGSHDFSGKMDGAIIYEVLSNVG 2fdrA 11 :CDGVLVDSEIIAAQVESRLLTEAGYPISVEEMGERFAGMTWKNILLQVESEA T0330 62 :LERAE 2fdrA 64 :IPLSA T0330 69 :DKFDKAKETYIALFRE 2fdrA 69 :SLLDKSEKLLDMRLER T0330 90 :DITLLEGVRELLDAL 2fdrA 85 :DVKIIDGVKFALSRL T0330 108 :S 2fdrA 100 :T T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHYF 2fdrA 101 :TPRCICSNSSSHRLDMMLTKVGLKPYF T0330 137 :PFGAFADDALDR 2fdrA 129 :PHIYSAKDLGAD T0330 149 :NELPHIALERARRM 2fdrA 143 :KPKPDIFLHGAAQF T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAVATGNFT 2fdrA 157 :GVSPDRVVVVEDSVHGIHGARAAGMRVIGFTGASHT T0330 202 :MEELARHKPGTLFKNFAETDEVLASIL 2fdrA 197 :ADRLTDAGAETVISRMQDLPAVIAAMA Number of specific fragments extracted= 11 number of extra gaps= 1 total=587 Number of alignments=50 # 2fdrA read from 2fdrA/merged-good-all-a2m # found chain 2fdrA in template set Warning: unaligning (T0330)S2 because first residue in template chain is (2fdrA)G3 Warning: unaligning (T0330)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2fdrA)D10 Warning: unaligning (T0330)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2fdrA)D10 Warning: unaligning (T0330)T229 because last residue in template chain is (2fdrA)E224 T0330 3 :RTLVL 2fdrA 4 :FDLII T0330 10 :IDGTLLKVESMNRRVLADALIEVYGTEGSTGSHDFSGKMDGAIIYEVLSNVG 2fdrA 11 :CDGVLVDSEIIAAQVESRLLTEAGYPISVEEMGERFAGMTWKNILLQVESEA T0330 64 :RAEIADKFDKAKETYIALFRER 2fdrA 63 :SIPLSASLLDKSEKLLDMRLER T0330 90 :DITLLEGVRELLDAL 2fdrA 85 :DVKIIDGVKFALSRL T0330 109 :DVLLGLLTGNFEASGRHKLKLPGIDHYF 2fdrA 100 :TTPRCICSNSSSHRLDMMLTKVGLKPYF T0330 137 :PFGAFADD 2fdrA 129 :PHIYSAKD T0330 145 :ALDRNELPHIALERARR 2fdrA 139 :ADRVKPKPDIFLHGAAQ T0330 165 :ANYSPSQIVIIGDTEHDIRCARELDARSIAVATGNFT 2fdrA 156 :FGVSPDRVVVVEDSVHGIHGARAAGMRVIGFTGASHT T0330 202 :MEELARHKPGTLFKNFAETDEVLASIL 2fdrA 197 :ADRLTDAGAETVISRMQDLPAVIAAMA Number of specific fragments extracted= 9 number of extra gaps= 1 total=596 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lvhA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1lvhA expands to /projects/compbio/data/pdb/1lvh.pdb.gz 1lvhA:Bad short name: P for alphabet: pdb_atoms Bad short name: OP1 for alphabet: pdb_atoms Bad short name: OP2 for alphabet: pdb_atoms Bad short name: OP3 for alphabet: pdb_atoms # T0330 read from 1lvhA/merged-good-all-a2m # 1lvhA read from 1lvhA/merged-good-all-a2m # adding 1lvhA to template set # found chain 1lvhA in template set Warning: unaligning (T0330)F8 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1lvhA)L9 Warning: unaligning (T0330)I10 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1lvhA)L9 T0330 1 :M 1lvhA 1 :M T0330 3 :RTLVL 1lvhA 2 :FKAVL T0330 11 :DGTLLKVESMNRRVLADAL 1lvhA 10 :DGVITDTAEYHFRAWKALA T0330 31 :EVYGTE 1lvhA 29 :EEIGIN T0330 37 :GSTGS 1lvhA 36 :VDRQF T0330 42 :HDFSGKMDGAIIYEVLSNVG 1lvhA 42 :EQLKGVSREDSLQKILDLAD T0330 62 :LERAEI 1lvhA 64 :VSAEEF T0330 72 :DKAKETYIALFRERA 1lvhA 70 :KELAKRKNDNYVKMI T0330 89 :EDIT 1lvhA 85 :QDVS T0330 93 :LLEGVRELLDALSSRS 1lvhA 92 :VYPGILQLLKDLRSNK T0330 110 :VLLGLLTGN 1lvhA 108 :IKIALASAS T0330 121 :ASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARRM 1lvhA 117 :KNGPFLLERMNLTGYFDAIADPAEVAASKPAPDIFIAAAHAV T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAV 1lvhA 159 :GVAPSESIGLEDSQAGIQAIKDSGALPIGV T0330 200 :FTMEELAR 1lvhA 189 :GRPEDLGD T0330 210 :PGTLFKNFAET 1lvhA 197 :DIVIVPDTSHY T0330 221 :DEVLASILT 1lvhA 209 :LEFLKEVWL Number of specific fragments extracted= 16 number of extra gaps= 0 total=612 Number of alignments=52 # 1lvhA read from 1lvhA/merged-good-all-a2m # found chain 1lvhA in template set Warning: unaligning (T0330)F8 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1lvhA)L9 Warning: unaligning (T0330)I10 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1lvhA)L9 T0330 1 :M 1lvhA 1 :M T0330 3 :RTLVL 1lvhA 2 :FKAVL T0330 11 :DGTLLKVESMNRRVLADALIEVYGTEGSTGSHDFSGKMDGAIIYEVLSNVG 1lvhA 10 :DGVITDTAEYHFRAWKALAEEIGINGVDRQFNEQLKGVSREDSLQKILDLA T0330 62 :LERAE 1lvhA 62 :KKVSA T0330 69 :DKFDKAKETYIALFRERA 1lvhA 67 :EEFKELAKRKNDNYVKMI T0330 87 :RREDITLLEGVRELLDALSSRS 1lvhA 86 :DVSPADVYPGILQLLKDLRSNK T0330 110 :VLLGLLTGN 1lvhA 108 :IKIALASAS T0330 121 :ASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARRM 1lvhA 117 :KNGPFLLERMNLTGYFDAIADPAEVAASKPAPDIFIAAAHAV T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAV 1lvhA 159 :GVAPSESIGLEDSQAGIQAIKDSGALPIGV T0330 200 :FTMEELAR 1lvhA 189 :GRPEDLGD T0330 210 :PGTLFKNFAET 1lvhA 197 :DIVIVPDTSHY T0330 221 :DEVLASILTP 1lvhA 209 :LEFLKEVWLQ Number of specific fragments extracted= 12 number of extra gaps= 0 total=624 Number of alignments=53 # 1lvhA read from 1lvhA/merged-good-all-a2m # found chain 1lvhA in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1lvhA)M1 Warning: unaligning (T0330)F8 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1lvhA)L9 Warning: unaligning (T0330)I10 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1lvhA)L9 T0330 3 :RTLVL 1lvhA 2 :FKAVL T0330 11 :DGTLLKVESMNRRVLADALIEVYGTEGSTGSHDFSGKMDGAIIYEVLSNVG 1lvhA 10 :DGVITDTAEYHFRAWKALAEEIGINGVDRQFNEQLKGVSREDSLQKILDLA T0330 64 :RAEIADKFDKAKETYIALFRERARREDIT 1lvhA 61 :DKKVSAEEFKELAKRKNDNYVKMIQDVSP T0330 93 :LLEGVRELLDALSS 1lvhA 92 :VYPGILQLLKDLRS T0330 108 :SDVLLGLLTGN 1lvhA 106 :NKIKIALASAS T0330 121 :ASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARR 1lvhA 117 :KNGPFLLERMNLTGYFDAIADPAEVAASKPAPDIFIAAAHA T0330 165 :ANYSPSQIVIIGDTEHDIRCARELDARSIAV 1lvhA 158 :VGVAPSESIGLEDSQAGIQAIKDSGALPIGV T0330 200 :FTMEELA 1lvhA 189 :GRPEDLG T0330 209 :KPGTLFKNFAE 1lvhA 196 :DDIVIVPDTSH T0330 221 :DEVLASILTPKH 1lvhA 209 :LEFLKEVWLQKQ Number of specific fragments extracted= 10 number of extra gaps= 0 total=634 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1f5sA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1f5sA expands to /projects/compbio/data/pdb/1f5s.pdb.gz 1f5sA:Skipped atom 82, because occupancy 0.500 <= existing 0.500 in 1f5sA Skipped atom 84, because occupancy 0.500 <= existing 0.500 in 1f5sA Skipped atom 86, because occupancy 0.500 <= existing 0.500 in 1f5sA Skipped atom 88, because occupancy 0.500 <= existing 0.500 in 1f5sA Skipped atom 90, because occupancy 0.500 <= existing 0.500 in 1f5sA Skipped atom 92, because occupancy 0.500 <= existing 0.500 in 1f5sA Skipped atom 94, because occupancy 0.500 <= existing 0.500 in 1f5sA Skipped atom 96, because occupancy 0.500 <= existing 0.500 in 1f5sA # T0330 read from 1f5sA/merged-good-all-a2m # 1f5sA read from 1f5sA/merged-good-all-a2m # adding 1f5sA to template set # found chain 1f5sA in template set T0330 2 :SRTLVLFDIDGTLLKVES 1f5sA 4 :KKKLILFDFDSTLVNNET T0330 25 :LADAL 1f5sA 22 :IDEIA T0330 31 :EVYGT 1f5sA 27 :REAGV T0330 46 :GKMDGAIIYEVLSNV 1f5sA 46 :KLNFEQSLRKRVSLL T0330 61 :GLERAEI 1f5sA 62 :DLPIEKV T0330 72 :DKAK 1f5sA 69 :EKAI T0330 89 :EDITLLEGVRELLDALSSRS 1f5sA 73 :KRITPTEGAEETIKELKNRG T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFA 1f5sA 93 :YVVAVVSGGFDIAVNKIKEKLGLDYAFANRLIV T0330 143 :DDALDRNELPHIALERARRM 1f5sA 136 :GEVLKENAKGEILEKIAKIE T0330 166 :NYSPSQIVIIGDTEHDIRCARELD 1f5sA 156 :GINLEDTVAVGDGANDISMFKKAG T0330 191 :RSIAVAT 1f5sA 180 :LKIAFCA T0330 202 :MEELARH 1f5sA 187 :KPILKEK T0330 210 :PGTLFK 1f5sA 194 :ADICIE T0330 216 :NFAETD 1f5sA 202 :DLREIL Number of specific fragments extracted= 14 number of extra gaps= 0 total=648 Number of alignments=55 # 1f5sA read from 1f5sA/merged-good-all-a2m # found chain 1f5sA in template set T0330 2 :SRTLVLFDIDGTLLKVES 1f5sA 4 :KKKLILFDFDSTLVNNET T0330 25 :LADALIEVY 1f5sA 22 :IDEIAREAG T0330 49 :DGAIIYEVLSNVGLERAEIADKFDKAKETY 1f5sA 31 :VEEEVKKITKEAMEGKLNFEQSLRKRVSLL T0330 79 :IALFRE 1f5sA 65 :IEKVEK T0330 87 :RREDITLLEGVRELLDALSSRS 1f5sA 71 :AIKRITPTEGAEETIKELKNRG T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHYF 1f5sA 93 :YVVAVVSGGFDIAVNKIKEKLGLDYAF T0330 137 :PFGAFADDAL 1f5sA 131 :TGDVEGEVLK T0330 147 :DRN 1f5sA 142 :NAK T0330 152 :PHIALERARRM 1f5sA 145 :GEILEKIAKIE T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIA 1f5sA 156 :GINLEDTVAVGDGANDISMFKKAGLKIAF T0330 200 :FTMEELARH 1f5sA 185 :CAKPILKEK T0330 210 :PGTLF 1f5sA 194 :ADICI T0330 215 :KNFAETD 1f5sA 201 :RDLREIL Number of specific fragments extracted= 13 number of extra gaps= 0 total=661 Number of alignments=56 # 1f5sA read from 1f5sA/merged-good-all-a2m # found chain 1f5sA in template set T0330 2 :SRTLVLFDIDGTLLKVESM 1f5sA 4 :KKKLILFDFDSTLVNNETI T0330 26 :ADALIEVYGTEGSTGSHDFS 1f5sA 23 :DEIAREAGVEEEVKKITKEA T0330 46 :GKMDGAIIYEVLSNVG 1f5sA 45 :GKLNFEQSLRKRVSLL T0330 65 :AEIA 1f5sA 61 :KDLP T0330 72 :DKAKETYIA 1f5sA 65 :IEKVEKAIK T0330 90 :DITLLEGVRELLDALSS 1f5sA 74 :RITPTEGAEETIKELKN T0330 108 :SDVLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADD 1f5sA 91 :RGYVVAVVSGGFDIAVNKIKEKLGLDYAFANRLIVKD T0330 145 :ALDRNELPHIALERARR 1f5sA 138 :VLKENAKGEILEKIAKI T0330 165 :ANYSPSQIVIIGDTEHDIRCARELDARSIA 1f5sA 155 :EGINLEDTVAVGDGANDISMFKKAGLKIAF T0330 200 :FTMEELAR 1f5sA 185 :CAKPILKE T0330 209 :KPGTLFKN 1f5sA 193 :KADICIEK Number of specific fragments extracted= 11 number of extra gaps= 0 total=672 Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b8eA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2b8eA expands to /projects/compbio/data/pdb/2b8e.pdb.gz 2b8eA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0330 read from 2b8eA/merged-good-all-a2m # 2b8eA read from 2b8eA/merged-good-all-a2m # adding 2b8eA to template set # found chain 2b8eA in template set Warning: unaligning (T0330)E179 because of BadResidue code BAD_PEPTIDE in next template residue (2b8eA)N621 Warning: unaligning (T0330)H180 because of BadResidue code BAD_PEPTIDE at template residue (2b8eA)N621 Warning: unaligning (T0330)D181 because of BadResidue code BAD_PEPTIDE at template residue (2b8eA)D622 Warning: unaligning (T0330)A196 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b8eA)S645 Warning: unaligning (T0330)T197 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b8eA)S645 T0330 4 :TLVLFDIDGTLLK 2b8eA 419 :TAVIFDKTGTLTK T0330 17 :VESMNRRVLADAL 2b8eA 460 :SEHPIAEAIVKKA T0330 31 :EVYGTEGSTGS 2b8eA 473 :LEHGIELGEPE T0330 42 :HDFSGK 2b8eA 486 :EVIAGE T0330 54 :YEVLSNVGLERA 2b8eA 503 :KRLMEDFGVAVS T0330 72 :DKAKETYIALFRERA 2b8eA 515 :NEVELALEKLEREAK T0330 91 :ITLLEGVRELLDALSSRS 2b8eA 548 :DTLKESAKPAVQELKRMG T0330 110 :VLLGLLTGNFEASGRHKLKLPGID 2b8eA 566 :IKVGMITGDNWRSAEAISRELNLD T0330 139 :GAFADDA 2b8eA 590 :LVIAEVL T0330 152 :PHIALERARRMTGA 2b8eA 597 :PHQKSEEVKKLQAK T0330 171 :QIVIIGDT 2b8eA 612 :VVAFVGDG T0330 182 :IRCARELD 2b8eA 623 :APALAQAD T0330 191 :RSIAV 2b8eA 631 :LGIAV T0330 198 :G 2b8eA 646 :G T0330 211 :GTLF 2b8eA 647 :DIVL T0330 215 :KNFAETDEVL 2b8eA 653 :DDLRDVVAAI Number of specific fragments extracted= 16 number of extra gaps= 2 total=688 Number of alignments=58 # 2b8eA read from 2b8eA/merged-good-all-a2m # found chain 2b8eA in template set Warning: unaligning (T0330)E179 because of BadResidue code BAD_PEPTIDE in next template residue (2b8eA)N621 Warning: unaligning (T0330)H180 because of BadResidue code BAD_PEPTIDE at template residue (2b8eA)N621 Warning: unaligning (T0330)D181 because of BadResidue code BAD_PEPTIDE at template residue (2b8eA)D622 Warning: unaligning (T0330)F200 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b8eA)S645 Warning: unaligning (T0330)T201 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b8eA)S645 T0330 4 :TLVLFDIDGTLLKVESMNR 2b8eA 419 :TAVIFDKTGTLTKGKPEVT T0330 23 :RVLADALIEVYGTEGSTGSHDFSGKM 2b8eA 466 :EAIVKKALEHGIELGEPEKVEVIAGE T0330 54 :YEVLSNVGLERAE 2b8eA 503 :KRLMEDFGVAVSN T0330 73 :KAKETYIALFRERA 2b8eA 516 :EVELALEKLEREAK T0330 91 :ITLLEGVRELLDALSSRS 2b8eA 548 :DTLKESAKPAVQELKRMG T0330 110 :VLLGLLTGNFEASGRHKLKLPGID 2b8eA 566 :IKVGMITGDNWRSAEAISRELNLD T0330 139 :GAFADDALDRN 2b8eA 590 :LVIAEVLPHQK T0330 156 :LERARRMTGA 2b8eA 601 :SEEVKKLQAK T0330 170 :SQIVIIGDT 2b8eA 611 :EVVAFVGDG T0330 182 :IRCARELDARSIA 2b8eA 623 :APALAQADLGIAV T0330 202 :M 2b8eA 646 :G T0330 211 :GTLF 2b8eA 647 :DIVL T0330 215 :KNFAETDEVL 2b8eA 653 :DDLRDVVAAI Number of specific fragments extracted= 13 number of extra gaps= 2 total=701 Number of alignments=59 # 2b8eA read from 2b8eA/merged-good-all-a2m # found chain 2b8eA in template set Warning: unaligning (T0330)E179 because of BadResidue code BAD_PEPTIDE in next template residue (2b8eA)N621 Warning: unaligning (T0330)H180 because of BadResidue code BAD_PEPTIDE at template residue (2b8eA)N621 Warning: unaligning (T0330)D181 because of BadResidue code BAD_PEPTIDE at template residue (2b8eA)D622 Warning: unaligning (T0330)A196 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2b8eA)S645 Warning: unaligning (T0330)T201 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2b8eA)S645 T0330 4 :TLVLFDIDGTLLK 2b8eA 419 :TAVIFDKTGTLTK T0330 22 :RRVLADALIEVYGTEGS 2b8eA 447 :RELLRLAAIAERRSEHP T0330 49 :DGAIIY 2b8eA 464 :IAEAIV T0330 55 :EVLSNVGL 2b8eA 504 :RLMEDFGV T0330 66 :EIADKFDKAKETYIA 2b8eA 512 :AVSNEVELALEKLER T0330 91 :ITLLEGVRELLDALSS 2b8eA 548 :DTLKESAKPAVQELKR T0330 108 :SDVLLGLLTGNFEASGRHKLKLPGID 2b8eA 564 :MGIKVGMITGDNWRSAEAISRELNLD T0330 139 :GAFADD 2b8eA 590 :LVIAEV T0330 151 :LPHIALERARRMTGA 2b8eA 596 :LPHQKSEEVKKLQAK T0330 170 :SQIVIIGDT 2b8eA 611 :EVVAFVGDG T0330 182 :IRCARELD 2b8eA 623 :APALAQAD T0330 191 :RSIAV 2b8eA 631 :LGIAV T0330 202 :M 2b8eA 646 :G T0330 211 :GTLF 2b8eA 647 :DIVL T0330 215 :KNFAETDEVL 2b8eA 653 :DDLRDVVAAI Number of specific fragments extracted= 15 number of extra gaps= 2 total=716 Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vj5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vj5A expands to /projects/compbio/data/pdb/1vj5.pdb.gz 1vj5A:# T0330 read from 1vj5A/merged-good-all-a2m # 1vj5A read from 1vj5A/merged-good-all-a2m # adding 1vj5A to template set # found chain 1vj5A in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1vj5A)T2 T0330 3 :RTLVLFDIDGTLL 1vj5A 3 :LRAAVFDLDGVLA T0330 17 :VESMNRRV 1vj5A 19 :VFGVLGRT T0330 29 :L 1vj5A 27 :E T0330 31 :EVYGTEGS 1vj5A 28 :EALALPRG T0330 52 :IIYE 1vj5A 36 :LLND T0330 56 :VLSNVGLERAEIADKFDKAKET 1vj5A 52 :RLMKGEITLSQWIPLMEENCRK T0330 78 :YIALFRERA 1vj5A 88 :IKEIFDKAI T0330 89 :EDITLLEGVRELLDALSSRS 1vj5A 97 :SARKINRPMLQAALMLRKKG T0330 110 :VLLGLLTG 1vj5A 117 :FTTAILTN T0330 118 :NFEASGRHKLKLPGI 1vj5A 131 :AERDGLAQLMCELKM T0330 135 :YFPFGAFADDALDRNELPHIALERARRM 1vj5A 146 :HFDFLIESCQVGMVKPEPQIYKFLLDTL T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSI 1vj5A 174 :KASPSEVVFLDDIGANLKPARDLGMVTI T0330 213 :LFKNFAETDEVLASILTP 1vj5A 202 :LVQDTDTALKELEKVTGI Number of specific fragments extracted= 13 number of extra gaps= 0 total=729 Number of alignments=61 # 1vj5A read from 1vj5A/merged-good-all-a2m # found chain 1vj5A in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1vj5A)T2 T0330 3 :RTLVLFDIDGTLLKVE 1vj5A 3 :LRAAVFDLDGVLALPA T0330 21 :NRRVLADALIEVYG 1vj5A 19 :VFGVLGRTEEALAL T0330 49 :DGAIIYEVLSNVG 1vj5A 33 :PRGLLNDAFQKGG T0330 62 :LERAEIADKFDKAKETY 1vj5A 58 :ITLSQWIPLMEENCRKC T0330 79 :IALFRE 1vj5A 89 :KEIFDK T0330 87 :RREDITLLEGVRELLDALSSRS 1vj5A 95 :AISARKINRPMLQAALMLRKKG T0330 110 :VLLGLLTGNF 1vj5A 117 :FTTAILTNTW T0330 120 :EASGRHKLKLPGID 1vj5A 133 :RDGLAQLMCELKMH T0330 136 :FPFGAFADDALDRNELPHIALERARRM 1vj5A 147 :FDFLIESCQVGMVKPEPQIYKFLLDTL T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIA 1vj5A 174 :KASPSEVVFLDDIGANLKPARDLGMVTIL T0330 214 :FKNFAETDEVLASILTPK 1vj5A 203 :VQDTDTALKELEKVTGIQ Number of specific fragments extracted= 11 number of extra gaps= 0 total=740 Number of alignments=62 # 1vj5A read from 1vj5A/merged-good-all-a2m # found chain 1vj5A in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1vj5A)T2 T0330 3 :RTLVLFDIDGTLL 1vj5A 3 :LRAAVFDLDGVLA T0330 16 :KVESMNRRV 1vj5A 18 :AVFGVLGRT T0330 25 :LADALI 1vj5A 37 :LNDAFQ T0330 33 :YGTEGSTGSHDFSGKMDGAIIYEVLS 1vj5A 43 :KGGPEGATTRLMKGEITLSQWIPLME T0330 69 :DKFDKAKETY 1vj5A 69 :ENCRKCSETA T0330 79 :IALFRERAR 1vj5A 88 :IKEIFDKAI T0330 89 :EDITLLEGVRELLDALSS 1vj5A 97 :SARKINRPMLQAALMLRK T0330 108 :SDVLLGLLTGNF 1vj5A 115 :KGFTTAILTNTW T0330 120 :EASGRHKLKLPG 1vj5A 133 :RDGLAQLMCELK T0330 134 :HYFPFGAFADDALDRNELPHIALERARR 1vj5A 145 :MHFDFLIESCQVGMVKPEPQIYKFLLDT T0330 165 :ANYSPSQIVIIGDTEHDIRCARELDARSI 1vj5A 173 :LKASPSEVVFLDDIGANLKPARDLGMVTI T0330 213 :LFKNFAETDEVLASIL 1vj5A 202 :LVQDTDTALKELEKVT Number of specific fragments extracted= 12 number of extra gaps= 0 total=752 Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o08A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0330 read from 1o08A/merged-good-all-a2m # 1o08A read from 1o08A/merged-good-all-a2m # found chain 1o08A in training set Warning: unaligning (T0330)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o08A)D1008 Warning: unaligning (T0330)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o08A)D1008 Warning: unaligning (T0330)P230 because of BadResidue code BAD_PEPTIDE in next template residue (1o08A)K1219 Warning: unaligning (T0330)K231 because of BadResidue code BAD_PEPTIDE at template residue (1o08A)K1219 Warning: unaligning (T0330)H232 because of BadResidue code BAD_PEPTIDE at template residue (1o08A)Q1220 T0330 1 :M 1o08A 1001 :M T0330 3 :RTLVL 1o08A 1002 :FKAVL T0330 10 :IDGTLLKVESMNRRVLADAL 1o08A 1009 :LDGVITDTAEYHFRAWKALA T0330 31 :EVYGTE 1o08A 1029 :EEIGIN T0330 37 :GSTGS 1o08A 1036 :VDRQF T0330 42 :HDFSGKMDGAIIYEVLSNVG 1o08A 1042 :EQLKGVSREDSLQKILDLAD T0330 62 :LERAEI 1o08A 1064 :VSAEEF T0330 72 :DKAKETYIALFRERA 1o08A 1070 :KELAKRKNDNYVKMI T0330 89 :EDIT 1o08A 1085 :QDVS T0330 93 :LLEGVRELLDALSSRS 1o08A 1092 :VYPGILQLLKDLRSNK T0330 110 :VLLGLLTGN 1o08A 1108 :IKIALASAS T0330 121 :ASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARRM 1o08A 1117 :KNGPFLLERMNLTGYFDAIADPAEVAASKPAPDIFIAAAHAV T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAV 1o08A 1159 :GVAPSESIGLEDSQAGIQAIKDSGALPIGV T0330 200 :FTMEELAR 1o08A 1189 :GRPEDLGD T0330 210 :PGTLFKNFAET 1o08A 1197 :DIVIVPDTSHY T0330 221 :DEVLASILT 1o08A 1209 :LEFLKEVWL Number of specific fragments extracted= 16 number of extra gaps= 2 total=768 Number of alignments=64 # 1o08A read from 1o08A/merged-good-all-a2m # found chain 1o08A in training set Warning: unaligning (T0330)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o08A)D1008 Warning: unaligning (T0330)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o08A)D1008 Warning: unaligning (T0330)P230 because of BadResidue code BAD_PEPTIDE in next template residue (1o08A)K1219 Warning: unaligning (T0330)K231 because of BadResidue code BAD_PEPTIDE at template residue (1o08A)K1219 Warning: unaligning (T0330)H232 because of BadResidue code BAD_PEPTIDE at template residue (1o08A)Q1220 T0330 1 :M 1o08A 1001 :M T0330 3 :RTLVL 1o08A 1002 :FKAVL T0330 10 :IDGTLLKVESMNRRVLADALIEVYGTEGSTGSHDFSGKMDGAIIYEVLSNVG 1o08A 1009 :LDGVITDTAEYHFRAWKALAEEIGINGVDRQFNEQLKGVSREDSLQKILDLA T0330 62 :LER 1o08A 1064 :VSA T0330 69 :DKFDKAKETYIALFRERA 1o08A 1067 :EEFKELAKRKNDNYVKMI T0330 87 :RREDITLLEGVRELLDALSSRS 1o08A 1086 :DVSPADVYPGILQLLKDLRSNK T0330 110 :VLLGLLTGN 1o08A 1108 :IKIALASAS T0330 121 :ASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARRM 1o08A 1117 :KNGPFLLERMNLTGYFDAIADPAEVAASKPAPDIFIAAAHAV T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAV 1o08A 1159 :GVAPSESIGLEDSQAGIQAIKDSGALPIGV T0330 200 :FTMEELAR 1o08A 1189 :GRPEDLGD T0330 210 :PGTLFKNFAET 1o08A 1197 :DIVIVPDTSHY T0330 221 :DEVLASILT 1o08A 1209 :LEFLKEVWL Number of specific fragments extracted= 12 number of extra gaps= 2 total=780 Number of alignments=65 # 1o08A read from 1o08A/merged-good-all-a2m # found chain 1o08A in training set Warning: unaligning (T0330)S2 because first residue in template chain is (1o08A)M1001 Warning: unaligning (T0330)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1o08A)D1008 Warning: unaligning (T0330)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o08A)D1008 Warning: unaligning (T0330)P230 because of BadResidue code BAD_PEPTIDE in next template residue (1o08A)K1219 Warning: unaligning (T0330)K231 because of BadResidue code BAD_PEPTIDE at template residue (1o08A)K1219 Warning: unaligning (T0330)H232 because of BadResidue code BAD_PEPTIDE at template residue (1o08A)Q1220 Warning: unaligning (T0330)S233 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1o08A)K1221 T0330 3 :RTLVL 1o08A 1002 :FKAVL T0330 10 :IDGTLLKVESMNRRVLADALIEVYGTEGSTGSHDFSGKMDGAIIYEVLSNVG 1o08A 1009 :LDGVITDTAEYHFRAWKALAEEIGINGVDRQFNEQLKGVSREDSLQKILDLA T0330 64 :RAEIADKFDKAKETYIALFRERARRE 1o08A 1061 :DKKVSAEEFKELAKRKNDNYVKMIQD T0330 90 :DITLLEGVRELLDALSS 1o08A 1089 :PADVYPGILQLLKDLRS T0330 108 :SDVLLGLLTGN 1o08A 1106 :NKIKIALASAS T0330 121 :ASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARR 1o08A 1117 :KNGPFLLERMNLTGYFDAIADPAEVAASKPAPDIFIAAAHA T0330 165 :ANYSPSQIVIIGDTEHDIRCARELDARSIAV 1o08A 1158 :VGVAPSESIGLEDSQAGIQAIKDSGALPIGV T0330 200 :FTMEELA 1o08A 1189 :GRPEDLG T0330 209 :KPGTLFKNFAET 1o08A 1196 :DDIVIVPDTSHY T0330 221 :DEVLASILT 1o08A 1209 :LEFLKEVWL Number of specific fragments extracted= 10 number of extra gaps= 2 total=790 Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2g09A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2g09A expands to /projects/compbio/data/pdb/2g09.pdb.gz 2g09A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1940, because occupancy 0.500 <= existing 0.500 in 2g09A Skipped atom 1942, because occupancy 0.500 <= existing 0.500 in 2g09A Skipped atom 1944, because occupancy 0.500 <= existing 0.500 in 2g09A Skipped atom 1946, because occupancy 0.500 <= existing 0.500 in 2g09A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0330 read from 2g09A/merged-good-all-a2m # 2g09A read from 2g09A/merged-good-all-a2m # adding 2g09A to template set # found chain 2g09A in template set Warning: unaligning (T0330)L5 because of BadResidue code BAD_PEPTIDE at template residue (2g09A)Q45 T0330 6 :VLFDIDGTLLKV 2g09A 46 :IITDFDMTLSRF T0330 25 :LADAL 2g09A 67 :CHNII T0330 31 :E 2g09A 72 :D T0330 34 :GTE 2g09A 73 :NCK T0330 37 :GSTG 2g09A 77 :VTDE T0330 49 :DGAIIYEVLSNV 2g09A 81 :CRRKLLQLKEQY T0330 61 :GLERAEIADKFDKAKETYIALFRE 2g09A 100 :VLTVEEKFPYMVEWYTKSHGLLIE T0330 85 :RARREDITLLEGVRELLDALSSRS 2g09A 134 :IVADSDVMLKEGYENFFGKLQQHG T0330 110 :VLLGLLTGNFEASGRHKLKLPGID 2g09A 158 :IPVFIFSAGIGDVLEEVIRQAGVY T0330 134 :HYFPFGAFA 2g09A 183 :SNVKVVSNF T0330 143 :D 2g09A 195 :D T0330 152 :PHIAL 2g09A 214 :HDGAL T0330 158 :RARRMTGA 2g09A 223 :YFSQLKDN T0330 170 :SQIVIIGDTEHDIRCA 2g09A 231 :SNIILLGDSQGDLRMA T0330 188 :LDAR 2g09A 247 :DGVA T0330 192 :SIAVATG 2g09A 257 :KIGYLND T0330 201 :TMEE 2g09A 264 :RVDE T0330 205 :LARH 2g09A 272 :YMDS T0330 210 :PGTLF 2g09A 276 :YDIVL T0330 215 :KNFAETDEVLA 2g09A 284 :ESLEVVNSILQ Number of specific fragments extracted= 20 number of extra gaps= 1 total=810 Number of alignments=67 # 2g09A read from 2g09A/merged-good-all-a2m # found chain 2g09A in template set Warning: unaligning (T0330)L5 because of BadResidue code BAD_PEPTIDE at template residue (2g09A)Q45 T0330 6 :VLFDIDGTLLKVE 2g09A 46 :IITDFDMTLSRFS T0330 25 :LADALIEV 2g09A 67 :CHNIIDNC T0330 36 :EGSTG 2g09A 76 :LVTDE T0330 49 :DGAIIYEVLSNVG 2g09A 81 :CRRKLLQLKEQYY T0330 62 :LERAEIADKFDKAKETYIALFRERA 2g09A 101 :LTVEEKFPYMVEWYTKSHGLLIEQG T0330 87 :RREDITLLEGVRELLDALSSRS 2g09A 136 :ADSDVMLKEGYENFFGKLQQHG T0330 110 :VLLGLLTGNFEASGRHKLKLPG 2g09A 158 :IPVFIFSAGIGDVLEEVIRQAG T0330 132 :IDHYFPFGAFA 2g09A 181 :YHSNVKVVSNF T0330 143 :DD 2g09A 195 :DE T0330 148 :RN 2g09A 219 :KN T0330 152 :PH 2g09A 221 :TD T0330 158 :RARRMT 2g09A 223 :YFSQLK T0330 166 :NY 2g09A 229 :DN T0330 170 :SQIVIIGDTEHDIRCAR 2g09A 231 :SNIILLGDSQGDLRMAD T0330 189 :DAR 2g09A 248 :GVA T0330 192 :SIAVAT 2g09A 257 :KIGYLN T0330 200 :FTMEELARHK 2g09A 263 :DRVDELLEKY T0330 210 :PGTLF 2g09A 276 :YDIVL T0330 215 :KNFAETDEVLAS 2g09A 284 :ESLEVVNSILQK Number of specific fragments extracted= 19 number of extra gaps= 1 total=829 Number of alignments=68 # 2g09A read from 2g09A/merged-good-all-a2m # found chain 2g09A in template set Warning: unaligning (T0330)L5 because of BadResidue code BAD_PEPTIDE at template residue (2g09A)Q45 T0330 6 :VLFDIDGTLLKV 2g09A 46 :IITDFDMTLSRF T0330 21 :NRRVLA 2g09A 67 :CHNIID T0330 33 :YGTEGSTGSHDFS 2g09A 73 :NCKLVTDECRRKL T0330 51 :AIIYEVLSNVGLERAEIADKFDKAKETYIALFRERARREDIT 2g09A 86 :LQLKEQYYAIEVDPVLTVEEKFPYMVEWYTKSHGLLIEQGIP T0330 93 :LLEGVRELLDALSS 2g09A 142 :LKEGYENFFGKLQQ T0330 108 :SDVLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFAD 2g09A 156 :HGIPVFIFSAGIGDVLEEVIRQAGVYHSNVKVVSNF T0330 145 :ALDRNELPHIAL 2g09A 207 :LIHVFNKHDGAL T0330 157 :ERARR 2g09A 223 :YFSQL T0330 165 :ANYS 2g09A 228 :KDNS T0330 171 :QIVIIGDTEHDIRC 2g09A 232 :NIILLGDSQGDLRM T0330 187 :ELDAR 2g09A 246 :ADGVA T0330 192 :SIAVATG 2g09A 257 :KIGYLND T0330 201 :TMEELA 2g09A 264 :RVDELL T0330 218 :AETDE 2g09A 270 :EKYMD Number of specific fragments extracted= 14 number of extra gaps= 1 total=843 Number of alignments=69 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b82A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2b82A expands to /projects/compbio/data/pdb/2b82.pdb.gz 2b82A:# T0330 read from 2b82A/merged-good-all-a2m # 2b82A read from 2b82A/merged-good-all-a2m # adding 2b82A to template set # found chain 2b82A in template set Warning: unaligning (T0330)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b82A)D44 Warning: unaligning (T0330)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b82A)D44 T0330 2 :SRTLVL 2b82A 37 :PPMAVG T0330 10 :IDGTLLKVESMNRRVL 2b82A 45 :IDDTVLFSSPGFWRGK T0330 31 :EVYG 2b82A 61 :KTFS T0330 39 :TGSHDFSG 2b82A 65 :PESEDYLK T0330 49 :DGAIIYEVLS 2b82A 73 :NPVFWEKMNN T0330 61 :GL 2b82A 83 :GW T0330 89 :EDITLLEGVRELLDALSSRS 2b82A 86 :EFSIPKEVARQLIDMHVRRG T0330 110 :VLLGLLTG 2b82A 106 :DAIFFVTG T0330 118 :NFEASGRHKLKLPG 2b82A 121 :TVSKTLADNFHIPA T0330 133 :DHYFPFGAFADDALD 2b82A 135 :TNMNPVIFAGDKPGQ T0330 148 :RN 2b82A 151 :TK T0330 156 :LERARRM 2b82A 153 :SQWLQDK T0330 166 :NYS 2b82A 160 :NIR T0330 173 :VIIGDTEHDIRCARELDARSIAVAT 2b82A 163 :IFYGDSDNDITAARDVGARGIRILR T0330 199 :N 2b82A 189 :S Number of specific fragments extracted= 15 number of extra gaps= 1 total=858 Number of alignments=70 # 2b82A read from 2b82A/merged-good-all-a2m # found chain 2b82A in template set Warning: unaligning (T0330)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b82A)D44 Warning: unaligning (T0330)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b82A)D44 T0330 2 :SRTLVL 2b82A 37 :PPMAVG T0330 10 :IDGTLLKVESMNRRVLAD 2b82A 45 :IDDTVLFSSPGFWRGKKT T0330 33 :YG 2b82A 63 :FS T0330 36 :EGSTGSHDFS 2b82A 65 :PESEDYLKNP T0330 69 :D 2b82A 75 :V T0330 78 :YIALFRER 2b82A 76 :FWEKMNNG T0330 87 :RREDITLLEGVRELLDALSSRS 2b82A 84 :WDEFSIPKEVARQLIDMHVRRG T0330 110 :VLLGLLTGNF 2b82A 106 :DAIFFVTGRS T0330 123 :GRHKLKLPGID 2b82A 123 :SKTLADNFHIP T0330 134 :HYFPFGAFADDAL 2b82A 136 :NMNPVIFAGDKPG T0330 147 :DRN 2b82A 150 :NTK T0330 156 :LERARRM 2b82A 153 :SQWLQDK T0330 166 :NYS 2b82A 160 :NIR T0330 173 :VIIGDTEHDIRCARELDARSIAVATG 2b82A 163 :IFYGDSDNDITAARDVGARGIRILRA Number of specific fragments extracted= 14 number of extra gaps= 1 total=872 Number of alignments=71 # 2b82A read from 2b82A/merged-good-all-a2m # found chain 2b82A in template set Warning: unaligning (T0330)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2b82A)D44 Warning: unaligning (T0330)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2b82A)D44 T0330 2 :SRTLVL 2b82A 37 :PPMAVG T0330 10 :IDGTLLKVESMNRR 2b82A 45 :IDDTVLFSSPGFWR T0330 53 :IYEVLSNVG 2b82A 59 :GKKTFSPES T0330 66 :EIADKFDKAKETY 2b82A 68 :EDYLKNPVFWEKM T0330 87 :RREDITLLEGVRELLDALSS 2b82A 84 :WDEFSIPKEVARQLIDMHVR T0330 108 :SDVLLGLLTGNF 2b82A 104 :RGDAIFFVTGRS T0330 122 :SGRHKL 2b82A 121 :TVSKTL T0330 128 :KLPGID 2b82A 128 :DNFHIP T0330 134 :HYFPFGAFADDALDRNEL 2b82A 135 :TNMNPVIFAGDKPGQNTK T0330 156 :LERARR 2b82A 153 :SQWLQD T0330 165 :ANYS 2b82A 159 :KNIR T0330 173 :VIIGDTEHDIRCARELDARSIAVA 2b82A 163 :IFYGDSDNDITAARDVGARGIRIL Number of specific fragments extracted= 12 number of extra gaps= 1 total=884 Number of alignments=72 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ah5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2ah5A expands to /projects/compbio/data/pdb/2ah5.pdb.gz 2ah5A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0330 read from 2ah5A/merged-good-all-a2m # 2ah5A read from 2ah5A/merged-good-all-a2m # adding 2ah5A to template set # found chain 2ah5A in template set Warning: unaligning (T0330)G117 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ah5A)K108 Warning: unaligning (T0330)N118 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ah5A)K108 T0330 3 :RTLVLFDIDGTLLKVESMNRRVLADAL 2ah5A 4 :ITAIFFDLDGTLVDSSIGIHNAFTYTF T0330 31 :EVYGTE 2ah5A 31 :KELGVP T0330 37 :GSTGS 2ah5A 38 :PDAKT T0330 42 :HDFSGKMDGAIIY 2ah5A 44 :RGFMGPPLESSFA T0330 60 :VGLERAEI 2ah5A 57 :TCLSKDQI T0330 72 :DKAKETYIALFRERAR 2ah5A 65 :SEAVQIYRSYYKAKGI T0330 89 :EDITLLEGVRELLDALSSR 2ah5A 81 :YEAQLFPQIIDLLEELSSS T0330 110 :VLLGLLT 2ah5A 100 :YPLYITT T0330 119 :FEASGRHKLKLPGIDHYFPFGAFADDALDRN 2ah5A 109 :DTSTAQDMAKNLEIHHFFDGIYGSSPEAPHK T0330 152 :PHIALERARRM 2ah5A 140 :ADVIHQALQTH T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAVATGNFTMEELARHKPGTLFKNFAETDEV 2ah5A 151 :QLAPEQAIIIGDTKFDMLGARETGIQKLAITWGFGEQADLLNYQPDYIAHKPLEVLAY Number of specific fragments extracted= 11 number of extra gaps= 1 total=895 Number of alignments=73 # 2ah5A read from 2ah5A/merged-good-all-a2m # found chain 2ah5A in template set Warning: unaligning (T0330)G117 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ah5A)K108 Warning: unaligning (T0330)N118 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ah5A)K108 T0330 3 :RTLVLFDIDGTLLKVESMNRRVLADALIEVYGTEGSTGSHDFS 2ah5A 4 :ITAIFFDLDGTLVDSSIGIHNAFTYTFKELGVPSPDAKTIRGF T0330 49 :DGAIIYEVLSNVG 2ah5A 47 :MGPPLESSFATCL T0330 63 :ER 2ah5A 60 :SK T0330 69 :DKFDKAKETYIALFRER 2ah5A 62 :DQISEAVQIYRSYYKAK T0330 87 :RREDITLLEGVRELLDALSSR 2ah5A 79 :GIYEAQLFPQIIDLLEELSSS T0330 110 :VLLGLLT 2ah5A 100 :YPLYITT T0330 119 :FEASGRHKLKLPGIDHYFPFGAFADDALDRN 2ah5A 109 :DTSTAQDMAKNLEIHHFFDGIYGSSPEAPHK T0330 152 :PHIALERARRM 2ah5A 140 :ADVIHQALQTH T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAVATGNFTMEELARHKPGTLFKNFAETDEV 2ah5A 151 :QLAPEQAIIIGDTKFDMLGARETGIQKLAITWGFGEQADLLNYQPDYIAHKPLEVLAY Number of specific fragments extracted= 9 number of extra gaps= 1 total=904 Number of alignments=74 # 2ah5A read from 2ah5A/merged-good-all-a2m # found chain 2ah5A in template set Warning: unaligning (T0330)G117 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ah5A)K108 Warning: unaligning (T0330)N118 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ah5A)K108 T0330 3 :RTLVLFDIDGTLLKVESMNRRVLADALIEVYGTEGSTGSHDFSGKMDGAIIYEV 2ah5A 4 :ITAIFFDLDGTLVDSSIGIHNAFTYTFKELGVPSPDAKTIRGFMGPPLESSFAT T0330 66 :EIADKFDKAKETYIALFRERARREDITLLEGVRELLDALSS 2ah5A 58 :CLSKDQISEAVQIYRSYYKAKGIYEAQLFPQIIDLLEELSS T0330 109 :DVLLGLLT 2ah5A 99 :SYPLYITT T0330 119 :FEASGRHKLKLPGIDHYFPFGAFADDALDRN 2ah5A 109 :DTSTAQDMAKNLEIHHFFDGIYGSSPEAPHK T0330 152 :PHIALERARR 2ah5A 140 :ADVIHQALQT T0330 165 :ANYSPSQIVIIGDTEHDIRCARELDARSIAVATGNFTMEELARHKPGTLFKNFAETDEV 2ah5A 150 :HQLAPEQAIIIGDTKFDMLGARETGIQKLAITWGFGEQADLLNYQPDYIAHKPLEVLAY Number of specific fragments extracted= 6 number of extra gaps= 1 total=910 Number of alignments=75 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zs9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zs9A expands to /projects/compbio/data/pdb/1zs9.pdb.gz 1zs9A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0330 read from 1zs9A/merged-good-all-a2m # 1zs9A read from 1zs9A/merged-good-all-a2m # adding 1zs9A to template set # found chain 1zs9A in template set Warning: unaligning (T0330)G61 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1zs9A)K106 Warning: unaligning (T0330)E63 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1zs9A)K106 T0330 3 :RTLVLFDIDGTLLK 1zs9A 10 :VTVILLDIEGTTTP T0330 17 :VESMNRRVLADALIEVYGT 1zs9A 31 :LFPYIEENVKEYLQTHWEE T0330 36 :EGSTGS 1zs9A 68 :HLDGAV T0330 42 :HDFSGKMDGAIIYE 1zs9A 75 :IPAASGNGVDDLQQ T0330 56 :VLSNV 1zs9A 97 :VCWQM T0330 64 :R 1zs9A 107 :T T0330 72 :DKAKETYIALFRERAR 1zs9A 108 :TALKQLQGHMWRAAFT T0330 88 :REDITLLEGVRELLDALSSRS 1zs9A 126 :RMKAEFFADVVPAVRKWREAG T0330 110 :VLLGLLTGNFEASGRHKLKLP 1zs9A 147 :MKVYIYSSGSVEAQKLLFGHS T0330 131 :GIDHYFPFGAF 1zs9A 171 :DILELVDGHFD T0330 144 :DALDRNELPHIALERARRM 1zs9A 182 :TKIGHKVESESYRKIADSI T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAVATGN 1zs9A 201 :GCSTNNILFLTDVTREASAAEEADVHVAVVVRPG T0330 200 :FTMEELARHK 1zs9A 238 :LTDDEKTYYS T0330 213 :LFKNFAET 1zs9A 248 :LITSFSEL Number of specific fragments extracted= 14 number of extra gaps= 0 total=924 Number of alignments=76 # 1zs9A read from 1zs9A/merged-good-all-a2m # found chain 1zs9A in template set T0330 3 :RTLVLFDIDGTLLKVESM 1zs9A 10 :VTVILLDIEGTTTPIAFV T0330 21 :NRRVLADALIEVYGTEGSTGSHDF 1zs9A 31 :LFPYIEENVKEYLQTHWEEEECQQ T0330 49 :DGAIIYEVLSNVG 1zs9A 55 :DVSLLRKQAEEDA T0330 62 :LERAEIADKFDKAKETY 1zs9A 81 :NGVDDLQQMIQAVVDNV T0330 79 :IALFRE 1zs9A 119 :RAAFTA T0330 87 :RREDITLLEGVRELLDALSSRS 1zs9A 125 :GRMKAEFFADVVPAVRKWREAG T0330 110 :VLLGLLTGNFEASGRHKLKLP 1zs9A 147 :MKVYIYSSGSVEAQKLLFGHS T0330 131 :GIDHYFPFGAFADDAL 1zs9A 171 :DILELVDGHFDTKIGH T0330 149 :NELPHIALERARRM 1zs9A 187 :KVESESYRKIADSI T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAVATG 1zs9A 201 :GCSTNNILFLTDVTREASAAEEADVHVAVVVRP T0330 199 :NFTMEELARHK 1zs9A 237 :GLTDDEKTYYS T0330 213 :LFKNFAET 1zs9A 248 :LITSFSEL Number of specific fragments extracted= 12 number of extra gaps= 0 total=936 Number of alignments=77 # 1zs9A read from 1zs9A/merged-good-all-a2m # found chain 1zs9A in template set Warning: unaligning (T0330)A65 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1zs9A)K106 Warning: unaligning (T0330)I67 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1zs9A)K106 T0330 3 :RTLVLFDIDGTLLK 1zs9A 10 :VTVILLDIEGTTTP T0330 17 :VESMNRRVLADALIEV 1zs9A 31 :LFPYIEENVKEYLQTH T0330 33 :YGTEGSTGSHDFSGKMDGAIIYEVLS 1zs9A 77 :AASGNGVDDLQQMIQAVVDNVCWQMS T0330 64 :R 1zs9A 103 :L T0330 68 :ADKFDKAKETYIALFRER 1zs9A 107 :TTALKQLQGHMWRAAFTA T0330 87 :RREDITLLEGVRELLDALSS 1zs9A 125 :GRMKAEFFADVVPAVRKWRE T0330 108 :SDVLLGLLTGNFEASGRHKLKLP 1zs9A 145 :AGMKVYIYSSGSVEAQKLLFGHS T0330 131 :GIDHYFPFGA 1zs9A 171 :DILELVDGHF T0330 143 :DDALDRNELPHIALERARR 1zs9A 181 :DTKIGHKVESESYRKIADS T0330 165 :ANYSPSQIVIIGDTEHDIRCARELDARSIAVATGNF 1zs9A 200 :IGCSTNNILFLTDVTREASAAEEADVHVAVVVRPGN T0330 201 :TMEELARH 1zs9A 239 :TDDEKTYY T0330 212 :TLFKNFAET 1zs9A 247 :SLITSFSEL Number of specific fragments extracted= 12 number of extra gaps= 0 total=948 Number of alignments=78 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1x42A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1x42A expands to /projects/compbio/data/pdb/1x42.pdb.gz 1x42A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0330 read from 1x42A/merged-good-all-a2m # 1x42A read from 1x42A/merged-good-all-a2m # adding 1x42A to template set # found chain 1x42A in template set Warning: unaligning (T0330)L228 because last residue in template chain is (1x42A)N230 T0330 1 :M 1x42A 1 :M T0330 3 :RTLVLFDIDGTLLK 1x42A 2 :IRAVFFDFVGTLLS T0330 17 :VESMNRRVLADALIEVYGTEGST 1x42A 41 :LLDEYEKLTREAFSNYAGKPYRP T0330 49 :DGAIIYEVLSNVGLERA 1x42A 68 :EEEVMRKLAEKYGFKYP T0330 72 :DKAKETYIALFR 1x42A 85 :ENFWEIHLRMHQ T0330 89 :EDITLLEGVRELLDALSSR 1x42A 97 :RYGELYPEVVEVLKSLKGK T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARRM 1x42A 116 :YHVGMITDSDTEYLMAHLDALGIKDLFDSITTSEEAGFFKPHPRIFELALKKA T0330 166 :NYSPSQIVIIGDTE 1x42A 169 :GVKGEEAVYVGDNP T0330 180 :HDIRCARELDARSIAVATGNFTMEEL 1x42A 184 :KDCGGSKNLGMTSILLDRKGEKREFW T0330 207 :RH 1x42A 210 :DK T0330 210 :PGTLFKNFAETDEVLASI 1x42A 212 :CDFIVSDLREVIKIVDEL Number of specific fragments extracted= 11 number of extra gaps= 0 total=959 Number of alignments=79 # 1x42A read from 1x42A/merged-good-all-a2m # found chain 1x42A in template set Warning: unaligning (T0330)L228 because last residue in template chain is (1x42A)N230 T0330 1 :M 1x42A 1 :M T0330 3 :RTLVLFDIDGTLLKVES 1x42A 2 :IRAVFFDFVGTLLSVEG T0330 21 :NRRVLADALIEVYGTEGS 1x42A 19 :EAKTHLKIMEEVLGDYPL T0330 49 :DGAIIYEVLSNVG 1x42A 37 :NPKTLLDEYEKLT T0330 62 :LERAEI 1x42A 62 :RPIRDI T0330 68 :ADKFDKAKETY 1x42A 69 :EEVMRKLAEKY T0330 79 :IALFRER 1x42A 88 :WEIHLRM T0330 87 :RREDITLLEGVRELLDALSSR 1x42A 95 :HQRYGELYPEVVEVLKSLKGK T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARRM 1x42A 116 :YHVGMITDSDTEYLMAHLDALGIKDLFDSITTSEEAGFFKPHPRIFELALKKA T0330 166 :NYSPSQIVIIGDTE 1x42A 169 :GVKGEEAVYVGDNP T0330 180 :HDIRCARELDARSIAVATGNFTMEELAR 1x42A 184 :KDCGGSKNLGMTSILLDRKGEKREFWDK T0330 210 :PGTLFKNFAETDEVLASI 1x42A 212 :CDFIVSDLREVIKIVDEL Number of specific fragments extracted= 12 number of extra gaps= 0 total=971 Number of alignments=80 # 1x42A read from 1x42A/merged-good-all-a2m # found chain 1x42A in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1x42A)M1 Warning: unaligning (T0330)L228 because last residue in template chain is (1x42A)N230 T0330 3 :RTLVLFDIDGTLLKVE 1x42A 2 :IRAVFFDFVGTLLSVE T0330 20 :MNRRVLADALIEV 1x42A 18 :GEAKTHLKIMEEV T0330 33 :YGTEGSTGSHDFSGKMDGAI 1x42A 33 :DYPLNPKTLLDEYEKLTREA T0330 57 :LSNV 1x42A 53 :FSNY T0330 61 :GLERAEIADKFDKAKETY 1x42A 58 :GKPYRPIRDIEEEVMRKL T0330 79 :IALFRERARREDITLLEGVRELLDALSS 1x42A 87 :FWEIHLRMHQRYGELYPEVVEVLKSLKG T0330 109 :DVLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARR 1x42A 115 :KYHVGMITDSDTEYLMAHLDALGIKDLFDSITTSEEAGFFKPHPRIFELALKK T0330 165 :ANYSPSQIVIIGDTE 1x42A 168 :AGVKGEEAVYVGDNP T0330 180 :HDIRCARELDARSIAVATGNFTMEELA 1x42A 184 :KDCGGSKNLGMTSILLDRKGEKREFWD T0330 209 :KPGTLFKNFAETDEVLASI 1x42A 211 :KCDFIVSDLREVIKIVDEL Number of specific fragments extracted= 10 number of extra gaps= 0 total=981 Number of alignments=81 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b0cA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2b0cA expands to /projects/compbio/data/pdb/2b0c.pdb.gz 2b0cA:# T0330 read from 2b0cA/merged-good-all-a2m # 2b0cA read from 2b0cA/merged-good-all-a2m # adding 2b0cA to template set # found chain 2b0cA in template set Warning: unaligning (T0330)S2 because first residue in template chain is (2b0cA)A6 T0330 3 :RTLVLFDIDGTLLKV 2b0cA 7 :KMLYIFDLGNVIVDI T0330 18 :ESMNRRVLA 2b0cA 23 :FNRVLGAWS T0330 31 :EVYGT 2b0cA 32 :DLTRI T0330 36 :EGSTGS 2b0cA 46 :HMGEAF T0330 42 :HDFSGKMDGAIIYEVLSNVGLERAE 2b0cA 54 :HERGEISDEAFAEALCHEMALPLSY T0330 72 :DKAKETYI 2b0cA 79 :EQFSHGWQ T0330 88 :REDITLLEGVRELLDALSSRS 2b0cA 87 :AVFVALRPEVIAIMHKLREQG T0330 110 :VLLGLLTGNFE 2b0cA 108 :HRVVVLSNTNR T0330 121 :ASGRHK 2b0cA 129 :PEIRDA T0330 136 :FPFGAFADDALDRNELPHIALERARRM 2b0cA 135 :ADHIYLSQDLGMRKPEARIYQHVLQAE T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARS 2b0cA 162 :GFSPSDTVFFDDNADNIEGANQLGITS T0330 212 :TLFKNFAETDEVLA 2b0cA 189 :ILVKDKTTIPDYFA Number of specific fragments extracted= 12 number of extra gaps= 0 total=993 Number of alignments=82 # 2b0cA read from 2b0cA/merged-good-all-a2m # found chain 2b0cA in template set Warning: unaligning (T0330)S2 because first residue in template chain is (2b0cA)A6 T0330 3 :RTLVLFDIDGTLLKVES 2b0cA 7 :KMLYIFDLGNVIVDIDF T0330 23 :RVLADALIEVYGTEGSTGSHDF 2b0cA 24 :NRVLGAWSDLTRIPLASLKKSF T0330 49 :DGAIIYEVLSNVGLERAEIA 2b0cA 46 :HMGEAFHQHERGEISDEAFA T0330 72 :DKAKETY 2b0cA 66 :EALCHEM T0330 79 :IALFRERARREDITLLEGVRELLDALSSRS 2b0cA 78 :YEQFSHGWQAVFVALRPEVIAIMHKLREQG T0330 110 :VLLGLLTGNF 2b0cA 108 :HRVVVLSNTN T0330 120 :EASGRHK 2b0cA 128 :YPEIRDA T0330 136 :FPFGAFADDALDRNELPHIALERARRM 2b0cA 135 :ADHIYLSQDLGMRKPEARIYQHVLQAE T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARS 2b0cA 162 :GFSPSDTVFFDDNADNIEGANQLGITS T0330 212 :TLFKNFAETDEVLA 2b0cA 189 :ILVKDKTTIPDYFA Number of specific fragments extracted= 10 number of extra gaps= 0 total=1003 Number of alignments=83 # 2b0cA read from 2b0cA/merged-good-all-a2m # found chain 2b0cA in template set Warning: unaligning (T0330)S2 because first residue in template chain is (2b0cA)A6 T0330 3 :RTLVLFDIDGTLLKV 2b0cA 7 :KMLYIFDLGNVIVDI T0330 18 :ESMNRRVLADA 2b0cA 23 :FNRVLGAWSDL T0330 36 :EGSTGSHDFSGKMDGAIIYEVLSNV 2b0cA 35 :RIPLASLKKSFHMGEAFHQHERGEI T0330 67 :IADKFDKAKETY 2b0cA 60 :SDEAFAEALCHE T0330 79 :IALFRERARREDITLLEGVRELLDALSS 2b0cA 78 :YEQFSHGWQAVFVALRPEVIAIMHKLRE T0330 108 :SDVLLGLLTGNF 2b0cA 106 :QGHRVVVLSNTN T0330 120 :EASGRHK 2b0cA 128 :YPEIRDA T0330 136 :FPFGAFADDALDRNELPHIALERARR 2b0cA 135 :ADHIYLSQDLGMRKPEARIYQHVLQA T0330 165 :ANYSPSQIVIIGDTEHDIRCARELDARS 2b0cA 161 :EGFSPSDTVFFDDNADNIEGANQLGITS T0330 212 :TLFKNFAETDEVLA 2b0cA 189 :ILVKDKTTIPDYFA Number of specific fragments extracted= 10 number of extra gaps= 0 total=1013 Number of alignments=84 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rkqA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0330 read from 1rkqA/merged-good-all-a2m # 1rkqA read from 1rkqA/merged-good-all-a2m # found chain 1rkqA in training set Warning: unaligning (T0330)P230 because last residue in template chain is (1rkqA)N271 T0330 2 :SRTLVLFDI 1rkqA 3 :AIKLIAIDM T0330 26 :ADAL 1rkqA 12 :DGTL T0330 86 :A 1rkqA 16 :L T0330 88 :REDITLLEGVRELLDALSSRS 1rkqA 17 :LPDHTISPAVKNAIAAARARG T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADDAL 1rkqA 38 :VNVVLTTGRPYAGVHNYLKELHMEQPGDYCITYNGAL T0330 150 :ELPHIALERARRM 1rkqA 197 :NKGTGVKSLADVL T0330 166 :NYSPSQIVIIGDTEHDIRCARELD 1rkqA 210 :GIKPEEIMAIGDQENDIAMIEYAG T0330 193 :IAVATGNFT 1rkqA 234 :VGVAVDNAI T0330 203 :EELARH 1rkqA 243 :PSVKEV T0330 210 :PGTLFKNFAE 1rkqA 249 :ANFVTKSNLE T0330 220 :TDEVLASILT 1rkqA 261 :VAFAIEKYVL Number of specific fragments extracted= 11 number of extra gaps= 0 total=1024 Number of alignments=85 # 1rkqA read from 1rkqA/merged-good-all-a2m # found chain 1rkqA in training set Warning: unaligning (T0330)P230 because last residue in template chain is (1rkqA)N271 T0330 2 :SRTLVLFDIDGTL 1rkqA 3 :AIKLIAIDMDGTL T0330 87 :RREDITLLEGVRELLDALSSRS 1rkqA 16 :LLPDHTISPAVKNAIAAARARG T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFA 1rkqA 38 :VNVVLTTGRPYAGVHNYLKELHMEQPGDYCITY T0330 145 :ALD 1rkqA 71 :NGA T0330 148 :RN 1rkqA 197 :NK T0330 152 :PHIALERARRM 1rkqA 199 :GTGVKSLADVL T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIA 1rkqA 210 :GIKPEEIMAIGDQENDIAMIEYAGVGVAV T0330 199 :NFTMEELARH 1rkqA 239 :DNAIPSVKEV T0330 210 :PGTLFKNFAE 1rkqA 249 :ANFVTKSNLE T0330 220 :TDEVLASILT 1rkqA 261 :VAFAIEKYVL Number of specific fragments extracted= 10 number of extra gaps= 0 total=1034 Number of alignments=86 # 1rkqA read from 1rkqA/merged-good-all-a2m # found chain 1rkqA in training set T0330 2 :SRTLVLFDIDGTLL 1rkqA 3 :AIKLIAIDMDGTLL T0330 88 :REDITLLEGVRELLDALSS 1rkqA 17 :LPDHTISPAVKNAIAAARA T0330 108 :SDVLLGLLTGNFEASGRHKLKLPGIDHYFP 1rkqA 36 :RGVNVVLTTGRPYAGVHNYLKELHMEQPGD T0330 146 :LDRNELPHIALERARR 1rkqA 193 :DKRVNKGTGVKSLADV T0330 165 :ANYSPSQIVIIGDTEHDIRCARELDARS 1rkqA 209 :LGIKPEEIMAIGDQENDIAMIEYAGVGV T0330 196 :ATGNF 1rkqA 237 :AVDNA T0330 202 :MEELARH 1rkqA 242 :IPSVKEV T0330 210 :PGTLFKNFAE 1rkqA 249 :ANFVTKSNLE Number of specific fragments extracted= 8 number of extra gaps= 0 total=1042 Number of alignments=87 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1swvA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1swvA expands to /projects/compbio/data/pdb/1swv.pdb.gz 1swvA:# T0330 read from 1swvA/merged-good-all-a2m # 1swvA read from 1swvA/merged-good-all-a2m # adding 1swvA to template set # found chain 1swvA in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1swvA)K5 Warning: unaligning (T0330)T229 because last residue in template chain is (1swvA)K261 T0330 3 :RTLVLFDIDGTLLK 1swvA 6 :IEAVIFAWAGTTVD T0330 17 :V 1swvA 25 :P T0330 22 :RRVLADAL 1swvA 26 :LEVFMEIF T0330 31 :EVYGTEGSTGS 1swvA 34 :HKRGVAITAEE T0330 42 :HDFSGKMDGAIIYE 1swvA 46 :RKPMGLLKIDHVRA T0330 56 :VLSNVG 1swvA 70 :WNRVFR T0330 62 :LERAEI 1swvA 78 :PTEADI T0330 72 :DKAKETYIALFRERAR 1swvA 84 :QEMYEEFEEILFAILP T0330 89 :EDITLLEGVRELLDALSSRS 1swvA 100 :RYASPINGVKEVIASLRERG T0330 110 :VLLGLLTGNFEASGR 1swvA 120 :IKIGSTTGYTREMMD T0330 125 :HKLKLPGID 1swvA 138 :KEAALQGYK T0330 136 :FPFGAFADDALDRNELPHIALERARRM 1swvA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMEL T0330 166 :NY 1swvA 174 :GV T0330 168 :SPSQIVIIGDTEHDIRCARELDARSIAVATG 1swvA 177 :PMNHMIKVGDTVSDMKEGRNAGMWTVGVILG T0330 199 :NFTMEE 1swvA 212 :GLTEEE T0330 205 :LARHKPGTLFKNFAETDEVLASIL 1swvA 237 :FVENGAHFTIETMQELESVMEHIE Number of specific fragments extracted= 16 number of extra gaps= 0 total=1058 Number of alignments=88 # 1swvA read from 1swvA/merged-good-all-a2m # found chain 1swvA in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1swvA)K5 Warning: unaligning (T0330)T229 because last residue in template chain is (1swvA)K261 T0330 3 :RTLVLFDIDGTLLKVE 1swvA 6 :IEAVIFAWAGTTVDYG T0330 19 :SMNRRVLADALIEVYGTEGSTGSHDFSGK 1swvA 23 :FAPLEVFMEIFHKRGVAITAEEARKPMGL T0330 49 :DGAIIYEVLSNVG 1swvA 52 :LKIDHVRALTEMP T0330 62 :LER 1swvA 78 :PTE T0330 69 :DKFDKAKETYIALFRER 1swvA 81 :ADIQEMYEEFEEILFAI T0330 87 :RREDITLLEGVRELLDALSSRS 1swvA 98 :LPRYASPINGVKEVIASLRERG T0330 110 :VLLGLLTGNFEASGRHKLKLP 1swvA 120 :IKIGSTTGYTREMMDIVAKEA T0330 131 :GID 1swvA 144 :GYK T0330 136 :FPFGAFADDALDRNELPHIALERARRM 1swvA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMEL T0330 166 :NY 1swvA 174 :GV T0330 168 :SPSQIVIIGDTEHDIRCARELDARSIAVATG 1swvA 177 :PMNHMIKVGDTVSDMKEGRNAGMWTVGVILG T0330 199 :NFTMEELARHK 1swvA 212 :GLTEEEVENMD T0330 210 :PGTLFKNFAETDEVLASIL 1swvA 242 :AHFTIETMQELESVMEHIE Number of specific fragments extracted= 13 number of extra gaps= 0 total=1071 Number of alignments=89 # 1swvA read from 1swvA/merged-good-all-a2m # found chain 1swvA in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1swvA)K5 Warning: unaligning (T0330)T229 because last residue in template chain is (1swvA)K261 T0330 3 :RTLVLFDIDGTLLK 1swvA 6 :IEAVIFAWAGTTVD T0330 22 :RRVLADALIEVYGTEGSTGSHDFSGKM 1swvA 26 :LEVFMEIFHKRGVAITAEEARKPMGLL T0330 50 :GAIIYEVLSNV 1swvA 53 :KIDHVRALTEM T0330 61 :GLERAEIADKFDKAKETYIALFRERARREDITLLEGVRELLDALSS 1swvA 72 :RVFRQLPTEADIQEMYEEFEEILFAILPRYASPINGVKEVIASLRE T0330 108 :SDVLLGLLTGNFEA 1swvA 118 :RGIKIGSTTGYTRE T0330 122 :SGRHKLKLPGID 1swvA 135 :IVAKEAALQGYK T0330 136 :FPFGAFADDALDRNELPHIALERARR 1swvA 147 :PDFLVTPDDVPAGRPYPWMCYKNAME T0330 165 :ANY 1swvA 173 :LGV T0330 168 :SPSQIVIIGDTEHDIRCARELDARSIAVATG 1swvA 177 :PMNHMIKVGDTVSDMKEGRNAGMWTVGVILG T0330 199 :NFTMEE 1swvA 212 :GLTEEE T0330 205 :LARHKPGTLFKNFAETDEVLASIL 1swvA 237 :FVENGAHFTIETMQELESVMEHIE Number of specific fragments extracted= 11 number of extra gaps= 0 total=1082 Number of alignments=90 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jud/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1jud expands to /projects/compbio/data/pdb/1jud.pdb.gz 1jud:Warning: there is no chain 1jud will retry with 1judA # T0330 read from 1jud/merged-good-all-a2m # 1jud read from 1jud/merged-good-all-a2m # adding 1jud to template set # found chain 1jud in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1jud)Y3 T0330 3 :RTLVLFDIDGTLLKVESMNRRV 1jud 4 :IKGIAFDLYGTLFDVHSVVGRC T0330 25 :LADALIEVY 1jud 40 :WRQKQLEYT T0330 40 :GSHDFSGKMDGAIIYEVLSNVGLERA 1jud 55 :NRYVNFQQATEDALRFTCRHLGLDLD T0330 72 :DKAKETYIALF 1jud 81 :ARTRSTLCDAY T0330 89 :EDITLLEGVRELLDALSSRS 1jud 92 :LRLAPFSEVPDSLRELKRRG T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARRM 1jud 112 :LKLAILSNGSPQSIDAVVSHAGLRDGFDHLLSVDPVQVYKPDNRVYELAEQAL T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAVATGNFT 1jud 165 :GLDRSAILFVSSNAWDATGARYFGFPTCWINRTGNV T0330 207 :RHKPGTLFKNFAETDE 1jud 205 :GQTPDWEVTSLRAVVE Number of specific fragments extracted= 8 number of extra gaps= 0 total=1090 Number of alignments=91 # 1jud read from 1jud/merged-good-all-a2m # found chain 1jud in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1jud)Y3 T0330 3 :RTLVLFDIDGTLLKVESMNR 1jud 4 :IKGIAFDLYGTLFDVHSVVG T0330 23 :RVLADALIEVYGTEGSTGSHDF 1jud 42 :QKQLEYTWLRSLMNRYVNFQQA T0330 49 :DGAIIYEVLSNVGLERAE 1jud 64 :TEDALRFTCRHLGLDLDA T0330 69 :DKFDKAKE 1jud 82 :RTRSTLCD T0330 87 :RREDITLLEGVRELLDALSSRS 1jud 90 :AYLRLAPFSEVPDSLRELKRRG T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARRM 1jud 112 :LKLAILSNGSPQSIDAVVSHAGLRDGFDHLLSVDPVQVYKPDNRVYELAEQAL T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAVATG 1jud 165 :GLDRSAILFVSSNAWDATGARYFGFPTCWINRT T0330 199 :NFT 1jud 205 :GQT T0330 210 :PGTLFKNFAETDE 1jud 208 :PDWEVTSLRAVVE Number of specific fragments extracted= 9 number of extra gaps= 0 total=1099 Number of alignments=92 # 1jud read from 1jud/merged-good-all-a2m # found chain 1jud in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1jud)Y3 T0330 3 :RTLVLFDIDGTLLKVESMNRRVLAD 1jud 4 :IKGIAFDLYGTLFDVHSVVGRCDEA T0330 34 :GTEGSTGSHDFSGKMDGAIIYEVLSNVG 1jud 29 :FPGRGREISALWRQKQLEYTWLRSLMNR T0330 68 :ADKFDKAKETYIALFRERA 1jud 57 :YVNFQQATEDALRFTCRHL T0330 88 :REDITLLEGVRELLDALSS 1jud 91 :YLRLAPFSEVPDSLRELKR T0330 108 :SDVLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARR 1jud 110 :RGLKLAILSNGSPQSIDAVVSHAGLRDGFDHLLSVDPVQVYKPDNRVYELAEQA T0330 165 :ANYSPSQIVIIGDTEHDIRCARELDARSIAVATGNF 1jud 164 :LGLDRSAILFVSSNAWDATGARYFGFPTCWINRTGN T0330 201 :TME 1jud 203 :EMG T0330 208 :HKPGTLFKNFAETDE 1jud 206 :QTPDWEVTSLRAVVE Number of specific fragments extracted= 8 number of extra gaps= 0 total=1107 Number of alignments=93 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vjrA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vjrA expands to /projects/compbio/data/pdb/1vjr.pdb.gz 1vjrA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 172, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 173, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 177, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 178, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 180, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 181, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 183, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 184, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 186, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 187, because occupancy 0.330 <= existing 0.340 in 1vjrA Skipped atom 237, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 241, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 243, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 245, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 247, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 249, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 271, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 275, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 277, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 279, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 281, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 283, because occupancy 0.500 <= existing 0.500 in 1vjrA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1601, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1605, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1607, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1609, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1611, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1613, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1616, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1620, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1622, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1624, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1626, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1628, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1630, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1632, because occupancy 0.500 <= existing 0.500 in 1vjrA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1868, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1872, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1874, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1876, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1878, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1880, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1912, because occupancy 0.350 <= existing 0.650 in 1vjrA Skipped atom 1914, because occupancy 0.350 <= existing 0.650 in 1vjrA Skipped atom 1916, because occupancy 0.350 <= existing 0.650 in 1vjrA Skipped atom 1918, because occupancy 0.350 <= existing 0.650 in 1vjrA Skipped atom 1920, because occupancy 0.350 <= existing 0.650 in 1vjrA Skipped atom 1922, because occupancy 0.350 <= existing 0.650 in 1vjrA Skipped atom 1930, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1934, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1936, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1938, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1940, because occupancy 0.500 <= existing 0.500 in 1vjrA Skipped atom 1942, because occupancy 0.500 <= existing 0.500 in 1vjrA # T0330 read from 1vjrA/merged-good-all-a2m # 1vjrA read from 1vjrA/merged-good-all-a2m # adding 1vjrA to template set # found chain 1vjrA in template set T0330 3 :RTLVLFDIDGTLLK 1vjrA 5 :IELFILDMDGTFYL T0330 17 :VESMNRRVLADA 1vjrA 22 :LLPGSLEFLETL T0330 31 :EVYGT 1vjrA 34 :KEKNK T0330 46 :GKMDGAIIYE 1vjrA 48 :SLGAQDYVRK T0330 57 :LSNVGLERAE 1vjrA 58 :LRNMGVDVPD T0330 89 :EDITLLEGV 1vjrA 68 :DAVVTSGEI T0330 100 :LLDAL 1vjrA 77 :TAEHM T0330 105 :SSRSDVLLGLLTG 1vjrA 83 :KRFGRCRIFLLGT T0330 121 :ASGRHKLKLPGID 1vjrA 96 :PQLKKVFEAYGHV T0330 134 :HYFPFGAFADDAL 1vjrA 112 :ENPDFVVLGFDKT T0330 147 :DRNELPHIALERARRM 1vjrA 181 :AGKPNPLVVDVISEKF T0330 166 :NYSPSQIVIIGDTE 1vjrA 197 :GVPKERMAMVGDRL T0330 180 :HDIRCARELDARSIAVATGNFTMEELARHK 1vjrA 212 :TDVKLGKNAGIVSILVLTGETTPEDLERAE T0330 210 :PGTLFKNFAETDEVL 1vjrA 244 :PDFVFKNLGELAKAV Number of specific fragments extracted= 14 number of extra gaps= 0 total=1121 Number of alignments=94 # 1vjrA read from 1vjrA/merged-good-all-a2m # found chain 1vjrA in template set T0330 3 :RTLVLFDIDGTLLKVESMNRRV 1vjrA 5 :IELFILDMDGTFYLDDSLLPGS T0330 26 :ADALIEVYGTEGSTGSHDFSGKMDGAIIYEVLSNVGLER 1vjrA 27 :LEFLETLKEKNKRFVFFTNNSSLGAQDYVRKLRNMGVDV T0330 87 :RREDITLLEGV 1vjrA 66 :PDDAVVTSGEI T0330 100 :LLDAL 1vjrA 77 :TAEHM T0330 105 :SSRSDVLLGLL 1vjrA 83 :KRFGRCRIFLL T0330 119 :FEASGRHKLKLPGID 1vjrA 94 :GTPQLKKVFEAYGHV T0330 136 :F 1vjrA 109 :I T0330 137 :PFGAFADDALD 1vjrA 115 :DFVVLGFDKTL T0330 148 :RNELPHIALERARRM 1vjrA 182 :GKPNPLVVDVISEKF T0330 166 :NYSPSQIVIIGDTE 1vjrA 197 :GVPKERMAMVGDRL T0330 180 :HDIRCARELDARSIAVATGNFTMEELARHK 1vjrA 212 :TDVKLGKNAGIVSILVLTGETTPEDLERAE T0330 210 :PGTLFKNFAETDEVL 1vjrA 244 :PDFVFKNLGELAKAV Number of specific fragments extracted= 12 number of extra gaps= 0 total=1133 Number of alignments=95 # 1vjrA read from 1vjrA/merged-good-all-a2m # found chain 1vjrA in template set T0330 3 :RTLVLFDIDGTLL 1vjrA 5 :IELFILDMDGTFY T0330 90 :DITLLEGVRELLDALSS 1vjrA 19 :DDSLLPGSLEFLETLKE T0330 108 :SDVLLGLLTGNF 1vjrA 36 :KNKRFVFFTNNS T0330 120 :EASGRHKLKLPGI 1vjrA 51 :AQDYVRKLRNMGV T0330 133 :DHYFP 1vjrA 67 :DDAVV T0330 148 :RNELPHIALERARR 1vjrA 182 :GKPNPLVVDVISEK T0330 165 :ANYSPSQIVIIGDTE 1vjrA 196 :FGVPKERMAMVGDRL T0330 180 :HDIRCARELDARSIAVATGNFTMEELARHK 1vjrA 212 :TDVKLGKNAGIVSILVLTGETTPEDLERAE T0330 210 :PGTLFKNFAETDEVL 1vjrA 244 :PDFVFKNLGELAKAV Number of specific fragments extracted= 9 number of extra gaps= 0 total=1142 Number of alignments=96 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bdeA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2bdeA expands to /projects/compbio/data/pdb/2bde.pdb.gz 2bdeA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0330 read from 2bdeA/merged-good-all-a2m # 2bdeA read from 2bdeA/merged-good-all-a2m # adding 2bdeA to template set # found chain 2bdeA in template set T0330 3 :RTLVLFDIDGTLLK 2bdeA 17 :IKLIGLDMDHTLIR T0330 17 :VESMNRRVLADALIEVYGT 2bdeA 36 :FESLVYDLVKERLAESFHY T0330 36 :EGSTGSHDFSGK 2bdeA 113 :YVDLGDPNYMAI T0330 48 :MDGAIIYEVLSNVG 2bdeA 131 :AFCILYGQLVDLKD T0330 62 :LERAEIADKFDKAKETYIAL 2bdeA 151 :PSYQAIAQDVQYCVDKVHSD T0330 82 :FRERAR 2bdeA 173 :LKNIII T0330 88 :REDITLLEGVRELLDALSSRS 2bdeA 182 :KKYVIREKEVVEGLKHFIRYG T0330 110 :VLLGLLTGNFEASGRHKLKLP 2bdeA 203 :KKIFILTNSEYSYSKLLLDYA T0330 131 :GIDHYFPFGAFADDAL 2bdeA 233 :HWQGLFEFVITLANKP T0330 155 :ALERARRM 2bdeA 284 :AKKFTEDL T0330 166 :NYSPSQIVIIGDTE 2bdeA 292 :GVGGDEILYIGDHI T0330 180 :HDIRCARELDARSIAVATG 2bdeA 308 :DILRLKKDCNWRTALVVEE T0330 202 :MEELARH 2bdeA 327 :LGEEIAS Number of specific fragments extracted= 13 number of extra gaps= 0 total=1155 Number of alignments=97 # 2bdeA read from 2bdeA/merged-good-all-a2m # found chain 2bdeA in template set T0330 3 :RTLVLFDIDGTLLKVESMNRRVL 2bdeA 17 :IKLIGLDMDHTLIRYNSKNFESL T0330 49 :DGAIIYEVLSNVG 2bdeA 40 :VYDLVKERLAESF T0330 62 :LERAEIADKFDKAKETY 2bdeA 151 :PSYQAIAQDVQYCVDKV T0330 81 :LFRERA 2bdeA 172 :TLKNII T0330 87 :RREDITLLEGVRELLDALSSRS 2bdeA 181 :LKKYVIREKEVVEGLKHFIRYG T0330 110 :VLLGLLTGNFEASGRHKLKLP 2bdeA 203 :KKIFILTNSEYSYSKLLLDYA T0330 131 :GIDHYFPFGAFADDALD 2bdeA 233 :HWQGLFEFVITLANKPR T0330 155 :ALERARRM 2bdeA 284 :AKKFTEDL T0330 166 :NYSPSQIVIIGDTE 2bdeA 292 :GVGGDEILYIGDHI T0330 180 :HDIRCARELDARSIAVATG 2bdeA 308 :DILRLKKDCNWRTALVVEE T0330 217 :FAETDEVLAS 2bdeA 327 :LGEEIASQIR Number of specific fragments extracted= 11 number of extra gaps= 0 total=1166 Number of alignments=98 # 2bdeA read from 2bdeA/merged-good-all-a2m # found chain 2bdeA in template set T0330 2 :SRTLVLFDIDGTLL 2bdeA 16 :KIKLIGLDMDHTLI T0330 16 :KVESMNRRVLADALIEV 2bdeA 35 :NFESLVYDLVKERLAES T0330 33 :YGTEGSTGSHDFS 2bdeA 96 :GTKQISFSDQKKI T0330 46 :GKMDGAIIYEVLSNVGLERAEI 2bdeA 132 :FCILYGQLVDLKDTNPDKMPSY T0330 69 :DKFDKAKETYIALFRERA 2bdeA 154 :QAIAQDVQYCVDKVHSDG T0330 87 :RREDITLLEGVRELLDALSS 2bdeA 181 :LKKYVIREKEVVEGLKHFIR T0330 108 :SDVLLGLLTGNFEASGRHKLKLP 2bdeA 201 :YGKKIFILTNSEYSYSKLLLDYA T0330 131 :GIDHYFPFGAFADD 2bdeA 233 :HWQGLFEFVITLAN T0330 151 :L 2bdeA 283 :N T0330 155 :ALERARR 2bdeA 284 :AKKFTED T0330 165 :ANYSPSQIVIIGDTE 2bdeA 291 :LGVGGDEILYIGDHI T0330 181 :D 2bdeA 307 :G T0330 182 :IRCARELDARSIAVATG 2bdeA 310 :LRLKKDCNWRTALVVEE Number of specific fragments extracted= 13 number of extra gaps= 0 total=1179 Number of alignments=99 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zrn/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zrn expands to /projects/compbio/data/pdb/1zrn.pdb.gz 1zrn:Warning: there is no chain 1zrn will retry with 1zrnA # T0330 read from 1zrn/merged-good-all-a2m # 1zrn read from 1zrn/merged-good-all-a2m # adding 1zrn to template set # found chain 1zrn in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1zrn)Y3 T0330 3 :RTLVLFDIDGTLLKVESMNRRV 1zrn 4 :IKGIAFDLYGTLFDVHSVVGRC T0330 25 :LADALIEVY 1zrn 40 :WRQKQLEYT T0330 34 :GT 1zrn 55 :NR T0330 42 :HDFSGKMDGAIIYEVLSNVGLERA 1zrn 57 :YVNFQQATEDALRFTCRHLGLDLD T0330 72 :DKAKETYIALF 1zrn 81 :ARTRSTLCDAY T0330 89 :EDITLLEGVRELLDALSSRS 1zrn 92 :LRLAPFSEVPDSLRELKRRG T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARRM 1zrn 112 :LKLAILSNGSPQSIDAVVSHAGLRDGFDHLLSVDPVQVYKPDNRVYELAEQAL T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAVATGNFT 1zrn 165 :GLDRSAILFVASNAWDATGARYFGFPTCWINRTGNV T0330 207 :RHKPGTLFKNFAETDE 1zrn 205 :GQTPDWEVTSLRAVVE Number of specific fragments extracted= 9 number of extra gaps= 0 total=1188 Number of alignments=100 # 1zrn read from 1zrn/merged-good-all-a2m # found chain 1zrn in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1zrn)Y3 T0330 3 :RTLVLFDIDGTLLKVESMNR 1zrn 4 :IKGIAFDLYGTLFDVHSVVG T0330 23 :RVLADALIEVYGTEGSTGSHDF 1zrn 42 :QKQLEYTWLRSLMNRYVNFQQA T0330 49 :DGAIIYEVLSNVGLERAE 1zrn 64 :TEDALRFTCRHLGLDLDA T0330 69 :DKFDKAKE 1zrn 82 :RTRSTLCD T0330 87 :RREDITLLEGVRELLDALSSRS 1zrn 90 :AYLRLAPFSEVPDSLRELKRRG T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARRM 1zrn 112 :LKLAILSNGSPQSIDAVVSHAGLRDGFDHLLSVDPVQVYKPDNRVYELAEQAL T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAVATG 1zrn 165 :GLDRSAILFVASNAWDATGARYFGFPTCWINRT T0330 199 :NFT 1zrn 205 :GQT T0330 210 :PGTLFKNFAETDE 1zrn 208 :PDWEVTSLRAVVE Number of specific fragments extracted= 9 number of extra gaps= 0 total=1197 Number of alignments=101 # 1zrn read from 1zrn/merged-good-all-a2m # found chain 1zrn in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1zrn)Y3 T0330 3 :RTLVLFDIDGTLLKVESMNRRVLAD 1zrn 4 :IKGIAFDLYGTLFDVHSVVGRCDEA T0330 34 :GTEGSTGSHDFSGKMDGAIIYEVLSNVG 1zrn 29 :FPGRGREISALWRQKQLEYTWLRSLMNR T0330 68 :ADKFDKAKETYIALFRERA 1zrn 57 :YVNFQQATEDALRFTCRHL T0330 87 :R 1zrn 88 :C T0330 89 :EDITLLEGVRELLDALSS 1zrn 92 :LRLAPFSEVPDSLRELKR T0330 108 :SDVLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARR 1zrn 110 :RGLKLAILSNGSPQSIDAVVSHAGLRDGFDHLLSVDPVQVYKPDNRVYELAEQA T0330 165 :ANYSPSQIVIIGDTEHDIRCARELDARSIAVATGNF 1zrn 164 :LGLDRSAILFVASNAWDATGARYFGFPTCWINRTGN T0330 201 :TME 1zrn 203 :EMG T0330 208 :HKPGTLFKNFAETDE 1zrn 206 :QTPDWEVTSLRAVVE Number of specific fragments extracted= 9 number of extra gaps= 0 total=1206 Number of alignments=102 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1k1eA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0330 read from 1k1eA/merged-good-all-a2m # 1k1eA read from 1k1eA/merged-good-all-a2m # found chain 1k1eA in training set T0330 3 :RTLVLFDIDGTLLK 1k1eA 8 :IKFVITDVDGVLTD T0330 39 :TGS 1k1eA 28 :ANG T0330 89 :EDITLLEGVRELLDALSSRS 1k1eA 32 :AIKSFHVRDGLGIKMLMDAD T0330 110 :VLLGLLTGNFEASGRHKLKLPGI 1k1eA 52 :IQVAVLSGRDSPILRRRIADLGI T0330 137 :PFGAFADD 1k1eA 75 :KLFFLGKL T0330 148 :RN 1k1eA 83 :EK T0330 152 :PHIALERARRM 1k1eA 85 :ETACFDLMKQA T0330 166 :NYSPSQIVIIGDTEHDIRCARELD 1k1eA 96 :GVTAEQTAYIGDDSVDLPAFAACG T0330 191 :RSIAV 1k1eA 120 :TSFAV T0330 198 :GNFTME 1k1eA 125 :ADAPIY T0330 205 :LARH 1k1eA 131 :VKNA T0330 210 :PGTLFKN 1k1eA 135 :VDHVLST T0330 217 :FAETDEVL 1k1eA 148 :FREMSDMI Number of specific fragments extracted= 13 number of extra gaps= 0 total=1219 Number of alignments=103 # 1k1eA read from 1k1eA/merged-good-all-a2m # found chain 1k1eA in training set T0330 3 :RTLVLFDIDGTLLKVES 1k1eA 8 :IKFVITDVDGVLTDGQL T0330 41 :SHDFS 1k1eA 25 :HYDAN T0330 87 :RREDITLLEGVRELLDALSSRS 1k1eA 30 :GEAIKSFHVRDGLGIKMLMDAD T0330 110 :VLLGLLTGNFEASGRHKLKLPGID 1k1eA 52 :IQVAVLSGRDSPILRRRIADLGIK T0330 138 :FGAFA 1k1eA 76 :LFFLG T0330 144 :DA 1k1eA 81 :KL T0330 148 :RN 1k1eA 83 :EK T0330 152 :PHIALERARRM 1k1eA 85 :ETACFDLMKQA T0330 166 :NYSPSQIVIIGDTEHDIRCARE 1k1eA 96 :GVTAEQTAYIGDDSVDLPAFAA T0330 190 :ARSIAVATG 1k1eA 118 :CGTSFAVAD T0330 200 :FTME 1k1eA 127 :APIY T0330 205 :LARH 1k1eA 131 :VKNA T0330 210 :PGTLFKN 1k1eA 135 :VDHVLST T0330 217 :FAETDEVLASILT 1k1eA 148 :FREMSDMILQAQG Number of specific fragments extracted= 14 number of extra gaps= 0 total=1233 Number of alignments=104 # 1k1eA read from 1k1eA/merged-good-all-a2m # found chain 1k1eA in training set T0330 3 :RTLVLFDIDGTLLKV 1k1eA 8 :IKFVITDVDGVLTDG T0330 95 :EGVRELLDALSS 1k1eA 38 :VRDGLGIKMLMD T0330 108 :SDVLLGLLTGNFEASGRHKLKLPGI 1k1eA 50 :ADIQVAVLSGRDSPILRRRIADLGI T0330 137 :PFGAFA 1k1eA 75 :KLFFLG T0330 148 :RNELPHIALERARR 1k1eA 81 :KLEKETACFDLMKQ T0330 165 :ANYSPSQIVIIGDTEHDIRCARE 1k1eA 95 :AGVTAEQTAYIGDDSVDLPAFAA T0330 190 :ARSIAV 1k1eA 118 :CGTSFA T0330 197 :TGNFTME 1k1eA 124 :VADAPIY T0330 205 :LARH 1k1eA 131 :VKNA T0330 210 :PGTLFKN 1k1eA 135 :VDHVLST Number of specific fragments extracted= 10 number of extra gaps= 0 total=1243 Number of alignments=105 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1u7pA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1u7pA expands to /projects/compbio/data/pdb/1u7p.pdb.gz 1u7pA:# T0330 read from 1u7pA/merged-good-all-a2m # 1u7pA read from 1u7pA/merged-good-all-a2m # adding 1u7pA to template set # found chain 1u7pA in template set T0330 1 :M 1u7pA 1 :M T0330 2 :SRTLVLFDIDGTLLKV 1u7pA 4 :LPKLAVFDLDYTLWPF T0330 36 :EGSTGS 1u7pA 20 :WVDTHV T0330 42 :HDFSGKMDG 1u7pA 27 :PPFHKSSDG T0330 72 :D 1u7pA 40 :R T0330 87 :RREDITLLEGVRELLDALSSRS 1u7pA 41 :RGQNIQLYPEVPEVLGRLQSLG T0330 110 :VLLGLLTG 1u7pA 63 :VPVAAASR T0330 118 :NFEASGRHKLKLPGIDHYFPFGAFADDAL 1u7pA 72 :SEIQGANQLLELFDLGKYFIQREIYPGSK T0330 152 :PHIALERARRM 1u7pA 101 :VTHFERLHHKT T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAV 1u7pA 112 :GVPFSQMVFFDDENRNIIDVGRLGVTCIHI T0330 197 :TGNFTMEELAR 1u7pA 142 :RDGMSLQTLTQ T0330 220 :TDEVLASILTP 1u7pA 153 :GLETFAKAQAG Number of specific fragments extracted= 12 number of extra gaps= 0 total=1255 Number of alignments=106 # 1u7pA read from 1u7pA/merged-good-all-a2m # found chain 1u7pA in template set T0330 3 :RTLVLFDIDGTLLKVES 1u7pA 5 :PKLAVFDLDYTLWPFWV T0330 34 :GTEGSTGSHDFSGKM 1u7pA 22 :DTHVDPPFHKSSDGT T0330 87 :RREDITLLEGVRELLDALSSRS 1u7pA 41 :RGQNIQLYPEVPEVLGRLQSLG T0330 110 :VLLGLLTG 1u7pA 63 :VPVAAASR T0330 118 :NFEASGRHKLKLPGIDHYFPFGAFADDA 1u7pA 72 :SEIQGANQLLELFDLGKYFIQREIYPGS T0330 149 :N 1u7pA 100 :K T0330 152 :PHIALERARRM 1u7pA 101 :VTHFERLHHKT T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAVATG 1u7pA 112 :GVPFSQMVFFDDENRNIIDVGRLGVTCIHIRDG T0330 200 :FTMEELAR 1u7pA 145 :MSLQTLTQ T0330 220 :TDEVLASILT 1u7pA 153 :GLETFAKAQA Number of specific fragments extracted= 10 number of extra gaps= 0 total=1265 Number of alignments=107 # 1u7pA read from 1u7pA/merged-good-all-a2m # found chain 1u7pA in template set T0330 2 :SRTLVLFDIDGTLLKV 1u7pA 4 :LPKLAVFDLDYTLWPF T0330 66 :EIADKFD 1u7pA 20 :WVDTHVD T0330 86 :ARREDITLLEGVRELLDALSS 1u7pA 40 :RRGQNIQLYPEVPEVLGRLQS T0330 108 :SDVLLGLLTG 1u7pA 61 :LGVPVAAASR T0330 118 :NFEASGRHKLKLPGIDHYFPFGAFA 1u7pA 72 :SEIQGANQLLELFDLGKYFIQREIY T0330 148 :RNELPHIALERARR 1u7pA 97 :PGSKVTHFERLHHK T0330 165 :ANYSPSQIVIIGDTEHDIRCARELDARSIA 1u7pA 111 :TGVPFSQMVFFDDENRNIIDVGRLGVTCIH T0330 196 :ATGNFTMEELAR 1u7pA 141 :IRDGMSLQTLTQ T0330 220 :TDEVLASILTP 1u7pA 153 :GLETFAKAQAG Number of specific fragments extracted= 9 number of extra gaps= 0 total=1274 Number of alignments=108 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rkuA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0330 read from 1rkuA/merged-good-all-a2m # 1rkuA read from 1rkuA/merged-good-all-a2m # found chain 1rkuA in training set Warning: unaligning (T0330)S2 because first residue in template chain is (1rkuA)D0 Warning: unaligning (T0330)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rkuA)D7 Warning: unaligning (T0330)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rkuA)D7 T0330 3 :RTLVL 1rkuA 1 :MEIAC T0330 10 :IDGTLLK 1rkuA 8 :LEGVLVP T0330 24 :VLADAL 1rkuA 16 :IWIAFA T0330 31 :EVYGTE 1rkuA 22 :EKTGID T0330 39 :TGSHDFSGK 1rkuA 28 :ALKATTRDI T0330 48 :MDGAIIYE 1rkuA 38 :DYDVLMKQ T0330 56 :VLSNVGLERAE 1rkuA 49 :ILDEHGLKLGD T0330 82 :FRERA 1rkuA 60 :IQEVI T0330 89 :EDITLLEGVRELLDALSSR 1rkuA 65 :ATLKPLEGAVEFVDWLRER T0330 110 :VLLGLLTGNFEASGRHKLKLPGI 1rkuA 84 :FQVVILSDTFYEFSQPLMRQLGF T0330 136 :FPFGAF 1rkuA 107 :PTLLCH T0330 142 :ADDA 1rkuA 116 :IDDS T0330 147 :DRNELPHIALERARRM 1rkuA 128 :RQKDPKRQSVIAFKSL T0330 166 :NY 1rkuA 144 :YY T0330 171 :QIVIIGDTEHDIRCARELD 1rkuA 146 :RVIAAGDSYNDTTMLSEAH T0330 191 :RSIAV 1rkuA 165 :AGILF T0330 199 :NFTMEELARHKPGTLFKNFAETDEVLASILTPKHS 1rkuA 170 :HAPENVIREFPQFPAVHTYEDLKREFLKASSRSLS Number of specific fragments extracted= 17 number of extra gaps= 1 total=1291 Number of alignments=109 # 1rkuA read from 1rkuA/merged-good-all-a2m # found chain 1rkuA in training set Warning: unaligning (T0330)S2 because first residue in template chain is (1rkuA)D0 Warning: unaligning (T0330)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rkuA)D7 Warning: unaligning (T0330)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rkuA)D7 T0330 3 :RTLVL 1rkuA 1 :MEIAC T0330 10 :IDGTLLKV 1rkuA 8 :LEGVLVPE T0330 24 :VLADALIEVYGT 1rkuA 16 :IWIAFAEKTGID T0330 39 :TGSHDFSGKM 1rkuA 28 :ALKATTRDIP T0330 49 :DGAIIYEVLSNVGLERAE 1rkuA 42 :LMKQRLRILDEHGLKLGD T0330 82 :FRE 1rkuA 60 :IQE T0330 87 :RREDITLLEGVRELLDALSSR 1rkuA 63 :VIATLKPLEGAVEFVDWLRER T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADDALD 1rkuA 84 :FQVVILSDTFYEFSQPLMRQLGFPTLLCHKLEIDDSDR T0330 148 :RN 1rkuA 129 :QK T0330 153 :HIALERARRMTGANY 1rkuA 131 :DPKRQSVIAFKSLYY T0330 171 :QIVIIGDTEHDIRCARELD 1rkuA 146 :RVIAAGDSYNDTTMLSEAH T0330 191 :RSIAV 1rkuA 165 :AGILF T0330 199 :NFTMEELARHKPGTLFKNFAETDEVLASILTPKHS 1rkuA 170 :HAPENVIREFPQFPAVHTYEDLKREFLKASSRSLS Number of specific fragments extracted= 13 number of extra gaps= 1 total=1304 Number of alignments=110 # 1rkuA read from 1rkuA/merged-good-all-a2m # found chain 1rkuA in training set Warning: unaligning (T0330)S2 because first residue in template chain is (1rkuA)D0 Warning: unaligning (T0330)F8 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1rkuA)D7 Warning: unaligning (T0330)D9 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1rkuA)D7 T0330 3 :RTLVL 1rkuA 1 :MEIAC T0330 10 :IDGTLLKV 1rkuA 8 :LEGVLVPE T0330 24 :VLADALIEVYGTEGS 1rkuA 16 :IWIAFAEKTGIDALK T0330 63 :ERAEIADKFDKAKETYIALFRE 1rkuA 31 :ATTRDIPDYDVLMKQRLRILDE T0330 85 :RARREDITLLEGVRELLDALSS 1rkuA 61 :QEVIATLKPLEGAVEFVDWLRE T0330 109 :DVLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADD 1rkuA 83 :RFQVVILSDTFYEFSQPLMRQLGFPTLLCHKLEIDD T0330 146 :LDRNELPHIALERARR 1rkuA 127 :LRQKDPKRQSVIAFKS T0330 165 :ANY 1rkuA 143 :LYY T0330 171 :QIVIIGDTEHDIRCARELD 1rkuA 146 :RVIAAGDSYNDTTMLSEAH T0330 191 :RSIAV 1rkuA 165 :AGILF T0330 199 :NFTMEELARHKPGTLFKNFAETDEVLASILTPKHS 1rkuA 170 :HAPENVIREFPQFPAVHTYEDLKREFLKASSRSLS Number of specific fragments extracted= 11 number of extra gaps= 1 total=1315 Number of alignments=111 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1te2A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0330 read from 1te2A/merged-good-all-a2m # 1te2A read from 1te2A/merged-good-all-a2m # found chain 1te2A in training set Warning: unaligning (T0330)L129 because of BadResidue code BAD_PEPTIDE in next template residue (1te2A)F129 Warning: unaligning (T0330)P130 because of BadResidue code BAD_PEPTIDE at template residue (1te2A)F129 T0330 2 :SRTLVLFDIDGTLLKVESMNRRVLADAL 1te2A 6 :QILAAIFDMDGLLIDSEPLWDRAELDVM T0330 31 :EVYGTEGSTGS 1te2A 34 :ASLGVDISRRN T0330 42 :HDFSGKMDGAIIYEVLSNVGLERAEI 1te2A 47 :PDTLGLRIDMVVDLWYARQPWNGPSR T0330 72 :DKAKETYIALFRERAR 1te2A 73 :QEVVERVIARAISLVE T0330 89 :EDITLLEGVRELLDALSSRS 1te2A 89 :ETRPLLPGVREAVALCKEQG T0330 110 :VLLGLLTGNFEASGRHKLK 1te2A 109 :LLVGLASASPLHMLEKVLT T0330 131 :GIDHYFPFGAFADDALDRNELPHIALERARRM 1te2A 130 :DLRDSFDALASAEKLPYSKPHPQVYLDCAAKL T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAVATGNF 1te2A 162 :GVDPLTCVALEDSVNGMIASKAARMRSIVVPAPEA T0330 201 :TMEELAR 1te2A 198 :NDPRFVL T0330 210 :PGTLFKNFAET 1te2A 205 :ANVKLSSLTEL T0330 221 :DEVLA 1te2A 217 :AKDLL Number of specific fragments extracted= 11 number of extra gaps= 1 total=1326 Number of alignments=112 # 1te2A read from 1te2A/merged-good-all-a2m # found chain 1te2A in training set Warning: unaligning (T0330)L129 because of BadResidue code BAD_PEPTIDE in next template residue (1te2A)F129 Warning: unaligning (T0330)P130 because of BadResidue code BAD_PEPTIDE at template residue (1te2A)F129 T0330 2 :SRTLVLFDIDGTLLKVESMNRRVLADALIEVYGTEGSTGSHDFSGKMDGAIIYEVLSNVG 1te2A 6 :QILAAIFDMDGLLIDSEPLWDRAELDVMASLGVDISRRNELPDTLGLRIDMVVDLWYARQ T0330 62 :LERA 1te2A 70 :PSRQ T0330 69 :DKFDKAKETYIALFRER 1te2A 74 :EVVERVIARAISLVEET T0330 91 :ITLLEGVRELLDALSSRS 1te2A 91 :RPLLPGVREAVALCKEQG T0330 110 :VLLGLLTGNFEASGRHKLK 1te2A 109 :LLVGLASASPLHMLEKVLT T0330 131 :GIDHYFPFGAFADDALDRNELPHIALERARRM 1te2A 130 :DLRDSFDALASAEKLPYSKPHPQVYLDCAAKL T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAVATG 1te2A 162 :GVDPLTCVALEDSVNGMIASKAARMRSIVVPAP T0330 210 :PGTLFKNFAET 1te2A 205 :ANVKLSSLTEL T0330 221 :DEVLA 1te2A 217 :AKDLL Number of specific fragments extracted= 9 number of extra gaps= 1 total=1335 Number of alignments=113 # 1te2A read from 1te2A/merged-good-all-a2m # found chain 1te2A in training set Warning: unaligning (T0330)L129 because of BadResidue code BAD_PEPTIDE in next template residue (1te2A)F129 Warning: unaligning (T0330)P130 because of BadResidue code BAD_PEPTIDE at template residue (1te2A)F129 T0330 2 :SRTLVLFDIDGTLLKVESMNRRVLADALIEVYGTEGSTGSHDFSGKMDGAIIYEVLSNVGLER 1te2A 6 :QILAAIFDMDGLLIDSEPLWDRAELDVMASLGVDISRRNELPDTLGLRIDMVVDLWYARQPWN T0330 68 :ADKFDKAKETYIALFRERARRED 1te2A 69 :GPSRQEVVERVIARAISLVEETR T0330 92 :TLLEGVRELLDALSS 1te2A 92 :PLLPGVREAVALCKE T0330 108 :SDVLLGLLTGNFEASGRHKLK 1te2A 107 :QGLLVGLASASPLHMLEKVLT T0330 131 :GIDHYFPFGAFADDALDRNELPHIALERARR 1te2A 130 :DLRDSFDALASAEKLPYSKPHPQVYLDCAAK T0330 165 :ANYSPSQIVIIGDTEHDIRCARELDARSIAVATGNF 1te2A 161 :LGVDPLTCVALEDSVNGMIASKAARMRSIVVPAPEA T0330 201 :TMEELA 1te2A 198 :NDPRFV T0330 209 :KPGTLFKNFAET 1te2A 204 :LANVKLSSLTEL Number of specific fragments extracted= 8 number of extra gaps= 1 total=1343 Number of alignments=114 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fezA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1fezA expands to /projects/compbio/data/pdb/1fez.pdb.gz 1fezA:# T0330 read from 1fezA/merged-good-all-a2m # 1fezA read from 1fezA/merged-good-all-a2m # adding 1fezA to template set # found chain 1fezA in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1fezA)K5 T0330 3 :RTLVLFDIDGTLLK 1fezA 6 :IEAVIFDWAGTTVD T0330 19 :SMNRRVLADAL 1fezA 23 :FAPLEVFMEIF T0330 31 :EVYGTEGSTGS 1fezA 34 :HKRGVAITAEE T0330 42 :HDFSGKMDGAIIYE 1fezA 46 :RKPMGLLKIDHVRA T0330 56 :VLSNVG 1fezA 70 :WNRVFR T0330 71 :FDKAKETYIALFRERAR 1fezA 83 :IQEMYEEFEEILFAILP T0330 89 :EDITLLEGVRELLDALSSRS 1fezA 100 :RYASPINAVKEVIASLRERG T0330 110 :VLLGLLTGNFEASGR 1fezA 120 :IKIGSTTGYTREMMD T0330 125 :HKLKLPGID 1fezA 138 :KEAALQGYK T0330 136 :FPFGAFADDALDRNELPHIALERARRM 1fezA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMEL T0330 166 :NY 1fezA 174 :GV T0330 168 :SPSQIVIIGDTEHDIRCARELDARSIAVAT 1fezA 177 :PMNHMIKVGDTVSDMKEGRNAGMWTVGVIL T0330 198 :GNFTMEE 1fezA 219 :ENMDSVE T0330 205 :LARHKPGTLFKNFAETDEVLASI 1fezA 237 :FVENGAHFTIETMQELESVMEHI Number of specific fragments extracted= 14 number of extra gaps= 0 total=1357 Number of alignments=115 # 1fezA read from 1fezA/merged-good-all-a2m # found chain 1fezA in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1fezA)K5 T0330 3 :RTLVLFDIDGTLLKVE 1fezA 6 :IEAVIFDWAGTTVDYG T0330 19 :SMNRRVLADALIEVYGTEGSTGSHDFSGKM 1fezA 23 :FAPLEVFMEIFHKRGVAITAEEARKPMGLL T0330 49 :DGAIIYEVLSNVG 1fezA 62 :EMPRIASEWNRVF T0330 62 :LER 1fezA 78 :PTE T0330 69 :DKFDKAKETYIALFRER 1fezA 81 :ADIQEMYEEFEEILFAI T0330 87 :RREDITLLEGVRELLDALSSRS 1fezA 98 :LPRYASPINAVKEVIASLRERG T0330 110 :VLLGLLTGNFEASGRHKLKLP 1fezA 120 :IKIGSTTGYTREMMDIVAKEA T0330 131 :GID 1fezA 144 :GYK T0330 136 :FPFGAFADDALDRNELPHIALERARRM 1fezA 147 :PDFLVTPDDVPAGRPYPWMCYKNAMEL T0330 166 :NY 1fezA 174 :GV T0330 168 :SPSQIVIIGDTEHDIRCARELDARSIAVATG 1fezA 177 :PMNHMIKVGDTVSDMKEGRNAGMWTVGVILG T0330 199 :NFTMEE 1fezA 220 :NMDSVE T0330 205 :LARHKPGTLFKNFAETDEVLASI 1fezA 237 :FVENGAHFTIETMQELESVMEHI Number of specific fragments extracted= 13 number of extra gaps= 0 total=1370 Number of alignments=116 # 1fezA read from 1fezA/merged-good-all-a2m # found chain 1fezA in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1fezA)K5 T0330 3 :RTLVLFDIDGTLLK 1fezA 6 :IEAVIFDWAGTTVD T0330 20 :MNRRVLADALIEVYGTEGSTGSHDFSGKMDGAI 1fezA 24 :APLEVFMEIFHKRGVAITAEEARKPMGLLKIDH T0330 53 :IYEVLSNVG 1fezA 66 :IASEWNRVF T0330 64 :RAEIADKFDKAKETYIALFRERARREDITLLEGVRELLDALSS 1fezA 75 :RQLPTEADIQEMYEEFEEILFAILPRYASPINAVKEVIASLRE T0330 108 :SDVLLGLLTGNFEA 1fezA 118 :RGIKIGSTTGYTRE T0330 122 :SGRHKLKLPGID 1fezA 135 :IVAKEAALQGYK T0330 136 :FPFGAFADDALDRNELPHIALERARR 1fezA 147 :PDFLVTPDDVPAGRPYPWMCYKNAME T0330 165 :ANY 1fezA 173 :LGV T0330 168 :SPSQIVIIGDTEHDIRCARELDARSIAVATGNF 1fezA 177 :PMNHMIKVGDTVSDMKEGRNAGMWTVGVILGSS T0330 202 :MEELARHKPGTLFKNFAETDEVLASI 1fezA 234 :RNRFVENGAHFTIETMQELESVMEHI Number of specific fragments extracted= 10 number of extra gaps= 0 total=1380 Number of alignments=117 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cr6B/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1cr6B expands to /projects/compbio/data/pdb/1cr6.pdb.gz 1cr6B:# T0330 read from 1cr6B/merged-good-all-a2m # 1cr6B read from 1cr6B/merged-good-all-a2m # adding 1cr6B to template set # found chain 1cr6B in template set Warning: unaligning (T0330)T4 because first residue in template chain is (1cr6B)R4 T0330 5 :LVLFDIDGTLLK 1cr6B 5 :VAAFDLDGVLAL T0330 19 :SMNRRVLADAL 1cr6B 17 :PSIAGAFRRSE T0330 31 :EVY 1cr6B 28 :EAL T0330 36 :EGSTGS 1cr6B 31 :ALPRDF T0330 42 :HDFSGKMD 1cr6B 38 :LGAYQTEF T0330 50 :GAIIYEVL 1cr6B 47 :EGPTEQLM T0330 59 :NVGLERAEIA 1cr6B 55 :KGKITFSQWV T0330 72 :DKAKETYIA 1cr6B 65 :PLMDESYRK T0330 81 :LFRERA 1cr6B 91 :IFSQAM T0330 89 :EDITLLEGVRELLDALSSRS 1cr6B 97 :AARSINRPMLQAAIALKKKG T0330 110 :VLLGLLTGN 1cr6B 117 :FTTCIVTNN T0330 119 :FEASGRHKLKLPG 1cr6B 132 :KRDSLAQMMCELS T0330 134 :HYFPFGAFADDALDRNELPHIALERARRM 1cr6B 145 :QHFDFLIESCQVGMIKPEPQIYNFLLDTL T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAVATG 1cr6B 174 :KAKPNEVVFLDDFGSNLKPARDMGMVTILVHNT T0330 200 :F 1cr6B 207 :A Number of specific fragments extracted= 15 number of extra gaps= 0 total=1395 Number of alignments=118 # 1cr6B read from 1cr6B/merged-good-all-a2m # found chain 1cr6B in template set Warning: unaligning (T0330)T4 because first residue in template chain is (1cr6B)R4 T0330 5 :LVLFDIDGTLLKVES 1cr6B 5 :VAAFDLDGVLALPSI T0330 26 :ADALIEVYGTEG 1cr6B 20 :AGAFRRSEEALA T0330 38 :STGSHDFSGKMDGAIIYEVLSNVGLERAEIADKFDKAKETY 1cr6B 34 :RDFLLGAYQTEFPEGPTEQLMKGKITFSQWVPLMDESYRKS T0330 79 :IALFRE 1cr6B 89 :SQIFSQ T0330 87 :RREDITLLEGVRELLDALSSRS 1cr6B 95 :AMAARSINRPMLQAAIALKKKG T0330 110 :VLLGLLTGNF 1cr6B 117 :FTTCIVTNNW T0330 120 :EASGRHKLKLPGID 1cr6B 133 :RDSLAQMMCELSQH T0330 136 :FPFGAFADDALDRNELPHIALERARRM 1cr6B 147 :FDFLIESCQVGMIKPEPQIYNFLLDTL T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAVATG 1cr6B 174 :KAKPNEVVFLDDFGSNLKPARDMGMVTILVHNT Number of specific fragments extracted= 9 number of extra gaps= 0 total=1404 Number of alignments=119 # 1cr6B read from 1cr6B/merged-good-all-a2m # found chain 1cr6B in template set Warning: unaligning (T0330)T4 because first residue in template chain is (1cr6B)R4 T0330 5 :LVLFDIDGTLL 1cr6B 5 :VAAFDLDGVLA T0330 16 :KVESMNRRV 1cr6B 18 :SIAGAFRRS T0330 33 :YGTEGSTGSHDFS 1cr6B 42 :QTEFPEGPTEQLM T0330 46 :GKMDGAIIY 1cr6B 56 :GKITFSQWV T0330 55 :EVLSNV 1cr6B 69 :ESYRKS T0330 63 :ERAEIADK 1cr6B 78 :CGANLPEN T0330 71 :FDKAKETYI 1cr6B 88 :ISQIFSQAM T0330 89 :EDITLLEGVRELLDALSS 1cr6B 97 :AARSINRPMLQAAIALKK T0330 108 :SDVLLGLLTGNF 1cr6B 115 :KGFTTCIVTNNW T0330 120 :EASGRHKLKLPG 1cr6B 133 :RDSLAQMMCELS T0330 134 :HYFPFGAFADDALDRNELPHIALERARR 1cr6B 145 :QHFDFLIESCQVGMIKPEPQIYNFLLDT T0330 165 :ANYSPSQIVIIGDTEHDIRCARELDARSI 1cr6B 173 :LKAKPNEVVFLDDFGSNLKPARDMGMVTI Number of specific fragments extracted= 12 number of extra gaps= 0 total=1416 Number of alignments=120 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2feaA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2feaA expands to /projects/compbio/data/pdb/2fea.pdb.gz 2feaA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 517, because occupancy 0.500 <= existing 0.500 in 2feaA Skipped atom 521, because occupancy 0.500 <= existing 0.500 in 2feaA Skipped atom 523, because occupancy 0.500 <= existing 0.500 in 2feaA Skipped atom 552, because occupancy 0.500 <= existing 0.500 in 2feaA Skipped atom 556, because occupancy 0.500 <= existing 0.500 in 2feaA Skipped atom 558, because occupancy 0.500 <= existing 0.500 in 2feaA Skipped atom 560, because occupancy 0.500 <= existing 0.500 in 2feaA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1319, because occupancy 0.500 <= existing 0.500 in 2feaA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1323, because occupancy 0.500 <= existing 0.500 in 2feaA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1325, because occupancy 0.500 <= existing 0.500 in 2feaA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1329, because occupancy 0.500 <= existing 0.500 in 2feaA Skipped atom 1566, because occupancy 0.300 <= existing 0.700 in 2feaA Skipped atom 1570, because occupancy 0.300 <= existing 0.700 in 2feaA Skipped atom 1572, because occupancy 0.300 <= existing 0.700 in 2feaA Skipped atom 1574, because occupancy 0.300 <= existing 0.700 in 2feaA Skipped atom 1576, because occupancy 0.300 <= existing 0.700 in 2feaA # T0330 read from 2feaA/merged-good-all-a2m # 2feaA read from 2feaA/merged-good-all-a2m # adding 2feaA to template set # found chain 2feaA in template set Warning: unaligning (T0330)L115 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2feaA)S99 Warning: unaligning (T0330)T116 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2feaA)S99 T0330 2 :SRTLVLFDIDGTLL 2feaA 4 :RKPFIICDFDGTIT T0330 19 :SM 2feaA 20 :DN T0330 25 :LADAL 2feaA 22 :IINIM T0330 31 :EVY 2feaA 27 :KTF T0330 37 :GSTGSHDF 2feaA 30 :APPEWMAL T0330 45 :SGKMDGAIIYEVLSNVGLERA 2feaA 44 :KTLSIKEGVGRMFGLLPSSLK T0330 72 :DKAKETYIAL 2feaA 65 :EEITSFVLED T0330 91 :ITLLEGVRELLDALSSRS 2feaA 75 :AKIREGFREFVAFINEHE T0330 110 :VLLGL 2feaA 93 :IPFYV T0330 117 :GNFEASGRHKLKLP 2feaA 100 :GGMDFFVYPLLEGI T0330 132 :IDHYFPFG 2feaA 115 :EKDRIYCN T0330 140 :AFADDAL 2feaA 124 :ASFDNDY T0330 155 :ALERARRM 2feaA 151 :KPSVIHEL T0330 167 :YSPS 2feaA 159 :SEPN T0330 171 :QIVIIGDTEHDIRCAR 2feaA 164 :YIIMIGDSVTDVEAAK T0330 190 :ARSIAVA 2feaA 181 :SDLCFAR T0330 202 :MEELARHKPGTL 2feaA 191 :LNECREQNLNHL T0330 214 :FKNFAETDEVLAS 2feaA 204 :YQDFYEIRKEIEN Number of specific fragments extracted= 18 number of extra gaps= 1 total=1434 Number of alignments=121 # 2feaA read from 2feaA/merged-good-all-a2m # found chain 2feaA in template set Warning: unaligning (T0330)L115 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2feaA)S99 Warning: unaligning (T0330)T116 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2feaA)S99 T0330 2 :SRTLVLFDIDGTLLKVES 2feaA 4 :RKPFIICDFDGTITMNDN T0330 25 :LADALIEVYGT 2feaA 22 :IINIMKTFAPP T0330 49 :DGAIIYEVLSNVGLERA 2feaA 33 :EWMALKDGVLSKTLSIK T0330 69 :DKFDKAK 2feaA 50 :EGVGRMF T0330 76 :ETYIALFRER 2feaA 65 :EEITSFVLED T0330 91 :ITLLEGVRELLDALSSRS 2feaA 75 :AKIREGFREFVAFINEHE T0330 110 :VLLGL 2feaA 93 :IPFYV T0330 117 :GNFEASGRHKLKLP 2feaA 100 :GGMDFFVYPLLEGI T0330 131 :GIDHYFPFGAFADDALD 2feaA 115 :EKDRIYCNHASFDNDYI T0330 148 :RN 2feaA 150 :CK T0330 156 :LERARRMTGANY 2feaA 152 :PSVIHELSEPNQ T0330 171 :QIVIIGDTEHDIRCARE 2feaA 164 :YIIMIGDSVTDVEAAKL T0330 190 :ARSIAVA 2feaA 181 :SDLCFAR T0330 202 :MEELARHKPGTL 2feaA 191 :LNECREQNLNHL T0330 214 :FKNFAETDEVLAS 2feaA 204 :YQDFYEIRKEIEN Number of specific fragments extracted= 15 number of extra gaps= 1 total=1449 Number of alignments=122 # 2feaA read from 2feaA/merged-good-all-a2m # found chain 2feaA in template set Warning: unaligning (T0330)L115 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2feaA)S99 Warning: unaligning (T0330)T116 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2feaA)S99 Warning: unaligning (T0330)P152 because of BadResidue code BAD_PEPTIDE in next template residue (2feaA)C149 Warning: unaligning (T0330)H153 because of BadResidue code BAD_PEPTIDE at template residue (2feaA)C149 T0330 2 :SRTLVLFDIDGTLL 2feaA 4 :RKPFIICDFDGTIT T0330 16 :K 2feaA 20 :D T0330 24 :VLADALIEVYGTEGSTGSHDFS 2feaA 21 :NIINIMKTFAPPEWMALKDGVL T0330 46 :GKMDGAIIYEVLSNVG 2feaA 44 :KTLSIKEGVGRMFGLL T0330 64 :RAEIADKFDKAKETY 2feaA 60 :PSSLKEEITSFVLED T0330 91 :ITLLEGVRELLDALSS 2feaA 75 :AKIREGFREFVAFINE T0330 108 :SDVLLGL 2feaA 91 :HEIPFYV T0330 117 :GNFEASGRHKLKLPGIDHYF 2feaA 100 :GGMDFFVYPLLEGIVEKDRI T0330 137 :PFGAFADD 2feaA 121 :CNHASFDN T0330 145 :ALDRNEL 2feaA 141 :GTCSNQC T0330 154 :IALERARRMTGANY 2feaA 150 :CKPSVIHELSEPNQ T0330 171 :QIVIIGDTEHDIRCARE 2feaA 164 :YIIMIGDSVTDVEAAKL T0330 190 :ARSIAVA 2feaA 181 :SDLCFAR T0330 202 :MEELARHKPGTL 2feaA 191 :LNECREQNLNHL T0330 214 :FKNFAETDEVLASI 2feaA 204 :YQDFYEIRKEIENV Number of specific fragments extracted= 15 number of extra gaps= 2 total=1464 Number of alignments=123 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ymqA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ymqA expands to /projects/compbio/data/pdb/1ymq.pdb.gz 1ymqA:# T0330 read from 1ymqA/merged-good-all-a2m # 1ymqA read from 1ymqA/merged-good-all-a2m # adding 1ymqA to template set # found chain 1ymqA in template set Warning: unaligning (T0330)R3 because first residue in template chain is (1ymqA)T2 T0330 4 :TLVLFDIDGTLLKV 1ymqA 3 :KALFFDIDGTLVSF T0330 89 :EDITLLEGVRELLDALSSRS 1ymqA 17 :ETHRIPSSTIEALEAAHAKG T0330 110 :VLLGLLTGNFEASGR 1ymqA 37 :LKIFIATGRPKAIIN T0330 125 :HKLKLPGI 1ymqA 54 :SELQDRNL T0330 136 :FPFGAFADDAL 1ymqA 62 :IDGYITMNGAY T0330 147 :DRNELPHIALERARRM 1ymqA 184 :KGDTKQKGIDEIIRHF T0330 166 :NYSPSQIVIIGDTEHDIRCARELD 1ymqA 200 :GIKLEETMSFGDGGNDISMLRHAA T0330 193 :IAVATGNFTME 1ymqA 224 :IGVAMGQAKED T0330 205 :LARH 1ymqA 235 :VKAA T0330 210 :PGTLFKNFAE 1ymqA 239 :ADYVTAPIDE T0330 220 :TDEVLASI 1ymqA 251 :ISKAMKHF Number of specific fragments extracted= 11 number of extra gaps= 0 total=1475 Number of alignments=124 # 1ymqA read from 1ymqA/merged-good-all-a2m # found chain 1ymqA in template set Warning: unaligning (T0330)R3 because first residue in template chain is (1ymqA)T2 T0330 4 :TLVLFDIDGTLL 1ymqA 3 :KALFFDIDGTLV T0330 87 :RREDITLLEGVRELLDALSSRS 1ymqA 15 :SFETHRIPSSTIEALEAAHAKG T0330 110 :VLLGLLTGNFEASGR 1ymqA 37 :LKIFIATGRPKAIIN T0330 125 :HKLKLPGI 1ymqA 54 :SELQDRNL T0330 136 :FPFGAFADDA 1ymqA 62 :IDGYITMNGA T0330 148 :RNELPHIALERARRM 1ymqA 185 :GDTKQKGIDEIIRHF T0330 166 :NYSPSQIVIIGDTEHDIRCARELD 1ymqA 200 :GIKLEETMSFGDGGNDISMLRHAA T0330 193 :IAVATGNFT 1ymqA 224 :IGVAMGQAK T0330 203 :EELARH 1ymqA 233 :EDVKAA T0330 210 :PGTLFKNFAE 1ymqA 239 :ADYVTAPIDE T0330 220 :TDEVLASI 1ymqA 251 :ISKAMKHF Number of specific fragments extracted= 11 number of extra gaps= 0 total=1486 Number of alignments=125 # 1ymqA read from 1ymqA/merged-good-all-a2m # found chain 1ymqA in template set Warning: unaligning (T0330)R3 because first residue in template chain is (1ymqA)T2 T0330 4 :TLVLFDIDGTLLK 1ymqA 3 :KALFFDIDGTLVS T0330 88 :REDITLLEGVRELLDALSS 1ymqA 16 :FETHRIPSSTIEALEAAHA T0330 108 :SDVLLGLLTGNFEASG 1ymqA 35 :KGLKIFIATGRPKAII T0330 125 :HKLKLPGI 1ymqA 54 :SELQDRNL T0330 136 :FPFGAFADD 1ymqA 62 :IDGYITMNG T0330 145 :ALDRNELPHIALERARR 1ymqA 182 :TAKGDTKQKGIDEIIRH T0330 165 :ANYSPSQIVIIGDTEHDIRCARELD 1ymqA 199 :FGIKLEETMSFGDGGNDISMLRHAA T0330 193 :IAVATGNFTME 1ymqA 224 :IGVAMGQAKED T0330 205 :LARH 1ymqA 235 :VKAA T0330 210 :PGTLFKNFAE 1ymqA 239 :ADYVTAPIDE T0330 220 :TDEVLASI 1ymqA 251 :ISKAMKHF Number of specific fragments extracted= 11 number of extra gaps= 0 total=1497 Number of alignments=126 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nf2A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1nf2A expands to /projects/compbio/data/pdb/1nf2.pdb.gz 1nf2A:# T0330 read from 1nf2A/merged-good-all-a2m # 1nf2A read from 1nf2A/merged-good-all-a2m # adding 1nf2A to template set # found chain 1nf2A in template set T0330 1 :M 1nf2A 1 :M T0330 3 :RTLVLFDIDGTLLK 1nf2A 2 :YRVFVFDLDGTLLN T0330 17 :VESMNRRVLADAL 1nf2A 20 :ISEKDRRNIEKLS T0330 31 :EVY 1nf2A 33 :RKC T0330 46 :GKMDGAIIYEVLSNVGLER 1nf2A 41 :SGRMLVSTLNVEKKYFKRT T0330 94 :LEGVRELLDALSSRS 1nf2A 85 :PEVAKDIIEYIKPLN T0330 110 :VLLG 1nf2A 100 :VHWQ T0330 114 :LLTGNFEASGRHKLKLPGID 1nf2A 110 :LYSEKDNEEIKSYARHSNVD T0330 136 :FP 1nf2A 130 :YR T0330 141 :FADDA 1nf2A 132 :VEPNL T0330 147 :DRNELPHIALERARRM 1nf2A 187 :KNVDKGKALRFLRERM T0330 166 :NYSPSQIVIIGDTEHDIRCARELDAR 1nf2A 203 :NWKKEEIVVFGDNENDLFMFEEAGLR T0330 195 :VATGNFT 1nf2A 229 :VAMENAI T0330 203 :EELARH 1nf2A 236 :EKVKEA T0330 210 :PGTLFKNFAE 1nf2A 242 :SDIVTLTNND T0330 220 :TDEVLASI 1nf2A 254 :VSYVLERI Number of specific fragments extracted= 16 number of extra gaps= 0 total=1513 Number of alignments=127 # 1nf2A read from 1nf2A/merged-good-all-a2m # found chain 1nf2A in template set T0330 1 :M 1nf2A 1 :M T0330 3 :RTLVLFDIDGTLLKVESMNRRVLADALIEVYGTEG 1nf2A 2 :YRVFVFDLDGTLLNDNLEISEKDRRNIEKLSRKCY T0330 39 :TGSHDFS 1nf2A 37 :VVFASGR T0330 49 :DGAIIYEVLSNVG 1nf2A 44 :MLVSTLNVEKKYF T0330 62 :LERAE 1nf2A 83 :IPPEV T0330 97 :VRELLDALSSRS 1nf2A 88 :AKDIIEYIKPLN T0330 110 :VLLG 1nf2A 100 :VHWQ T0330 114 :LLTGNFEASGRHKLKLPGID 1nf2A 110 :LYSEKDNEEIKSYARHSNVD T0330 136 :FPF 1nf2A 130 :YRV T0330 142 :ADDALD 1nf2A 133 :EPNLSE T0330 148 :RN 1nf2A 190 :DK T0330 152 :PHIALERARRM 1nf2A 192 :GKALRFLRERM T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIA 1nf2A 203 :NWKKEEIVVFGDNENDLFMFEEAGLRVAM T0330 199 :NFTMEELARH 1nf2A 232 :ENAIEKVKEA T0330 210 :PGTLFKNFAE 1nf2A 242 :SDIVTLTNND T0330 220 :TDEVLAS 1nf2A 254 :VSYVLER Number of specific fragments extracted= 16 number of extra gaps= 0 total=1529 Number of alignments=128 # 1nf2A read from 1nf2A/merged-good-all-a2m # found chain 1nf2A in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1nf2A)M1 T0330 3 :RTLVLFDIDGTLLK 1nf2A 2 :YRVFVFDLDGTLLN T0330 33 :YGTEGSTGSHDFS 1nf2A 16 :DNLEISEKDRRNI T0330 46 :GKMDGAIIYEVLSNVGLERAE 1nf2A 41 :SGRMLVSTLNVEKKYFKRTFP T0330 95 :EGVRELLDALSS 1nf2A 86 :EVAKDIIEYIKP T0330 108 :SDVLLG 1nf2A 98 :LNVHWQ T0330 114 :LLTGNFEASGRHKLKLPGIDHYFP 1nf2A 110 :LYSEKDNEEIKSYARHSNVDYRVE T0330 145 :ALDRNELPHIALERARR 1nf2A 185 :VPKNVDKGKALRFLRER T0330 165 :ANYSPSQIVIIGDTEHDIRCARELDARSI 1nf2A 202 :MNWKKEEIVVFGDNENDLFMFEEAGLRVA T0330 197 :TGNFT 1nf2A 231 :MENAI T0330 203 :EELARH 1nf2A 236 :EKVKEA T0330 210 :PGTLFKNFAE 1nf2A 242 :SDIVTLTNND T0330 220 :TDEVLAS 1nf2A 254 :VSYVLER Number of specific fragments extracted= 12 number of extra gaps= 0 total=1541 Number of alignments=129 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qq5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0330 read from 1qq5A/merged-good-all-a2m # 1qq5A read from 1qq5A/merged-good-all-a2m # found chain 1qq5A in training set Warning: unaligning (T0330)L228 because last residue in template chain is (1qq5A)A245 T0330 1 :M 1qq5A 1 :M T0330 3 :RTLVLFDIDGTLLK 1qq5A 2 :IKAVVFDAYGTLFD T0330 17 :VESMNRRV 1qq5A 19 :VADATERA T0330 25 :LADAL 1qq5A 39 :RQKQL T0330 31 :EVY 1qq5A 44 :EYS T0330 34 :GTEGSTG 1qq5A 53 :GRYADFW T0330 47 :KMDGAIIYEVLSNVGLERAE 1qq5A 60 :SVTREALAYTLGTLGLEPDE T0330 72 :DKAK 1qq5A 80 :SFLA T0330 84 :ERAR 1qq5A 84 :DMAQ T0330 88 :REDITLLEGVRELLDALS 1qq5A 89 :YNRLTPYPDAAQCLAELA T0330 108 :S 1qq5A 107 :P T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARRM 1qq5A 108 :LKRAILSNGAPDMLQALVANAGLTDSFDAVISVDAKRVFKPHPDSYALVEEVL T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAVAT 1qq5A 161 :GVTPAEVLFVSSNGFDVGGAKNFGFSVARVAR T0330 200 :FTMEE 1qq5A 193 :LSQEA T0330 209 :KPGTLFKNFAETDEVLASI 1qq5A 226 :APDFVVPALGDLPRLVRGM Number of specific fragments extracted= 15 number of extra gaps= 0 total=1556 Number of alignments=130 # 1qq5A read from 1qq5A/merged-good-all-a2m # found chain 1qq5A in training set T0330 1 :M 1qq5A 1 :M T0330 3 :RTLVLFDIDGTLLKVESMNR 1qq5A 2 :IKAVVFDAYGTLFDVQSVAD T0330 23 :RVLADALIEVYGTEGSTGSHDF 1qq5A 40 :QKQLEYSWLRALMGRYADFWSV T0330 49 :DGAIIYEVLSNVGLERAE 1qq5A 62 :TREALAYTLGTLGLEPDE T0330 69 :DKFDKAKE 1qq5A 80 :SFLADMAQ T0330 87 :RREDITLLEGVRELLDALS 1qq5A 88 :AYNRLTPYPDAAQCLAELA T0330 108 :S 1qq5A 107 :P T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARRM 1qq5A 108 :LKRAILSNGAPDMLQALVANAGLTDSFDAVISVDAKRVFKPHPDSYALVEEVL T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAVAT 1qq5A 161 :GVTPAEVLFVSSNGFDVGGAKNFGFSVARVAR T0330 200 :FTMEELARHK 1qq5A 193 :LSQEALAREL T0330 210 :PGTLFKNFAETDEVLASI 1qq5A 227 :PDFVVPALGDLPRLVRGM Number of specific fragments extracted= 11 number of extra gaps= 0 total=1567 Number of alignments=131 # 1qq5A read from 1qq5A/merged-good-all-a2m # found chain 1qq5A in training set Warning: unaligning (T0330)S2 because first residue in template chain is (1qq5A)M1 Warning: unaligning (T0330)L228 because last residue in template chain is (1qq5A)A245 T0330 3 :RTLVLFDIDGTLLK 1qq5A 2 :IKAVVFDAYGTLFD T0330 17 :VESMNRRV 1qq5A 19 :VADATERA T0330 34 :GTEGSTGSHDFSGKMDGAIIYEVLSNVG 1qq5A 27 :YPGRGEYITQVWRQKQLEYSWLRALMGR T0330 64 :RAEIADKFDKAKETYIAL 1qq5A 55 :YADFWSVTREALAYTLGT T0330 82 :FRERARR 1qq5A 81 :FLADMAQ T0330 89 :EDITLLEGVRELLDAL 1qq5A 90 :NRLTPYPDAAQCLAEL T0330 108 :SDVLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARR 1qq5A 106 :APLKRAILSNGAPDMLQALVANAGLTDSFDAVISVDAKRVFKPHPDSYALVEEV T0330 165 :ANYSPSQIVIIGDTEHDIRCARELDARSIAVA 1qq5A 160 :LGVTPAEVLFVSSNGFDVGGAKNFGFSVARVA T0330 199 :NFTMEELARH 1qq5A 192 :RLSQEALARE T0330 209 :KPGTLFKNFAETDEVLASI 1qq5A 226 :APDFVVPALGDLPRLVRGM Number of specific fragments extracted= 10 number of extra gaps= 0 total=1577 Number of alignments=132 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fi1A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fi1A expands to /projects/compbio/data/pdb/2fi1.pdb.gz 2fi1A:# T0330 read from 2fi1A/merged-good-all-a2m # 2fi1A read from 2fi1A/merged-good-all-a2m # adding 2fi1A to template set # found chain 2fi1A in template set T0330 1 :MSRTLVLFDIDGTLLKVESMNRRVLADAL 2fi1A 4 :MKYHDYIWDLGGTLLDNYETSTAAFVETL T0330 31 :EVYGTEGSTGS 2fi1A 33 :ALYGITQDHDS T0330 56 :VLSNVGLERAEIADKF 2fi1A 44 :VYQALKVSTPFAIETF T0330 72 :DKAKETYIALFRERA 2fi1A 64 :ENFLEKYKENEAREL T0330 89 :EDITLLEGVRELLDALSSRS 2fi1A 79 :EHPILFEGVSDLLEDISNQG T0330 110 :VLLGLLTGNF 2fi1A 99 :GRHFLVSHRN T0330 121 :ASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARRM 2fi1A 109 :DQVLEILEKTSIAAYFTEVVTSSSGFKRKPNPESMLYLREKY T0330 166 :NY 2fi1A 151 :QI T0330 170 :SQIVIIGDTEHDIRCARELDARS 2fi1A 153 :SSGLVIGDRPIDIEAGQAAGLDT T0330 212 :TLFKNFAETDEVL 2fi1A 176 :HLFTSIVNLRQVL Number of specific fragments extracted= 10 number of extra gaps= 0 total=1587 Number of alignments=133 # 2fi1A read from 2fi1A/merged-good-all-a2m # found chain 2fi1A in template set T0330 1 :MSRTLVLFDIDGTLLKVESMNRRVLADALIEVYGTE 2fi1A 4 :MKYHDYIWDLGGTLLDNYETSTAAFVETLALYGITQ T0330 49 :DGAIIYEVLSN 2fi1A 40 :DHDSVYQALKV T0330 63 :ERAEIADKF 2fi1A 51 :STPFAIETF T0330 72 :DKAKETYIALFRE 2fi1A 64 :ENFLEKYKENEAR T0330 87 :RREDITLLEGVRELLDALSSRS 2fi1A 77 :ELEHPILFEGVSDLLEDISNQG T0330 110 :VLLGLLTGNFEA 2fi1A 99 :GRHFLVSHRNDQ T0330 123 :GRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARRM 2fi1A 111 :VLEILEKTSIAAYFTEVVTSSSGFKRKPNPESMLYLREKY T0330 166 :NY 2fi1A 151 :QI T0330 170 :SQIVIIGDTEHDIRCARELDARS 2fi1A 153 :SSGLVIGDRPIDIEAGQAAGLDT T0330 212 :TLFKNFAETDEVL 2fi1A 176 :HLFTSIVNLRQVL Number of specific fragments extracted= 10 number of extra gaps= 0 total=1597 Number of alignments=134 # 2fi1A read from 2fi1A/merged-good-all-a2m # found chain 2fi1A in template set T0330 1 :MSRTLVLFDIDGTLLKVESMNRRVLADALIEVYGTEGSTGSHDFS 2fi1A 4 :MKYHDYIWDLGGTLLDNYETSTAAFVETLALYGITQDHDSVYQAL T0330 47 :KMDGAIIYEVLSNV 2fi1A 49 :KVSTPFAIETFAPN T0330 68 :ADKFDKAKETYIALF 2fi1A 63 :LENFLEKYKENEARE T0330 88 :REDITLLEGVRELLDALSS 2fi1A 78 :LEHPILFEGVSDLLEDISN T0330 108 :SDVLLGLLTGNFEA 2fi1A 97 :QGGRHFLVSHRNDQ T0330 123 :GRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARR 2fi1A 111 :VLEILEKTSIAAYFTEVVTSSSGFKRKPNPESMLYLREK T0330 165 :ANYS 2fi1A 150 :YQIS T0330 171 :QIVIIGDTEHDIRCARELDARS 2fi1A 154 :SGLVIGDRPIDIEAGQAAGLDT T0330 212 :TLFKNFAETDEVL 2fi1A 176 :HLFTSIVNLRQVL Number of specific fragments extracted= 9 number of extra gaps= 0 total=1606 Number of alignments=135 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1q92A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0330 read from 1q92A/merged-good-all-a2m # 1q92A read from 1q92A/merged-good-all-a2m # found chain 1q92A in training set Warning: unaligning (T0330)E31 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)F61 Warning: unaligning (T0330)V32 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)F61 Warning: unaligning (T0330)T39 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)E70 Warning: unaligning (T0330)G40 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)E70 Warning: unaligning (T0330)H42 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)G74 Warning: unaligning (T0330)D43 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)G74 Warning: unaligning (T0330)S58 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)R83 Warning: unaligning (T0330)N59 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)R83 Warning: unaligning (T0330)L94 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)P109 Warning: unaligning (T0330)E95 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)P109 Warning: unaligning (T0330)L104 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)A119 Warning: unaligning (T0330)S105 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)A119 Warning: unaligning (T0330)P130 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)F151 Warning: unaligning (T0330)A190 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1q92A)E190 Warning: unaligning (T0330)R191 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1q92A)E190 Warning: unaligning (T0330)A196 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)A196 Warning: unaligning (T0330)T197 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)A196 Warning: unaligning (T0330)L213 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1q92A)L211 Warning: unaligning (T0330)F214 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1q92A)L211 Warning: unaligning (T0330)T229 because last residue in template chain is (1q92A)P227 T0330 2 :SRTLVLFDIDGTLLKVESMNRRVLAD 1q92A 34 :RALRVLVDMDGVLADFEGGFLRKFRA T0330 33 :YGTE 1q92A 62 :PDQP T0330 37 :GS 1q92A 67 :IA T0330 41 :S 1q92A 71 :D T0330 44 :FS 1q92A 75 :FW T0330 53 :IYEVL 1q92A 77 :VSEQY T0330 60 :VGLERA 1q92A 84 :LRPGLS T0330 76 :E 1q92A 90 :E T0330 81 :LFRERAR 1q92A 91 :KAISIWE T0330 88 :REDITL 1q92A 102 :FFELEP T0330 96 :GVRELLDA 1q92A 110 :GAVEAVKE T0330 106 :SRSDVLLGLLTG 1q92A 120 :SLQNTDVFICTS T0330 118 :NFEASGRHKLKL 1q92A 138 :YCPYEKYAWVEK T0330 133 :DHYFPFGAFADDAL 1q92A 153 :PDFLEQIVLTRDKT T0330 166 :NYSPS 1q92A 167 :VVSAD T0330 173 :VIIGDTE 1q92A 172 :LLIDDRP T0330 180 :H 1q92A 181 :T T0330 189 :D 1q92A 188 :S T0330 192 :SIAV 1q92A 191 :HVLF T0330 198 :GNF 1q92A 197 :CHN T0330 206 :ARHK 1q92A 200 :QHLQ T0330 210 :PGT 1q92A 207 :PRR T0330 215 :KNFAE 1q92A 212 :HSWAD T0330 220 :TDEVLASIL 1q92A 218 :WKAILDSKR Number of specific fragments extracted= 24 number of extra gaps= 10 total=1630 Number of alignments=136 # 1q92A read from 1q92A/merged-good-all-a2m # found chain 1q92A in training set Warning: unaligning (T0330)V32 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)F61 Warning: unaligning (T0330)Y33 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)F61 Warning: unaligning (T0330)S41 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)E70 Warning: unaligning (T0330)H42 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)E70 Warning: unaligning (T0330)D49 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)G74 Warning: unaligning (T0330)G50 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)G74 Warning: unaligning (T0330)S58 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)R83 Warning: unaligning (T0330)N59 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)R83 Warning: unaligning (T0330)L94 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)P109 Warning: unaligning (T0330)E95 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)P109 Warning: unaligning (T0330)L104 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)A119 Warning: unaligning (T0330)S105 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)A119 Warning: unaligning (T0330)P130 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)F151 Warning: unaligning (T0330)A190 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1q92A)E190 Warning: unaligning (T0330)R191 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1q92A)E190 Warning: unaligning (T0330)A196 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)A196 Warning: unaligning (T0330)T197 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)A196 Warning: unaligning (T0330)L213 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1q92A)L211 Warning: unaligning (T0330)F214 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1q92A)L211 Warning: unaligning (T0330)T229 because last residue in template chain is (1q92A)P227 T0330 2 :SRTLVLFDIDGTLLKVESMNRRV 1q92A 34 :RALRVLVDMDGVLADFEGGFLRK T0330 29 :LIE 1q92A 57 :FRA T0330 34 :GTEGSTG 1q92A 62 :PDQPFIA T0330 43 :D 1q92A 71 :D T0330 45 :S 1q92A 72 :R T0330 51 :AIIYEVL 1q92A 75 :FWVSEQY T0330 60 :VGLERAE 1q92A 84 :LRPGLSE T0330 81 :LFRERA 1q92A 91 :KAISIW T0330 87 :RREDITL 1q92A 101 :FFFELEP T0330 96 :GVRELLDA 1q92A 110 :GAVEAVKE T0330 106 :SRSDVLLGLLTGNF 1q92A 120 :SLQNTDVFICTSPI T0330 120 :EASGRHKLKL 1q92A 140 :PYEKYAWVEK T0330 131 :G 1q92A 152 :G T0330 133 :DHYFPFGAFADDAL 1q92A 153 :PDFLEQIVLTRDKT T0330 166 :NYSPS 1q92A 167 :VVSAD T0330 173 :VIIGDTE 1q92A 172 :LLIDDRP T0330 189 :D 1q92A 188 :S T0330 192 :SIAV 1q92A 191 :HVLF T0330 198 :GNF 1q92A 197 :CHN T0330 206 :ARH 1q92A 200 :QHL T0330 210 :PGT 1q92A 207 :PRR T0330 215 :KNFAE 1q92A 212 :HSWAD T0330 220 :TDEVLASIL 1q92A 218 :WKAILDSKR Number of specific fragments extracted= 23 number of extra gaps= 10 total=1653 Number of alignments=137 # 1q92A read from 1q92A/merged-good-all-a2m # found chain 1q92A in training set Warning: unaligning (T0330)A28 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)F61 Warning: unaligning (T0330)V32 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)F61 Warning: unaligning (T0330)T39 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)E70 Warning: unaligning (T0330)G40 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)E70 Warning: unaligning (T0330)D43 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)R83 Warning: unaligning (T0330)F44 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)R83 Warning: unaligning (T0330)L94 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)P109 Warning: unaligning (T0330)E95 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)P109 Warning: unaligning (T0330)L104 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)A119 Warning: unaligning (T0330)S105 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)A119 Warning: unaligning (T0330)P130 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)F151 Warning: unaligning (T0330)G131 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)F151 Warning: unaligning (T0330)A190 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1q92A)E190 Warning: unaligning (T0330)R191 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1q92A)E190 Warning: unaligning (T0330)A196 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1q92A)A196 Warning: unaligning (T0330)T197 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1q92A)A196 Warning: unaligning (T0330)L213 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (1q92A)L211 Warning: unaligning (T0330)F214 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (1q92A)L211 Warning: unaligning (T0330)T229 because last residue in template chain is (1q92A)P227 T0330 3 :RTLVLFDIDGTLLKVESMNRRVLAD 1q92A 35 :ALRVLVDMDGVLADFEGGFLRKFRA T0330 33 :YGTEGS 1q92A 63 :DQPFIA T0330 41 :SH 1q92A 80 :QY T0330 45 :SGKMDGAIIYEVLSNVG 1q92A 84 :LRPGLSEKAISIWESKN T0330 87 :RREDITL 1q92A 101 :FFFELEP T0330 96 :GVRELLDA 1q92A 110 :GAVEAVKE T0330 106 :SRSDVLLGLLTGNF 1q92A 120 :SLQNTDVFICTSPI T0330 120 :EASGRHKLKL 1q92A 140 :PYEKYAWVEK T0330 132 :IDHYFPFGAFADDALDRNEL 1q92A 152 :GPDFLEQIVLTRDKTVVSAD T0330 173 :VIIGDTE 1q92A 172 :LLIDDRP T0330 189 :D 1q92A 188 :S T0330 192 :SIAV 1q92A 191 :HVLF T0330 198 :GNF 1q92A 197 :CHN T0330 209 :KPGT 1q92A 206 :PPRR T0330 215 :KNFAE 1q92A 212 :HSWAD T0330 220 :TDEVLASIL 1q92A 218 :WKAILDSKR Number of specific fragments extracted= 16 number of extra gaps= 9 total=1669 Number of alignments=138 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qq7A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1qq7A expands to /projects/compbio/data/pdb/1qq7.pdb.gz 1qq7A:Bad short name: C2 for alphabet: pdb_atoms Bad short name: C1 for alphabet: pdb_atoms Bad short name: O1 for alphabet: pdb_atoms Bad short name: O2 for alphabet: pdb_atoms Skipped atom 191, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 193, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 195, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 197, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 199, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 201, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 203, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 763, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 765, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 767, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 882, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 884, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 886, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 888, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 890, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1206, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1208, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1357, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1359, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1459, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1461, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1619, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1621, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1623, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1625, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1627, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1629, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1631, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1633, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1635, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1637, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1639, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1641, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1643, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1645, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1647, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1649, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1651, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1653, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1655, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1657, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1659, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1661, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1663, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1665, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1667, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1669, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1671, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1673, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1675, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1677, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1679, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1681, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1683, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1685, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1687, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1689, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1691, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1693, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1695, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1697, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1699, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1701, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1703, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1705, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1707, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1709, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1748, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1750, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1752, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1754, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1789, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1791, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1793, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1816, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1818, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1820, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1822, because occupancy 0.500 <= existing 0.500 in 1qq7A Skipped atom 1824, because occupancy 0.500 <= existing 0.500 in 1qq7A # T0330 read from 1qq7A/merged-good-all-a2m # 1qq7A read from 1qq7A/merged-good-all-a2m # adding 1qq7A to template set # found chain 1qq7A in template set Warning: unaligning (T0330)F8 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1qq7A)A9 Warning: unaligning (T0330)I10 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1qq7A)A9 Warning: unaligning (T0330)L228 because last residue in template chain is (1qq7A)A245 T0330 1 :M 1qq7A 1 :M T0330 3 :RTLVL 1qq7A 2 :IKAVV T0330 11 :DGTLLK 1qq7A 10 :YGTLFD T0330 17 :VESMNRRV 1qq7A 19 :VADATERA T0330 25 :LADALIEVY 1qq7A 38 :WRQKQLEYS T0330 34 :GTEGS 1qq7A 53 :GRYAD T0330 45 :SGKMDGAIIYEVLSNVGLERAE 1qq7A 58 :FWSVTREALAYTLGTLGLEPDE T0330 72 :DKA 1qq7A 80 :SFL T0330 83 :RERAR 1qq7A 83 :ADMAQ T0330 88 :REDITLLEGVRELLDALS 1qq7A 89 :YNRLTPYPDAAQCLAELA T0330 108 :S 1qq7A 107 :P T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARRM 1qq7A 108 :LKRAILSNGAPDMLQALVANAGLTDSFDAVISVDAKRVFKPHPDSYALVEEVL T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAVAT 1qq7A 161 :GVTPAEVLFVSSNGFDVGGAKNFGFSVARVAR T0330 200 :FTMEE 1qq7A 193 :LSQEA T0330 209 :KPGTLFKNFAETDEVLASI 1qq7A 226 :APDFVVPALGDLPRLVRGM Number of specific fragments extracted= 15 number of extra gaps= 0 total=1684 Number of alignments=139 # 1qq7A read from 1qq7A/merged-good-all-a2m # found chain 1qq7A in template set Warning: unaligning (T0330)F8 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1qq7A)A9 Warning: unaligning (T0330)I10 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1qq7A)A9 T0330 1 :M 1qq7A 1 :M T0330 3 :RTLVL 1qq7A 2 :IKAVV T0330 11 :DGTLLKVESMNR 1qq7A 10 :YGTLFDVQSVAD T0330 23 :RVLADALIEVYGTEGSTGSHDF 1qq7A 40 :QKQLEYSWLRALMGRYADFWSV T0330 49 :DGAIIYEVLSNVGLERAE 1qq7A 62 :TREALAYTLGTLGLEPDE T0330 69 :DKFDKAKE 1qq7A 80 :SFLADMAQ T0330 87 :RREDITLLEGVRELLDALS 1qq7A 88 :AYNRLTPYPDAAQCLAELA T0330 108 :S 1qq7A 107 :P T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARRM 1qq7A 108 :LKRAILSNGAPDMLQALVANAGLTDSFDAVISVDAKRVFKPHPDSYALVEEVL T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAVAT 1qq7A 161 :GVTPAEVLFVSSNGFDVGGAKNFGFSVARVAR T0330 200 :FTMEELARHK 1qq7A 193 :LSQEALAREL T0330 210 :PGTLFKNFAETDEVLASI 1qq7A 227 :PDFVVPALGDLPRLVRGM Number of specific fragments extracted= 12 number of extra gaps= 0 total=1696 Number of alignments=140 # 1qq7A read from 1qq7A/merged-good-all-a2m # found chain 1qq7A in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1qq7A)M1 Warning: unaligning (T0330)F8 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1qq7A)A9 Warning: unaligning (T0330)I10 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1qq7A)A9 Warning: unaligning (T0330)L228 because last residue in template chain is (1qq7A)A245 T0330 3 :RTLVL 1qq7A 2 :IKAVV T0330 11 :DGTLLKV 1qq7A 10 :YGTLFDV T0330 18 :ESMNRRV 1qq7A 20 :ADATERA T0330 34 :GTEGSTGSHDFSGKMDGAIIYEVLSNVG 1qq7A 27 :YPGRGEYITQVWRQKQLEYSWLRALMGR T0330 68 :ADKFDKAKETYIALFR 1qq7A 55 :YADFWSVTREALAYTL T0330 84 :ERARR 1qq7A 83 :ADMAQ T0330 89 :EDITLLEGVRELLDAL 1qq7A 90 :NRLTPYPDAAQCLAEL T0330 108 :SDVLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARR 1qq7A 106 :APLKRAILSNGAPDMLQALVANAGLTDSFDAVISVDAKRVFKPHPDSYALVEEV T0330 165 :ANYSPSQIVIIGDTEHDIRCARELDARSIAVA 1qq7A 160 :LGVTPAEVLFVSSNGFDVGGAKNFGFSVARVA T0330 199 :NFTMEELARH 1qq7A 192 :RLSQEALARE T0330 209 :KPGTLFKNFAETDEVLASI 1qq7A 226 :APDFVVPALGDLPRLVRGM Number of specific fragments extracted= 11 number of extra gaps= 0 total=1707 Number of alignments=141 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1aq6A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1aq6A expands to /projects/compbio/data/pdb/1aq6.pdb.gz 1aq6A:# T0330 read from 1aq6A/merged-good-all-a2m # 1aq6A read from 1aq6A/merged-good-all-a2m # adding 1aq6A to template set # found chain 1aq6A in template set Warning: unaligning (T0330)L228 because last residue in template chain is (1aq6A)A245 T0330 1 :M 1aq6A 1 :M T0330 3 :RTLVLFDIDGTLLK 1aq6A 2 :IKAVVFDAYGTLFD T0330 17 :VESMNRRV 1aq6A 19 :VADATERA T0330 25 :LADALIEVY 1aq6A 38 :WRQKQLEYS T0330 34 :GT 1aq6A 53 :GR T0330 47 :KMDGAIIYEVLSNVGLERAE 1aq6A 60 :GVTREALAYTLGTLGLEPDE T0330 72 :DKA 1aq6A 80 :SFL T0330 76 :E 1aq6A 83 :A T0330 84 :ERAR 1aq6A 84 :DMAQ T0330 88 :REDITLLEGVRELLDALS 1aq6A 89 :YNRLTPYPDAAQCLAELA T0330 108 :S 1aq6A 107 :P T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARRM 1aq6A 108 :LKRAILSNGAPDMLQALVANAGLTDSFDAVISVDAKRVFKPHPDSYALVEEVL T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAVAT 1aq6A 161 :GVTPAEVLFVSSNGFDVGGAKNFGFSVARVAR T0330 200 :FTMEE 1aq6A 193 :LSQEA T0330 209 :KPGTLFKNFAETDEVLASI 1aq6A 226 :APDFVVPALGDLPRLVRGM Number of specific fragments extracted= 15 number of extra gaps= 0 total=1722 Number of alignments=142 # 1aq6A read from 1aq6A/merged-good-all-a2m # found chain 1aq6A in template set T0330 1 :M 1aq6A 1 :M T0330 3 :RTLVLFDIDGTLLKVESMNR 1aq6A 2 :IKAVVFDAYGTLFDVQSVAD T0330 23 :RVLADALIEVYGTEGSTGSHDF 1aq6A 40 :QKQLEYSWLRALMGRYADFWGV T0330 49 :DGAIIYEVLSNVGLERAE 1aq6A 62 :TREALAYTLGTLGLEPDE T0330 69 :DKFDKAKE 1aq6A 80 :SFLADMAQ T0330 87 :RREDITLLEGVRELLDALS 1aq6A 88 :AYNRLTPYPDAAQCLAELA T0330 108 :S 1aq6A 107 :P T0330 110 :VLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARRM 1aq6A 108 :LKRAILSNGAPDMLQALVANAGLTDSFDAVISVDAKRVFKPHPDSYALVEEVL T0330 166 :NYSPSQIVIIGDTEHDIRCARELDARSIAVAT 1aq6A 161 :GVTPAEVLFVSSNGFDVGGAKNFGFSVARVAR T0330 200 :FTMEELARHK 1aq6A 193 :LSQEALAREL T0330 210 :PGTLFKNFAETDEVLAS 1aq6A 227 :PDFVVPALGDLPRLVRG Number of specific fragments extracted= 11 number of extra gaps= 0 total=1733 Number of alignments=143 # 1aq6A read from 1aq6A/merged-good-all-a2m # found chain 1aq6A in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1aq6A)M1 Warning: unaligning (T0330)L228 because last residue in template chain is (1aq6A)A245 T0330 3 :RTLVLFDIDGTLLK 1aq6A 2 :IKAVVFDAYGTLFD T0330 17 :VESMNRRV 1aq6A 19 :VADATERA T0330 34 :GTEGSTGSHDFSGKMDGAIIYEVLSNVG 1aq6A 27 :YPGRGEYITQVWRQKQLEYSWLRALMGR T0330 64 :RAEIADKFDKAKETYIAL 1aq6A 55 :YADFWGVTREALAYTLGT T0330 82 :FRERARR 1aq6A 81 :FLADMAQ T0330 89 :EDITLLEGVRELLDAL 1aq6A 90 :NRLTPYPDAAQCLAEL T0330 108 :SDVLLGLLTGNFEASGRHKLKLPGIDHYFPFGAFADDALDRNELPHIALERARR 1aq6A 106 :APLKRAILSNGAPDMLQALVANAGLTDSFDAVISVDAKRVFKPHPDSYALVEEV T0330 165 :ANYSPSQIVIIGDTEHDIRCARELDARSIAVA 1aq6A 160 :LGVTPAEVLFVSSNGFDVGGAKNFGFSVARVA T0330 199 :NFTMEELARH 1aq6A 192 :RLSQEALARE T0330 209 :KPGTLFKNFAETDEVLASI 1aq6A 226 :APDFVVPALGDLPRLVRGM Number of specific fragments extracted= 10 number of extra gaps= 0 total=1743 Number of alignments=144 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mh9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1mh9A expands to /projects/compbio/data/pdb/1mh9.pdb.gz 1mh9A:# T0330 read from 1mh9A/merged-good-all-a2m # 1mh9A read from 1mh9A/merged-good-all-a2m # adding 1mh9A to template set # found chain 1mh9A in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1mh9A)R34 Warning: unaligning (T0330)T229 because last residue in template chain is (1mh9A)P227 T0330 3 :RTLVLFDIDGTLLKVESMNRRVLAD 1mh9A 35 :ALRVLVDMDGVLADFEGGFLRKFRA T0330 32 :VY 1mh9A 60 :RF T0330 34 :GTE 1mh9A 63 :DQP T0330 37 :GSTGS 1mh9A 67 :IALED T0330 42 :H 1mh9A 73 :R T0330 46 :GKMDGAIIYE 1mh9A 74 :GFWVSEQYGR T0330 60 :VGLER 1mh9A 84 :LRPGL T0330 75 :K 1mh9A 89 :S T0330 80 :ALFRERAR 1mh9A 90 :EKAISIWE T0330 88 :REDITLLEGVRELLDALSSRSDVLLGLLTGN 1mh9A 102 :FFELEPLPGAVEAVKEMASLQNTDVFICTSP T0330 119 :FEASGRHKLKLP 1mh9A 139 :CPYEKYAWVEKY T0330 133 :DHYFPFGAFADDALD 1mh9A 153 :PDFLEQIVLTRDKTV T0330 166 :NYS 1mh9A 169 :SAD T0330 173 :VIIGDTE 1mh9A 172 :LLIDDRP T0330 180 :H 1mh9A 181 :T T0330 189 :DARSIAVATGNF 1mh9A 188 :SWEHVLFTACHN T0330 206 :ARHK 1mh9A 200 :QHLQ T0330 210 :PGTLFKNFAE 1mh9A 207 :PRRRLHSWAD T0330 220 :TDEVLASIL 1mh9A 218 :WKAILDSKR Number of specific fragments extracted= 19 number of extra gaps= 0 total=1762 Number of alignments=145 # 1mh9A read from 1mh9A/merged-good-all-a2m # found chain 1mh9A in template set Warning: unaligning (T0330)S2 because first residue in template chain is (1mh9A)R34 T0330 3 :RTLVLFDIDGTLLKVESMNRRV 1mh9A 35 :ALRVLVDMDGVLADFEGGFLRK T0330 29 :LIEVYGT 1mh9A 57 :FRARFPD T0330 37 :GSTGSHDFS 1mh9A 64 :QPFIALEDR T0330 49 :DGAIIYEVLSNVGLERAE 1mh9A 73 :RGFWVSEQYGRLRPGLSE T0330 81 :LFRERA 1mh9A 91 :KAISIW T0330 87 :RREDITLLEGVRELLDALSSRSDVLLGLLTGNF 1mh9A 101 :FFFELEPLPGAVEAVKEMASLQNTDVFICTSPI T0330 120 :EASGRHKLKLP 1mh9A 140 :PYEKYAWVEKY T0330 131 :G 1mh9A 152 :G T0330 133 :DHYFPFGAFADDALDR 1mh9A 153 :PDFLEQIVLTRDKTVV T0330 166 :NYS 1mh9A 169 :SAD T0330 173 :VIIGDTE 1mh9A 172 :LLIDDRP T0330 189 :DARSIAVATGNF 1mh9A 188 :SWEHVLFTACHN T0330 206 :ARH 1mh9A 200 :QHL T0330 210 :PGTLFKNFAE 1mh9A 207 :PRRRLHSWAD T0330 220 :TDEVLASIL 1mh9A 218 :WKAILDSKR Number of specific fragments extracted= 15 number of extra gaps= 0 total=1777 Number of alignments=146 # 1mh9A read from 1mh9A/merged-good-all-a2m # found chain 1mh9A in template set Warning: unaligning (T0330)K209 because of BadResidue code BAD_PEPTIDE at template residue (1mh9A)P206 Warning: unaligning (T0330)T229 because last residue in template chain is (1mh9A)P227 T0330 4 :TLVLFDIDGTLLKVESMNRRVLADA 1mh9A 36 :LRVLVDMDGVLADFEGGFLRKFRAR T0330 32 :V 1mh9A 61 :F T0330 33 :YGTEGSTGSHDFSGKMDGAIIYEVLSNVG 1mh9A 72 :RRGFWVSEQYGRLRPGLSEKAISIWESKN T0330 87 :RREDITLLEGVRELLDALSSRSDVLLGLLTGNF 1mh9A 101 :FFFELEPLPGAVEAVKEMASLQNTDVFICTSPI T0330 120 :EASGRHKLKLPGIDHYFPFGAFADDALDRNEL 1mh9A 140 :PYEKYAWVEKYFGPDFLEQIVLTRDKTVVSAD T0330 173 :VIIGDTE 1mh9A 172 :LLIDDRP T0330 189 :DARSIAVATGNF 1mh9A 188 :SWEHVLFTACHN T0330 210 :PGTLFKNFAE 1mh9A 207 :PRRRLHSWAD T0330 220 :TDEVLASIL 1mh9A 218 :WKAILDSKR Number of specific fragments extracted= 9 number of extra gaps= 1 total=1786 Number of alignments=147 # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0330//projects/compbio/experiments/protein-predict/casp7/T0330/align.constraints_v3.costfcn or /projects/compbio/experiments/protein-predict/casp7/T0330//projects/compbio/experiments/protein-predict/casp7/T0330/align.constraints_v3.costfcn.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/T0330/align.constraints_v3.costfcn # reading script from file /projects/compbio/experiments/protein-predict/casp7/T0330/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((T0330)L7.CB, (T0330)I175.CB) [> 4.2709 = 7.1182 < 9.2537] w=1.0000 to align # Constraint # added constraint: constraint((T0330)L7.CB, (T0330)I174.CB) [> 2.8268 = 4.7113 < 6.1246] w=1.0000 to align # Constraint # added constraint: constraint((T0330)L7.CB, (T0330)V173.CB) [> 4.1968 = 6.9947 < 9.0931] w=1.0000 to align # Constraint # added constraint: constraint((T0330)V6.CB, (T0330)V173.CB) [> 3.0169 = 5.0281 < 6.5365] w=1.0000 to align # Constraint # added constraint: constraint((T0330)T13.CB, (T0330)D177.CB) [> 3.0679 = 5.1132 < 6.6472] w=0.9930 to align # Constraint # added constraint: constraint((T0330)T13.CB, (T0330)G176.CA) [> 2.8713 = 4.7854 < 6.2211] w=0.9930 to align # Constraint # added constraint: constraint((T0330)T13.CB, (T0330)I175.CB) [> 3.5994 = 5.9990 < 7.7987] w=0.9930 to align # Constraint # added constraint: constraint((T0330)G12.CA, (T0330)D177.CB) [> 2.8721 = 4.7869 < 6.2229] w=0.9930 to align # Constraint # added constraint: constraint((T0330)V6.CB, (T0330)I175.CB) [> 4.0936 = 6.8227 < 8.8695] w=0.9792 to align # Constraint # added constraint: constraint((T0330)L101.CB, (T0330)L112.CB) [> 3.6942 = 6.1570 < 8.0041] w=0.9578 to align # Constraint # added constraint: constraint((T0330)L7.CB, (T0330)I172.CB) [> 3.6775 = 6.1292 < 7.9679] w=0.9431 to align # Constraint # added constraint: constraint((T0330)I174.CB, (T0330)S192.CB) [> 3.2663 = 5.4438 < 7.0770] w=0.9369 to align # Constraint # added constraint: constraint((T0330)L5.CB, (T0330)V173.CB) [> 4.3969 = 7.3281 < 9.5266] w=0.9367 to align # Constraint # added constraint: constraint((T0330)V6.CB, (T0330)V110.CB) [> 3.4110 = 5.6850 < 7.3905] w=0.9296 to align # Constraint # added constraint: constraint((T0330)V6.CB, (T0330)L112.CB) [> 3.2092 = 5.3487 < 6.9533] w=0.9296 to align # Constraint # added constraint: constraint((T0330)V6.CB, (T0330)G113.CA) [> 4.1050 = 6.8417 < 8.8942] w=0.9296 to align # Constraint # added constraint: constraint((T0330)L7.CB, (T0330)G113.CA) [> 3.2019 = 5.3365 < 6.9375] w=0.9296 to align # Constraint # added constraint: constraint((T0330)V173.CB, (T0330)R191.CB) [> 3.0573 = 5.0954 < 6.6241] w=0.9227 to align # Constraint # added constraint: constraint((T0330)L14.CB, (T0330)V97.CB) [> 3.2274 = 5.3790 < 6.9926] w=0.9226 to align # Constraint # added constraint: constraint((T0330)L5.CB, (T0330)I172.CB) [> 2.8493 = 4.7488 < 6.1735] w=0.9220 to align # Constraint # added constraint: constraint((T0330)I174.CB, (T0330)A185.CB) [> 2.6616 = 4.4360 < 5.7668] w=0.9220 to align # Constraint # added constraint: constraint((T0330)L5.CB, (T0330)L111.CB) [> 2.5860 = 4.3101 < 5.6031] w=0.9085 to align # Constraint # added constraint: constraint((T0330)L5.CB, (T0330)V110.CB) [> 3.9484 = 6.5806 < 8.5548] w=0.9085 to align # Constraint # added constraint: constraint((T0330)V6.CB, (T0330)L104.CB) [> 3.5469 = 5.9115 < 7.6849] w=0.9085 to align # Constraint # added constraint: constraint((T0330)V6.CB, (T0330)L111.CB) [> 4.3281 = 7.2135 < 9.3775] w=0.9085 to align # Constraint # added constraint: constraint((T0330)L5.CB, (T0330)Q171.CB) [> 3.9557 = 6.5929 < 8.5708] w=0.9079 to align # Constraint # added constraint: constraint((T0330)V6.CB, (T0330)I172.CB) [> 4.4397 = 7.3994 < 9.6193] w=0.9008 to align # Constraint # added constraint: constraint((T0330)V173.CB, (T0330)S192.CB) [> 4.3268 = 7.2114 < 9.3749] w=0.8927 to align # Constraint # added constraint: constraint((T0330)L5.CB, (T0330)Y167.CB) [> 2.9426 = 4.9043 < 6.3756] w=0.8896 to align # Constraint # added constraint: constraint((T0330)G176.CA, (T0330)I193.CB) [> 4.1986 = 6.9977 < 9.0970] w=0.8877 to align # Constraint # added constraint: constraint((T0330)L7.CB, (T0330)L115.CB) [> 3.1633 = 5.2722 < 6.8539] w=0.8874 to align # Constraint # added constraint: constraint((T0330)D11.CB, (T0330)T116.CB) [> 4.1371 = 6.8951 < 8.9636] w=0.8803 to align # Constraint # added constraint: constraint((T0330)I175.CB, (T0330)I193.CB) [> 3.0299 = 5.0497 < 6.5647] w=0.8736 to align # Constraint # added constraint: constraint((T0330)T4.CB, (T0330)L111.CB) [> 3.9457 = 6.5762 < 8.5491] w=0.8735 to align # Constraint # added constraint: constraint((T0330)T4.CB, (T0330)V110.CB) [> 3.6806 = 6.1343 < 7.9746] w=0.8735 to align # Constraint # added constraint: constraint((T0330)L5.CB, (T0330)G113.CA) [> 4.2853 = 7.1422 < 9.2849] w=0.8733 to align # Constraint # added constraint: constraint((T0330)T4.CB, (T0330)Q171.CB) [> 2.8480 = 4.7466 < 6.1706] w=0.8729 to align # Constraint # added constraint: constraint((T0330)A155.CB, (T0330)C184.CB) [> 3.5052 = 5.8421 < 7.5947] w=0.8727 to align # Constraint # added constraint: constraint((T0330)I174.CB, (T0330)R191.CB) [> 4.1239 = 6.8731 < 8.9350] w=0.8594 to align # Constraint # added constraint: constraint((T0330)L14.CB, (T0330)L93.CB) [> 3.7841 = 6.3068 < 8.1989] w=0.8592 to align # Constraint # added constraint: constraint((T0330)G176.CA, (T0330)A194.CB) [> 3.6869 = 6.1449 < 7.9884] w=0.8548 to align # Constraint # added constraint: constraint((T0330)L15.CB, (T0330)L93.CB) [> 3.4728 = 5.7880 < 7.5244] w=0.8522 to align # Constraint # added constraint: constraint((T0330)I10.CB, (T0330)T116.CB) [> 2.6576 = 4.4294 < 5.7583] w=0.8451 to align # Constraint # added constraint: constraint((T0330)I10.CB, (T0330)L114.CB) [> 3.4727 = 5.7878 < 7.5241] w=0.8451 to align # Constraint # added constraint: constraint((T0330)I174.CB, (T0330)A190.CB) [> 3.1302 = 5.2170 < 6.7821] w=0.8382 to align # Constraint # added constraint: constraint((T0330)V173.CB, (T0330)A190.CB) [> 3.8298 = 6.3830 < 8.2979] w=0.8382 to align # Constraint # added constraint: constraint((T0330)V173.CB, (T0330)I193.CB) [> 3.6945 = 6.1575 < 8.0048] w=0.8314 to align # Constraint # added constraint: constraint((T0330)I174.CB, (T0330)I193.CB) [> 4.1363 = 6.8938 < 8.9619] w=0.8314 to align # Constraint # added constraint: constraint((T0330)L7.CB, (T0330)L114.CB) [> 4.3647 = 7.2744 < 9.4567] w=0.8311 to align # Constraint # added constraint: constraint((T0330)A159.CB, (T0330)I172.CB) [> 3.7385 = 6.2308 < 8.1001] w=0.8305 to align # Constraint # added constraint: constraint((T0330)L5.CB, (T0330)L112.CB) [> 4.4068 = 7.3446 < 9.5480] w=0.8241 to align # Constraint # added constraint: constraint((T0330)L15.CB, (T0330)I91.CB) [> 3.2531 = 5.4218 < 7.0484] w=0.8240 to align # Constraint # added constraint: constraint((T0330)T4.CB, (T0330)I172.CB) [> 4.4223 = 7.3705 < 9.5816] w=0.8236 to align # Constraint # added constraint: constraint((T0330)P152.CB, (T0330)C184.CB) [> 3.4710 = 5.7850 < 7.5205] w=0.8235 to align # Constraint # added constraint: constraint((T0330)I172.CB, (T0330)A190.CB) [> 3.0026 = 5.0043 < 6.5056] w=0.8234 to align # Constraint # added constraint: constraint((T0330)A155.CB, (T0330)L188.CB) [> 2.9493 = 4.9155 < 6.3901] w=0.8164 to align # Constraint # added constraint: constraint((T0330)D9.CB, (T0330)D177.CB) [> 3.7958 = 6.3263 < 8.2242] w=0.8099 to align # Constraint # added constraint: constraint((T0330)D9.CB, (T0330)G176.CA) [> 2.4161 = 4.0268 < 5.2348] w=0.8099 to align # Constraint # added constraint: constraint((T0330)D9.CB, (T0330)I175.CB) [> 3.9277 = 6.5462 < 8.5100] w=0.8099 to align # Constraint # added constraint: constraint((T0330)F8.CB, (T0330)G176.CA) [> 4.2712 = 7.1186 < 9.2542] w=0.8099 to align # Constraint # added constraint: constraint((T0330)F8.CB, (T0330)I175.CB) [> 3.1026 = 5.1711 < 6.7224] w=0.8099 to align # Constraint # added constraint: constraint((T0330)L7.CB, (T0330)R158.CB) [> 3.7117 = 6.1862 < 8.0421] w=0.8024 to align # Constraint # added constraint: constraint((T0330)T116.CB, (T0330)A140.CB) [> 4.3174 = 7.1957 < 9.3544] w=0.7959 to align # Constraint # added constraint: constraint((T0330)G113.CA, (T0330)G139.CA) [> 3.4464 = 5.7440 < 7.4671] w=0.7959 to align # Constraint # added constraint: constraint((T0330)G176.CA, (T0330)V195.CB) [> 3.4197 = 5.6994 < 7.4093] w=0.7914 to align # Constraint # added constraint: constraint((T0330)L114.CB, (T0330)G139.CA) [> 2.9218 = 4.8698 < 6.3307] w=0.7888 to align # Constraint # added constraint: constraint((T0330)L15.CB, (T0330)T92.CB) [> 3.8572 = 6.4287 < 8.3574] w=0.7888 to align # Constraint # added constraint: constraint((T0330)A159.CB, (T0330)P169.CB) [> 3.6005 = 6.0009 < 7.8011] w=0.7883 to align # Constraint # added constraint: constraint((T0330)G113.CA, (T0330)F138.CB) [> 2.9950 = 4.9917 < 6.4892] w=0.7818 to align # Constraint # added constraint: constraint((T0330)L14.CB, (T0330)L94.CB) [> 3.7706 = 6.2844 < 8.1697] w=0.7818 to align # Constraint # added constraint: constraint((T0330)G113.CA, (T0330)F136.CB) [> 3.1699 = 5.2831 < 6.8681] w=0.7812 to align # Constraint # added constraint: constraint((T0330)P169.CB, (T0330)D189.CB) [> 2.8675 = 4.7792 < 6.2130] w=0.7812 to align # Constraint # added constraint: constraint((T0330)L114.CB, (T0330)F136.CB) [> 3.3677 = 5.6129 < 7.2967] w=0.7812 to align # Constraint # added constraint: constraint((T0330)I193.CB, (T0330)T212.CB) [> 3.1436 = 5.2394 < 6.8112] w=0.7790 to align # Constraint # added constraint: constraint((T0330)D177.CB, (T0330)A194.CB) [> 4.0726 = 6.7876 < 8.8239] w=0.7773 to align # Constraint # added constraint: constraint((T0330)I172.CB, (T0330)R191.CB) [> 4.1273 = 6.8788 < 8.9424] w=0.7743 to align # Constraint # added constraint: constraint((T0330)G117.CA, (T0330)A142.CB) [> 2.9938 = 4.9897 < 6.4866] w=0.7677 to align # Constraint # added constraint: constraint((T0330)T4.CB, (T0330)Y167.CB) [> 3.3164 = 5.5273 < 7.1856] w=0.7673 to align # Constraint # added constraint: constraint((T0330)G12.CA, (T0330)G176.CA) [> 4.5887 = 7.6479 < 9.9423] w=0.7607 to align # Constraint # added constraint: constraint((T0330)L114.CB, (T0330)A140.CB) [> 3.9154 = 6.5257 < 8.4835] w=0.7607 to align # Constraint # added constraint: constraint((T0330)L115.CB, (T0330)G139.CA) [> 4.3374 = 7.2290 < 9.3977] w=0.7607 to align # Constraint # added constraint: constraint((T0330)L15.CB, (T0330)L94.CB) [> 3.8274 = 6.3789 < 8.2926] w=0.7536 to align # Constraint # added constraint: constraint((T0330)L14.CB, (T0330)L114.CB) [> 4.2719 = 7.1198 < 9.2557] w=0.7536 to align # Constraint # added constraint: constraint((T0330)D177.CB, (T0330)V195.CB) [> 3.0213 = 5.0355 < 6.5461] w=0.7492 to align # Constraint # added constraint: constraint((T0330)I193.CB, (T0330)G211.CA) [> 4.1509 = 6.9181 < 8.9936] w=0.7468 to align # Constraint # added constraint: constraint((T0330)I175.CB, (T0330)V195.CB) [> 3.6697 = 6.1161 < 7.9509] w=0.7422 to align # Constraint # added constraint: constraint((T0330)L115.CB, (T0330)A140.CB) [> 3.0256 = 5.0426 < 6.5554] w=0.7396 to align # Constraint # added constraint: constraint((T0330)T116.CB, (T0330)F141.CB) [> 3.5860 = 5.9767 < 7.7696] w=0.7396 to align # Constraint # added constraint: constraint((T0330)D11.CB, (T0330)D177.CB) [> 4.5776 = 7.6293 < 9.9181] w=0.7396 to align # Constraint # added constraint: constraint((T0330)F8.CB, (T0330)L114.CB) [> 3.2722 = 5.4536 < 7.0897] w=0.7395 to align # Constraint # added constraint: constraint((T0330)F8.CB, (T0330)G113.CA) [> 3.7861 = 6.3102 < 8.2033] w=0.7395 to align # Constraint # added constraint: constraint((T0330)A155.CB, (T0330)I174.CB) [> 4.2193 = 7.0321 < 9.1417] w=0.7392 to align # Constraint # added constraint: constraint((T0330)R3.CB, (T0330)Q171.CB) [> 3.8202 = 6.3670 < 8.2770] w=0.7392 to align # Constraint # added constraint: constraint((T0330)A194.CB, (T0330)F214.CB) [> 4.1711 = 6.9518 < 9.0373] w=0.7327 to align # Constraint # added constraint: constraint((T0330)S192.CB, (T0330)G211.CA) [> 3.4955 = 5.8257 < 7.5735] w=0.7327 to align # Constraint # added constraint: constraint((T0330)D9.CB, (T0330)D181.CB) [> 3.4692 = 5.7819 < 7.5165] w=0.7319 to align # Constraint # added constraint: constraint((T0330)V97.CB, (T0330)F217.CB) [> 3.2848 = 5.4748 < 7.1172] w=0.7307 to align # Constraint # added constraint: constraint((T0330)I193.CB, (T0330)F214.CB) [> 3.8111 = 6.3519 < 8.2574] w=0.7257 to align # Constraint # added constraint: constraint((T0330)D9.CB, (T0330)T178.CB) [> 4.3481 = 7.2469 < 9.4209] w=0.7233 to align # Constraint # added constraint: constraint((T0330)L93.CB, (T0330)P130.CB) [> 3.4422 = 5.7371 < 7.4582] w=0.7206 to align # Constraint # added constraint: constraint((T0330)D9.CB, (T0330)T116.CB) [> 3.9115 = 6.5191 < 8.4749] w=0.7184 to align # Constraint # added constraint: constraint((T0330)D9.CB, (T0330)L115.CB) [> 3.8292 = 6.3820 < 8.2966] w=0.7184 to align # Constraint # added constraint: constraint((T0330)P152.CB, (T0330)E187.CB) [> 2.9725 = 4.9542 < 6.4404] w=0.7180 to align # Constraint # added constraint: constraint((T0330)P169.CB, (T0330)L188.CB) [> 3.4373 = 5.7288 < 7.4475] w=0.7179 to align # Constraint # added constraint: constraint((T0330)F8.CB, (T0330)L112.CB) [> 4.2184 = 7.0307 < 9.1399] w=0.7166 to align # Constraint # added constraint: constraint((T0330)S170.CB, (T0330)D189.CB) [> 3.3860 = 5.6433 < 7.3363] w=0.7108 to align # Constraint # added constraint: constraint((T0330)E150.CB, (T0330)R183.CB) [> 3.1067 = 5.1779 < 6.7312] w=0.7038 to align # Constraint # added constraint: constraint((T0330)I193.CB, (T0330)L213.CB) [> 4.1831 = 6.9718 < 9.0633] w=0.7016 to align # Constraint # added constraint: constraint((T0330)V195.CB, (T0330)F214.CB) [> 3.4498 = 5.7496 < 7.4745] w=0.6975 to align # Constraint # added constraint: constraint((T0330)A194.CB, (T0330)T212.CB) [> 4.2668 = 7.1114 < 9.2448] w=0.6975 to align # Constraint # added constraint: constraint((T0330)G176.CA, (T0330)S192.CB) [> 4.4782 = 7.4637 < 9.7029] w=0.6974 to align # Constraint # added constraint: constraint((T0330)T116.CB, (T0330)A142.CB) [> 4.2209 = 7.0349 < 9.1454] w=0.6974 to align # Constraint # added constraint: constraint((T0330)N149.CB, (T0330)C184.CB) [> 3.1605 = 5.2675 < 6.8477] w=0.6950 to align # Constraint # added constraint: constraint((T0330)K16.CB, (T0330)L94.CB) [> 3.6102 = 6.0170 < 7.8222] w=0.6927 to align # Constraint # added constraint: constraint((T0330)L111.CB, (T0330)Y167.CB) [> 4.1451 = 6.9086 < 8.9811] w=0.6900 to align # Constraint # added constraint: constraint((T0330)N149.CB, (T0330)D181.CB) [> 3.5884 = 5.9807 < 7.7749] w=0.6897 to align # Constraint # added constraint: constraint((T0330)G96.CA, (T0330)F217.CB) [> 3.1940 = 5.3233 < 6.9203] w=0.6885 to align # Constraint # added constraint: constraint((T0330)I175.CB, (T0330)A194.CB) [> 4.2986 = 7.1644 < 9.3137] w=0.6768 to align # Constraint # added constraint: constraint((T0330)A194.CB, (T0330)L213.CB) [> 3.0452 = 5.0753 < 6.5979] w=0.6764 to align # Constraint # added constraint: constraint((T0330)L101.CB, (T0330)I132.CB) [> 4.0372 = 6.7286 < 8.7472] w=0.6758 to align # Constraint # added constraint: constraint((T0330)L112.CB, (T0330)F136.CB) [> 3.1660 = 5.2766 < 6.8595] w=0.6756 to align # Constraint # added constraint: constraint((T0330)I10.CB, (T0330)N118.CB) [> 3.9646 = 6.6076 < 8.5899] w=0.6755 to align # Constraint # added constraint: constraint((T0330)S192.CB, (T0330)T212.CB) [> 4.2082 = 7.0136 < 9.1177] w=0.6728 to align # Constraint # added constraint: constraint((T0330)G117.CA, (T0330)F141.CB) [> 3.8537 = 6.4228 < 8.3497] w=0.6692 to align # Constraint # added constraint: constraint((T0330)L15.CB, (T0330)K126.CB) [> 3.9433 = 6.5722 < 8.5439] w=0.6691 to align # Constraint # added constraint: constraint((T0330)I182.CB, (T0330)S192.CB) [> 2.9891 = 4.9818 < 6.4763] w=0.6689 to align # Constraint # added constraint: constraint((T0330)G113.CA, (T0330)P137.CB) [> 3.4555 = 5.7591 < 7.4869] w=0.6686 to align # Constraint # added constraint: constraint((T0330)L100.CB, (T0330)D221.CB) [> 3.6040 = 6.0068 < 7.8088] w=0.6668 to align # Constraint # added constraint: constraint((T0330)R3.CB, (T0330)V110.CB) [> 4.0241 = 6.7069 < 8.7189] w=0.6644 to align # Constraint # added constraint: constraint((T0330)A159.CB, (T0330)S168.CB) [> 4.1316 = 6.8859 < 8.9517] w=0.6615 to align # Constraint # added constraint: constraint((T0330)F8.CB, (T0330)L115.CB) [> 4.3057 = 7.1761 < 9.3289] w=0.6553 to align # Constraint # added constraint: constraint((T0330)L151.CB, (T0330)C184.CB) [> 3.7516 = 6.2526 < 8.1284] w=0.6547 to align # Constraint # added constraint: constraint((T0330)I175.CB, (T0330)S192.CB) [> 4.3357 = 7.2262 < 9.3941] w=0.6547 to align # Constraint # added constraint: constraint((T0330)I174.CB, (T0330)C184.CB) [> 3.5086 = 5.8476 < 7.6019] w=0.6546 to align # Constraint # added constraint: constraint((T0330)I10.CB, (T0330)G123.CA) [> 4.1020 = 6.8367 < 8.8877] w=0.6482 to align # Constraint # added constraint: constraint((T0330)L114.CB, (T0330)L127.CB) [> 4.1326 = 6.8877 < 8.9541] w=0.6412 to align # Constraint # added constraint: constraint((T0330)L7.CB, (T0330)A190.CB) [> 4.3836 = 7.3060 < 9.4978] w=0.6412 to align # Constraint # added constraint: constraint((T0330)L100.CB, (T0330)F217.CB) [> 2.8676 = 4.7793 < 6.2131] w=0.6392 to align # Constraint # added constraint: constraint((T0330)L115.CB, (T0330)A155.CB) [> 3.9147 = 6.5245 < 8.4818] w=0.6386 to align # Constraint # added constraint: constraint((T0330)G113.CA, (T0330)A140.CB) [> 4.2421 = 7.0702 < 9.1913] w=0.6270 to align # Constraint # added constraint: constraint((T0330)L111.CB, (T0330)P137.CB) [> 3.1092 = 5.1820 < 6.7366] w=0.6263 to align # Constraint # added constraint: constraint((T0330)L112.CB, (T0330)P137.CB) [> 3.3089 = 5.5149 < 7.1693] w=0.6263 to align # Constraint # added constraint: constraint((T0330)K16.CB, (T0330)I91.CB) [> 4.0841 = 6.8068 < 8.8489] w=0.6230 to align # Constraint # added constraint: constraint((T0330)L115.CB, (T0330)I174.CB) [> 4.4108 = 7.3513 < 9.5567] w=0.6199 to align # Constraint # added constraint: constraint((T0330)I10.CB, (T0330)K126.CB) [> 4.1614 = 6.9357 < 9.0164] w=0.6151 to align # Constraint # added constraint: constraint((T0330)D177.CB, (T0330)A196.CB) [> 4.1384 = 6.8973 < 8.9665] w=0.6084 to align # Constraint # added constraint: constraint((T0330)A155.CB, (T0330)A190.CB) [> 3.8756 = 6.4593 < 8.3971] w=0.6072 to align # Constraint # added constraint: constraint((T0330)L156.CB, (T0330)L188.CB) [> 3.8314 = 6.3857 < 8.3014] w=0.6072 to align # Constraint # added constraint: constraint((T0330)P169.CB, (T0330)A190.CB) [> 3.0220 = 5.0366 < 6.5476] w=0.6053 to align # Constraint # added constraint: constraint((T0330)L5.CB, (T0330)M162.CB) [> 3.4511 = 5.7519 < 7.4775] w=0.6006 to align # Constraint # added constraint: constraint((T0330)L7.CB, (T0330)A155.CB) [> 3.7092 = 6.1819 < 8.0365] w=0.5984 to align # Constraint # added constraint: constraint((T0330)I193.CB, (T0330)P210.CB) [> 3.6690 = 6.1149 < 7.9494] w=0.5983 to align # Constraint # added constraint: constraint((T0330)D11.CB, (T0330)N118.CB) [> 4.0584 = 6.7640 < 8.7932] w=0.5983 to align # Constraint # added constraint: constraint((T0330)N118.CB, (T0330)F141.CB) [> 3.6562 = 6.0936 < 7.9217] w=0.5948 to align # Constraint # added constraint: constraint((T0330)D9.CB, (T0330)L114.CB) [> 4.5216 = 7.5360 < 9.7969] w=0.5917 to align # Constraint # added constraint: constraint((T0330)S192.CB, (T0330)P210.CB) [> 3.1552 = 5.2587 < 6.8363] w=0.5913 to align # Constraint # added constraint: constraint((T0330)G117.CA, (T0330)N149.CB) [> 3.8317 = 6.3861 < 8.3019] w=0.5912 to align # Constraint # added constraint: constraint((T0330)P152.CB, (T0330)L188.CB) [> 2.9630 = 4.9384 < 6.4199] w=0.5864 to align # Constraint # added constraint: constraint((T0330)V6.CB, (T0330)I174.CB) [> 4.6467 = 7.7444 < 10.0678] w=0.5848 to align # Constraint # added constraint: constraint((T0330)A155.CB, (T0330)A185.CB) [> 3.7589 = 6.2649 < 8.1443] w=0.5841 to align # Constraint # added constraint: constraint((T0330)G113.CA, (T0330)R158.CB) [> 3.9295 = 6.5491 < 8.5138] w=0.5772 to align # Constraint # added constraint: constraint((T0330)F138.CB, (T0330)R161.CB) [> 3.3999 = 5.6664 < 7.3664] w=0.5771 to align # Constraint # added constraint: constraint((T0330)I182.CB, (T0330)A194.CB) [> 3.4407 = 5.7345 < 7.4549] w=0.5726 to align # Constraint # added constraint: constraint((T0330)V195.CB, (T0330)K215.CB) [> 4.4248 = 7.3746 < 9.5870] w=0.5578 to align # Constraint # added constraint: constraint((T0330)A194.CB, (T0330)G211.CA) [> 4.3724 = 7.2873 < 9.4735] w=0.5567 to align # Constraint # added constraint: constraint((T0330)E120.CB, (T0330)F141.CB) [> 2.9590 = 4.9316 < 6.4111] w=0.5567 to align # Constraint # added constraint: constraint((T0330)G12.CA, (T0330)L94.CB) [> 4.2918 = 7.1529 < 9.2988] w=0.5565 to align # Constraint # added constraint: constraint((T0330)T13.CB, (T0330)L94.CB) [> 4.3546 = 7.2576 < 9.4349] w=0.5565 to align # Constraint # added constraint: constraint((T0330)A196.CB, (T0330)F214.CB) [> 4.1968 = 6.9946 < 9.0930] w=0.5427 to align # Constraint # added constraint: constraint((T0330)T116.CB, (T0330)G139.CA) [> 4.4976 = 7.4959 < 9.7447] w=0.5426 to align # Constraint # added constraint: constraint((T0330)L127.CB, (T0330)F136.CB) [> 3.9507 = 6.5845 < 8.5598] w=0.5356 to align # Constraint # added constraint: constraint((T0330)A103.CB, (T0330)D221.CB) [> 3.3372 = 5.5620 < 7.2306] w=0.5350 to align # Constraint # added constraint: constraint((T0330)F119.CB, (T0330)F141.CB) [> 3.5648 = 5.9413 < 7.7236] w=0.5279 to align # Constraint # added constraint: constraint((T0330)L112.CB, (T0330)Y135.CB) [> 3.7095 = 6.1825 < 8.0373] w=0.5271 to align # Constraint # added constraint: constraint((T0330)A196.CB, (T0330)L213.CB) [> 3.6605 = 6.1008 < 7.9310] w=0.5216 to align # Constraint # added constraint: constraint((T0330)A145.CB, (T0330)I154.CB) [> 3.5036 = 5.8394 < 7.5912] w=0.5208 to align # Constraint # added constraint: constraint((T0330)V195.CB, (T0330)F217.CB) [> 3.8813 = 6.4689 < 8.4095] w=0.5079 to align # Constraint # added constraint: constraint((T0330)F214.CB, (T0330)V223.CB) [> 3.8329 = 6.3882 < 8.3047] w=0.5075 to align # Constraint # added constraint: constraint((T0330)T212.CB, (T0330)V223.CB) [> 3.4576 = 5.7626 < 7.4914] w=0.5075 to align # Constraint # added constraint: constraint((T0330)R3.CB, (T0330)R191.CB) [> 4.1609 = 6.9349 < 9.0153] w=0.5069 to align # Constraint # added constraint: constraint((T0330)L111.CB, (T0330)F138.CB) [> 4.4427 = 7.4044 < 9.6258] w=0.5003 to align # Constraint # added constraint: constraint((T0330)G117.CA, (T0330)D143.CB) [> 3.9112 = 6.5187 < 8.4743] w=0.5002 to align # Constraint # added constraint: constraint((T0330)G117.CA, (T0330)R148.CB) [> 3.6288 = 6.0480 < 7.8624] w=0.4996 to align # Constraint # added constraint: constraint((T0330)R98.CB, (T0330)I132.CB) [> 4.0276 = 6.7126 < 8.7264] w=0.4976 to align # Constraint # added constraint: constraint((T0330)L7.CB, (T0330)L112.CB) [> 4.6603 = 7.7671 < 10.0972] w=0.4952 to align # Constraint # added constraint: constraint((T0330)V17.CB, (T0330)I91.CB) [> 3.5504 = 5.9174 < 7.6926] w=0.4917 to align # Constraint # added constraint: constraint((T0330)V173.CB, (T0330)L224.CB) [> 3.9038 = 6.5063 < 8.4582] w=0.4914 to align # Constraint # added constraint: constraint((T0330)L112.CB, (T0330)F138.CB) [> 4.3046 = 7.1744 < 9.3267] w=0.4882 to align # Constraint # added constraint: constraint((T0330)A155.CB, (T0330)P169.CB) [> 4.3251 = 7.2085 < 9.3711] w=0.4879 to align # Constraint # added constraint: constraint((T0330)A140.CB, (T0330)I154.CB) [> 3.2780 = 5.4634 < 7.1024] w=0.4856 to align # Constraint # added constraint: constraint((T0330)A196.CB, (T0330)K215.CB) [> 3.3187 = 5.5312 < 7.1906] w=0.4804 to align # Constraint # added constraint: constraint((T0330)D177.CB, (T0330)T197.CB) [> 3.5223 = 5.8705 < 7.6316] w=0.4793 to align # Constraint # added constraint: constraint((T0330)F8.CB, (T0330)I174.CB) [> 4.5883 = 7.6472 < 9.9414] w=0.4789 to align # Constraint # added constraint: constraint((T0330)E179.CB, (T0330)L205.CB) [> 4.1040 = 6.8400 < 8.8920] w=0.4787 to align # Constraint # added constraint: constraint((T0330)G12.CA, (T0330)V195.CB) [> 4.3184 = 7.1974 < 9.3567] w=0.4746 to align # Constraint # added constraint: constraint((T0330)A142.CB, (T0330)I154.CB) [> 3.6477 = 6.0795 < 7.9034] w=0.4715 to align # Constraint # added constraint: constraint((T0330)L15.CB, (T0330)V97.CB) [> 4.5472 = 7.5786 < 9.8522] w=0.4652 to align # Constraint # added constraint: constraint((T0330)L5.CB, (T0330)R158.CB) [> 4.3874 = 7.3123 < 9.5061] w=0.4646 to align # Constraint # added constraint: constraint((T0330)L101.CB, (T0330)Y135.CB) [> 2.8673 = 4.7789 < 6.2125] w=0.4638 to align # Constraint # added constraint: constraint((T0330)T13.CB, (T0330)F217.CB) [> 4.1134 = 6.8557 < 8.9124] w=0.4556 to align # Constraint # added constraint: constraint((T0330)V195.CB, (T0330)L213.CB) [> 4.4122 = 7.3537 < 9.5598] w=0.4512 to align # Constraint # added constraint: constraint((T0330)L5.CB, (T0330)A159.CB) [> 3.9597 = 6.5995 < 8.5793] w=0.4505 to align # Constraint # added constraint: constraint((T0330)I172.CB, (T0330)L188.CB) [> 3.7207 = 6.2012 < 8.0616] w=0.4505 to align # Constraint # added constraint: constraint((T0330)G176.CA, (T0330)A185.CB) [> 4.4365 = 7.3941 < 9.6123] w=0.4435 to align # Constraint # added constraint: constraint((T0330)D177.CB, (T0330)F200.CB) [> 3.2706 = 5.4509 < 7.0862] w=0.4371 to align # Constraint # added constraint: constraint((T0330)L15.CB, (T0330)P130.CB) [> 4.0171 = 6.6951 < 8.7036] w=0.4365 to align # Constraint # added constraint: constraint((T0330)E120.CB, (T0330)D143.CB) [> 3.4950 = 5.8250 < 7.5725] w=0.4365 to align # Constraint # added constraint: constraint((T0330)I182.CB, (T0330)P210.CB) [> 3.1462 = 5.2437 < 6.8168] w=0.4365 to align # Constraint # added constraint: constraint((T0330)G123.CA, (T0330)F141.CB) [> 4.1698 = 6.9496 < 9.0345] w=0.4365 to align # Constraint # added constraint: constraint((T0330)I193.CB, (T0330)V223.CB) [> 3.5466 = 5.9110 < 7.6844] w=0.4351 to align # Constraint # added constraint: constraint((T0330)F138.CB, (T0330)R158.CB) [> 3.7840 = 6.3067 < 8.1987] w=0.4342 to align # Constraint # added constraint: constraint((T0330)V6.CB, (T0330)L224.CB) [> 4.2516 = 7.0860 < 9.2118] w=0.4300 to align # Constraint # added constraint: constraint((T0330)T197.CB, (T0330)N216.CB) [> 3.6135 = 6.0224 < 7.8292] w=0.4295 to align # Constraint # added constraint: constraint((T0330)S170.CB, (T0330)A190.CB) [> 4.2647 = 7.1079 < 9.2402] w=0.4292 to align # Constraint # added constraint: constraint((T0330)L14.CB, (T0330)F217.CB) [> 4.2879 = 7.1465 < 9.2904] w=0.4223 to align # Constraint # added constraint: constraint((T0330)D102.CB, (T0330)Y135.CB) [> 4.1689 = 6.9482 < 9.0326] w=0.4215 to align # Constraint # added constraint: constraint((T0330)T13.CB, (T0330)D181.CB) [> 4.6250 = 7.7084 < 10.0209] w=0.4153 to align # Constraint # added constraint: constraint((T0330)R191.CB, (T0330)T212.CB) [> 4.4279 = 7.3799 < 9.5939] w=0.4089 to align # Constraint # added constraint: constraint((T0330)S170.CB, (T0330)R191.CB) [> 4.2608 = 7.1014 < 9.2318] w=0.4082 to align # Constraint # added constraint: constraint((T0330)S105.CB, (T0330)Y135.CB) [> 3.8273 = 6.3788 < 8.2925] w=0.4009 to align # Constraint # added constraint: constraint((T0330)N118.CB, (T0330)A142.CB) [> 3.8929 = 6.4882 < 8.4347] w=0.3971 to align # Constraint # added constraint: constraint((T0330)R98.CB, (T0330)P130.CB) [> 3.8160 = 6.3600 < 8.2680] w=0.3968 to align # Constraint # added constraint: constraint((T0330)I182.CB, (T0330)L205.CB) [> 3.6535 = 6.0892 < 7.9160] w=0.3942 to align # Constraint # added constraint: constraint((T0330)V97.CB, (T0330)I132.CB) [> 4.2245 = 7.0408 < 9.1531] w=0.3872 to align # Constraint # added constraint: constraint((T0330)A159.CB, (T0330)L188.CB) [> 4.1775 = 6.9626 < 9.0513] w=0.3849 to align # Constraint # added constraint: constraint((T0330)F119.CB, (T0330)A142.CB) [> 3.6236 = 6.0394 < 7.8512] w=0.3823 to align # Constraint # added constraint: constraint((T0330)G12.CA, (T0330)T178.CB) [> 4.5031 = 7.5051 < 9.7566] w=0.3731 to align # Constraint # added constraint: constraint((T0330)L115.CB, (T0330)C184.CB) [> 4.0674 = 6.7790 < 8.8128] w=0.3730 to align # Constraint # added constraint: constraint((T0330)R3.CB, (T0330)L224.CB) [> 3.5894 = 5.9823 < 7.7769] w=0.3591 to align # Constraint # added constraint: constraint((T0330)R124.CB, (T0330)D133.CB) [> 4.1054 = 6.8423 < 8.8950] w=0.3590 to align # Constraint # added constraint: constraint((T0330)L14.CB, (T0330)P130.CB) [> 4.3674 = 7.2791 < 9.4628] w=0.3546 to align # Constraint # added constraint: constraint((T0330)I175.CB, (T0330)F214.CB) [> 4.1742 = 6.9569 < 9.0440] w=0.3526 to align # Constraint # added constraint: constraint((T0330)D177.CB, (T0330)G198.CA) [> 3.6237 = 6.0394 < 7.8512] w=0.3520 to align # Constraint # added constraint: constraint((T0330)E179.CB, (T0330)A194.CB) [> 3.9628 = 6.6047 < 8.5861] w=0.3480 to align # Constraint # added constraint: constraint((T0330)I175.CB, (T0330)F217.CB) [> 4.3818 = 7.3029 < 9.4938] w=0.3450 to align # Constraint # added constraint: constraint((T0330)I10.CB, (T0330)L127.CB) [> 4.5108 = 7.5180 < 9.7734] w=0.3385 to align # Constraint # added constraint: constraint((T0330)L104.CB, (T0330)L224.CB) [> 4.2777 = 7.1295 < 9.2684] w=0.3315 to align # Constraint # added constraint: constraint((T0330)A28.CB, (T0330)Y78.CB) [> 3.2007 = 5.3345 < 6.9348] w=0.3309 to align # Constraint # added constraint: constraint((T0330)L93.CB, (T0330)K126.CB) [> 4.0995 = 6.8324 < 8.8822] w=0.3306 to align # Constraint # added constraint: constraint((T0330)D177.CB, (T0330)N199.CB) [> 3.5969 = 5.9948 < 7.7933] w=0.3245 to align # Constraint # added constraint: constraint((T0330)T178.CB, (T0330)F200.CB) [> 3.9400 = 6.5667 < 8.5367] w=0.3174 to align # Constraint # added constraint: constraint((T0330)G113.CA, (T0330)M162.CB) [> 4.2263 = 7.0438 < 9.1570] w=0.3168 to align # Constraint # added constraint: constraint((T0330)I91.CB, (T0330)L129.CB) [> 3.6201 = 6.0335 < 7.8436] w=0.3168 to align # Constraint # added constraint: constraint((T0330)A185.CB, (T0330)P210.CB) [> 4.0982 = 6.8304 < 8.8795] w=0.3168 to align # Constraint # added constraint: constraint((T0330)V173.CB, (T0330)I227.CB) [> 3.9900 = 6.6501 < 8.6451] w=0.3154 to align # Constraint # added constraint: constraint((T0330)L104.CB, (T0330)T220.CB) [> 4.3555 = 7.2591 < 9.4368] w=0.3104 to align # Constraint # added constraint: constraint((T0330)A159.CB, (T0330)A190.CB) [> 4.2802 = 7.1337 < 9.2739] w=0.3097 to align # Constraint # added constraint: constraint((T0330)M20.CB, (T0330)D90.CB) [> 3.3284 = 5.5473 < 7.2115] w=0.3040 to align # Constraint # added constraint: constraint((T0330)G12.CA, (T0330)T197.CB) [> 3.6790 = 6.1316 < 7.9711] w=0.3033 to align # Constraint # added constraint: constraint((T0330)L151.CB, (T0330)E187.CB) [> 4.2781 = 7.1302 < 9.2692] w=0.3027 to align # Constraint # added constraint: constraint((T0330)G139.CA, (T0330)R158.CB) [> 4.0917 = 6.8195 < 8.8653] w=0.3027 to align # Constraint # added constraint: constraint((T0330)L5.CB, (T0330)P137.CB) [> 4.6375 = 7.7292 < 10.0480] w=0.2957 to align # Constraint # added constraint: constraint((T0330)R191.CB, (T0330)I227.CB) [> 3.6187 = 6.0311 < 7.8405] w=0.2943 to align # Constraint # added constraint: constraint((T0330)V24.CB, (T0330)F82.CB) [> 2.9088 = 4.8480 < 6.3024] w=0.2886 to align # Constraint # added constraint: constraint((T0330)P152.CB, (T0330)A185.CB) [> 4.5520 = 7.5867 < 9.8628] w=0.2886 to align # Constraint # added constraint: constraint((T0330)G12.CA, (T0330)N199.CB) [> 3.8608 = 6.4346 < 8.3650] w=0.2816 to align # Constraint # added constraint: constraint((T0330)L156.CB, (T0330)E187.CB) [> 3.4141 = 5.6901 < 7.3972] w=0.2816 to align # Constraint # added constraint: constraint((T0330)L115.CB, (T0330)A142.CB) [> 4.3210 = 7.2016 < 9.3621] w=0.2802 to align # Constraint # added constraint: constraint((T0330)L14.CB, (T0330)L101.CB) [> 4.4249 = 7.3748 < 9.5872] w=0.2750 to align # Constraint # added constraint: constraint((T0330)L7.CB, (T0330)C184.CB) [> 3.7560 = 6.2600 < 8.1380] w=0.2745 to align # Constraint # added constraint: constraint((T0330)I10.CB, (T0330)G117.CA) [> 4.6734 = 7.7890 < 10.1257] w=0.2742 to align # Constraint # added constraint: constraint((T0330)N118.CB, (T0330)D143.CB) [> 3.8116 = 6.3526 < 8.2584] w=0.2711 to align # Constraint # added constraint: constraint((T0330)S168.CB, (T0330)D189.CB) [> 4.4512 = 7.4186 < 9.6442] w=0.2701 to align # Constraint # added constraint: constraint((T0330)L93.CB, (T0330)L129.CB) [> 4.1171 = 6.8618 < 8.9204] w=0.2673 to align # Constraint # added constraint: constraint((T0330)L25.CB, (T0330)I53.CB) [> 4.0030 = 6.6716 < 8.6731] w=0.2654 to align # Constraint # added constraint: constraint((T0330)A28.CB, (T0330)L81.CB) [> 4.0293 = 6.7155 < 8.7302] w=0.2619 to align # Constraint # added constraint: constraint((T0330)G123.CA, (T0330)G139.CA) [> 4.4198 = 7.3663 < 9.5762] w=0.2605 to align # Constraint # added constraint: constraint((T0330)R3.CB, (T0330)I227.CB) [> 3.9027 = 6.5045 < 8.4558] w=0.2605 to align # Constraint # added constraint: constraint((T0330)I172.CB, (T0330)D189.CB) [> 3.4784 = 5.7973 < 7.5365] w=0.2604 to align # Constraint # added constraint: constraint((T0330)V24.CB, (T0330)L81.CB) [> 3.1594 = 5.2657 < 6.8454] w=0.2541 to align # Constraint # added constraint: constraint((T0330)V110.CB, (T0330)L224.CB) [> 4.2883 = 7.1471 < 9.2912] w=0.2541 to align # Constraint # added constraint: constraint((T0330)L127.CB, (T0330)G139.CA) [> 4.3838 = 7.3064 < 9.4983] w=0.2540 to align # Constraint # added constraint: constraint((T0330)R186.CB, (T0330)H208.CB) [> 3.7228 = 6.2046 < 8.0660] w=0.2534 to align # Constraint # added constraint: constraint((T0330)I10.CB, (T0330)L115.CB) [> 4.4874 = 7.4790 < 9.7227] w=0.2534 to align # Constraint # added constraint: constraint((T0330)I53.CB, (T0330)A74.CB) [> 3.4157 = 5.6928 < 7.4006] w=0.2478 to align # Constraint # added constraint: constraint((T0330)G12.CA, (T0330)G198.CA) [> 3.0056 = 5.0093 < 6.5121] w=0.2464 to align # Constraint # added constraint: constraint((T0330)L7.CB, (T0330)A185.CB) [> 4.4770 = 7.4616 < 9.7001] w=0.2464 to align # Constraint # added constraint: constraint((T0330)V24.CB, (T0330)Y78.CB) [> 3.2306 = 5.3843 < 6.9996] w=0.2401 to align # Constraint # added constraint: constraint((T0330)V173.CB, (T0330)V223.CB) [> 4.4974 = 7.4956 < 9.7443] w=0.2399 to align # Constraint # added constraint: constraint((T0330)M20.CB, (T0330)F82.CB) [> 3.7647 = 6.2745 < 8.1569] w=0.2394 to align # Constraint # added constraint: constraint((T0330)T4.CB, (T0330)S108.CB) [> 4.3902 = 7.3170 < 9.5122] w=0.2393 to align # Constraint # added constraint: constraint((T0330)D11.CB, (T0330)I91.CB) [> 4.0393 = 6.7322 < 8.7518] w=0.2350 to align # Constraint # added constraint: constraint((T0330)F8.CB, (T0330)L101.CB) [> 4.1941 = 6.9903 < 9.0873] w=0.2327 to align # Constraint # added constraint: constraint((T0330)L112.CB, (T0330)I132.CB) [> 3.4045 = 5.6742 < 7.3765] w=0.2323 to align # Constraint # added constraint: constraint((T0330)I174.CB, (T0330)E187.CB) [> 4.4209 = 7.3681 < 9.5786] w=0.2323 to align # Constraint # added constraint: constraint((T0330)L114.CB, (T0330)F141.CB) [> 4.4397 = 7.3996 < 9.6194] w=0.2321 to align # Constraint # added constraint: constraint((T0330)R83.CB, (T0330)S122.CB) [> 4.0709 = 6.7849 < 8.8204] w=0.2253 to align # Constraint # added constraint: constraint((T0330)D11.CB, (T0330)T178.CB) [> 4.5362 = 7.5603 < 9.8285] w=0.2230 to align # Constraint # added constraint: constraint((T0330)V24.CB, (T0330)R85.CB) [> 3.6895 = 6.1491 < 7.9939] w=0.2217 to align # Constraint # added constraint: constraint((T0330)P152.CB, (T0330)D189.CB) [> 4.4335 = 7.3891 < 9.6058] w=0.2182 to align # Constraint # added constraint: constraint((T0330)A185.CB, (T0330)H208.CB) [> 3.5522 = 5.9203 < 7.6964] w=0.2182 to align # Constraint # added constraint: constraint((T0330)Q171.CB, (T0330)D189.CB) [> 3.5582 = 5.9303 < 7.7094] w=0.2182 to align # Constraint # added constraint: constraint((T0330)A196.CB, (T0330)L205.CB) [> 3.8642 = 6.4404 < 8.3725] w=0.2182 to align # Constraint # added constraint: constraint((T0330)R186.CB, (T0330)P210.CB) [> 4.1958 = 6.9930 < 9.0909] w=0.2112 to align # Constraint # added constraint: constraint((T0330)V173.CB, (T0330)A185.CB) [> 4.6386 = 7.7311 < 10.0504] w=0.2112 to align # Constraint # added constraint: constraint((T0330)T197.CB, (T0330)F217.CB) [> 4.0021 = 6.6701 < 8.6711] w=0.2112 to align # Constraint # added constraint: constraint((T0330)M20.CB, (T0330)R85.CB) [> 3.4401 = 5.7335 < 7.4535] w=0.2112 to align # Constraint # added constraint: constraint((T0330)L14.CB, (T0330)K126.CB) [> 4.2298 = 7.0496 < 9.1645] w=0.2112 to align # Constraint # added constraint: constraint((T0330)I172.CB, (T0330)E187.CB) [> 4.3967 = 7.3278 < 9.5262] w=0.2111 to align # Constraint # added constraint: constraint((T0330)G117.CA, (T0330)A145.CB) [> 3.6823 = 6.1372 < 7.9784] w=0.2047 to align # Constraint # added constraint: constraint((T0330)R186.CB, (T0330)K209.CB) [> 3.5919 = 5.9866 < 7.7825] w=0.2042 to align # Constraint # added constraint: constraint((T0330)L14.CB, (T0330)L127.CB) [> 4.5135 = 7.5226 < 9.7794] w=0.2042 to align # Constraint # added constraint: constraint((T0330)A196.CB, (T0330)N216.CB) [> 4.2910 = 7.1517 < 9.2972] w=0.1977 to align # Constraint # added constraint: constraint((T0330)T212.CB, (T0330)I227.CB) [> 4.0090 = 6.6816 < 8.6861] w=0.1971 to align # Constraint # added constraint: constraint((T0330)S2.CB, (T0330)Q171.CB) [> 3.8451 = 6.4086 < 8.3312] w=0.1971 to align # Constraint # added constraint: constraint((T0330)G50.CA, (T0330)K75.CB) [> 3.5797 = 5.9662 < 7.7561] w=0.1950 to align # Constraint # added constraint: constraint((T0330)L115.CB, (T0330)F141.CB) [> 3.9288 = 6.5480 < 8.5123] w=0.1905 to align # Constraint # added constraint: constraint((T0330)F141.CB, (T0330)I154.CB) [> 4.3741 = 7.2902 < 9.4773] w=0.1901 to align # Constraint # added constraint: constraint((T0330)T13.CB, (T0330)T197.CB) [> 3.8263 = 6.3771 < 8.2903] w=0.1901 to align # Constraint # added constraint: constraint((T0330)M20.CB, (T0330)A86.CB) [> 3.4299 = 5.7165 < 7.4315] w=0.1830 to align # Constraint # added constraint: constraint((T0330)S192.CB, (T0330)L213.CB) [> 4.4063 = 7.3438 < 9.5470] w=0.1830 to align # Constraint # added constraint: constraint((T0330)L101.CB, (T0330)G131.CA) [> 4.2513 = 7.0856 < 9.2112] w=0.1829 to align # Constraint # added constraint: constraint((T0330)R22.CB, (T0330)H42.CB) [> 3.5412 = 5.9020 < 7.6726] w=0.1816 to align # Constraint # added constraint: constraint((T0330)V17.CB, (T0330)D90.CB) [> 3.9756 = 6.6261 < 8.6139] w=0.1807 to align # Constraint # added constraint: constraint((T0330)D27.CB, (T0330)L81.CB) [> 3.4556 = 5.7594 < 7.4872] w=0.1760 to align # Constraint # added constraint: constraint((T0330)A28.CB, (T0330)T77.CB) [> 3.3733 = 5.6222 < 7.3089] w=0.1760 to align # Constraint # added constraint: constraint((T0330)F8.CB, (T0330)F136.CB) [> 4.3997 = 7.3328 < 9.5326] w=0.1760 to align # Constraint # added constraint: constraint((T0330)L151.CB, (T0330)D181.CB) [> 3.7701 = 6.2835 < 8.1685] w=0.1760 to align # Constraint # added constraint: constraint((T0330)Y54.CB, (T0330)R64.CB) [> 3.6685 = 6.1142 < 7.9485] w=0.1739 to align # Constraint # added constraint: constraint((T0330)D11.CB, (T0330)N21.CB) [> 4.1231 = 6.8719 < 8.9335] w=0.1696 to align # Constraint # added constraint: constraint((T0330)D49.CB, (T0330)K75.CB) [> 3.7113 = 6.1855 < 8.0412] w=0.1689 to align # Constraint # added constraint: constraint((T0330)T178.CB, (T0330)T201.CB) [> 4.3689 = 7.2815 < 9.4659] w=0.1689 to align # Constraint # added constraint: constraint((T0330)G117.CA, (T0330)H180.CB) [> 3.9830 = 6.6383 < 8.6299] w=0.1689 to align # Constraint # added constraint: constraint((T0330)A86.CB, (T0330)S122.CB) [> 3.8581 = 6.4301 < 8.3592] w=0.1666 to align # Constraint # added constraint: constraint((T0330)G113.CA, (T0330)I132.CB) [> 3.4291 = 5.7152 < 7.4298] w=0.1619 to align # Constraint # added constraint: constraint((T0330)G113.CA, (T0330)Y135.CB) [> 3.6823 = 6.1372 < 7.9784] w=0.1619 to align # Constraint # added constraint: constraint((T0330)F119.CB, (T0330)A140.CB) [> 3.4395 = 5.7324 < 7.4521] w=0.1618 to align # Constraint # added constraint: constraint((T0330)F8.CB, (T0330)V97.CB) [> 4.3812 = 7.3020 < 9.4926] w=0.1617 to align # Constraint # added constraint: constraint((T0330)R3.CB, (T0330)L111.CB) [> 3.7269 = 6.2115 < 8.0749] w=0.1576 to align # Constraint # added constraint: constraint((T0330)T197.CB, (T0330)F214.CB) [> 3.7607 = 6.2678 < 8.1482] w=0.1549 to align # Constraint # added constraint: constraint((T0330)G117.CA, (T0330)D144.CB) [> 3.1727 = 5.2877 < 6.8741] w=0.1548 to align # Constraint # added constraint: constraint((T0330)L151.CB, (T0330)R183.CB) [> 3.2611 = 5.4352 < 7.0658] w=0.1548 to align # Constraint # added constraint: constraint((T0330)S105.CB, (T0330)P137.CB) [> 4.3094 = 7.1823 < 9.3370] w=0.1547 to align # Constraint # added constraint: constraint((T0330)I182.CB, (T0330)I193.CB) [> 4.5028 = 7.5047 < 9.7561] w=0.1499 to align # Constraint # added constraint: constraint((T0330)Y54.CB, (T0330)F71.CB) [> 3.8344 = 6.3906 < 8.3078] w=0.1492 to align # Constraint # added constraint: constraint((T0330)N21.CB, (T0330)S45.CB) [> 4.1404 = 6.9007 < 8.9708] w=0.1486 to align # Constraint # added constraint: constraint((T0330)A145.CB, (T0330)L156.CB) [> 4.4903 = 7.4839 < 9.7290] w=0.1478 to align # Constraint # added constraint: constraint((T0330)M202.CB, (T0330)L213.CB) [> 3.4817 = 5.8029 < 7.5437] w=0.1478 to align # Constraint # added constraint: constraint((T0330)L29.CB, (T0330)L57.CB) [> 3.9637 = 6.6062 < 8.5881] w=0.1478 to align # Constraint # added constraint: constraint((T0330)V32.CB, (T0330)A74.CB) [> 4.1590 = 6.9316 < 9.0111] w=0.1478 to align # Constraint # added constraint: constraint((T0330)L114.CB, (T0330)Y135.CB) [> 3.0914 = 5.1523 < 6.6981] w=0.1478 to align # Constraint # added constraint: constraint((T0330)T178.CB, (T0330)M202.CB) [> 3.5520 = 5.9200 < 7.6961] w=0.1478 to align # Constraint # added constraint: constraint((T0330)T116.CB, (T0330)F136.CB) [> 4.2138 = 7.0230 < 9.1298] w=0.1478 to align # Constraint # added constraint: constraint((T0330)D9.CB, (T0330)C184.CB) [> 4.4119 = 7.3531 < 9.5590] w=0.1477 to align # Constraint # added constraint: constraint((T0330)R64.CB, (T0330)A74.CB) [> 3.4748 = 5.7914 < 7.5288] w=0.1408 to align # Constraint # added constraint: constraint((T0330)V24.CB, (T0330)I79.CB) [> 3.6573 = 6.0955 < 7.9241] w=0.1408 to align # Constraint # added constraint: constraint((T0330)L25.CB, (T0330)L57.CB) [> 4.0639 = 6.7732 < 8.8052] w=0.1408 to align # Constraint # added constraint: constraint((T0330)D177.CB, (T0330)M202.CB) [> 4.0270 = 6.7117 < 8.7252] w=0.1408 to align # Constraint # added constraint: constraint((T0330)Y33.CB, (T0330)V60.CB) [> 3.5105 = 5.8508 < 7.6061] w=0.1338 to align # Constraint # added constraint: constraint((T0330)T4.CB, (T0330)D109.CB) [> 4.1923 = 6.9872 < 9.0833] w=0.1273 to align # Constraint # added constraint: constraint((T0330)Q171.CB, (T0330)R191.CB) [> 3.9039 = 6.5065 < 8.4584] w=0.1267 to align # Constraint # added constraint: constraint((T0330)A185.CB, (T0330)G211.CA) [> 4.4115 = 7.3525 < 9.5582] w=0.1267 to align # Constraint # added constraint: constraint((T0330)L29.CB, (T0330)I53.CB) [> 3.7991 = 6.3318 < 8.2313] w=0.1267 to align # Constraint # added constraint: constraint((T0330)L115.CB, (T0330)F136.CB) [> 3.4212 = 5.7020 < 7.4125] w=0.1267 to align # Constraint # added constraint: constraint((T0330)V17.CB, (T0330)A86.CB) [> 3.9688 = 6.6147 < 8.5991] w=0.1224 to align # Constraint # added constraint: constraint((T0330)L7.CB, (T0330)A140.CB) [> 4.5185 = 7.5309 < 9.7902] w=0.1224 to align # Constraint # added constraint: constraint((T0330)L57.CB, (T0330)I67.CB) [> 3.5203 = 5.8672 < 7.6274] w=0.1211 to align # Constraint # added constraint: constraint((T0330)M1.CB, (T0330)Q171.CB) [> 3.9495 = 6.5825 < 8.5572] w=0.1197 to align # Constraint # added constraint: constraint((T0330)Q171.CB, (T0330)A190.CB) [> 4.6691 = 7.7818 < 10.1164] w=0.1197 to align # Constraint # added constraint: constraint((T0330)L114.CB, (T0330)H134.CB) [> 3.9505 = 6.5841 < 8.5593] w=0.1196 to align # Constraint # added constraint: constraint((T0330)L112.CB, (T0330)H134.CB) [> 4.0513 = 6.7521 < 8.7777] w=0.1196 to align # Constraint # added constraint: constraint((T0330)V56.CB, (T0330)A74.CB) [> 3.7307 = 6.2178 < 8.0832] w=0.1196 to align # Constraint # added constraint: constraint((T0330)T116.CB, (T0330)F138.CB) [> 4.3212 = 7.2020 < 9.3626] w=0.1196 to align # Constraint # added constraint: constraint((T0330)L25.CB, (T0330)V56.CB) [> 3.4799 = 5.7998 < 7.5397] w=0.1175 to align # Constraint # added constraint: constraint((T0330)L25.CB, (T0330)S41.CB) [> 3.4060 = 5.6767 < 7.3797] w=0.1126 to align # Constraint # added constraint: constraint((T0330)V17.CB, (T0330)A26.CB) [> 4.0713 = 6.7855 < 8.8211] w=0.1126 to align # Constraint # added constraint: constraint((T0330)L57.CB, (T0330)A74.CB) [> 3.7674 = 6.2791 < 8.1628] w=0.1126 to align # Constraint # added constraint: constraint((T0330)I53.CB, (T0330)F71.CB) [> 3.6574 = 6.0957 < 7.9244] w=0.1063 to align # Constraint # added constraint: constraint((T0330)G50.CA, (T0330)A74.CB) [> 4.0143 = 6.6905 < 8.6977] w=0.1056 to align # Constraint # added constraint: constraint((T0330)G96.CA, (T0330)T220.CB) [> 4.3664 = 7.2774 < 9.4606] w=0.1056 to align # Constraint # added constraint: constraint((T0330)F44.CB, (T0330)V56.CB) [> 3.8289 = 6.3815 < 8.2959] w=0.1056 to align # Constraint # added constraint: constraint((T0330)I175.CB, (T0330)A185.CB) [> 4.7298 = 7.8829 < 10.2478] w=0.1056 to align # Constraint # added constraint: constraint((T0330)G176.CA, (T0330)A196.CB) [> 3.5718 = 5.9530 < 7.7389] w=0.1056 to align # Constraint # added constraint: constraint((T0330)G198.CA, (T0330)F214.CB) [> 3.5827 = 5.9712 < 7.7626] w=0.1056 to align # Constraint # added constraint: constraint((T0330)D9.CB, (T0330)H180.CB) [> 4.5794 = 7.6323 < 9.9220] w=0.1056 to align # Constraint # added constraint: constraint((T0330)K16.CB, (T0330)T197.CB) [> 4.2672 = 7.1120 < 9.2456] w=0.1056 to align # Constraint # added constraint: constraint((T0330)T116.CB, (T0330)D143.CB) [> 4.3300 = 7.2167 < 9.3817] w=0.1056 to align # Constraint # added constraint: constraint((T0330)I172.CB, (T0330)A185.CB) [> 4.5080 = 7.5134 < 9.7674] w=0.1056 to align # Constraint # added constraint: constraint((T0330)L104.CB, (T0330)Y135.CB) [> 4.4215 = 7.3692 < 9.5799] w=0.1056 to align # Constraint # added constraint: constraint((T0330)L93.CB, (T0330)L127.CB) [> 4.3233 = 7.2055 < 9.3672] w=0.1055 to align # Constraint # added constraint: constraint((T0330)L29.CB, (T0330)S41.CB) [> 3.9845 = 6.6409 < 8.6332] w=0.1000 to align # Constraint # added constraint: constraint((T0330)L57.CB, (T0330)F71.CB) [> 3.9239 = 6.5398 < 8.5017] w=0.0992 to align # Constraint # added constraint: constraint((T0330)E18.CB, (T0330)G198.CA) [> 3.6700 = 6.1166 < 7.9516] w=0.0992 to align # Constraint # added constraint: constraint((T0330)V195.CB, (T0330)T212.CB) [> 3.4872 = 5.8121 < 7.5557] w=0.0986 to align # Constraint # added constraint: constraint((T0330)Y33.CB, (T0330)L62.CB) [> 3.4797 = 5.7995 < 7.5394] w=0.0985 to align # Constraint # added constraint: constraint((T0330)G176.CA, (T0330)T197.CB) [> 3.6591 = 6.0985 < 7.9280] w=0.0985 to align # Constraint # added constraint: constraint((T0330)L29.CB, (T0330)A74.CB) [> 4.2809 = 7.1348 < 9.2752] w=0.0985 to align # Constraint # added constraint: constraint((T0330)F119.CB, (T0330)G139.CA) [> 3.1748 = 5.2914 < 6.8788] w=0.0985 to align # Constraint # added constraint: constraint((T0330)L29.CB, (T0330)V60.CB) [> 4.3109 = 7.1848 < 9.3403] w=0.0985 to align # Constraint # added constraint: constraint((T0330)R148.CB, (T0330)R183.CB) [> 3.5795 = 5.9658 < 7.7555] w=0.0985 to align # Constraint # added constraint: constraint((T0330)L25.CB, (T0330)N118.CB) [> 4.0059 = 6.6766 < 8.6796] w=0.0985 to align # Constraint # added constraint: constraint((T0330)N118.CB, (T0330)D144.CB) [> 4.4150 = 7.3584 < 9.5659] w=0.0944 to align # Constraint # added constraint: constraint((T0330)N21.CB, (T0330)I53.CB) [> 3.8586 = 6.4310 < 8.3602] w=0.0943 to align # Constraint # added constraint: constraint((T0330)T178.CB, (T0330)G198.CA) [> 4.4749 = 7.4582 < 9.6957] w=0.0915 to align # Constraint # added constraint: constraint((T0330)I174.CB, (T0330)A194.CB) [> 3.7673 = 6.2787 < 8.1624] w=0.0915 to align # Constraint # added constraint: constraint((T0330)V173.CB, (T0330)A194.CB) [> 4.2349 = 7.0581 < 9.1756] w=0.0915 to align # Constraint # added constraint: constraint((T0330)L29.CB, (T0330)V56.CB) [> 4.1160 = 6.8601 < 8.9181] w=0.0915 to align # Constraint # added constraint: constraint((T0330)N118.CB, (T0330)F138.CB) [> 3.7953 = 6.3255 < 8.2231] w=0.0915 to align # Constraint # added constraint: constraint((T0330)S192.CB, (T0330)F214.CB) [> 3.7924 = 6.3206 < 8.2168] w=0.0915 to align # Constraint # added constraint: constraint((T0330)V110.CB, (T0330)L228.CB) [> 4.4186 = 7.3643 < 9.5736] w=0.0895 to align # Constraint # added constraint: constraint((T0330)D177.CB, (T0330)F214.CB) [> 2.8604 = 4.7673 < 6.1975] w=0.0885 to align # Constraint # added constraint: constraint((T0330)F44.CB, (T0330)I53.CB) [> 3.4441 = 5.7401 < 7.4622] w=0.0866 to align # Constraint # added constraint: constraint((T0330)L114.CB, (T0330)P130.CB) [> 4.2707 = 7.1178 < 9.2531] w=0.0865 to align # Constraint # added constraint: constraint((T0330)A26.CB, (T0330)H42.CB) [> 3.9519 = 6.5866 < 8.5625] w=0.0859 to align # Constraint # added constraint: constraint((T0330)A185.CB, (T0330)A194.CB) [> 3.2663 = 5.4438 < 7.0769] w=0.0845 to align # Constraint # added constraint: constraint((T0330)V17.CB, (T0330)F82.CB) [> 4.1948 = 6.9913 < 9.0887] w=0.0845 to align # Constraint # added constraint: constraint((T0330)E31.CB, (T0330)Y78.CB) [> 3.9760 = 6.6267 < 8.6148] w=0.0845 to align # Constraint # added constraint: constraint((T0330)V195.CB, (T0330)E219.CB) [> 4.6390 = 7.7317 < 10.0512] w=0.0845 to align # Constraint # added constraint: constraint((T0330)A103.CB, (T0330)A218.CB) [> 4.7173 = 7.8622 < 10.2209] w=0.0845 to align # Constraint # added constraint: constraint((T0330)D177.CB, (T0330)I193.CB) [> 4.1371 = 6.8951 < 8.9636] w=0.0845 to align # Constraint # added constraint: constraint((T0330)T4.CB, (T0330)R107.CB) [> 4.4928 = 7.4879 < 9.7343] w=0.0844 to align # Constraint # added constraint: constraint((T0330)A103.CB, (T0330)L224.CB) [> 4.1772 = 6.9621 < 9.0507] w=0.0844 to align # Constraint # added constraint: constraint((T0330)G117.CA, (T0330)L146.CB) [> 4.1212 = 6.8686 < 8.9292] w=0.0844 to align # Constraint # added constraint: constraint((T0330)L25.CB, (T0330)F119.CB) [> 4.2716 = 7.1193 < 9.2551] w=0.0844 to align # Constraint # added constraint: constraint((T0330)I53.CB, (T0330)I67.CB) [> 3.6740 = 6.1233 < 7.9603] w=0.0788 to align # Constraint # added constraint: constraint((T0330)N21.CB, (T0330)Y78.CB) [> 3.9212 = 6.5354 < 8.4960] w=0.0781 to align # Constraint # added constraint: constraint((T0330)A28.CB, (T0330)I52.CB) [> 2.8975 = 4.8292 < 6.2779] w=0.0774 to align # Constraint # added constraint: constraint((T0330)L25.CB, (T0330)F44.CB) [> 3.7682 = 6.2804 < 8.1645] w=0.0774 to align # Constraint # added constraint: constraint((T0330)T4.CB, (T0330)S170.CB) [> 3.4276 = 5.7126 < 7.4264] w=0.0774 to align # Constraint # added constraint: constraint((T0330)A28.CB, (T0330)I79.CB) [> 3.4912 = 5.8187 < 7.5644] w=0.0774 to align # Constraint # added constraint: constraint((T0330)V32.CB, (T0330)L62.CB) [> 4.0640 = 6.7733 < 8.8053] w=0.0774 to align # Constraint # added constraint: constraint((T0330)L25.CB, (T0330)A74.CB) [> 3.7759 = 6.2932 < 8.1812] w=0.0774 to align # Constraint # added constraint: constraint((T0330)G176.CA, (T0330)T201.CB) [> 3.6972 = 6.1620 < 8.0105] w=0.0774 to align # Constraint # added constraint: constraint((T0330)L14.CB, (T0330)I175.CB) [> 4.5164 = 7.5273 < 9.7855] w=0.0774 to align # Constraint # added constraint: constraint((T0330)N21.CB, (T0330)A86.CB) [> 3.8642 = 6.4403 < 8.3724] w=0.0739 to align # Constraint # added constraint: constraint((T0330)L25.CB, (T0330)H42.CB) [> 3.8241 = 6.3735 < 8.2856] w=0.0711 to align # Constraint # added constraint: constraint((T0330)L62.CB, (T0330)A74.CB) [> 3.8522 = 6.4203 < 8.3464] w=0.0704 to align # Constraint # added constraint: constraint((T0330)L14.CB, (T0330)T220.CB) [> 3.6075 = 6.0124 < 7.8162] w=0.0704 to align # Constraint # added constraint: constraint((T0330)L25.CB, (T0330)I79.CB) [> 4.0334 = 6.7224 < 8.7391] w=0.0704 to align # Constraint # added constraint: constraint((T0330)T13.CB, (T0330)A196.CB) [> 3.8753 = 6.4588 < 8.3964] w=0.0704 to align # Constraint # added constraint: constraint((T0330)G12.CA, (T0330)A196.CB) [> 4.5252 = 7.5420 < 9.8046] w=0.0704 to align # Constraint # added constraint: constraint((T0330)L115.CB, (T0330)F138.CB) [> 4.2864 = 7.1440 < 9.2872] w=0.0701 to align # Constraint # added constraint: constraint((T0330)A103.CB, (T0330)T220.CB) [> 4.4057 = 7.3427 < 9.5456] w=0.0634 to align # Constraint # added constraint: constraint((T0330)L100.CB, (T0330)N216.CB) [> 4.7433 = 7.9056 < 10.2772] w=0.0634 to align # Constraint # added constraint: constraint((T0330)L127.CB, (T0330)A140.CB) [> 3.5250 = 5.8749 < 7.6374] w=0.0634 to align # Constraint # added constraint: constraint((T0330)G123.CA, (T0330)A142.CB) [> 3.4212 = 5.7020 < 7.4126] w=0.0634 to align # Constraint # added constraint: constraint((T0330)L112.CB, (T0330)G139.CA) [> 3.7679 = 6.2799 < 8.1639] w=0.0634 to align # Constraint # added constraint: constraint((T0330)F71.CB, (T0330)G117.CA) [> 3.8477 = 6.4129 < 8.3367] w=0.0633 to align # Constraint # added constraint: constraint((T0330)R191.CB, (T0330)H208.CB) [> 3.9256 = 6.5427 < 8.5055] w=0.0633 to align # Constraint # added constraint: constraint((T0330)A103.CB, (T0330)A225.CB) [> 4.4472 = 7.4120 < 9.6356] w=0.0633 to align # Constraint # added constraint: constraint((T0330)T4.CB, (T0330)L104.CB) [> 4.4762 = 7.4603 < 9.6984] w=0.0633 to align # Constraint # added constraint: constraint((T0330)E18.CB, (T0330)H42.CB) [> 3.4827 = 5.8045 < 7.5459] w=0.0612 to align # Constraint # added constraint: constraint((T0330)F44.CB, (T0330)H180.CB) [> 4.1325 = 6.8875 < 8.9537] w=0.0563 to align # Constraint # added constraint: constraint((T0330)I67.CB, (T0330)G117.CA) [> 4.0964 = 6.8273 < 8.8754] w=0.0563 to align # Constraint # added constraint: constraint((T0330)S45.CB, (T0330)A142.CB) [> 4.0506 = 6.7509 < 8.7762] w=0.0499 to align # Constraint # added constraint: constraint((T0330)R3.CB, (T0330)S170.CB) [> 4.7381 = 7.8968 < 10.2658] w=0.0493 to align # Constraint # added constraint: constraint((T0330)N21.CB, (T0330)H42.CB) [> 3.3452 = 5.5753 < 7.2479] w=0.0493 to align # Constraint # added constraint: constraint((T0330)A196.CB, (T0330)T212.CB) [> 4.4736 = 7.4559 < 9.6927] w=0.0493 to align # Constraint # added constraint: constraint((T0330)R22.CB, (T0330)Y54.CB) [> 3.8449 = 6.4081 < 8.3306] w=0.0493 to align # Constraint # added constraint: constraint((T0330)A68.CB, (T0330)L146.CB) [> 3.3713 = 5.6188 < 7.3044] w=0.0493 to align # Constraint # added constraint: constraint((T0330)I10.CB, (T0330)P137.CB) [> 4.6957 = 7.8262 < 10.1740] w=0.0493 to align # Constraint # added constraint: constraint((T0330)I175.CB, (T0330)R191.CB) [> 4.7271 = 7.8785 < 10.2421] w=0.0493 to align # Constraint # added constraint: constraint((T0330)G123.CA, (T0330)A140.CB) [> 3.7582 = 6.2636 < 8.1427] w=0.0492 to align # Constraint # added constraint: constraint((T0330)G117.CA, (T0330)A140.CB) [> 3.5720 = 5.9533 < 7.7393] w=0.0492 to align # Constraint # added constraint: constraint((T0330)R183.CB, (T0330)S192.CB) [> 4.5782 = 7.6303 < 9.9194] w=0.0443 to align # Constraint # added constraint: constraint((T0330)V60.CB, (T0330)L146.CB) [> 3.4339 = 5.7231 < 7.4401] w=0.0435 to align # Constraint # added constraint: constraint((T0330)V60.CB, (T0330)A142.CB) [> 4.2266 = 7.0443 < 9.1576] w=0.0435 to align # Constraint # added constraint: constraint((T0330)V24.CB, (T0330)D90.CB) [> 3.6098 = 6.0163 < 7.8212] w=0.0429 to align # Constraint # added constraint: constraint((T0330)S58.CB, (T0330)A142.CB) [> 3.4204 = 5.7007 < 7.4109] w=0.0429 to align # Constraint # added constraint: constraint((T0330)V32.CB, (T0330)L57.CB) [> 4.6688 = 7.7813 < 10.1157] w=0.0422 to align # Constraint # added constraint: constraint((T0330)I174.CB, (T0330)V195.CB) [> 3.9907 = 6.6512 < 8.6465] w=0.0422 to align # Constraint # added constraint: constraint((T0330)V97.CB, (T0330)V195.CB) [> 4.6717 = 7.7861 < 10.1220] w=0.0362 to align # Constraint # added constraint: constraint((T0330)Q171.CB, (T0330)S192.CB) [> 4.4308 = 7.3846 < 9.6000] w=0.0352 to align # Constraint # added constraint: constraint((T0330)A74.CB, (T0330)A86.CB) [> 3.3525 = 5.5874 < 7.2637] w=0.0352 to align # Constraint # added constraint: constraint((T0330)L14.CB, (T0330)L100.CB) [> 4.4870 = 7.4783 < 9.7218] w=0.0352 to align # Constraint # added constraint: constraint((T0330)I30.CB, (T0330)H180.CB) [> 4.6845 = 7.8075 < 10.1498] w=0.0352 to align # Constraint # added constraint: constraint((T0330)M1.CB, (T0330)S170.CB) [> 4.1419 = 6.9032 < 8.9742] w=0.0352 to align # Constraint # added constraint: constraint((T0330)L112.CB, (T0330)A140.CB) [> 3.0170 = 5.0283 < 6.5368] w=0.0352 to align # Constraint # added constraint: constraint((T0330)C184.CB, (T0330)A194.CB) [> 4.4066 = 7.3444 < 9.5477] w=0.0352 to align # Constraint # added constraint: constraint((T0330)D147.CB, (T0330)R183.CB) [> 3.6294 = 6.0490 < 7.8637] w=0.0352 to align # Constraint # added constraint: constraint((T0330)M48.CB, (T0330)G117.CA) [> 3.4180 = 5.6967 < 7.4057] w=0.0282 to align # Constraint # added constraint: constraint((T0330)R23.CB, (T0330)Y78.CB) [> 4.1757 = 6.9595 < 9.0473] w=0.0282 to align # Constraint # added constraint: constraint((T0330)L104.CB, (T0330)F138.CB) [> 4.2203 = 7.0338 < 9.1439] w=0.0282 to align # Constraint # added constraint: constraint((T0330)A103.CB, (T0330)E157.CB) [> 4.3830 = 7.3050 < 9.4965] w=0.0282 to align # Constraint # added constraint: constraint((T0330)A103.CB, (T0330)H153.CB) [> 4.1761 = 6.9602 < 9.0482] w=0.0282 to align # Constraint # added constraint: constraint((T0330)L100.CB, (T0330)A140.CB) [> 4.1161 = 6.8603 < 8.9183] w=0.0282 to align # Constraint # added constraint: constraint((T0330)L7.CB, (T0330)F141.CB) [> 4.7032 = 7.8387 < 10.1903] w=0.0282 to align # Constraint # added constraint: constraint((T0330)L111.CB, (T0330)G139.CA) [> 4.3605 = 7.2676 < 9.4478] w=0.0282 to align # Constraint # added constraint: constraint((T0330)V6.CB, (T0330)V32.CB) [> 3.6416 = 6.0694 < 7.8902] w=0.0282 to align # Constraint # added constraint: constraint((T0330)I10.CB, (T0330)D43.CB) [> 2.9057 = 4.8429 < 6.2957] w=0.0282 to align # Constraint # added constraint: constraint((T0330)A145.CB, (T0330)H180.CB) [> 4.3085 = 7.1809 < 9.3352] w=0.0282 to align # Constraint # added constraint: constraint((T0330)F71.CB, (T0330)A140.CB) [> 3.7520 = 6.2534 < 8.1294] w=0.0281 to align # Constraint # added constraint: constraint((T0330)G139.CA, (T0330)I154.CB) [> 4.4995 = 7.4992 < 9.7490] w=0.0281 to align # Constraint # added constraint: constraint((T0330)A103.CB, (T0330)K231.CB) [> 3.7613 = 6.2688 < 8.1494] w=0.0262 to align # Constraint # added constraint: constraint((T0330)I182.CB, (T0330)T212.CB) [> 4.3789 = 7.2982 < 9.4876] w=0.0252 to align # Constraint # added constraint: constraint((T0330)I52.CB, (T0330)K70.CB) [> 2.9443 = 4.9071 < 6.3793] w=0.0218 to align # Constraint # added constraint: constraint((T0330)I182.CB, (T0330)V195.CB) [> 3.7566 = 6.2609 < 8.1392] w=0.0211 to align # Constraint # added constraint: constraint((T0330)M1.CB, (T0330)L111.CB) [> 4.4972 = 7.4953 < 9.7439] w=0.0211 to align # Constraint # added constraint: constraint((T0330)E99.CB, (T0330)T220.CB) [> 4.6928 = 7.8213 < 10.1677] w=0.0211 to align # Constraint # added constraint: constraint((T0330)A103.CB, (T0330)L205.CB) [> 3.8613 = 6.4356 < 8.3662] w=0.0211 to align # Constraint # added constraint: constraint((T0330)A103.CB, (T0330)M202.CB) [> 4.1230 = 6.8717 < 8.9333] w=0.0211 to align # Constraint # added constraint: constraint((T0330)F44.CB, (T0330)F82.CB) [> 2.7617 = 4.6029 < 5.9838] w=0.0211 to align # Constraint # added constraint: constraint((T0330)G117.CA, (T0330)G139.CA) [> 3.4846 = 5.8077 < 7.5500] w=0.0211 to align # Constraint # added constraint: constraint((T0330)L25.CB, (T0330)G117.CA) [> 4.7197 = 7.8661 < 10.2260] w=0.0211 to align # Constraint # added constraint: constraint((T0330)I67.CB, (T0330)T116.CB) [> 4.6838 = 7.8063 < 10.1482] w=0.0211 to align # Constraint # added constraint: constraint((T0330)M48.CB, (T0330)A74.CB) [> 2.4757 = 4.1262 < 5.3641] w=0.0211 to align # Constraint # added constraint: constraint((T0330)R107.CB, (T0330)F138.CB) [> 4.4531 = 7.4219 < 9.6485] w=0.0211 to align # Constraint # added constraint: constraint((T0330)L14.CB, (T0330)L25.CB) [> 3.9395 = 6.5658 < 8.5355] w=0.0211 to align # Constraint # added constraint: constraint((T0330)F8.CB, (T0330)L25.CB) [> 4.6265 = 7.7108 < 10.0241] w=0.0211 to align # Constraint # added constraint: constraint((T0330)G96.CA, (T0330)V195.CB) [> 4.3721 = 7.2869 < 9.4730] w=0.0211 to align # Constraint # added constraint: constraint((T0330)G61.CA, (T0330)A74.CB) [> 4.2683 = 7.1138 < 9.2480] w=0.0211 to align # Constraint # added constraint: constraint((T0330)D11.CB, (T0330)G176.CA) [> 4.1586 = 6.9310 < 9.0103] w=0.0208 to align # Constraint # added constraint: constraint((T0330)V6.CB, (T0330)R107.CB) [> 4.6711 = 7.7851 < 10.1206] w=0.0141 to align # Constraint # added constraint: constraint((T0330)A103.CB, (T0330)D147.CB) [> 3.4098 = 5.6831 < 7.3880] w=0.0141 to align # Constraint # added constraint: constraint((T0330)G139.CA, (T0330)M162.CB) [> 3.6687 = 6.1146 < 7.9489] w=0.0141 to align # Constraint # added constraint: constraint((T0330)A103.CB, (T0330)E222.CB) [> 4.6962 = 7.8271 < 10.1752] w=0.0141 to align # Constraint # added constraint: constraint((T0330)A145.CB, (T0330)R183.CB) [> 4.4505 = 7.4175 < 9.6428] w=0.0141 to align # Constraint # added constraint: constraint((T0330)R3.CB, (T0330)S192.CB) [> 3.9942 = 6.6570 < 8.6541] w=0.0141 to align # Constraint # added constraint: constraint((T0330)L25.CB, (T0330)T116.CB) [> 4.3011 = 7.1685 < 9.3191] w=0.0140 to align # Constraint # added constraint: constraint((T0330)A103.CB, (T0330)L228.CB) [> 4.6121 = 7.6868 < 9.9929] w=0.0121 to align # Constraint # added constraint: constraint((T0330)F8.CB, (T0330)V32.CB) [> 4.7886 = 7.9810 < 10.3753] w=0.0070 to align # Constraint # added constraint: constraint((T0330)G61.CA, (T0330)D177.CB) [> 4.7220 = 7.8700 < 10.2310] w=0.0070 to align # Constraint # added constraint: constraint((T0330)A74.CB, (T0330)T116.CB) [> 4.3672 = 7.2787 < 9.4624] w=0.0070 to align # Constraint # added constraint: constraint((T0330)L114.CB, (T0330)K128.CB) [> 4.6979 = 7.8298 < 10.1788] w=0.0070 to align # Constraint # added constraint: constraint((T0330)F8.CB, (T0330)V195.CB) [> 4.4451 = 7.4085 < 9.6310] w=0.0014 to align # Constraint # added constraint: constraint((T0330)M162.CB, (T0330)Q171.CB) [> 4.7478 = 7.9130 < 10.2869] w=0.0014 to align # SetCost created cost = # ( 1.0000 * align ) # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0330/ # command:# reading script from file servers-clean.under # Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0330/decoys/ # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 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 T0330 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 T0330 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 T0330 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 T0330 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_TS5 # ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1 # Found a chain break before 199 # 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 209 # 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 107 # 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 209 # 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 109 # 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 229 # 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 215 # 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 225 # 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 230 # 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 228 # 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 149 # 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 209 # 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 # Found a chain break before 201 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS2 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS3.pdb.gz looking for model 1 # Found a chain break before 131 # 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 149 # 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 116 # 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 229 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS1 # ReadConformPDB reading from PDB file servers/CIRCLE_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS2 # ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1 # Found a chain break before 223 # 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 T0330 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS4 # ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation CIRCLE_TS5 # ReadConformPDB reading from PDB file servers/CPHmodels_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation CPHmodels_TS1 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 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 T0330 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 T0330 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS3 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS4 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS5 # ReadConformPDB reading from PDB file servers/Distill_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 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 T0330 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 T0330 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 T0330 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 T0330 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 212 # 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 T0330 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 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation FAMSD_TS3 # ReadConformPDB reading from PDB file servers/FAMSD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 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 T0330 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 229 # copying to AlignedFragments data structure # naming current conformation FAMS_TS1 # ReadConformPDB reading from PDB file servers/FAMS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation FAMS_TS2 # ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1 # Found a chain break before 229 # copying to AlignedFragments data structure # naming current conformation FAMS_TS3 # ReadConformPDB reading from PDB file servers/FAMS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation FAMS_TS4 # ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation FAMS_TS5 # ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1 # naming current conformation FOLDpro_TS1 # ReadConformPDB reading from PDB file servers/FOLDpro_TS2.pdb.gz looking for model 1 # Found a chain break before 213 # 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 140 # 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 167 # 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 192 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS5 # ReadConformPDB reading from PDB file servers/FORTE1_AL1.pdb.gz looking for model 1 Skipped atom 15, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 328, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz # WARNING: incomplete conformation T0330 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 Skipped atom 38, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 40, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 42, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 44, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 102, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 104, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 106, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 108, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 206, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 208, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 210, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 212, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 262, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 264, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 266, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 268, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 506, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 508, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 510, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz Skipped atom 512, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz # WARNING: incomplete conformation T0330 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 T0330 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 830, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 832, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 834, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 836, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 838, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 840, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 842, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 844, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 846, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 848, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 850, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 852, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 854, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 856, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 858, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 860, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 862, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 864, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 866, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 868, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 870, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 872, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 874, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz Skipped atom 876, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL4.pdb.gz # WARNING: incomplete conformation T0330 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 T0330 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 Skipped atom 15, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 328, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz # WARNING: incomplete conformation T0330 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 Skipped atom 38, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 40, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 42, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 44, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 102, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 104, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 106, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 108, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 206, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 208, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 210, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 212, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 262, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 264, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 266, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 268, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 506, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 508, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 510, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz Skipped atom 512, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz # WARNING: incomplete conformation T0330 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 T0330 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 # WARNING: incomplete conformation T0330 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 T0330 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 208 # 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 208 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS2 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS3.pdb.gz looking for model 1 # Found a chain break before 190 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS3 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS4.pdb.gz looking for model 1 # Found a chain break before 155 # 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 232 # 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 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS1 # ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS2 # ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS3 # ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS4 # ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 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 T0330 can't currently be optimized by undertaker # naming current conformation FUGUE_AL1 # ReadConformPDB reading from PDB file servers/FUGUE_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 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 T0330 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 T0330 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 T0330 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 229 # 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 229 # 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 229 # 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 229 # 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 232 # 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 215 # 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 211 # 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 190 # 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 191 # 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 206 # copying to AlignedFragments data structure # naming current conformation Frankenstein_TS5 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1 # Found a chain break before 195 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS1 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS2 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 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 T0330 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 # Found a chain break before 161 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS5 # ReadConformPDB reading from PDB file servers/HHpred1_TS1.pdb.gz looking for model 1 # Found a chain break before 209 # 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 161 # copying to AlignedFragments data structure # naming current conformation HHpred2_TS1 # ReadConformPDB reading from PDB file servers/HHpred3_TS1.pdb.gz looking for model 1 # Found a chain break before 149 # copying to AlignedFragments data structure # naming current conformation HHpred3_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 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 T0330 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 T0330 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 T0330 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 T0330 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 T0330 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 T0330 can't currently be optimized by undertaker # naming current conformation LOOPP_TS2 # ReadConformPDB reading from PDB file servers/LOOPP_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 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 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation LOOPP_TS4 # ReadConformPDB reading from PDB file servers/LOOPP_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation LOOPP_TS5 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS1.pdb.gz looking for model 1 # Found a chain break before 164 # 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 226 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS3.pdb.gz looking for model 1 # Found a chain break before 232 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server2_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS4.pdb.gz looking for model 1 # Found a chain break before 149 # 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 149 # 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 149 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS2.pdb.gz looking for model 1 # Found a chain break before 232 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS3.pdb.gz looking for model 1 # Found a chain break before 214 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS4.pdb.gz looking for model 1 # Found a chain break before 149 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS5.pdb.gz looking for model 1 # Found a chain break before 149 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS5 # ReadConformPDB reading from PDB file servers/MetaTasser_TS1.pdb.gz looking for model 1 # Found a chain break before 213 # 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 213 # 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 215 # 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 213 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS4 # ReadConformPDB reading from PDB file servers/NN_PUT_lab_TS1.pdb.gz looking for model 1 # Found a chain break before 195 # copying to AlignedFragments data structure # naming current conformation NN_PUT_lab_TS1 # ReadConformPDB reading from PDB file servers/POMYSL_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation POMYSL_TS1 # ReadConformPDB reading from PDB file servers/POMYSL_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation POMYSL_TS2 # ReadConformPDB reading from PDB file servers/POMYSL_TS3.pdb.gz looking for model 1 WARNING: atom 1 has residue number 2 < previous residue 233 in servers/POMYSL_TS3.pdb.gz # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation POMYSL_TS3 # ReadConformPDB reading from PDB file servers/POMYSL_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation POMYSL_TS4 # ReadConformPDB reading from PDB file servers/POMYSL_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation POMYSL_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS1.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS2.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS3.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS4.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS5.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO_TS1.pdb.gz looking for model 1 # Found a chain break before 204 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1 # Found a chain break before 166 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1 # Found a chain break before 149 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1 # Found a chain break before 203 # 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 149 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS5 # ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation Pcons6_TS1 # ReadConformPDB reading from PDB file servers/Pcons6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation Pcons6_TS2 # ReadConformPDB reading from PDB file servers/Pcons6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 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 T0330 can't currently be optimized by undertaker # naming current conformation Pcons6_TS4 # ReadConformPDB reading from PDB file servers/Pcons6_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation Pcons6_TS5 # ReadConformPDB reading from PDB file servers/Phyre-1_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 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 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # 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 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # 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 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # 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 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # 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 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # 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 # Found a chain break before 145 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS1 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1 # Found a chain break before 117 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS2 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1 # Found a chain break before 142 # 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 T0330 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS4 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS5.pdb.gz looking for model 1 # Found a chain break before 162 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS1.pdb.gz looking for model 1 # Found a chain break before 195 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS2.pdb.gz looking for model 1 # Found a chain break before 195 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # 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 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # 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 149 # 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 209 # 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 90 # 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 227 # 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 107 # 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 227 # 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 209 # 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 201 # 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 199 # 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 205 # 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 149 # 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 145 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS1 # ReadConformPDB reading from PDB file servers/ROBETTA_TS2.pdb.gz looking for model 1 # Found a chain break before 162 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS2 # ReadConformPDB reading from PDB file servers/ROBETTA_TS3.pdb.gz looking for model 1 # Found a chain break before 142 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS3 # ReadConformPDB reading from PDB file servers/ROBETTA_TS4.pdb.gz looking for model 1 # Found a chain break before 117 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS4 # ReadConformPDB reading from PDB file servers/ROBETTA_TS5.pdb.gz looking for model 1 # Found a chain break before 89 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS5 # ReadConformPDB reading from PDB file servers/ROKKY_TS1.pdb.gz looking for model 1 # Found a chain break before 201 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS1 # ReadConformPDB reading from PDB file servers/ROKKY_TS2.pdb.gz looking for model 1 # Found a chain break before 223 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS2 # ReadConformPDB reading from PDB file servers/ROKKY_TS3.pdb.gz looking for model 1 # Found a chain break before 208 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS3 # ReadConformPDB reading from PDB file servers/ROKKY_TS4.pdb.gz looking for model 1 # Found a chain break before 207 # copying to AlignedFragments data structure # naming current conformation ROKKY_TS4 # ReadConformPDB reading from PDB file servers/ROKKY_TS5.pdb.gz looking for model 1 # Found a chain break before 149 # 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 T0330 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 Skipped atom 310, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 312, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 314, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 316, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 362, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 364, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 366, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 368, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 382, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 384, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 386, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 388, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 390, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 392, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 394, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 396, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 670, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 672, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 674, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz Skipped atom 676, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz # WARNING: incomplete conformation T0330 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 T0330 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 Skipped atom 11, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz Skipped atom 304, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL4 # ReadConformPDB reading from PDB file servers/SAM-T02_AL5.pdb.gz looking for model 1 Skipped atom 30, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 32, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 34, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 36, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 94, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 96, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 98, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 100, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 202, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 204, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 206, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 208, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 258, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 260, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 262, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 264, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 502, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 504, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 506, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz Skipped atom 508, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL5 # ReadConformPDB reading from PDB file servers/SAM-T99_AL1.pdb.gz looking for model 1 Skipped atom 182, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 184, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 186, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 188, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 190, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 192, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 194, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 196, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 278, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 280, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 282, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz Skipped atom 284, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL1.pdb.gz # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL1 # ReadConformPDB reading from PDB file servers/SAM-T99_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL2 # ReadConformPDB reading from PDB file servers/SAM-T99_AL3.pdb.gz looking for model 1 Skipped atom 106, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 108, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 110, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 112, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 118, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 120, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 122, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 124, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 142, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 144, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 146, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 148, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 278, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 280, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 282, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 284, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 382, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 384, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 386, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 388, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 430, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 432, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 434, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 436, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 590, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 592, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 594, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 596, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 886, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 888, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz Skipped atom 890, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL3.pdb.gz # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL3 # ReadConformPDB reading from PDB file servers/SAM-T99_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL4 # ReadConformPDB reading from PDB file servers/SAM-T99_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL5 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS1.pdb.gz looking for model 1 # Found a chain break before 215 # 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 T0330 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 T0330 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 T0330 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 T0330 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 195 # 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 149 # 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 149 # 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 149 # 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 164 # copying to AlignedFragments data structure # naming current conformation SP3_TS5 # ReadConformPDB reading from PDB file servers/SP4_TS1.pdb.gz looking for model 1 # naming current conformation SP4_TS1 # ReadConformPDB reading from PDB file servers/SP4_TS2.pdb.gz looking for model 1 # Found a chain break before 149 # 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 164 # copying to AlignedFragments data structure # naming current conformation SP4_TS3 # ReadConformPDB reading from PDB file servers/SP4_TS4.pdb.gz looking for model 1 # Found a chain break before 149 # copying to AlignedFragments data structure # naming current conformation SP4_TS4 # ReadConformPDB reading from PDB file servers/SP4_TS5.pdb.gz looking for model 1 # naming current conformation SP4_TS5 # ReadConformPDB reading from PDB file servers/SPARKS2_TS1.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS1 # ReadConformPDB reading from PDB file servers/SPARKS2_TS2.pdb.gz looking for model 1 # Found a chain break before 149 # 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 149 # 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 229 # 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 217 # 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 T0330 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 T0330 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 T0330 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 T0330 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 T0330 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 T0330 can't currently be optimized by undertaker # copying to AlignedFragments data structure # 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 T0330 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 Skipped atom 34, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 36, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 38, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 40, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 98, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 100, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 102, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 104, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 202, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 204, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 206, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 208, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 258, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 260, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 262, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 264, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 502, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 504, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 506, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 508, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz # WARNING: incomplete conformation T0330 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 # WARNING: incomplete conformation T0330 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 Skipped atom 306, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 308, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 310, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 312, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 358, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 360, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 362, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 364, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 378, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 380, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 382, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 384, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 386, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 388, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 390, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 392, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 666, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 668, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 670, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz Skipped atom 672, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL4.pdb.gz # WARNING: incomplete conformation T0330 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 T0330 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 208 # 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 165 # 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 166 # 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 165 # 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 125 # 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 230 # 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 T0330 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 T0330 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 T0330 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 T0330 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 T0330 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 T0330 can't currently be optimized by undertaker # naming current conformation forecast-s_AL5 # ReadConformPDB reading from PDB file servers/gtg_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation gtg_AL1 # ReadConformPDB reading from PDB file servers/gtg_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation gtg_AL2 # ReadConformPDB reading from PDB file servers/gtg_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation gtg_AL3 # ReadConformPDB reading from PDB file servers/gtg_AL4.pdb.gz looking for model 1 Skipped atom 38, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 40, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 42, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 44, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 102, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 104, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 106, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 108, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 210, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 212, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 214, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 216, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 498, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 500, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 502, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz Skipped atom 504, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL4.pdb.gz # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation gtg_AL4 # ReadConformPDB reading from PDB file servers/gtg_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation gtg_AL5 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1 # Found a chain break before 149 # 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 149 # 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 200 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS4.pdb.gz looking for model 1 # Found a chain break before 149 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS5.pdb.gz looking for model 1 # Found a chain break before 226 # 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 227 # 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 230 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS3.pdb.gz looking for model 1 # Found a chain break before 230 # 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 # Found a chain break before 230 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS5.pdb.gz looking for model 1 # Found a chain break before 230 # 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 T0330 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 T0330 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 T0330 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 T0330 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 T0330 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 # Found a chain break before 230 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS1 # ReadConformPDB reading from PDB file servers/keasar-server_TS2.pdb.gz looking for model 1 # Found a chain break before 226 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS2 # ReadConformPDB reading from PDB file servers/keasar-server_TS3.pdb.gz looking for model 1 # Found a chain break before 184 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS3 # ReadConformPDB reading from PDB file servers/keasar-server_TS4.pdb.gz looking for model 1 # Found a chain break before 153 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS4 # ReadConformPDB reading from PDB file servers/keasar-server_TS5.pdb.gz looking for model 1 # Found a chain break before 227 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS5 # ReadConformPDB reading from PDB file servers/mGen-3D_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 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 T0330 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 T0330 can't currently be optimized by undertaker # naming current conformation nFOLD_TS2 # ReadConformPDB reading from PDB file servers/nFOLD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 can't currently be optimized by undertaker # naming current conformation nFOLD_TS3 # ReadConformPDB reading from PDB file servers/nFOLD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0330 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 T0330 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 T0330 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 # Found a chain break before 231 # copying to AlignedFragments data structure # naming current conformation shub_TS1 # command:Using radius: 8.0000 Using models AND alignments for constraints model score 0.2955 model score 0.3090 model score 0.8862 model score 0.2167 model score 0.2695 model score 0.0463 model score 0.0987 model score 0.0415 model score 0.3194 model score 0.5109 model score 0.1406 model score 0.2728 model score 0.2770 model score 0.5014 model score 0.5054 model score -0.5769 model score 0.0408 model score 0.5614 model score 1.8520 model score -0.0028 model score 1.6668 model score 1.8098 model score 1.8347 model score 1.6263 model score 1.6731 model score -0.5686 model score -0.4940 model score -0.4642 model score -0.4704 model score -0.2867 model score -0.3215 model score -0.5177 model score -0.5199 model score -0.5191 model score -0.5152 model score -0.3470 model score -0.2023 model score 0.1975 model score 0.1164 model score -0.4773 model score -0.3710 model score -0.1790 model score 1.2575 model score 1.2565 model score 1.2648 model score 1.2616 model score 1.2601 model score -0.5216 model score -0.5199 model score -0.4327 model score -0.4007 model score -0.4699 model score -0.4803 model score -0.3470 model score -0.5177 model score -0.5199 model score -0.5199 model score -0.5635 model score 1.1017 model score 1.1581 model score -0.0009 model score 1.4593 model score 1.2626 model score 1.2591 model score 1.2589 model score 1.2620 model score 1.2589 model score 1.2626 model score 1.2617 model score 1.2619 model score 1.2589 model score 1.2615 model score 1.8603 model score 1.8605 model score 2.6341 model score 2.1457 model score 2.5848 model score -0.5084 model score -0.1873 model score -0.0656 model score 0.0230 model score -0.0802 model score 1.2537 model score 1.2573 model score 1.2552 model score 1.2559 model score 1.2601 model score -0.4897 model score -0.4797 model score -0.3440 model score -0.3493 model score -0.4030 model score -0.0795 model score -0.1967 model score -0.2330 model score 0.3255 model score -0.2194 model score -0.4905 model score -0.4595 model score -0.3331 model score -0.4200 model score -0.4245 model score -0.5274 model score -0.5651 model score -0.5686 model score 0.0106 model score 0.1258 model score 0.2267 model score 0.0762 model score 0.1891 model score -0.0904 model score 0.0886 model score -0.0225 model score 0.1568 model score -0.1917 model score -0.4562 model score -0.4836 model score -0.4265 model score -0.4665 model score -0.3902 model score -0.4587 model score -0.4265 model score -0.4589 model score -0.4665 model score -0.4535 model score -0.6217 model score -0.5265 model score -0.4670 model score -0.6160 model score -0.5029 model score 1.2856 model score 1.2903 model score 1.2891 model score 1.3039 model score 1.3072 model score -0.4765 model score -0.5035 model score -0.4925 model score -0.4956 model score -0.4682 model score -0.4041 model score -0.3944 model score -0.4820 model score -0.3926 model score -0.5048 model score -0.4042 model score -0.4883 model score -0.3871 model score -0.4664 model score -0.4391 model score -0.4555 model score -0.4661 model score -0.4661 model score -0.4661 model score -0.4660 model score -0.4660 model score -0.3501 model score -0.3730 model score -0.3898 model score -0.4450 model score -0.2814 model score -0.4946 model score -0.5029 model score -0.4718 model score -0.4544 model score -0.4404 model score -0.3682 model score -0.3928 model score -0.4542 model score -0.4130 model score -0.4029 model score -0.4643 model score -0.4559 model score -0.4978 model score -0.4391 model score -0.5122 model score -0.3501 model score -0.2814 model score -0.3898 model score -0.3730 model score -0.3268 model score -0.4064 model score -0.4492 model score -0.2918 model score -0.3351 model score -0.4091 model score 1.2537 model score 1.2553 model score 1.2583 model score 1.2584 model score 1.2566 model score 1.2567 model score 1.2584 model score 1.2579 model score 1.2586 model score 1.2583 model score -0.3997 model score -0.0570 model score -0.3120 model score -0.0852 model score -0.3452 model score -0.5029 model score -0.3345 model score -0.2845 model score 0.0452 model score 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eval: 0.0000 min: 0.0000 max: 0.0022 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0022 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0022 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0022 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0022 USE_EVALUE, weight: 0.9992 eval: 0.0000 min: 0.0000 max: 0.0022 USE_EVALUE, weight: 0.9992 eval: 0.0000 min: 0.0000 max: 0.0022 USE_EVALUE, weight: 0.9992 eval: 0.0000 min: 0.0000 max: 0.0022 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0022 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0022 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0022 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0022 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0022 USE_EVALUE, weight: 1.0000 eval: 0.0000 min: 0.0000 max: 0.0022 USE_EVALUE, weight: 0.6960 eval: 0.0008 min: 0.0000 max: 0.0022 USE_EVALUE, weight: 0.6960 eval: 0.0008 min: 0.0000 max: 0.0022 USE_EVALUE, weight: 0.6960 eval: 0.0008 min: 0.0000 max: 0.0022 Number of contacts in models: 272 Number of contacts in alignments: 147 NUMB_ALIGNS: 147 Adding 8929 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: -384.9337, CN propb: -384.9337 weights: 0.3567 constraints: 648 # command:Found ConstraintSet # PrintContacts align.constraints_meta03 Number of constraints in align3.constraints 648 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_meta03 Number of constraints in align3.constraints.bonus 648 # command:Found ConstraintSet # PrintContacts rejected.constraints_meta03 Number of constraints in rejected3.constraints 8281 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_meta03 Number of constraints in rejected3.constraints.bonus 8281 # 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 8929 # command: