# 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/T0314/ # command:# Making conformation for sequence T0314 numbered 1 through 106 Created new target T0314 from T0314.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0314/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0314//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0314/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0314//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0314/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0314/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0314/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1b89A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1b89A expands to /projects/compbio/data/pdb/1b89.pdb.gz 1b89A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0314 read from 1b89A/merged-good-all-a2m # 1b89A read from 1b89A/merged-good-all-a2m # adding 1b89A to template set # found chain 1b89A in template set T0314 4 :TSTDICQAADAL 1b89A 1344 :NIPKVLRAAEQA # choosing archetypes in rotamer library Number of specific fragments extracted= 1 number of extra gaps= 0 total=1 # 1b89A read from 1b89A/merged-good-all-a2m # found chain 1b89A in template set T0314 6 :TDICQAADAL 1b89A 1346 :PKVLRAAEQA Number of specific fragments extracted= 1 number of extra gaps= 0 total=2 # 1b89A read from 1b89A/merged-good-all-a2m # found chain 1b89A in template set T0314 4 :TSTDICQAADAL 1b89A 1344 :NIPKVLRAAEQA Number of specific fragments extracted= 1 number of extra gaps= 0 total=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rypJ/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1rypJ expands to /projects/compbio/data/pdb/1ryp.pdb.gz 1rypJ:# T0314 read from 1rypJ/merged-good-all-a2m # 1rypJ read from 1rypJ/merged-good-all-a2m # adding 1rypJ to template set # found chain 1rypJ in template set T0314 2 :SITSTDICQAADA 1rypJ 72 :AIEPETFTQLVSS T0314 15 :LKG 1rypJ 86 :LYE T0314 18 :FVGFNRKTGRYIVRFSE 1rypJ 100 :VAGINSKSGKPFIAGFD T0314 42 :ADDSITPTSEFVWSSV 1rypJ 117 :LIGCIDEAKDFIVSGT T0314 64 :LGREQLQILLEQNI 1rypJ 149 :LEPEDLFETISQAL T0314 78 :NERLNIGEPLLVYLRRQD 1rypJ 167 :DRDALSGWGAVVYIIKKD T0314 98 :EITAQ 1rypJ 185 :EVVKR Number of specific fragments extracted= 7 number of extra gaps= 0 total=10 Number of alignments=1 # 1rypJ read from 1rypJ/merged-good-all-a2m # found chain 1rypJ in template set T0314 8 :ICQAADALK 1rypJ 82 :VSSSLYERR T0314 18 :FVGFNRKTGRYIVRFSE 1rypJ 100 :VAGINSKSGKPFIAGFD T0314 42 :ADDSITPTSEFVWSS 1rypJ 117 :LIGCIDEAKDFIVSG T0314 58 :RD 1rypJ 146 :EP T0314 64 :LGREQLQILLEQNINERLN 1rypJ 149 :LEPEDLFETISQALLNAAD T0314 83 :IGEPLLVYLRRQD 1rypJ 172 :SGWGAVVYIIKKD T0314 98 :EITAQ 1rypJ 185 :EVVKR Number of specific fragments extracted= 7 number of extra gaps= 0 total=17 Number of alignments=2 # 1rypJ read from 1rypJ/merged-good-all-a2m # found chain 1rypJ in template set T0314 2 :SITSTDICQAADA 1rypJ 72 :AIEPETFTQLVSS T0314 15 :LKG 1rypJ 86 :LYE T0314 18 :FVGFNRKTGRYIVRFSE 1rypJ 100 :VAGINSKSGKPFIAGFD T0314 42 :ADDSITPTSEFVWSSVRDDVM 1rypJ 117 :LIGCIDEAKDFIVSGTASDQL T0314 63 :RLGREQLQILLEQNI 1rypJ 148 :NLEPEDLFETISQAL T0314 78 :NERLNIGEPLLVYLRRQD 1rypJ 167 :DRDALSGWGAVVYIIKKD T0314 98 :EITAQ 1rypJ 185 :EVVKR Number of specific fragments extracted= 7 number of extra gaps= 0 total=24 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1wjxA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0314 read from 1wjxA/merged-good-all-a2m # 1wjxA read from 1wjxA/merged-good-all-a2m # found chain 1wjxA in training set Warning: unaligning (T0314)P48 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1wjxA)V70 Warning: unaligning (T0314)V57 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1wjxA)V70 T0314 17 :GFVGF 1wjxA 43 :SFARF T0314 24 :KTGRYIVR 1wjxA 48 :EDGELYLE T0314 43 :DDSIT 1wjxA 56 :NLYIA T0314 58 :RDD 1wjxA 71 :DPR T0314 61 :VMRLGREQLQILLEQNINERLNI 1wjxA 77 :KLLLHKHELRRLLGKVEQKGLTL T0314 85 :EPLLVYLRRQDLPEITAQ 1wjxA 100 :VPLKIYFNERGYAKVLLG Number of specific fragments extracted= 6 number of extra gaps= 0 total=30 Number of alignments=4 # 1wjxA read from 1wjxA/merged-good-all-a2m # found chain 1wjxA in training set Warning: unaligning (T0314)P48 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1wjxA)V70 Warning: unaligning (T0314)V57 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1wjxA)V70 T0314 16 :KGFVGFNR 1wjxA 35 :AGKVDFTG T0314 24 :KTGRYIVR 1wjxA 48 :EDGELYLE T0314 43 :DDSIT 1wjxA 56 :NLYIA T0314 58 :RDD 1wjxA 71 :DPR T0314 61 :VMRLGREQLQILLEQNINERLNI 1wjxA 77 :KLLLHKHELRRLLGKVEQKGLTL T0314 85 :EPLLVYLRRQDL 1wjxA 100 :VPLKIYFNERGY Number of specific fragments extracted= 6 number of extra gaps= 0 total=36 Number of alignments=5 # 1wjxA read from 1wjxA/merged-good-all-a2m # found chain 1wjxA in training set Warning: unaligning (T0314)P48 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1wjxA)V70 Warning: unaligning (T0314)V57 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1wjxA)V70 T0314 18 :FVGF 1wjxA 44 :FARF T0314 24 :KTGRYIVR 1wjxA 48 :EDGELYLE T0314 43 :DDSIT 1wjxA 56 :NLYIA T0314 58 :RDD 1wjxA 71 :DPR T0314 61 :VMRLGREQLQILLEQNINERLNI 1wjxA 77 :KLLLHKHELRRLLGKVEQKGLTL T0314 85 :EPLLVYLRRQDLPEIT 1wjxA 100 :VPLKIYFNERGYAKVL Number of specific fragments extracted= 6 number of extra gaps= 0 total=42 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2f1kA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2f1kA expands to /projects/compbio/data/pdb/2f1k.pdb.gz 2f1kA:Skipped atom 152, because occupancy 0.4 <= existing 0.600 in 2f1kA Skipped atom 444, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 446, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 448, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 450, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 452, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 807, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 809, because occupancy 0.500 <= existing 0.500 in 2f1kA Bad short name: OD3 for alphabet: pdb_atoms Skipped atom 1215, because occupancy 0.400 <= existing 0.600 in 2f1kA Skipped atom 1217, because occupancy 0.400 <= existing 0.600 in 2f1kA Skipped atom 1219, because occupancy 0.400 <= existing 0.600 in 2f1kA Skipped atom 1221, because occupancy 0.400 <= existing 0.600 in 2f1kA Skipped atom 1223, because occupancy 0.400 <= existing 0.600 in 2f1kA Skipped atom 1576, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1578, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1703, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1705, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1707, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1717, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1719, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1721, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1723, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1725, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1727, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1729, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1731, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1858, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1860, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1862, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1864, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1866, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1868, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1870, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1872, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1874, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1876, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1878, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1967, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1969, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1988, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1990, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1992, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1994, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1996, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 1998, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 2000, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 2002, because occupancy 0.500 <= existing 0.500 in 2f1kA Skipped atom 2004, because occupancy 0.500 <= existing 0.500 in 2f1kA # T0314 read from 2f1kA/merged-good-all-a2m # 2f1kA read from 2f1kA/merged-good-all-a2m # adding 2f1kA to template set # found chain 2f1kA in template set Warning: unaligning (T0314)R23 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2f1kA)A115 Warning: unaligning (T0314)T25 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2f1kA)A115 Warning: unaligning (T0314)G26 because of BadResidue code BAD_PEPTIDE in next template residue (2f1kA)T117 Warning: unaligning (T0314)E34 because of BadResidue code BAD_PEPTIDE at template residue (2f1kA)T117 Warning: unaligning (T0314)D35 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f1kA)A118 Warning: unaligning (T0314)S36 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2f1kA)Q120 Warning: unaligning (T0314)F37 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f1kA)Q120 Warning: unaligning (T0314)Q70 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2f1kA)L151 Warning: unaligning (T0314)L72 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2f1kA)L151 T0314 3 :ITSTDICQAADALKGFVGFN 2f1kA 93 :VKTAIAEPASQLWSGFIGGH T0314 38 :GMDVADDSITPTSEFVWSSVRD 2f1kA 121 :GIDGAEENLFVNAPYVLTPTEY T0314 64 :LGREQL 2f1kA 143 :TDPEQL T0314 73 :L 2f1kA 152 :R Number of specific fragments extracted= 4 number of extra gaps= 0 total=46 Number of alignments=7 # 2f1kA read from 2f1kA/merged-good-all-a2m # found chain 2f1kA in template set Warning: unaligning (T0314)R23 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2f1kA)A115 Warning: unaligning (T0314)T25 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2f1kA)A115 Warning: unaligning (T0314)G26 because of BadResidue code BAD_PEPTIDE in next template residue (2f1kA)T117 Warning: unaligning (T0314)E34 because of BadResidue code BAD_PEPTIDE at template residue (2f1kA)T117 Warning: unaligning (T0314)D35 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f1kA)A118 Warning: unaligning (T0314)S36 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2f1kA)Q120 Warning: unaligning (T0314)F37 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f1kA)Q120 Warning: unaligning (T0314)Q70 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2f1kA)L151 Warning: unaligning (T0314)L72 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2f1kA)L151 T0314 9 :CQAADALKGFVGFN 2f1kA 99 :EPASQLWSGFIGGH T0314 38 :GMDVADDSITPTSEFVWSSVRD 2f1kA 121 :GIDGAEENLFVNAPYVLTPTEY T0314 64 :LGREQL 2f1kA 143 :TDPEQL T0314 73 :LE 2f1kA 152 :RS Number of specific fragments extracted= 4 number of extra gaps= 0 total=50 Number of alignments=8 # 2f1kA read from 2f1kA/merged-good-all-a2m # found chain 2f1kA in template set Warning: unaligning (T0314)R23 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2f1kA)A115 Warning: unaligning (T0314)T25 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2f1kA)A115 Warning: unaligning (T0314)G26 because of BadResidue code BAD_PEPTIDE in next template residue (2f1kA)T117 Warning: unaligning (T0314)E34 because of BadResidue code BAD_PEPTIDE at template residue (2f1kA)T117 Warning: unaligning (T0314)D35 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f1kA)A118 Warning: unaligning (T0314)S36 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2f1kA)Q120 Warning: unaligning (T0314)F37 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2f1kA)Q120 Warning: unaligning (T0314)Q70 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2f1kA)L151 Warning: unaligning (T0314)L72 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2f1kA)L151 T0314 3 :ITSTDICQAADALKGFVGFN 2f1kA 93 :VKTAIAEPASQLWSGFIGGH T0314 38 :GMDVADDSITPTSEFVWSSVRD 2f1kA 121 :GIDGAEENLFVNAPYVLTPTEY T0314 64 :LGREQL 2f1kA 143 :TDPEQL T0314 73 :L 2f1kA 152 :R Number of specific fragments extracted= 4 number of extra gaps= 0 total=54 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mw7A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1mw7A expands to /projects/compbio/data/pdb/1mw7.pdb.gz 1mw7A:# T0314 read from 1mw7A/merged-good-all-a2m # 1mw7A read from 1mw7A/merged-good-all-a2m # adding 1mw7A to template set # found chain 1mw7A in template set T0314 3 :ITSTDICQAADAL 1mw7A 149 :LSLEDLEFALIDY T0314 17 :GFVGFNRKTGRYIVRFSEDSF 1mw7A 162 :GLEELEEVEDKIIIRGDYNSF T0314 44 :DSITPTSEFVWSSVRDDVMRLGREQLQI 1mw7A 191 :SLKLPILKASLQRIATTPIELNDEQMEL T0314 73 :LEQNINERLNIGEPLLVYLR 1mw7A 219 :TEKLLDRIEDDDDVVALYTN Number of specific fragments extracted= 4 number of extra gaps= 0 total=58 Number of alignments=10 # 1mw7A read from 1mw7A/merged-good-all-a2m # found chain 1mw7A in template set T0314 3 :ITSTDICQAADAL 1mw7A 149 :LSLEDLEFALIDY T0314 17 :GFVGFNRKTGRYIVRFSEDSF 1mw7A 162 :GLEELEEVEDKIIIRGDYNSF T0314 44 :DSITPTSEFVWSSVRDDVMRLGREQLQIL 1mw7A 191 :SLKLPILKASLQRIATTPIELNDEQMELT T0314 74 :EQNINERLNIGEPLLVYL 1mw7A 220 :EKLLDRIEDDDDVVALYT Number of specific fragments extracted= 4 number of extra gaps= 0 total=62 Number of alignments=11 # 1mw7A read from 1mw7A/merged-good-all-a2m # found chain 1mw7A in template set T0314 3 :ITSTDICQAADAL 1mw7A 149 :LSLEDLEFALIDY T0314 17 :GFVGFNRKTGRYIVRFSEDSF 1mw7A 162 :GLEELEEVEDKIIIRGDYNSF T0314 44 :DSITPTSEFVWSSVRDDVMRLGREQLQI 1mw7A 191 :SLKLPILKASLQRIATTPIELNDEQMEL T0314 73 :LEQNINERLNIGEPLLVYLR 1mw7A 219 :TEKLLDRIEDDDDVVALYTN Number of specific fragments extracted= 4 number of extra gaps= 0 total=66 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kshA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1kshA expands to /projects/compbio/data/pdb/1ksh.pdb.gz 1kshA:Skipped atom 280, because occupancy 0.400 <= existing 0.600 in 1kshA Skipped atom 282, because occupancy 0.400 <= existing 0.600 in 1kshA Skipped atom 284, because occupancy 0.400 <= existing 0.600 in 1kshA Skipped atom 286, because occupancy 0.400 <= existing 0.600 in 1kshA Skipped atom 288, because occupancy 0.400 <= existing 0.600 in 1kshA Skipped atom 290, because occupancy 0.400 <= existing 0.600 in 1kshA Skipped atom 292, because occupancy 0.400 <= existing 0.600 in 1kshA Skipped atom 294, because occupancy 0.400 <= existing 0.600 in 1kshA Skipped atom 353, because occupancy 0.500 <= existing 0.500 in 1kshA Skipped atom 355, because occupancy 0.500 <= existing 0.500 in 1kshA Skipped atom 357, because occupancy 0.500 <= existing 0.500 in 1kshA Skipped atom 359, because occupancy 0.500 <= existing 0.500 in 1kshA Skipped atom 361, because occupancy 0.500 <= existing 0.500 in 1kshA Skipped atom 1048, because occupancy 0.500 <= existing 0.500 in 1kshA Skipped atom 1050, because occupancy 0.500 <= existing 0.500 in 1kshA Skipped atom 1052, because occupancy 0.500 <= existing 0.500 in 1kshA Skipped atom 1054, because occupancy 0.500 <= existing 0.500 in 1kshA Skipped atom 1091, because occupancy 0.300 <= existing 0.700 in 1kshA Skipped atom 1093, because occupancy 0.300 <= existing 0.700 in 1kshA Skipped atom 1095, because occupancy 0.300 <= existing 0.700 in 1kshA Skipped atom 1097, because occupancy 0.300 <= existing 0.700 in 1kshA Skipped atom 1099, because occupancy 0.300 <= existing 0.700 in 1kshA Skipped atom 1101, because occupancy 0.300 <= existing 0.700 in 1kshA Skipped atom 1150, because occupancy 0.300 <= existing 0.700 in 1kshA Skipped atom 1152, because occupancy 0.300 <= existing 0.700 in 1kshA Skipped atom 1154, because occupancy 0.300 <= existing 0.700 in 1kshA Skipped atom 1156, because occupancy 0.300 <= existing 0.700 in 1kshA # T0314 read from 1kshA/merged-good-all-a2m # 1kshA read from 1kshA/merged-good-all-a2m # adding 1kshA to template set # found chain 1kshA in template set T0314 44 :DSITPTSEFVW 1kshA 42 :DTISPTLGFNI T0314 55 :SSVRDDVMR 1kshA 55 :LEHRGFKLN Number of specific fragments extracted= 2 number of extra gaps= 0 total=68 Number of alignments=13 # 1kshA read from 1kshA/merged-good-all-a2m # found chain 1kshA in template set Number of specific fragments extracted= 0 number of extra gaps= 0 total=68 # 1kshA read from 1kshA/merged-good-all-a2m # found chain 1kshA in template set T0314 21 :FNRKTGRYIVRFSED 1kshA 56 :EHRGFKLNIWDVGGQ T0314 36 :SFGMDV 1kshA 75 :SYWRNY T0314 43 :DDSIT 1kshA 81 :FESTD T0314 52 :FVWSSVRDDVMRLGREQLQILLEQ 1kshA 89 :WVVDSADRQRMQDCQRELQSLLVE T0314 79 :ERLN 1kshA 113 :ERLA T0314 84 :GEPLLVYLRRQDLP 1kshA 117 :GATLLIFANKQDLP Number of specific fragments extracted= 6 number of extra gaps= 0 total=74 Number of alignments=14 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zicA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0314/1zicA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0314/1zicA/merged-good-all-a2m.gz for input Trying 1zicA/merged-good-all-a2m Error: Couldn't open file 1zicA/merged-good-all-a2m or 1zicA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vemA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vemA expands to /projects/compbio/data/pdb/1vem.pdb.gz 1vemA:Skipped atom 2616, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2618, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2620, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2622, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2624, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2626, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2628, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2630, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2632, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2634, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2636, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2638, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2640, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2642, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2644, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2646, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2648, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2650, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2652, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2654, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2656, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2658, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2660, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2662, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2664, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2666, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2668, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2670, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2672, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2674, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2676, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2678, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2680, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2682, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2684, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2686, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2688, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2690, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2692, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2694, because occupancy 0.500 <= existing 0.500 in 1vemA Skipped atom 2696, because occupancy 0.500 <= existing 0.500 in 1vemA # T0314 read from 1vemA/merged-good-all-a2m # 1vemA read from 1vemA/merged-good-all-a2m # adding 1vemA to template set # found chain 1vemA in template set T0314 6 :TDICQAADALKGFVGF 1vemA 405 :NSLMGKFKDLLGVTPV T0314 23 :RKTGRYIVRFSEDSFGMDVADDSITPT 1vemA 432 :TIGDTVYITGNRAELGSWDTKQYPIQL T0314 53 :VWSSVRDD 1vemA 459 :YYDSHSND T0314 61 :VMRLGR 1vemA 470 :NVVLPA T0314 82 :NIGEPLLVYLRRQDLP 1vemA 476 :ERNIEFKAFIKSKDGT Number of specific fragments extracted= 5 number of extra gaps= 0 total=79 Number of alignments=15 # 1vemA read from 1vemA/merged-good-all-a2m # found chain 1vemA in template set T0314 23 :RKTGRYIVRFSEDSFGMDVADDSIT 1vemA 432 :TIGDTVYITGNRAELGSWDTKQYPI T0314 51 :EFVWSSVRDD 1vemA 457 :QLYYDSHSND T0314 61 :VMRLGR 1vemA 470 :NVVLPA T0314 82 :NIGEPLLVYLRRQDLP 1vemA 476 :ERNIEFKAFIKSKDGT Number of specific fragments extracted= 4 number of extra gaps= 0 total=83 Number of alignments=16 # 1vemA read from 1vemA/merged-good-all-a2m # found chain 1vemA in template set Number of specific fragments extracted= 0 number of extra gaps= 0 total=83 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1o17A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1o17A expands to /projects/compbio/data/pdb/1o17.pdb.gz 1o17A:# T0314 read from 1o17A/merged-good-all-a2m # 1o17A read from 1o17A/merged-good-all-a2m # adding 1o17A to template set # found chain 1o17A in template set T0314 6 :TDICQAADALK 1o17A 199 :DLLSKSAYELD T0314 25 :TGRYIVRFSEDSF 1o17A 210 :FNKIILVYGEPGI T0314 44 :DSITPTSEF 1o17A 223 :DEVSPIGNT T0314 53 :VWSSVRDDVMRLG 1o17A 235 :IVSKRGIEEVKLN Number of specific fragments extracted= 4 number of extra gaps= 0 total=87 Number of alignments=17 # 1o17A read from 1o17A/merged-good-all-a2m # found chain 1o17A in template set T0314 8 :ICQAADALK 1o17A 201 :LSKSAYELD T0314 21 :F 1o17A 210 :F T0314 26 :GRYIVRFSEDSF 1o17A 211 :NKIILVYGEPGI T0314 44 :DSITPTSEFVWSS 1o17A 223 :DEVSPIGNTFMKI T0314 57 :VRDDVMRLG 1o17A 237 :SKRGIEEVK Number of specific fragments extracted= 5 number of extra gaps= 0 total=92 Number of alignments=18 # 1o17A read from 1o17A/merged-good-all-a2m # found chain 1o17A in template set T0314 6 :TDICQAADALK 1o17A 199 :DLLSKSAYELD T0314 25 :TGRYIVRFSEDSF 1o17A 210 :FNKIILVYGEPGI T0314 44 :DSITPTSEF 1o17A 223 :DEVSPIGNT T0314 53 :VWSSVRDDVMRLG 1o17A 235 :IVSKRGIEEVKLN Number of specific fragments extracted= 4 number of extra gaps= 0 total=96 Number of alignments=19 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cb2A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2cb2A expands to /projects/compbio/data/pdb/2cb2.pdb.gz 2cb2A:Skipped atom 164, because occupancy 0.430 <= existing 0.570 in 2cb2A Skipped atom 166, because occupancy 0.430 <= existing 0.570 in 2cb2A Skipped atom 168, because occupancy 0.430 <= existing 0.570 in 2cb2A Skipped atom 170, because occupancy 0.430 <= existing 0.570 in 2cb2A Skipped atom 172, because occupancy 0.430 <= existing 0.570 in 2cb2A Skipped atom 174, because occupancy 0.430 <= existing 0.570 in 2cb2A Skipped atom 176, because occupancy 0.430 <= existing 0.570 in 2cb2A Skipped atom 178, because occupancy 0.430 <= existing 0.570 in 2cb2A Skipped atom 262, because occupancy 0.490 <= existing 0.510 in 2cb2A Skipped atom 264, because occupancy 0.490 <= existing 0.510 in 2cb2A Skipped atom 266, because occupancy 0.490 <= existing 0.510 in 2cb2A Skipped atom 369, because occupancy 0.480 <= existing 0.520 in 2cb2A Skipped atom 371, because occupancy 0.480 <= existing 0.520 in 2cb2A Skipped atom 373, because occupancy 0.480 <= existing 0.520 in 2cb2A Skipped atom 375, because occupancy 0.480 <= existing 0.520 in 2cb2A Skipped atom 542, because occupancy 0.310 <= existing 0.690 in 2cb2A Skipped atom 544, because occupancy 0.310 <= existing 0.690 in 2cb2A Skipped atom 847, because occupancy 0.490 <= existing 0.510 in 2cb2A Skipped atom 849, because occupancy 0.490 <= existing 0.510 in 2cb2A Skipped atom 851, because occupancy 0.490 <= existing 0.510 in 2cb2A Skipped atom 853, because occupancy 0.490 <= existing 0.510 in 2cb2A Skipped atom 855, because occupancy 0.490 <= existing 0.510 in 2cb2A Skipped atom 857, because occupancy 0.490 <= existing 0.510 in 2cb2A Skipped atom 859, because occupancy 0.490 <= existing 0.510 in 2cb2A Skipped atom 861, because occupancy 0.490 <= existing 0.510 in 2cb2A Skipped atom 1372, because occupancy 0.410 <= existing 0.590 in 2cb2A Skipped atom 1374, because occupancy 0.410 <= existing 0.590 in 2cb2A Skipped atom 1462, because occupancy 0.380 <= existing 0.620 in 2cb2A Skipped atom 1464, because occupancy 0.380 <= existing 0.620 in 2cb2A Skipped atom 1466, because occupancy 0.380 <= existing 0.620 in 2cb2A Skipped atom 1468, because occupancy 0.380 <= existing 0.620 in 2cb2A Skipped atom 1495, because occupancy 0.380 <= existing 0.620 in 2cb2A Skipped atom 1497, because occupancy 0.380 <= existing 0.620 in 2cb2A Skipped atom 1499, because occupancy 0.380 <= existing 0.620 in 2cb2A Skipped atom 1501, because occupancy 0.380 <= existing 0.620 in 2cb2A Skipped atom 1503, because occupancy 0.380 <= existing 0.620 in 2cb2A Skipped atom 1505, because occupancy 0.380 <= existing 0.620 in 2cb2A Skipped atom 1702, because occupancy 0.450 <= existing 0.550 in 2cb2A Skipped atom 1704, because occupancy 0.450 <= existing 0.550 in 2cb2A Skipped atom 1706, because occupancy 0.450 <= existing 0.550 in 2cb2A Skipped atom 1958, because occupancy 0.420 <= existing 0.580 in 2cb2A Skipped atom 1960, because occupancy 0.420 <= existing 0.580 in 2cb2A Skipped atom 1962, because occupancy 0.420 <= existing 0.580 in 2cb2A Skipped atom 1964, because occupancy 0.420 <= existing 0.580 in 2cb2A Skipped atom 2015, because occupancy 0.340 <= existing 0.660 in 2cb2A Skipped atom 2018, because occupancy 0.340 <= existing 0.660 in 2cb2A Skipped atom 2401, because occupancy 0.500 <= existing 0.500 in 2cb2A Skipped atom 2403, because occupancy 0.500 <= existing 0.500 in 2cb2A Skipped atom 2405, because occupancy 0.500 <= existing 0.500 in 2cb2A Skipped atom 2407, because occupancy 0.500 <= existing 0.500 in 2cb2A # T0314 read from 2cb2A/merged-good-all-a2m # 2cb2A read from 2cb2A/merged-good-all-a2m # adding 2cb2A to template set # found chain 2cb2A in template set Warning: unaligning (T0314)I8 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2cb2A)M32 Warning: unaligning (T0314)Q10 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2cb2A)M32 T0314 5 :STD 2cb2A 27 :GPK T0314 11 :AADALKGFVGF 2cb2A 33 :VTARHPGFVGF T0314 27 :RYIVRFSEDSFGMDVADDSITPTSE 2cb2A 44 :QNHIQIGILPFGNRYGGAKMDMTKE T0314 59 :DDVMRL 2cb2A 69 :SSTVRV T0314 65 :GREQLQILLEQNINE 2cb2A 82 :DWKDHEEMHRQNWSY Number of specific fragments extracted= 5 number of extra gaps= 0 total=101 Number of alignments=20 # 2cb2A read from 2cb2A/merged-good-all-a2m # found chain 2cb2A in template set Warning: unaligning (T0314)I8 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2cb2A)M32 Warning: unaligning (T0314)Q10 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2cb2A)M32 T0314 6 :TD 2cb2A 28 :PK T0314 11 :AADALKGFVGFN 2cb2A 33 :VTARHPGFVGFQ T0314 28 :YIVRFSEDSFGMDVADDSITPTSE 2cb2A 45 :NHIQIGILPFGNRYGGAKMDMTKE T0314 59 :DDVMRL 2cb2A 69 :SSTVRV T0314 65 :GREQLQILLEQNIN 2cb2A 82 :DWKDHEEMHRQNWS Number of specific fragments extracted= 5 number of extra gaps= 0 total=106 Number of alignments=21 # 2cb2A read from 2cb2A/merged-good-all-a2m # found chain 2cb2A in template set Warning: unaligning (T0314)I8 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2cb2A)M32 Warning: unaligning (T0314)Q10 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2cb2A)M32 T0314 5 :STD 2cb2A 27 :GPK T0314 11 :AADALKGFVGF 2cb2A 33 :VTARHPGFVGF T0314 27 :RYIVRFSEDSFGMDVADDSITPTSE 2cb2A 44 :QNHIQIGILPFGNRYGGAKMDMTKE T0314 59 :DDVMRL 2cb2A 69 :SSTVRV T0314 65 :GREQLQILLEQNINE 2cb2A 82 :DWKDHEEMHRQNWSY Number of specific fragments extracted= 5 number of extra gaps= 0 total=111 Number of alignments=22 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1din/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0314 read from 1din/merged-good-all-a2m # 1din read from 1din/merged-good-all-a2m # found chain 1din in training set T0314 17 :GFVGFNRKTGRYIVRFSEDSFGMD 1din 18 :ALVGSPAKAPAPVIVIAQEIFGVN T0314 66 :REQLQILLEQNI 1din 45 :RETVSWLVDQGY Number of specific fragments extracted= 2 number of extra gaps= 0 total=113 Number of alignments=23 # 1din read from 1din/merged-good-all-a2m # found chain 1din in training set T0314 18 :FVGFNRKTGRYIVRFSEDSFGMDV 1din 19 :LVGSPAKAPAPVIVIAQEIFGVNA T0314 66 :REQLQILLEQNI 1din 45 :RETVSWLVDQGY Number of specific fragments extracted= 2 number of extra gaps= 0 total=115 Number of alignments=24 # 1din read from 1din/merged-good-all-a2m # found chain 1din in training set T0314 17 :GFVGFNRKTGRYIVRFSEDSFGMD 1din 18 :ALVGSPAKAPAPVIVIAQEIFGVN T0314 64 :LGREQLQILLEQNI 1din 43 :FMRETVSWLVDQGY Number of specific fragments extracted= 2 number of extra gaps= 0 total=117 Number of alignments=25 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1veoA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0314/1veoA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0314/1veoA/merged-good-all-a2m.gz for input Trying 1veoA/merged-good-all-a2m Error: Couldn't open file 1veoA/merged-good-all-a2m or 1veoA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 4icb/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 4icb expands to /projects/compbio/data/pdb/4icb.pdb.gz 4icb:Warning: there is no chain 4icb will retry with 4icbA Skipped atom 243, because occupancy 0.330 <= existing 0.670 in 4icb Skipped atom 245, because occupancy 0.330 <= existing 0.670 in 4icb Skipped atom 247, because occupancy 0.330 <= existing 0.670 in 4icb Skipped atom 249, because occupancy 0.330 <= existing 0.670 in 4icb Skipped atom 332, because occupancy 0.500 <= existing 0.500 in 4icb Skipped atom 334, because occupancy 0.500 <= existing 0.500 in 4icb Skipped atom 336, because occupancy 0.500 <= existing 0.500 in 4icb Skipped atom 338, because occupancy 0.500 <= existing 0.500 in 4icb Skipped atom 340, because occupancy 0.500 <= existing 0.500 in 4icb Skipped atom 342, because occupancy 0.500 <= existing 0.500 in 4icb Skipped atom 344, because occupancy 0.500 <= existing 0.500 in 4icb Skipped atom 346, because occupancy 0.500 <= existing 0.500 in 4icb Skipped atom 348, because occupancy 0.500 <= existing 0.500 in 4icb Skipped atom 350, because occupancy 0.500 <= existing 0.500 in 4icb Skipped atom 352, because occupancy 0.500 <= existing 0.500 in 4icb Skipped atom 354, because occupancy 0.500 <= existing 0.500 in 4icb Skipped atom 356, because occupancy 0.500 <= existing 0.500 in 4icb Skipped atom 358, because occupancy 0.500 <= existing 0.500 in 4icb Skipped atom 360, because occupancy 0.500 <= existing 0.500 in 4icb Skipped atom 362, because occupancy 0.500 <= existing 0.500 in 4icb Skipped atom 364, because occupancy 0.500 <= existing 0.500 in 4icb Skipped atom 366, because occupancy 0.500 <= existing 0.500 in 4icb Skipped atom 368, because occupancy 0.500 <= existing 0.500 in 4icb Skipped atom 370, because occupancy 0.500 <= existing 0.500 in 4icb Skipped atom 562, because occupancy 0.400 <= existing 0.600 in 4icb Skipped atom 564, because occupancy 0.400 <= existing 0.600 in 4icb Skipped atom 566, because occupancy 0.400 <= existing 0.600 in 4icb Skipped atom 568, because occupancy 0.400 <= existing 0.600 in 4icb Skipped atom 570, because occupancy 0.400 <= existing 0.600 in 4icb Skipped atom 630, because occupancy 0.500 <= existing 0.500 in 4icb Skipped atom 632, because occupancy 0.500 <= existing 0.500 in 4icb Skipped atom 634, because occupancy 0.500 <= existing 0.500 in 4icb Skipped atom 636, because occupancy 0.500 <= existing 0.500 in 4icb Skipped atom 638, because occupancy 0.500 <= existing 0.500 in 4icb # T0314 read from 4icb/merged-good-all-a2m # 4icb read from 4icb/merged-good-all-a2m # adding 4icb to template set # found chain 4icb in template set T0314 64 :LGREQLQILLEQNINERLNIGEPL 4icb 23 :LSKEELKLLLQTEFPSLLKGPSTL Number of specific fragments extracted= 1 number of extra gaps= 0 total=118 Number of alignments=26 # 4icb read from 4icb/merged-good-all-a2m # found chain 4icb in template set T0314 3 :ITSTDICQAADALKG 4icb 1 :KSPEELKGIFEKYAA T0314 24 :KTG 4icb 16 :KEG T0314 43 :DDS 4icb 19 :DPN T0314 60 :D 4icb 22 :Q T0314 64 :LGREQLQILLEQNINERLNIGEP 4icb 23 :LSKEELKLLLQTEFPSLLKGPST Number of specific fragments extracted= 5 number of extra gaps= 0 total=123 Number of alignments=27 # 4icb read from 4icb/merged-good-all-a2m # found chain 4icb in template set T0314 64 :LGREQLQILLEQNINERLNIGEPL 4icb 23 :LSKEELKLLLQTEFPSLLKGPSTL Number of specific fragments extracted= 1 number of extra gaps= 0 total=124 Number of alignments=28 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1itcA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1itcA expands to /projects/compbio/data/pdb/1itc.pdb.gz 1itcA:# T0314 read from 1itcA/merged-good-all-a2m # 1itcA read from 1itcA/merged-good-all-a2m # adding 1itcA to template set # found chain 1itcA in template set T0314 6 :TDICQAADALKGFVGF 1itcA 405 :NSLMGKFKDLLGVTPV T0314 22 :NRKTGRYIVRFSEDSFGMDVADDSI 1itcA 431 :TTIGDTVYITGNRAELGSWDTKQYP T0314 50 :SEFVWSSVRDD 1itcA 456 :IQLYYDSHSND T0314 61 :VMRLGR 1itcA 470 :NVVLPA T0314 82 :NIGEPLLVYLRRQDLP 1itcA 476 :ERNIEFKAFIKSKDGT Number of specific fragments extracted= 5 number of extra gaps= 0 total=129 Number of alignments=29 # 1itcA read from 1itcA/merged-good-all-a2m # found chain 1itcA in template set T0314 22 :NRKTGRYIVRFSEDSFGMDVADDSI 1itcA 431 :TTIGDTVYITGNRAELGSWDTKQYP T0314 50 :SEFVWSSVRDD 1itcA 456 :IQLYYDSHSND T0314 61 :VMRLGR 1itcA 470 :NVVLPA T0314 82 :NIGEPLLVYLRRQDLP 1itcA 476 :ERNIEFKAFIKSKDGT Number of specific fragments extracted= 4 number of extra gaps= 0 total=133 Number of alignments=30 # 1itcA read from 1itcA/merged-good-all-a2m # found chain 1itcA in template set Number of specific fragments extracted= 0 number of extra gaps= 0 total=133 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i6uA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1i6uA expands to /projects/compbio/data/pdb/1i6u.pdb.gz 1i6uA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0314 read from 1i6uA/merged-good-all-a2m # 1i6uA read from 1i6uA/merged-good-all-a2m # adding 1i6uA to template set # found chain 1i6uA in template set T0314 4 :TSTDICQAADAL 1i6uA 30 :ASKLIGRVLKVM T0314 16 :KGFVG 1i6uA 44 :NGYIG T0314 22 :NRKTGRYIVRFSEDSFGMDVADDS 1i6uA 55 :DGRAGIFKVELIGKINKCGAIKPR T0314 55 :SSVRDDVMRLGR 1i6uA 79 :FPVKKFGYEKFE T0314 74 :EQNINE 1i6uA 91 :KRYLPA T0314 84 :GEPLLVYLR 1i6uA 97 :RDFGILIVS Number of specific fragments extracted= 6 number of extra gaps= 0 total=139 Number of alignments=31 # 1i6uA read from 1i6uA/merged-good-all-a2m # found chain 1i6uA in template set T0314 4 :TSTDICQAADAL 1i6uA 30 :ASKLIGRVLKVM T0314 16 :KGFVG 1i6uA 44 :NGYIG T0314 22 :NRKTGRYIVRFSEDSFGMDVADDS 1i6uA 55 :DGRAGIFKVELIGKINKCGAIKPR T0314 55 :SSVRDDVMRLGR 1i6uA 79 :FPVKKFGYEKFE T0314 74 :EQNINE 1i6uA 91 :KRYLPA T0314 84 :GEPLLVYLR 1i6uA 97 :RDFGILIVS Number of specific fragments extracted= 6 number of extra gaps= 0 total=145 Number of alignments=32 # 1i6uA read from 1i6uA/merged-good-all-a2m # found chain 1i6uA in template set T0314 4 :TSTDICQAADAL 1i6uA 30 :ASKLIGRVLKVM T0314 16 :KGFVG 1i6uA 44 :NGYIG T0314 22 :NRKTGRYIVRFSEDSFGMDVADDS 1i6uA 55 :DGRAGIFKVELIGKINKCGAIKPR T0314 47 :T 1i6uA 79 :F T0314 56 :SVRDDVMRLG 1i6uA 80 :PVKKFGYEKF T0314 73 :LEQNINER 1i6uA 90 :EKRYLPAR T0314 84 :GEPL 1i6uA 98 :DFGI T0314 89 :VYL 1i6uA 102 :LIV Number of specific fragments extracted= 8 number of extra gaps= 0 total=153 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2sak/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0314 read from 2sak/merged-good-all-a2m # 2sak read from 2sak/merged-good-all-a2m # found chain 2sak in training set T0314 25 :TGRYI 2sak 21 :TGPYL T0314 30 :VRFS 2sak 27 :VNVT T0314 34 :EDSFGMDV 2sak 32 :VDSKGNEL T0314 48 :PTSEFVWSSVRDDV 2sak 40 :LSPHYVEFPIKPGT T0314 63 :RLGREQLQILLEQNINER 2sak 54 :TLTKEKIEYYVEWALDAT T0314 81 :LNIGEPLLVYL 2sak 81 :LDPSAKIEVTY T0314 92 :RRQDLPEITAQRQL 2sak 93 :DKNKKKEETKSFPI Number of specific fragments extracted= 7 number of extra gaps= 0 total=160 Number of alignments=34 # 2sak read from 2sak/merged-good-all-a2m # found chain 2sak in training set T0314 22 :NRKTGRYIVRFS 2sak 19 :EPTGPYLMVNVT T0314 35 :DSFGMDVA 2sak 33 :DSKGNELL T0314 49 :TSEFVWSSVRDDV 2sak 41 :SPHYVEFPIKPGT T0314 63 :RLGREQLQILLEQNINER 2sak 54 :TLTKEKIEYYVEWALDAT T0314 81 :LNIGEPLLVYLRRQD 2sak 81 :LDPSAKIEVTYYDKN T0314 96 :LPEITAQRQ 2sak 97 :KKEETKSFP Number of specific fragments extracted= 6 number of extra gaps= 0 total=166 Number of alignments=35 # 2sak read from 2sak/merged-good-all-a2m # found chain 2sak in training set T0314 25 :TGRYI 2sak 21 :TGPYL T0314 30 :VRFS 2sak 27 :VNVT T0314 35 :DSFGMDV 2sak 33 :DSKGNEL T0314 48 :PTSEFVWSSVRDDV 2sak 40 :LSPHYVEFPIKPGT T0314 63 :RLGREQLQILLEQNINER 2sak 54 :TLTKEKIEYYVEWALDAT T0314 81 :LNIGEPLLVYL 2sak 81 :LDPSAKIEVTY T0314 92 :RRQDLPEITAQRQLR 2sak 93 :DKNKKKEETKSFPIT Number of specific fragments extracted= 7 number of extra gaps= 0 total=173 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1go4A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1go4A expands to /projects/compbio/data/pdb/1go4.pdb.gz 1go4A:# T0314 read from 1go4A/merged-good-all-a2m # 1go4A read from 1go4A/merged-good-all-a2m # adding 1go4A to template set # found chain 1go4A in template set Warning: unaligning (T0314)S2 because of BadResidue code BAD_PEPTIDE at template residue (1go4A)G10 T0314 3 :ITSTDICQAADALKGF 1go4A 11 :ITLRGSAEIVAEFFSF T0314 41 :VADDSITPTSEFVWSSVRDDVMRLG 1go4A 32 :LYQRGIYPSETFTRVQKYGLTLLVT T0314 66 :REQLQILLEQNINERLNIG 1go4A 62 :IKYLNNVVEQLKDWLYKCS T0314 85 :EPLLVYLRRQDLPEITAQRQ 1go4A 82 :QKLVVVISNIESGEVLERWQ Number of specific fragments extracted= 4 number of extra gaps= 1 total=177 Number of alignments=37 # 1go4A read from 1go4A/merged-good-all-a2m # found chain 1go4A in template set Warning: unaligning (T0314)M1 because of BadResidue code BAD_PEPTIDE in next template residue (1go4A)G10 Warning: unaligning (T0314)S2 because of BadResidue code BAD_PEPTIDE at template residue (1go4A)G10 T0314 3 :ITSTDICQAADAL 1go4A 11 :ITLRGSAEIVAEF T0314 41 :VADDSITPTSEFVWSSVRDDVMRLG 1go4A 32 :LYQRGIYPSETFTRVQKYGLTLLVT T0314 66 :REQLQILLEQ 1go4A 62 :IKYLNNVVEQ T0314 77 :INERLNIG 1go4A 72 :LKDWLYKC T0314 85 :EPLLVYLRRQDLPEITAQ 1go4A 82 :QKLVVVISNIESGEVLER Number of specific fragments extracted= 5 number of extra gaps= 1 total=182 Number of alignments=38 # 1go4A read from 1go4A/merged-good-all-a2m # found chain 1go4A in template set Warning: unaligning (T0314)S2 because of BadResidue code BAD_PEPTIDE at template residue (1go4A)G10 T0314 3 :ITSTDICQAADALKGF 1go4A 11 :ITLRGSAEIVAEFFSF T0314 41 :VADDSITPTSEFVWSSVRDDVMRLG 1go4A 32 :LYQRGIYPSETFTRVQKYGLTLLVT T0314 66 :REQLQILLEQNINERLNIG 1go4A 62 :IKYLNNVVEQLKDWLYKCS T0314 85 :EPLLVYLRRQDLPEITAQRQ 1go4A 82 :QKLVVVISNIESGEVLERWQ Number of specific fragments extracted= 4 number of extra gaps= 1 total=186 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zi6A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0314/1zi6A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0314/1zi6A/merged-good-all-a2m.gz for input Trying 1zi6A/merged-good-all-a2m Error: Couldn't open file 1zi6A/merged-good-all-a2m or 1zi6A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yyaA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0314 read from 1yyaA/merged-good-all-a2m # 1yyaA read from 1yyaA/merged-good-all-a2m # found chain 1yyaA in training set T0314 3 :ITSTDICQAADAL 1yyaA 103 :ETDALVAEKAKRL Number of specific fragments extracted= 1 number of extra gaps= 0 total=187 # 1yyaA read from 1yyaA/merged-good-all-a2m # found chain 1yyaA in training set T0314 3 :ITSTDICQAADAL 1yyaA 103 :ETDALVAEKAKRL Number of specific fragments extracted= 1 number of extra gaps= 0 total=188 # 1yyaA read from 1yyaA/merged-good-all-a2m # found chain 1yyaA in training set T0314 3 :ITSTDICQAADAL 1yyaA 103 :ETDALVAEKAKRL Number of specific fragments extracted= 1 number of extra gaps= 0 total=189 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ggvA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ggvA expands to /projects/compbio/data/pdb/1ggv.pdb.gz 1ggvA:Bad short name: CI2 for alphabet: pdb_atoms Bad short name: CJ for alphabet: pdb_atoms Bad short name: CI1 for alphabet: pdb_atoms Bad short name: CH1 for alphabet: pdb_atoms # T0314 read from 1ggvA/merged-good-all-a2m # 1ggvA read from 1ggvA/merged-good-all-a2m # adding 1ggvA to template set # found chain 1ggvA in template set T0314 17 :GFVGFNRKTGRYIVRFSEDSFGMD 1ggvA 18 :ALVGSPAKAPAPVIVIAQEIFGVN T0314 66 :REQLQILLEQNI 1ggvA 45 :RETVSWLVDQGY Number of specific fragments extracted= 2 number of extra gaps= 0 total=191 Number of alignments=40 # 1ggvA read from 1ggvA/merged-good-all-a2m # found chain 1ggvA in template set T0314 18 :FVGFNRKTGRYIVRFSEDSFGMDV 1ggvA 19 :LVGSPAKAPAPVIVIAQEIFGVNA T0314 66 :REQLQILLEQNI 1ggvA 45 :RETVSWLVDQGY Number of specific fragments extracted= 2 number of extra gaps= 0 total=193 Number of alignments=41 # 1ggvA read from 1ggvA/merged-good-all-a2m # found chain 1ggvA in template set T0314 17 :GFVGFNRKTGRYIVRFSEDSFGMD 1ggvA 18 :ALVGSPAKAPAPVIVIAQEIFGVN T0314 64 :LGREQLQILLEQNI 1ggvA 43 :FMRETVSWLVDQGY Number of specific fragments extracted= 2 number of extra gaps= 0 total=195 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b5iC/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2b5iC expands to /projects/compbio/data/pdb/2b5i.pdb.gz 2b5iC:# T0314 read from 2b5iC/merged-good-all-a2m # 2b5iC read from 2b5iC/merged-good-all-a2m # adding 2b5iC to template set # found chain 2b5iC in template set T0314 28 :YIVRFSED 2b5iC 65 :LHYWYKNS T0314 42 :ADDSITPTSEFVWSSVRDDVMRLG 2b5iC 73 :DNDKVQKCSHYLFSEEITSGCQLQ T0314 78 :NERLNIGEPLLVYLRRQDLPEITAQRQLR 2b5iC 97 :KKEIHLYQTFVVQLQDPREPRRQATQMLK Number of specific fragments extracted= 3 number of extra gaps= 0 total=198 Number of alignments=43 # 2b5iC read from 2b5iC/merged-good-all-a2m # found chain 2b5iC in template set T0314 27 :RYIVRFSED 2b5iC 64 :TLHYWYKNS T0314 42 :ADDSITPTSEFVWSSVRDDVMRLG 2b5iC 73 :DNDKVQKCSHYLFSEEITSGCQLQ T0314 78 :NERLNIGEPLLVYLRRQDLPEITAQRQLR 2b5iC 97 :KKEIHLYQTFVVQLQDPREPRRQATQMLK Number of specific fragments extracted= 3 number of extra gaps= 0 total=201 Number of alignments=44 # 2b5iC read from 2b5iC/merged-good-all-a2m # found chain 2b5iC in template set T0314 28 :YIVRFSED 2b5iC 65 :LHYWYKNS T0314 42 :ADDSITPTSEFVWSSVRDDVMRLG 2b5iC 73 :DNDKVQKCSHYLFSEEITSGCQLQ T0314 78 :NERLNIGEPLLVYLRRQDLPEITAQRQLR 2b5iC 97 :KKEIHLYQTFVVQLQDPREPRRQATQMLK Number of specific fragments extracted= 3 number of extra gaps= 0 total=204 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zi8A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zi8A expands to /projects/compbio/data/pdb/1zi8.pdb.gz 1zi8A:# T0314 read from 1zi8A/merged-good-all-a2m # 1zi8A read from 1zi8A/merged-good-all-a2m # adding 1zi8A to template set # found chain 1zi8A in template set T0314 17 :GFVGFNRKTGRYIVRFSEDSFGMD 1zi8A 18 :ALVGSPAKAPAPVIVIAQDIFGVN T0314 66 :REQLQILLEQNI 1zi8A 45 :RETVSWLVDQGY Number of specific fragments extracted= 2 number of extra gaps= 0 total=206 Number of alignments=46 # 1zi8A read from 1zi8A/merged-good-all-a2m # found chain 1zi8A in template set T0314 18 :FVGFNRKTGRYIVRFSEDSFGMDV 1zi8A 19 :LVGSPAKAPAPVIVIAQDIFGVNA T0314 66 :REQLQILLEQNI 1zi8A 45 :RETVSWLVDQGY Number of specific fragments extracted= 2 number of extra gaps= 0 total=208 Number of alignments=47 # 1zi8A read from 1zi8A/merged-good-all-a2m # found chain 1zi8A in template set T0314 17 :GFVGFNRKTGRYIVRFSEDSFGMD 1zi8A 18 :ALVGSPAKAPAPVIVIAQDIFGVN T0314 64 :LGREQLQILLEQNI 1zi8A 43 :FMRETVSWLVDQGY Number of specific fragments extracted= 2 number of extra gaps= 0 total=210 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fsrA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fsrA expands to /projects/compbio/data/pdb/2fsr.pdb.gz 2fsrA:Skipped atom 26, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 28, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 30, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 32, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 34, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 36, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 38, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 40, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 109, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 111, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 113, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 115, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 117, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 119, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 121, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 123, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 125, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 127, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 129, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 138, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 140, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 142, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 144, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 146, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 148, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 150, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 152, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 154, because occupancy 0.400 <= existing 0.600 in 2fsrA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 333, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 335, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 337, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 339, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 341, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 343, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 345, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 347, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 349, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 351, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 353, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 361, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 363, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 365, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 367, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 369, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 371, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 373, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 436, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 438, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 440, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 442, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 444, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 446, because occupancy 0.400 <= existing 0.600 in 2fsrA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 897, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 899, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 901, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 903, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 905, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 907, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 909, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 911, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 913, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 915, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 917, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1057, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1059, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1061, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1063, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1065, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1067, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1069, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1071, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1135, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1137, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1139, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1141, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1143, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1145, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1154, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1156, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1158, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1160, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1162, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1164, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1166, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1168, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1170, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1228, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1230, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1232, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1234, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1236, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1238, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1240, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1242, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1244, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1246, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1248, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1250, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1252, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1254, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1256, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1258, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1260, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1262, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1264, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1266, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1284, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1286, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1288, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1290, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1292, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1294, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1296, because occupancy 0.400 <= existing 0.600 in 2fsrA Skipped atom 1352, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1354, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1356, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1358, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1360, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1362, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1379, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 1381, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 1383, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 1385, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 1387, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 1389, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 1391, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 1393, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 1395, because occupancy 0.300 <= existing 0.700 in 2fsrA Skipped atom 1455, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1457, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1459, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1461, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1463, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1465, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1467, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1469, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1471, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1473, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1475, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1477, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1479, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1481, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1483, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1485, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1487, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1489, because occupancy 0.500 <= existing 0.500 in 2fsrA Skipped atom 1491, because occupancy 0.500 <= existing 0.500 in 2fsrA # T0314 read from 2fsrA/merged-good-all-a2m # 2fsrA read from 2fsrA/merged-good-all-a2m # adding 2fsrA to template set # found chain 2fsrA in template set T0314 7 :DICQAADALKGFVGF 2fsrA 53 :HDLANWHFFGHGALM T0314 22 :NRKTGRYIVRFS 2fsrA 70 :LGETGECIGQIG T0314 41 :VADDSITPTSEFVWSSVRDDV 2fsrA 82 :INHGPLFPEKELGWLLYEGHE T0314 64 :LGREQLQILLEQNIN 2fsrA 106 :YAAEAAVALRDWAFE T0314 80 :RLNIG 2fsrA 121 :TLNLP T0314 86 :PLLVYLRRQ 2fsrA 126 :TLVSYVSPQ Number of specific fragments extracted= 6 number of extra gaps= 0 total=216 Number of alignments=49 # 2fsrA read from 2fsrA/merged-good-all-a2m # found chain 2fsrA in template set T0314 3 :ITSTDICQAADALKG 2fsrA 42 :YDLPSTWGVFCHDLA T0314 18 :FVGFNRKTGRYIVRFS 2fsrA 66 :LMIDLGETGECIGQIG T0314 41 :VADDSITPTSEFVWSSVRDDV 2fsrA 82 :INHGPLFPEKELGWLLYEGHE T0314 64 :LGREQLQILLEQNI 2fsrA 106 :YAAEAAVALRDWAF T0314 79 :ERLNIG 2fsrA 120 :ETLNLP T0314 86 :PLLVYLRRQ 2fsrA 126 :TLVSYVSPQ Number of specific fragments extracted= 6 number of extra gaps= 0 total=222 Number of alignments=50 # 2fsrA read from 2fsrA/merged-good-all-a2m # found chain 2fsrA in template set T0314 7 :DICQAADALKGFVGF 2fsrA 53 :HDLANWHFFGHGALM T0314 22 :NRKTGRYIVRFS 2fsrA 70 :LGETGECIGQIG T0314 41 :VADDSITPTSEFVWSSVRDDV 2fsrA 82 :INHGPLFPEKELGWLLYEGHE T0314 63 :RLGREQLQILLEQNIN 2fsrA 105 :GYAAEAAVALRDWAFE T0314 80 :RLNIG 2fsrA 121 :TLNLP T0314 86 :PLLVYLRRQ 2fsrA 126 :TLVSYVSPQ Number of specific fragments extracted= 6 number of extra gaps= 0 total=228 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1g5bA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1g5bA expands to /projects/compbio/data/pdb/1g5b.pdb.gz 1g5bA:# T0314 read from 1g5bA/merged-good-all-a2m # 1g5bA read from 1g5bA/merged-good-all-a2m # adding 1g5bA to template set # found chain 1g5bA in template set T0314 5 :STDICQAADALKGFVGFNRKTGRYIVRFSEDSFG 1g5bA 112 :AKALAHKADELPLIIELVSKDKKYVICHADYPFD T0314 45 :SI 1g5bA 146 :EY Number of specific fragments extracted= 2 number of extra gaps= 0 total=230 Number of alignments=52 # 1g5bA read from 1g5bA/merged-good-all-a2m # found chain 1g5bA in template set T0314 6 :TDICQAADALKGFVGFNRKTGRYIVRFSEDSFGMDVADDSIT 1g5bA 113 :KALAHKADELPLIIELVSKDKKYVICHADYPFDEYEFGKPVD T0314 59 :DDV 1g5bA 155 :HQQ T0314 65 :GREQLQILLEQNINER 1g5bA 161 :NRERISNSQNGIVKEI Number of specific fragments extracted= 3 number of extra gaps= 0 total=233 Number of alignments=53 # 1g5bA read from 1g5bA/merged-good-all-a2m # found chain 1g5bA in template set T0314 5 :STDICQAADALKGFVGFNRKTGRYIVRFSEDSFG 1g5bA 112 :AKALAHKADELPLIIELVSKDKKYVICHADYPFD T0314 45 :SIT 1g5bA 146 :EYE Number of specific fragments extracted= 2 number of extra gaps= 0 total=235 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ig5A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0314 read from 1ig5A/merged-good-all-a2m # 1ig5A read from 1ig5A/merged-good-all-a2m # found chain 1ig5A in training set T0314 63 :RLGREQLQILLEQNINERLNIGEP 1ig5A 22 :QLSKEELKLLLQTEFPSLLKGPST Number of specific fragments extracted= 1 number of extra gaps= 0 total=236 Number of alignments=55 # 1ig5A read from 1ig5A/merged-good-all-a2m # found chain 1ig5A in training set T0314 4 :TSTDICQAADALKGF 1ig5A 2 :SPEELKGIFEKYAAK T0314 25 :TG 1ig5A 17 :EG T0314 60 :DVMRLGREQLQILLEQNINERLNIGEP 1ig5A 19 :DPNQLSKEELKLLLQTEFPSLLKGPST Number of specific fragments extracted= 3 number of extra gaps= 0 total=239 Number of alignments=56 # 1ig5A read from 1ig5A/merged-good-all-a2m # found chain 1ig5A in training set T0314 61 :VMRLGREQLQILLEQNINERLNIGEP 1ig5A 20 :PNQLSKEELKLLLQTEFPSLLKGPST Number of specific fragments extracted= 1 number of extra gaps= 0 total=240 Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1exnA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1exnA expands to /projects/compbio/data/pdb/1exn.pdb.gz 1exnA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0314 read from 1exnA/merged-good-all-a2m # 1exnA read from 1exnA/merged-good-all-a2m # adding 1exnA to template set # found chain 1exnA in template set T0314 25 :TGRYIVRFSEDSFGMDVADDSI 1exnA 143 :LYDHVWLISTDGDWDTLLTDKV T0314 52 :FVWSSVRDDVMRL 1exnA 165 :SRFSFTTRREYHL Number of specific fragments extracted= 2 number of extra gaps= 0 total=242 Number of alignments=58 # 1exnA read from 1exnA/merged-good-all-a2m # found chain 1exnA in template set Number of specific fragments extracted= 0 number of extra gaps= 0 total=242 # 1exnA read from 1exnA/merged-good-all-a2m # found chain 1exnA in template set T0314 25 :TGRYIVRFSEDSFGMDVADDSI 1exnA 143 :LYDHVWLISTDGDWDTLLTDKV T0314 52 :FVWSSVRDDVMRL 1exnA 165 :SRFSFTTRREYHL T0314 65 :GREQL 1exnA 188 :DVEQF Number of specific fragments extracted= 3 number of extra gaps= 0 total=245 Number of alignments=59 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1khxA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0314 read from 1khxA/merged-good-all-a2m # 1khxA read from 1khxA/merged-good-all-a2m # found chain 1khxA in training set T0314 5 :STDICQAADALKGFVGFNRKTGRYIVRFSEDS 1khxA 322 :NATVEMTRRHIGRGVRLYYIGGEVFAECLSDS T0314 37 :FG 1khxA 366 :YG T0314 47 :TPTSEFVWSS 1khxA 368 :WHPATVCKIP T0314 58 :RDDVMR 1khxA 378 :PGCNLK T0314 64 :LGREQLQILLEQNINE 1khxA 385 :FNNQEFAALLAQSVNQ T0314 80 :RLNIGEPLLVYLRR 1khxA 407 :QLTRMCTIRMSFVK Number of specific fragments extracted= 6 number of extra gaps= 0 total=251 Number of alignments=60 # 1khxA read from 1khxA/merged-good-all-a2m # found chain 1khxA in training set T0314 5 :STDICQAADALKGFVGFNRKTGRYIVRFSEDS 1khxA 322 :NATVEMTRRHIGRGVRLYYIGGEVFAECLSDS T0314 37 :FGMDVA 1khxA 366 :YGWHPA T0314 51 :EFVWSS 1khxA 372 :TVCKIP T0314 58 :RDDVMR 1khxA 378 :PGCNLK T0314 64 :LGREQLQILLEQNINE 1khxA 385 :FNNQEFAALLAQSVNQ T0314 80 :RLNIGEPLLVYL 1khxA 407 :QLTRMCTIRMSF Number of specific fragments extracted= 6 number of extra gaps= 0 total=257 Number of alignments=61 # 1khxA read from 1khxA/merged-good-all-a2m # found chain 1khxA in training set T0314 5 :STDICQAADALKGFVGFNRKTGRYIVRFSEDS 1khxA 322 :NATVEMTRRHIGRGVRLYYIGGEVFAECLSDS T0314 37 :FG 1khxA 366 :YG T0314 47 :TPTSEFVWSS 1khxA 368 :WHPATVCKIP T0314 58 :RDDVMR 1khxA 378 :PGCNLK T0314 64 :LGREQLQILLEQNINE 1khxA 385 :FNNQEFAALLAQSVNQ T0314 80 :RLNIGEPLLVYLRR 1khxA 407 :QLTRMCTIRMSFVK Number of specific fragments extracted= 6 number of extra gaps= 0 total=263 Number of alignments=62 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1venA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0314/1venA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0314/1venA/merged-good-all-a2m.gz for input Trying 1venA/merged-good-all-a2m Error: Couldn't open file 1venA/merged-good-all-a2m or 1venA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ziyA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0314/1ziyA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0314/1ziyA/merged-good-all-a2m.gz for input Trying 1ziyA/merged-good-all-a2m Error: Couldn't open file 1ziyA/merged-good-all-a2m or 1ziyA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vepA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0314/1vepA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0314/1vepA/merged-good-all-a2m.gz for input Trying 1vepA/merged-good-all-a2m Error: Couldn't open file 1vepA/merged-good-all-a2m or 1vepA/merged-good-all-a2m.gz for input # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0314//projects/compbio/experiments/protein-predict/casp7/T0314/align.constraints_v3.costfcn or /projects/compbio/experiments/protein-predict/casp7/T0314//projects/compbio/experiments/protein-predict/casp7/T0314/align.constraints_v3.costfcn.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/T0314/align.constraints_v3.costfcn # reading script from file /projects/compbio/experiments/protein-predict/casp7/T0314/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((T0314)V30.CB, (T0314)M62.CB) [> 3.9388 = 6.5647 < 8.5341] w=1.0000 to align # Constraint # added constraint: constraint((T0314)V19.CB, (T0314)L69.CB) [> 4.4205 = 7.3675 < 9.5778] w=0.7862 to align # Constraint # added constraint: constraint((T0314)R31.CB, (T0314)I46.CB) [> 3.2098 = 5.3497 < 6.9546] w=0.7773 to align # Constraint # added constraint: constraint((T0314)I29.CB, (T0314)I46.CB) [> 2.6683 = 4.4472 < 5.7813] w=0.7589 to align # Constraint # added constraint: constraint((T0314)F18.CB, (T0314)R66.CB) [> 4.0105 = 6.6842 < 8.6895] w=0.7356 to align # Constraint # added constraint: constraint((T0314)G20.CA, (T0314)V30.CB) [> 4.1590 = 6.9317 < 9.0112] w=0.6934 to align # Constraint # added constraint: constraint((T0314)V19.CB, (T0314)R31.CB) [> 4.0023 = 6.6706 < 8.6717] w=0.6934 to align # Constraint # added constraint: constraint((T0314)F32.CB, (T0314)L72.CB) [> 4.2461 = 7.0769 < 9.2000] w=0.6660 to align # Constraint # added constraint: constraint((T0314)F32.CB, (T0314)L69.CB) [> 4.0616 = 6.7694 < 8.8002] w=0.6660 to align # Constraint # added constraint: constraint((T0314)F32.CB, (T0314)Q68.CB) [> 3.1236 = 5.2060 < 6.7679] w=0.6660 to align # Constraint # added constraint: constraint((T0314)F18.CB, (T0314)M39.CB) [> 3.3063 = 5.5104 < 7.1636] w=0.6506 to align # Constraint # added constraint: constraint((T0314)V30.CB, (T0314)I46.CB) [> 4.3019 = 7.1698 < 9.3208] w=0.6459 to align # Constraint # added constraint: constraint((T0314)D40.CB, (T0314)R66.CB) [> 4.1887 = 6.9812 < 9.0755] w=0.6300 to align # Constraint # added constraint: constraint((T0314)M39.CB, (T0314)R66.CB) [> 4.5798 = 7.6331 < 9.9230] w=0.6300 to align # Constraint # added constraint: constraint((T0314)V30.CB, (T0314)L72.CB) [> 3.1341 = 5.2235 < 6.7905] w=0.6079 to align # Constraint # added constraint: constraint((T0314)E34.CB, (T0314)G65.CA) [> 4.3817 = 7.3028 < 9.4937] w=0.6027 to align # Constraint # added constraint: constraint((T0314)F18.CB, (T0314)R31.CB) [> 3.5955 = 5.9925 < 7.7903] w=0.5643 to align # Constraint # added constraint: constraint((T0314)V30.CB, (T0314)I77.CB) [> 2.9397 = 4.8994 < 6.3692] w=0.5550 to align # Constraint # added constraint: constraint((T0314)I29.CB, (T0314)I77.CB) [> 4.0130 = 6.6883 < 8.6948] w=0.5550 to align # Constraint # added constraint: constraint((T0314)Y28.CB, (T0314)I77.CB) [> 3.8727 = 6.4546 < 8.3909] w=0.5550 to align # Constraint # added constraint: constraint((T0314)R27.CB, (T0314)I77.CB) [> 3.5524 = 5.9207 < 7.6969] w=0.5550 to align # Constraint # added constraint: constraint((T0314)R27.CB, (T0314)N76.CB) [> 3.6561 = 6.0935 < 7.9216] w=0.5550 to align # Constraint # added constraint: constraint((T0314)F21.CB, (T0314)L73.CB) [> 4.3981 = 7.3302 < 9.5293] w=0.5550 to align # Constraint # added constraint: constraint((T0314)G20.CA, (T0314)L73.CB) [> 3.2402 = 5.4003 < 7.0204] w=0.5550 to align # Constraint # added constraint: constraint((T0314)G20.CA, (T0314)L69.CB) [> 3.2815 = 5.4692 < 7.1099] w=0.5550 to align # Constraint # added constraint: constraint((T0314)F18.CB, (T0314)L69.CB) [> 3.5188 = 5.8646 < 7.6240] w=0.5550 to align # Constraint # added constraint: constraint((T0314)R31.CB, (T0314)S45.CB) [> 4.1210 = 6.8684 < 8.9289] w=0.5534 to align # Constraint # added constraint: constraint((T0314)V19.CB, (T0314)V30.CB) [> 3.0743 = 5.1239 < 6.6611] w=0.5472 to align # Constraint # added constraint: constraint((T0314)F37.CB, (T0314)L64.CB) [> 4.5301 = 7.5501 < 9.8152] w=0.5462 to align # Constraint # added constraint: constraint((T0314)Y28.CB, (T0314)F52.CB) [> 3.3930 = 5.6550 < 7.3515] w=0.5343 to align # Constraint # added constraint: constraint((T0314)V30.CB, (T0314)V89.CB) [> 3.3011 = 5.5018 < 7.1524] w=0.5294 to align # Constraint # added constraint: constraint((T0314)F18.CB, (T0314)V30.CB) [> 3.9922 = 6.6537 < 8.6498] w=0.5273 to align # Constraint # added constraint: constraint((T0314)V30.CB, (T0314)F52.CB) [> 3.9289 = 6.5482 < 8.5126] w=0.5265 to align # Constraint # added constraint: constraint((T0314)G20.CA, (T0314)R31.CB) [> 3.4207 = 5.7012 < 7.4116] w=0.5239 to align # Constraint # added constraint: constraint((T0314)Y28.CB, (T0314)L64.CB) [> 3.8123 = 6.3538 < 8.2599] w=0.5217 to align # Constraint # added constraint: constraint((T0314)G17.CA, (T0314)Q68.CB) [> 3.3702 = 5.6170 < 7.3021] w=0.5113 to align # Constraint # added constraint: constraint((T0314)R31.CB, (T0314)V41.CB) [> 3.7170 = 6.1951 < 8.0536] w=0.5112 to align # Constraint # added constraint: constraint((T0314)V30.CB, (T0314)L64.CB) [> 3.8417 = 6.4029 < 8.3237] w=0.5100 to align # Constraint # added constraint: constraint((T0314)Y28.CB, (T0314)V89.CB) [> 3.6857 = 6.1428 < 7.9857] w=0.4960 to align # Constraint # added constraint: constraint((T0314)Y28.CB, (T0314)Y90.CB) [> 4.3411 = 7.2351 < 9.4057] w=0.4960 to align # Constraint # added constraint: constraint((T0314)Y28.CB, (T0314)L91.CB) [> 3.7020 = 6.1699 < 8.0209] w=0.4960 to align # Constraint # added constraint: constraint((T0314)Y28.CB, (T0314)R92.CB) [> 4.6325 = 7.7209 < 10.0371] w=0.4960 to align # Constraint # added constraint: constraint((T0314)I29.CB, (T0314)V89.CB) [> 4.2626 = 7.1044 < 9.2357] w=0.4960 to align # Constraint # added constraint: constraint((T0314)I29.CB, (T0314)Y90.CB) [> 2.9940 = 4.9901 < 6.4871] w=0.4960 to align # Constraint # added constraint: constraint((T0314)I29.CB, (T0314)R92.CB) [> 3.6799 = 6.1332 < 7.9732] w=0.4960 to align # Constraint # added constraint: constraint((T0314)V30.CB, (T0314)L88.CB) [> 4.0469 = 6.7448 < 8.7683] w=0.4960 to align # Constraint # added constraint: constraint((T0314)V30.CB, (T0314)Y90.CB) [> 4.4356 = 7.3927 < 9.6105] w=0.4960 to align # Constraint # added constraint: constraint((T0314)R31.CB, (T0314)L88.CB) [> 3.7612 = 6.2687 < 8.1493] w=0.4960 to align # Constraint # added constraint: constraint((T0314)F32.CB, (T0314)L88.CB) [> 4.6287 = 7.7145 < 10.0288] w=0.4960 to align # Constraint # added constraint: constraint((T0314)S33.CB, (T0314)E85.CB) [> 4.1878 = 6.9797 < 9.0736] w=0.4960 to align # Constraint # added constraint: constraint((T0314)S33.CB, (T0314)P86.CB) [> 2.7621 = 4.6034 < 5.9845] w=0.4960 to align # Constraint # added constraint: constraint((T0314)S33.CB, (T0314)L87.CB) [> 4.4750 = 7.4584 < 9.6959] w=0.4960 to align # Constraint # added constraint: constraint((T0314)I46.CB, (T0314)Y90.CB) [> 4.5322 = 7.5536 < 9.8197] w=0.4960 to align # Constraint # added constraint: constraint((T0314)G17.CA, (T0314)G65.CA) [> 3.9420 = 6.5700 < 8.5409] w=0.4954 to align # Constraint # added constraint: constraint((T0314)E34.CB, (T0314)D44.CB) [> 3.1630 = 5.2717 < 6.8533] w=0.4730 to align # Constraint # added constraint: constraint((T0314)Y28.CB, (T0314)W54.CB) [> 4.1728 = 6.9547 < 9.0412] w=0.4524 to align # Constraint # added constraint: constraint((T0314)G20.CA, (T0314)I29.CB) [> 3.2570 = 5.4283 < 7.0568] w=0.4516 to align # Constraint # added constraint: constraint((T0314)G26.CA, (T0314)Q94.CB) [> 3.6229 = 6.0381 < 7.8496] w=0.4352 to align # Constraint # added constraint: constraint((T0314)D35.CB, (T0314)I46.CB) [> 3.9488 = 6.5813 < 8.5557] w=0.4337 to align # Constraint # added constraint: constraint((T0314)F52.CB, (T0314)V89.CB) [> 3.8352 = 6.3921 < 8.3097] w=0.4332 to align # Constraint # added constraint: constraint((T0314)R31.CB, (T0314)T47.CB) [> 4.0091 = 6.6818 < 8.6863] w=0.4319 to align # Constraint # added constraint: constraint((T0314)A12.CB, (T0314)F21.CB) [> 4.3596 = 7.2660 < 9.4458] w=0.4295 to align # Constraint # added constraint: constraint((T0314)F21.CB, (T0314)V30.CB) [> 3.8613 = 6.4355 < 8.3662] w=0.4232 to align # Constraint # added constraint: constraint((T0314)F18.CB, (T0314)S36.CB) [> 4.2061 = 7.0101 < 9.1132] w=0.4224 to align # Constraint # added constraint: constraint((T0314)S36.CB, (T0314)G65.CA) [> 3.5524 = 5.9206 < 7.6968] w=0.4177 to align # Constraint # added constraint: constraint((T0314)I29.CB, (T0314)F52.CB) [> 4.1157 = 6.8595 < 8.9173] w=0.4172 to align # Constraint # added constraint: constraint((T0314)R31.CB, (T0314)V53.CB) [> 3.8821 = 6.4701 < 8.4112] w=0.4071 to align # Constraint # added constraint: constraint((T0314)R27.CB, (T0314)R92.CB) [> 3.0605 = 5.1009 < 6.6311] w=0.4061 to align # Constraint # added constraint: constraint((T0314)R27.CB, (T0314)L91.CB) [> 4.3954 = 7.3256 < 9.5233] w=0.4061 to align # Constraint # added constraint: constraint((T0314)T49.CB, (T0314)M62.CB) [> 3.9395 = 6.5659 < 8.5356] w=0.3989 to align # Constraint # added constraint: constraint((T0314)D35.CB, (T0314)D44.CB) [> 3.9482 = 6.5804 < 8.5545] w=0.3989 to align # Constraint # added constraint: constraint((T0314)S33.CB, (T0314)T47.CB) [> 2.9021 = 4.8369 < 6.2879] w=0.3956 to align # Constraint # added constraint: constraint((T0314)S33.CB, (T0314)S45.CB) [> 3.3164 = 5.5274 < 7.1856] w=0.3956 to align # Constraint # added constraint: constraint((T0314)A42.CB, (T0314)F52.CB) [> 3.9203 = 6.5338 < 8.4939] w=0.3818 to align # Constraint # added constraint: constraint((T0314)L88.CB, (T0314)Q102.CB) [> 3.6419 = 6.0698 < 7.8907] w=0.3713 to align # Constraint # added constraint: constraint((T0314)V30.CB, (T0314)W54.CB) [> 3.9196 = 6.5326 < 8.4924] w=0.3713 to align # Constraint # added constraint: constraint((T0314)G17.CA, (T0314)M39.CB) [> 3.9976 = 6.6626 < 8.6614] w=0.3700 to align # Constraint # added constraint: constraint((T0314)F18.CB, (T0314)G65.CA) [> 3.4470 = 5.7450 < 7.4685] w=0.3656 to align # Constraint # added constraint: constraint((T0314)E34.CB, (T0314)E85.CB) [> 3.4592 = 5.7654 < 7.4950] w=0.3612 to align # Constraint # added constraint: constraint((T0314)E34.CB, (T0314)G84.CA) [> 4.6326 = 7.7210 < 10.0373] w=0.3612 to align # Constraint # added constraint: constraint((T0314)E34.CB, (T0314)I83.CB) [> 4.0297 = 6.7161 < 8.7309] w=0.3612 to align # Constraint # added constraint: constraint((T0314)R31.CB, (T0314)L87.CB) [> 3.8498 = 6.4163 < 8.3412] w=0.3612 to align # Constraint # added constraint: constraint((T0314)R31.CB, (T0314)A42.CB) [> 3.5170 = 5.8616 < 7.6201] w=0.3612 to align # Constraint # added constraint: constraint((T0314)R31.CB, (T0314)D40.CB) [> 3.2750 = 5.4584 < 7.0959] w=0.3612 to align # Constraint # added constraint: constraint((T0314)I29.CB, (T0314)L91.CB) [> 4.6467 = 7.7445 < 10.0679] w=0.3612 to align # Constraint # added constraint: constraint((T0314)I29.CB, (T0314)A42.CB) [> 4.0964 = 6.8274 < 8.8756] w=0.3612 to align # Constraint # added constraint: constraint((T0314)G26.CA, (T0314)R93.CB) [> 3.6330 = 6.0550 < 7.8715] w=0.3612 to align # Constraint # added constraint: constraint((T0314)G26.CA, (T0314)L91.CB) [> 3.6305 = 6.0508 < 7.8661] w=0.3612 to align # Constraint # added constraint: constraint((T0314)G65.CA, (T0314)I83.CB) [> 2.8575 = 4.7625 < 6.1912] w=0.3612 to align # Constraint # added constraint: constraint((T0314)G65.CA, (T0314)N82.CB) [> 4.3675 = 7.2791 < 9.4628] w=0.3612 to align # Constraint # added constraint: constraint((T0314)L64.CB, (T0314)I83.CB) [> 4.4346 = 7.3910 < 9.6082] w=0.3612 to align # Constraint # added constraint: constraint((T0314)A42.CB, (T0314)Y90.CB) [> 3.7641 = 6.2734 < 8.1555] w=0.3612 to align # Constraint # added constraint: constraint((T0314)F37.CB, (T0314)L87.CB) [> 3.3018 = 5.5030 < 7.1540] w=0.3612 to align # Constraint # added constraint: constraint((T0314)F37.CB, (T0314)E85.CB) [> 3.7733 = 6.2888 < 8.1755] w=0.3612 to align # Constraint # added constraint: constraint((T0314)S36.CB, (T0314)I83.CB) [> 4.7453 = 7.9088 < 10.2815] w=0.3612 to align # Constraint # added constraint: constraint((T0314)F37.CB, (T0314)T47.CB) [> 4.1144 = 6.8573 < 8.9146] w=0.3594 to align # Constraint # added constraint: constraint((T0314)I29.CB, (T0314)T47.CB) [> 3.8153 = 6.3588 < 8.2664] w=0.3579 to align # Constraint # added constraint: constraint((T0314)V53.CB, (T0314)M62.CB) [> 3.0656 = 5.1093 < 6.6421] w=0.3564 to align # Constraint # added constraint: constraint((T0314)L15.CB, (T0314)L72.CB) [> 2.3664 = 3.9440 < 5.1272] w=0.3544 to align # Constraint # added constraint: constraint((T0314)L15.CB, (T0314)I71.CB) [> 3.9683 = 6.6137 < 8.5979] w=0.3544 to align # Constraint # added constraint: constraint((T0314)L15.CB, (T0314)Q68.CB) [> 3.3770 = 5.6283 < 7.3169] w=0.3544 to align # Constraint # added constraint: constraint((T0314)A12.CB, (T0314)L72.CB) [> 3.9470 = 6.5784 < 8.5519] w=0.3544 to align # Constraint # added constraint: constraint((T0314)F32.CB, (T0314)W54.CB) [> 3.5117 = 5.8527 < 7.6086] w=0.3541 to align # Constraint # added constraint: constraint((T0314)V19.CB, (T0314)S33.CB) [> 3.3414 = 5.5691 < 7.2398] w=0.3493 to align # Constraint # added constraint: constraint((T0314)V19.CB, (T0314)F32.CB) [> 3.5948 = 5.9913 < 7.7887] w=0.3493 to align # Constraint # added constraint: constraint((T0314)A14.CB, (T0314)L72.CB) [> 4.3000 = 7.1667 < 9.3168] w=0.3385 to align # Constraint # added constraint: constraint((T0314)E34.CB, (T0314)S45.CB) [> 4.0583 = 6.7638 < 8.7929] w=0.3382 to align # Constraint # added constraint: constraint((T0314)F32.CB, (T0314)T49.CB) [> 3.5120 = 5.8534 < 7.6094] w=0.3382 to align # Constraint # added constraint: constraint((T0314)R31.CB, (T0314)P48.CB) [> 4.3799 = 7.2999 < 9.4899] w=0.3382 to align # Constraint # added constraint: constraint((T0314)S5.CB, (T0314)Y28.CB) [> 4.1040 = 6.8400 < 8.8920] w=0.3223 to align # Constraint # added constraint: constraint((T0314)V30.CB, (T0314)T49.CB) [> 4.1857 = 6.9762 < 9.0690] w=0.3204 to align # Constraint # added constraint: constraint((T0314)I29.CB, (T0314)P48.CB) [> 3.9842 = 6.6404 < 8.6325] w=0.3204 to align # Constraint # added constraint: constraint((T0314)L91.CB, (T0314)T100.CB) [> 3.5272 = 5.8787 < 7.6423] w=0.3184 to align # Constraint # added constraint: constraint((T0314)Y90.CB, (T0314)A101.CB) [> 4.2060 = 7.0100 < 9.1131] w=0.3184 to align # Constraint # added constraint: constraint((T0314)V89.CB, (T0314)Q102.CB) [> 3.8106 = 6.3510 < 8.2563] w=0.3184 to align # Constraint # added constraint: constraint((T0314)F18.CB, (T0314)I83.CB) [> 3.8442 = 6.4070 < 8.3291] w=0.3182 to align # Constraint # added constraint: constraint((T0314)S33.CB, (T0314)T49.CB) [> 4.3850 = 7.3083 < 9.5008] w=0.3171 to align # Constraint # added constraint: constraint((T0314)R23.CB, (T0314)L73.CB) [> 4.0443 = 6.7406 < 8.7627] w=0.3075 to align # Constraint # added constraint: constraint((T0314)I8.CB, (T0314)F18.CB) [> 3.8612 = 6.4354 < 8.3660] w=0.3022 to align # Constraint # added constraint: constraint((T0314)A12.CB, (T0314)V30.CB) [> 3.8562 = 6.4270 < 8.3552] w=0.2992 to align # Constraint # added constraint: constraint((T0314)F32.CB, (T0314)G65.CA) [> 4.0999 = 6.8332 < 8.8832] w=0.2960 to align # Constraint # added constraint: constraint((T0314)F52.CB, (T0314)V61.CB) [> 3.9160 = 6.5267 < 8.4847] w=0.2847 to align # Constraint # added constraint: constraint((T0314)F52.CB, (T0314)M62.CB) [> 3.7355 = 6.2258 < 8.0935] w=0.2847 to align # Constraint # added constraint: constraint((T0314)Q70.CB, (T0314)L81.CB) [> 4.6080 = 7.6800 < 9.9840] w=0.2759 to align # Constraint # added constraint: constraint((T0314)L15.CB, (T0314)S36.CB) [> 4.5330 = 7.5550 < 9.8215] w=0.2753 to align # Constraint # added constraint: constraint((T0314)L15.CB, (T0314)D44.CB) [> 4.0562 = 6.7604 < 8.7885] w=0.2696 to align # Constraint # added constraint: constraint((T0314)C9.CB, (T0314)F18.CB) [> 3.7124 = 6.1874 < 8.0436] w=0.2696 to align # Constraint # added constraint: constraint((T0314)A14.CB, (T0314)Q75.CB) [> 4.5226 = 7.5377 < 9.7990] w=0.2642 to align # Constraint # added constraint: constraint((T0314)G17.CA, (T0314)L72.CB) [> 4.6495 = 7.7491 < 10.0739] w=0.2642 to align # Constraint # added constraint: constraint((T0314)F32.CB, (T0314)P48.CB) [> 3.8989 = 6.4982 < 8.4476] w=0.2642 to align # Constraint # added constraint: constraint((T0314)E34.CB, (T0314)I46.CB) [> 4.4377 = 7.3962 < 9.6151] w=0.2642 to align # Constraint # added constraint: constraint((T0314)E34.CB, (T0314)P48.CB) [> 3.9367 = 6.5611 < 8.5294] w=0.2642 to align # Constraint # added constraint: constraint((T0314)S36.CB, (T0314)S45.CB) [> 3.7696 = 6.2826 < 8.1674] w=0.2642 to align # Constraint # added constraint: constraint((T0314)A42.CB, (T0314)V53.CB) [> 3.7916 = 6.3193 < 8.2151] w=0.2610 to align # Constraint # added constraint: constraint((T0314)V41.CB, (T0314)V53.CB) [> 4.6746 = 7.7909 < 10.1282] w=0.2610 to align # Constraint # added constraint: constraint((T0314)P86.CB, (T0314)Q104.CB) [> 3.7396 = 6.2326 < 8.1025] w=0.2607 to align # Constraint # added constraint: constraint((T0314)L87.CB, (T0314)Q104.CB) [> 4.5861 = 7.6435 < 9.9365] w=0.2607 to align # Constraint # added constraint: constraint((T0314)L88.CB, (T0314)R103.CB) [> 4.3285 = 7.2141 < 9.3783] w=0.2607 to align # Constraint # added constraint: constraint((T0314)R31.CB, (T0314)F52.CB) [> 3.7947 = 6.3245 < 8.2218] w=0.2603 to align # Constraint # added constraint: constraint((T0314)A42.CB, (T0314)L64.CB) [> 3.6303 = 6.0505 < 7.8656] w=0.2596 to align # Constraint # added constraint: constraint((T0314)I29.CB, (T0314)E51.CB) [> 3.5896 = 5.9827 < 7.7775] w=0.2496 to align # Constraint # added constraint: constraint((T0314)Y28.CB, (T0314)E51.CB) [> 4.5398 = 7.5664 < 9.8363] w=0.2496 to align # Constraint # added constraint: constraint((T0314)R27.CB, (T0314)F52.CB) [> 4.5200 = 7.5334 < 9.7934] w=0.2496 to align # Constraint # added constraint: constraint((T0314)R27.CB, (T0314)E51.CB) [> 3.9917 = 6.6528 < 8.6487] w=0.2496 to align # Constraint # added constraint: constraint((T0314)I29.CB, (T0314)T49.CB) [> 4.2446 = 7.0744 < 9.1967] w=0.2463 to align # Constraint # added constraint: constraint((T0314)Y28.CB, (T0314)T49.CB) [> 2.5621 = 4.2702 < 5.5512] w=0.2463 to align # Constraint # added constraint: constraint((T0314)Y28.CB, (T0314)P48.CB) [> 4.6611 = 7.7685 < 10.0991] w=0.2463 to align # Constraint # added constraint: constraint((T0314)G38.CA, (T0314)T47.CB) [> 4.4060 = 7.3433 < 9.5463] w=0.2455 to align # Constraint # added constraint: constraint((T0314)A11.CB, (T0314)D44.CB) [> 4.5042 = 7.5070 < 9.7591] w=0.2449 to align # Constraint # added constraint: constraint((T0314)L91.CB, (T0314)A101.CB) [> 2.6648 = 4.4413 < 5.7737] w=0.2444 to align # Constraint # added constraint: constraint((T0314)Y90.CB, (T0314)Q102.CB) [> 2.9835 = 4.9724 < 6.4642] w=0.2444 to align # Constraint # added constraint: constraint((T0314)I8.CB, (T0314)Y28.CB) [> 4.1114 = 6.8523 < 8.9080] w=0.2418 to align # Constraint # added constraint: constraint((T0314)I29.CB, (T0314)V61.CB) [> 3.4749 = 5.7916 < 7.5290] w=0.2399 to align # Constraint # added constraint: constraint((T0314)V30.CB, (T0314)V61.CB) [> 4.6686 = 7.7810 < 10.1153] w=0.2399 to align # Constraint # added constraint: constraint((T0314)Y90.CB, (T0314)I99.CB) [> 3.7471 = 6.2453 < 8.1188] w=0.2366 to align # Constraint # added constraint: constraint((T0314)V89.CB, (T0314)A101.CB) [> 4.2283 = 7.0472 < 9.1614] w=0.2366 to align # Constraint # added constraint: constraint((T0314)V19.CB, (T0314)S56.CB) [> 3.4195 = 5.6992 < 7.4089] w=0.2312 to align # Constraint # added constraint: constraint((T0314)K16.CB, (T0314)V57.CB) [> 4.5486 = 7.5810 < 9.8553] w=0.2312 to align # Constraint # added constraint: constraint((T0314)C9.CB, (T0314)V57.CB) [> 4.6785 = 7.7975 < 10.1367] w=0.2312 to align # Constraint # added constraint: constraint((T0314)G20.CA, (T0314)W54.CB) [> 3.7513 = 6.2522 < 8.1279] w=0.2312 to align # Constraint # added constraint: constraint((T0314)F21.CB, (T0314)F52.CB) [> 4.2418 = 7.0697 < 9.1906] w=0.2312 to align # Constraint # added constraint: constraint((T0314)F21.CB, (T0314)V53.CB) [> 4.1215 = 6.8692 < 8.9299] w=0.2312 to align # Constraint # added constraint: constraint((T0314)F21.CB, (T0314)W54.CB) [> 3.5244 = 5.8741 < 7.6363] w=0.2312 to align # Constraint # added constraint: constraint((T0314)W54.CB, (T0314)L73.CB) [> 4.4348 = 7.3914 < 9.6088] w=0.2312 to align # Constraint # added constraint: constraint((T0314)I8.CB, (T0314)G20.CA) [> 3.3247 = 5.5411 < 7.2035] w=0.2281 to align # Constraint # added constraint: constraint((T0314)V41.CB, (T0314)F52.CB) [> 3.9826 = 6.6377 < 8.6291] w=0.2207 to align # Constraint # added constraint: constraint((T0314)V30.CB, (T0314)S55.CB) [> 3.5485 = 5.9141 < 7.6883] w=0.2165 to align # Constraint # added constraint: constraint((T0314)L73.CB, (T0314)L87.CB) [> 4.0639 = 6.7732 < 8.8051] w=0.2154 to align # Constraint # added constraint: constraint((T0314)V89.CB, (T0314)R103.CB) [> 3.0555 = 5.0924 < 6.6202] w=0.2078 to align # Constraint # added constraint: constraint((T0314)R27.CB, (T0314)V61.CB) [> 3.2514 = 5.4190 < 7.0447] w=0.2064 to align # Constraint # added constraint: constraint((T0314)R31.CB, (T0314)D43.CB) [> 2.8292 = 4.7154 < 6.1300] w=0.2064 to align # Constraint # added constraint: constraint((T0314)L72.CB, (T0314)I83.CB) [> 4.7113 = 7.8522 < 10.2078] w=0.2064 to align # Constraint # added constraint: constraint((T0314)I8.CB, (T0314)V30.CB) [> 4.3621 = 7.2702 < 9.4512] w=0.2036 to align # Constraint # added constraint: constraint((T0314)T4.CB, (T0314)N22.CB) [> 3.7006 = 6.1676 < 8.0179] w=0.2035 to align # Constraint # added constraint: constraint((T0314)S33.CB, (T0314)A42.CB) [> 3.9846 = 6.6411 < 8.6334] w=0.2027 to align # Constraint # added constraint: constraint((T0314)S5.CB, (T0314)F21.CB) [> 4.0726 = 6.7877 < 8.8240] w=0.1956 to align # Constraint # added constraint: constraint((T0314)R31.CB, (T0314)S50.CB) [> 3.9680 = 6.6132 < 8.5972] w=0.1909 to align # Constraint # added constraint: constraint((T0314)V89.CB, (T0314)T100.CB) [> 4.5285 = 7.5475 < 9.8117] w=0.1905 to align # Constraint # added constraint: constraint((T0314)V41.CB, (T0314)E67.CB) [> 3.7091 = 6.1819 < 8.0365] w=0.1850 to align # Constraint # added constraint: constraint((T0314)D40.CB, (T0314)G65.CA) [> 3.5257 = 5.8762 < 7.6391] w=0.1850 to align # Constraint # added constraint: constraint((T0314)M39.CB, (T0314)G65.CA) [> 3.4529 = 5.7549 < 7.4814] w=0.1850 to align # Constraint # added constraint: constraint((T0314)V19.CB, (T0314)N82.CB) [> 4.5686 = 7.6143 < 9.8986] w=0.1806 to align # Constraint # added constraint: constraint((T0314)F21.CB, (T0314)L64.CB) [> 3.5310 = 5.8850 < 7.6505] w=0.1806 to align # Constraint # added constraint: constraint((T0314)L87.CB, (T0314)L105.CB) [> 2.9338 = 4.8897 < 6.3566] w=0.1700 to align # Constraint # added constraint: constraint((T0314)P86.CB, (T0314)L105.CB) [> 4.4893 = 7.4822 < 9.7269] w=0.1700 to align # Constraint # added constraint: constraint((T0314)F37.CB, (T0314)I46.CB) [> 3.9490 = 6.5817 < 8.5562] w=0.1695 to align # Constraint # added constraint: constraint((T0314)E51.CB, (T0314)G65.CA) [> 3.5357 = 5.8928 < 7.6607] w=0.1670 to align # Constraint # added constraint: constraint((T0314)M39.CB, (T0314)V53.CB) [> 3.6510 = 6.0850 < 7.9105] w=0.1611 to align # Constraint # added constraint: constraint((T0314)G17.CA, (T0314)D43.CB) [> 3.7652 = 6.2752 < 8.1578] w=0.1587 to align # Constraint # added constraint: constraint((T0314)R27.CB, (T0314)T49.CB) [> 4.4513 = 7.4188 < 9.6445] w=0.1565 to align # Constraint # added constraint: constraint((T0314)T4.CB, (T0314)V53.CB) [> 4.4552 = 7.4254 < 9.6530] w=0.1541 to align # Constraint # added constraint: constraint((T0314)D7.CB, (T0314)G20.CA) [> 4.0874 = 6.8124 < 8.8561] w=0.1541 to align # Constraint # added constraint: constraint((T0314)I8.CB, (T0314)S55.CB) [> 3.3487 = 5.5812 < 7.2556] w=0.1541 to align # Constraint # added constraint: constraint((T0314)I8.CB, (T0314)V57.CB) [> 3.8240 = 6.3734 < 8.2854] w=0.1541 to align # Constraint # added constraint: constraint((T0314)A12.CB, (T0314)Y28.CB) [> 3.6151 = 6.0253 < 7.8328] w=0.1530 to align # Constraint # added constraint: constraint((T0314)G38.CA, (T0314)V53.CB) [> 4.0075 = 6.6791 < 8.6829] w=0.1500 to align # Constraint # added constraint: constraint((T0314)D43.CB, (T0314)L64.CB) [> 3.5565 = 5.9276 < 7.7058] w=0.1500 to align # Constraint # added constraint: constraint((T0314)C9.CB, (T0314)F21.CB) [> 2.8560 = 4.7599 < 6.1879] w=0.1462 to align # Constraint # added constraint: constraint((T0314)I8.CB, (T0314)T47.CB) [> 4.5979 = 7.6632 < 9.9621] w=0.1462 to align # Constraint # added constraint: constraint((T0314)S5.CB, (T0314)R23.CB) [> 4.5029 = 7.5049 < 9.7563] w=0.1462 to align # Constraint # added constraint: constraint((T0314)F37.CB, (T0314)W54.CB) [> 3.8214 = 6.3689 < 8.2796] w=0.1462 to align # Constraint # added constraint: constraint((T0314)F37.CB, (T0314)F52.CB) [> 4.5947 = 7.6579 < 9.9553] w=0.1462 to align # Constraint # added constraint: constraint((T0314)A42.CB, (T0314)E51.CB) [> 2.8352 = 4.7254 < 6.1430] w=0.1398 to align # Constraint # added constraint: constraint((T0314)V30.CB, (T0314)S50.CB) [> 3.3207 = 5.5345 < 7.1949] w=0.1380 to align # Constraint # added constraint: constraint((T0314)G38.CA, (T0314)S50.CB) [> 4.5417 = 7.5696 < 9.8404] w=0.1380 to align # Constraint # added constraint: constraint((T0314)V19.CB, (T0314)I83.CB) [> 2.6588 = 4.4313 < 5.7607] w=0.1376 to align # Constraint # added constraint: constraint((T0314)V30.CB, (T0314)I99.CB) [> 3.9182 = 6.5303 < 8.4894] w=0.1376 to align # Constraint # added constraint: constraint((T0314)M62.CB, (T0314)I99.CB) [> 4.0053 = 6.6755 < 8.6782] w=0.1376 to align # Constraint # added constraint: constraint((T0314)P86.CB, (T0314)I99.CB) [> 3.2478 = 5.4130 < 7.0369] w=0.1376 to align # Constraint # added constraint: constraint((T0314)L88.CB, (T0314)I99.CB) [> 4.4433 = 7.4055 < 9.6271] w=0.1376 to align # Constraint # added constraint: constraint((T0314)V89.CB, (T0314)L105.CB) [> 3.9205 = 6.5342 < 8.4944] w=0.1347 to align # Constraint # added constraint: constraint((T0314)P86.CB, (T0314)R106.CB) [> 4.0892 = 6.8153 < 8.8598] w=0.1347 to align # Constraint # added constraint: constraint((T0314)G84.CA, (T0314)R106.CB) [> 4.1316 = 6.8861 < 8.9519] w=0.1347 to align # Constraint # added constraint: constraint((T0314)K16.CB, (T0314)G26.CA) [> 4.6986 = 7.8311 < 10.1804] w=0.1317 to align # Constraint # added constraint: constraint((T0314)M39.CB, (T0314)R80.CB) [> 4.2723 = 7.1205 < 9.2566] w=0.1290 to align # Constraint # added constraint: constraint((T0314)V41.CB, (T0314)E51.CB) [> 4.0057 = 6.6762 < 8.6791] w=0.1222 to align # Constraint # added constraint: constraint((T0314)V41.CB, (T0314)S50.CB) [> 3.4813 = 5.8021 < 7.5428] w=0.1110 to align # Constraint # added constraint: constraint((T0314)F32.CB, (T0314)I71.CB) [> 4.5759 = 7.6266 < 9.9145] w=0.1110 to align # Constraint # added constraint: constraint((T0314)V30.CB, (T0314)Q68.CB) [> 4.1394 = 6.8990 < 8.9687] w=0.1110 to align # Constraint # added constraint: constraint((T0314)V30.CB, (T0314)G65.CA) [> 4.0768 = 6.7946 < 8.8330] w=0.1110 to align # Constraint # added constraint: constraint((T0314)E51.CB, (T0314)V89.CB) [> 3.7140 = 6.1900 < 8.0471] w=0.1110 to align # Constraint # added constraint: constraint((T0314)S33.CB, (T0314)E51.CB) [> 4.5681 = 7.6135 < 9.8975] w=0.1103 to align # Constraint # added constraint: constraint((T0314)S33.CB, (T0314)S50.CB) [> 3.8436 = 6.4059 < 8.3277] w=0.1103 to align # Constraint # added constraint: constraint((T0314)C9.CB, (T0314)L81.CB) [> 2.5679 = 4.2799 < 5.5639] w=0.1096 to align # Constraint # added constraint: constraint((T0314)D13.CB, (T0314)E74.CB) [> 4.7742 = 7.9570 < 10.3441] w=0.1096 to align # Constraint # added constraint: constraint((T0314)V41.CB, (T0314)G65.CA) [> 4.4954 = 7.4923 < 9.7400] w=0.1096 to align # Constraint # added constraint: constraint((T0314)T4.CB, (T0314)T25.CB) [> 3.3167 = 5.5278 < 7.1861] w=0.0956 to align # Constraint # added constraint: constraint((T0314)S5.CB, (T0314)T25.CB) [> 4.1294 = 6.8823 < 8.9470] w=0.0956 to align # Constraint # added constraint: constraint((T0314)C9.CB, (T0314)Y28.CB) [> 4.1129 = 6.8548 < 8.9112] w=0.0956 to align # Constraint # added constraint: constraint((T0314)M39.CB, (T0314)L69.CB) [> 3.9049 = 6.5082 < 8.4606] w=0.0750 to align # Constraint # added constraint: constraint((T0314)A12.CB, (T0314)S33.CB) [> 3.6518 = 6.0863 < 7.9122] w=0.0740 to align # Constraint # added constraint: constraint((T0314)F21.CB, (T0314)R93.CB) [> 4.3677 = 7.2796 < 9.4634] w=0.0740 to align # Constraint # added constraint: constraint((T0314)Q70.CB, (T0314)L91.CB) [> 3.1460 = 5.2434 < 6.8164] w=0.0740 to align # Constraint # added constraint: constraint((T0314)D7.CB, (T0314)D44.CB) [> 4.2118 = 7.0197 < 9.1256] w=0.0740 to align # Constraint # added constraint: constraint((T0314)A11.CB, (T0314)S33.CB) [> 4.3172 = 7.1953 < 9.3539] w=0.0740 to align # Constraint # added constraint: constraint((T0314)A11.CB, (T0314)V41.CB) [> 4.3545 = 7.2575 < 9.4348] w=0.0740 to align # Constraint # added constraint: constraint((T0314)A11.CB, (T0314)D43.CB) [> 3.4990 = 5.8316 < 7.5810] w=0.0740 to align # Constraint # added constraint: constraint((T0314)S5.CB, (T0314)I83.CB) [> 4.4222 = 7.3703 < 9.5814] w=0.0731 to align # Constraint # added constraint: constraint((T0314)T6.CB, (T0314)L81.CB) [> 3.6394 = 6.0656 < 7.8853] w=0.0731 to align # Constraint # added constraint: constraint((T0314)L91.CB, (T0314)R103.CB) [> 4.7941 = 7.9901 < 10.3871] w=0.0731 to align # Constraint # added constraint: constraint((T0314)D43.CB, (T0314)L81.CB) [> 3.1507 = 5.2512 < 6.8266] w=0.0725 to align # Constraint # added constraint: constraint((T0314)D43.CB, (T0314)R80.CB) [> 2.3516 = 3.9193 < 5.0951] w=0.0725 to align # Constraint # added constraint: constraint((T0314)V30.CB, (T0314)V41.CB) [> 3.4762 = 5.7937 < 7.5318] w=0.0725 to align # Constraint # added constraint: constraint((T0314)S56.CB, (T0314)L96.CB) [> 4.1143 = 6.8572 < 8.9143] w=0.0725 to align # Constraint # added constraint: constraint((T0314)V57.CB, (T0314)L96.CB) [> 2.3653 = 3.9422 < 5.1248] w=0.0725 to align # Constraint # added constraint: constraint((T0314)V19.CB, (T0314)A101.CB) [> 3.3165 = 5.5274 < 7.1856] w=0.0688 to align # Constraint # added constraint: constraint((T0314)I83.CB, (T0314)A101.CB) [> 3.2039 = 5.3399 < 6.9418] w=0.0688 to align # Constraint # added constraint: constraint((T0314)N22.CB, (T0314)D43.CB) [> 4.7739 = 7.9565 < 10.3435] w=0.0688 to align # Constraint # added constraint: constraint((T0314)I29.CB, (T0314)D40.CB) [> 3.5601 = 5.9335 < 7.7135] w=0.0565 to align # Constraint # added constraint: constraint((T0314)S33.CB, (T0314)G65.CA) [> 2.8280 = 4.7134 < 6.1274] w=0.0565 to align # Constraint # added constraint: constraint((T0314)G38.CA, (T0314)R80.CB) [> 3.0911 = 5.1519 < 6.6975] w=0.0565 to align # Constraint # added constraint: constraint((T0314)D40.CB, (T0314)R80.CB) [> 3.5310 = 5.8850 < 7.6505] w=0.0565 to align # Constraint # added constraint: constraint((T0314)V30.CB, (T0314)L73.CB) [> 3.6649 = 6.1082 < 7.9406] w=0.0529 to align # Constraint # added constraint: constraint((T0314)D40.CB, (T0314)T49.CB) [> 4.1574 = 6.9291 < 9.0078] w=0.0529 to align # Constraint # added constraint: constraint((T0314)Q10.CB, (T0314)I46.CB) [> 4.7994 = 7.9990 < 10.3987] w=0.0494 to align # Constraint # added constraint: constraint((T0314)S50.CB, (T0314)G65.CA) [> 3.9202 = 6.5337 < 8.4938] w=0.0383 to align # Constraint # added constraint: constraint((T0314)G65.CA, (T0314)L105.CB) [> 4.0270 = 6.7117 < 8.7252] w=0.0353 to align # Constraint # added constraint: constraint((T0314)L81.CB, (T0314)L105.CB) [> 4.1677 = 6.9461 < 9.0299] w=0.0353 to align # Constraint # added constraint: constraint((T0314)A11.CB, (T0314)L91.CB) [> 3.9296 = 6.5494 < 8.5142] w=0.0335 to align # Constraint # added constraint: constraint((T0314)L69.CB, (T0314)G84.CA) [> 4.1377 = 6.8962 < 8.9650] w=0.0335 to align # Constraint # added constraint: constraint((T0314)Y28.CB, (T0314)G65.CA) [> 3.9410 = 6.5684 < 8.5389] w=0.0335 to align # Constraint # added constraint: constraint((T0314)A11.CB, (T0314)R93.CB) [> 3.7475 = 6.2458 < 8.1195] w=0.0223 to align # Constraint # added constraint: constraint((T0314)K24.CB, (T0314)I71.CB) [> 4.3377 = 7.2295 < 9.3984] w=0.0159 to align # SetCost created cost = # ( 1.0000 * align ) # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0314/ # command:# reading script from file servers-clean.under # Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0314/decoys/ # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0314 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 # Found a chain break before 84 # copying to AlignedFragments data structure # 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 T0314 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_POPULUS_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS4.pdb.gz looking for model 1 # Found a chain break before 91 # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS5.pdb.gz looking for model 1 # Found a chain break before 100 # copying to AlignedFragments data structure # 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 T0314 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 T0314 can't currently be optimized by undertaker # naming current conformation 3D-JIGSAW_RECOM_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0314 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 T0314 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 T0314 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 T0314 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 T0314 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 50 # 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 64 # 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 73 # 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 70 # 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 64 # 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 96 # 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 85 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS2 # ReadConformPDB reading from PDB file servers/ABIpro_TS3.pdb.gz looking for model 1 # naming current conformation ABIpro_TS3 # ReadConformPDB reading from PDB file servers/ABIpro_TS4.pdb.gz looking for model 1 # Found a chain break before 85 # 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 85 # 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 45 # 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 105 # 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 105 # 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 105 # 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 105 # 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 105 # 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 97 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS1 # ReadConformPDB reading from PDB file servers/CIRCLE_TS2.pdb.gz looking for model 1 # Found a chain break before 100 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS2 # ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1 # Found a chain break before 85 # 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 T0314 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS4 # ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1 # Found a chain break before 96 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS5 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0314 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 T0314 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 T0314 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 T0314 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation CaspIta-FOX_TS4 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0314 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 T0314 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 T0314 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 T0314 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 T0314 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 T0314 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 95 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS1 # ReadConformPDB reading from PDB file servers/FAMSD_TS2.pdb.gz looking for model 1 # Found a chain break before 98 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS2 # ReadConformPDB reading from PDB file servers/FAMSD_TS3.pdb.gz looking for model 1 # Found a chain break before 96 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS3 # ReadConformPDB reading from PDB file servers/FAMSD_TS4.pdb.gz looking for model 1 # Found a chain break before 93 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS4 # ReadConformPDB reading from PDB file servers/FAMSD_TS5.pdb.gz looking for model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS5 # ReadConformPDB reading from PDB file servers/FAMS_TS1.pdb.gz looking for model 1 # Found a chain break before 101 # copying to AlignedFragments data structure # naming current conformation FAMS_TS1 # ReadConformPDB reading from PDB file servers/FAMS_TS2.pdb.gz looking for model 1 # Found a chain break before 94 # copying to AlignedFragments data structure # naming current conformation FAMS_TS2 # ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # naming current conformation FAMS_TS3 # ReadConformPDB reading from PDB file servers/FAMS_TS4.pdb.gz looking for model 1 # Found a chain break before 96 # copying to AlignedFragments data structure # naming current conformation FAMS_TS4 # ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1 # Found a chain break before 98 # copying to AlignedFragments data structure # naming current conformation FAMS_TS5 # ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1 # Found a chain break before 31 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS1 # ReadConformPDB reading from PDB file servers/FOLDpro_TS2.pdb.gz looking for model 1 # Found a chain break before 53 # 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 47 # 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 101 # 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 97 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS5 # ReadConformPDB reading from PDB file servers/FORTE1_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0314 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL1 # ReadConformPDB reading from PDB file servers/FORTE1_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0314 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 T0314 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL3 # ReadConformPDB reading from PDB file servers/FORTE1_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0314 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL4 # ReadConformPDB reading from PDB file servers/FORTE1_AL5.pdb.gz looking for model 1 Skipped atom 138, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz Skipped atom 140, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz Skipped atom 142, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz Skipped atom 144, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz Skipped atom 338, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz Skipped atom 340, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz Skipped atom 342, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz Skipped atom 344, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz # WARNING: incomplete conformation T0314 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL5 # ReadConformPDB reading from PDB file servers/FORTE2_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0314 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE2_AL1 # ReadConformPDB reading from PDB file servers/FORTE2_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0314 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 T0314 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE2_AL3 # ReadConformPDB reading from PDB file servers/FORTE2_AL4.pdb.gz looking for model 1 Skipped atom 138, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 140, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 142, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 144, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 338, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 340, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 342, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz Skipped atom 344, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz # WARNING: incomplete conformation T0314 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE2_AL4 # ReadConformPDB reading from PDB file servers/FORTE2_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0314 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 # naming current conformation FPSOLVER-SERVER_TS1 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS2.pdb.gz looking for model 1 # Found a chain break before 105 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS2 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS3.pdb.gz looking for model 1 # Found a chain break before 47 # 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 90 # 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 105 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS5 # ReadConformPDB reading from PDB file servers/FUGUE_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0314 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGUE_AL1 # ReadConformPDB reading from PDB file servers/FUGUE_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0314 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGUE_AL2 # ReadConformPDB reading from PDB file servers/FUGUE_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0314 can't currently be optimized by undertaker # naming current conformation FUGUE_AL3 # ReadConformPDB reading from PDB file servers/FUGUE_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0314 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGUE_AL4 # ReadConformPDB reading from PDB file servers/FUGUE_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0314 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 99 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS1 # ReadConformPDB reading from PDB file servers/FUNCTION_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0314 can't currently be optimized by undertaker # naming current conformation FUNCTION_TS2 # ReadConformPDB reading from PDB file servers/FUNCTION_TS3.pdb.gz looking for model 1 # Found a chain break before 102 # 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 94 # 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 96 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS5 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1 # naming current conformation GeneSilicoMetaServer_TS1 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS2.pdb.gz looking for model 1 # Found a chain break before 82 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS2 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1 # naming current conformation GeneSilicoMetaServer_TS3 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS4.pdb.gz looking for model 1 # Found a chain break before 45 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS4 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS5.pdb.gz looking for model 1 # naming current conformation GeneSilicoMetaServer_TS5 # ReadConformPDB reading from PDB file servers/HHpred1_TS1.pdb.gz looking for model 1 # Found a chain break before 16 # copying to AlignedFragments data structure # naming current conformation HHpred1_TS1 # ReadConformPDB reading from PDB file servers/HHpred2_TS1.pdb.gz looking for model 1 # naming current conformation HHpred2_TS1 # ReadConformPDB reading from PDB file servers/HHpred3_TS1.pdb.gz looking for model 1 # naming current conformation HHpred3_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0314 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 T0314 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 T0314 can't currently be optimized by undertaker # copying to AlignedFragments data structure # 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 T0314 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 T0314 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 T0314 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 T0314 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 T0314 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 T0314 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 T0314 can't currently be optimized by undertaker # naming current conformation LOOPP_TS5 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS1.pdb.gz looking for model 1 # Found a chain break before 79 # 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 29 # 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 95 # 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 # 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 42 # 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 105 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS1 # ReadConformPDB reading from PDB file servers/MetaTasser_TS2.pdb.gz looking for model 1 # Found a chain break before 105 # 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 105 # 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 105 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS4 # ReadConformPDB reading from PDB file servers/MetaTasser_TS5.pdb.gz looking for model 1 # Found a chain break before 102 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS5 # ReadConformPDB reading from PDB file servers/NN_PUT_lab_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0314 can't currently be optimized by undertaker # naming current conformation NN_PUT_lab_TS1 # ReadConformPDB reading from PDB file servers/POMYSL_TS1.pdb.gz looking for model 1 WARNING: atom 1 has residue number 10 < previous residue 106 in servers/POMYSL_TS1.pdb.gz # WARNING: incomplete conformation T0314 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: atom 1 has residue number 10 < previous residue 106 in servers/POMYSL_TS2.pdb.gz # WARNING: incomplete conformation T0314 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 # Found a chain break before 32 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS3 # ReadConformPDB reading from PDB file servers/POMYSL_TS4.pdb.gz looking for model 1 # Found a chain break before 98 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS4 # ReadConformPDB reading from PDB file servers/POMYSL_TS5.pdb.gz looking for model 1 # Found a chain break before 103 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS1.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS2.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS3.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS4.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS5.pdb.gz looking for model 1 # Found a chain break before 100 # copying to AlignedFragments data structure # 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 97 # 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 86 # 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 98 # copying to AlignedFragments data structure # naming current conformation PROTINFO_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1 # naming current conformation PROTINFO_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1 # naming current conformation PROTINFO_TS5 # ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1 # naming current conformation Pcons6_TS1 # ReadConformPDB reading from PDB file servers/Pcons6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0314 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 # Found a chain break before 95 # copying to AlignedFragments data structure # naming current conformation Pcons6_TS3 # ReadConformPDB reading from PDB file servers/Pcons6_TS4.pdb.gz looking for model 1 # naming current conformation Pcons6_TS4 # ReadConformPDB reading from PDB file servers/Pcons6_TS5.pdb.gz looking for model 1 # Found a chain break before 97 # copying to AlignedFragments data structure # naming current conformation Pcons6_TS5 # ReadConformPDB reading from PDB file servers/Phyre-1_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0314 can't currently be optimized by undertaker # naming current conformation Phyre-1_TS1 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS1.pdb.gz looking for model 1 # Found a chain break before 96 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS1 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1 # naming current conformation Pmodeller6_TS2 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0314 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS3 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0314 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 97 # 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 # naming current conformation RAPTOR-ACE_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS2.pdb.gz looking for model 1 # naming current conformation RAPTOR-ACE_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS3.pdb.gz looking for model 1 # Found a chain break before 51 # 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 # 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 82 # 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 87 # 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 103 # 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 83 # 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 85 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS4 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS5.pdb.gz looking for model 1 # naming current conformation RAPTORESS_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR_TS1.pdb.gz looking for model 1 # naming current conformation RAPTOR_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR_TS2.pdb.gz looking for model 1 # Found a chain break before 18 # 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 15 # 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 78 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR_TS5.pdb.gz looking for model 1 # naming current conformation RAPTOR_TS5 # ReadConformPDB reading from PDB file servers/ROBETTA_TS1.pdb.gz looking for model 1 # naming current conformation ROBETTA_TS1 # ReadConformPDB reading from PDB file servers/ROBETTA_TS2.pdb.gz looking for model 1 # Found a chain break before 1 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS2 # ReadConformPDB reading from PDB file servers/ROBETTA_TS3.pdb.gz looking for model 1 # naming current conformation ROBETTA_TS3 # ReadConformPDB reading from PDB file servers/ROBETTA_TS4.pdb.gz looking for model 1 # naming current conformation ROBETTA_TS4 # ReadConformPDB reading from PDB file servers/ROBETTA_TS5.pdb.gz looking for model 1 # naming current conformation ROBETTA_TS5 # ReadConformPDB reading from PDB file servers/ROKKY_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0314 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS1 # ReadConformPDB reading from PDB file servers/ROKKY_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0314 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS2 # ReadConformPDB reading from PDB file servers/ROKKY_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0314 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS3 # ReadConformPDB reading from PDB file servers/ROKKY_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0314 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS4 # ReadConformPDB reading from PDB file servers/ROKKY_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0314 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS5 # ReadConformPDB reading from PDB file servers/SAM-T02_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0314 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL1 # ReadConformPDB reading from PDB file servers/SAM-T02_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0314 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 T0314 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL3 # ReadConformPDB reading from PDB file servers/SAM-T02_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0314 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL4 # ReadConformPDB reading from PDB file servers/SAM-T02_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0314 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL5 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS1.pdb.gz looking for model 1 # Found a chain break before 96 # 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 T0314 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 T0314 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 T0314 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 T0314 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 38 # copying to AlignedFragments data structure # naming current conformation SP3_TS1 # ReadConformPDB reading from PDB file servers/SP3_TS2.pdb.gz looking for model 1 # naming current conformation SP3_TS2 # ReadConformPDB reading from PDB file servers/SP3_TS3.pdb.gz looking for model 1 # naming current conformation SP3_TS3 # ReadConformPDB reading from PDB file servers/SP3_TS4.pdb.gz looking for model 1 # Found a chain break before 58 # 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 29 # 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 # naming current conformation SP4_TS2 # ReadConformPDB reading from PDB file servers/SP4_TS3.pdb.gz looking for model 1 # naming current conformation SP4_TS3 # ReadConformPDB reading from PDB file servers/SP4_TS4.pdb.gz looking for model 1 # naming current conformation SP4_TS4 # ReadConformPDB reading from PDB file servers/SP4_TS5.pdb.gz looking for model 1 # Found a chain break before 32 # copying to AlignedFragments data structure # naming current conformation SP4_TS5 # ReadConformPDB reading from PDB file servers/SPARKS2_TS1.pdb.gz looking for model 1 # Found a chain break before 79 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS1 # ReadConformPDB reading from PDB file servers/SPARKS2_TS2.pdb.gz looking for model 1 # Found a chain break before 30 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS2 # ReadConformPDB reading from PDB file servers/SPARKS2_TS3.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS3 # ReadConformPDB reading from PDB file servers/SPARKS2_TS4.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS4 # ReadConformPDB reading from PDB file servers/SPARKS2_TS5.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0314 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 T0314 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 T0314 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 T0314 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 T0314 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 T0314 can't currently be optimized by undertaker # naming current conformation UNI-EID_expm_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0314 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 54, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 56, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 58, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 60, 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 210, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz Skipped atom 212, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz # WARNING: incomplete conformation T0314 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 T0314 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL3 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0314 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 T0314 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 95 # 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 76 # 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 95 # 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 104 # 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 96 # 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 # WARNING: incomplete conformation T0314 can't currently be optimized by undertaker # naming current conformation beautshot_TS1 # ReadConformPDB reading from PDB file servers/beautshotbase_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0314 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 T0314 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 T0314 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 Skipped atom 6, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 8, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 10, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 12, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 238, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 240, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 242, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 244, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 278, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 280, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 282, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 284, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 338, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 340, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 342, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 344, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 346, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 348, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 350, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 352, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 402, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 404, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 406, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz Skipped atom 408, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz # WARNING: incomplete conformation T0314 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 T0314 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 T0314 can't currently be optimized by undertaker # naming current conformation forecast-s_AL5 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1 # Found a chain break before 91 # 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 54 # 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 22 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS4.pdb.gz looking for model 1 # naming current conformation karypis.srv.2_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS5.pdb.gz looking for model 1 # Found a chain break before 46 # 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 103 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS2.pdb.gz looking for model 1 WARNING: atoms too close: (T0314)R103.O and (T0314)Q104.N only 0.000 apart, marking (T0314)Q104.N as missing # WARNING: incomplete conformation T0314 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS3.pdb.gz looking for model 1 # Found a chain break before 103 # 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 103 # 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 103 # 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 T0314 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0314 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 T0314 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 T0314 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 T0314 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 33 # 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 61 # 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 72 # 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 7 # 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 49 # 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 T0314 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 T0314 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation nFOLD_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0314 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 T0314 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation nFOLD_TS3 # ReadConformPDB reading from PDB file servers/nFOLD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0314 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 T0314 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 T0314 can't currently be optimized by undertaker # naming current conformation panther2_TS1 # ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0314 can't currently be optimized by undertaker # naming current conformation shub_TS1 # command:Using radius: 8.0000 Using models AND alignments for constraints model score 1.8984 model score 2.2201 model score 2.0313 model score 1.9008 model score 2.0187 model score 1.6778 model score 1.4760 model score 1.6690 model score 1.8646 model score 1.8402 model score 1.5416 model score 1.8306 model score 1.9229 model score 1.7675 model score 1.5727 model score 1.8276 model score 1.7387 model score 1.4250 model score 1.6264 model score 1.6077 model score 1.3264 model score 1.6097 model score 1.6224 model score 2.1340 model score 2.1466 model score 2.1056 model score 2.1213 model score 2.1322 model score 1.4496 model score 1.4622 model score 1.8557 model score 1.7123 model score 1.8230 model score 1.3456 model score 2.5757 model score 1.5429 model score 1.7618 model score 1.6957 model score 1.2792 model score 1.2764 model score 1.2751 model score 1.2762 model score 1.2749 model score 1.7124 model score 1.7372 model score 1.6618 model score 1.8486 model score 1.7635 model score 1.4269 model score 1.7377 model score 1.4496 model score 1.8230 model score 1.7372 model score 1.6993 model score 1.9712 model score 1.4962 model score 1.8448 model score 1.3976 model score 1.2852 model score 1.2881 model score 1.2866 model score 1.2740 model score 1.2861 model score 1.2852 model score 1.2881 model score 1.2866 model score 1.2861 model score 1.2870 model score 1.9131 model score 2.0648 model score 1.8552 model score 2.0076 model score 2.1195 model score 1.2756 model score 1.2878 model score 1.2860 model score 1.2874 model score 1.2771 model score 2.0315 model score 1.6715 model score 1.7177 model score 1.7377 model score 1.6884 model score 2.1819 model score 1.7514 model score 2.1040 model score 1.5713 model score 2.2835 model score 1.9579 model score 1.6712 model score 1.6712 model score 1.5934 model score 1.2294 model score 1.5471 model score 1.6112 model score 1.5252 model score 1.6774 model score 1.5732 model score 1.6688 model score 1.3952 model score 1.5815 model score 1.7291 model score 1.5813 model score 1.6932 model score 2.1284 model score 1.8678 model score 1.1866 model score 1.2372 model score 1.1781 model score 1.2328 model score 1.1753 model score 1.6774 model score 1.3147 model score 1.3612 model score 1.9021 model score 1.7669 model score 1.7471 model score 1.3321 model score 1.2758 model score 1.3166 model score 1.2824 model score 1.1064 model score 1.9023 model score 2.5544 model score 1.6571 model score 1.3321 model score 1.3076 model score 1.5144 model score 2.0334 model score 2.1482 model score 1.4475 model score 1.6992 model score 1.4048 model score 1.5634 model score 1.7390 model score 2.4880 model score 2.4880 model score 1.8501 model score 1.8044 model score 2.0449 model score 1.3807 model score 2.1790 model score 1.8133 model score 1.7449 model score 1.6942 model score 1.7258 model score 1.5025 model score 1.8145 model score 1.6969 model score 1.7170 model score 1.7131 model score 1.4937 model score 1.7999 model score 1.5144 model score 1.7008 model score 1.5952 model score 1.6659 model score 1.4114 model score 1.2843 model score 1.2848 model score 1.2825 model score 1.2823 model score 1.2703 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2756 model score 1.2771 model score 1.5247 model score 1.5159 model score 1.5148 model score 1.5115 model score 0.8633 model score 1.3127 model score 1.7352 model score 1.6576 model score 1.9234 model score 1.7926 model score 1.3883 model score 1.7696 model score 1.4358 model score 1.6659 model score 1.6708 model score 1.5479 model score 1.7631 model score 1.5346 model score 1.6849 model score 1.5365 model score 1.2848 model score 1.2771 model score 1.2845 model score 1.2848 model score 1.2855 model score 1.7406 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2853 model score 1.2771 model score 1.0354 model score 1.1668 model score 0.9938 model score 1.0513 model score 0.9330 model score 1.5570 model score 1.5691 model score 1.2771 model score 1.2723 model score 1.2676 model score 1.2771 model score 1.2855 model score 1.7630 model score 1.7620 model score 1.4901 model score 1.7044 model score 1.8407 model score 1.9068 model score 1.9684 model score 2.0824 model score 1.7110 model score 1.7440 model score 1.6626 model score 1.4854 model score 1.6361 model score 1.3926 model score 1.3013 model score 1.7069 model score 1.7027 model score 1.8821 model score 1.9598 model score 2.1501 model score 1.7005 model score 1.8294 model score 1.7052 model score 2.1540 model score 1.5064 model score 1.6499 model score 1.3066 model score 1.5109 USE_META, weight: 0.4560 cost: 1.8984 min: 0.8633 max: 2.5757 USE_META, weight: 0.2869 cost: 2.2201 min: 0.8633 max: 2.5757 USE_META, weight: 0.3861 cost: 2.0313 min: 0.8633 max: 2.5757 USE_META, weight: 0.4547 cost: 1.9008 min: 0.8633 max: 2.5757 USE_META, weight: 0.3928 cost: 2.0187 min: 0.8633 max: 2.5757 USE_META, weight: 0.5719 cost: 1.6778 min: 0.8633 max: 2.5757 USE_META, weight: 0.6780 cost: 1.4760 min: 0.8633 max: 2.5757 USE_META, weight: 0.5765 cost: 1.6690 min: 0.8633 max: 2.5757 USE_META, weight: 0.4737 cost: 1.8646 min: 0.8633 max: 2.5757 USE_META, weight: 0.4866 cost: 1.8402 min: 0.8633 max: 2.5757 USE_META, weight: 0.6435 cost: 1.5416 min: 0.8633 max: 2.5757 USE_META, weight: 0.4916 cost: 1.8306 min: 0.8633 max: 2.5757 USE_META, weight: 0.4431 cost: 1.9229 min: 0.8633 max: 2.5757 USE_META, weight: 0.5248 cost: 1.7675 min: 0.8633 max: 2.5757 USE_META, weight: 0.6272 cost: 1.5727 min: 0.8633 max: 2.5757 USE_META, weight: 0.4932 cost: 1.8276 min: 0.8633 max: 2.5757 USE_META, weight: 0.5399 cost: 1.7387 min: 0.8633 max: 2.5757 USE_META, weight: 0.7048 cost: 1.4250 min: 0.8633 max: 2.5757 USE_META, weight: 0.5990 cost: 1.6264 min: 0.8633 max: 2.5757 USE_META, weight: 0.6087 cost: 1.6077 min: 0.8633 max: 2.5757 USE_META, weight: 0.7566 cost: 1.3264 min: 0.8633 max: 2.5757 USE_META, weight: 0.6077 cost: 1.6097 min: 0.8633 max: 2.5757 USE_META, weight: 0.6011 cost: 1.6224 min: 0.8633 max: 2.5757 USE_META, weight: 0.3322 cost: 2.1340 min: 0.8633 max: 2.5757 USE_META, weight: 0.3255 cost: 2.1466 min: 0.8633 max: 2.5757 USE_META, weight: 0.3470 cost: 2.1056 min: 0.8633 max: 2.5757 USE_META, weight: 0.3388 cost: 2.1213 min: 0.8633 max: 2.5757 USE_META, weight: 0.3331 cost: 2.1322 min: 0.8633 max: 2.5757 USE_META, weight: 0.6919 cost: 1.4496 min: 0.8633 max: 2.5757 USE_META, weight: 0.6852 cost: 1.4622 min: 0.8633 max: 2.5757 USE_META, weight: 0.4784 cost: 1.8557 min: 0.8633 max: 2.5757 USE_META, weight: 0.5538 cost: 1.7123 min: 0.8633 max: 2.5757 USE_META, weight: 0.4956 cost: 1.8230 min: 0.8633 max: 2.5757 USE_META, weight: 0.7465 cost: 1.3456 min: 0.8633 max: 2.5757 USE_META, weight: 0.1000 cost: 2.5757 min: 0.8633 max: 2.5757 USE_META, weight: 0.6428 cost: 1.5429 min: 0.8633 max: 2.5757 USE_META, weight: 0.5278 cost: 1.7618 min: 0.8633 max: 2.5757 USE_META, weight: 0.5625 cost: 1.6957 min: 0.8633 max: 2.5757 USE_META, weight: 0.7814 cost: 1.2792 min: 0.8633 max: 2.5757 USE_META, weight: 0.7829 cost: 1.2764 min: 0.8633 max: 2.5757 USE_META, weight: 0.7836 cost: 1.2751 min: 0.8633 max: 2.5757 USE_META, weight: 0.7830 cost: 1.2762 min: 0.8633 max: 2.5757 USE_META, weight: 0.7837 cost: 1.2749 min: 0.8633 max: 2.5757 USE_META, weight: 0.5537 cost: 1.7124 min: 0.8633 max: 2.5757 USE_META, weight: 0.5407 cost: 1.7372 min: 0.8633 max: 2.5757 USE_META, weight: 0.5803 cost: 1.6618 min: 0.8633 max: 2.5757 USE_META, weight: 0.4822 cost: 1.8486 min: 0.8633 max: 2.5757 USE_META, weight: 0.5269 cost: 1.7635 min: 0.8633 max: 2.5757 USE_META, weight: 0.7038 cost: 1.4269 min: 0.8633 max: 2.5757 USE_META, weight: 0.5405 cost: 1.7377 min: 0.8633 max: 2.5757 USE_META, weight: 0.6919 cost: 1.4496 min: 0.8633 max: 2.5757 USE_META, weight: 0.4956 cost: 1.8230 min: 0.8633 max: 2.5757 USE_META, weight: 0.5407 cost: 1.7372 min: 0.8633 max: 2.5757 USE_META, weight: 0.5606 cost: 1.6993 min: 0.8633 max: 2.5757 USE_META, weight: 0.4177 cost: 1.9712 min: 0.8633 max: 2.5757 USE_META, weight: 0.6674 cost: 1.4962 min: 0.8633 max: 2.5757 USE_META, weight: 0.4841 cost: 1.8448 min: 0.8633 max: 2.5757 USE_META, weight: 0.7192 cost: 1.3976 min: 0.8633 max: 2.5757 USE_META, weight: 0.7783 cost: 1.2852 min: 0.8633 max: 2.5757 USE_META, weight: 0.7767 cost: 1.2881 min: 0.8633 max: 2.5757 USE_META, weight: 0.7775 cost: 1.2866 min: 0.8633 max: 2.5757 USE_META, weight: 0.7842 cost: 1.2740 min: 0.8633 max: 2.5757 USE_META, weight: 0.7778 cost: 1.2861 min: 0.8633 max: 2.5757 USE_META, weight: 0.7783 cost: 1.2852 min: 0.8633 max: 2.5757 USE_META, weight: 0.7767 cost: 1.2881 min: 0.8633 max: 2.5757 USE_META, weight: 0.7775 cost: 1.2866 min: 0.8633 max: 2.5757 USE_META, weight: 0.7778 cost: 1.2861 min: 0.8633 max: 2.5757 USE_META, weight: 0.7773 cost: 1.2870 min: 0.8633 max: 2.5757 USE_META, weight: 0.4482 cost: 1.9131 min: 0.8633 max: 2.5757 USE_META, weight: 0.3685 cost: 2.0648 min: 0.8633 max: 2.5757 USE_META, weight: 0.4787 cost: 1.8552 min: 0.8633 max: 2.5757 USE_META, weight: 0.3986 cost: 2.0076 min: 0.8633 max: 2.5757 USE_META, weight: 0.3397 cost: 2.1195 min: 0.8633 max: 2.5757 USE_META, weight: 0.7833 cost: 1.2756 min: 0.8633 max: 2.5757 USE_META, weight: 0.7769 cost: 1.2878 min: 0.8633 max: 2.5757 USE_META, weight: 0.7778 cost: 1.2860 min: 0.8633 max: 2.5757 USE_META, weight: 0.7771 cost: 1.2874 min: 0.8633 max: 2.5757 USE_META, weight: 0.7825 cost: 1.2771 min: 0.8633 max: 2.5757 USE_META, weight: 0.3860 cost: 2.0315 min: 0.8633 max: 2.5757 USE_META, weight: 0.5753 cost: 1.6715 min: 0.8633 max: 2.5757 USE_META, weight: 0.5510 cost: 1.7177 min: 0.8633 max: 2.5757 USE_META, weight: 0.5405 cost: 1.7377 min: 0.8633 max: 2.5757 USE_META, weight: 0.5663 cost: 1.6884 min: 0.8633 max: 2.5757 USE_META, weight: 0.3069 cost: 2.1819 min: 0.8633 max: 2.5757 USE_META, weight: 0.5333 cost: 1.7514 min: 0.8633 max: 2.5757 USE_META, weight: 0.3479 cost: 2.1040 min: 0.8633 max: 2.5757 USE_META, weight: 0.6279 cost: 1.5713 min: 0.8633 max: 2.5757 USE_META, weight: 0.2536 cost: 2.2835 min: 0.8633 max: 2.5757 USE_META, weight: 0.4247 cost: 1.9579 min: 0.8633 max: 2.5757 USE_META, weight: 0.5754 cost: 1.6712 min: 0.8633 max: 2.5757 USE_META, weight: 0.5754 cost: 1.6712 min: 0.8633 max: 2.5757 USE_META, weight: 0.6163 cost: 1.5934 min: 0.8633 max: 2.5757 USE_META, weight: 0.8076 cost: 1.2294 min: 0.8633 max: 2.5757 USE_META, weight: 0.6406 cost: 1.5471 min: 0.8633 max: 2.5757 USE_META, weight: 0.6069 cost: 1.6112 min: 0.8633 max: 2.5757 USE_META, weight: 0.6521 cost: 1.5252 min: 0.8633 max: 2.5757 USE_META, weight: 0.5721 cost: 1.6774 min: 0.8633 max: 2.5757 USE_META, weight: 0.6269 cost: 1.5732 min: 0.8633 max: 2.5757 USE_META, weight: 0.5766 cost: 1.6688 min: 0.8633 max: 2.5757 USE_META, weight: 0.7205 cost: 1.3952 min: 0.8633 max: 2.5757 USE_META, weight: 0.6226 cost: 1.5815 min: 0.8633 max: 2.5757 USE_META, weight: 0.5449 cost: 1.7291 min: 0.8633 max: 2.5757 USE_META, weight: 0.6227 cost: 1.5813 min: 0.8633 max: 2.5757 USE_META, weight: 0.5638 cost: 1.6932 min: 0.8633 max: 2.5757 USE_META, weight: 0.3351 cost: 2.1284 min: 0.8633 max: 2.5757 USE_META, weight: 0.4720 cost: 1.8678 min: 0.8633 max: 2.5757 USE_META, weight: 0.8301 cost: 1.1866 min: 0.8633 max: 2.5757 USE_META, weight: 0.8035 cost: 1.2372 min: 0.8633 max: 2.5757 USE_META, weight: 0.8346 cost: 1.1781 min: 0.8633 max: 2.5757 USE_META, weight: 0.8058 cost: 1.2328 min: 0.8633 max: 2.5757 USE_META, weight: 0.8361 cost: 1.1753 min: 0.8633 max: 2.5757 USE_META, weight: 0.5721 cost: 1.6774 min: 0.8633 max: 2.5757 USE_META, weight: 0.7628 cost: 1.3147 min: 0.8633 max: 2.5757 USE_META, weight: 0.7383 cost: 1.3612 min: 0.8633 max: 2.5757 USE_META, weight: 0.4540 cost: 1.9021 min: 0.8633 max: 2.5757 USE_META, weight: 0.5251 cost: 1.7669 min: 0.8633 max: 2.5757 USE_META, weight: 0.5355 cost: 1.7471 min: 0.8633 max: 2.5757 USE_META, weight: 0.7536 cost: 1.3321 min: 0.8633 max: 2.5757 USE_META, weight: 0.7832 cost: 1.2758 min: 0.8633 max: 2.5757 USE_META, weight: 0.7618 cost: 1.3166 min: 0.8633 max: 2.5757 USE_META, weight: 0.7797 cost: 1.2824 min: 0.8633 max: 2.5757 USE_META, weight: 0.8723 cost: 1.1064 min: 0.8633 max: 2.5757 USE_META, weight: 0.4539 cost: 1.9023 min: 0.8633 max: 2.5757 USE_META, weight: 0.1112 cost: 2.5544 min: 0.8633 max: 2.5757 USE_META, weight: 0.5828 cost: 1.6571 min: 0.8633 max: 2.5757 USE_META, weight: 0.7536 cost: 1.3321 min: 0.8633 max: 2.5757 USE_META, weight: 0.7665 cost: 1.3076 min: 0.8633 max: 2.5757 USE_META, weight: 0.6578 cost: 1.5144 min: 0.8633 max: 2.5757 USE_META, weight: 0.3850 cost: 2.0334 min: 0.8633 max: 2.5757 USE_META, weight: 0.3247 cost: 2.1482 min: 0.8633 max: 2.5757 USE_META, weight: 0.6930 cost: 1.4475 min: 0.8633 max: 2.5757 USE_META, weight: 0.5607 cost: 1.6992 min: 0.8633 max: 2.5757 USE_META, weight: 0.7154 cost: 1.4048 min: 0.8633 max: 2.5757 USE_META, weight: 0.6321 cost: 1.5634 min: 0.8633 max: 2.5757 USE_META, weight: 0.5398 cost: 1.7390 min: 0.8633 max: 2.5757 USE_META, weight: 0.1461 cost: 2.4880 min: 0.8633 max: 2.5757 USE_META, weight: 0.1461 cost: 2.4880 min: 0.8633 max: 2.5757 USE_META, weight: 0.4813 cost: 1.8501 min: 0.8633 max: 2.5757 USE_META, weight: 0.5054 cost: 1.8044 min: 0.8633 max: 2.5757 USE_META, weight: 0.3790 cost: 2.0449 min: 0.8633 max: 2.5757 USE_META, weight: 0.7281 cost: 1.3807 min: 0.8633 max: 2.5757 USE_META, weight: 0.3085 cost: 2.1790 min: 0.8633 max: 2.5757 USE_META, weight: 0.5007 cost: 1.8133 min: 0.8633 max: 2.5757 USE_META, weight: 0.5367 cost: 1.7449 min: 0.8633 max: 2.5757 USE_META, weight: 0.5633 cost: 1.6942 min: 0.8633 max: 2.5757 USE_META, weight: 0.5467 cost: 1.7258 min: 0.8633 max: 2.5757 USE_META, weight: 0.6641 cost: 1.5025 min: 0.8633 max: 2.5757 USE_META, weight: 0.5001 cost: 1.8145 min: 0.8633 max: 2.5757 USE_META, weight: 0.5619 cost: 1.6969 min: 0.8633 max: 2.5757 USE_META, weight: 0.5513 cost: 1.7170 min: 0.8633 max: 2.5757 USE_META, weight: 0.5534 cost: 1.7131 min: 0.8633 max: 2.5757 USE_META, weight: 0.6687 cost: 1.4937 min: 0.8633 max: 2.5757 USE_META, weight: 0.5077 cost: 1.7999 min: 0.8633 max: 2.5757 USE_META, weight: 0.6578 cost: 1.5144 min: 0.8633 max: 2.5757 USE_META, weight: 0.5598 cost: 1.7008 min: 0.8633 max: 2.5757 USE_META, weight: 0.6153 cost: 1.5952 min: 0.8633 max: 2.5757 USE_META, weight: 0.5782 cost: 1.6659 min: 0.8633 max: 2.5757 USE_META, weight: 0.7119 cost: 1.4114 min: 0.8633 max: 2.5757 USE_META, weight: 0.7787 cost: 1.2843 min: 0.8633 max: 2.5757 USE_META, weight: 0.7785 cost: 1.2848 min: 0.8633 max: 2.5757 USE_META, weight: 0.7797 cost: 1.2825 min: 0.8633 max: 2.5757 USE_META, weight: 0.7798 cost: 1.2823 min: 0.8633 max: 2.5757 USE_META, weight: 0.7861 cost: 1.2703 min: 0.8633 max: 2.5757 USE_META, weight: 0.7825 cost: 1.2771 min: 0.8633 max: 2.5757 USE_META, weight: 0.7825 cost: 1.2771 min: 0.8633 max: 2.5757 USE_META, weight: 0.7825 cost: 1.2771 min: 0.8633 max: 2.5757 USE_META, weight: 0.7833 cost: 1.2756 min: 0.8633 max: 2.5757 USE_META, weight: 0.7825 cost: 1.2771 min: 0.8633 max: 2.5757 USE_META, weight: 0.6524 cost: 1.5247 min: 0.8633 max: 2.5757 USE_META, weight: 0.6570 cost: 1.5159 min: 0.8633 max: 2.5757 USE_META, weight: 0.6576 cost: 1.5148 min: 0.8633 max: 2.5757 USE_META, weight: 0.6593 cost: 1.5115 min: 0.8633 max: 2.5757 USE_META, weight: 1.0000 cost: 0.8633 min: 0.8633 max: 2.5757 USE_META, weight: 0.7638 cost: 1.3127 min: 0.8633 max: 2.5757 USE_META, weight: 0.5417 cost: 1.7352 min: 0.8633 max: 2.5757 USE_META, weight: 0.5825 cost: 1.6576 min: 0.8633 max: 2.5757 USE_META, weight: 0.4428 cost: 1.9234 min: 0.8633 max: 2.5757 USE_META, weight: 0.5116 cost: 1.7926 min: 0.8633 max: 2.5757 USE_META, weight: 0.7241 cost: 1.3883 min: 0.8633 max: 2.5757 USE_META, weight: 0.5237 cost: 1.7696 min: 0.8633 max: 2.5757 USE_META, weight: 0.6991 cost: 1.4358 min: 0.8633 max: 2.5757 USE_META, weight: 0.5782 cost: 1.6659 min: 0.8633 max: 2.5757 USE_META, weight: 0.5756 cost: 1.6708 min: 0.8633 max: 2.5757 USE_META, weight: 0.6402 cost: 1.5479 min: 0.8633 max: 2.5757 USE_META, weight: 0.5271 cost: 1.7631 min: 0.8633 max: 2.5757 USE_META, weight: 0.6472 cost: 1.5346 min: 0.8633 max: 2.5757 USE_META, weight: 0.5682 cost: 1.6849 min: 0.8633 max: 2.5757 USE_META, weight: 0.6462 cost: 1.5365 min: 0.8633 max: 2.5757 USE_META, weight: 0.7785 cost: 1.2848 min: 0.8633 max: 2.5757 USE_META, weight: 0.7825 cost: 1.2771 min: 0.8633 max: 2.5757 USE_META, weight: 0.7786 cost: 1.2845 min: 0.8633 max: 2.5757 USE_META, weight: 0.7785 cost: 1.2848 min: 0.8633 max: 2.5757 USE_META, weight: 0.7781 cost: 1.2855 min: 0.8633 max: 2.5757 USE_META, weight: 0.5389 cost: 1.7406 min: 0.8633 max: 2.5757 USE_META, weight: 0.7825 cost: 1.2771 min: 0.8633 max: 2.5757 USE_META, weight: 0.7825 cost: 1.2771 min: 0.8633 max: 2.5757 USE_META, weight: 0.7825 cost: 1.2771 min: 0.8633 max: 2.5757 USE_META, weight: 0.7782 cost: 1.2853 min: 0.8633 max: 2.5757 USE_META, weight: 0.7825 cost: 1.2771 min: 0.8633 max: 2.5757 USE_META, weight: 0.9095 cost: 1.0354 min: 0.8633 max: 2.5757 USE_META, weight: 0.8405 cost: 1.1668 min: 0.8633 max: 2.5757 USE_META, weight: 0.9314 cost: 0.9938 min: 0.8633 max: 2.5757 USE_META, weight: 0.9012 cost: 1.0513 min: 0.8633 max: 2.5757 USE_META, weight: 0.9634 cost: 0.9330 min: 0.8633 max: 2.5757 USE_META, weight: 0.6354 cost: 1.5570 min: 0.8633 max: 2.5757 USE_META, weight: 0.6291 cost: 1.5691 min: 0.8633 max: 2.5757 USE_META, weight: 0.7825 cost: 1.2771 min: 0.8633 max: 2.5757 USE_META, weight: 0.7851 cost: 1.2723 min: 0.8633 max: 2.5757 USE_META, weight: 0.7875 cost: 1.2676 min: 0.8633 max: 2.5757 USE_META, weight: 0.7825 cost: 1.2771 min: 0.8633 max: 2.5757 USE_META, weight: 0.7781 cost: 1.2855 min: 0.8633 max: 2.5757 USE_META, weight: 0.5271 cost: 1.7630 min: 0.8633 max: 2.5757 USE_META, weight: 0.5277 cost: 1.7620 min: 0.8633 max: 2.5757 USE_META, weight: 0.6706 cost: 1.4901 min: 0.8633 max: 2.5757 USE_META, weight: 0.5579 cost: 1.7044 min: 0.8633 max: 2.5757 USE_META, weight: 0.4863 cost: 1.8407 min: 0.8633 max: 2.5757 USE_META, weight: 0.4516 cost: 1.9068 min: 0.8633 max: 2.5757 USE_META, weight: 0.4192 cost: 1.9684 min: 0.8633 max: 2.5757 USE_META, weight: 0.3593 cost: 2.0824 min: 0.8633 max: 2.5757 USE_META, weight: 0.5545 cost: 1.7110 min: 0.8633 max: 2.5757 USE_META, weight: 0.5371 cost: 1.7440 min: 0.8633 max: 2.5757 USE_META, weight: 0.5799 cost: 1.6626 min: 0.8633 max: 2.5757 USE_META, weight: 0.6731 cost: 1.4854 min: 0.8633 max: 2.5757 USE_META, weight: 0.5938 cost: 1.6361 min: 0.8633 max: 2.5757 USE_META, weight: 0.7218 cost: 1.3926 min: 0.8633 max: 2.5757 USE_META, weight: 0.7698 cost: 1.3013 min: 0.8633 max: 2.5757 USE_META, weight: 0.5566 cost: 1.7069 min: 0.8633 max: 2.5757 USE_META, weight: 0.5588 cost: 1.7027 min: 0.8633 max: 2.5757 USE_META, weight: 0.4646 cost: 1.8821 min: 0.8633 max: 2.5757 USE_META, weight: 0.4237 cost: 1.9598 min: 0.8633 max: 2.5757 USE_META, weight: 0.3237 cost: 2.1501 min: 0.8633 max: 2.5757 USE_META, weight: 0.5600 cost: 1.7005 min: 0.8633 max: 2.5757 USE_META, weight: 0.4923 cost: 1.8294 min: 0.8633 max: 2.5757 USE_META, weight: 0.5575 cost: 1.7052 min: 0.8633 max: 2.5757 USE_META, weight: 0.3216 cost: 2.1540 min: 0.8633 max: 2.5757 USE_META, weight: 0.6620 cost: 1.5064 min: 0.8633 max: 2.5757 USE_META, weight: 0.5866 cost: 1.6499 min: 0.8633 max: 2.5757 USE_META, weight: 0.7670 cost: 1.3066 min: 0.8633 max: 2.5757 USE_META, weight: 0.6596 cost: 1.5109 min: 0.8633 max: 2.5757 USE_EVALUE, weight: 0.2211 eval: 32.7140 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.2211 eval: 32.7140 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.2211 eval: 32.7140 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.6165 eval: 19.1070 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.6165 eval: 19.1070 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.6165 eval: 19.1070 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.6906 eval: 16.5580 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.6906 eval: 16.5580 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.6906 eval: 16.5580 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.4368 eval: 25.2920 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.4368 eval: 25.2920 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.4368 eval: 25.2920 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.6500 eval: 17.9530 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.6500 eval: 17.9530 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 1.0000 eval: 5.9094 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 1.0000 eval: 5.9094 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.1715 eval: 34.4230 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.1715 eval: 34.4230 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.1715 eval: 34.4230 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.7892 eval: 13.1650 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.7892 eval: 13.1650 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.7892 eval: 13.1650 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.7506 eval: 14.4930 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.7506 eval: 14.4930 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.7506 eval: 14.4930 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.1427 eval: 35.4130 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.1427 eval: 35.4130 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.1427 eval: 35.4130 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.6185 eval: 19.0380 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.6185 eval: 19.0380 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.2855 eval: 30.5000 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.2855 eval: 30.5000 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.2855 eval: 30.5000 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.1580 eval: 34.8860 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.1580 eval: 34.8860 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.1580 eval: 34.8860 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.3275 eval: 29.0530 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.3275 eval: 29.0530 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.3275 eval: 29.0530 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.1681 eval: 34.5410 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.1681 eval: 34.5410 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.1681 eval: 34.5410 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.4025 eval: 26.4720 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.4025 eval: 26.4720 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.4025 eval: 26.4720 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.7393 eval: 14.8820 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.7393 eval: 14.8820 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.7393 eval: 14.8820 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.3317 eval: 28.9100 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.3317 eval: 28.9100 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.3317 eval: 28.9100 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.5063 eval: 22.9000 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.5063 eval: 22.9000 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.5063 eval: 22.9000 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.6662 eval: 17.3980 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.6662 eval: 17.3980 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.6662 eval: 17.3980 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.6719 eval: 17.2000 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.6719 eval: 17.2000 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.1000 eval: 36.8830 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.1000 eval: 36.8830 min: 5.9094 max: 36.8830 USE_EVALUE, weight: 0.1000 eval: 36.8830 min: 5.9094 max: 36.8830 Number of contacts in models: 239 Number of contacts in alignments: 62 NUMB_ALIGNS: 62 Adding 4332 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: -200.8321, CN propb: -200.8321 weights: 0.3234 constraints: 273 # command:Found ConstraintSet # PrintContacts align.constraints_meta03 Number of constraints in align3.constraints 273 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_meta03 Number of constraints in align3.constraints.bonus 273 # command:Found ConstraintSet # PrintContacts rejected.constraints_meta03 Number of constraints in rejected3.constraints 4059 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_meta03 Number of constraints in rejected3.constraints.bonus 4059 # 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 4332 # command: