# 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/T0307/ # command:# Making conformation for sequence T0307 numbered 1 through 133 Created new target T0307 from T0307.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0307/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0307//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0307/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0307//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0307/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0307/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0307/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1oksA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0307 read from 1oksA/merged-good-all-a2m # 1oksA read from 1oksA/merged-good-all-a2m # found chain 1oksA in training set Warning: unaligning (T0307)N132 because of BadResidue code BAD_PEPTIDE in next template residue (1oksA)H54 Warning: unaligning (T0307)L133 because of BadResidue code BAD_PEPTIDE at template residue (1oksA)H54 T0307 68 :EASQAVALIAR 1oksA 3 :SRSVIRSIIKS # choosing archetypes in rotamer library T0307 79 :MDEERKKYVASYLGVI 1oksA 16 :LEEDRKRYLMTLLDDI T0307 101 :IDDNELALWTL 1oksA 32 :KGANDLAKFHQ T0307 122 :TVMEAINNMK 1oksA 43 :MLVKIIMKHH Number of specific fragments extracted= 4 number of extra gaps= 1 total=4 Number of alignments=1 # 1oksA read from 1oksA/merged-good-all-a2m # found chain 1oksA in training set Warning: unaligning (T0307)N132 because of BadResidue code BAD_PEPTIDE in next template residue (1oksA)H54 Warning: unaligning (T0307)L133 because of BadResidue code BAD_PEPTIDE at template residue (1oksA)H54 T0307 68 :EASQAVALIAR 1oksA 3 :SRSVIRSIIKS T0307 79 :MDEERKKYVASYLGVI 1oksA 16 :LEEDRKRYLMTLLDDI T0307 101 :IDDNELALWTL 1oksA 32 :KGANDLAKFHQ T0307 122 :TVMEAINNMK 1oksA 43 :MLVKIIMKHH Number of specific fragments extracted= 4 number of extra gaps= 1 total=8 Number of alignments=2 # 1oksA read from 1oksA/merged-good-all-a2m # found chain 1oksA in training set T0307 42 :VMTREFMRFGILQDQVDLLLKASDSIEASQAVALI 1oksA 6 :VIRSIIKSSRLEEDRKRYLMTLLDDIKGANDLAKF T0307 84 :KKYVASYLGVI 1oksA 41 :HQMLVKIIMKH Number of specific fragments extracted= 2 number of extra gaps= 0 total=10 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1top/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1top expands to /projects/compbio/data/pdb/1top.pdb.gz 1top:Warning: there is no chain 1top will retry with 1topA Skipped atom 474, because occupancy 0.5 <= existing 0.500 in 1top Skipped atom 476, because occupancy 0.500 <= existing 0.500 in 1top Skipped atom 478, because occupancy 0.500 <= existing 0.500 in 1top Skipped atom 480, because occupancy 0.500 <= existing 0.500 in 1top Skipped atom 482, because occupancy 0.500 <= existing 0.500 in 1top Skipped atom 779, because occupancy 0.500 <= existing 0.500 in 1top Skipped atom 781, because occupancy 0.500 <= existing 0.500 in 1top Skipped atom 960, because occupancy 0.500 <= existing 0.500 in 1top Skipped atom 962, because occupancy 0.500 <= existing 0.500 in 1top Skipped atom 964, because occupancy 0.500 <= existing 0.500 in 1top Skipped atom 966, because occupancy 0.500 <= existing 0.500 in 1top Skipped atom 968, because occupancy 0.500 <= existing 0.500 in 1top Skipped atom 970, because occupancy 0.500 <= existing 0.500 in 1top Skipped atom 972, because occupancy 0.500 <= existing 0.500 in 1top Skipped atom 1103, because occupancy 0.500 <= existing 0.500 in 1top Skipped atom 1105, because occupancy 0.500 <= existing 0.500 in 1top Skipped atom 1107, because occupancy 0.500 <= existing 0.500 in 1top Skipped atom 1109, because occupancy 0.500 <= existing 0.500 in 1top Skipped atom 1204, because occupancy 0.500 <= existing 0.500 in 1top Skipped atom 1206, because occupancy 0.500 <= existing 0.500 in 1top Skipped atom 1208, because occupancy 0.500 <= existing 0.500 in 1top Skipped atom 1210, because occupancy 0.500 <= existing 0.500 in 1top # T0307 read from 1top/merged-good-all-a2m # 1top read from 1top/merged-good-all-a2m # adding 1top to template set # found chain 1top in template set T0307 17 :ELTAIIKMAKSMVMADGK 1top 17 :EMIAEFKAAFDMFDADGG T0307 35 :IKPAEIAVMTREF 1top 37 :ISTKELGTVMRML T0307 51 :GILQDQVDLLLKA 1top 52 :NPTKEELDAIIEE T0307 64 :SDSIEASQAVALIARMDEERKK 1top 70 :SGTIDFEEFLVMMVRQMKEDAK T0307 86 :YVASYLGVIM 1top 97 :ELANCFRIFD T0307 96 :ASDGDIDDNELALW 1top 108 :NADGFIDIEELGEI T0307 111 :LISTLCGLPTMTVMEAINNM 1top 122 :LRATGEHVTEEDIEDLMKDS Number of specific fragments extracted= 7 number of extra gaps= 0 total=17 Number of alignments=4 # 1top read from 1top/merged-good-all-a2m # found chain 1top in template set T0307 15 :GQELTAIIKMAKSMVMADGK 1top 15 :SEEMIAEFKAAFDMFDADGG T0307 35 :IKPAEIAVMTREF 1top 37 :ISTKELGTVMRML T0307 49 :RFGILQDQVDLLLKA 1top 50 :GQNPTKEELDAIIEE T0307 64 :SDSIEASQAVALIARMDEERKK 1top 70 :SGTIDFEEFLVMMVRQMKEDAK T0307 86 :YVASYLGVI 1top 97 :ELANCFRIF T0307 95 :MASDGDIDDNELALW 1top 107 :KNADGFIDIEELGEI T0307 111 :LISTLCGLPTMTVMEAINNM 1top 122 :LRATGEHVTEEDIEDLMKDS Number of specific fragments extracted= 7 number of extra gaps= 0 total=24 Number of alignments=5 # 1top read from 1top/merged-good-all-a2m # found chain 1top in template set T0307 14 :SGQELTAIIKMA 1top 2 :SMTDQQAEARAF T0307 35 :IKPAEIAVMTREFMRF 1top 14 :LSEEMIAEFKAAFDMF T0307 51 :GILQDQVDLLLKASDS 1top 52 :NPTKEELDAIIEEVDE T0307 67 :IEASQAVALI 1top 73 :IDFEEFLVMM T0307 77 :ARMDEERKKYVASYLGVI 1top 88 :EDAKGKSEEELANCFRIF T0307 95 :MASDGDIDDNE 1top 107 :KNADGFIDIEE T0307 109 :WTLISTLCG 1top 118 :LGEILRATG Number of specific fragments extracted= 7 number of extra gaps= 0 total=31 Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1tn4/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1tn4 expands to /projects/compbio/data/pdb/1tn4.pdb.gz 1tn4:Warning: there is no chain 1tn4 will retry with 1tn4A # T0307 read from 1tn4/merged-good-all-a2m # 1tn4 read from 1tn4/merged-good-all-a2m # adding 1tn4 to template set # found chain 1tn4 in template set T0307 15 :GQELTAIIKMAKSMVMADGK 1tn4 12 :SEEMIAEFKAAFDMFDADGG T0307 35 :IKPAEIAVMTRE 1tn4 34 :ISVKELGTVMRM T0307 50 :FG 1tn4 46 :LG T0307 52 :ILQDQVDLLLKA 1tn4 50 :PTKEELDAIIEE T0307 64 :SDSIEASQAVAL 1tn4 67 :SGTIDFEEFLVM T0307 76 :IARMDEERK 1tn4 80 :VRQMKEDAK T0307 85 :KYVASYLGVIM 1tn4 93 :EELAELFRIFD T0307 96 :ASDGDIDDNELALW 1tn4 105 :NADGYIDAEELAEI T0307 112 :ISTLCG 1tn4 119 :FRASGE T0307 118 :LPTMTVMEAINNM 1tn4 126 :VTDEEIESLMKDG Number of specific fragments extracted= 10 number of extra gaps= 0 total=41 Number of alignments=7 # 1tn4 read from 1tn4/merged-good-all-a2m # found chain 1tn4 in template set T0307 15 :GQELTAIIKMAKSMVMADGK 1tn4 12 :SEEMIAEFKAAFDMFDADGG T0307 35 :IKPAEIAVMTREF 1tn4 34 :ISVKELGTVMRML T0307 51 :G 1tn4 47 :G T0307 52 :ILQDQVDLLLKA 1tn4 50 :PTKEELDAIIEE T0307 64 :SDSIEASQAVALIAR 1tn4 67 :SGTIDFEEFLVMMVR T0307 79 :MDEERKKYVASYLG 1tn4 83 :MKEDAKGKSEEELA T0307 93 :VI 1tn4 101 :IF T0307 95 :MASDGDIDDNELALWT 1tn4 104 :RNADGYIDAEELAEIF T0307 112 :ISTLCGLPTMTVMEAINNM 1tn4 120 :RASGEHVTDEEIESLMKDG Number of specific fragments extracted= 9 number of extra gaps= 0 total=50 Number of alignments=8 # 1tn4 read from 1tn4/merged-good-all-a2m # found chain 1tn4 in template set T0307 16 :QELTAIIKMAKSMVMADGK 1tn4 13 :EEMIAEFKAAFDMFDADGG T0307 35 :IKPAE 1tn4 34 :ISVKE T0307 43 :MTREFMRFGI 1tn4 39 :LGTVMRMLGQ T0307 53 :LQDQVDLLLKASDS 1tn4 51 :TKEELDAIIEEVDE T0307 67 :IEASQAVA 1tn4 70 :IDFEEFLV T0307 75 :LIARMDEERKKY 1tn4 79 :MVRQMKEDAKGK T0307 87 :VAS 1tn4 95 :LAE T0307 90 :YLGVIMASDGD 1tn4 114 :ELAEIFRASGE T0307 101 :IDDNELALWT 1tn4 126 :VTDEEIESLM Number of specific fragments extracted= 9 number of extra gaps= 0 total=59 Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fkiA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fkiA expands to /projects/compbio/data/pdb/2fki.pdb.gz 2fkiA:# T0307 read from 2fkiA/merged-good-all-a2m # 2fkiA read from 2fkiA/merged-good-all-a2m # adding 2fkiA to template set # found chain 2fkiA in template set Warning: unaligning (T0307)Y90 because last residue in template chain is (2fkiA)L118 T0307 5 :RQSLNI 2fkiA 45 :RPAVSL T0307 13 :FSGQELTAIIKMAKSMVMADGKIKPAEIAVMT 2fkiA 51 :KTSPELAELLRQQHSDVRPSRHLNKAHWSTVY T0307 48 :MRFGILQDQVDLLLKAS 2fkiA 83 :LDGSLPDSQIYYLVDAS T0307 72 :AVALIARMDEERKKYVAS 2fkiA 100 :YQQAVNLLPEEKRKLLVQ Number of specific fragments extracted= 4 number of extra gaps= 0 total=63 Number of alignments=10 # 2fkiA read from 2fkiA/merged-good-all-a2m # found chain 2fkiA in template set Warning: unaligning (T0307)Y90 because last residue in template chain is (2fkiA)L118 T0307 4 :GRQSLNIMT 2fkiA 44 :NRPAVSLKT T0307 15 :GQELTAIIKMAKSMVMADGKIKPAEIAVMT 2fkiA 53 :SPELAELLRQQHSDVRPSRHLNKAHWSTVY T0307 48 :MRFGILQDQVDLLLKAS 2fkiA 83 :LDGSLPDSQIYYLVDAS T0307 72 :AVALIARMDEERKKYVAS 2fkiA 100 :YQQAVNLLPEEKRKLLVQ Number of specific fragments extracted= 4 number of extra gaps= 0 total=67 Number of alignments=11 # 2fkiA read from 2fkiA/merged-good-all-a2m # found chain 2fkiA in template set Warning: unaligning (T0307)Y90 because last residue in template chain is (2fkiA)L118 T0307 51 :GILQDQVDLLLKASDS 2fkiA 86 :SLPDSQIYYLVDASYQ T0307 74 :ALIARMDEERKKYVAS 2fkiA 102 :QAVNLLPEEKRKLLVQ Number of specific fragments extracted= 2 number of extra gaps= 0 total=69 Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1s6cA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1s6cA expands to /projects/compbio/data/pdb/1s6c.pdb.gz 1s6cA:Bad short name: AS for alphabet: pdb_atoms Bad short name: AS for alphabet: pdb_atoms # T0307 read from 1s6cA/merged-good-all-a2m # 1s6cA read from 1s6cA/merged-good-all-a2m # adding 1s6cA to template set # found chain 1s6cA in template set Warning: unaligning (T0307)M28 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1s6cA)P65 Warning: unaligning (T0307)A31 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1s6cA)P65 Warning: unaligning (T0307)G117 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1s6cA)P171 T0307 13 :FSGQELTAIIKMAKS 1s6cA 48 :FTKRELQVLYRGFKN T0307 32 :DGKIKPAEIAVMTREFMRFGILQDQVDLLLKA 1s6cA 66 :SGVVNEETFKQIYAQFFPHGDASTYAHYLFNA T0307 64 :SDSIEASQAVA 1s6cA 103 :TGSVKFEDFVT T0307 75 :LIARM 1s6cA 117 :ILLRG T0307 80 :DEERKKYVASYLGV 1s6cA 123 :VHEKLRWTFNLYDI T0307 96 :ASDGDIDDNELA 1s6cA 137 :NKDGYINKEEMM T0307 108 :LWTLISTLC 1s6cA 150 :IVKAIYDMM Number of specific fragments extracted= 7 number of extra gaps= 0 total=76 Number of alignments=13 # 1s6cA read from 1s6cA/merged-good-all-a2m # found chain 1s6cA in template set Warning: unaligning (T0307)M28 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1s6cA)P65 Warning: unaligning (T0307)A31 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1s6cA)P65 Warning: unaligning (T0307)G117 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1s6cA)P171 Warning: unaligning (T0307)P119 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1s6cA)P171 T0307 13 :FSGQELTAIIKMAKS 1s6cA 48 :FTKRELQVLYRGFKN T0307 32 :DGKIKPAEIAVMTREFMRFGILQDQVDLLLKA 1s6cA 66 :SGVVNEETFKQIYAQFFPHGDASTYAHYLFNA T0307 64 :SDSIEAS 1s6cA 103 :TGSVKFE T0307 71 :QAVALIARMD 1s6cA 113 :TALSILLRGT T0307 81 :EERKKYVASYLG 1s6cA 124 :HEKLRWTFNLYD T0307 95 :MASDGDIDDNEL 1s6cA 136 :INKDGYINKEEM T0307 107 :ALWTLISTLC 1s6cA 149 :DIVKAIYDMM T0307 120 :TMTVMEAINNM 1s6cA 172 :RQHVDVFFQKM Number of specific fragments extracted= 8 number of extra gaps= 0 total=84 Number of alignments=14 # 1s6cA read from 1s6cA/merged-good-all-a2m # found chain 1s6cA in template set Warning: unaligning (T0307)I52 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1s6cA)P171 Warning: unaligning (T0307)E68 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1s6cA)P171 T0307 14 :SGQELTAIIKMAKS 1s6cA 122 :TVHEKLRWTFNLYD T0307 29 :VMADGKIKPAEIAVMTREFMRFG 1s6cA 136 :INKDGYINKEEMMDIVKAIYDMM T0307 69 :AS 1s6cA 172 :RQ Number of specific fragments extracted= 3 number of extra gaps= 0 total=87 Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cosA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2cosA expands to /projects/compbio/data/pdb/2cos.pdb.gz 2cosA:# T0307 read from 2cosA/merged-good-all-a2m # 2cosA read from 2cosA/merged-good-all-a2m # adding 2cosA to template set # found chain 2cosA in template set T0307 43 :MTREFMRFGILQDQVDLLLKASDSIEASQAVALIARM 2cosA 12 :MLQELVNAGCDQEMAGRALKQTGSRSIEAALEYISKM Number of specific fragments extracted= 1 number of extra gaps= 0 total=88 Number of alignments=16 # 2cosA read from 2cosA/merged-good-all-a2m # found chain 2cosA in template set T0307 42 :VMTREFMRFGILQDQVDLLLKASDSIEASQAVALIARM 2cosA 11 :QMLQELVNAGCDQEMAGRALKQTGSRSIEAALEYISKM Number of specific fragments extracted= 1 number of extra gaps= 0 total=89 Number of alignments=17 # 2cosA read from 2cosA/merged-good-all-a2m # found chain 2cosA in template set T0307 34 :KIKPAEIAVMTR 2cosA 7 :GVNRQMLQELVN T0307 50 :FGILQDQVDLLLKASDSIEASQAVALIARM 2cosA 19 :AGCDQEMAGRALKQTGSRSIEAALEYISKM Number of specific fragments extracted= 2 number of extra gaps= 0 total=91 Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1u61A/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/T0307/1u61A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0307/1u61A/merged-good-all-a2m.gz for input Trying 1u61A/merged-good-all-a2m Error: Couldn't open file 1u61A/merged-good-all-a2m or 1u61A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 487dL/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 487dL expands to /projects/compbio/data/pdb/487d.pdb.gz 487dL:# T0307 read from 487dL/merged-good-all-a2m # 487dL read from 487dL/merged-good-all-a2m # adding 487dL to template set # found chain 487dL in template set T0307 7 :SLNIMTFSGQELT 487dL 55 :PVVITVYEDKSFT T0307 34 :KIKPAEIAVMTREFMRFGILQD 487dL 69 :IIKTPPASFLLKKAAGIEKGSS T0307 62 :KASDSIEA 487dL 91 :EPKRKIVG T0307 78 :R 487dL 99 :K T0307 79 :MDEERKKYVASYLG 487dL 101 :TRKQIEEIAKTKMP T0307 98 :DGDIDDNELALWTLISTLC 487dL 115 :DLNANSLEAAMKIIEGTAK Number of specific fragments extracted= 6 number of extra gaps= 0 total=97 Number of alignments=19 # 487dL read from 487dL/merged-good-all-a2m # found chain 487dL in template set T0307 4 :GRQSLNIMT 487dL 62 :EDKSFTFII T0307 14 :SGQELTAIIKMAKSMVMADGKIKPAEIAVMTREFM 487dL 71 :KTPPASFLLKKAAGIEKGSSEPKRKIVGKVTRKQI T0307 54 :QDQVDLLLKASDSIEASQAVALIAR 487dL 106 :EEIAKTKMPDLNANSLEAAMKIIEG Number of specific fragments extracted= 3 number of extra gaps= 0 total=100 Number of alignments=20 # 487dL read from 487dL/merged-good-all-a2m # found chain 487dL in template set T0307 24 :MAKSMVMAD 487dL 78 :LLKKAAGIE T0307 33 :GKIKPAEIAVMTREFMR 487dL 98 :GKVTRKQIEEIAKTKMP T0307 50 :FGILQDQVDLLLKASDS 487dL 118 :ANSLEAAMKIIEGTAKS Number of specific fragments extracted= 3 number of extra gaps= 0 total=103 Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1e7lA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0307 read from 1e7lA/merged-good-all-a2m # 1e7lA read from 1e7lA/merged-good-all-a2m # found chain 1e7lA in training set T0307 15 :GQELTAIIKMAKSMV 1e7lA 81 :GVDYLEWLENLLTYL T0307 30 :MADGKIKPAEIAVMTREFMRFG 1e7lA 99 :YTQNNIHPNFVGDKSKEFSRLG T0307 120 :TMTVMEAINNMK 1e7lA 121 :KEEMMAEMLQRG Number of specific fragments extracted= 3 number of extra gaps= 0 total=106 Number of alignments=22 # 1e7lA read from 1e7lA/merged-good-all-a2m # found chain 1e7lA in training set T0307 65 :DSIEASQAV 1e7lA 80 :QGVDYLEWL T0307 81 :EERKKYVAS 1e7lA 89 :ENLLTYLKS T0307 96 :ASDGDIDDNELALW 1e7lA 99 :YTQNNIHPNFVGDK T0307 112 :ISTLCGLPTMTVMEAINNMK 1e7lA 113 :SKEFSRLGKEEMMAEMLQRG Number of specific fragments extracted= 4 number of extra gaps= 0 total=110 Number of alignments=23 # 1e7lA read from 1e7lA/merged-good-all-a2m # found chain 1e7lA in training set T0307 33 :GKIKPAEIAVMTREFMR 1e7lA 81 :GVDYLEWLENLLTYLKS T0307 50 :FGILQDQVDLLLKASDSIEASQAVALIARM 1e7lA 102 :NNIHPNFVGDKSKEFSRLGKEEMMAEMLQR T0307 80 :DEERKKYVASYLGV 1e7lA 141 :KTQLIASFKKQLRK Number of specific fragments extracted= 3 number of extra gaps= 0 total=113 Number of alignments=24 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ap1A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2ap1A expands to /projects/compbio/data/pdb/2ap1.pdb.gz 2ap1A:Skipped atom 67, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 69, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 71, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 319, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 655, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 728, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 730, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 732, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 734, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 736, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 738, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 740, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 742, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 744, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 746, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 748, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 759, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 763, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 765, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 767, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 769, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 833, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 837, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 839, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 841, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 843, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1053, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1055, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1376, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1380, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1382, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1384, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1386, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1388, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1390, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1392, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1718, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1722, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1724, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1726, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1728, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1730, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1869, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1873, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1875, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1877, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1983, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1987, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1989, because occupancy 0.500 <= existing 0.500 in 2ap1A Skipped atom 1991, because occupancy 0.500 <= existing 0.500 in 2ap1A # T0307 read from 2ap1A/merged-good-all-a2m # 2ap1A read from 2ap1A/merged-good-all-a2m # adding 2ap1A to template set # found chain 2ap1A in template set T0307 54 :QDQVDLLLK 2ap1A 191 :GRGFAWLYQ T0307 63 :ASDSIEASQAVALIARMDEERKKYVASYLGVI 2ap1A 202 :YDQSLQAPEIIALWEQGDEQAHAHVERYLDLL T0307 105 :ELALWTLIST 2ap1A 234 :AVCLGNILTI Number of specific fragments extracted= 3 number of extra gaps= 0 total=116 Number of alignments=25 # 2ap1A read from 2ap1A/merged-good-all-a2m # found chain 2ap1A in template set T0307 57 :VDLLLK 2ap1A 194 :FAWLYQ T0307 63 :ASDSIEASQAVALIARMDEERKKYVASYLGVI 2ap1A 202 :YDQSLQAPEIIALWEQGDEQAHAHVERYLDLL T0307 105 :ELALWTLIST 2ap1A 234 :AVCLGNILTI Number of specific fragments extracted= 3 number of extra gaps= 0 total=119 Number of alignments=26 # 2ap1A read from 2ap1A/merged-good-all-a2m # found chain 2ap1A in template set T0307 34 :KIKPAEIAVM 2ap1A 159 :RLPVDALTLM T0307 50 :FGILQDQ 2ap1A 170 :FDFPLRR T0307 57 :VDLLLKASD 2ap1A 194 :FAWLYQHYY T0307 66 :SIEASQAVALIARMDEERKKYVASYLGVIMA 2ap1A 205 :SLQAPEIIALWEQGDEQAHAHVERYLDLLAV T0307 108 :LWTLISTLCGL 2ap1A 236 :CLGNILTIVDP T0307 122 :TVMEAINNMKN 2ap1A 247 :DLLVIGGGLSN Number of specific fragments extracted= 6 number of extra gaps= 0 total=125 Number of alignments=27 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1auiB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1auiB expands to /projects/compbio/data/pdb/1aui.pdb.gz 1auiB:# T0307 read from 1auiB/merged-good-all-a2m # 1auiB read from 1auiB/merged-good-all-a2m # adding 1auiB to template set # found chain 1auiB in template set T0307 12 :TFSGQELTAIIKMAKSMVMADGKIKPAEIAVMTREFMRFGILQDQVDLLL 1auiB 13 :HFDADEIKRLGKRFKKLDLDNSGSLSVEEFMSLPELQQNPLVQRVIDIFD T0307 62 :KASDSIEASQAVALIA 1auiB 64 :DGNGEVDFKEFIEGVS T0307 78 :RM 1auiB 84 :KG T0307 80 :DEERKKYVASYL 1auiB 87 :KEQKLRFAFRIY T0307 94 :IMASDGDIDDNELALWTLISTLCGLPTMTVMEAINN 1auiB 99 :DMDKDGYISNGELFQVLKMMVGNNLKDTQLQQIVDK Number of specific fragments extracted= 5 number of extra gaps= 0 total=130 Number of alignments=28 # 1auiB read from 1auiB/merged-good-all-a2m # found chain 1auiB in template set T0307 12 :TFSGQELTAIIKMAKSMVMADGKIKPAEIAVMTREFMRFGILQDQVDLLL 1auiB 13 :HFDADEIKRLGKRFKKLDLDNSGSLSVEEFMSLPELQQNPLVQRVIDIFD T0307 62 :KASDSIEASQAVALIA 1auiB 64 :DGNGEVDFKEFIEGVS T0307 78 :RMDEERK 1auiB 84 :KGDKEQK T0307 85 :KYVASYL 1auiB 92 :RFAFRIY T0307 94 :IMASDGDIDDNELALWTLISTLCGLPTMTVMEAINN 1auiB 99 :DMDKDGYISNGELFQVLKMMVGNNLKDTQLQQIVDK Number of specific fragments extracted= 5 number of extra gaps= 0 total=135 Number of alignments=29 # 1auiB read from 1auiB/merged-good-all-a2m # found chain 1auiB in template set T0307 34 :KIKPAEIAVMTREFMRFGI 1auiB 13 :HFDADEIKRLGKRFKKLDL T0307 53 :LQDQ 1auiB 38 :SVEE T0307 57 :VDLLLK 1auiB 71 :FKEFIE T0307 63 :ASDSIEASQAVALI 1auiB 81 :FSVKGDKEQKLRFA T0307 77 :ARM 1auiB 96 :RIY T0307 84 :KKYVASYLG 1auiB 108 :NGELFQVLK T0307 95 :MASDGDIDDNELA 1auiB 117 :MMVGNNLKDTQLQ Number of specific fragments extracted= 7 number of extra gaps= 0 total=142 Number of alignments=30 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ugpA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0307 read from 1ugpA/merged-good-all-a2m # 1ugpA read from 1ugpA/merged-good-all-a2m # found chain 1ugpA in training set T0307 16 :QELTAIIKMAKSMVMADGKIKPAEIAVMTREFM 1ugpA 15 :KEITARVKALESMLIEQGILTTSMIDRMAEIYE T0307 65 :DSIEASQAVALIAR 1ugpA 48 :NEVGPHLGAKVVVK T0307 79 :MDEERKKYVAS 1ugpA 64 :TDPEFKKRLLA Number of specific fragments extracted= 3 number of extra gaps= 0 total=145 Number of alignments=31 # 1ugpA read from 1ugpA/merged-good-all-a2m # found chain 1ugpA in training set T0307 16 :QELTAIIKMAKSMVMADGKIKPAEIAVMTREF 1ugpA 15 :KEITARVKALESMLIEQGILTTSMIDRMAEIY T0307 62 :KASDSIEASQAVALIARMDEERKKYVAS 1ugpA 47 :ENEVGPHLGAKVVVKAWTDPEFKKRLLA Number of specific fragments extracted= 2 number of extra gaps= 0 total=147 Number of alignments=32 # 1ugpA read from 1ugpA/merged-good-all-a2m # found chain 1ugpA in training set T0307 16 :QELTAIIKMAKSMVMADGKIKPAEIAVMTREFM 1ugpA 15 :KEITARVKALESMLIEQGILTTSMIDRMAEIYE T0307 65 :DSIEASQAVALIARM 1ugpA 48 :NEVGPHLGAKVVVKA T0307 80 :DEERKKYVASYL 1ugpA 65 :DPEFKKRLLADG T0307 110 :TLISTLCGLPTMTV 1ugpA 77 :TEACKELGIGGLQG Number of specific fragments extracted= 4 number of extra gaps= 0 total=151 Number of alignments=33 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gwxA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2gwxA expands to /projects/compbio/data/pdb/2gwx.pdb.gz 2gwxA:# T0307 read from 2gwxA/merged-good-all-a2m # 2gwxA read from 2gwxA/merged-good-all-a2m # adding 2gwxA to template set # found chain 2gwxA in template set T0307 27 :SMVMADGK 2gwxA 338 :GLLVANGS T0307 41 :AVMTREFMRF 2gwxA 346 :GFVTREFLRS T0307 55 :D 2gwxA 358 :K T0307 62 :KASDSIEA 2gwxA 359 :PFSDIIEP T0307 83 :RKKYVASYLG 2gwxA 367 :KFEFAVKFNA T0307 99 :GDIDDNELALWTLISTLCG 2gwxA 377 :LELDDSDLALFIAAIILCG T0307 118 :LPTMTVMEAINN 2gwxA 401 :MNVPRVEAIQDT Number of specific fragments extracted= 7 number of extra gaps= 0 total=158 Number of alignments=34 # 2gwxA read from 2gwxA/merged-good-all-a2m # found chain 2gwxA in template set T0307 33 :GKIKPAEIAVMTREFMRF 2gwxA 399 :GLMNVPRVEAIQDTILRA T0307 53 :LQDQVDLLLKASDSI 2gwxA 417 :LEFHLQANHPDAQQL T0307 69 :ASQAVALIARMDEERKKYV 2gwxA 432 :FPKLLQKMADLRQLVTEHA T0307 106 :LALWTLISTLCGLPTMTVMEAINN 2gwxA 451 :QMMQRIKKTETETSLHPLLQEIYK Number of specific fragments extracted= 4 number of extra gaps= 0 total=162 Number of alignments=35 # 2gwxA read from 2gwxA/merged-good-all-a2m # found chain 2gwxA in template set T0307 15 :G 2gwxA 381 :D T0307 19 :TAIIKMAKSMVMADG 2gwxA 382 :SDLALFIAAIILCGD T0307 34 :KIKPAEIAVMTREFM 2gwxA 400 :LMNVPRVEAIQDTIL T0307 55 :DQVDLLLKASDS 2gwxA 415 :RALEFHLQANHP T0307 67 :IE 2gwxA 428 :AQ T0307 69 :ASQAVALIARMDE 2gwxA 432 :FPKLLQKMADLRQ T0307 83 :RKKYVASYLGVIMA 2gwxA 445 :LVTEHAQMMQRIKK T0307 97 :SDGDIDDNELALW 2gwxA 461 :TETSLHPLLQEIY Number of specific fragments extracted= 8 number of extra gaps= 0 total=170 Number of alignments=36 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1n25A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1n25A expands to /projects/compbio/data/pdb/1n25.pdb.gz 1n25A:# T0307 read from 1n25A/merged-good-all-a2m # 1n25A read from 1n25A/merged-good-all-a2m # adding 1n25A to template set # found chain 1n25A in template set T0307 16 :QELTAIIKMAKSMVMA 1n25A 331 :KNQKTICQQAVDTVLA T0307 38 :AEIAVMTREFM 1n25A 350 :VDSLQLTREQM T0307 49 :RFGILQDQVDLLLKASDSIEASQAVALIA 1n25A 364 :RFNDLLDRMDIMFGSTGSADIEEWMAGVA T0307 78 :RMDEERKKYVASYLG 1n25A 400 :KMDSVVYDFLKCMVY T0307 99 :GDIDDNELALWTLISTLCG 1n25A 426 :GPIDSGKTTLAAALLELCG T0307 118 :LPTMTVMEAINNM 1n25A 452 :LPLDRLNFELGVA Number of specific fragments extracted= 6 number of extra gaps= 0 total=176 Number of alignments=37 # 1n25A read from 1n25A/merged-good-all-a2m # found chain 1n25A in template set T0307 16 :QELTAIIKMAKSMVMA 1n25A 331 :KNQKTICQQAVDTVLA T0307 38 :AEIAVMTREFM 1n25A 350 :VDSLQLTREQM T0307 49 :RFGILQDQVDLLLKASDSIEASQAVALIARMD 1n25A 364 :RFNDLLDRMDIMFGSTGSADIEEWMAGVAWLH T0307 81 :EERKKYVASYLGVIM 1n25A 399 :PKMDSVVYDFLKCMV T0307 97 :S 1n25A 416 :I T0307 99 :GDIDDNELALWTLISTLCG 1n25A 426 :GPIDSGKTTLAAALLELCG T0307 118 :LPTMTVMEAI 1n25A 452 :LPLDRLNFEL Number of specific fragments extracted= 7 number of extra gaps= 0 total=183 Number of alignments=38 # 1n25A read from 1n25A/merged-good-all-a2m # found chain 1n25A in template set T0307 20 :AIIKMA 1n25A 322 :ANAAIF T0307 31 :ADGKIKPAEIAVMTREFMRFG 1n25A 328 :ADSKNQKTICQQAVDTVLAKK T0307 61 :LKASDSIEASQAVA 1n25A 349 :RVDSLQLTREQMLT T0307 75 :LIARMD 1n25A 368 :LLDRMD T0307 84 :KKYVASYLGVIMASDGDIDDNELALWTLIST 1n25A 384 :IEEWMAGVAWLHCLLPKMDSVVYDFLKCMVY Number of specific fragments extracted= 5 number of extra gaps= 0 total=188 Number of alignments=39 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1s1eA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1s1eA expands to /projects/compbio/data/pdb/1s1e.pdb.gz 1s1eA:# T0307 read from 1s1eA/merged-good-all-a2m # 1s1eA read from 1s1eA/merged-good-all-a2m # adding 1s1eA to template set # found chain 1s1eA in template set T0307 13 :FSGQELTAIIKMAKSM 1s1eA 48 :FTKRELQVLYRGFKNE T0307 30 :MADGKIKPAEIAVMTREFMRFGILQDQVDLLLKA 1s1eA 64 :CPSGVVNEETFKQIYAQFFPHGDASTYAHYLFNA T0307 64 :SDSIEASQAVALIARM 1s1eA 103 :TGSVKFEDFVTALSIL T0307 80 :DEERKKYVASYLGV 1s1eA 123 :VHEKLRWTFNLYDI T0307 96 :ASDGDIDDNELA 1s1eA 137 :NKDGYINKEEMM T0307 108 :LWTLISTLCGLPT 1s1eA 150 :IVKAIYDMMGKYT Number of specific fragments extracted= 6 number of extra gaps= 0 total=194 Number of alignments=40 # 1s1eA read from 1s1eA/merged-good-all-a2m # found chain 1s1eA in template set T0307 13 :FSGQELTAIIKMAKSM 1s1eA 48 :FTKRELQVLYRGFKNE T0307 30 :MADGKIKPAEIAVMTREFMRFGILQDQVDLLLKA 1s1eA 64 :CPSGVVNEETFKQIYAQFFPHGDASTYAHYLFNA T0307 64 :SDSIEASQAVALIARM 1s1eA 103 :TGSVKFEDFVTALSIL T0307 80 :DEERKKYVASYLGV 1s1eA 123 :VHEKLRWTFNLYDI T0307 96 :ASDGDIDDNEL 1s1eA 137 :NKDGYINKEEM T0307 107 :ALWTLISTLCGLPT 1s1eA 149 :DIVKAIYDMMGKYT Number of specific fragments extracted= 6 number of extra gaps= 0 total=200 Number of alignments=41 # 1s1eA read from 1s1eA/merged-good-all-a2m # found chain 1s1eA in template set T0307 12 :TFSGQELTAIIKMAKS 1s1eA 47 :NFTKRELQVLYRGFKN T0307 32 :DGKIKPA 1s1eA 66 :SGVVNEE T0307 42 :VMTREFMRF 1s1eA 73 :TFKQIYAQF T0307 51 :GILQDQ 1s1eA 84 :HGDAST T0307 57 :VDLLLKASD 1s1eA 91 :AHYLFNAFD T0307 66 :SIEASQAVALIARM 1s1eA 105 :SVKFEDFVTALSIL T0307 80 :D 1s1eA 122 :T T0307 81 :EERKKYVASYLG 1s1eA 124 :HEKLRWTFNLYD T0307 98 :DGDIDDNE 1s1eA 139 :DGYINKEE T0307 106 :LALWTLISTLCGLPTMTVM 1s1eA 148 :MDIVKAIYDMMGKYTYPVL Number of specific fragments extracted= 10 number of extra gaps= 0 total=210 Number of alignments=42 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b50A/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/T0307/2b50A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0307/2b50A/merged-good-all-a2m.gz for input Trying 2b50A/merged-good-all-a2m Error: Couldn't open file 2b50A/merged-good-all-a2m or 2b50A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1svmA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1svmA expands to /projects/compbio/data/pdb/1svm.pdb.gz 1svmA:# T0307 read from 1svmA/merged-good-all-a2m # 1svmA read from 1svmA/merged-good-all-a2m # adding 1svmA to template set # found chain 1svmA in template set T0307 16 :QELTAIIKMAKSMVMA 1svmA 331 :KNQKTICQQAVDTVLA T0307 37 :PAEIAVMTREFM 1svmA 349 :RVDSLQLTREQM T0307 49 :RFGILQDQVDLLLKASDSIEASQAVALIA 1svmA 364 :RFNDLLDRMDIMFGSTGSADIEEWMAGVA T0307 78 :RMDEERKKYVASYLG 1svmA 400 :KMDSVVYDFLKCMVY T0307 99 :GDIDDNELALWTLISTLCG 1svmA 426 :GPIDSGKTTLAAALLELCG Number of specific fragments extracted= 5 number of extra gaps= 0 total=215 Number of alignments=43 # 1svmA read from 1svmA/merged-good-all-a2m # found chain 1svmA in template set T0307 16 :QELTAIIKMAKSMVMA 1svmA 331 :KNQKTICQQAVDTVLA T0307 37 :PAEIAVMTREFM 1svmA 349 :RVDSLQLTREQM T0307 49 :RFGILQDQVDLLLKASDSIEASQAVALIARMD 1svmA 364 :RFNDLLDRMDIMFGSTGSADIEEWMAGVAWLH T0307 81 :EERKKYVASYLGVIM 1svmA 399 :PKMDSVVYDFLKCMV T0307 96 :ASD 1svmA 415 :NIP T0307 99 :GDIDDNELALWTLISTLCG 1svmA 426 :GPIDSGKTTLAAALLELCG T0307 118 :LPTMTVMEAIN 1svmA 452 :LPLDRLNFELG Number of specific fragments extracted= 7 number of extra gaps= 0 total=222 Number of alignments=44 # 1svmA read from 1svmA/merged-good-all-a2m # found chain 1svmA in template set T0307 24 :MA 1svmA 326 :IF T0307 31 :ADGKIKPAEIAVMTREFMR 1svmA 328 :ADSKNQKTICQQAVDTVLA T0307 50 :FGILQDQ 1svmA 353 :LQLTREQ T0307 57 :VDLLLKASD 1svmA 365 :FNDLLDRMD T0307 66 :SIEASQAVA 1svmA 381 :SADIEEWMA T0307 75 :LIARMDEERKKYVASYLGVIMAS 1svmA 393 :WLHCLLPKMDSVVYDFLKCMVYN Number of specific fragments extracted= 6 number of extra gaps= 0 total=228 Number of alignments=45 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mvwB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1mvwB expands to /projects/compbio/data/pdb/1mvw.pdb.gz 1mvwB:# T0307 read from 1mvwB/merged-good-all-a2m # 1mvwB read from 1mvwB/merged-good-all-a2m # adding 1mvwB to template set # found chain 1mvwB in template set Warning: unaligning (T0307)F13 because first residue in template chain is (1mvwB)F19 Warning: unaligning (T0307)M121 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1mvwB)E131 Warning: unaligning (T0307)E125 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1mvwB)E131 T0307 14 :SGQELTAIIKMAKSMV 1mvwB 20 :DETEIEDFKEAFTVID T0307 30 :MADGKIKPAEIAVMTREFMRFGILQDQVDLLLK 1mvwB 37 :NADGIIDKDDLRETFAAMGRLNVKNEELDAMIK T0307 63 :ASDSIEASQAVALIAR 1mvwB 71 :ASGPINFTVFLTMFGE T0307 80 :DEERKKYVASY 1mvwB 94 :EDVIMGAFKVL T0307 96 :ASDGDIDDNELALWTLISTLCGLPT 1mvwB 105 :DPDGKGSIKKSFLEELLTTGGGRFT T0307 126 :AINNM 1mvwB 132 :EIKNM Number of specific fragments extracted= 6 number of extra gaps= 1 total=234 Number of alignments=46 # 1mvwB read from 1mvwB/merged-good-all-a2m # found chain 1mvwB in template set Warning: unaligning (T0307)M121 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1mvwB)E131 Warning: unaligning (T0307)T122 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1mvwB)E131 T0307 14 :SGQELTAIIKMAKSMV 1mvwB 20 :DETEIEDFKEAFTVID T0307 30 :MADGKIKPAEIAVMTREFMRFGILQDQVDLLLK 1mvwB 37 :NADGIIDKDDLRETFAAMGRLNVKNEELDAMIK T0307 63 :ASDSIEASQAVALIARM 1mvwB 71 :ASGPINFTVFLTMFGEK T0307 80 :DEERKKYVASY 1mvwB 94 :EDVIMGAFKVL T0307 96 :ASDGDIDDNELALWTLISTLCGLPT 1mvwB 105 :DPDGKGSIKKSFLEELLTTGGGRFT T0307 123 :VMEAI 1mvwB 132 :EIKNM Number of specific fragments extracted= 6 number of extra gaps= 1 total=240 Number of alignments=47 # 1mvwB read from 1mvwB/merged-good-all-a2m # found chain 1mvwB in template set Warning: unaligning (T0307)F13 because first residue in template chain is (1mvwB)F19 Warning: unaligning (T0307)D103 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (1mvwB)E131 Warning: unaligning (T0307)N104 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (1mvwB)E131 T0307 14 :SGQELTAIIKMAKS 1mvwB 20 :DETEIEDFKEAFTV T0307 30 :MADGKIKPAEIAVMTREFMRFGILQDQ 1mvwB 37 :NADGIIDKDDLRETFAAMGRLNVKNEE T0307 57 :VDLLLKASD 1mvwB 77 :FTVFLTMFG T0307 66 :S 1mvwB 90 :G T0307 67 :IEASQAVALIARMDEE 1mvwB 92 :DPEDVIMGAFKVLDPD T0307 83 :RKKYVASYLG 1mvwB 113 :KKSFLEELLT T0307 97 :SDGDID 1mvwB 124 :GGGRFT T0307 105 :ELALW 1mvwB 132 :EIKNM Number of specific fragments extracted= 8 number of extra gaps= 1 total=248 Number of alignments=48 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3gwxA/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/T0307/3gwxA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0307/3gwxA/merged-good-all-a2m.gz for input Trying 3gwxA/merged-good-all-a2m Error: Couldn't open file 3gwxA/merged-good-all-a2m or 3gwxA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 256bA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0307 read from 256bA/merged-good-all-a2m # 256bA read from 256bA/merged-good-all-a2m # found chain 256bA in training set T0307 17 :ELTAIIKMAKSMVMADGKIKPAEI 256bA 25 :QVKDALTKMRAAALDAQKATPPKL T0307 41 :AVMTREFMRFGILQDQVDLLLKASDSIEASQAVALIARMDEERKKYVASY 256bA 56 :PEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYHQKY Number of specific fragments extracted= 2 number of extra gaps= 0 total=250 Number of alignments=49 # 256bA read from 256bA/merged-good-all-a2m # found chain 256bA in training set T0307 16 :QELTAIIKMAKSMVMADGKIKPAEI 256bA 24 :AQVKDALTKMRAAALDAQKATPPKL T0307 41 :AVMTREFMRFGILQDQVDLLLKASDSIEASQAVALIARMDEERKKYVASY 256bA 56 :PEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYHQKY Number of specific fragments extracted= 2 number of extra gaps= 0 total=252 Number of alignments=50 # 256bA read from 256bA/merged-good-all-a2m # found chain 256bA in training set T0307 15 :GQELTAIIKMAKSMVMADGKIKP 256bA 24 :AQVKDALTKMRAAALDAQKATPP T0307 38 :AEIAVMTREFMRF 256bA 56 :PEMKDFRHGFDIL T0307 54 :QDQVDLLLKASDSIEASQAVALIARMDEERKKY 256bA 69 :VGQIDDALKLANEGKVKEAQAAAEQLKTTRNAY Number of specific fragments extracted= 3 number of extra gaps= 0 total=255 Number of alignments=51 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1jk0A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1jk0A expands to /projects/compbio/data/pdb/1jk0.pdb.gz 1jk0A:# T0307 read from 1jk0A/merged-good-all-a2m # 1jk0A read from 1jk0A/merged-good-all-a2m # adding 1jk0A to template set # found chain 1jk0A in template set T0307 34 :KIKPAEIAVMTREFMRFG 1jk0A 90 :PIKYHEIWQAYKRAEASF T0307 62 :KASDSIEASQAVALIA 1jk0A 108 :WTAEEIDLSKDIHDWN T0307 78 :RMDEERKKYVASYLGVIMASDG 1jk0A 125 :RMNENERFFISRVLAFFAASDG T0307 106 :LALWTLISTLCGLPTMTVMEAIN 1jk0A 147 :IVNENLVENFSTEVQIPEAKSFY Number of specific fragments extracted= 4 number of extra gaps= 0 total=259 Number of alignments=52 # 1jk0A read from 1jk0A/merged-good-all-a2m # found chain 1jk0A in template set T0307 15 :GQELTAIIKMAKSMVMADGKIKPAEIAVMTR 1jk0A 93 :YHEIWQAYKRAEASFWTAEEIDLSKDIHDWN T0307 46 :EFMRF 1jk0A 128 :ENERF T0307 51 :GILQDQ 1jk0A 146 :GIVNEN T0307 57 :VDLLLKASDSIEASQAVALIARMDEERKKYVASYLGVIMA 1jk0A 153 :VENFSTEVQIPEAKSFYGFQIMIENIHSETYSLLIDTYIK T0307 102 :DDNEL 1jk0A 193 :DPKES T0307 109 :WTLISTLCGLPTMTVM 1jk0A 198 :EFLFNAIHTIPEIGEK Number of specific fragments extracted= 6 number of extra gaps= 0 total=265 Number of alignments=53 # 1jk0A read from 1jk0A/merged-good-all-a2m # found chain 1jk0A in template set T0307 13 :FSGQELTAIIKMAKSMVMADGK 1jk0A 126 :MNENERFFISRVLAFFAASDGI T0307 39 :EIAVMTREFMRF 1jk0A 148 :VNENLVENFSTE T0307 52 :ILQDQVDLLLKASDSIE 1jk0A 160 :VQIPEAKSFYGFQIMIE T0307 69 :ASQAVA 1jk0A 179 :HSETYS T0307 75 :LIARM 1jk0A 186 :LIDTY T0307 80 :DEERKKYVASYLG 1jk0A 193 :DPKESEFLFNAIH T0307 104 :NELALWTL 1jk0A 208 :PEIGEKAE Number of specific fragments extracted= 7 number of extra gaps= 0 total=272 Number of alignments=54 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1uhnA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1uhnA expands to /projects/compbio/data/pdb/1uhn.pdb.gz 1uhnA:# T0307 read from 1uhnA/merged-good-all-a2m # 1uhnA read from 1uhnA/merged-good-all-a2m # adding 1uhnA to template set # found chain 1uhnA in template set T0307 13 :FSGQELTAIIKMAKSMVMA 1uhnA 42 :FSVSEIEALYELFKKISSA T0307 32 :DGKIKPAEIAVM 1uhnA 64 :DGLINKEEFQLA T0307 49 :RFGILQDQVDLLLKASDSI 1uhnA 83 :ESLFADRVFDLFDTKHNGI T0307 68 :EASQAVALIARM 1uhnA 103 :GFEEFARALSVF T0307 80 :DEERKKYVASYLG 1uhnA 120 :IDDKIHFSFQLYD T0307 95 :MASDGDIDDNELA 1uhnA 133 :LKQQGFIERQEVK T0307 108 :LWTLISTLCGLPTMTVMEAINNM 1uhnA 149 :VATLAESGMNLKDTVIEDIIDKT Number of specific fragments extracted= 7 number of extra gaps= 0 total=279 Number of alignments=55 # 1uhnA read from 1uhnA/merged-good-all-a2m # found chain 1uhnA in template set T0307 17 :ELTAIIKMAKSMVMADGKIKPAEIAVM 1uhnA 49 :ALYELFKKISSAVIDDGLINKEEFQLA T0307 49 :RFGILQDQVDLLLKASDSI 1uhnA 83 :ESLFADRVFDLFDTKHNGI T0307 68 :EASQAVALIARM 1uhnA 103 :GFEEFARALSVF T0307 80 :DEERKKYVASYLG 1uhnA 120 :IDDKIHFSFQLYD T0307 95 :MASDGDIDDNELA 1uhnA 133 :LKQQGFIERQEVK T0307 108 :LWTLISTLCGLPTMTVMEAINNM 1uhnA 149 :VATLAESGMNLKDTVIEDIIDKT Number of specific fragments extracted= 6 number of extra gaps= 0 total=285 Number of alignments=56 # 1uhnA read from 1uhnA/merged-good-all-a2m # found chain 1uhnA in template set T0307 12 :TFSGQELTAIIKMAKSMVMA 1uhnA 41 :VFSVSEIEALYELFKKISSA T0307 32 :DGKIKPAEIAVM 1uhnA 64 :DGLINKEEFQLA T0307 50 :FGILQDQ 1uhnA 76 :LFKTNKK T0307 57 :VDLLLKASDS 1uhnA 87 :ADRVFDLFDT T0307 67 :IEASQAVALIARM 1uhnA 102 :LGFEEFARALSVF T0307 80 :DEERKKYVASYL 1uhnA 120 :IDDKIHFSFQLY T0307 96 :ASDGDIDDNE 1uhnA 134 :KQQGFIERQE T0307 106 :LALWTLISTLCGLPTMT 1uhnA 145 :KQMVVATLAESGMNLKD Number of specific fragments extracted= 8 number of extra gaps= 0 total=293 Number of alignments=57 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2awhA/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/T0307/2awhA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0307/2awhA/merged-good-all-a2m.gz for input Trying 2awhA/merged-good-all-a2m Error: Couldn't open file 2awhA/merged-good-all-a2m or 2awhA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 2mysB/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2mysB expands to /projects/compbio/data/pdb-ca-mod/2mys.brk_ca_mod.gz 2mysB:# T0307 read from 2mysB/merged-good-all-a2m # 2mysB read from 2mysB/merged-good-all-a2m # adding 2mysB to template set # found chain 2mysB in template set Warning: unaligning (T0307)S14 because first residue in template chain is (2mysB)F19 Warning: unaligning (T0307)M24 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2mysB)A30 Warning: unaligning (T0307)A25 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)A30 Warning: unaligning (T0307)K36 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2mysB)K44 Warning: unaligning (T0307)P37 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)K44 Warning: unaligning (T0307)R45 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2mysB)A53 Warning: unaligning (T0307)E46 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)A53 Warning: unaligning (T0307)F47 because of BadResidue code BAD_PEPTIDE in next template residue (2mysB)G55 Warning: unaligning (T0307)M48 because of BadResidue code BAD_PEPTIDE at template residue (2mysB)G55 Warning: unaligning (T0307)R49 because of BadResidue code BAD_PEPTIDE in next template residue (2mysB)L57 Warning: unaligning (T0307)F50 because of BadResidue code BAD_PEPTIDE at template residue (2mysB)L57 Warning: unaligning (T0307)D58 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2mysB)A66 Warning: unaligning (T0307)L59 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)A66 Warning: unaligning (T0307)V73 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2mysB)T82 Warning: unaligning (T0307)A74 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2mysB)T82 Warning: unaligning (T0307)A77 because of BadResidue code BAD_PEPTIDE in next template residue (2mysB)E86 Warning: unaligning (T0307)R78 because of BadResidue code BAD_PEPTIDE at template residue (2mysB)E86 Warning: unaligning (T0307)D80 because of BadResidue code BAD_PEPTIDE in next template residue (2mysB)E94 Warning: unaligning (T0307)E81 because of BadResidue code BAD_PEPTIDE at template residue (2mysB)E94 Warning: unaligning (T0307)K85 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2mysB)G99 Warning: unaligning (T0307)Y86 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)G99 Warning: unaligning (T0307)A88 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2mysB)K102 Warning: unaligning (T0307)S89 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)K102 Warning: unaligning (T0307)G99 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2mysB)K109 Warning: unaligning (T0307)D100 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)K109 Warning: unaligning (T0307)I101 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)G110 Warning: unaligning (T0307)D102 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2mysB)I112 Warning: unaligning (T0307)D103 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)I112 Warning: unaligning (T0307)N104 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)K113 Warning: unaligning (T0307)S113 because of BadResidue code BAD_PEPTIDE in next template residue (2mysB)T123 Warning: unaligning (T0307)T114 because of BadResidue code BAD_PEPTIDE at template residue (2mysB)T123 Warning: unaligning (T0307)T120 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2mysB)P130 Warning: unaligning (T0307)M121 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)P130 T0307 15 :GQELTAIIK 2mysB 20 :DETEIEDFK T0307 26 :KSMVM 2mysB 31 :FTVID T0307 31 :ADGKI 2mysB 38 :ADGII T0307 38 :AEIAVMT 2mysB 45 :DDLRETF T0307 51 :GILQDQV 2mysB 58 :NVKNEEL T0307 60 :LLK 2mysB 67 :MIK T0307 63 :ASDSIEASQA 2mysB 71 :ASGPINFTVF T0307 75 :LI 2mysB 83 :MF T0307 79 :M 2mysB 87 :K T0307 82 :ERK 2mysB 95 :DVI T0307 87 :V 2mysB 100 :A T0307 94 :IMASD 2mysB 103 :VLDPD T0307 105 :ELALWTLI 2mysB 114 :KSFLEELL T0307 115 :LCG 2mysB 124 :GGG T0307 119 :P 2mysB 128 :F T0307 122 :TVMEAIN 2mysB 131 :EEIKNMW Number of specific fragments extracted= 16 number of extra gaps= 12 total=309 Number of alignments=58 # 2mysB read from 2mysB/merged-good-all-a2m # found chain 2mysB in template set Warning: unaligning (T0307)S14 because first residue in template chain is (2mysB)F19 Warning: unaligning (T0307)M24 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2mysB)A30 Warning: unaligning (T0307)A25 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)A30 Warning: unaligning (T0307)K36 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2mysB)K44 Warning: unaligning (T0307)P37 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)K44 Warning: unaligning (T0307)R45 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2mysB)A53 Warning: unaligning (T0307)E46 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)A53 Warning: unaligning (T0307)F47 because of BadResidue code BAD_PEPTIDE in next template residue (2mysB)G55 Warning: unaligning (T0307)M48 because of BadResidue code BAD_PEPTIDE at template residue (2mysB)G55 Warning: unaligning (T0307)R49 because of BadResidue code BAD_PEPTIDE in next template residue (2mysB)L57 Warning: unaligning (T0307)F50 because of BadResidue code BAD_PEPTIDE at template residue (2mysB)L57 Warning: unaligning (T0307)D58 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2mysB)A66 Warning: unaligning (T0307)L59 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)A66 Warning: unaligning (T0307)V73 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2mysB)T82 Warning: unaligning (T0307)A74 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2mysB)T82 Warning: unaligning (T0307)A77 because of BadResidue code BAD_PEPTIDE in next template residue (2mysB)E86 Warning: unaligning (T0307)R78 because of BadResidue code BAD_PEPTIDE at template residue (2mysB)E86 Warning: unaligning (T0307)D80 because of BadResidue code BAD_PEPTIDE in next template residue (2mysB)E94 Warning: unaligning (T0307)E81 because of BadResidue code BAD_PEPTIDE at template residue (2mysB)E94 Warning: unaligning (T0307)K85 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2mysB)G99 Warning: unaligning (T0307)Y86 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)G99 Warning: unaligning (T0307)A88 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2mysB)K102 Warning: unaligning (T0307)S89 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)K102 Warning: unaligning (T0307)G99 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2mysB)K109 Warning: unaligning (T0307)D100 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)K109 Warning: unaligning (T0307)I101 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)G110 Warning: unaligning (T0307)D102 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2mysB)I112 Warning: unaligning (T0307)D103 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)I112 Warning: unaligning (T0307)N104 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)K113 Warning: unaligning (T0307)S113 because of BadResidue code BAD_PEPTIDE in next template residue (2mysB)T123 Warning: unaligning (T0307)T114 because of BadResidue code BAD_PEPTIDE at template residue (2mysB)T123 Warning: unaligning (T0307)T120 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2mysB)P130 Warning: unaligning (T0307)M121 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)P130 T0307 15 :GQELTAIIK 2mysB 20 :DETEIEDFK T0307 26 :KSMVM 2mysB 31 :FTVID T0307 31 :ADGKI 2mysB 38 :ADGII T0307 38 :AEIAVMT 2mysB 45 :DDLRETF T0307 51 :GILQDQV 2mysB 58 :NVKNEEL T0307 60 :LLK 2mysB 67 :MIK T0307 63 :ASDSIEASQA 2mysB 71 :ASGPINFTVF T0307 75 :LI 2mysB 83 :MF T0307 79 :M 2mysB 87 :K T0307 82 :ERK 2mysB 95 :DVI T0307 87 :V 2mysB 100 :A T0307 94 :IMASD 2mysB 103 :VLDPD T0307 105 :ELALWTLI 2mysB 114 :KSFLEELL T0307 115 :LCG 2mysB 124 :GGG T0307 119 :P 2mysB 128 :F T0307 122 :TVMEAIN 2mysB 131 :EEIKNMW Number of specific fragments extracted= 16 number of extra gaps= 12 total=325 Number of alignments=59 # 2mysB read from 2mysB/merged-good-all-a2m # found chain 2mysB in template set Warning: unaligning (T0307)S14 because first residue in template chain is (2mysB)F19 Warning: unaligning (T0307)M24 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2mysB)A30 Warning: unaligning (T0307)A25 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)A30 Warning: unaligning (T0307)K36 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2mysB)K44 Warning: unaligning (T0307)P37 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)K44 Warning: unaligning (T0307)R45 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2mysB)A53 Warning: unaligning (T0307)E46 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)A53 Warning: unaligning (T0307)F47 because of BadResidue code BAD_PEPTIDE in next template residue (2mysB)G55 Warning: unaligning (T0307)M48 because of BadResidue code BAD_PEPTIDE at template residue (2mysB)G55 Warning: unaligning (T0307)R49 because of BadResidue code BAD_PEPTIDE in next template residue (2mysB)L57 Warning: unaligning (T0307)F50 because of BadResidue code BAD_PEPTIDE at template residue (2mysB)L57 Warning: unaligning (T0307)D58 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2mysB)A66 Warning: unaligning (T0307)L59 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)A66 Warning: unaligning (T0307)V73 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2mysB)T82 Warning: unaligning (T0307)A74 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2mysB)T82 Warning: unaligning (T0307)A77 because of BadResidue code BAD_PEPTIDE in next template residue (2mysB)E86 Warning: unaligning (T0307)E82 because of BadResidue code BAD_PEPTIDE at template residue (2mysB)E86 Warning: unaligning (T0307)K84 because of BadResidue code BAD_PEPTIDE at template residue (2mysB)E94 Warning: unaligning (T0307)A88 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2mysB)G99 Warning: unaligning (T0307)S89 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)G99 Warning: unaligning (T0307)L91 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2mysB)K102 Warning: unaligning (T0307)G92 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)K102 Warning: unaligning (T0307)S97 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2mysB)K109 Warning: unaligning (T0307)D98 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)K109 Warning: unaligning (T0307)G99 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)G110 Warning: unaligning (T0307)D100 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2mysB)I112 Warning: unaligning (T0307)I101 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)I112 Warning: unaligning (T0307)D102 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2mysB)K113 Warning: unaligning (T0307)T114 because of BadResidue code BAD_PEPTIDE in next template residue (2mysB)T123 Warning: unaligning (T0307)L115 because of BadResidue code BAD_PEPTIDE at template residue (2mysB)T123 T0307 15 :GQELTAIIK 2mysB 20 :DETEIEDFK T0307 26 :KSMV 2mysB 31 :FTVI T0307 30 :MADGKI 2mysB 37 :NADGII T0307 38 :AEIAVMT 2mysB 45 :DDLRETF T0307 51 :GILQDQV 2mysB 58 :NVKNEEL T0307 60 :LLKASDS 2mysB 67 :MIKEASG T0307 67 :IEASQA 2mysB 75 :INFTVF T0307 75 :LI 2mysB 83 :MF T0307 83 :R 2mysB 87 :K T0307 85 :KYV 2mysB 95 :DVI T0307 90 :Y 2mysB 100 :A T0307 93 :VI 2mysB 103 :VL T0307 95 :MA 2mysB 106 :PD T0307 103 :DN 2mysB 114 :KS T0307 108 :LWTLIS 2mysB 116 :FLEELL T0307 116 :CGL 2mysB 124 :GGG Number of specific fragments extracted= 16 number of extra gaps= 11 total=341 Number of alignments=60 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ncx/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ncx expands to /projects/compbio/data/pdb/1ncx.pdb.gz 1ncx:Warning: there is no chain 1ncx will retry with 1ncxA # T0307 read from 1ncx/merged-good-all-a2m # 1ncx read from 1ncx/merged-good-all-a2m # adding 1ncx to template set # found chain 1ncx in template set T0307 33 :GKIKPAEIAVMTREF 1ncx 35 :GDISTKELGTVMRML T0307 51 :GILQDQVDLLLKA 1ncx 52 :NPTKEELDAIIEE T0307 64 :SDSIEASQAVALIARM 1ncx 70 :SGTIDFEEFLVMMVRQ T0307 80 :DEERKKYVASYL 1ncx 95 :EEELANCFRIFD T0307 95 :MASDGDIDDNELALW 1ncx 107 :KNADGFIDIEELGEI T0307 111 :LISTLCGLPTMTVMEAINNM 1ncx 122 :LRATGEHVTEEDIEDLMKDS Number of specific fragments extracted= 6 number of extra gaps= 0 total=347 Number of alignments=61 # 1ncx read from 1ncx/merged-good-all-a2m # found chain 1ncx in template set T0307 16 :QELTAIIKMAKSMVMADGK 1ncx 16 :EEMIAEFKAAFDMFDADGG T0307 35 :IKPAEIAVMTREF 1ncx 37 :ISTKELGTVMRML T0307 49 :RFGILQDQVDLLLKA 1ncx 50 :GQNPTKEELDAIIEE T0307 64 :SDSIEASQAVALIARMDEERKKY 1ncx 70 :SGTIDFEEFLVMMVRQMKEDAKG T0307 87 :VASYLGVI 1ncx 98 :LANCFRIF T0307 95 :MASDGDIDDNELALW 1ncx 107 :KNADGFIDIEELGEI T0307 111 :LISTLCGLPTMTVMEAINNM 1ncx 122 :LRATGEHVTEEDIEDLMKDS Number of specific fragments extracted= 7 number of extra gaps= 0 total=354 Number of alignments=62 # 1ncx read from 1ncx/merged-good-all-a2m # found chain 1ncx in template set T0307 14 :SGQELTAIIKMA 1ncx 2 :SMTDQQAEARAF T0307 35 :IKPAEIAVMTREFMRFGIL 1ncx 14 :LSEEMIAEFKAAFDMFDAD T0307 54 :QDQVDLLLKASD 1ncx 39 :TKELGTVMRMLG T0307 66 :SIEASQAVALIARMDEE 1ncx 52 :NPTKEELDAIIEEVDED T0307 84 :KKYVASYLGVIMA 1ncx 75 :FEEFLVMMVRQMK T0307 97 :SDGDIDDNELALWT 1ncx 109 :ADGFIDIEELGEIL Number of specific fragments extracted= 6 number of extra gaps= 0 total=360 Number of alignments=63 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2aaoA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2aaoA expands to /projects/compbio/data/pdb/2aao.pdb.gz 2aaoA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 113, because occupancy 0.500 <= existing 0.500 in 2aaoA Skipped atom 115, because occupancy 0.500 <= existing 0.500 in 2aaoA Skipped atom 117, because occupancy 0.500 <= existing 0.500 in 2aaoA Skipped atom 119, because occupancy 0.500 <= existing 0.500 in 2aaoA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 334, because occupancy 0.500 <= existing 0.500 in 2aaoA Skipped atom 336, because occupancy 0.500 <= existing 0.500 in 2aaoA Skipped atom 338, because occupancy 0.500 <= existing 0.500 in 2aaoA Skipped atom 340, because occupancy 0.500 <= existing 0.500 in 2aaoA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0307 read from 2aaoA/merged-good-all-a2m # 2aaoA read from 2aaoA/merged-good-all-a2m # adding 2aaoA to template set # found chain 2aaoA in template set T0307 15 :GQELTAIIKMAKSMVMAD 2aaoA 22 :SEEEIAGLKEMFNMIDAD T0307 33 :GKIKPAEIAVMTREF 2aaoA 42 :GQITFEELKAGLKRV T0307 49 :RFGILQDQVDLLLKA 2aaoA 57 :GANLKESEILDLMQA T0307 64 :SDSIEASQAVALIARMDEERK 2aaoA 77 :SGTIDYKEFIAATLHLNKIER T0307 85 :KYVASYLGVIMASDGDIDDNELA 2aaoA 100 :HLFAAFTYFDKDGSGYITPDELQ Number of specific fragments extracted= 5 number of extra gaps= 0 total=365 Number of alignments=64 # 2aaoA read from 2aaoA/merged-good-all-a2m # found chain 2aaoA in template set Warning: unaligning (T0307)S64 because first residue in template chain is (2aaoA)M6 T0307 65 :DSIEASQAVALIARMDEERKKYVASYLGVIMASD 2aaoA 7 :NKFKKMALRVIAESLSEEEIAGLKEMFNMIDADK T0307 99 :GDIDDNELALW 2aaoA 42 :GQITFEELKAG T0307 113 :STLCGLPTMTVMEAINNM 2aaoA 55 :RVGANLKESEILDLMQAA Number of specific fragments extracted= 3 number of extra gaps= 0 total=368 Number of alignments=65 # 2aaoA read from 2aaoA/merged-good-all-a2m # found chain 2aaoA in template set T0307 16 :QELTAIIKMAKSMVMAD 2aaoA 23 :EEEIAGLKEMFNMIDAD T0307 33 :GKIKPAEIA 2aaoA 42 :GQITFEELK T0307 45 :REFMRF 2aaoA 51 :AGLKRV T0307 51 :GILQDQVDLLLKASD 2aaoA 59 :NLKESEILDLMQAAD T0307 66 :SIEASQAVALIARMDE 2aaoA 79 :TIDYKEFIAATLHLNK T0307 83 :RKKYVASYLGVIMASDGDIDDNELA 2aaoA 98 :EDHLFAAFTYFDKDGSGYITPDELQ Number of specific fragments extracted= 6 number of extra gaps= 0 total=374 Number of alignments=66 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1y0sA/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/T0307/1y0sA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0307/1y0sA/merged-good-all-a2m.gz for input Trying 1y0sA/merged-good-all-a2m Error: Couldn't open file 1y0sA/merged-good-all-a2m or 1y0sA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ff9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ff9A expands to /projects/compbio/data/pdb/1ff9.pdb.gz 1ff9A:# T0307 read from 1ff9A/merged-good-all-a2m # 1ff9A read from 1ff9A/merged-good-all-a2m # adding 1ff9A to template set # found chain 1ff9A in template set T0307 16 :QELTAIIKMAKSMVMADGKIKPA 1ff9A 249 :QGFPQFIKVLVDIGFLSDEEQPF T0307 51 :GILQDQVDLLLKAS 1ff9A 276 :IPWKEATQKIVKAS T0307 66 :SIEASQAVALIAR 1ff9A 290 :SASEQDIVSTIVS T0307 80 :DEERKKYVASYLGVIMASDGDIDDNELALWTLISTL 1ff9A 309 :TEEQKRIVAGLKWLGIFSDKKITPRGNALDTLCATL Number of specific fragments extracted= 4 number of extra gaps= 0 total=378 Number of alignments=67 # 1ff9A read from 1ff9A/merged-good-all-a2m # found chain 1ff9A in template set T0307 54 :QDQVDLLLKAS 1ff9A 279 :KEATQKIVKAS T0307 66 :SIEASQAVALIARM 1ff9A 290 :SASEQDIVSTIVSN T0307 80 :DEERKKYVASYLGVI 1ff9A 308 :STEEQKRIVAGLKWL T0307 95 :MASDGDIDDNELALWTLISTL 1ff9A 324 :IFSDKKITPRGNALDTLCATL Number of specific fragments extracted= 4 number of extra gaps= 0 total=382 Number of alignments=68 # 1ff9A read from 1ff9A/merged-good-all-a2m # found chain 1ff9A in template set T0307 18 :LTAIIKMAKSMVMADGKIKP 1ff9A 251 :FPQFIKVLVDIGFLSDEEQP T0307 43 :MTR 1ff9A 278 :WKE T0307 46 :EFMRFG 1ff9A 282 :TQKIVK T0307 64 :SDSIEASQAVALI 1ff9A 288 :ASSASEQDIVSTI T0307 77 :ARM 1ff9A 302 :SNA T0307 80 :DEERKKYVASYLGVI 1ff9A 308 :STEEQKRIVAGLKWL T0307 95 :MASDGDID 1ff9A 324 :IFSDKKIT T0307 104 :NELALWTLISTL 1ff9A 335 :NALDTLCATLEE Number of specific fragments extracted= 8 number of extra gaps= 0 total=390 Number of alignments=69 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1afvA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1afvA expands to /projects/compbio/data/pdb/1afv.pdb.gz 1afvA:# T0307 read from 1afvA/merged-good-all-a2m # 1afvA read from 1afvA/merged-good-all-a2m # adding 1afvA to template set # found chain 1afvA in template set Warning: unaligning (T0307)L118 because of BadResidue code BAD_PEPTIDE in next template residue (1afvA)P122 Warning: unaligning (T0307)P119 because of BadResidue code BAD_PEPTIDE at template residue (1afvA)P122 T0307 13 :FSGQELTAIIKMAKSMVMADG 1afvA 15 :ISPRTLNAWVKVVEEKAFSPE T0307 40 :I 1afvA 36 :V T0307 44 :TREFMRF 1afvA 37 :IPMFSAL T0307 51 :GILQDQVDLLLKASD 1afvA 46 :GATPQDLNTMLNTVG T0307 66 :SIEASQAV 1afvA 62 :HQAAMQML T0307 76 :IARMDEERKKYVA 1afvA 70 :KETINEEAAEWDR T0307 93 :VIMASDGDIDDNEL 1afvA 83 :LHPVHAGPIAPGQM T0307 108 :LWTLISTLCG 1afvA 111 :LQEQIGWMTH T0307 120 :TMTVMEA 1afvA 123 :PIPVGEI Number of specific fragments extracted= 9 number of extra gaps= 1 total=399 Number of alignments=70 # 1afvA read from 1afvA/merged-good-all-a2m # found chain 1afvA in template set T0307 12 :TFSGQELTAIIKMAKSMVMADG 1afvA 14 :AISPRTLNAWVKVVEEKAFSPE T0307 40 :IAVMTREFMRFGILQDQVDLLLKASDSIEASQA 1afvA 36 :VIPMFSALSEGATPQDLNTMLNTVGGHQAAMQM T0307 79 :MDEERKKYVASYLGVIMASDGDIDDNE 1afvA 69 :LKETINEEAAEWDRLHPVHAGPIAPGQ Number of specific fragments extracted= 3 number of extra gaps= 0 total=402 Number of alignments=71 # 1afvA read from 1afvA/merged-good-all-a2m # found chain 1afvA in template set T0307 34 :KIKPAEIAVMTREFMRFGILQDQVDLLLKASDSIEASQAVALIARM 1afvA 14 :AISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTV T0307 80 :DEERKKYVASYLGVIMA 1afvA 62 :HQAAMQMLKETINEEAA Number of specific fragments extracted= 2 number of extra gaps= 0 total=404 Number of alignments=72 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1a2xA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1a2xA expands to /projects/compbio/data/pdb/1a2x.pdb.gz 1a2xA:# T0307 read from 1a2xA/merged-good-all-a2m # 1a2xA read from 1a2xA/merged-good-all-a2m # adding 1a2xA to template set # found chain 1a2xA in template set T0307 16 :QELTAIIKM 1a2xA 37 :KELGTVMRM T0307 31 :ADGKIKPAEIAVMTREFMR 1a2xA 46 :LGQTPTKEELDAIIEEVDE T0307 63 :ASDSIEASQAVALIARM 1a2xA 66 :GSGTIDFEEFLVMMVRQ T0307 80 :DEERKKYVASYLG 1a2xA 92 :EEELAECFRIFDR T0307 96 :ASDGDIDDNELALW 1a2xA 105 :NADGYIDAEELAEI T0307 115 :LCG 1a2xA 119 :FRA T0307 118 :LPTMTVMEA 1a2xA 126 :VTDEEIESL Number of specific fragments extracted= 7 number of extra gaps= 0 total=411 Number of alignments=73 # 1a2xA read from 1a2xA/merged-good-all-a2m # found chain 1a2xA in template set T0307 16 :QELTAIIKMAKSMVMAD 1a2xA 13 :EEMIAEFKAAFDMFDAD T0307 33 :GKIKPAEIAVMTRE 1a2xA 32 :GDISVKELGTVMRM T0307 48 :MRFGILQDQVDLLLKA 1a2xA 46 :LGQTPTKEELDAIIEE T0307 64 :SDSIEASQAVALIARM 1a2xA 67 :SGTIDFEEFLVMMVRQ T0307 80 :DEERKKYVASYLG 1a2xA 92 :EEELAECFRIFDR T0307 96 :ASDGDIDDNELALW 1a2xA 105 :NADGYIDAEELAEI T0307 114 :TLCGLPTMTVMEAINNM 1a2xA 119 :FRASGEHVTDEEIESLM Number of specific fragments extracted= 7 number of extra gaps= 0 total=418 Number of alignments=74 # 1a2xA read from 1a2xA/merged-good-all-a2m # found chain 1a2xA in template set T0307 12 :TFSGQELTAIIKM 1a2xA 33 :DISVKELGTVMRM T0307 31 :ADGKIKPAEIAVMTREFMRFGIL 1a2xA 46 :LGQTPTKEELDAIIEEVDEDGSG T0307 54 :QDQ 1a2xA 72 :FEE T0307 57 :VDLLLKASDSIEASQAVALIARMD 1a2xA 80 :VRQMKEDAKGKSEEELAECFRIFD T0307 88 :ASYLGVIMASDGD 1a2xA 112 :AEELAEIFRASGE T0307 101 :IDDNELALWTL 1a2xA 126 :VTDEEIESLMK Number of specific fragments extracted= 6 number of extra gaps= 0 total=424 Number of alignments=75 # command:Using radius: 8.0000 Alignment mode NUMB_ALIGNS: 75 Adding 1385 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: -251.6243, CN propb: -251.6243 weights: 0.2337 constraints: 205 # command:Found ConstraintSet # PrintContacts align.constraints_v3 Number of constraints in align.constraints 205 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_v3 Number of constraints in align.constraints.bonus 205 # command:Found ConstraintSet # PrintContacts rejected.constraints_v3 Number of constraints in rejected.constraints 1180 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_v3 Number of constraints in rejected.constraints.bonus 1180 # 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 1385 # command: