# 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/T0357/ # command:# Making conformation for sequence T0357 numbered 1 through 141 Created new target T0357 from T0357.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0357/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0357//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0357/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0357//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0357/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0357/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0357/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1q1gA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1q1gA expands to /projects/compbio/data/pdb/1q1g.pdb.gz 1q1gA:# T0357 read from 1q1gA/merged-good-all-a2m # 1q1gA read from 1q1gA/merged-good-all-a2m # adding 1q1gA to template set # found chain 1q1gA in template set T0357 7 :RAITRGRAEGEALVT 1q1gA 40 :DLAYNREYKSVECHY # choosing archetypes in rotamer library T0357 45 :KGESV 1q1gA 55 :KGQKF T0357 54 :LVFPGGKGSTVGSYVLLNLRKNGV 1q1gA 60 :LCVSHGVGSAGCAVCFEELCQNGA T0357 80 :KAIINK 1q1gA 84 :KVIIRA T0357 86 :KTETIIAVGAAMAE 1q1gA 101 :KRGDICICNAAVRE T0357 100 :IPLV 1q1gA 126 :FPAV T0357 106 :RDEKFFEAVK 1q1gA 130 :GDFDVYDTLN Number of specific fragments extracted= 7 number of extra gaps= 0 total=7 Number of alignments=1 # 1q1gA read from 1q1gA/merged-good-all-a2m # found chain 1q1gA in template set T0357 6 :CRAITRGRAEGEALVT 1q1gA 39 :VDLAYNREYKSVECHY T0357 45 :KGES 1q1gA 55 :KGQK T0357 53 :ILVFPGGKGSTVGSYVLLNLRKNGV 1q1gA 59 :FLCVSHGVGSAGCAVCFEELCQNGA T0357 80 :KAIINK 1q1gA 84 :KVIIRA T0357 86 :KTETIIAVGAAMAE 1q1gA 101 :KRGDICICNAAVRE T0357 100 :IPLV 1q1gA 126 :FPAV T0357 106 :RDEKFFEAVK 1q1gA 130 :GDFDVYDTLN Number of specific fragments extracted= 7 number of extra gaps= 0 total=14 Number of alignments=2 # 1q1gA read from 1q1gA/merged-good-all-a2m # found chain 1q1gA in template set T0357 7 :RAITRGRAEGEALVT 1q1gA 40 :DLAYNREYKSVECHY T0357 45 :KGESV 1q1gA 55 :KGQKF T0357 54 :LVFPGGKGSTVGSYVLLNLRKNGV 1q1gA 60 :LCVSHGVGSAGCAVCFEELCQNGA T0357 80 :KAIIN 1q1gA 84 :KVIIR Number of specific fragments extracted= 4 number of extra gaps= 0 total=18 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2d13A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2d13A expands to /projects/compbio/data/pdb/2d13.pdb.gz 2d13A:# T0357 read from 2d13A/merged-good-all-a2m # 2d13A read from 2d13A/merged-good-all-a2m # adding 2d13A to template set # found chain 2d13A in template set Warning: unaligning (T0357)T89 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2d13A)N51 Warning: unaligning (T0357)D107 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2d13A)E74 T0357 53 :ILVF 2d13A 7 :VAVL T0357 59 :GKGSTVGSYVLLNLRKNGVAPKAIINKKTE 2d13A 11 :YSGGKDSNYALYWALKSGLRVRYLVSMVSE T0357 100 :IPLVEVR 2d13A 64 :IPIIKGF T0357 108 :EKFFEAVKT 2d13A 80 :EDLKNVLEG Number of specific fragments extracted= 4 number of extra gaps= 0 total=22 Number of alignments=4 # 2d13A read from 2d13A/merged-good-all-a2m # found chain 2d13A in template set Warning: unaligning (T0357)T89 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2d13A)N51 Warning: unaligning (T0357)D107 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2d13A)E74 T0357 52 :RILVF 2d13A 6 :DVAVL T0357 59 :GKGSTVGSYVLLNLRKNGVAPKAIINKKTE 2d13A 11 :YSGGKDSNYALYWALKSGLRVRYLVSMVSE T0357 100 :IPLVEVR 2d13A 64 :IPIIKGF T0357 108 :EKFFEAVKT 2d13A 80 :EDLKNVLEG Number of specific fragments extracted= 4 number of extra gaps= 0 total=26 Number of alignments=5 # 2d13A read from 2d13A/merged-good-all-a2m # found chain 2d13A in template set Warning: unaligning (T0357)T89 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2d13A)N51 T0357 52 :RILVFP 2d13A 6 :DVAVLY T0357 60 :KGSTVGSYVLLNLRKNGVAPKAIINKKTE 2d13A 12 :SGGKDSNYALYWALKSGLRVRYLVSMVSE Number of specific fragments extracted= 2 number of extra gaps= 0 total=28 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1bg6/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1bg6 expands to /projects/compbio/data/pdb/1bg6.pdb.gz 1bg6:Warning: there is no chain 1bg6 will retry with 1bg6A # T0357 read from 1bg6/merged-good-all-a2m # 1bg6 read from 1bg6/merged-good-all-a2m # adding 1bg6 to template set # found chain 1bg6 in template set T0357 105 :VRDEKFFEAVKTGDRVVVNADEGYVE 1bg6 34 :DIDAQRIKEIQDRGAIIAEGPGLAGT Number of specific fragments extracted= 1 number of extra gaps= 0 total=29 Number of alignments=7 # 1bg6 read from 1bg6/merged-good-all-a2m # found chain 1bg6 in template set T0357 50 :AGRILVF 1bg6 101 :EGQLIIL T0357 59 :GKGSTVGSYVLLN 1bg6 108 :NPGATGGALEFRK Number of specific fragments extracted= 2 number of extra gaps= 0 total=31 Number of alignments=8 # 1bg6 read from 1bg6/merged-good-all-a2m # found chain 1bg6 in template set T0357 50 :AGRILVF 1bg6 101 :EGQLIIL T0357 59 :GKGSTVGSYVLLN 1bg6 108 :NPGATGGALEFRK T0357 72 :LRKNGVAPKAIIN 1bg6 122 :LRENGAPEVTIGE Number of specific fragments extracted= 3 number of extra gaps= 0 total=34 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vbkA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vbkA expands to /projects/compbio/data/pdb/1vbk.pdb.gz 1vbkA:# T0357 read from 1vbkA/merged-good-all-a2m # 1vbkA read from 1vbkA/merged-good-all-a2m # adding 1vbkA to template set # found chain 1vbkA in template set T0357 8 :AITRG 1vbkA 155 :EIMQG T0357 17 :EALVTKEYISFLGGIDKET 1vbkA 160 :KAYIYTEKIKGWGGLPIGT T0357 50 :AGRILVFPGG 1vbkA 179 :EGRMIGILHD T0357 63 :TVGSYVLLNLRKNGVAPKAIINKKTE 1vbkA 189 :ELSALAIFLMMKRGVEVIPVYIGKDD T0357 100 :IPLVEVRDEK 1vbkA 236 :GFLVVAESFD T0357 110 :FFEAVKT 1vbkA 247 :VLKLIRD Number of specific fragments extracted= 6 number of extra gaps= 0 total=40 Number of alignments=10 # 1vbkA read from 1vbkA/merged-good-all-a2m # found chain 1vbkA in template set T0357 8 :AITRG 1vbkA 155 :EIMQG T0357 17 :EALVTKEYISFLGGIDKETG 1vbkA 160 :KAYIYTEKIKGWGGLPIGTE T0357 51 :GRILVFPGG 1vbkA 180 :GRMIGILHD T0357 63 :TVGSYVLLNLRKNGVA 1vbkA 189 :ELSALAIFLMMKRGVE T0357 92 :AVGAAMAE 1vbkA 205 :VIPVYIGK T0357 100 :IPLVEVRD 1vbkA 236 :GFLVVAES T0357 108 :EKFFEAVKT 1vbkA 245 :DRVLKLIRD Number of specific fragments extracted= 7 number of extra gaps= 0 total=47 Number of alignments=11 # 1vbkA read from 1vbkA/merged-good-all-a2m # found chain 1vbkA in template set T0357 2 :VKFACR 1vbkA 150 :IEIGIE T0357 9 :ITRG 1vbkA 156 :IMQG T0357 17 :EALVTKEYISFLGGIDKET 1vbkA 160 :KAYIYTEKIKGWGGLPIGT T0357 50 :AGRILVFPGG 1vbkA 179 :EGRMIGILHD T0357 63 :TVGSYVLLNLRKNGVAPKAIINKKTET 1vbkA 189 :ELSALAIFLMMKRGVEVIPVYIGKDDK Number of specific fragments extracted= 5 number of extra gaps= 0 total=52 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yavA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1yavA expands to /projects/compbio/data/pdb/1yav.pdb.gz 1yavA:# T0357 read from 1yavA/merged-good-all-a2m # 1yavA read from 1yavA/merged-good-all-a2m # adding 1yavA to template set # found chain 1yavA in template set T0357 37 :IVKEDCE 1yavA 28 :HVQVGNN T0357 65 :GSYVLLNLRKNGVAPKAIINKKTE 1yavA 35 :LEHALLVLTKTGYTAIPVLDPSYR T0357 92 :AVGAA 1yavA 59 :LHGLI T0357 99 :E 1yavA 64 :G T0357 100 :IPLVEVRD 1yavA 96 :IPRLHIND T0357 108 :EKFFEAVKTGDRVVVNADEGYVELI 1yavA 106 :MKGFGMVINNGFVCVENDEQVFEGI Number of specific fragments extracted= 6 number of extra gaps= 0 total=58 Number of alignments=13 # 1yavA read from 1yavA/merged-good-all-a2m # found chain 1yavA in template set T0357 38 :VKEDCE 1yavA 29 :VQVGNN T0357 65 :GSYVLLNLRKNGVAPKAIINKKTE 1yavA 35 :LEHALLVLTKTGYTAIPVLDPSYR T0357 92 :AVGAAM 1yavA 59 :LHGLIG T0357 100 :IPLVEVRD 1yavA 96 :IPRLHIND T0357 108 :EKFFEAVKTGDRVVVNADEGYVEL 1yavA 106 :MKGFGMVINNGFVCVENDEQVFEG Number of specific fragments extracted= 5 number of extra gaps= 0 total=63 Number of alignments=14 # 1yavA read from 1yavA/merged-good-all-a2m # found chain 1yavA in template set T0357 66 :SYVLLNLRKNGVAPKAIINKK 1yavA 36 :EHALLVLTKTGYTAIPVLDPS Number of specific fragments extracted= 1 number of extra gaps= 0 total=64 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1hx3A/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/T0357/1hx3A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0357/1hx3A/merged-good-all-a2m.gz for input Trying 1hx3A/merged-good-all-a2m Error: Couldn't open file 1hx3A/merged-good-all-a2m or 1hx3A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2g74A/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/T0357/2g74A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0357/2g74A/merged-good-all-a2m.gz for input Trying 2g74A/merged-good-all-a2m Error: Couldn't open file 2g74A/merged-good-all-a2m or 2g74A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1p3rA/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/T0357/1p3rA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0357/1p3rA/merged-good-all-a2m.gz for input Trying 1p3rA/merged-good-all-a2m Error: Couldn't open file 1p3rA/merged-good-all-a2m or 1p3rA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2f1dA/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/T0357/2f1dA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0357/2f1dA/merged-good-all-a2m.gz for input Trying 2f1dA/merged-good-all-a2m Error: Couldn't open file 2f1dA/merged-good-all-a2m or 2f1dA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1rxyA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0357 read from 1rxyA/merged-good-all-a2m # 1rxyA read from 1rxyA/merged-good-all-a2m # found chain 1rxyA in training set T0357 19 :LVTKEYISFLG 1rxyA 44 :LASHREFTTWR T0357 42 :CEIKGES 1rxyA 55 :AELDGKP T0357 53 :ILVFPGGKGSTVGSYVLLNLRKNGV 1rxyA 62 :VIVCSTGIGGPSTSIAVEELAQLGI T0357 78 :APKAIINK 1rxyA 93 :GTTGAIQP T0357 86 :KTETIIAVGAAMAE 1rxyA 103 :NVGDVLVTTASVRL T0357 100 :IPLV 1rxyA 128 :FPAV T0357 106 :RDEKFFEAVK 1rxyA 132 :ADFECTTALV Number of specific fragments extracted= 7 number of extra gaps= 0 total=71 Number of alignments=16 # 1rxyA read from 1rxyA/merged-good-all-a2m # found chain 1rxyA in training set T0357 19 :LVTKEYISFL 1rxyA 44 :LASHREFTTW T0357 43 :EIKGES 1rxyA 56 :ELDGKP T0357 53 :ILVFPGGKGSTVGSYVLLNLRKNGV 1rxyA 62 :VIVCSTGIGGPSTSIAVEELAQLGI T0357 78 :APKAIINK 1rxyA 93 :GTTGAIQP T0357 86 :KTETIIAVGAA 1rxyA 103 :NVGDVLVTTAS T0357 100 :IPLV 1rxyA 128 :FPAV T0357 106 :RDEKFFEAV 1rxyA 132 :ADFECTTAL Number of specific fragments extracted= 7 number of extra gaps= 0 total=78 Number of alignments=17 # 1rxyA read from 1rxyA/merged-good-all-a2m # found chain 1rxyA in training set T0357 19 :LVTKEYISFLGG 1rxyA 44 :LASHREFTTWRA T0357 43 :EIKGESV 1rxyA 56 :ELDGKPV T0357 54 :LVFPGGKGSTVGSYVLLNLRKNGV 1rxyA 63 :IVCSTGIGGPSTSIAVEELAQLGI Number of specific fragments extracted= 3 number of extra gaps= 0 total=81 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qdlB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1qdlB expands to /projects/compbio/data/pdb/1qdl.pdb.gz 1qdlB:# T0357 read from 1qdlB/merged-good-all-a2m # 1qdlB read from 1qdlB/merged-good-all-a2m # adding 1qdlB to template set # found chain 1qdlB in template set T0357 3 :KFACRAITRGR 1qdlB 98 :IRRARKVFHGK T0357 15 :EGEALV 1qdlB 109 :ISNIIL T0357 21 :TKEYISFLGGI 1qdlB 116 :NNSPLSLYYGI T0357 37 :IVKE 1qdlB 139 :VVDE T0357 59 :GK 1qdlB 143 :VH T0357 76 :GVAPKAIINKKTETIIAV 1qdlB 145 :RPLIVDAISAEDNEIMAI T0357 97 :MAE 1qdlB 163 :HHE T0357 100 :IPLVE 1qdlB 167 :YPIYG Number of specific fragments extracted= 8 number of extra gaps= 0 total=89 Number of alignments=19 # 1qdlB read from 1qdlB/merged-good-all-a2m # found chain 1qdlB in template set T0357 4 :FACRAITRGR 1qdlB 99 :RRARKVFHGK T0357 15 :EGEALVT 1qdlB 109 :ISNIILV T0357 22 :KEYISFLGGI 1qdlB 117 :NSPLSLYYGI T0357 36 :G 1qdlB 137 :S T0357 37 :IVKE 1qdlB 139 :VVDE T0357 49 :VA 1qdlB 143 :VH T0357 76 :GVAPKAIINKKTETIIA 1qdlB 145 :RPLIVDAISAEDNEIMA T0357 96 :AMAE 1qdlB 162 :IHHE T0357 100 :IPLVEV 1qdlB 167 :YPIYGV Number of specific fragments extracted= 9 number of extra gaps= 0 total=98 Number of alignments=20 # 1qdlB read from 1qdlB/merged-good-all-a2m # found chain 1qdlB in template set T0357 51 :GRILVFPGGKGS 1qdlB 47 :DRLIISPGPGTP T0357 63 :TVGSYVLLNLR 1qdlB 65 :GVSLDVIKYLG T0357 76 :GVAPKAIIN 1qdlB 76 :KRTPILGVC T0357 91 :IAVGAAMAEIP 1qdlB 85 :LGHQAIGYAFG T0357 106 :RD 1qdlB 96 :AK T0357 111 :FEAVKT 1qdlB 98 :IRRARK T0357 121 :VVNADEGY 1qdlB 104 :VFHGKISN T0357 132 :IELEHHHH 1qdlB 112 :IILVNNSP Number of specific fragments extracted= 8 number of extra gaps= 0 total=106 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ganA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2ganA expands to /projects/compbio/data/pdb/2gan.pdb.gz 2ganA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0357 read from 2ganA/merged-good-all-a2m # 2ganA read from 2ganA/merged-good-all-a2m # adding 2ganA to template set # found chain 2ganA in template set T0357 8 :AITRGRAEGEALVTKEYI 2ganA 72 :YQKDNRIIGTIALVYKRI T0357 33 :KETG 2ganA 90 :KEKG T0357 37 :IVKEDCEIKGESVAGRILVFPGGKGSTVGSYVLL 2ganA 96 :WVPEELMNEKVGLIEFFVVDPEFQGKGIGSTLLE T0357 71 :NLRKNGVAPKAIINKK 2ganA 134 :RLRSLGKDPYVVTFPN T0357 106 :RDEKFFEAVKTGDR 2ganA 150 :LEAYSYYYMKKGFR T0357 121 :VVNADEGYVELIELE 2ganA 164 :EIMRYKEFVILKFNH Number of specific fragments extracted= 6 number of extra gaps= 0 total=112 Number of alignments=22 # 2ganA read from 2ganA/merged-good-all-a2m # found chain 2ganA in template set T0357 7 :RAITRGRAEGEALVTKEYI 2ganA 71 :TYQKDNRIIGTIALVYKRI T0357 33 :KETGI 2ganA 90 :KEKGI T0357 38 :VKEDCEIKGESVAGRILVFPGGKGSTVGSYVLL 2ganA 97 :VPEELMNEKVGLIEFFVVDPEFQGKGIGSTLLE T0357 71 :NLRKNGVAPKAIINKKT 2ganA 134 :RLRSLGKDPYVVTFPNL T0357 107 :DEKFFEAVKTG 2ganA 151 :EAYSYYYMKKG T0357 129 :VELIELEHHH 2ganA 162 :FREIMRYKEF Number of specific fragments extracted= 6 number of extra gaps= 0 total=118 Number of alignments=23 # 2ganA read from 2ganA/merged-good-all-a2m # found chain 2ganA in template set T0357 8 :AITRGRAEGEALVTKEYI 2ganA 72 :YQKDNRIIGTIALVYKRI T0357 28 :LGGIDKETG 2ganA 94 :IWWVPEELM T0357 37 :IVKEDC 2ganA 113 :VVDPEF T0357 45 :KGESV 2ganA 119 :QGKGI T0357 61 :GSTVGSYVLLNLRKNGVAPKAIINKKTETIIAV 2ganA 124 :GSTLLEFAVKRLRSLGKDPYVVTFPNLEAYSYY T0357 102 :LVEV 2ganA 158 :MKKG T0357 111 :FEAV 2ganA 162 :FREI T0357 121 :VVNADEGYVE 2ganA 166 :MRYKEFVILK Number of specific fragments extracted= 8 number of extra gaps= 0 total=126 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1x83A/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/T0357/1x83A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0357/1x83A/merged-good-all-a2m.gz for input Trying 1x83A/merged-good-all-a2m Error: Couldn't open file 1x83A/merged-good-all-a2m or 1x83A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1q54A/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/T0357/1q54A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0357/1q54A/merged-good-all-a2m.gz for input Trying 1q54A/merged-good-all-a2m Error: Couldn't open file 1q54A/merged-good-all-a2m or 1q54A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2etlA/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/T0357/2etlA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0357/2etlA/merged-good-all-a2m.gz for input Trying 2etlA/merged-good-all-a2m Error: Couldn't open file 2etlA/merged-good-all-a2m or 2etlA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ppvA/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/T0357/1ppvA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0357/1ppvA/merged-good-all-a2m.gz for input Trying 1ppvA/merged-good-all-a2m Error: Couldn't open file 1ppvA/merged-good-all-a2m or 1ppvA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vi4A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vi4A expands to /projects/compbio/data/pdb/1vi4.pdb.gz 1vi4A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 187, because occupancy 0.5 <= existing 0.500 in 1vi4A Skipped atom 189, because occupancy 0.500 <= existing 0.500 in 1vi4A Skipped atom 191, because occupancy 0.500 <= existing 0.500 in 1vi4A Skipped atom 193, because occupancy 0.500 <= existing 0.500 in 1vi4A Skipped atom 195, because occupancy 0.500 <= existing 0.500 in 1vi4A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0357 read from 1vi4A/merged-good-all-a2m # 1vi4A read from 1vi4A/merged-good-all-a2m # adding 1vi4A to template set # found chain 1vi4A in template set T0357 46 :GESVAGRILVFP 1vi4A 54 :SQNGKGKVLVVD T0357 59 :GKGST 1vi4A 66 :GHGSC T0357 64 :VGSYVLLNLRKNGVA 1vi4A 75 :MGDQLAILAIKNDWE T0357 89 :TIIAVGAA 1vi4A 90 :GVIIYGAV T0357 100 :IPLVEVRD 1vi4A 110 :IKALGTSP T0357 113 :AVKTGDRVVVNADEGYV 1vi4A 138 :IVEPGDYLYADWNGILM Number of specific fragments extracted= 6 number of extra gaps= 0 total=132 Number of alignments=25 # 1vi4A read from 1vi4A/merged-good-all-a2m # found chain 1vi4A in template set T0357 47 :ESVAGRILVFP 1vi4A 55 :QNGKGKVLVVD T0357 59 :GKGST 1vi4A 66 :GHGSC T0357 64 :VGSYVLLNLRKNGV 1vi4A 75 :MGDQLAILAIKNDW T0357 88 :ETIIAVGAA 1vi4A 89 :EGVIIYGAV T0357 101 :PLVEVRD 1vi4A 130 :VTLTMQN T0357 112 :EAVKTGDRVVVNADEGYVE 1vi4A 137 :QIVEPGDYLYADWNGILMS T0357 133 :E 1vi4A 156 :E Number of specific fragments extracted= 7 number of extra gaps= 0 total=139 Number of alignments=26 # 1vi4A read from 1vi4A/merged-good-all-a2m # found chain 1vi4A in template set T0357 47 :ESVAGRILVFP 1vi4A 55 :QNGKGKVLVVD T0357 59 :GKGST 1vi4A 66 :GHGSC T0357 65 :GSYVLLNLRKNGVA 1vi4A 76 :GDQLAILAIKNDWE T0357 80 :KAIINKKTETIIAV 1vi4A 90 :GVIIYGAVRDVVAM T0357 94 :GAAMAEIPLVEVRDEKFF 1vi4A 109 :GIKALGTSPFKTEKRGAG T0357 112 :EAVKTGDRVVVNADEGYV 1vi4A 137 :QIVEPGDYLYADWNGILM Number of specific fragments extracted= 6 number of extra gaps= 0 total=145 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r67A/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/T0357/1r67A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0357/1r67A/merged-good-all-a2m.gz for input Trying 1r67A/merged-good-all-a2m Error: Couldn't open file 1r67A/merged-good-all-a2m or 1r67A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qmeA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1qmeA expands to /projects/compbio/data/pdb/1qme.pdb.gz 1qmeA:# T0357 read from 1qmeA/merged-good-all-a2m # 1qmeA read from 1qmeA/merged-good-all-a2m # adding 1qmeA to template set # found chain 1qmeA in template set Number of specific fragments extracted= 0 number of extra gaps= 0 total=145 # 1qmeA read from 1qmeA/merged-good-all-a2m # found chain 1qmeA in template set T0357 59 :GKGSTVGSYVLLNLRKNGVAP 1qmeA 334 :EPGSTMKVMMLAAAIDNNTFP T0357 116 :TGDRVV 1qmeA 355 :GGEVFN T0357 122 :VNADEGYV 1qmeA 364 :LKIADATI Number of specific fragments extracted= 3 number of extra gaps= 0 total=148 Number of alignments=28 # 1qmeA read from 1qmeA/merged-good-all-a2m # found chain 1qmeA in template set T0357 17 :EALVTKE 1qmeA 292 :TLVSAKT T0357 24 :YISFLGGIDKETG 1qmeA 303 :ATTQRPTFDADTK T0357 37 :IVKEDCEIK 1qmeA 317 :GITEDFVWR T0357 57 :PGGKGSTVGSYVLLNLRKNGVAP 1qmeA 332 :NYEPGSTMKVMMLAAAIDNNTFP T0357 105 :VRDEKFFEAVK 1qmeA 355 :GGEVFNSSELK Number of specific fragments extracted= 5 number of extra gaps= 0 total=153 Number of alignments=29 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1nbwA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1nbwA expands to /projects/compbio/data/pdb/1nbw.pdb.gz 1nbwA:# T0357 read from 1nbwA/merged-good-all-a2m # 1nbwA read from 1nbwA/merged-good-all-a2m # adding 1nbwA to template set # found chain 1nbwA in template set T0357 12 :GRAEGEAL 1nbwA 109 :GVGVGTTI T0357 24 :YISFLGGIDKETG 1nbwA 117 :ALGRLATLPAAQY T0357 50 :AGRILVFPGGKGSTVGSYVLLNLRKNGVAPKAIINKKT 1nbwA 131 :EGWIVLIDDAVDFLDAVWWLNEALDRGINVVAAILKKD T0357 100 :IPLVEVRD 1nbwA 181 :LPVVDEVT T0357 110 :FFEAVKTGDRVVVN 1nbwA 189 :LLEQVPEGVMAAVE T0357 124 :ADE 1nbwA 205 :APG Number of specific fragments extracted= 6 number of extra gaps= 0 total=159 Number of alignments=30 # 1nbwA read from 1nbwA/merged-good-all-a2m # found chain 1nbwA in template set T0357 50 :AGRILVFPGGKGSTVGSYVLLNLRKNGVAPKAIINKKTE 1nbwA 131 :EGWIVLIDDAVDFLDAVWWLNEALDRGINVVAAILKKDD T0357 89 :TIIA 1nbwA 180 :TLPV T0357 93 :VGAAMAE 1nbwA 199 :AAVEVAA T0357 106 :RDEKFFEAVK 1nbwA 225 :LSPEETQAIV T0357 116 :TGDR 1nbwA 241 :IGNR T0357 120 :VVVNADEGYVELIELEH 1nbwA 247 :VVLKTPQGDVQSRVIPA Number of specific fragments extracted= 6 number of extra gaps= 0 total=165 Number of alignments=31 # 1nbwA read from 1nbwA/merged-good-all-a2m # found chain 1nbwA in template set T0357 47 :ESVAGRILVFPGGKGSTVGSYVLLNLRKNGVAPKAIINKKTETIIAV 1nbwA 128 :QYAEGWIVLIDDAVDFLDAVWWLNEALDRGINVVAAILKKDDGVLVN T0357 96 :AMAEIPLVE 1nbwA 183 :VVDEVTLLE T0357 113 :AVKTGDRVVV 1nbwA 192 :QVPEGVMAAV Number of specific fragments extracted= 3 number of extra gaps= 0 total=168 Number of alignments=32 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1v7lA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1v7lA expands to /projects/compbio/data/pdb/1v7l.pdb.gz 1v7lA:# T0357 read from 1v7lA/merged-good-all-a2m # 1v7lA read from 1v7lA/merged-good-all-a2m # adding 1v7lA to template set # found chain 1v7lA in template set T0357 13 :RAEGEALVTKEYISFLGGIDKETG 1v7lA 2 :ITTGKVWKFGDDISTDEITPGRYN T0357 39 :KEDC 1v7lA 27 :TKDP T0357 50 :AGRILVFPGGKG 1v7lA 51 :PGDVVVAGKNFG T0357 62 :ST 1v7lA 65 :SS T0357 64 :VGSYVLLNL 1v7lA 69 :SAALALKAL T0357 76 :GV 1v7lA 78 :GI T0357 94 :GAAMAE 1v7lA 80 :AGVIAE T0357 100 :IPLVEVRDEK 1v7lA 100 :IPLLLGKTEG T0357 114 :VKTGDRVVVNADEGYV 1v7lA 110 :LKDGDLVTVNWETGEV T0357 130 :ELIELEHHH 1v7lA 130 :EILMFEPLE Number of specific fragments extracted= 10 number of extra gaps= 0 total=178 Number of alignments=33 # 1v7lA read from 1v7lA/merged-good-all-a2m # found chain 1v7lA in template set T0357 50 :AGRILVFPG 1v7lA 51 :PGDVVVAGK T0357 59 :GKGST 1v7lA 62 :GIGSS T0357 64 :VGSYVLLNL 1v7lA 69 :SAALALKAL T0357 76 :GVA 1v7lA 78 :GIA T0357 95 :AAMAE 1v7lA 81 :GVIAE T0357 100 :IPLVEVRDE 1v7lA 100 :IPLLLGKTE T0357 113 :AVKTGDRVVVNADEGYVE 1v7lA 109 :GLKDGDLVTVNWETGEVR T0357 131 :LIELEHHH 1v7lA 131 :ILMFEPLE Number of specific fragments extracted= 8 number of extra gaps= 0 total=186 Number of alignments=34 # 1v7lA read from 1v7lA/merged-good-all-a2m # found chain 1v7lA in template set T0357 50 :AGRILVFPG 1v7lA 51 :PGDVVVAGK T0357 59 :GKGST 1v7lA 62 :GIGSS T0357 64 :VGSYVLLNL 1v7lA 69 :SAALALKAL T0357 79 :PKAIINKKTETIIAVGAAMAEIPLVEVR 1v7lA 79 :IAGVIAESFGRIFYRNAINIGIPLLLGK T0357 111 :FEAVKTGDRVVVNADEGYVEL 1v7lA 107 :TEGLKDGDLVTVNWETGEVRK Number of specific fragments extracted= 5 number of extra gaps= 0 total=191 Number of alignments=35 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2bsxA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2bsxA expands to /projects/compbio/data/pdb/2bsx.pdb.gz 2bsxA:# T0357 read from 2bsxA/merged-good-all-a2m # 2bsxA read from 2bsxA/merged-good-all-a2m # adding 2bsxA to template set # found chain 2bsxA in template set Warning: unaligning (T0357)E15 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bsxA)V50 Warning: unaligning (T0357)G16 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bsxA)V50 Warning: unaligning (T0357)G61 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bsxA)S68 Warning: unaligning (T0357)S62 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bsxA)S68 Warning: unaligning (T0357)P101 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bsxA)A128 Warning: unaligning (T0357)L102 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bsxA)A128 T0357 4 :FACRAITRGRA 2bsxA 38 :YVDLAYNREYK T0357 17 :EALV 2bsxA 51 :ECHY T0357 45 :KGES 2bsxA 55 :KGQK T0357 53 :ILVFPGGK 2bsxA 59 :FLCVSHGV T0357 63 :TVGSYVLLNLRKNGV 2bsxA 69 :AGCAVCFEELCQNGA T0357 80 :KAIINK 2bsxA 84 :KVIIRA T0357 86 :KTETIIAVGAAMAE 2bsxA 101 :KRGDICICNAAVRE T0357 100 :I 2bsxA 126 :F T0357 103 :V 2bsxA 129 :V T0357 106 :RDEKFFEAVK 2bsxA 130 :GDFDVYDTLN Number of specific fragments extracted= 10 number of extra gaps= 3 total=201 Number of alignments=36 # 2bsxA read from 2bsxA/merged-good-all-a2m # found chain 2bsxA in template set Warning: unaligning (T0357)E15 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bsxA)V50 Warning: unaligning (T0357)G16 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bsxA)V50 Warning: unaligning (T0357)G61 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bsxA)S68 Warning: unaligning (T0357)S62 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bsxA)S68 Warning: unaligning (T0357)P101 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bsxA)A128 Warning: unaligning (T0357)L102 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bsxA)A128 T0357 4 :FACRAITRGRA 2bsxA 38 :YVDLAYNREYK T0357 17 :EALV 2bsxA 51 :ECHY T0357 45 :KGE 2bsxA 55 :KGQ T0357 52 :RILVFPGGK 2bsxA 58 :KFLCVSHGV T0357 63 :TVGSYVLLNLRKNGV 2bsxA 69 :AGCAVCFEELCQNGA T0357 80 :KAIINK 2bsxA 84 :KVIIRA T0357 86 :KTETIIAVGAAMAE 2bsxA 101 :KRGDICICNAAVRE T0357 100 :I 2bsxA 126 :F T0357 103 :V 2bsxA 129 :V T0357 106 :RDEKFFEAVK 2bsxA 130 :GDFDVYDTLN Number of specific fragments extracted= 10 number of extra gaps= 3 total=211 Number of alignments=37 # 2bsxA read from 2bsxA/merged-good-all-a2m # found chain 2bsxA in template set Warning: unaligning (T0357)G16 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bsxA)V50 Warning: unaligning (T0357)E17 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bsxA)V50 Warning: unaligning (T0357)G61 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2bsxA)S68 Warning: unaligning (T0357)S62 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2bsxA)S68 T0357 7 :RAITRGRAE 2bsxA 40 :DLAYNREYK T0357 18 :ALVT 2bsxA 51 :ECHY T0357 45 :KGESV 2bsxA 55 :KGQKF T0357 54 :LVFPGGK 2bsxA 60 :LCVSHGV T0357 63 :TVGSYVLLNLRKNGV 2bsxA 69 :AGCAVCFEELCQNGA T0357 80 :KAIIN 2bsxA 84 :KVIIR Number of specific fragments extracted= 6 number of extra gaps= 2 total=217 Number of alignments=38 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1i9aA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1i9aA expands to /projects/compbio/data/pdb/1i9a.pdb.gz 1i9aA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0357 read from 1i9aA/merged-good-all-a2m # 1i9aA read from 1i9aA/merged-good-all-a2m # adding 1i9aA to template set # found chain 1i9aA in template set T0357 116 :TGDRVVVNADEGYVELI 1i9aA 100 :PDFRYRATDPSGIVENE Number of specific fragments extracted= 1 number of extra gaps= 0 total=218 # 1i9aA read from 1i9aA/merged-good-all-a2m # found chain 1i9aA in template set T0357 116 :TGDRVVVNADEGYVELI 1i9aA 100 :PDFRYRATDPSGIVENE Number of specific fragments extracted= 1 number of extra gaps= 0 total=219 # 1i9aA read from 1i9aA/merged-good-all-a2m # found chain 1i9aA in template set T0357 106 :RDEKFFEAVKTGDRVVVNADEGYVELIE 1i9aA 90 :VEITPPESIYPDFRYRATDPSGIVENEV Number of specific fragments extracted= 1 number of extra gaps= 0 total=220 Number of alignments=39 # command:Using radius: 8.0000 Alignment mode NUMB_ALIGNS: 39 Adding 1148 constraints to all.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all.constraints maxweight: 1.0000 Optimizing... Probability sum: -274.9974, CN propb: -274.9974 weights: 0.2090 constraints: 565 # command:Found ConstraintSet # PrintContacts align.constraints_v3 Number of constraints in align.constraints 565 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_v3 Number of constraints in align.constraints.bonus 565 # command:Found ConstraintSet # PrintContacts rejected.constraints_v3 Number of constraints in rejected.constraints 583 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_v3 Number of constraints in rejected.constraints.bonus 583 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_v3 Number of constraints in noncontact.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_v3 Number of constraints in noncontact.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_v3 Number of constraints in all.constraints 1148 # command: