# 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:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0307//projects/compbio/experiments/protein-predict/casp7/T0307/align.constraints_v3.costfcn or /projects/compbio/experiments/protein-predict/casp7/T0307//projects/compbio/experiments/protein-predict/casp7/T0307/align.constraints_v3.costfcn.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/T0307/align.constraints_v3.costfcn # reading script from file /projects/compbio/experiments/protein-predict/casp7/T0307/align.constraints_v3.costfcn # future Constraint commands -> align # future HelixConstraint commands -> align # future StrandConstraint commands -> align # future SheetConstraint commands -> align # future Hbond commands -> align # future SSbond commands -> align # Constraint # added constraint: constraint((T0307)I35.CB, (T0307)I67.CB) [> 3.0874 = 5.1456 < 6.6894] w=1.0000 to align # Constraint # added constraint: constraint((T0307)A63.CB, (T0307)L75.CB) [> 3.8153 = 6.3589 < 8.2665] w=0.9258 to align # Constraint # added constraint: constraint((T0307)I40.CB, (T0307)V57.CB) [> 3.2850 = 5.4750 < 7.1175] w=0.8849 to align # Constraint # added constraint: constraint((T0307)L60.CB, (T0307)L75.CB) [> 3.1339 = 5.2231 < 6.7901] w=0.8640 to align # Constraint # added constraint: constraint((T0307)I40.CB, (T0307)L61.CB) [> 3.7319 = 6.2198 < 8.0857] w=0.8441 to align # Constraint # added constraint: constraint((T0307)I35.CB, (T0307)A72.CB) [> 4.0914 = 6.8191 < 8.8648] w=0.8436 to align # Constraint # added constraint: constraint((T0307)L91.CB, (T0307)I101.CB) [> 3.4373 = 5.7288 < 7.4474] w=0.8180 to align # Constraint # added constraint: constraint((T0307)A96.CB, (T0307)E105.CB) [> 4.4225 = 7.3708 < 9.5820] w=0.8140 to align # Constraint # added constraint: constraint((T0307)K36.CB, (T0307)S66.CB) [> 3.7674 = 6.2790 < 8.1627] w=0.8068 to align # Constraint # added constraint: constraint((T0307)L61.CB, (T0307)A72.CB) [> 3.9206 = 6.5343 < 8.4946] w=0.8004 to align # Constraint # added constraint: constraint((T0307)K34.CB, (T0307)E68.CB) [> 3.6444 = 6.0739 < 7.8961] w=0.7308 to align # Constraint # added constraint: constraint((T0307)T44.CB, (T0307)V57.CB) [> 3.5090 = 5.8484 < 7.6029] w=0.7279 to align # Constraint # added constraint: constraint((T0307)V29.CB, (T0307)E39.CB) [> 3.2745 = 5.4575 < 7.0948] w=0.6993 to align # Constraint # added constraint: constraint((T0307)K34.CB, (T0307)I67.CB) [> 3.6458 = 6.0763 < 7.8992] w=0.6885 to align # Constraint # added constraint: constraint((T0307)P37.CB, (T0307)L61.CB) [> 3.1922 = 5.3204 < 6.9165] w=0.6851 to align # Constraint # added constraint: constraint((T0307)S64.CB, (T0307)L75.CB) [> 3.5483 = 5.9138 < 7.6880] w=0.6460 to align # Constraint # added constraint: constraint((T0307)I22.CB, (T0307)A69.CB) [> 4.0437 = 6.7395 < 8.7614] w=0.6316 to align # Constraint # added constraint: constraint((T0307)M28.CB, (T0307)M43.CB) [> 3.8226 = 6.3709 < 8.2822] w=0.6245 to align # Constraint # added constraint: constraint((T0307)M30.CB, (T0307)E39.CB) [> 3.7483 = 6.2472 < 8.1213] w=0.6150 to align # Constraint # added constraint: constraint((T0307)I22.CB, (T0307)A72.CB) [> 4.2395 = 7.0659 < 9.1857] w=0.5998 to align # Constraint # added constraint: constraint((T0307)I22.CB, (T0307)I76.CB) [> 4.0705 = 6.7842 < 8.8195] w=0.5960 to align # Constraint # added constraint: constraint((T0307)M95.CB, (T0307)E105.CB) [> 3.2750 = 5.4584 < 7.0960] w=0.5929 to align # Constraint # added constraint: constraint((T0307)A41.CB, (T0307)I52.CB) [> 3.6571 = 6.0952 < 7.9237] w=0.5408 to align # Constraint # added constraint: constraint((T0307)L18.CB, (T0307)V73.CB) [> 3.8660 = 6.4434 < 8.3764] w=0.5176 to align # Constraint # added constraint: constraint((T0307)P37.CB, (T0307)V57.CB) [> 3.6600 = 6.0999 < 7.9299] w=0.5132 to align # Constraint # added constraint: constraint((T0307)I94.CB, (T0307)E105.CB) [> 3.4660 = 5.7766 < 7.5096] w=0.5127 to align # Constraint # added constraint: constraint((T0307)A25.CB, (T0307)A72.CB) [> 3.7183 = 6.1971 < 8.0563] w=0.5100 to align # Constraint # added constraint: constraint((T0307)P37.CB, (T0307)D58.CB) [> 3.8949 = 6.4914 < 8.4388] w=0.4946 to align # Constraint # added constraint: constraint((T0307)A63.CB, (T0307)A72.CB) [> 3.6153 = 6.0255 < 7.8331] w=0.4846 to align # Constraint # added constraint: constraint((T0307)I21.CB, (T0307)A72.CB) [> 4.4864 = 7.4774 < 9.7206] w=0.4815 to align # Constraint # added constraint: constraint((T0307)A107.CB, (T0307)V123.CB) [> 3.2564 = 5.4273 < 7.0555] w=0.4754 to align # Constraint # added constraint: constraint((T0307)L106.CB, (T0307)I127.CB) [> 3.4529 = 5.7549 < 7.4813] w=0.4750 to align # Constraint # added constraint: constraint((T0307)K26.CB, (T0307)A69.CB) [> 3.3779 = 5.6298 < 7.3188] w=0.4608 to align # Constraint # added constraint: constraint((T0307)K23.CB, (T0307)A69.CB) [> 3.9853 = 6.6421 < 8.6348] w=0.4608 to align # Constraint # added constraint: constraint((T0307)I40.CB, (T0307)I67.CB) [> 3.9437 = 6.5728 < 8.5446] w=0.4555 to align # Constraint # added constraint: constraint((T0307)A41.CB, (T0307)L53.CB) [> 3.7604 = 6.2674 < 8.1476] w=0.4432 to align # Constraint # added constraint: constraint((T0307)I21.CB, (T0307)I76.CB) [> 4.1344 = 6.8908 < 8.9580] w=0.4347 to align # Constraint # added constraint: constraint((T0307)G92.CA, (T0307)I101.CB) [> 3.3536 = 5.5894 < 7.2662] w=0.4283 to align # Constraint # added constraint: constraint((T0307)A25.CB, (T0307)A69.CB) [> 3.1981 = 5.3302 < 6.9293] w=0.4274 to align # Constraint # added constraint: constraint((T0307)I21.CB, (T0307)V73.CB) [> 3.5408 = 5.9014 < 7.6718] w=0.4274 to align # Constraint # added constraint: constraint((T0307)I22.CB, (T0307)V73.CB) [> 3.8128 = 6.3547 < 8.2612] w=0.4258 to align # Constraint # added constraint: constraint((T0307)V29.CB, (T0307)I40.CB) [> 4.0376 = 6.7294 < 8.7482] w=0.4169 to align # Constraint # added constraint: constraint((T0307)I76.CB, (T0307)V87.CB) [> 3.7478 = 6.2463 < 8.1202] w=0.4011 to align # Constraint # added constraint: constraint((T0307)I94.CB, (T0307)W109.CB) [> 3.6116 = 6.0194 < 7.8252] w=0.3960 to align # Constraint # added constraint: constraint((T0307)L59.CB, (T0307)Y90.CB) [> 3.8513 = 6.4189 < 8.3445] w=0.3942 to align # Constraint # added constraint: constraint((T0307)F13.CB, (T0307)V73.CB) [> 4.0531 = 6.7552 < 8.7817] w=0.3526 to align # Constraint # added constraint: constraint((T0307)L106.CB, (T0307)V123.CB) [> 3.4362 = 5.7270 < 7.4451] w=0.3467 to align # Constraint # added constraint: constraint((T0307)Q56.CB, (T0307)M79.CB) [> 4.0383 = 6.7305 < 8.7497] w=0.3221 to align # Constraint # added constraint: constraint((T0307)M95.CB, (T0307)L108.CB) [> 4.3181 = 7.1968 < 9.3559] w=0.3177 to align # Constraint # added constraint: constraint((T0307)V29.CB, (T0307)V42.CB) [> 4.3230 = 7.2050 < 9.3665] w=0.3153 to align # Constraint # added constraint: constraint((T0307)T19.CB, (T0307)V73.CB) [> 4.0900 = 6.8166 < 8.8616] w=0.3139 to align # Constraint # added constraint: constraint((T0307)L59.CB, (T0307)L75.CB) [> 3.9909 = 6.6515 < 8.6469] w=0.2993 to align # Constraint # added constraint: constraint((T0307)Q56.CB, (T0307)L75.CB) [> 4.3006 = 7.1677 < 9.3179] w=0.2993 to align # Constraint # added constraint: constraint((T0307)M95.CB, (T0307)W109.CB) [> 4.2669 = 7.1115 < 9.2450] w=0.2874 to align # Constraint # added constraint: constraint((T0307)F47.CB, (T0307)V57.CB) [> 3.4069 = 5.6782 < 7.3816] w=0.2785 to align # Constraint # added constraint: constraint((T0307)A31.CB, (T0307)V42.CB) [> 3.8146 = 6.3576 < 8.2649] w=0.2784 to align # Constraint # added constraint: constraint((T0307)L111.CB, (T0307)V123.CB) [> 3.5683 = 5.9472 < 7.7314] w=0.2776 to align # Constraint # added constraint: constraint((T0307)L60.CB, (T0307)Q71.CB) [> 3.6476 = 6.0794 < 7.9032] w=0.2775 to align # Constraint # added constraint: constraint((T0307)F13.CB, (T0307)A77.CB) [> 3.6485 = 6.0808 < 7.9050] w=0.2745 to align # Constraint # added constraint: constraint((T0307)Y90.CB, (T0307)I101.CB) [> 3.8348 = 6.3914 < 8.3088] w=0.2709 to align # Constraint # added constraint: constraint((T0307)I21.CB, (T0307)A69.CB) [> 4.7507 = 7.9179 < 10.2933] w=0.2679 to align # Constraint # added constraint: constraint((T0307)A63.CB, (T0307)Y86.CB) [> 4.3766 = 7.2943 < 9.4826] w=0.2648 to align # Constraint # added constraint: constraint((T0307)I112.CB, (T0307)V123.CB) [> 4.7287 = 7.8811 < 10.2455] w=0.2647 to align # Constraint # added constraint: constraint((T0307)G92.CA, (T0307)L106.CB) [> 3.7062 = 6.1769 < 8.0300] w=0.2597 to align # Constraint # added constraint: constraint((T0307)Y90.CB, (T0307)L108.CB) [> 4.5111 = 7.5186 < 9.7742] w=0.2597 to align # Constraint # added constraint: constraint((T0307)M28.CB, (T0307)E39.CB) [> 3.0492 = 5.0820 < 6.6066] w=0.2418 to align # Constraint # added constraint: constraint((T0307)L18.CB, (T0307)L60.CB) [> 4.2601 = 7.1002 < 9.2302] w=0.2409 to align # Constraint # added constraint: constraint((T0307)I76.CB, (T0307)Y86.CB) [> 4.4334 = 7.3890 < 9.6057] w=0.2383 to align # Constraint # added constraint: constraint((T0307)D58.CB, (T0307)I67.CB) [> 3.4063 = 5.6772 < 7.3804] w=0.2374 to align # Constraint # added constraint: constraint((T0307)F50.CB, (T0307)M79.CB) [> 3.7275 = 6.2124 < 8.0762] w=0.2356 to align # Constraint # added constraint: constraint((T0307)F47.CB, (T0307)L60.CB) [> 3.9246 = 6.5410 < 8.5034] w=0.2303 to align # Constraint # added constraint: constraint((T0307)T44.CB, (T0307)L53.CB) [> 3.3461 = 5.5768 < 7.2499] w=0.2282 to align # Constraint # added constraint: constraint((T0307)Q56.CB, (T0307)T114.CB) [> 3.9502 = 6.5837 < 8.5589] w=0.2264 to align # Constraint # added constraint: constraint((T0307)A63.CB, (T0307)S89.CB) [> 3.8219 = 6.3698 < 8.2808] w=0.2264 to align # Constraint # added constraint: constraint((T0307)A63.CB, (T0307)Y90.CB) [> 2.8612 = 4.7687 < 6.1993] w=0.2264 to align # Constraint # added constraint: constraint((T0307)L91.CB, (T0307)L108.CB) [> 3.0737 = 5.1228 < 6.6596] w=0.2264 to align # Constraint # added constraint: constraint((T0307)L91.CB, (T0307)W109.CB) [> 3.3654 = 5.6089 < 7.2916] w=0.2212 to align # Constraint # added constraint: constraint((T0307)M28.CB, (T0307)V42.CB) [> 3.8619 = 6.4364 < 8.3673] w=0.2135 to align # Constraint # added constraint: constraint((T0307)M30.CB, (T0307)M43.CB) [> 3.7188 = 6.1980 < 8.0574] w=0.2130 to align # Constraint # added constraint: constraint((T0307)M24.CB, (T0307)I76.CB) [> 4.6174 = 7.6957 < 10.0044] w=0.2097 to align # Constraint # added constraint: constraint((T0307)D55.CB, (T0307)M95.CB) [> 4.4295 = 7.3824 < 9.5971] w=0.2079 to align # Constraint # added constraint: constraint((T0307)M95.CB, (T0307)L111.CB) [> 4.5478 = 7.5797 < 9.8536] w=0.2040 to align # Constraint # added constraint: constraint((T0307)F47.CB, (T0307)Q56.CB) [> 3.6737 = 6.1229 < 7.9597] w=0.2035 to align # Constraint # added constraint: constraint((T0307)I22.CB, (T0307)A31.CB) [> 3.6120 = 6.0200 < 7.8260] w=0.1944 to align # Constraint # added constraint: constraint((T0307)I94.CB, (T0307)L108.CB) [> 4.0395 = 6.7324 < 8.7522] w=0.1932 to align # Constraint # added constraint: constraint((T0307)R45.CB, (T0307)Q54.CB) [> 4.0347 = 6.7245 < 8.7418] w=0.1916 to align # Constraint # added constraint: constraint((T0307)A88.CB, (T0307)S97.CB) [> 4.3404 = 7.2340 < 9.4043] w=0.1914 to align # Constraint # added constraint: constraint((T0307)A25.CB, (T0307)F47.CB) [> 3.2144 = 5.3573 < 6.9646] w=0.1909 to align # Constraint # added constraint: constraint((T0307)A107.CB, (T0307)T120.CB) [> 4.0806 = 6.8011 < 8.8414] w=0.1861 to align # Constraint # added constraint: constraint((T0307)L59.CB, (T0307)L111.CB) [> 3.6604 = 6.1006 < 7.9308] w=0.1849 to align # Constraint # added constraint: constraint((T0307)L59.CB, (T0307)L108.CB) [> 3.7154 = 6.1923 < 8.0500] w=0.1849 to align # Constraint # added constraint: constraint((T0307)I52.CB, (T0307)L115.CB) [> 3.8475 = 6.4125 < 8.3362] w=0.1849 to align # Constraint # added constraint: constraint((T0307)A25.CB, (T0307)V73.CB) [> 4.6838 = 7.8063 < 10.1481] w=0.1775 to align # Constraint # added constraint: constraint((T0307)L18.CB, (T0307)I76.CB) [> 4.1073 = 6.8455 < 8.8991] w=0.1716 to align # Constraint # added constraint: constraint((T0307)I52.CB, (T0307)I112.CB) [> 4.1533 = 6.9222 < 8.9989] w=0.1678 to align # Constraint # added constraint: constraint((T0307)L60.CB, (T0307)A74.CB) [> 4.1035 = 6.8392 < 8.8910] w=0.1678 to align # Constraint # added constraint: constraint((T0307)A107.CB, (T0307)I127.CB) [> 3.2860 = 5.4767 < 7.1197] w=0.1678 to align # Constraint # added constraint: constraint((T0307)A25.CB, (T0307)K36.CB) [> 4.0483 = 6.7472 < 8.7713] w=0.1620 to align # Constraint # added constraint: constraint((T0307)T12.CB, (T0307)R78.CB) [> 3.4451 = 5.7418 < 7.4643] w=0.1618 to align # Constraint # added constraint: constraint((T0307)T12.CB, (T0307)A77.CB) [> 2.9280 = 4.8800 < 6.3440] w=0.1618 to align # Constraint # added constraint: constraint((T0307)L111.CB, (T0307)T122.CB) [> 4.5345 = 7.5575 < 9.8247] w=0.1603 to align # Constraint # added constraint: constraint((T0307)I21.CB, (T0307)A31.CB) [> 4.3111 = 7.1852 < 9.3407] w=0.1572 to align # Constraint # added constraint: constraint((T0307)F50.CB, (T0307)I76.CB) [> 3.9313 = 6.5522 < 8.5179] w=0.1550 to align # Constraint # added constraint: constraint((T0307)R49.CB, (T0307)C116.CB) [> 3.7332 = 6.2221 < 8.0887] w=0.1547 to align # Constraint # added constraint: constraint((T0307)V87.CB, (T0307)L115.CB) [> 4.6058 = 7.6764 < 9.9793] w=0.1547 to align # Constraint # added constraint: constraint((T0307)L111.CB, (T0307)A126.CB) [> 4.4886 = 7.4810 < 9.7253] w=0.1509 to align # Constraint # added constraint: constraint((T0307)V93.CB, (T0307)L106.CB) [> 3.9082 = 6.5137 < 8.4678] w=0.1502 to align # Constraint # added constraint: constraint((T0307)V93.CB, (T0307)L108.CB) [> 4.3138 = 7.1896 < 9.3465] w=0.1502 to align # Constraint # added constraint: constraint((T0307)I112.CB, (T0307)M124.CB) [> 3.9464 = 6.5774 < 8.5506] w=0.1493 to align # Constraint # added constraint: constraint((T0307)T110.CB, (T0307)V123.CB) [> 3.9836 = 6.6393 < 8.6312] w=0.1357 to align # Constraint # added constraint: constraint((T0307)T19.CB, (T0307)S64.CB) [> 3.3027 = 5.5045 < 7.1558] w=0.1343 to align # Constraint # added constraint: constraint((T0307)I22.CB, (T0307)L61.CB) [> 3.3143 = 5.5238 < 7.1809] w=0.1316 to align # Constraint # added constraint: constraint((T0307)V42.CB, (T0307)L53.CB) [> 4.0093 = 6.6822 < 8.6869] w=0.1262 to align # Constraint # added constraint: constraint((T0307)L106.CB, (T0307)M130.CB) [> 3.3927 = 5.6545 < 7.3508] w=0.1226 to align # Constraint # added constraint: constraint((T0307)Q54.CB, (T0307)A96.CB) [> 4.0484 = 6.7473 < 8.7715] w=0.1202 to align # Constraint # added constraint: constraint((T0307)V73.CB, (T0307)A96.CB) [> 4.5362 = 7.5604 < 9.8285] w=0.1200 to align # Constraint # added constraint: constraint((T0307)T114.CB, (T0307)V123.CB) [> 3.4533 = 5.7555 < 7.4822] w=0.1174 to align # Constraint # added constraint: constraint((T0307)V93.CB, (T0307)W109.CB) [> 3.7320 = 6.2201 < 8.0861] w=0.1172 to align # Constraint # added constraint: constraint((T0307)I94.CB, (T0307)I112.CB) [> 3.9040 = 6.5066 < 8.4586] w=0.1161 to align # Constraint # added constraint: constraint((T0307)V93.CB, (T0307)A107.CB) [> 3.8499 = 6.4164 < 8.3413] w=0.1155 to align # Constraint # added constraint: constraint((T0307)M95.CB, (T0307)A107.CB) [> 4.3546 = 7.2577 < 9.4350] w=0.1154 to align # Constraint # added constraint: constraint((T0307)S113.CB, (T0307)M124.CB) [> 4.4761 = 7.4602 < 9.6983] w=0.1129 to align # Constraint # added constraint: constraint((T0307)M24.CB, (T0307)L91.CB) [> 3.1145 = 5.1908 < 6.7480] w=0.1103 to align # Constraint # added constraint: constraint((T0307)M24.CB, (T0307)V87.CB) [> 3.6442 = 6.0736 < 7.8957] w=0.1103 to align # Constraint # added constraint: constraint((T0307)I21.CB, (T0307)Y90.CB) [> 3.9514 = 6.5857 < 8.5614] w=0.1103 to align # Constraint # added constraint: constraint((T0307)L59.CB, (T0307)V93.CB) [> 4.1210 = 6.8684 < 8.9289] w=0.1102 to align # Constraint # added constraint: constraint((T0307)A38.CB, (T0307)V57.CB) [> 3.6049 = 6.0081 < 7.8106] w=0.0847 to align # Constraint # added constraint: constraint((T0307)T110.CB, (T0307)I127.CB) [> 4.0089 = 6.6815 < 8.6859] w=0.0847 to align # Constraint # added constraint: constraint((T0307)I112.CB, (T0307)I127.CB) [> 3.7696 = 6.2827 < 8.1675] w=0.0840 to align # Constraint # added constraint: constraint((T0307)Y86.CB, (T0307)L111.CB) [> 3.6372 = 6.0620 < 7.8806] w=0.0840 to align # Constraint # added constraint: constraint((T0307)F13.CB, (T0307)I76.CB) [> 4.7943 = 7.9904 < 10.3875] w=0.0831 to align # Constraint # added constraint: constraint((T0307)L115.CB, (T0307)A126.CB) [> 3.3038 = 5.5064 < 7.1583] w=0.0823 to align # Constraint # added constraint: constraint((T0307)I101.CB, (T0307)M130.CB) [> 4.6813 = 7.8022 < 10.1429] w=0.0820 to align # Constraint # added constraint: constraint((T0307)A77.CB, (T0307)V87.CB) [> 3.6327 = 6.0545 < 7.8708] w=0.0817 to align # Constraint # added constraint: constraint((T0307)I21.CB, (T0307)L61.CB) [> 3.2545 = 5.4242 < 7.0514] w=0.0813 to align # Constraint # added constraint: constraint((T0307)L18.CB, (T0307)L61.CB) [> 3.9645 = 6.6076 < 8.5898] w=0.0813 to align # Constraint # added constraint: constraint((T0307)G92.CA, (T0307)L108.CB) [> 4.7785 = 7.9642 < 10.3534] w=0.0791 to align # Constraint # added constraint: constraint((T0307)S7.CB, (T0307)M48.CB) [> 3.6179 = 6.0298 < 7.8387] w=0.0781 to align # Constraint # added constraint: constraint((T0307)L8.CB, (T0307)V42.CB) [> 4.1284 = 6.8807 < 8.9449] w=0.0781 to align # Constraint # added constraint: constraint((T0307)L8.CB, (T0307)M43.CB) [> 3.2675 = 5.4458 < 7.0795] w=0.0781 to align # Constraint # added constraint: constraint((T0307)L8.CB, (T0307)M48.CB) [> 3.6707 = 6.1178 < 7.9531] w=0.0781 to align # Constraint # added constraint: constraint((T0307)L8.CB, (T0307)L60.CB) [> 4.5409 = 7.5681 < 9.8386] w=0.0781 to align # Constraint # added constraint: constraint((T0307)N9.CB, (T0307)I35.CB) [> 3.4911 = 5.8184 < 7.5640] w=0.0781 to align # Constraint # added constraint: constraint((T0307)S7.CB, (T0307)V42.CB) [> 3.3416 = 5.5694 < 7.2402] w=0.0781 to align # Constraint # added constraint: constraint((T0307)Q6.CB, (T0307)F50.CB) [> 3.6716 = 6.1194 < 7.9552] w=0.0781 to align # Constraint # added constraint: constraint((T0307)Q6.CB, (T0307)T44.CB) [> 4.4438 = 7.4064 < 9.6283] w=0.0781 to align # Constraint # added constraint: constraint((T0307)R5.CB, (T0307)F50.CB) [> 4.2123 = 7.0205 < 9.1266] w=0.0781 to align # Constraint # added constraint: constraint((T0307)R5.CB, (T0307)M48.CB) [> 4.4449 = 7.4082 < 9.6306] w=0.0781 to align # Constraint # added constraint: constraint((T0307)I10.CB, (T0307)L60.CB) [> 4.3225 = 7.2041 < 9.3654] w=0.0781 to align # Constraint # added constraint: constraint((T0307)I10.CB, (T0307)M43.CB) [> 4.1258 = 6.8762 < 8.9391] w=0.0781 to align # Constraint # added constraint: constraint((T0307)I10.CB, (T0307)V42.CB) [> 4.5396 = 7.5660 < 9.8358] w=0.0781 to align # Constraint # added constraint: constraint((T0307)I10.CB, (T0307)A41.CB) [> 2.7377 = 4.5629 < 5.9317] w=0.0781 to align # Constraint # added constraint: constraint((T0307)I10.CB, (T0307)I40.CB) [> 4.2057 = 7.0095 < 9.1123] w=0.0781 to align # Constraint # added constraint: constraint((T0307)F13.CB, (T0307)A74.CB) [> 3.9087 = 6.5145 < 8.4688] w=0.0781 to align # Constraint # added constraint: constraint((T0307)R45.CB, (T0307)G92.CA) [> 3.7801 = 6.3002 < 8.1902] w=0.0773 to align # Constraint # added constraint: constraint((T0307)Y90.CB, (T0307)C116.CB) [> 3.5164 = 5.8607 < 7.6189] w=0.0773 to align # Constraint # added constraint: constraint((T0307)L91.CB, (T0307)L115.CB) [> 4.6935 = 7.8224 < 10.1692] w=0.0773 to align # Constraint # added constraint: constraint((T0307)L91.CB, (T0307)C116.CB) [> 4.3667 = 7.2779 < 9.4613] w=0.0773 to align # Constraint # added constraint: constraint((T0307)I94.CB, (T0307)C116.CB) [> 3.5081 = 5.8468 < 7.6009] w=0.0773 to align # Constraint # added constraint: constraint((T0307)M24.CB, (T0307)I35.CB) [> 4.4889 = 7.4815 < 9.7259] w=0.0755 to align # Constraint # added constraint: constraint((T0307)A96.CB, (T0307)L108.CB) [> 3.6778 = 6.1296 < 7.9685] w=0.0751 to align # Constraint # added constraint: constraint((T0307)V29.CB, (T0307)I67.CB) [> 4.7716 = 7.9527 < 10.3385] w=0.0748 to align # Constraint # added constraint: constraint((T0307)E17.CB, (T0307)G92.CA) [> 4.7395 = 7.8992 < 10.2690] w=0.0703 to align # Constraint # added constraint: constraint((T0307)L18.CB, (T0307)A88.CB) [> 3.0376 = 5.0627 < 6.5814] w=0.0703 to align # Constraint # added constraint: constraint((T0307)A20.CB, (T0307)A88.CB) [> 3.9651 = 6.6085 < 8.5910] w=0.0703 to align # Constraint # added constraint: constraint((T0307)A20.CB, (T0307)L91.CB) [> 3.2564 = 5.4274 < 7.0556] w=0.0703 to align # Constraint # added constraint: constraint((T0307)M24.CB, (T0307)I94.CB) [> 4.3902 = 7.3170 < 9.5120] w=0.0703 to align # Constraint # added constraint: constraint((T0307)S27.CB, (T0307)S97.CB) [> 3.7950 = 6.3250 < 8.2226] w=0.0703 to align # Constraint # added constraint: constraint((T0307)F13.CB, (T0307)L59.CB) [> 4.2414 = 7.0690 < 9.1896] w=0.0654 to align # Constraint # added constraint: constraint((T0307)W109.CB, (T0307)V123.CB) [> 3.3608 = 5.6013 < 7.2818] w=0.0484 to align # Constraint # added constraint: constraint((T0307)P37.CB, (T0307)G92.CA) [> 3.9808 = 6.6346 < 8.6250] w=0.0423 to align # Constraint # added constraint: constraint((T0307)S7.CB, (T0307)A38.CB) [> 4.3239 = 7.2065 < 9.3685] w=0.0423 to align # Constraint # added constraint: constraint((T0307)L8.CB, (T0307)I35.CB) [> 3.3820 = 5.6367 < 7.3277] w=0.0423 to align # Constraint # added constraint: constraint((T0307)S14.CB, (T0307)K62.CB) [> 4.5876 = 7.6460 < 9.9398] w=0.0423 to align # Constraint # added constraint: constraint((T0307)L111.CB, (T0307)M124.CB) [> 3.9189 = 6.5316 < 8.4910] w=0.0420 to align # Constraint # added constraint: constraint((T0307)A74.CB, (T0307)C116.CB) [> 3.5634 = 5.9389 < 7.7206] w=0.0417 to align # Constraint # added constraint: constraint((T0307)L91.CB, (T0307)I112.CB) [> 3.3942 = 5.6571 < 7.3542] w=0.0417 to align # Constraint # added constraint: constraint((T0307)M28.CB, (T0307)A38.CB) [> 4.5960 = 7.6600 < 9.9580] w=0.0415 to align # Constraint # added constraint: constraint((T0307)A38.CB, (T0307)L53.CB) [> 4.6246 = 7.7077 < 10.0201] w=0.0415 to align # Constraint # added constraint: constraint((T0307)A20.CB, (T0307)V87.CB) [> 3.8123 = 6.3538 < 8.2600] w=0.0400 to align # Constraint # added constraint: constraint((T0307)I52.CB, (T0307)S97.CB) [> 4.4149 = 7.3582 < 9.5656] w=0.0400 to align # Constraint # added constraint: constraint((T0307)L53.CB, (T0307)D98.CB) [> 4.4776 = 7.4626 < 9.7014] w=0.0400 to align # Constraint # added constraint: constraint((T0307)V93.CB, (T0307)L115.CB) [> 4.6133 = 7.6888 < 9.9954] w=0.0400 to align # Constraint # added constraint: constraint((T0307)I94.CB, (T0307)L115.CB) [> 4.6332 = 7.7221 < 10.0387] w=0.0400 to align # Constraint # added constraint: constraint((T0307)A38.CB, (T0307)L59.CB) [> 3.4698 = 5.7829 < 7.5178] w=0.0400 to align # Constraint # added constraint: constraint((T0307)E46.CB, (T0307)A96.CB) [> 3.9476 = 6.5794 < 8.5532] w=0.0400 to align # Constraint # added constraint: constraint((T0307)V57.CB, (T0307)M130.CB) [> 3.8010 = 6.3349 < 8.2354] w=0.0400 to align # Constraint # added constraint: constraint((T0307)M43.CB, (T0307)V93.CB) [> 4.0262 = 6.7103 < 8.7234] w=0.0400 to align # Constraint # added constraint: constraint((T0307)M11.CB, (T0307)A74.CB) [> 4.1320 = 6.8867 < 8.9527] w=0.0391 to align # Constraint # added constraint: constraint((T0307)M11.CB, (T0307)A41.CB) [> 4.6757 = 7.7929 < 10.1308] w=0.0391 to align # Constraint # added constraint: constraint((T0307)M11.CB, (T0307)I40.CB) [> 4.2579 = 7.0965 < 9.2254] w=0.0391 to align # Constraint # added constraint: constraint((T0307)S14.CB, (T0307)A41.CB) [> 4.3344 = 7.2241 < 9.3913] w=0.0391 to align # Constraint # added constraint: constraint((T0307)K62.CB, (T0307)V93.CB) [> 4.3035 = 7.1725 < 9.3242] w=0.0391 to align # Constraint # added constraint: constraint((T0307)L18.CB, (T0307)A74.CB) [> 2.9094 = 4.8490 < 6.3038] w=0.0379 to align # Constraint # added constraint: constraint((T0307)W109.CB, (T0307)I127.CB) [> 3.0681 = 5.1136 < 6.6476] w=0.0374 to align # Constraint # added constraint: constraint((T0307)F50.CB, (T0307)T120.CB) [> 4.5202 = 7.5337 < 9.7938] w=0.0357 to align # Constraint # added constraint: constraint((T0307)V93.CB, (T0307)S113.CB) [> 3.4607 = 5.7679 < 7.4983] w=0.0351 to align # Constraint # added constraint: constraint((T0307)I35.CB, (T0307)A74.CB) [> 3.9662 = 6.6102 < 8.5933] w=0.0327 to align # Constraint # added constraint: constraint((T0307)Y86.CB, (T0307)A126.CB) [> 4.5882 = 7.6470 < 9.9411] w=0.0327 to align # Constraint # added constraint: constraint((T0307)M30.CB, (T0307)G92.CA) [> 4.3677 = 7.2795 < 9.4634] w=0.0098 to align # Constraint # added constraint: constraint((T0307)V29.CB, (T0307)S70.CB) [> 4.4281 = 7.3801 < 9.5942] w=0.0098 to align # Constraint # added constraint: constraint((T0307)V29.CB, (T0307)A74.CB) [> 3.6731 = 6.1218 < 7.9584] w=0.0098 to align # Constraint # added constraint: constraint((T0307)C116.CB, (T0307)E125.CB) [> 3.9659 = 6.6098 < 8.5927] w=0.0098 to align # Constraint # added constraint: constraint((T0307)M79.CB, (T0307)M130.CB) [> 3.9771 = 6.6285 < 8.6170] w=0.0093 to align # Constraint # added constraint: constraint((T0307)I52.CB, (T0307)I94.CB) [> 4.1192 = 6.8653 < 8.9249] w=0.0047 to align # SetCost created cost = # ( 1.0000 * align ) # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0307/ # command:# reading script from file servers-clean.under # Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0307/decoys/ # ReadConformPDB reading from PDB file edit2.pdb.gz looking for model 1 # Found a chain break before 129 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file edit3.pdb.gz looking for model 1 # Found a chain break before 129 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file edit9.pdb.gz looking for model 1 # Found a chain break before 129 # copying to AlignedFragments data structure # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS2 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS3 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS4 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_POPULUS_TS5 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_RECOM_TS1 # ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation 3D-JIGSAW_TS1 # ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1 # Found a chain break before 119 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS1 # ReadConformPDB reading from PDB file servers/3Dpro_TS2.pdb.gz looking for model 1 # Found a chain break before 85 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS2 # ReadConformPDB reading from PDB file servers/3Dpro_TS3.pdb.gz looking for model 1 # Found a chain break before 40 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS3 # ReadConformPDB reading from PDB file servers/3Dpro_TS4.pdb.gz looking for model 1 # Found a chain break before 87 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS4 # ReadConformPDB reading from PDB file servers/3Dpro_TS5.pdb.gz looking for model 1 # Found a chain break before 82 # copying to AlignedFragments data structure # naming current conformation 3Dpro_TS5 # ReadConformPDB reading from PDB file servers/ABIpro_TS1.pdb.gz looking for model 1 # Found a chain break before 87 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS1 # ReadConformPDB reading from PDB file servers/ABIpro_TS2.pdb.gz looking for model 1 # Found a chain break before 82 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS2 # ReadConformPDB reading from PDB file servers/ABIpro_TS3.pdb.gz looking for model 1 # Found a chain break before 129 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS3 # ReadConformPDB reading from PDB file servers/ABIpro_TS4.pdb.gz looking for model 1 # Found a chain break before 86 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS4 # ReadConformPDB reading from PDB file servers/ABIpro_TS5.pdb.gz looking for model 1 # Found a chain break before 113 # copying to AlignedFragments data structure # naming current conformation ABIpro_TS5 # ReadConformPDB reading from PDB file servers/BayesHH_TS1.pdb.gz looking for model 1 # naming current conformation BayesHH_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS1.pdb.gz looking for model 1 # Found a chain break before 132 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS1 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS2.pdb.gz looking for model 1 # naming current conformation Bilab-ENABLE_TS2 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS3.pdb.gz looking for model 1 # Found a chain break before 132 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS3 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS4.pdb.gz looking for model 1 # naming current conformation Bilab-ENABLE_TS4 # ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS5.pdb.gz looking for model 1 # Found a chain break before 132 # copying to AlignedFragments data structure # naming current conformation Bilab-ENABLE_TS5 # ReadConformPDB reading from PDB file servers/CIRCLE_TS1.pdb.gz looking for model 1 # Found a chain break before 122 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS1 # ReadConformPDB reading from PDB file servers/CIRCLE_TS2.pdb.gz looking for model 1 # Found a chain break before 122 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS2 # ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1 # Found a chain break before 128 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS3 # ReadConformPDB reading from PDB file servers/CIRCLE_TS4.pdb.gz looking for model 1 # Found a chain break before 130 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS4 # ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1 # Found a chain break before 119 # copying to AlignedFragments data structure # naming current conformation CIRCLE_TS5 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1 # Found a chain break before 119 # copying to AlignedFragments data structure # naming current conformation CaspIta-FOX_TS1 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS2 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS3 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS4 # ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS5.pdb.gz looking for model 1 WARNING: atoms too close: (T0307)V93.C and (T0307)I94.N only 0.000 apart, marking (T0307)I94.N as missing WARNING: atoms too close: (T0307)I94.N and (T0307)I94.CA only 0.000 apart, marking (T0307)I94.CA as missing WARNING: atoms too close: (T0307)V93.C and (T0307)I94.CA only 0.000 apart, marking (T0307)I94.CA as missing WARNING: atoms too close: (T0307)I94.CA and (T0307)I94.CB only 0.000 apart, marking (T0307)I94.CB as missing WARNING: atoms too close: (T0307)I94.N and (T0307)I94.CB only 0.000 apart, marking (T0307)I94.CB as missing WARNING: atoms too close: (T0307)V93.C and (T0307)I94.CB only 0.000 apart, marking (T0307)I94.CB as missing WARNING: atoms too close: (T0307)I94.CB and (T0307)I94.CG1 only 0.000 apart, marking (T0307)I94.CG1 as missing WARNING: atoms too close: (T0307)I94.CA and (T0307)I94.CG1 only 0.000 apart, marking (T0307)I94.CG1 as missing WARNING: atoms too close: (T0307)I94.N and (T0307)I94.CG1 only 0.000 apart, marking (T0307)I94.CG1 as missing WARNING: atoms too close: (T0307)V93.C and (T0307)I94.CG1 only 0.000 apart, marking (T0307)I94.CG1 as missing WARNING: atoms too close: (T0307)I94.CG1 and (T0307)I94.CG2 only 0.000 apart, marking (T0307)I94.CG2 as missing WARNING: atoms too close: (T0307)I94.CB and (T0307)I94.CG2 only 0.000 apart, marking (T0307)I94.CG2 as missing WARNING: atoms too close: (T0307)I94.CA and (T0307)I94.CG2 only 0.000 apart, marking (T0307)I94.CG2 as missing WARNING: atoms too close: (T0307)I94.N and (T0307)I94.CG2 only 0.000 apart, marking (T0307)I94.CG2 as missing WARNING: atoms too close: (T0307)V93.C and (T0307)I94.CG2 only 0.000 apart, marking (T0307)I94.CG2 as missing WARNING: atoms too close: (T0307)I94.CG2 and (T0307)I94.CD1 only 0.000 apart, marking (T0307)I94.CD1 as missing WARNING: atoms too close: (T0307)I94.CG1 and (T0307)I94.CD1 only 0.000 apart, marking (T0307)I94.CD1 as missing WARNING: atoms too close: (T0307)I94.CB and (T0307)I94.CD1 only 0.000 apart, marking (T0307)I94.CD1 as missing WARNING: atoms too close: (T0307)I94.CA and (T0307)I94.CD1 only 0.000 apart, marking (T0307)I94.CD1 as missing WARNING: atoms too close: (T0307)I94.N and (T0307)I94.CD1 only 0.000 apart, marking (T0307)I94.CD1 as missing WARNING: atoms too close: (T0307)V93.C and (T0307)I94.CD1 only 0.000 apart, marking (T0307)I94.CD1 as missing WARNING: atoms too close: (T0307)I94.CD1 and (T0307)I94.O only 0.000 apart, marking (T0307)I94.O as missing WARNING: atoms too close: (T0307)I94.CG2 and (T0307)I94.O only 0.000 apart, marking (T0307)I94.O as missing WARNING: atoms too close: (T0307)I94.CG1 and (T0307)I94.O only 0.000 apart, marking (T0307)I94.O as missing WARNING: atoms too close: (T0307)I94.CB and (T0307)I94.O only 0.000 apart, marking (T0307)I94.O as missing WARNING: atoms too close: (T0307)I94.CA and (T0307)I94.O only 0.000 apart, marking (T0307)I94.O as missing WARNING: atoms too close: (T0307)I94.N and (T0307)I94.O only 0.000 apart, marking (T0307)I94.O as missing WARNING: atoms too close: (T0307)V93.C and (T0307)I94.O only 0.000 apart, marking (T0307)I94.O as missing WARNING: atoms too close: (T0307)I94.O and (T0307)I94.C only 0.000 apart, marking (T0307)I94.C as missing WARNING: atoms too close: (T0307)I94.CD1 and (T0307)I94.C only 0.000 apart, marking (T0307)I94.C as missing WARNING: atoms too close: (T0307)I94.CG2 and (T0307)I94.C only 0.000 apart, marking (T0307)I94.C as missing WARNING: atoms too close: (T0307)I94.CG1 and (T0307)I94.C only 0.000 apart, marking (T0307)I94.C as missing WARNING: atoms too close: (T0307)I94.CB and (T0307)I94.C only 0.000 apart, marking (T0307)I94.C as missing WARNING: atoms too close: (T0307)I94.CA and (T0307)I94.C only 0.000 apart, marking (T0307)I94.C as missing WARNING: atoms too close: (T0307)I94.N and (T0307)I94.C only 0.000 apart, marking (T0307)I94.C as missing WARNING: atoms too close: (T0307)V93.C and (T0307)I94.C only 0.000 apart, marking (T0307)I94.C as missing WARNING: atoms too close: (T0307)I94.C and (T0307)M95.N only 0.000 apart, marking (T0307)I94.C as missing WARNING: atoms too close: (T0307)I94.O and (T0307)M95.N only 0.000 apart, marking (T0307)I94.O as missing WARNING: atoms too close: (T0307)I94.CD1 and (T0307)M95.N only 0.000 apart, marking (T0307)I94.CD1 as missing WARNING: atoms too close: (T0307)I94.CG2 and (T0307)M95.N only 0.000 apart, marking (T0307)I94.CG2 as missing WARNING: atoms too close: (T0307)I94.CG1 and (T0307)M95.N only 0.000 apart, marking (T0307)I94.CG1 as missing WARNING: atoms too close: (T0307)I94.CB and (T0307)M95.N only 0.000 apart, marking (T0307)I94.CB as missing WARNING: atoms too close: (T0307)I94.CA and (T0307)M95.N only 0.000 apart, marking (T0307)I94.CA as missing WARNING: atoms too close: (T0307)I94.N and (T0307)M95.N only 0.000 apart, marking (T0307)I94.N as missing WARNING: atoms too close: (T0307)V93.C and (T0307)M95.N only 0.000 apart, marking (T0307)M95.N as missing WARNING: atoms too close: (T0307)M95.N and (T0307)M95.CA only 0.000 apart, marking (T0307)M95.CA as missing WARNING: atoms too close: (T0307)I94.C and (T0307)M95.CA only 0.000 apart, marking (T0307)M95.CA as missing WARNING: atoms too close: (T0307)I94.O and (T0307)M95.CA only 0.000 apart, marking (T0307)M95.CA as missing WARNING: atoms too close: (T0307)I94.CD1 and (T0307)M95.CA only 0.000 apart, marking (T0307)M95.CA as missing WARNING: atoms too close: (T0307)I94.CG2 and (T0307)M95.CA only 0.000 apart, marking (T0307)M95.CA as missing WARNING: atoms too close: (T0307)I94.CG1 and (T0307)M95.CA only 0.000 apart, marking (T0307)M95.CA as missing WARNING: atoms too close: (T0307)I94.CB and (T0307)M95.CA only 0.000 apart, marking (T0307)M95.CA as missing WARNING: atoms too close: (T0307)I94.CA and (T0307)M95.CA only 0.000 apart, marking (T0307)M95.CA as missing WARNING: atoms too close: (T0307)I94.N and (T0307)M95.CA only 0.000 apart, marking (T0307)M95.CA as missing WARNING: atoms too close: (T0307)V93.C and (T0307)M95.CA only 0.000 apart, marking (T0307)M95.CA as missing WARNING: atoms too close: (T0307)M95.CA and (T0307)M95.CB only 0.000 apart, marking (T0307)M95.CB as missing WARNING: atoms too close: (T0307)M95.N and (T0307)M95.CB only 0.000 apart, marking (T0307)M95.CB as missing WARNING: atoms too close: (T0307)I94.C and (T0307)M95.CB only 0.000 apart, marking (T0307)M95.CB as missing WARNING: atoms too close: (T0307)I94.O and (T0307)M95.CB only 0.000 apart, marking (T0307)M95.CB as missing WARNING: atoms too close: (T0307)I94.CD1 and (T0307)M95.CB only 0.000 apart, marking (T0307)M95.CB as missing WARNING: atoms too close: (T0307)I94.CG2 and (T0307)M95.CB only 0.000 apart, marking (T0307)M95.CB as missing WARNING: atoms too close: (T0307)I94.CG1 and (T0307)M95.CB only 0.000 apart, marking (T0307)M95.CB as missing WARNING: atoms too close: (T0307)I94.CB and (T0307)M95.CB only 0.000 apart, marking (T0307)M95.CB as missing WARNING: atoms too close: (T0307)I94.CA and (T0307)M95.CB only 0.000 apart, marking (T0307)M95.CB as missing WARNING: atoms too close: (T0307)I94.N and (T0307)M95.CB only 0.000 apart, marking (T0307)M95.CB as missing WARNING: atoms too close: (T0307)V93.C and (T0307)M95.CB only 0.000 apart, marking (T0307)M95.CB as missing WARNING: atoms too close: (T0307)M95.CB and (T0307)M95.CG only 0.000 apart, marking (T0307)M95.CG as missing WARNING: atoms too close: (T0307)M95.CA and (T0307)M95.CG only 0.000 apart, marking (T0307)M95.CG as missing WARNING: atoms too close: (T0307)M95.N and (T0307)M95.CG only 0.000 apart, marking (T0307)M95.CG as missing WARNING: atoms too close: (T0307)I94.C and (T0307)M95.CG only 0.000 apart, marking (T0307)M95.CG as missing WARNING: atoms too close: (T0307)I94.O and (T0307)M95.CG only 0.000 apart, marking (T0307)M95.CG as missing WARNING: atoms too close: (T0307)I94.CD1 and (T0307)M95.CG only 0.000 apart, marking (T0307)M95.CG as missing WARNING: atoms too close: (T0307)I94.CG2 and (T0307)M95.CG only 0.000 apart, marking (T0307)M95.CG as missing WARNING: atoms too close: (T0307)I94.CG1 and (T0307)M95.CG only 0.000 apart, marking (T0307)M95.CG as missing WARNING: atoms too close: (T0307)I94.CB and (T0307)M95.CG only 0.000 apart, marking (T0307)M95.CG as missing WARNING: atoms too close: (T0307)I94.CA and (T0307)M95.CG only 0.000 apart, marking (T0307)M95.CG as missing WARNING: atoms too close: (T0307)I94.N and (T0307)M95.CG only 0.000 apart, marking (T0307)M95.CG as missing WARNING: atoms too close: (T0307)V93.C and (T0307)M95.CG only 0.000 apart, marking (T0307)M95.CG as missing WARNING: atoms too close: (T0307)M95.CG and (T0307)M95.SD only 0.000 apart, marking (T0307)M95.SD as missing WARNING: atoms too close: (T0307)M95.CB and (T0307)M95.SD only 0.000 apart, marking (T0307)M95.SD as missing WARNING: atoms too close: (T0307)M95.CA and (T0307)M95.SD only 0.000 apart, marking (T0307)M95.SD as missing WARNING: atoms too close: (T0307)M95.N and (T0307)M95.SD only 0.000 apart, marking (T0307)M95.SD as missing WARNING: atoms too close: (T0307)I94.C and (T0307)M95.SD only 0.000 apart, marking (T0307)M95.SD as missing WARNING: atoms too close: (T0307)I94.O and (T0307)M95.SD only 0.000 apart, marking (T0307)M95.SD as missing WARNING: atoms too close: (T0307)I94.CD1 and (T0307)M95.SD only 0.000 apart, marking (T0307)M95.SD as missing WARNING: atoms too close: (T0307)I94.CG2 and (T0307)M95.SD only 0.000 apart, marking (T0307)M95.SD as missing WARNING: atoms too close: (T0307)I94.CG1 and (T0307)M95.SD only 0.000 apart, marking (T0307)M95.SD as missing WARNING: atoms too close: (T0307)I94.CB and (T0307)M95.SD only 0.000 apart, marking (T0307)M95.SD as missing WARNING: atoms too close: (T0307)I94.CA and (T0307)M95.SD only 0.000 apart, marking (T0307)M95.SD as missing WARNING: atoms too close: (T0307)I94.N and (T0307)M95.SD only 0.000 apart, marking (T0307)M95.SD as missing WARNING: atoms too close: (T0307)V93.C and (T0307)M95.SD only 0.000 apart, marking (T0307)M95.SD as missing WARNING: atoms too close: (T0307)M95.SD and (T0307)M95.CE only 0.000 apart, marking (T0307)M95.CE as missing WARNING: atoms too close: (T0307)M95.CG and (T0307)M95.CE only 0.000 apart, marking (T0307)M95.CE as missing WARNING: atoms too close: (T0307)M95.CB and (T0307)M95.CE only 0.000 apart, marking (T0307)M95.CE as missing WARNING: atoms too close: (T0307)M95.CA and (T0307)M95.CE only 0.000 apart, marking (T0307)M95.CE as missing WARNING: atoms too close: (T0307)M95.N and (T0307)M95.CE only 0.000 apart, marking (T0307)M95.CE as missing WARNING: atoms too close: (T0307)I94.C and (T0307)M95.CE only 0.000 apart, marking (T0307)M95.CE as missing WARNING: atoms too close: (T0307)I94.O and (T0307)M95.CE only 0.000 apart, marking (T0307)M95.CE as missing WARNING: atoms too close: (T0307)I94.CD1 and (T0307)M95.CE only 0.000 apart, marking (T0307)M95.CE as missing WARNING: atoms too close: (T0307)I94.CG2 and (T0307)M95.CE only 0.000 apart, marking (T0307)M95.CE as missing WARNING: atoms too close: (T0307)I94.CG1 and (T0307)M95.CE only 0.000 apart, marking (T0307)M95.CE as missing WARNING: atoms too close: (T0307)I94.CB and (T0307)M95.CE only 0.000 apart, marking (T0307)M95.CE as missing WARNING: atoms too close: (T0307)I94.CA and (T0307)M95.CE only 0.000 apart, marking (T0307)M95.CE as missing WARNING: atoms too close: (T0307)I94.N and (T0307)M95.CE only 0.000 apart, marking (T0307)M95.CE as missing WARNING: atoms too close: (T0307)V93.C and (T0307)M95.CE only 0.000 apart, marking (T0307)M95.CE as missing WARNING: atoms too close: (T0307)M95.CE and (T0307)M95.O only 0.000 apart, marking (T0307)M95.O as missing WARNING: atoms too close: (T0307)M95.SD and (T0307)M95.O only 0.000 apart, marking (T0307)M95.O as missing WARNING: atoms too close: (T0307)M95.CG and (T0307)M95.O only 0.000 apart, marking (T0307)M95.O as missing WARNING: atoms too close: (T0307)M95.CB and (T0307)M95.O only 0.000 apart, marking (T0307)M95.O as missing WARNING: atoms too close: (T0307)M95.CA and (T0307)M95.O only 0.000 apart, marking (T0307)M95.O as missing WARNING: atoms too close: (T0307)M95.N and (T0307)M95.O only 0.000 apart, marking (T0307)M95.O as missing WARNING: atoms too close: (T0307)I94.C and (T0307)M95.O only 0.000 apart, marking (T0307)M95.O as missing WARNING: atoms too close: (T0307)I94.O and (T0307)M95.O only 0.000 apart, marking (T0307)M95.O as missing WARNING: atoms too close: (T0307)I94.CD1 and (T0307)M95.O only 0.000 apart, marking (T0307)M95.O as missing WARNING: atoms too close: (T0307)I94.CG2 and (T0307)M95.O only 0.000 apart, marking (T0307)M95.O as missing WARNING: atoms too close: (T0307)I94.CG1 and (T0307)M95.O only 0.000 apart, marking (T0307)M95.O as missing WARNING: atoms too close: (T0307)I94.CB and (T0307)M95.O only 0.000 apart, marking (T0307)M95.O as missing WARNING: atoms too close: (T0307)I94.CA and (T0307)M95.O only 0.000 apart, marking (T0307)M95.O as missing WARNING: atoms too close: (T0307)I94.N and (T0307)M95.O only 0.000 apart, marking (T0307)M95.O as missing WARNING: atoms too close: (T0307)V93.C and (T0307)M95.O only 0.000 apart, marking (T0307)M95.O as missing WARNING: atoms too close: (T0307)M95.O and (T0307)M95.C only 0.000 apart, marking (T0307)M95.C as missing WARNING: atoms too close: (T0307)M95.CE and (T0307)M95.C only 0.000 apart, marking (T0307)M95.C as missing WARNING: atoms too close: (T0307)M95.SD and (T0307)M95.C only 0.000 apart, marking (T0307)M95.C as missing WARNING: atoms too close: (T0307)M95.CG and (T0307)M95.C only 0.000 apart, marking (T0307)M95.C as missing WARNING: atoms too close: (T0307)M95.CB and (T0307)M95.C only 0.000 apart, marking (T0307)M95.C as missing WARNING: atoms too close: (T0307)M95.CA and (T0307)M95.C only 0.000 apart, marking (T0307)M95.C as missing WARNING: atoms too close: (T0307)M95.N and (T0307)M95.C only 0.000 apart, marking (T0307)M95.C as missing WARNING: atoms too close: (T0307)I94.C and (T0307)M95.C only 0.000 apart, marking (T0307)M95.C as missing WARNING: atoms too close: (T0307)I94.O and (T0307)M95.C only 0.000 apart, marking (T0307)M95.C as missing WARNING: atoms too close: (T0307)I94.CD1 and (T0307)M95.C only 0.000 apart, marking (T0307)M95.C as missing WARNING: atoms too close: (T0307)I94.CG2 and (T0307)M95.C only 0.000 apart, marking (T0307)M95.C as missing WARNING: atoms too close: (T0307)I94.CG1 and (T0307)M95.C only 0.000 apart, marking (T0307)M95.C as missing WARNING: atoms too close: (T0307)I94.CB and (T0307)M95.C only 0.000 apart, marking (T0307)M95.C as missing WARNING: atoms too close: (T0307)I94.CA and (T0307)M95.C only 0.000 apart, marking (T0307)M95.C as missing WARNING: atoms too close: (T0307)I94.N and (T0307)M95.C only 0.000 apart, marking (T0307)M95.C as missing WARNING: atoms too close: (T0307)V93.C and (T0307)M95.C only 0.000 apart, marking (T0307)M95.C as missing WARNING: atoms too close: (T0307)M95.C and (T0307)A96.N only 0.000 apart, marking (T0307)M95.C as missing WARNING: atoms too close: (T0307)M95.O and (T0307)A96.N only 0.000 apart, marking (T0307)M95.O as missing WARNING: atoms too close: (T0307)M95.CE and (T0307)A96.N only 0.000 apart, marking (T0307)M95.CE as missing WARNING: atoms too close: (T0307)M95.SD and (T0307)A96.N only 0.000 apart, marking (T0307)M95.SD as missing WARNING: atoms too close: (T0307)M95.CG and (T0307)A96.N only 0.000 apart, marking (T0307)M95.CG as missing WARNING: atoms too close: (T0307)M95.CB and (T0307)A96.N only 0.000 apart, marking (T0307)M95.CB as missing WARNING: atoms too close: (T0307)M95.CA and (T0307)A96.N only 0.000 apart, marking (T0307)M95.CA as missing WARNING: atoms too close: (T0307)M95.N and (T0307)A96.N only 0.000 apart, marking (T0307)M95.N as missing WARNING: atoms too close: (T0307)I94.C and (T0307)A96.N only 0.000 apart, marking (T0307)I94.C as missing WARNING: atoms too close: (T0307)I94.O and (T0307)A96.N only 0.000 apart, marking (T0307)I94.O as missing WARNING: atoms too close: (T0307)I94.CD1 and (T0307)A96.N only 0.000 apart, marking (T0307)I94.CD1 as missing WARNING: atoms too close: (T0307)I94.CG2 and (T0307)A96.N only 0.000 apart, marking (T0307)I94.CG2 as missing WARNING: atoms too close: (T0307)I94.CG1 and (T0307)A96.N only 0.000 apart, marking (T0307)I94.CG1 as missing WARNING: atoms too close: (T0307)I94.CB and (T0307)A96.N only 0.000 apart, marking (T0307)I94.CB as missing WARNING: atoms too close: (T0307)I94.CA and (T0307)A96.N only 0.000 apart, marking (T0307)I94.CA as missing WARNING: atoms too close: (T0307)I94.N and (T0307)A96.N only 0.000 apart, marking (T0307)I94.N as missing WARNING: atoms too close: (T0307)V93.C and (T0307)A96.N only 0.000 apart, marking (T0307)A96.N as missing WARNING: atoms too close: (T0307)A96.N and (T0307)A96.CA only 0.000 apart, marking (T0307)A96.CA as missing WARNING: atoms too close: (T0307)M95.C and (T0307)A96.CA only 0.000 apart, marking (T0307)A96.CA as missing WARNING: atoms too close: (T0307)M95.O and (T0307)A96.CA only 0.000 apart, marking (T0307)A96.CA as missing WARNING: atoms too close: (T0307)M95.CE and (T0307)A96.CA only 0.000 apart, marking (T0307)A96.CA as missing WARNING: atoms too close: (T0307)M95.SD and (T0307)A96.CA only 0.000 apart, marking (T0307)A96.CA as missing WARNING: atoms too close: (T0307)M95.CG and (T0307)A96.CA only 0.000 apart, marking (T0307)A96.CA as missing WARNING: atoms too close: (T0307)M95.CB and (T0307)A96.CA only 0.000 apart, marking (T0307)A96.CA as missing WARNING: atoms too close: (T0307)M95.CA and (T0307)A96.CA only 0.000 apart, marking (T0307)A96.CA as missing WARNING: atoms too close: (T0307)M95.N and (T0307)A96.CA only 0.000 apart, marking (T0307)A96.CA as missing WARNING: atoms too close: (T0307)I94.C and (T0307)A96.CA only 0.000 apart, marking (T0307)A96.CA as missing WARNING: atoms too close: (T0307)I94.O and (T0307)A96.CA only 0.000 apart, marking (T0307)A96.CA as missing WARNING: atoms too close: (T0307)I94.CD1 and (T0307)A96.CA only 0.000 apart, marking (T0307)A96.CA as missing WARNING: atoms too close: (T0307)I94.CG2 and (T0307)A96.CA only 0.000 apart, marking (T0307)A96.CA as missing WARNING: atoms too close: (T0307)I94.CG1 and (T0307)A96.CA only 0.000 apart, marking (T0307)A96.CA as missing WARNING: atoms too close: (T0307)I94.CB and (T0307)A96.CA only 0.000 apart, marking (T0307)A96.CA as missing WARNING: atoms too close: (T0307)I94.CA and (T0307)A96.CA only 0.000 apart, marking (T0307)A96.CA as missing WARNING: atoms too close: (T0307)I94.N and (T0307)A96.CA only 0.000 apart, marking (T0307)A96.CA as missing WARNING: atoms too close: (T0307)V93.C and (T0307)A96.CA only 0.000 apart, marking (T0307)A96.CA as missing WARNING: atoms too close: (T0307)A96.CA and (T0307)A96.CB only 0.000 apart, marking (T0307)A96.CB as missing WARNING: atoms too close: (T0307)A96.N and (T0307)A96.CB only 0.000 apart, marking (T0307)A96.CB as missing WARNING: atoms too close: (T0307)M95.C and (T0307)A96.CB only 0.000 apart, marking (T0307)A96.CB as missing WARNING: atoms too close: (T0307)M95.O and (T0307)A96.CB only 0.000 apart, marking (T0307)A96.CB as missing WARNING: atoms too close: (T0307)M95.CE and (T0307)A96.CB only 0.000 apart, marking (T0307)A96.CB as missing WARNING: atoms too close: (T0307)M95.SD and (T0307)A96.CB only 0.000 apart, marking (T0307)A96.CB as missing WARNING: atoms too close: (T0307)M95.CG and (T0307)A96.CB only 0.000 apart, marking (T0307)A96.CB as missing WARNING: atoms too close: (T0307)M95.CB and (T0307)A96.CB only 0.000 apart, marking (T0307)A96.CB as missing WARNING: atoms too close: (T0307)M95.CA and (T0307)A96.CB only 0.000 apart, marking (T0307)A96.CB as missing WARNING: atoms too close: (T0307)M95.N and (T0307)A96.CB only 0.000 apart, marking (T0307)A96.CB as missing WARNING: atoms too close: (T0307)I94.C and (T0307)A96.CB only 0.000 apart, marking (T0307)A96.CB as missing WARNING: atoms too close: (T0307)I94.O and (T0307)A96.CB only 0.000 apart, marking (T0307)A96.CB as missing WARNING: atoms too close: (T0307)I94.CD1 and (T0307)A96.CB only 0.000 apart, marking (T0307)A96.CB as missing WARNING: atoms too close: (T0307)I94.CG2 and (T0307)A96.CB only 0.000 apart, marking (T0307)A96.CB as missing WARNING: atoms too close: (T0307)I94.CG1 and (T0307)A96.CB only 0.000 apart, marking (T0307)A96.CB as missing WARNING: atoms too close: (T0307)I94.CB and (T0307)A96.CB only 0.000 apart, marking (T0307)A96.CB as missing WARNING: atoms too close: (T0307)I94.CA and (T0307)A96.CB only 0.000 apart, marking (T0307)A96.CB as missing WARNING: atoms too close: (T0307)I94.N and (T0307)A96.CB only 0.000 apart, marking (T0307)A96.CB as missing WARNING: atoms too close: (T0307)V93.C and (T0307)A96.CB only 0.000 apart, marking (T0307)A96.CB as missing WARNING: atoms too close: (T0307)A96.CB and (T0307)A96.O only 0.000 apart, marking (T0307)A96.O as missing WARNING: atoms too close: (T0307)A96.CA and (T0307)A96.O only 0.000 apart, marking (T0307)A96.O as missing WARNING: atoms too close: (T0307)A96.N and (T0307)A96.O only 0.000 apart, marking (T0307)A96.O as missing WARNING: atoms too close: (T0307)M95.C and (T0307)A96.O only 0.000 apart, marking (T0307)A96.O as missing WARNING: atoms too close: (T0307)M95.O and (T0307)A96.O only 0.000 apart, marking (T0307)A96.O as missing WARNING: atoms too close: (T0307)M95.CE and (T0307)A96.O only 0.000 apart, marking (T0307)A96.O as missing WARNING: atoms too close: (T0307)M95.SD and (T0307)A96.O only 0.000 apart, marking (T0307)A96.O as missing WARNING: atoms too close: (T0307)M95.CG and (T0307)A96.O only 0.000 apart, marking (T0307)A96.O as missing WARNING: atoms too close: (T0307)M95.CB and (T0307)A96.O only 0.000 apart, marking (T0307)A96.O as missing WARNING: atoms too close: (T0307)M95.CA and (T0307)A96.O only 0.000 apart, marking (T0307)A96.O as missing WARNING: atoms too close: (T0307)M95.N and (T0307)A96.O only 0.000 apart, marking (T0307)A96.O as missing WARNING: atoms too close: (T0307)I94.C and (T0307)A96.O only 0.000 apart, marking (T0307)A96.O as missing WARNING: atoms too close: (T0307)I94.O and (T0307)A96.O only 0.000 apart, marking (T0307)A96.O as missing WARNING: atoms too close: (T0307)I94.CD1 and (T0307)A96.O only 0.000 apart, marking (T0307)A96.O as missing WARNING: atoms too close: (T0307)I94.CG2 and (T0307)A96.O only 0.000 apart, marking (T0307)A96.O as missing WARNING: atoms too close: (T0307)I94.CG1 and (T0307)A96.O only 0.000 apart, marking (T0307)A96.O as missing WARNING: atoms too close: (T0307)I94.CB and (T0307)A96.O only 0.000 apart, marking (T0307)A96.O as missing WARNING: atoms too close: (T0307)I94.CA and (T0307)A96.O only 0.000 apart, marking (T0307)A96.O as missing WARNING: atoms too close: (T0307)I94.N and (T0307)A96.O only 0.000 apart, marking (T0307)A96.O as missing WARNING: atoms too close: (T0307)V93.C and (T0307)A96.O only 0.000 apart, marking (T0307)A96.O as missing WARNING: atoms too close: (T0307)A96.O and (T0307)A96.C only 0.000 apart, marking (T0307)A96.C as missing WARNING: atoms too close: (T0307)A96.CB and (T0307)A96.C only 0.000 apart, marking (T0307)A96.C as missing WARNING: atoms too close: (T0307)A96.CA and (T0307)A96.C only 0.000 apart, marking (T0307)A96.C as missing WARNING: atoms too close: (T0307)A96.N and (T0307)A96.C only 0.000 apart, marking (T0307)A96.C as missing WARNING: atoms too close: (T0307)M95.C and (T0307)A96.C only 0.000 apart, marking (T0307)A96.C as missing WARNING: atoms too close: (T0307)M95.O and (T0307)A96.C only 0.000 apart, marking (T0307)A96.C as missing WARNING: atoms too close: (T0307)M95.CE and (T0307)A96.C only 0.000 apart, marking (T0307)A96.C as missing WARNING: atoms too close: (T0307)M95.SD and (T0307)A96.C only 0.000 apart, marking (T0307)A96.C as missing WARNING: atoms too close: (T0307)M95.CG and (T0307)A96.C only 0.000 apart, marking (T0307)A96.C as missing WARNING: atoms too close: (T0307)M95.CB and (T0307)A96.C only 0.000 apart, marking (T0307)A96.C as missing WARNING: atoms too close: (T0307)M95.CA and (T0307)A96.C only 0.000 apart, marking (T0307)A96.C as missing WARNING: atoms too close: (T0307)M95.N and (T0307)A96.C only 0.000 apart, marking (T0307)A96.C as missing WARNING: atoms too close: (T0307)I94.C and (T0307)A96.C only 0.000 apart, marking (T0307)A96.C as missing WARNING: atoms too close: (T0307)I94.O and (T0307)A96.C only 0.000 apart, marking (T0307)A96.C as missing WARNING: atoms too close: (T0307)I94.CD1 and (T0307)A96.C only 0.000 apart, marking (T0307)A96.C as missing WARNING: atoms too close: (T0307)I94.CG2 and (T0307)A96.C only 0.000 apart, marking (T0307)A96.C as missing WARNING: atoms too close: (T0307)I94.CG1 and (T0307)A96.C only 0.000 apart, marking (T0307)A96.C as missing WARNING: atoms too close: (T0307)I94.CB and (T0307)A96.C only 0.000 apart, marking (T0307)A96.C as missing WARNING: atoms too close: (T0307)I94.CA and (T0307)A96.C only 0.000 apart, marking (T0307)A96.C as missing WARNING: atoms too close: (T0307)I94.N and (T0307)A96.C only 0.000 apart, marking (T0307)A96.C as missing WARNING: atoms too close: (T0307)V93.C and (T0307)A96.C only 0.000 apart, marking (T0307)A96.C as missing WARNING: atoms too close: (T0307)A96.C and (T0307)S97.N only 0.000 apart, marking (T0307)A96.C as missing WARNING: atoms too close: (T0307)A96.O and (T0307)S97.N only 0.000 apart, marking (T0307)A96.O as missing WARNING: atoms too close: (T0307)A96.CB and (T0307)S97.N only 0.000 apart, marking (T0307)A96.CB as missing WARNING: atoms too close: (T0307)A96.CA and (T0307)S97.N only 0.000 apart, marking (T0307)A96.CA as missing WARNING: atoms too close: (T0307)A96.N and (T0307)S97.N only 0.000 apart, marking (T0307)A96.N as missing WARNING: atoms too close: (T0307)M95.C and (T0307)S97.N only 0.000 apart, marking (T0307)M95.C as missing WARNING: atoms too close: (T0307)M95.O and (T0307)S97.N only 0.000 apart, marking (T0307)M95.O as missing WARNING: atoms too close: (T0307)M95.CE and (T0307)S97.N only 0.000 apart, marking (T0307)M95.CE as missing WARNING: atoms too close: (T0307)M95.SD and (T0307)S97.N only 0.000 apart, marking (T0307)M95.SD as missing WARNING: atoms too close: (T0307)M95.CG and (T0307)S97.N only 0.000 apart, marking (T0307)M95.CG as missing WARNING: atoms too close: (T0307)M95.CB and (T0307)S97.N only 0.000 apart, marking (T0307)M95.CB as missing WARNING: atoms too close: (T0307)M95.CA and (T0307)S97.N only 0.000 apart, marking (T0307)M95.CA as missing WARNING: atoms too close: (T0307)M95.N and (T0307)S97.N only 0.000 apart, marking (T0307)M95.N as missing WARNING: atoms too close: (T0307)I94.C and (T0307)S97.N only 0.000 apart, marking (T0307)I94.C as missing WARNING: atoms too close: (T0307)I94.O and (T0307)S97.N only 0.000 apart, marking (T0307)I94.O as missing WARNING: atoms too close: (T0307)I94.CD1 and (T0307)S97.N only 0.000 apart, marking (T0307)I94.CD1 as missing WARNING: atoms too close: (T0307)I94.CG2 and (T0307)S97.N only 0.000 apart, marking (T0307)I94.CG2 as missing WARNING: atoms too close: (T0307)I94.CG1 and (T0307)S97.N only 0.000 apart, marking (T0307)I94.CG1 as missing WARNING: atoms too close: (T0307)I94.CB and (T0307)S97.N only 0.000 apart, marking (T0307)I94.CB as missing WARNING: atoms too close: (T0307)I94.CA and (T0307)S97.N only 0.000 apart, marking (T0307)I94.CA as missing WARNING: atoms too close: (T0307)I94.N and (T0307)S97.N only 0.000 apart, marking (T0307)I94.N as missing WARNING: atoms too close: (T0307)V93.C and (T0307)S97.N only 0.000 apart, marking (T0307)S97.N as missing WARNING: atoms too close: (T0307)S97.N and (T0307)S97.CA only 0.000 apart, marking (T0307)S97.CA as missing WARNING: atoms too close: (T0307)A96.C and (T0307)S97.CA only 0.000 apart, marking (T0307)S97.CA as missing WARNING: atoms too close: (T0307)A96.O and (T0307)S97.CA only 0.000 apart, marking (T0307)S97.CA as missing WARNING: atoms too close: (T0307)A96.CB and (T0307)S97.CA only 0.000 apart, marking (T0307)S97.CA as missing WARNING: atoms too close: (T0307)A96.CA and (T0307)S97.CA only 0.000 apart, marking (T0307)S97.CA as missing WARNING: atoms too close: (T0307)A96.N and (T0307)S97.CA only 0.000 apart, marking (T0307)S97.CA as missing WARNING: atoms too close: (T0307)M95.C and (T0307)S97.CA only 0.000 apart, marking (T0307)S97.CA as missing WARNING: atoms too close: (T0307)M95.O and (T0307)S97.CA only 0.000 apart, marking (T0307)S97.CA as missing WARNING: atoms too close: (T0307)M95.CE and (T0307)S97.CA only 0.000 apart, marking (T0307)S97.CA as missing WARNING: atoms too close: (T0307)M95.SD and (T0307)S97.CA only 0.000 apart, marking (T0307)S97.CA as missing WARNING: atoms too close: (T0307)M95.CG and (T0307)S97.CA only 0.000 apart, marking (T0307)S97.CA as missing WARNING: atoms too close: (T0307)M95.CB and (T0307)S97.CA only 0.000 apart, marking (T0307)S97.CA as missing WARNING: atoms too close: (T0307)M95.CA and (T0307)S97.CA only 0.000 apart, marking (T0307)S97.CA as missing WARNING: atoms too close: (T0307)M95.N and (T0307)S97.CA only 0.000 apart, marking (T0307)S97.CA as missing WARNING: atoms too close: (T0307)I94.C and (T0307)S97.CA only 0.000 apart, marking (T0307)S97.CA as missing WARNING: atoms too close: (T0307)I94.O and (T0307)S97.CA only 0.000 apart, marking (T0307)S97.CA as missing WARNING: atoms too close: (T0307)I94.CD1 and (T0307)S97.CA only 0.000 apart, marking (T0307)S97.CA as missing WARNING: atoms too close: (T0307)I94.CG2 and (T0307)S97.CA only 0.000 apart, marking (T0307)S97.CA as missing WARNING: atoms too close: (T0307)I94.CG1 and (T0307)S97.CA only 0.000 apart, marking (T0307)S97.CA as missing WARNING: atoms too close: (T0307)I94.CB and (T0307)S97.CA only 0.000 apart, marking (T0307)S97.CA as missing WARNING: atoms too close: (T0307)I94.CA and (T0307)S97.CA only 0.000 apart, marking (T0307)S97.CA as missing WARNING: atoms too close: (T0307)I94.N and (T0307)S97.CA only 0.000 apart, marking (T0307)S97.CA as missing WARNING: atoms too close: (T0307)V93.C and (T0307)S97.CA only 0.000 apart, marking (T0307)S97.CA as missing WARNING: atoms too close: (T0307)S97.CA and (T0307)S97.CB only 0.000 apart, marking (T0307)S97.CB as missing WARNING: atoms too close: (T0307)S97.N and (T0307)S97.CB only 0.000 apart, marking (T0307)S97.CB as missing WARNING: atoms too close: (T0307)A96.C and (T0307)S97.CB only 0.000 apart, marking (T0307)S97.CB as missing WARNING: atoms too close: (T0307)A96.O and (T0307)S97.CB only 0.000 apart, marking (T0307)S97.CB as missing WARNING: atoms too close: (T0307)A96.CB and (T0307)S97.CB only 0.000 apart, marking (T0307)S97.CB as missing WARNING: atoms too close: (T0307)A96.CA and (T0307)S97.CB only 0.000 apart, marking (T0307)S97.CB as missing WARNING: atoms too close: (T0307)A96.N and (T0307)S97.CB only 0.000 apart, marking (T0307)S97.CB as missing WARNING: atoms too close: (T0307)M95.C and (T0307)S97.CB only 0.000 apart, marking (T0307)S97.CB as missing WARNING: atoms too close: (T0307)M95.O and (T0307)S97.CB only 0.000 apart, marking (T0307)S97.CB as missing WARNING: atoms too close: (T0307)M95.CE and (T0307)S97.CB only 0.000 apart, marking (T0307)S97.CB as missing WARNING: atoms too close: (T0307)M95.SD and (T0307)S97.CB only 0.000 apart, marking (T0307)S97.CB as missing WARNING: atoms too close: (T0307)M95.CG and (T0307)S97.CB only 0.000 apart, marking (T0307)S97.CB as missing WARNING: atoms too close: (T0307)M95.CB and (T0307)S97.CB only 0.000 apart, marking (T0307)S97.CB as missing WARNING: atoms too close: (T0307)M95.CA and (T0307)S97.CB only 0.000 apart, marking (T0307)S97.CB as missing WARNING: atoms too close: (T0307)M95.N and (T0307)S97.CB only 0.000 apart, marking (T0307)S97.CB as missing WARNING: atoms too close: (T0307)I94.C and (T0307)S97.CB only 0.000 apart, marking (T0307)S97.CB as missing WARNING: atoms too close: (T0307)I94.O and (T0307)S97.CB only 0.000 apart, marking (T0307)S97.CB as missing WARNING: atoms too close: (T0307)I94.CD1 and (T0307)S97.CB only 0.000 apart, marking (T0307)S97.CB as missing WARNING: atoms too close: (T0307)I94.CG2 and (T0307)S97.CB only 0.000 apart, marking (T0307)S97.CB as missing WARNING: atoms too close: (T0307)I94.CG1 and (T0307)S97.CB only 0.000 apart, marking (T0307)S97.CB as missing WARNING: atoms too close: (T0307)I94.CB and (T0307)S97.CB only 0.000 apart, marking (T0307)S97.CB as missing WARNING: atoms too close: (T0307)I94.CA and (T0307)S97.CB only 0.000 apart, marking (T0307)S97.CB as missing WARNING: atoms too close: (T0307)I94.N and (T0307)S97.CB only 0.000 apart, marking (T0307)S97.CB as missing WARNING: atoms too close: (T0307)V93.C and (T0307)S97.CB only 0.000 apart, marking (T0307)S97.CB as missing WARNING: atoms too close: (T0307)S97.CB and (T0307)S97.OG only 0.000 apart, marking (T0307)S97.OG as missing WARNING: atoms too close: (T0307)S97.CA and (T0307)S97.OG only 0.000 apart, marking (T0307)S97.OG as missing WARNING: atoms too close: (T0307)S97.N and (T0307)S97.OG only 0.000 apart, marking (T0307)S97.OG as missing WARNING: atoms too close: (T0307)A96.C and (T0307)S97.OG only 0.000 apart, marking (T0307)S97.OG as missing WARNING: atoms too close: (T0307)A96.O and (T0307)S97.OG only 0.000 apart, marking (T0307)S97.OG as missing WARNING: atoms too close: (T0307)A96.CB and (T0307)S97.OG only 0.000 apart, marking (T0307)S97.OG as missing WARNING: atoms too close: (T0307)A96.CA and (T0307)S97.OG only 0.000 apart, marking (T0307)S97.OG as missing WARNING: atoms too close: (T0307)A96.N and (T0307)S97.OG only 0.000 apart, marking (T0307)S97.OG as missing WARNING: atoms too close: (T0307)M95.C and (T0307)S97.OG only 0.000 apart, marking (T0307)S97.OG as missing WARNING: atoms too close: (T0307)M95.O and (T0307)S97.OG only 0.000 apart, marking (T0307)S97.OG as missing WARNING: atoms too close: (T0307)M95.CE and (T0307)S97.OG only 0.000 apart, marking (T0307)S97.OG as missing WARNING: atoms too close: (T0307)M95.SD and (T0307)S97.OG only 0.000 apart, marking (T0307)S97.OG as missing WARNING: atoms too close: (T0307)M95.CG and (T0307)S97.OG only 0.000 apart, marking (T0307)S97.OG as missing WARNING: atoms too close: (T0307)M95.CB and (T0307)S97.OG only 0.000 apart, marking (T0307)S97.OG as missing WARNING: atoms too close: (T0307)M95.CA and (T0307)S97.OG only 0.000 apart, marking (T0307)S97.OG as missing WARNING: atoms too close: (T0307)M95.N and (T0307)S97.OG only 0.000 apart, marking (T0307)S97.OG as missing WARNING: atoms too close: (T0307)I94.C and (T0307)S97.OG only 0.000 apart, marking (T0307)S97.OG as missing WARNING: atoms too close: (T0307)I94.O and (T0307)S97.OG only 0.000 apart, marking (T0307)S97.OG as missing WARNING: atoms too close: (T0307)I94.CD1 and (T0307)S97.OG only 0.000 apart, marking (T0307)S97.OG as missing WARNING: atoms too close: (T0307)I94.CG2 and (T0307)S97.OG only 0.000 apart, marking (T0307)S97.OG as missing WARNING: atoms too close: (T0307)I94.CG1 and (T0307)S97.OG only 0.000 apart, marking (T0307)S97.OG as missing WARNING: atoms too close: (T0307)I94.CB and (T0307)S97.OG only 0.000 apart, marking (T0307)S97.OG as missing WARNING: atoms too close: (T0307)I94.CA and (T0307)S97.OG only 0.000 apart, marking (T0307)S97.OG as missing WARNING: atoms too close: (T0307)I94.N and (T0307)S97.OG only 0.000 apart, marking (T0307)S97.OG as missing WARNING: atoms too close: (T0307)V93.C and (T0307)S97.OG only 0.000 apart, marking (T0307)S97.OG as missing WARNING: atoms too close: (T0307)S97.OG and (T0307)S97.O only 0.000 apart, marking (T0307)S97.O as missing WARNING: atoms too close: (T0307)S97.CB and (T0307)S97.O only 0.000 apart, marking (T0307)S97.O as missing WARNING: atoms too close: (T0307)S97.CA and (T0307)S97.O only 0.000 apart, marking (T0307)S97.O as missing WARNING: atoms too close: (T0307)S97.N and (T0307)S97.O only 0.000 apart, marking (T0307)S97.O as missing WARNING: atoms too close: (T0307)A96.C and (T0307)S97.O only 0.000 apart, marking (T0307)S97.O as missing WARNING: atoms too close: (T0307)A96.O and (T0307)S97.O only 0.000 apart, marking (T0307)S97.O as missing WARNING: atoms too close: (T0307)A96.CB and (T0307)S97.O only 0.000 apart, marking (T0307)S97.O as missing WARNING: atoms too close: (T0307)A96.CA and (T0307)S97.O only 0.000 apart, marking (T0307)S97.O as missing WARNING: atoms too close: (T0307)A96.N and (T0307)S97.O only 0.000 apart, marking (T0307)S97.O as missing WARNING: atoms too close: (T0307)M95.C and (T0307)S97.O only 0.000 apart, marking (T0307)S97.O as missing WARNING: atoms too close: (T0307)M95.O and (T0307)S97.O only 0.000 apart, marking (T0307)S97.O as missing WARNING: atoms too close: (T0307)M95.CE and (T0307)S97.O only 0.000 apart, marking (T0307)S97.O as missing WARNING: atoms too close: (T0307)M95.SD and (T0307)S97.O only 0.000 apart, marking (T0307)S97.O as missing WARNING: atoms too close: (T0307)M95.CG and (T0307)S97.O only 0.000 apart, marking (T0307)S97.O as missing WARNING: atoms too close: (T0307)M95.CB and (T0307)S97.O only 0.000 apart, marking (T0307)S97.O as missing WARNING: atoms too close: (T0307)M95.CA and (T0307)S97.O only 0.000 apart, marking (T0307)S97.O as missing WARNING: atoms too close: (T0307)M95.N and (T0307)S97.O only 0.000 apart, marking (T0307)S97.O as missing WARNING: atoms too close: (T0307)I94.C and (T0307)S97.O only 0.000 apart, marking (T0307)S97.O as missing WARNING: atoms too close: (T0307)I94.O and (T0307)S97.O only 0.000 apart, marking (T0307)S97.O as missing WARNING: atoms too close: (T0307)I94.CD1 and (T0307)S97.O only 0.000 apart, marking (T0307)S97.O as missing WARNING: atoms too close: (T0307)I94.CG2 and (T0307)S97.O only 0.000 apart, marking (T0307)S97.O as missing WARNING: atoms too close: (T0307)I94.CG1 and (T0307)S97.O only 0.000 apart, marking (T0307)S97.O as missing WARNING: atoms too close: (T0307)I94.CB and (T0307)S97.O only 0.000 apart, marking (T0307)S97.O as missing WARNING: atoms too close: (T0307)I94.CA and (T0307)S97.O only 0.000 apart, marking (T0307)S97.O as missing WARNING: atoms too close: (T0307)I94.N and (T0307)S97.O only 0.000 apart, marking (T0307)S97.O as missing WARNING: atoms too close: (T0307)V93.C and (T0307)S97.O only 0.000 apart, marking (T0307)S97.O as missing WARNING: atoms too close: (T0307)S97.O and (T0307)S97.C only 0.000 apart, marking (T0307)S97.C as missing WARNING: atoms too close: (T0307)S97.OG and (T0307)S97.C only 0.000 apart, marking (T0307)S97.C as missing WARNING: atoms too close: (T0307)S97.CB and (T0307)S97.C only 0.000 apart, marking (T0307)S97.C as missing WARNING: atoms too close: (T0307)S97.CA and (T0307)S97.C only 0.000 apart, marking (T0307)S97.C as missing WARNING: atoms too close: (T0307)S97.N and (T0307)S97.C only 0.000 apart, marking (T0307)S97.C as missing WARNING: atoms too close: (T0307)A96.C and (T0307)S97.C only 0.000 apart, marking (T0307)S97.C as missing WARNING: atoms too close: (T0307)A96.O and (T0307)S97.C only 0.000 apart, marking (T0307)S97.C as missing WARNING: atoms too close: (T0307)A96.CB and (T0307)S97.C only 0.000 apart, marking (T0307)S97.C as missing WARNING: atoms too close: (T0307)A96.CA and (T0307)S97.C only 0.000 apart, marking (T0307)S97.C as missing WARNING: atoms too close: (T0307)A96.N and (T0307)S97.C only 0.000 apart, marking (T0307)S97.C as missing WARNING: atoms too close: (T0307)M95.C and (T0307)S97.C only 0.000 apart, marking (T0307)S97.C as missing WARNING: atoms too close: (T0307)M95.O and (T0307)S97.C only 0.000 apart, marking (T0307)S97.C as missing WARNING: atoms too close: (T0307)M95.CE and (T0307)S97.C only 0.000 apart, marking (T0307)S97.C as missing WARNING: atoms too close: (T0307)M95.SD and (T0307)S97.C only 0.000 apart, marking (T0307)S97.C as missing WARNING: atoms too close: (T0307)M95.CG and (T0307)S97.C only 0.000 apart, marking (T0307)S97.C as missing WARNING: atoms too close: (T0307)M95.CB and (T0307)S97.C only 0.000 apart, marking (T0307)S97.C as missing WARNING: atoms too close: (T0307)M95.CA and (T0307)S97.C only 0.000 apart, marking (T0307)S97.C as missing WARNING: atoms too close: (T0307)M95.N and (T0307)S97.C only 0.000 apart, marking (T0307)S97.C as missing WARNING: atoms too close: (T0307)I94.C and (T0307)S97.C only 0.000 apart, marking (T0307)S97.C as missing WARNING: atoms too close: (T0307)I94.O and (T0307)S97.C only 0.000 apart, marking (T0307)S97.C as missing WARNING: atoms too close: (T0307)I94.CD1 and (T0307)S97.C only 0.000 apart, marking (T0307)S97.C as missing WARNING: atoms too close: (T0307)I94.CG2 and (T0307)S97.C only 0.000 apart, marking (T0307)S97.C as missing WARNING: atoms too close: (T0307)I94.CG1 and (T0307)S97.C only 0.000 apart, marking (T0307)S97.C as missing WARNING: atoms too close: (T0307)I94.CB and (T0307)S97.C only 0.000 apart, marking (T0307)S97.C as missing WARNING: atoms too close: (T0307)I94.CA and (T0307)S97.C only 0.000 apart, marking (T0307)S97.C as missing WARNING: atoms too close: (T0307)I94.N and (T0307)S97.C only 0.000 apart, marking (T0307)S97.C as missing WARNING: atoms too close: (T0307)V93.C and (T0307)S97.C only 0.000 apart, marking (T0307)S97.C as missing WARNING: atoms too close: (T0307)S97.C and (T0307)D98.N only 0.000 apart, marking (T0307)S97.C as missing WARNING: atoms too close: (T0307)S97.O and (T0307)D98.N only 0.000 apart, marking (T0307)S97.O as missing WARNING: atoms too close: (T0307)S97.OG and (T0307)D98.N only 0.000 apart, marking (T0307)S97.OG as missing WARNING: atoms too close: (T0307)S97.CB and (T0307)D98.N only 0.000 apart, marking (T0307)S97.CB as missing WARNING: atoms too close: (T0307)S97.CA and (T0307)D98.N only 0.000 apart, marking (T0307)S97.CA as missing WARNING: atoms too close: (T0307)S97.N and (T0307)D98.N only 0.000 apart, marking (T0307)S97.N as missing WARNING: atoms too close: (T0307)A96.C and (T0307)D98.N only 0.000 apart, marking (T0307)A96.C as missing WARNING: atoms too close: (T0307)A96.O and (T0307)D98.N only 0.000 apart, marking (T0307)A96.O as missing WARNING: atoms too close: (T0307)A96.CB and (T0307)D98.N only 0.000 apart, marking (T0307)A96.CB as missing WARNING: atoms too close: (T0307)A96.CA and (T0307)D98.N only 0.000 apart, marking (T0307)A96.CA as missing WARNING: atoms too close: (T0307)A96.N and (T0307)D98.N only 0.000 apart, marking (T0307)A96.N as missing WARNING: atoms too close: (T0307)M95.C and (T0307)D98.N only 0.000 apart, marking (T0307)M95.C as missing WARNING: atoms too close: (T0307)M95.O and (T0307)D98.N only 0.000 apart, marking (T0307)M95.O as missing WARNING: atoms too close: (T0307)M95.CE and (T0307)D98.N only 0.000 apart, marking (T0307)M95.CE as missing WARNING: atoms too close: (T0307)M95.SD and (T0307)D98.N only 0.000 apart, marking (T0307)M95.SD as missing WARNING: atoms too close: (T0307)M95.CG and (T0307)D98.N only 0.000 apart, marking (T0307)M95.CG as missing WARNING: atoms too close: (T0307)M95.CB and (T0307)D98.N only 0.000 apart, marking (T0307)M95.CB as missing WARNING: atoms too close: (T0307)M95.CA and (T0307)D98.N only 0.000 apart, marking (T0307)M95.CA as missing WARNING: atoms too close: (T0307)M95.N and (T0307)D98.N only 0.000 apart, marking (T0307)M95.N as missing WARNING: atoms too close: (T0307)I94.C and (T0307)D98.N only 0.000 apart, marking (T0307)I94.C as missing WARNING: atoms too close: (T0307)I94.O and (T0307)D98.N only 0.000 apart, marking (T0307)I94.O as missing WARNING: atoms too close: (T0307)I94.CD1 and (T0307)D98.N only 0.000 apart, marking (T0307)I94.CD1 as missing WARNING: atoms too close: (T0307)I94.CG2 and (T0307)D98.N only 0.000 apart, marking (T0307)I94.CG2 as missing WARNING: atoms too close: (T0307)I94.CG1 and (T0307)D98.N only 0.000 apart, marking (T0307)I94.CG1 as missing WARNING: atoms too close: (T0307)I94.CB and (T0307)D98.N only 0.000 apart, marking (T0307)I94.CB as missing WARNING: atoms too close: (T0307)I94.CA and (T0307)D98.N only 0.000 apart, marking (T0307)I94.CA as missing WARNING: atoms too close: (T0307)I94.N and (T0307)D98.N only 0.000 apart, marking (T0307)I94.N as missing WARNING: atoms too close: (T0307)V93.C and (T0307)D98.N only 0.000 apart, marking (T0307)D98.N as missing WARNING: atoms too close: (T0307)D98.N and (T0307)D98.CA only 0.000 apart, marking (T0307)D98.CA as missing WARNING: atoms too close: (T0307)S97.C and (T0307)D98.CA only 0.000 apart, marking (T0307)D98.CA as missing WARNING: atoms too close: (T0307)S97.O and (T0307)D98.CA only 0.000 apart, marking (T0307)D98.CA as missing WARNING: atoms too close: (T0307)S97.OG and (T0307)D98.CA only 0.000 apart, marking (T0307)D98.CA as missing WARNING: atoms too close: (T0307)S97.CB and (T0307)D98.CA only 0.000 apart, marking (T0307)D98.CA as missing WARNING: atoms too close: (T0307)S97.CA and (T0307)D98.CA only 0.000 apart, marking (T0307)D98.CA as missing WARNING: atoms too close: (T0307)S97.N and (T0307)D98.CA only 0.000 apart, marking (T0307)D98.CA as missing WARNING: atoms too close: (T0307)A96.C and (T0307)D98.CA only 0.000 apart, marking (T0307)D98.CA as missing WARNING: atoms too close: (T0307)A96.O and (T0307)D98.CA only 0.000 apart, marking (T0307)D98.CA as missing WARNING: atoms too close: (T0307)A96.CB and (T0307)D98.CA only 0.000 apart, marking (T0307)D98.CA as missing WARNING: atoms too close: (T0307)A96.CA and (T0307)D98.CA only 0.000 apart, marking (T0307)D98.CA as missing WARNING: atoms too close: (T0307)A96.N and (T0307)D98.CA only 0.000 apart, marking (T0307)D98.CA as missing WARNING: atoms too close: (T0307)M95.C and (T0307)D98.CA only 0.000 apart, marking (T0307)D98.CA as missing WARNING: atoms too close: (T0307)M95.O and (T0307)D98.CA only 0.000 apart, marking (T0307)D98.CA as missing WARNING: atoms too close: (T0307)M95.CE and (T0307)D98.CA only 0.000 apart, marking (T0307)D98.CA as missing WARNING: atoms too close: (T0307)M95.SD and (T0307)D98.CA only 0.000 apart, marking (T0307)D98.CA as missing WARNING: atoms too close: (T0307)M95.CG and (T0307)D98.CA only 0.000 apart, marking (T0307)D98.CA as missing WARNING: atoms too close: (T0307)M95.CB and (T0307)D98.CA only 0.000 apart, marking (T0307)D98.CA as missing WARNING: atoms too close: (T0307)M95.CA and (T0307)D98.CA only 0.000 apart, marking (T0307)D98.CA as missing WARNING: atoms too close: (T0307)M95.N and (T0307)D98.CA only 0.000 apart, marking (T0307)D98.CA as missing WARNING: atoms too close: (T0307)I94.C and (T0307)D98.CA only 0.000 apart, marking (T0307)D98.CA as missing WARNING: atoms too close: (T0307)I94.O and (T0307)D98.CA only 0.000 apart, marking (T0307)D98.CA as missing WARNING: atoms too close: (T0307)I94.CD1 and (T0307)D98.CA only 0.000 apart, marking (T0307)D98.CA as missing WARNING: atoms too close: (T0307)I94.CG2 and (T0307)D98.CA only 0.000 apart, marking (T0307)D98.CA as missing WARNING: atoms too close: (T0307)I94.CG1 and (T0307)D98.CA only 0.000 apart, marking (T0307)D98.CA as missing WARNING: atoms too close: (T0307)I94.CB and (T0307)D98.CA only 0.000 apart, marking (T0307)D98.CA as missing WARNING: atoms too close: (T0307)I94.CA and (T0307)D98.CA only 0.000 apart, marking (T0307)D98.CA as missing WARNING: atoms too close: (T0307)I94.N and (T0307)D98.CA only 0.000 apart, marking (T0307)D98.CA as missing WARNING: atoms too close: (T0307)V93.C and (T0307)D98.CA only 0.000 apart, marking (T0307)D98.CA as missing WARNING: atoms too close: (T0307)D98.CA and (T0307)D98.CB only 0.000 apart, marking (T0307)D98.CB as missing WARNING: atoms too close: (T0307)D98.N and (T0307)D98.CB only 0.000 apart, marking (T0307)D98.CB as missing WARNING: atoms too close: (T0307)S97.C and (T0307)D98.CB only 0.000 apart, marking (T0307)D98.CB as missing WARNING: atoms too close: (T0307)S97.O and (T0307)D98.CB only 0.000 apart, marking (T0307)D98.CB as missing WARNING: atoms too close: (T0307)S97.OG and (T0307)D98.CB only 0.000 apart, marking (T0307)D98.CB as missing WARNING: atoms too close: (T0307)S97.CB and (T0307)D98.CB only 0.000 apart, marking (T0307)D98.CB as missing WARNING: atoms too close: (T0307)S97.CA and (T0307)D98.CB only 0.000 apart, marking (T0307)D98.CB as missing WARNING: atoms too close: (T0307)S97.N and (T0307)D98.CB only 0.000 apart, marking (T0307)D98.CB as missing WARNING: atoms too close: (T0307)A96.C and (T0307)D98.CB only 0.000 apart, marking (T0307)D98.CB as missing WARNING: atoms too close: (T0307)A96.O and (T0307)D98.CB only 0.000 apart, marking (T0307)D98.CB as missing WARNING: atoms too close: (T0307)A96.CB and (T0307)D98.CB only 0.000 apart, marking (T0307)D98.CB as missing WARNING: atoms too close: (T0307)A96.CA and (T0307)D98.CB only 0.000 apart, marking (T0307)D98.CB as missing WARNING: atoms too close: (T0307)A96.N and (T0307)D98.CB only 0.000 apart, marking (T0307)D98.CB as missing WARNING: atoms too close: (T0307)M95.C and (T0307)D98.CB only 0.000 apart, marking (T0307)D98.CB as missing WARNING: atoms too close: (T0307)M95.O and (T0307)D98.CB only 0.000 apart, marking (T0307)D98.CB as missing WARNING: atoms too close: (T0307)M95.CE and (T0307)D98.CB only 0.000 apart, marking (T0307)D98.CB as missing WARNING: atoms too close: (T0307)M95.SD and (T0307)D98.CB only 0.000 apart, marking (T0307)D98.CB as missing WARNING: atoms too close: (T0307)M95.CG and (T0307)D98.CB only 0.000 apart, marking (T0307)D98.CB as missing WARNING: atoms too close: (T0307)M95.CB and (T0307)D98.CB only 0.000 apart, marking (T0307)D98.CB as missing WARNING: atoms too close: (T0307)M95.CA and (T0307)D98.CB only 0.000 apart, marking (T0307)D98.CB as missing WARNING: atoms too close: (T0307)M95.N and (T0307)D98.CB only 0.000 apart, marking (T0307)D98.CB as missing WARNING: atoms too close: (T0307)I94.C and (T0307)D98.CB only 0.000 apart, marking (T0307)D98.CB as missing WARNING: atoms too close: (T0307)I94.O and (T0307)D98.CB only 0.000 apart, marking (T0307)D98.CB as missing WARNING: atoms too close: (T0307)I94.CD1 and (T0307)D98.CB only 0.000 apart, marking (T0307)D98.CB as missing WARNING: atoms too close: (T0307)I94.CG2 and (T0307)D98.CB only 0.000 apart, marking (T0307)D98.CB as missing WARNING: atoms too close: (T0307)I94.CG1 and (T0307)D98.CB only 0.000 apart, marking (T0307)D98.CB as missing WARNING: atoms too close: (T0307)I94.CB and (T0307)D98.CB only 0.000 apart, marking (T0307)D98.CB as missing WARNING: atoms too close: (T0307)I94.CA and (T0307)D98.CB only 0.000 apart, marking (T0307)D98.CB as missing WARNING: atoms too close: (T0307)I94.N and (T0307)D98.CB only 0.000 apart, marking (T0307)D98.CB as missing WARNING: atoms too close: (T0307)V93.C and (T0307)D98.CB only 0.000 apart, marking (T0307)D98.CB as missing WARNING: atoms too close: (T0307)D98.CB and (T0307)D98.CG only 0.000 apart, marking (T0307)D98.CG as missing WARNING: atoms too close: (T0307)D98.CA and (T0307)D98.CG only 0.000 apart, marking (T0307)D98.CG as missing WARNING: atoms too close: (T0307)D98.N and (T0307)D98.CG only 0.000 apart, marking (T0307)D98.CG as missing WARNING: atoms too close: (T0307)S97.C and (T0307)D98.CG only 0.000 apart, marking (T0307)D98.CG as missing WARNING: atoms too close: (T0307)S97.O and (T0307)D98.CG only 0.000 apart, marking (T0307)D98.CG as missing WARNING: atoms too close: (T0307)S97.OG and (T0307)D98.CG only 0.000 apart, marking (T0307)D98.CG as missing WARNING: atoms too close: (T0307)S97.CB and (T0307)D98.CG only 0.000 apart, marking (T0307)D98.CG as missing WARNING: atoms too close: (T0307)S97.CA and (T0307)D98.CG only 0.000 apart, marking (T0307)D98.CG as missing WARNING: atoms too close: (T0307)S97.N and (T0307)D98.CG only 0.000 apart, marking (T0307)D98.CG as missing WARNING: atoms too close: (T0307)A96.C and (T0307)D98.CG only 0.000 apart, marking (T0307)D98.CG as missing WARNING: atoms too close: (T0307)A96.O and (T0307)D98.CG only 0.000 apart, marking (T0307)D98.CG as missing WARNING: atoms too close: (T0307)A96.CB and (T0307)D98.CG only 0.000 apart, marking (T0307)D98.CG as missing WARNING: atoms too close: (T0307)A96.CA and (T0307)D98.CG only 0.000 apart, marking (T0307)D98.CG as missing WARNING: atoms too close: (T0307)A96.N and (T0307)D98.CG only 0.000 apart, marking (T0307)D98.CG as missing WARNING: atoms too close: (T0307)M95.C and (T0307)D98.CG only 0.000 apart, marking (T0307)D98.CG as missing WARNING: atoms too close: (T0307)M95.O and (T0307)D98.CG only 0.000 apart, marking (T0307)D98.CG as missing WARNING: atoms too close: (T0307)M95.CE and (T0307)D98.CG only 0.000 apart, marking (T0307)D98.CG as missing WARNING: atoms too close: (T0307)M95.SD and (T0307)D98.CG only 0.000 apart, marking (T0307)D98.CG as missing WARNING: atoms too close: (T0307)M95.CG and (T0307)D98.CG only 0.000 apart, marking (T0307)D98.CG as missing WARNING: atoms too close: (T0307)M95.CB and (T0307)D98.CG only 0.000 apart, marking (T0307)D98.CG as missing WARNING: atoms too close: (T0307)M95.CA and (T0307)D98.CG only 0.000 apart, marking (T0307)D98.CG as missing WARNING: atoms too close: (T0307)M95.N and (T0307)D98.CG only 0.000 apart, marking (T0307)D98.CG as missing WARNING: atoms too close: (T0307)I94.C and (T0307)D98.CG only 0.000 apart, marking (T0307)D98.CG as missing WARNING: atoms too close: (T0307)I94.O and (T0307)D98.CG only 0.000 apart, marking (T0307)D98.CG as missing WARNING: atoms too close: (T0307)I94.CD1 and (T0307)D98.CG only 0.000 apart, marking (T0307)D98.CG as missing WARNING: atoms too close: (T0307)I94.CG2 and (T0307)D98.CG only 0.000 apart, marking (T0307)D98.CG as missing WARNING: atoms too close: (T0307)I94.CG1 and (T0307)D98.CG only 0.000 apart, marking (T0307)D98.CG as missing WARNING: atoms too close: (T0307)I94.CB and (T0307)D98.CG only 0.000 apart, marking (T0307)D98.CG as missing WARNING: atoms too close: (T0307)I94.CA and (T0307)D98.CG only 0.000 apart, marking (T0307)D98.CG as missing WARNING: atoms too close: (T0307)I94.N and (T0307)D98.CG only 0.000 apart, marking (T0307)D98.CG as missing WARNING: atoms too close: (T0307)V93.C and (T0307)D98.CG only 0.000 apart, marking (T0307)D98.CG as missing WARNING: atoms too close: (T0307)D98.CG and (T0307)D98.OD1 only 0.000 apart, marking (T0307)D98.OD1 as missing WARNING: atoms too close: (T0307)D98.CB and (T0307)D98.OD1 only 0.000 apart, marking (T0307)D98.OD1 as missing WARNING: atoms too close: (T0307)D98.CA and (T0307)D98.OD1 only 0.000 apart, marking (T0307)D98.OD1 as missing WARNING: atoms too close: (T0307)D98.N and (T0307)D98.OD1 only 0.000 apart, marking (T0307)D98.OD1 as missing WARNING: atoms too close: (T0307)S97.C and (T0307)D98.OD1 only 0.000 apart, marking (T0307)D98.OD1 as missing WARNING: atoms too close: (T0307)S97.O and (T0307)D98.OD1 only 0.000 apart, marking (T0307)D98.OD1 as missing WARNING: atoms too close: (T0307)S97.OG and (T0307)D98.OD1 only 0.000 apart, marking (T0307)D98.OD1 as missing WARNING: atoms too close: (T0307)S97.CB and (T0307)D98.OD1 only 0.000 apart, marking (T0307)D98.OD1 as missing WARNING: atoms too close: (T0307)S97.CA and (T0307)D98.OD1 only 0.000 apart, marking (T0307)D98.OD1 as missing WARNING: atoms too close: (T0307)S97.N and (T0307)D98.OD1 only 0.000 apart, marking (T0307)D98.OD1 as missing WARNING: atoms too close: (T0307)A96.C and (T0307)D98.OD1 only 0.000 apart, marking (T0307)D98.OD1 as missing WARNING: atoms too close: (T0307)A96.O and (T0307)D98.OD1 only 0.000 apart, marking (T0307)D98.OD1 as missing WARNING: atoms too close: (T0307)A96.CB and (T0307)D98.OD1 only 0.000 apart, marking (T0307)D98.OD1 as missing WARNING: atoms too close: (T0307)A96.CA and (T0307)D98.OD1 only 0.000 apart, marking (T0307)D98.OD1 as missing WARNING: atoms too close: (T0307)A96.N and (T0307)D98.OD1 only 0.000 apart, marking (T0307)D98.OD1 as missing WARNING: atoms too close: (T0307)M95.C and (T0307)D98.OD1 only 0.000 apart, marking (T0307)D98.OD1 as missing WARNING: atoms too close: (T0307)M95.O and (T0307)D98.OD1 only 0.000 apart, marking (T0307)D98.OD1 as missing WARNING: atoms too close: (T0307)M95.CE and (T0307)D98.OD1 only 0.000 apart, marking (T0307)D98.OD1 as missing WARNING: atoms too close: (T0307)M95.SD and (T0307)D98.OD1 only 0.000 apart, marking (T0307)D98.OD1 as missing WARNING: atoms too close: (T0307)M95.CG and (T0307)D98.OD1 only 0.000 apart, marking (T0307)D98.OD1 as missing WARNING: atoms too close: (T0307)M95.CB and (T0307)D98.OD1 only 0.000 apart, marking (T0307)D98.OD1 as missing WARNING: atoms too close: (T0307)M95.CA and (T0307)D98.OD1 only 0.000 apart, marking (T0307)D98.OD1 as missing WARNING: atoms too close: (T0307)M95.N and (T0307)D98.OD1 only 0.000 apart, marking (T0307)D98.OD1 as missing WARNING: atoms too close: (T0307)I94.C and (T0307)D98.OD1 only 0.000 apart, marking (T0307)D98.OD1 as missing WARNING: atoms too close: (T0307)I94.O and (T0307)D98.OD1 only 0.000 apart, marking (T0307)D98.OD1 as missing WARNING: atoms too close: (T0307)I94.CD1 and (T0307)D98.OD1 only 0.000 apart, marking (T0307)D98.OD1 as missing WARNING: atoms too close: (T0307)I94.CG2 and (T0307)D98.OD1 only 0.000 apart, marking (T0307)D98.OD1 as missing WARNING: atoms too close: (T0307)I94.CG1 and (T0307)D98.OD1 only 0.000 apart, marking (T0307)D98.OD1 as missing WARNING: atoms too close: (T0307)I94.CB and (T0307)D98.OD1 only 0.000 apart, marking (T0307)D98.OD1 as missing WARNING: atoms too close: (T0307)I94.CA and (T0307)D98.OD1 only 0.000 apart, marking (T0307)D98.OD1 as missing WARNING: atoms too close: (T0307)I94.N and (T0307)D98.OD1 only 0.000 apart, marking (T0307)D98.OD1 as missing WARNING: atoms too close: (T0307)V93.C and (T0307)D98.OD1 only 0.000 apart, marking (T0307)D98.OD1 as missing WARNING: atoms too close: (T0307)D98.OD1 and (T0307)D98.OD2 only 0.000 apart, marking (T0307)D98.OD2 as missing WARNING: atoms too close: (T0307)D98.CG and (T0307)D98.OD2 only 0.000 apart, marking (T0307)D98.OD2 as missing WARNING: atoms too close: (T0307)D98.CB and (T0307)D98.OD2 only 0.000 apart, marking (T0307)D98.OD2 as missing WARNING: atoms too close: (T0307)D98.CA and (T0307)D98.OD2 only 0.000 apart, marking (T0307)D98.OD2 as missing WARNING: atoms too close: (T0307)D98.N and (T0307)D98.OD2 only 0.000 apart, marking (T0307)D98.OD2 as missing WARNING: atoms too close: (T0307)S97.C and (T0307)D98.OD2 only 0.000 apart, marking (T0307)D98.OD2 as missing WARNING: atoms too close: (T0307)S97.O and (T0307)D98.OD2 only 0.000 apart, marking (T0307)D98.OD2 as missing WARNING: atoms too close: (T0307)S97.OG and (T0307)D98.OD2 only 0.000 apart, marking (T0307)D98.OD2 as missing WARNING: atoms too close: (T0307)S97.CB and (T0307)D98.OD2 only 0.000 apart, marking (T0307)D98.OD2 as missing WARNING: atoms too close: (T0307)S97.CA and (T0307)D98.OD2 only 0.000 apart, marking (T0307)D98.OD2 as missing WARNING: atoms too close: (T0307)S97.N and (T0307)D98.OD2 only 0.000 apart, marking (T0307)D98.OD2 as missing WARNING: atoms too close: (T0307)A96.C and (T0307)D98.OD2 only 0.000 apart, marking (T0307)D98.OD2 as missing WARNING: atoms too close: (T0307)A96.O and (T0307)D98.OD2 only 0.000 apart, marking (T0307)D98.OD2 as missing WARNING: atoms too close: (T0307)A96.CB and (T0307)D98.OD2 only 0.000 apart, marking (T0307)D98.OD2 as missing WARNING: atoms too close: (T0307)A96.CA and (T0307)D98.OD2 only 0.000 apart, marking (T0307)D98.OD2 as missing WARNING: atoms too close: (T0307)A96.N and (T0307)D98.OD2 only 0.000 apart, marking (T0307)D98.OD2 as missing WARNING: atoms too close: (T0307)M95.C and (T0307)D98.OD2 only 0.000 apart, marking (T0307)D98.OD2 as missing WARNING: atoms too close: (T0307)M95.O and (T0307)D98.OD2 only 0.000 apart, marking (T0307)D98.OD2 as missing WARNING: atoms too close: (T0307)M95.CE and (T0307)D98.OD2 only 0.000 apart, marking (T0307)D98.OD2 as missing WARNING: atoms too close: (T0307)M95.SD and (T0307)D98.OD2 only 0.000 apart, marking (T0307)D98.OD2 as missing WARNING: atoms too close: (T0307)M95.CG and (T0307)D98.OD2 only 0.000 apart, marking (T0307)D98.OD2 as missing WARNING: atoms too close: (T0307)M95.CB and (T0307)D98.OD2 only 0.000 apart, marking (T0307)D98.OD2 as missing WARNING: atoms too close: (T0307)M95.CA and (T0307)D98.OD2 only 0.000 apart, marking (T0307)D98.OD2 as missing WARNING: atoms too close: (T0307)M95.N and (T0307)D98.OD2 only 0.000 apart, marking (T0307)D98.OD2 as missing WARNING: atoms too close: (T0307)I94.C and (T0307)D98.OD2 only 0.000 apart, marking (T0307)D98.OD2 as missing WARNING: atoms too close: (T0307)I94.O and (T0307)D98.OD2 only 0.000 apart, marking (T0307)D98.OD2 as missing WARNING: atoms too close: (T0307)I94.CD1 and (T0307)D98.OD2 only 0.000 apart, marking (T0307)D98.OD2 as missing WARNING: atoms too close: (T0307)I94.CG2 and (T0307)D98.OD2 only 0.000 apart, marking (T0307)D98.OD2 as missing WARNING: atoms too close: (T0307)I94.CG1 and (T0307)D98.OD2 only 0.000 apart, marking (T0307)D98.OD2 as missing WARNING: atoms too close: (T0307)I94.CB and (T0307)D98.OD2 only 0.000 apart, marking (T0307)D98.OD2 as missing WARNING: atoms too close: (T0307)I94.CA and (T0307)D98.OD2 only 0.000 apart, marking (T0307)D98.OD2 as missing WARNING: atoms too close: (T0307)I94.N and (T0307)D98.OD2 only 0.000 apart, marking (T0307)D98.OD2 as missing WARNING: atoms too close: (T0307)V93.C and (T0307)D98.OD2 only 0.000 apart, marking (T0307)D98.OD2 as missing WARNING: atoms too close: (T0307)D98.OD2 and (T0307)D98.O only 0.000 apart, marking (T0307)D98.O as missing WARNING: atoms too close: (T0307)D98.OD1 and (T0307)D98.O only 0.000 apart, marking (T0307)D98.O as missing WARNING: atoms too close: (T0307)D98.CG and (T0307)D98.O only 0.000 apart, marking (T0307)D98.O as missing WARNING: atoms too close: (T0307)D98.CB and (T0307)D98.O only 0.000 apart, marking (T0307)D98.O as missing WARNING: atoms too close: (T0307)D98.CA and (T0307)D98.O only 0.000 apart, marking (T0307)D98.O as missing WARNING: atoms too close: (T0307)D98.N and (T0307)D98.O only 0.000 apart, marking (T0307)D98.O as missing WARNING: atoms too close: (T0307)S97.C and (T0307)D98.O only 0.000 apart, marking (T0307)D98.O as missing WARNING: atoms too close: (T0307)S97.O and (T0307)D98.O only 0.000 apart, marking (T0307)D98.O as missing WARNING: atoms too close: (T0307)S97.OG and (T0307)D98.O only 0.000 apart, marking (T0307)D98.O as missing WARNING: atoms too close: (T0307)S97.CB and (T0307)D98.O only 0.000 apart, marking (T0307)D98.O as missing WARNING: atoms too close: (T0307)S97.CA and (T0307)D98.O only 0.000 apart, marking (T0307)D98.O as missing WARNING: atoms too close: (T0307)S97.N and (T0307)D98.O only 0.000 apart, marking (T0307)D98.O as missing WARNING: atoms too close: (T0307)A96.C and (T0307)D98.O only 0.000 apart, marking (T0307)D98.O as missing WARNING: atoms too close: (T0307)A96.O and (T0307)D98.O only 0.000 apart, marking (T0307)D98.O as missing WARNING: atoms too close: (T0307)A96.CB and (T0307)D98.O only 0.000 apart, marking (T0307)D98.O as missing WARNING: atoms too close: (T0307)A96.CA and (T0307)D98.O only 0.000 apart, marking (T0307)D98.O as missing WARNING: atoms too close: (T0307)A96.N and (T0307)D98.O only 0.000 apart, marking (T0307)D98.O as missing WARNING: atoms too close: (T0307)M95.C and (T0307)D98.O only 0.000 apart, marking (T0307)D98.O as missing WARNING: atoms too close: (T0307)M95.O and (T0307)D98.O only 0.000 apart, marking (T0307)D98.O as missing WARNING: atoms too close: (T0307)M95.CE and (T0307)D98.O only 0.000 apart, marking (T0307)D98.O as missing WARNING: atoms too close: (T0307)M95.SD and (T0307)D98.O only 0.000 apart, marking (T0307)D98.O as missing WARNING: atoms too close: (T0307)M95.CG and (T0307)D98.O only 0.000 apart, marking (T0307)D98.O as missing WARNING: atoms too close: (T0307)M95.CB and (T0307)D98.O only 0.000 apart, marking (T0307)D98.O as missing WARNING: atoms too close: (T0307)M95.CA and (T0307)D98.O only 0.000 apart, marking (T0307)D98.O as missing WARNING: atoms too close: (T0307)M95.N and (T0307)D98.O only 0.000 apart, marking (T0307)D98.O as missing WARNING: atoms too close: (T0307)I94.C and (T0307)D98.O only 0.000 apart, marking (T0307)D98.O as missing WARNING: atoms too close: (T0307)I94.O and (T0307)D98.O only 0.000 apart, marking (T0307)D98.O as missing WARNING: atoms too close: (T0307)I94.CD1 and (T0307)D98.O only 0.000 apart, marking (T0307)D98.O as missing WARNING: atoms too close: (T0307)I94.CG2 and (T0307)D98.O only 0.000 apart, marking (T0307)D98.O as missing WARNING: atoms too close: (T0307)I94.CG1 and (T0307)D98.O only 0.000 apart, marking (T0307)D98.O as missing WARNING: atoms too close: (T0307)I94.CB and (T0307)D98.O only 0.000 apart, marking (T0307)D98.O as missing WARNING: atoms too close: (T0307)I94.CA and (T0307)D98.O only 0.000 apart, marking (T0307)D98.O as missing WARNING: atoms too close: (T0307)I94.N and (T0307)D98.O only 0.000 apart, marking (T0307)D98.O as missing WARNING: atoms too close: (T0307)V93.C and (T0307)D98.O only 0.000 apart, marking (T0307)D98.O as missing WARNING: atoms too close: (T0307)D98.O and (T0307)D98.C only 0.000 apart, marking (T0307)D98.C as missing WARNING: atoms too close: (T0307)D98.OD2 and (T0307)D98.C only 0.000 apart, marking (T0307)D98.C as missing WARNING: atoms too close: (T0307)D98.OD1 and (T0307)D98.C only 0.000 apart, marking (T0307)D98.C as missing WARNING: atoms too close: (T0307)D98.CG and (T0307)D98.C only 0.000 apart, marking (T0307)D98.C as missing WARNING: atoms too close: (T0307)D98.CB and (T0307)D98.C only 0.000 apart, marking (T0307)D98.C as missing WARNING: atoms too close: (T0307)D98.CA and (T0307)D98.C only 0.000 apart, marking (T0307)D98.C as missing WARNING: atoms too close: (T0307)D98.N and (T0307)D98.C only 0.000 apart, marking (T0307)D98.C as missing WARNING: atoms too close: (T0307)S97.C and (T0307)D98.C only 0.000 apart, marking (T0307)D98.C as missing WARNING: atoms too close: (T0307)S97.O and (T0307)D98.C only 0.000 apart, marking (T0307)D98.C as missing WARNING: atoms too close: (T0307)S97.OG and (T0307)D98.C only 0.000 apart, marking (T0307)D98.C as missing WARNING: atoms too close: (T0307)S97.CB and (T0307)D98.C only 0.000 apart, marking (T0307)D98.C as missing WARNING: atoms too close: (T0307)S97.CA and (T0307)D98.C only 0.000 apart, marking (T0307)D98.C as missing WARNING: atoms too close: (T0307)S97.N and (T0307)D98.C only 0.000 apart, marking (T0307)D98.C as missing WARNING: atoms too close: (T0307)A96.C and (T0307)D98.C only 0.000 apart, marking (T0307)D98.C as missing WARNING: atoms too close: (T0307)A96.O and (T0307)D98.C only 0.000 apart, marking (T0307)D98.C as missing WARNING: atoms too close: (T0307)A96.CB and (T0307)D98.C only 0.000 apart, marking (T0307)D98.C as missing WARNING: atoms too close: (T0307)A96.CA and (T0307)D98.C only 0.000 apart, marking (T0307)D98.C as missing WARNING: atoms too close: (T0307)A96.N and (T0307)D98.C only 0.000 apart, marking (T0307)D98.C as missing WARNING: atoms too close: (T0307)M95.C and (T0307)D98.C only 0.000 apart, marking (T0307)D98.C as missing WARNING: atoms too close: (T0307)M95.O and (T0307)D98.C only 0.000 apart, marking (T0307)D98.C as missing WARNING: atoms too close: (T0307)M95.CE and (T0307)D98.C only 0.000 apart, marking (T0307)D98.C as missing WARNING: atoms too close: (T0307)M95.SD and (T0307)D98.C only 0.000 apart, marking (T0307)D98.C as missing WARNING: atoms too close: (T0307)M95.CG and (T0307)D98.C only 0.000 apart, marking (T0307)D98.C as missing WARNING: atoms too close: (T0307)M95.CB and (T0307)D98.C only 0.000 apart, marking (T0307)D98.C as missing WARNING: atoms too close: (T0307)M95.CA and (T0307)D98.C only 0.000 apart, marking (T0307)D98.C as missing WARNING: atoms too close: (T0307)M95.N and (T0307)D98.C only 0.000 apart, marking (T0307)D98.C as missing WARNING: atoms too close: (T0307)I94.C and (T0307)D98.C only 0.000 apart, marking (T0307)D98.C as missing WARNING: atoms too close: (T0307)I94.O and (T0307)D98.C only 0.000 apart, marking (T0307)D98.C as missing WARNING: atoms too close: (T0307)I94.CD1 and (T0307)D98.C only 0.000 apart, marking (T0307)D98.C as missing WARNING: atoms too close: (T0307)I94.CG2 and (T0307)D98.C only 0.000 apart, marking (T0307)D98.C as missing WARNING: atoms too close: (T0307)I94.CG1 and (T0307)D98.C only 0.000 apart, marking (T0307)D98.C as missing WARNING: atoms too close: (T0307)I94.CB and (T0307)D98.C only 0.000 apart, marking (T0307)D98.C as missing WARNING: atoms too close: (T0307)I94.CA and (T0307)D98.C only 0.000 apart, marking (T0307)D98.C as missing WARNING: atoms too close: (T0307)I94.N and (T0307)D98.C only 0.000 apart, marking (T0307)D98.C as missing WARNING: atoms too close: (T0307)V93.C and (T0307)D98.C only 0.000 apart, marking (T0307)D98.C as missing # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation CaspIta-FOX_TS5 # ReadConformPDB reading from PDB file servers/Distill_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation Distill_TS1 # ReadConformPDB reading from PDB file servers/Distill_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation Distill_TS2 # ReadConformPDB reading from PDB file servers/Distill_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation Distill_TS3 # ReadConformPDB reading from PDB file servers/Distill_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation Distill_TS4 # ReadConformPDB reading from PDB file servers/Distill_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation Distill_TS5 # ReadConformPDB reading from PDB file servers/FAMSD_TS1.pdb.gz looking for model 1 # Found a chain break before 122 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS1 # ReadConformPDB reading from PDB file servers/FAMSD_TS2.pdb.gz looking for model 1 # Found a chain break before 124 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS2 # ReadConformPDB reading from PDB file servers/FAMSD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation FAMSD_TS3 # ReadConformPDB reading from PDB file servers/FAMSD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FAMSD_TS4 # ReadConformPDB reading from PDB file servers/FAMSD_TS5.pdb.gz looking for model 1 # Found a chain break before 119 # copying to AlignedFragments data structure # naming current conformation FAMSD_TS5 # ReadConformPDB reading from PDB file servers/FAMS_TS1.pdb.gz looking for model 1 # Found a chain break before 130 # copying to AlignedFragments data structure # naming current conformation FAMS_TS1 # ReadConformPDB reading from PDB file servers/FAMS_TS2.pdb.gz looking for model 1 # Found a chain break before 122 # copying to AlignedFragments data structure # naming current conformation FAMS_TS2 # ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1 # Found a chain break before 122 # copying to AlignedFragments data structure # naming current conformation FAMS_TS3 # ReadConformPDB reading from PDB file servers/FAMS_TS4.pdb.gz looking for model 1 # Found a chain break before 122 # copying to AlignedFragments data structure # naming current conformation FAMS_TS4 # ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1 # Found a chain break before 130 # copying to AlignedFragments data structure # naming current conformation FAMS_TS5 # ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1 # Found a chain break before 65 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS1 # ReadConformPDB reading from PDB file servers/FOLDpro_TS2.pdb.gz looking for model 1 # Found a chain break before 125 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS2 # ReadConformPDB reading from PDB file servers/FOLDpro_TS3.pdb.gz looking for model 1 # Found a chain break before 128 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS3 # ReadConformPDB reading from PDB file servers/FOLDpro_TS4.pdb.gz looking for model 1 # Found a chain break before 77 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS4 # ReadConformPDB reading from PDB file servers/FOLDpro_TS5.pdb.gz looking for model 1 # Found a chain break before 38 # copying to AlignedFragments data structure # naming current conformation FOLDpro_TS5 # ReadConformPDB reading from PDB file servers/FORTE1_AL1.pdb.gz looking for model 1 Skipped atom 258, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 260, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 262, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz Skipped atom 264, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL1 # ReadConformPDB reading from PDB file servers/FORTE1_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation FORTE1_AL2 # ReadConformPDB reading from PDB file servers/FORTE1_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE1_AL3 # ReadConformPDB reading from PDB file servers/FORTE1_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation FORTE1_AL4 # ReadConformPDB reading from PDB file servers/FORTE1_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation FORTE1_AL5 # ReadConformPDB reading from PDB file servers/FORTE2_AL1.pdb.gz looking for model 1 Skipped atom 258, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 260, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 262, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz Skipped atom 264, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FORTE2_AL1 # ReadConformPDB reading from PDB file servers/FORTE2_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation FORTE2_AL2 # ReadConformPDB reading from PDB file servers/FORTE2_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation FORTE2_AL3 # ReadConformPDB reading from PDB file servers/FORTE2_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation FORTE2_AL4 # ReadConformPDB reading from PDB file servers/FORTE2_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation FORTE2_AL5 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS1.pdb.gz looking for model 1 # Found a chain break before 83 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS1 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS2.pdb.gz looking for model 1 # Found a chain break before 102 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS2 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS3.pdb.gz looking for model 1 # Found a chain break before 81 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS3 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS4.pdb.gz looking for model 1 # Found a chain break before 46 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS4 # ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS5.pdb.gz looking for model 1 # Found a chain break before 56 # copying to AlignedFragments data structure # naming current conformation FPSOLVER-SERVER_TS5 # ReadConformPDB reading from PDB file servers/FUGMOD_TS1.pdb.gz looking for model 1 # Found a chain break before 117 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS1 # ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1 # Found a chain break before 66 # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS2 # ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGMOD_TS3 # ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation FUGMOD_TS4 # ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1 # naming current conformation FUGMOD_TS5 # ReadConformPDB reading from PDB file servers/FUGUE_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation FUGUE_AL1 # ReadConformPDB reading from PDB file servers/FUGUE_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGUE_AL2 # ReadConformPDB reading from PDB file servers/FUGUE_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation FUGUE_AL3 # ReadConformPDB reading from PDB file servers/FUGUE_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation FUGUE_AL4 # ReadConformPDB reading from PDB file servers/FUGUE_AL5.pdb.gz looking for model 1 Skipped atom 175, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL5.pdb.gz Skipped atom 260, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL5.pdb.gz Skipped atom 273, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL5.pdb.gz # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation FUGUE_AL5 # ReadConformPDB reading from PDB file servers/FUNCTION_TS1.pdb.gz looking for model 1 # Found a chain break before 124 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS1 # ReadConformPDB reading from PDB file servers/FUNCTION_TS2.pdb.gz looking for model 1 # Found a chain break before 124 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS2 # ReadConformPDB reading from PDB file servers/FUNCTION_TS3.pdb.gz looking for model 1 # Found a chain break before 130 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS3 # ReadConformPDB reading from PDB file servers/FUNCTION_TS4.pdb.gz looking for model 1 # Found a chain break before 120 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS4 # ReadConformPDB reading from PDB file servers/FUNCTION_TS5.pdb.gz looking for model 1 # Found a chain break before 123 # copying to AlignedFragments data structure # naming current conformation FUNCTION_TS5 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1 # naming current conformation GeneSilicoMetaServer_TS1 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS2 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS3 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS4.pdb.gz looking for model 1 # Found a chain break before 73 # copying to AlignedFragments data structure # naming current conformation GeneSilicoMetaServer_TS4 # ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation GeneSilicoMetaServer_TS5 # ReadConformPDB reading from PDB file servers/HHpred1_TS1.pdb.gz looking for model 1 # naming current conformation HHpred1_TS1 # ReadConformPDB reading from PDB file servers/HHpred2_TS1.pdb.gz looking for model 1 # naming current conformation HHpred2_TS1 # ReadConformPDB reading from PDB file servers/HHpred3_TS1.pdb.gz looking for model 1 # Found a chain break before 116 # copying to AlignedFragments data structure # naming current conformation HHpred3_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS1 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS2 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS3 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS4 # ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation Huber-Torda-Server_TS5 # ReadConformPDB reading from PDB file servers/LOOPP_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation LOOPP_TS1 # ReadConformPDB reading from PDB file servers/LOOPP_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation LOOPP_TS2 # ReadConformPDB reading from PDB file servers/LOOPP_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation LOOPP_TS3 # ReadConformPDB reading from PDB file servers/LOOPP_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation LOOPP_TS4 # ReadConformPDB reading from PDB file servers/LOOPP_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation LOOPP_TS5 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS1.pdb.gz looking for model 1 # Found a chain break before 89 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS1 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS2.pdb.gz looking for model 1 # naming current conformation Ma-OPUS-server_TS2 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS3.pdb.gz looking for model 1 # Found a chain break before 117 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS3 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS4.pdb.gz looking for model 1 # Found a chain break before 108 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS4 # ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS5.pdb.gz looking for model 1 # Found a chain break before 90 # copying to AlignedFragments data structure # naming current conformation Ma-OPUS-server_TS5 # ReadConformPDB reading from PDB file servers/MetaTasser_TS1.pdb.gz looking for model 1 # Found a chain break before 131 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS1 # ReadConformPDB reading from PDB file servers/MetaTasser_TS2.pdb.gz looking for model 1 # Found a chain break before 132 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS2 # ReadConformPDB reading from PDB file servers/MetaTasser_TS3.pdb.gz looking for model 1 # Found a chain break before 131 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS3 # ReadConformPDB reading from PDB file servers/MetaTasser_TS4.pdb.gz looking for model 1 # Found a chain break before 132 # copying to AlignedFragments data structure # naming current conformation MetaTasser_TS4 # ReadConformPDB reading from PDB file servers/NN_PUT_lab_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation NN_PUT_lab_TS1 # ReadConformPDB reading from PDB file servers/POMYSL_TS1.pdb.gz looking for model 1 # Found a chain break before 128 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS1 # ReadConformPDB reading from PDB file servers/POMYSL_TS2.pdb.gz looking for model 1 # Found a chain break before 128 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS2 # ReadConformPDB reading from PDB file servers/POMYSL_TS3.pdb.gz looking for model 1 # Found a chain break before 89 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS3 # ReadConformPDB reading from PDB file servers/POMYSL_TS4.pdb.gz looking for model 1 # Found a chain break before 126 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS4 # ReadConformPDB reading from PDB file servers/POMYSL_TS5.pdb.gz looking for model 1 # Found a chain break before 60 # copying to AlignedFragments data structure # naming current conformation POMYSL_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS1.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS2.pdb.gz looking for model 1 # naming current conformation PROTINFO-AB_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation PROTINFO-AB_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation PROTINFO-AB_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation PROTINFO-AB_TS5 # ReadConformPDB reading from PDB file servers/PROTINFO_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS1 # ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS2 # ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1 # naming current conformation PROTINFO_TS3 # ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS4 # ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation PROTINFO_TS5 # ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation Pcons6_TS1 # ReadConformPDB reading from PDB file servers/Pcons6_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation Pcons6_TS2 # ReadConformPDB reading from PDB file servers/Pcons6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation Pcons6_TS3 # ReadConformPDB reading from PDB file servers/Pcons6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation Pcons6_TS4 # ReadConformPDB reading from PDB file servers/Pcons6_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation Pcons6_TS5 # ReadConformPDB reading from PDB file servers/Phyre-1_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation Phyre-1_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS1 # ReadConformPDB reading from PDB file servers/Phyre-2_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS2 # ReadConformPDB reading from PDB file servers/Phyre-2_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS3 # ReadConformPDB reading from PDB file servers/Phyre-2_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS4 # ReadConformPDB reading from PDB file servers/Phyre-2_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation Phyre-2_TS5 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS1.pdb.gz looking for model 1 # Found a chain break before 12 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS1 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1 # Found a chain break before 12 # copying to AlignedFragments data structure # naming current conformation Pmodeller6_TS2 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS3 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS4 # ReadConformPDB reading from PDB file servers/Pmodeller6_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation Pmodeller6_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS1.pdb.gz looking for model 1 # Found a chain break before 16 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS2.pdb.gz looking for model 1 # naming current conformation RAPTOR-ACE_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS4.pdb.gz looking for model 1 # naming current conformation RAPTOR-ACE_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS5.pdb.gz looking for model 1 # Found a chain break before 107 # copying to AlignedFragments data structure # naming current conformation RAPTOR-ACE_TS5 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS1.pdb.gz looking for model 1 # Found a chain break before 115 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS1 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS2.pdb.gz looking for model 1 # Found a chain break before 115 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS2 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS3.pdb.gz looking for model 1 # Found a chain break before 61 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS3 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS4.pdb.gz looking for model 1 # Found a chain break before 36 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS4 # ReadConformPDB reading from PDB file servers/RAPTORESS_TS5.pdb.gz looking for model 1 # Found a chain break before 36 # copying to AlignedFragments data structure # naming current conformation RAPTORESS_TS5 # ReadConformPDB reading from PDB file servers/RAPTOR_TS1.pdb.gz looking for model 1 # Found a chain break before 115 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS1 # ReadConformPDB reading from PDB file servers/RAPTOR_TS2.pdb.gz looking for model 1 # Found a chain break before 51 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS2 # ReadConformPDB reading from PDB file servers/RAPTOR_TS3.pdb.gz looking for model 1 # Found a chain break before 108 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS3 # ReadConformPDB reading from PDB file servers/RAPTOR_TS4.pdb.gz looking for model 1 # Found a chain break before 119 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS4 # ReadConformPDB reading from PDB file servers/RAPTOR_TS5.pdb.gz looking for model 1 # Found a chain break before 89 # copying to AlignedFragments data structure # naming current conformation RAPTOR_TS5 # ReadConformPDB reading from PDB file servers/ROBETTA_TS1.pdb.gz looking for model 1 # Found a chain break before 12 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS1 # ReadConformPDB reading from PDB file servers/ROBETTA_TS2.pdb.gz looking for model 1 # Found a chain break before 12 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS2 # ReadConformPDB reading from PDB file servers/ROBETTA_TS3.pdb.gz looking for model 1 # Found a chain break before 12 # copying to AlignedFragments data structure # naming current conformation ROBETTA_TS3 # ReadConformPDB reading from PDB file servers/ROBETTA_TS4.pdb.gz looking for model 1 # naming current conformation ROBETTA_TS4 # ReadConformPDB reading from PDB file servers/ROBETTA_TS5.pdb.gz looking for model 1 # naming current conformation ROBETTA_TS5 # ReadConformPDB reading from PDB file servers/ROKKY_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS1 # ReadConformPDB reading from PDB file servers/ROKKY_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS2 # ReadConformPDB reading from PDB file servers/ROKKY_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS3 # ReadConformPDB reading from PDB file servers/ROKKY_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS4 # ReadConformPDB reading from PDB file servers/ROKKY_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation ROKKY_TS5 # ReadConformPDB reading from PDB file servers/SAM-T02_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL1 # ReadConformPDB reading from PDB file servers/SAM-T02_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL2 # ReadConformPDB reading from PDB file servers/SAM-T02_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL3 # ReadConformPDB reading from PDB file servers/SAM-T02_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL4 # ReadConformPDB reading from PDB file servers/SAM-T02_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation SAM-T02_AL5 # ReadConformPDB reading from PDB file servers/SAM-T99_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL1 # ReadConformPDB reading from PDB file servers/SAM-T99_AL2.pdb.gz looking for model 1 Skipped atom 13, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL2.pdb.gz Skipped atom 38, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL2.pdb.gz Skipped atom 39, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL2.pdb.gz Skipped atom 40, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL2.pdb.gz Skipped atom 41, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL2.pdb.gz Skipped atom 102, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL2.pdb.gz Skipped atom 127, because occupancy 1.000 <= existing 1.000 in servers/SAM-T99_AL2.pdb.gz # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation SAM-T99_AL2 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS1.pdb.gz looking for model 1 # Found a chain break before 96 # copying to AlignedFragments data structure # naming current conformation SAM_T06_server_TS1 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS2 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS3 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS4 # ReadConformPDB reading from PDB file servers/SAM_T06_server_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation SAM_T06_server_TS5 # ReadConformPDB reading from PDB file servers/SP3_TS1.pdb.gz looking for model 1 # naming current conformation SP3_TS1 # ReadConformPDB reading from PDB file servers/SP3_TS2.pdb.gz looking for model 1 # Found a chain break before 16 # copying to AlignedFragments data structure # naming current conformation SP3_TS2 # ReadConformPDB reading from PDB file servers/SP3_TS3.pdb.gz looking for model 1 # Found a chain break before 84 # copying to AlignedFragments data structure # naming current conformation SP3_TS3 # ReadConformPDB reading from PDB file servers/SP3_TS4.pdb.gz looking for model 1 # Found a chain break before 49 # copying to AlignedFragments data structure # naming current conformation SP3_TS4 # ReadConformPDB reading from PDB file servers/SP3_TS5.pdb.gz looking for model 1 # Found a chain break before 86 # copying to AlignedFragments data structure # naming current conformation SP3_TS5 # ReadConformPDB reading from PDB file servers/SP4_TS1.pdb.gz looking for model 1 # Found a chain break before 84 # copying to AlignedFragments data structure # naming current conformation SP4_TS1 # ReadConformPDB reading from PDB file servers/SP4_TS2.pdb.gz looking for model 1 # Found a chain break before 29 # copying to AlignedFragments data structure # naming current conformation SP4_TS2 # ReadConformPDB reading from PDB file servers/SP4_TS3.pdb.gz looking for model 1 # Found a chain break before 66 # copying to AlignedFragments data structure # naming current conformation SP4_TS3 # ReadConformPDB reading from PDB file servers/SP4_TS4.pdb.gz looking for model 1 # Found a chain break before 52 # copying to AlignedFragments data structure # naming current conformation SP4_TS4 # ReadConformPDB reading from PDB file servers/SP4_TS5.pdb.gz looking for model 1 # naming current conformation SP4_TS5 # ReadConformPDB reading from PDB file servers/SPARKS2_TS1.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS1 # ReadConformPDB reading from PDB file servers/SPARKS2_TS2.pdb.gz looking for model 1 # Found a chain break before 92 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS2 # ReadConformPDB reading from PDB file servers/SPARKS2_TS3.pdb.gz looking for model 1 # Found a chain break before 66 # copying to AlignedFragments data structure # naming current conformation SPARKS2_TS3 # ReadConformPDB reading from PDB file servers/SPARKS2_TS4.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS4 # ReadConformPDB reading from PDB file servers/SPARKS2_TS5.pdb.gz looking for model 1 # naming current conformation SPARKS2_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS2 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS3 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS4 # ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation UNI-EID_bnmx_TS5 # ReadConformPDB reading from PDB file servers/UNI-EID_expm_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation UNI-EID_expm_TS1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL1 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL2 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL3 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL4 # ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation UNI-EID_sfst_AL5 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS1.pdb.gz looking for model 1 # Found a chain break before 128 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS1 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS2.pdb.gz looking for model 1 # Found a chain break before 119 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS2 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS3.pdb.gz looking for model 1 # Found a chain break before 108 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS3 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS4.pdb.gz looking for model 1 # Found a chain break before 132 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS4 # ReadConformPDB reading from PDB file servers/Zhang-Server_TS5.pdb.gz looking for model 1 # Found a chain break before 119 # copying to AlignedFragments data structure # naming current conformation Zhang-Server_TS5 # ReadConformPDB reading from PDB file servers/beautshot_TS1.pdb.gz looking for model 1 # Found a chain break before 131 # copying to AlignedFragments data structure # naming current conformation beautshot_TS1 # ReadConformPDB reading from PDB file servers/beautshotbase_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation beautshotbase_TS1 # ReadConformPDB reading from PDB file servers/forecast-s_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation forecast-s_AL1 # ReadConformPDB reading from PDB file servers/forecast-s_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation forecast-s_AL2 # ReadConformPDB reading from PDB file servers/forecast-s_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation forecast-s_AL3 # ReadConformPDB reading from PDB file servers/forecast-s_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation forecast-s_AL4 # ReadConformPDB reading from PDB file servers/forecast-s_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation forecast-s_AL5 # ReadConformPDB reading from PDB file servers/gtg_AL1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation gtg_AL1 # ReadConformPDB reading from PDB file servers/gtg_AL2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation gtg_AL2 # ReadConformPDB reading from PDB file servers/gtg_AL3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation gtg_AL3 # ReadConformPDB reading from PDB file servers/gtg_AL4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation gtg_AL4 # ReadConformPDB reading from PDB file servers/gtg_AL5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation gtg_AL5 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1 # Found a chain break before 77 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS2.pdb.gz looking for model 1 # Found a chain break before 45 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS3.pdb.gz looking for model 1 # Found a chain break before 118 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS4.pdb.gz looking for model 1 # Found a chain break before 119 # copying to AlignedFragments data structure # naming current conformation karypis.srv.2_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.2_TS5.pdb.gz looking for model 1 # naming current conformation karypis.srv.2_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS1.pdb.gz looking for model 1 # Found a chain break before 130 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS2.pdb.gz looking for model 1 # Found a chain break before 130 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS3.pdb.gz looking for model 1 WARNING: atoms too close: (T0307)S7.O and (T0307)L8.N only 0.000 apart, marking (T0307)L8.N as missing # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS4.pdb.gz looking for model 1 # Found a chain break before 130 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv.4_TS5.pdb.gz looking for model 1 # Found a chain break before 126 # copying to AlignedFragments data structure # naming current conformation karypis.srv.4_TS5 # ReadConformPDB reading from PDB file servers/karypis.srv_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS1 # ReadConformPDB reading from PDB file servers/karypis.srv_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS2 # ReadConformPDB reading from PDB file servers/karypis.srv_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation karypis.srv_TS3 # ReadConformPDB reading from PDB file servers/karypis.srv_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS4 # ReadConformPDB reading from PDB file servers/karypis.srv_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation karypis.srv_TS5 # ReadConformPDB reading from PDB file servers/keasar-server_TS1.pdb.gz looking for model 1 # Found a chain break before 108 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS1 # ReadConformPDB reading from PDB file servers/keasar-server_TS2.pdb.gz looking for model 1 # Found a chain break before 102 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS2 # ReadConformPDB reading from PDB file servers/keasar-server_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation keasar-server_TS3 # ReadConformPDB reading from PDB file servers/keasar-server_TS5.pdb.gz looking for model 1 # Found a chain break before 103 # copying to AlignedFragments data structure # naming current conformation keasar-server_TS5 # ReadConformPDB reading from PDB file servers/mGen-3D_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation mGen-3D_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation nFOLD_TS1 # ReadConformPDB reading from PDB file servers/nFOLD_TS2.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation nFOLD_TS2 # ReadConformPDB reading from PDB file servers/nFOLD_TS3.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # copying to AlignedFragments data structure # naming current conformation nFOLD_TS3 # ReadConformPDB reading from PDB file servers/nFOLD_TS4.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation nFOLD_TS4 # ReadConformPDB reading from PDB file servers/nFOLD_TS5.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation nFOLD_TS5 # ReadConformPDB reading from PDB file servers/panther2_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation panther2_TS1 # ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1 # WARNING: incomplete conformation T0307 can't currently be optimized by undertaker # naming current conformation shub_TS1 # command:Using radius: 8.0000 Using models AND alignments for constraints model score 2.0121 model score 2.1526 model score 2.0366 model score 2.1157 model score 2.1157 model score 2.1157 model score 2.1157 model score 2.1157 model score 2.1157 model score 2.1157 model score 0.6674 model score 1.6163 model score 1.3229 model score 1.3038 model score 1.1429 model score 1.3038 model score 1.1429 model score 1.0523 model score 1.2643 model score 0.9539 model score 0.7503 model score 1.5880 model score 1.9910 model score 1.6360 model score 1.5088 model score 1.5789 model score 1.2790 model score 1.2796 model score 0.2956 model score 1.5825 model score 1.7620 model score 0.8205 model score 2.4182 model score 0.8162 model score 0.8206 model score 1.8003 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2790 model score 1.9914 model score 1.8720 model score 1.8057 model score 1.5217 model score 0.5040 model score 1.2790 model score 1.2790 model score 1.2796 model score 1.5825 model score 1.7648 model score 1.4221 model score 1.7024 model score 1.6706 model score 1.5985 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.7267 model score 2.0355 model score 2.0478 model score 1.9258 model score 1.9146 model score 1.6500 model score 0.7038 model score 2.0084 model score 1.8180 model score 2.3138 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.8586 model score 1.9876 model score 1.1455 model score 1.7935 model score 1.8025 model score 0.7167 model score 0.6040 model score 0.5339 model score 0.8645 model score 0.8752 model score 2.0752 model score 2.0752 model score 0.7317 model score 1.3646 model score 1.7434 model score 1.4593 model score 1.4868 model score 1.1662 model score 1.6176 model score 0.9015 model score 1.7688 model score 1.7303 model score 1.6394 model score 1.6579 model score 1.8522 model score 1.8449 model score 1.7764 model score 1.6513 model score 0.2888 model score 0.4103 model score 0.4732 model score 0.3188 model score 1.6176 model score 1.6390 model score 1.6390 model score 1.3613 model score 1.0019 model score 1.4578 model score 0.5980 model score 0.5848 model score 1.5245 model score 1.4044 model score 1.6378 model score 1.4198 model score 0.5985 model score 0.6046 model score 0.7260 model score 0.6441 model score 1.9725 model score 1.9358 model score 1.9759 model score 2.0236 model score 2.0210 model score 1.7258 model score 2.1637 model score 2.2024 model score 2.1161 model score 1.6526 model score 1.7540 model score 1.8950 model score 1.6767 model score 1.9966 model score 2.0073 model score 1.9994 model score 1.3340 model score 1.2724 model score 1.1460 model score 1.9144 model score 1.7867 model score 1.8876 model score 1.2567 model score 1.9290 model score 1.3555 model score 2.1791 model score 1.8045 model score 1.1388 model score 1.8723 model score 1.0535 model score 1.3299 model score 1.6767 model score 1.6921 model score 1.8950 model score 1.6323 model score 1.2610 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.4927 model score 1.8325 model score 0.9861 model score 0.8039 model score 1.1637 model score 0.6545 model score 1.3340 model score 1.4093 model score 0.4089 model score 0.8486 model score 1.4093 model score 0.6473 model score 0.4612 model score 1.0464 model score 1.8367 model score 1.9190 model score 0.3894 model score 0.3034 model score 2.0471 model score 1.7515 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.5238 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 0.0997 model score 1.3926 model score 1.2104 model score 0.2665 model score 1.3160 model score 0.6139 model score 0.7053 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 1.2771 model score 0.5676 model score 0.5153 model score 1.4783 model score 1.6032 model score 1.7721 model score 1.6167 model score 1.8308 model score 1.6705 model score 1.1813 model score 1.7333 model score 1.5604 model score 1.4801 model score 1.5851 model score 1.4829 model score 1.5592 model score 1.6095 model score 2.1826 model score 0.5356 model score 2.1419 model score 1.5207 model score 1.9294 model score 1.7802 model score 1.9527 model score 1.4864 model score 1.4334 model score 1.1382 model score 0.8707 USE_META, weight: 0.2576 cost: 2.0121 min: 0.0997 max: 2.4182 USE_META, weight: 0.2031 cost: 2.1526 min: 0.0997 max: 2.4182 USE_META, weight: 0.2481 cost: 2.0366 min: 0.0997 max: 2.4182 USE_META, weight: 0.2174 cost: 2.1157 min: 0.0997 max: 2.4182 USE_META, weight: 0.2174 cost: 2.1157 min: 0.0997 max: 2.4182 USE_META, weight: 0.2174 cost: 2.1157 min: 0.0997 max: 2.4182 USE_META, weight: 0.2174 cost: 2.1157 min: 0.0997 max: 2.4182 USE_META, weight: 0.2174 cost: 2.1157 min: 0.0997 max: 2.4182 USE_META, weight: 0.2174 cost: 2.1157 min: 0.0997 max: 2.4182 USE_META, weight: 0.2174 cost: 2.1157 min: 0.0997 max: 2.4182 USE_META, weight: 0.7796 cost: 0.6674 min: 0.0997 max: 2.4182 USE_META, weight: 0.4113 cost: 1.6163 min: 0.0997 max: 2.4182 USE_META, weight: 0.5252 cost: 1.3229 min: 0.0997 max: 2.4182 USE_META, weight: 0.5326 cost: 1.3038 min: 0.0997 max: 2.4182 USE_META, weight: 0.5950 cost: 1.1429 min: 0.0997 max: 2.4182 USE_META, weight: 0.5326 cost: 1.3038 min: 0.0997 max: 2.4182 USE_META, weight: 0.5950 cost: 1.1429 min: 0.0997 max: 2.4182 USE_META, weight: 0.6302 cost: 1.0523 min: 0.0997 max: 2.4182 USE_META, weight: 0.5479 cost: 1.2643 min: 0.0997 max: 2.4182 USE_META, weight: 0.6684 cost: 0.9539 min: 0.0997 max: 2.4182 USE_META, weight: 0.7475 cost: 0.7503 min: 0.0997 max: 2.4182 USE_META, weight: 0.4222 cost: 1.5880 min: 0.0997 max: 2.4182 USE_META, weight: 0.2658 cost: 1.9910 min: 0.0997 max: 2.4182 USE_META, weight: 0.4036 cost: 1.6360 min: 0.0997 max: 2.4182 USE_META, weight: 0.4530 cost: 1.5088 min: 0.0997 max: 2.4182 USE_META, weight: 0.4258 cost: 1.5789 min: 0.0997 max: 2.4182 USE_META, weight: 0.5422 cost: 1.2790 min: 0.0997 max: 2.4182 USE_META, weight: 0.5420 cost: 1.2796 min: 0.0997 max: 2.4182 USE_META, weight: 0.9239 cost: 0.2956 min: 0.0997 max: 2.4182 USE_META, weight: 0.4244 cost: 1.5825 min: 0.0997 max: 2.4182 USE_META, weight: 0.3547 cost: 1.7620 min: 0.0997 max: 2.4182 USE_META, weight: 0.7202 cost: 0.8205 min: 0.0997 max: 2.4182 USE_META, weight: 0.1000 cost: 2.4182 min: 0.0997 max: 2.4182 USE_META, weight: 0.7219 cost: 0.8162 min: 0.0997 max: 2.4182 USE_META, weight: 0.7202 cost: 0.8206 min: 0.0997 max: 2.4182 USE_META, weight: 0.3399 cost: 1.8003 min: 0.0997 max: 2.4182 USE_META, weight: 0.5430 cost: 1.2771 min: 0.0997 max: 2.4182 USE_META, weight: 0.5430 cost: 1.2771 min: 0.0997 max: 2.4182 USE_META, weight: 0.5430 cost: 1.2771 min: 0.0997 max: 2.4182 USE_META, weight: 0.5430 cost: 1.2771 min: 0.0997 max: 2.4182 USE_META, weight: 0.5430 cost: 1.2771 min: 0.0997 max: 2.4182 USE_META, weight: 0.5422 cost: 1.2790 min: 0.0997 max: 2.4182 USE_META, weight: 0.2657 cost: 1.9914 min: 0.0997 max: 2.4182 USE_META, weight: 0.3120 cost: 1.8720 min: 0.0997 max: 2.4182 USE_META, weight: 0.3377 cost: 1.8057 min: 0.0997 max: 2.4182 USE_META, weight: 0.4480 cost: 1.5217 min: 0.0997 max: 2.4182 USE_META, weight: 0.8430 cost: 0.5040 min: 0.0997 max: 2.4182 USE_META, weight: 0.5422 cost: 1.2790 min: 0.0997 max: 2.4182 USE_META, weight: 0.5422 cost: 1.2790 min: 0.0997 max: 2.4182 USE_META, weight: 0.5420 cost: 1.2796 min: 0.0997 max: 2.4182 USE_META, weight: 0.4244 cost: 1.5825 min: 0.0997 max: 2.4182 USE_META, weight: 0.3536 cost: 1.7648 min: 0.0997 max: 2.4182 USE_META, weight: 0.4867 cost: 1.4221 min: 0.0997 max: 2.4182 USE_META, weight: 0.3778 cost: 1.7024 min: 0.0997 max: 2.4182 USE_META, weight: 0.3902 cost: 1.6706 min: 0.0997 max: 2.4182 USE_META, weight: 0.4182 cost: 1.5985 min: 0.0997 max: 2.4182 USE_META, weight: 0.5430 cost: 1.2771 min: 0.0997 max: 2.4182 USE_META, weight: 0.5430 cost: 1.2771 min: 0.0997 max: 2.4182 USE_META, weight: 0.5430 cost: 1.2771 min: 0.0997 max: 2.4182 USE_META, weight: 0.5430 cost: 1.2771 min: 0.0997 max: 2.4182 USE_META, weight: 0.5430 cost: 1.2771 min: 0.0997 max: 2.4182 USE_META, weight: 0.5430 cost: 1.2771 min: 0.0997 max: 2.4182 USE_META, weight: 0.5430 cost: 1.2771 min: 0.0997 max: 2.4182 USE_META, weight: 0.5430 cost: 1.2771 min: 0.0997 max: 2.4182 USE_META, weight: 0.5430 cost: 1.2771 min: 0.0997 max: 2.4182 USE_META, weight: 0.5430 cost: 1.2771 min: 0.0997 max: 2.4182 USE_META, weight: 0.3684 cost: 1.7267 min: 0.0997 max: 2.4182 USE_META, weight: 0.2486 cost: 2.0355 min: 0.0997 max: 2.4182 USE_META, weight: 0.2438 cost: 2.0478 min: 0.0997 max: 2.4182 USE_META, weight: 0.2911 cost: 1.9258 min: 0.0997 max: 2.4182 USE_META, weight: 0.2955 cost: 1.9146 min: 0.0997 max: 2.4182 USE_META, weight: 0.3982 cost: 1.6500 min: 0.0997 max: 2.4182 USE_META, weight: 0.7655 cost: 0.7038 min: 0.0997 max: 2.4182 USE_META, weight: 0.2591 cost: 2.0084 min: 0.0997 max: 2.4182 USE_META, weight: 0.3330 cost: 1.8180 min: 0.0997 max: 2.4182 USE_META, weight: 0.1405 cost: 2.3138 min: 0.0997 max: 2.4182 USE_META, weight: 0.5430 cost: 1.2771 min: 0.0997 max: 2.4182 USE_META, weight: 0.5430 cost: 1.2771 min: 0.0997 max: 2.4182 USE_META, weight: 0.5430 cost: 1.2771 min: 0.0997 max: 2.4182 USE_META, weight: 0.5430 cost: 1.2771 min: 0.0997 max: 2.4182 USE_META, weight: 0.5430 cost: 1.2771 min: 0.0997 max: 2.4182 USE_META, weight: 0.3172 cost: 1.8586 min: 0.0997 max: 2.4182 USE_META, weight: 0.2671 cost: 1.9876 min: 0.0997 max: 2.4182 USE_META, weight: 0.5940 cost: 1.1455 min: 0.0997 max: 2.4182 USE_META, weight: 0.3425 cost: 1.7935 min: 0.0997 max: 2.4182 USE_META, weight: 0.3390 cost: 1.8025 min: 0.0997 max: 2.4182 USE_META, weight: 0.7605 cost: 0.7167 min: 0.0997 max: 2.4182 USE_META, weight: 0.8042 cost: 0.6040 min: 0.0997 max: 2.4182 USE_META, weight: 0.8314 cost: 0.5339 min: 0.0997 max: 2.4182 USE_META, weight: 0.7031 cost: 0.8645 min: 0.0997 max: 2.4182 USE_META, weight: 0.6989 cost: 0.8752 min: 0.0997 max: 2.4182 USE_META, weight: 0.2331 cost: 2.0752 min: 0.0997 max: 2.4182 USE_META, weight: 0.2331 cost: 2.0752 min: 0.0997 max: 2.4182 USE_META, weight: 0.7547 cost: 0.7317 min: 0.0997 max: 2.4182 USE_META, weight: 0.5090 cost: 1.3646 min: 0.0997 max: 2.4182 USE_META, weight: 0.3619 cost: 1.7434 min: 0.0997 max: 2.4182 USE_META, weight: 0.4722 cost: 1.4593 min: 0.0997 max: 2.4182 USE_META, weight: 0.4615 cost: 1.4868 min: 0.0997 max: 2.4182 USE_META, weight: 0.5860 cost: 1.1662 min: 0.0997 max: 2.4182 USE_META, weight: 0.4108 cost: 1.6176 min: 0.0997 max: 2.4182 USE_META, weight: 0.6887 cost: 0.9015 min: 0.0997 max: 2.4182 USE_META, weight: 0.3521 cost: 1.7688 min: 0.0997 max: 2.4182 USE_META, weight: 0.3670 cost: 1.7303 min: 0.0997 max: 2.4182 USE_META, weight: 0.4023 cost: 1.6394 min: 0.0997 max: 2.4182 USE_META, weight: 0.3951 cost: 1.6579 min: 0.0997 max: 2.4182 USE_META, weight: 0.3197 cost: 1.8522 min: 0.0997 max: 2.4182 USE_META, weight: 0.3225 cost: 1.8449 min: 0.0997 max: 2.4182 USE_META, weight: 0.3491 cost: 1.7764 min: 0.0997 max: 2.4182 USE_META, weight: 0.3977 cost: 1.6513 min: 0.0997 max: 2.4182 USE_META, weight: 0.9266 cost: 0.2888 min: 0.0997 max: 2.4182 USE_META, weight: 0.8794 cost: 0.4103 min: 0.0997 max: 2.4182 USE_META, weight: 0.8550 cost: 0.4732 min: 0.0997 max: 2.4182 USE_META, weight: 0.9149 cost: 0.3188 min: 0.0997 max: 2.4182 USE_META, weight: 0.4108 cost: 1.6176 min: 0.0997 max: 2.4182 USE_META, weight: 0.4025 cost: 1.6390 min: 0.0997 max: 2.4182 USE_META, weight: 0.4025 cost: 1.6390 min: 0.0997 max: 2.4182 USE_META, weight: 0.5102 cost: 1.3613 min: 0.0997 max: 2.4182 USE_META, weight: 0.6498 cost: 1.0019 min: 0.0997 max: 2.4182 USE_META, weight: 0.4728 cost: 1.4578 min: 0.0997 max: 2.4182 USE_META, weight: 0.8065 cost: 0.5980 min: 0.0997 max: 2.4182 USE_META, weight: 0.8117 cost: 0.5848 min: 0.0997 max: 2.4182 USE_META, weight: 0.4469 cost: 1.5245 min: 0.0997 max: 2.4182 USE_META, weight: 0.4935 cost: 1.4044 min: 0.0997 max: 2.4182 USE_META, weight: 0.4029 cost: 1.6378 min: 0.0997 max: 2.4182 USE_META, weight: 0.4876 cost: 1.4198 min: 0.0997 max: 2.4182 USE_META, weight: 0.8064 cost: 0.5985 min: 0.0997 max: 2.4182 USE_META, weight: 0.8040 cost: 0.6046 min: 0.0997 max: 2.4182 USE_META, weight: 0.7569 cost: 0.7260 min: 0.0997 max: 2.4182 USE_META, weight: 0.7887 cost: 0.6441 min: 0.0997 max: 2.4182 USE_META, weight: 0.2730 cost: 1.9725 min: 0.0997 max: 2.4182 USE_META, weight: 0.2872 cost: 1.9358 min: 0.0997 max: 2.4182 USE_META, weight: 0.2717 cost: 1.9759 min: 0.0997 max: 2.4182 USE_META, weight: 0.2532 cost: 2.0236 min: 0.0997 max: 2.4182 USE_META, weight: 0.2542 cost: 2.0210 min: 0.0997 max: 2.4182 USE_META, weight: 0.3688 cost: 1.7258 min: 0.0997 max: 2.4182 USE_META, weight: 0.1988 cost: 2.1637 min: 0.0997 max: 2.4182 USE_META, weight: 0.1838 cost: 2.2024 min: 0.0997 max: 2.4182 USE_META, weight: 0.2173 cost: 2.1161 min: 0.0997 max: 2.4182 USE_META, weight: 0.3972 cost: 1.6526 min: 0.0997 max: 2.4182 USE_META, weight: 0.3578 cost: 1.7540 min: 0.0997 max: 2.4182 USE_META, weight: 0.3031 cost: 1.8950 min: 0.0997 max: 2.4182 USE_META, weight: 0.3878 cost: 1.6767 min: 0.0997 max: 2.4182 USE_META, weight: 0.2636 cost: 1.9966 min: 0.0997 max: 2.4182 USE_META, weight: 0.2595 cost: 2.0073 min: 0.0997 max: 2.4182 USE_META, weight: 0.2626 cost: 1.9994 min: 0.0997 max: 2.4182 USE_META, weight: 0.5208 cost: 1.3340 min: 0.0997 max: 2.4182 USE_META, weight: 0.5448 cost: 1.2724 min: 0.0997 max: 2.4182 USE_META, weight: 0.5938 cost: 1.1460 min: 0.0997 max: 2.4182 USE_META, weight: 0.2955 cost: 1.9144 min: 0.0997 max: 2.4182 USE_META, weight: 0.3451 cost: 1.7867 min: 0.0997 max: 2.4182 USE_META, weight: 0.3059 cost: 1.8876 min: 0.0997 max: 2.4182 USE_META, weight: 0.5508 cost: 1.2567 min: 0.0997 max: 2.4182 USE_META, weight: 0.2899 cost: 1.9290 min: 0.0997 max: 2.4182 USE_META, weight: 0.5125 cost: 1.3555 min: 0.0997 max: 2.4182 USE_META, weight: 0.1928 cost: 2.1791 min: 0.0997 max: 2.4182 USE_META, weight: 0.3382 cost: 1.8045 min: 0.0997 max: 2.4182 USE_META, weight: 0.5966 cost: 1.1388 min: 0.0997 max: 2.4182 USE_META, weight: 0.3119 cost: 1.8723 min: 0.0997 max: 2.4182 USE_META, weight: 0.6297 cost: 1.0535 min: 0.0997 max: 2.4182 USE_META, weight: 0.5225 cost: 1.3299 min: 0.0997 max: 2.4182 USE_META, weight: 0.3878 cost: 1.6767 min: 0.0997 max: 2.4182 USE_META, weight: 0.3818 cost: 1.6921 min: 0.0997 max: 2.4182 USE_META, weight: 0.3031 cost: 1.8950 min: 0.0997 max: 2.4182 USE_META, weight: 0.4051 cost: 1.6323 min: 0.0997 max: 2.4182 USE_META, weight: 0.5492 cost: 1.2610 min: 0.0997 max: 2.4182 USE_META, weight: 0.5430 cost: 1.2771 min: 0.0997 max: 2.4182 USE_META, weight: 0.5430 cost: 1.2771 min: 0.0997 max: 2.4182 USE_META, weight: 0.5430 cost: 1.2771 min: 0.0997 max: 2.4182 USE_META, weight: 0.5430 cost: 1.2771 min: 0.0997 max: 2.4182 USE_META, weight: 0.5430 cost: 1.2771 min: 0.0997 max: 2.4182 USE_META, weight: 0.5430 cost: 1.2771 min: 0.0997 max: 2.4182 USE_META, weight: 0.5430 cost: 1.2771 min: 0.0997 max: 2.4182 USE_META, weight: 0.5430 cost: 1.2771 min: 0.0997 max: 2.4182 USE_META, weight: 0.5430 cost: 1.2771 min: 0.0997 max: 2.4182 USE_META, weight: 0.5430 cost: 1.2771 min: 0.0997 max: 2.4182 USE_META, weight: 0.5430 cost: 1.2771 min: 0.0997 max: 2.4182 USE_META, weight: 0.5430 cost: 1.2771 min: 0.0997 max: 2.4182 USE_META, weight: 0.4592 cost: 1.4927 min: 0.0997 max: 2.4182 USE_META, weight: 0.3274 cost: 1.8325 min: 0.0997 max: 2.4182 USE_META, weight: 0.6559 cost: 0.9861 min: 0.0997 max: 2.4182 USE_META, weight: 0.7266 cost: 0.8039 min: 0.0997 max: 2.4182 USE_META, weight: 0.5869 cost: 1.1637 min: 0.0997 max: 2.4182 USE_META, weight: 0.7846 cost: 0.6545 min: 0.0997 max: 2.4182 USE_META, weight: 0.5208 cost: 1.3340 min: 0.0997 max: 2.4182 USE_META, weight: 0.4916 cost: 1.4093 min: 0.0997 max: 2.4182 USE_META, weight: 0.8799 cost: 0.4089 min: 0.0997 max: 2.4182 USE_META, weight: 0.7093 cost: 0.8486 min: 0.0997 max: 2.4182 USE_META, weight: 0.4916 cost: 1.4093 min: 0.0997 max: 2.4182 USE_META, weight: 0.7874 cost: 0.6473 min: 0.0997 max: 2.4182 USE_META, weight: 0.8596 cost: 0.4612 min: 0.0997 max: 2.4182 USE_META, weight: 0.6325 cost: 1.0464 min: 0.0997 max: 2.4182 USE_META, weight: 0.3257 cost: 1.8367 min: 0.0997 max: 2.4182 USE_META, weight: 0.2938 cost: 1.9190 min: 0.0997 max: 2.4182 USE_META, weight: 0.8875 cost: 0.3894 min: 0.0997 max: 2.4182 USE_META, weight: 0.9209 cost: 0.3034 min: 0.0997 max: 2.4182 USE_META, weight: 0.2440 cost: 2.0471 min: 0.0997 max: 2.4182 USE_META, weight: 0.3588 cost: 1.7515 min: 0.0997 max: 2.4182 USE_META, weight: 0.5430 cost: 1.2771 min: 0.0997 max: 2.4182 USE_META, weight: 0.5430 cost: 1.2771 min: 0.0997 max: 2.4182 USE_META, weight: 0.5430 cost: 1.2771 min: 0.0997 max: 2.4182 USE_META, weight: 0.5430 cost: 1.2771 min: 0.0997 max: 2.4182 USE_META, weight: 0.5430 cost: 1.2771 min: 0.0997 max: 2.4182 USE_META, weight: 0.4472 cost: 1.5238 min: 0.0997 max: 2.4182 USE_META, weight: 0.5430 cost: 1.2771 min: 0.0997 max: 2.4182 USE_META, weight: 0.5430 cost: 1.2771 min: 0.0997 max: 2.4182 USE_META, weight: 0.5430 cost: 1.2771 min: 0.0997 max: 2.4182 USE_META, weight: 0.5430 cost: 1.2771 min: 0.0997 max: 2.4182 USE_META, weight: 0.5430 cost: 1.2771 min: 0.0997 max: 2.4182 USE_META, weight: 1.0000 cost: 0.0997 min: 0.0997 max: 2.4182 USE_META, weight: 0.4981 cost: 1.3926 min: 0.0997 max: 2.4182 USE_META, weight: 0.5688 cost: 1.2104 min: 0.0997 max: 2.4182 USE_META, weight: 0.9352 cost: 0.2665 min: 0.0997 max: 2.4182 USE_META, weight: 0.5279 cost: 1.3160 min: 0.0997 max: 2.4182 USE_META, weight: 0.8004 cost: 0.6139 min: 0.0997 max: 2.4182 USE_META, weight: 0.7649 cost: 0.7053 min: 0.0997 max: 2.4182 USE_META, weight: 0.5430 cost: 1.2771 min: 0.0997 max: 2.4182 USE_META, weight: 0.5430 cost: 1.2771 min: 0.0997 max: 2.4182 USE_META, weight: 0.5430 cost: 1.2771 min: 0.0997 max: 2.4182 USE_META, weight: 0.5430 cost: 1.2771 min: 0.0997 max: 2.4182 USE_META, weight: 0.5430 cost: 1.2771 min: 0.0997 max: 2.4182 USE_META, weight: 0.5430 cost: 1.2771 min: 0.0997 max: 2.4182 USE_META, weight: 0.5430 cost: 1.2771 min: 0.0997 max: 2.4182 USE_META, weight: 0.5430 cost: 1.2771 min: 0.0997 max: 2.4182 USE_META, weight: 0.5430 cost: 1.2771 min: 0.0997 max: 2.4182 USE_META, weight: 0.5430 cost: 1.2771 min: 0.0997 max: 2.4182 USE_META, weight: 0.8184 cost: 0.5676 min: 0.0997 max: 2.4182 USE_META, weight: 0.8387 cost: 0.5153 min: 0.0997 max: 2.4182 USE_META, weight: 0.4649 cost: 1.4783 min: 0.0997 max: 2.4182 USE_META, weight: 0.4164 cost: 1.6032 min: 0.0997 max: 2.4182 USE_META, weight: 0.3508 cost: 1.7721 min: 0.0997 max: 2.4182 USE_META, weight: 0.4111 cost: 1.6167 min: 0.0997 max: 2.4182 USE_META, weight: 0.3280 cost: 1.8308 min: 0.0997 max: 2.4182 USE_META, weight: 0.3902 cost: 1.6705 min: 0.0997 max: 2.4182 USE_META, weight: 0.5801 cost: 1.1813 min: 0.0997 max: 2.4182 USE_META, weight: 0.3659 cost: 1.7333 min: 0.0997 max: 2.4182 USE_META, weight: 0.4330 cost: 1.5604 min: 0.0997 max: 2.4182 USE_META, weight: 0.4641 cost: 1.4801 min: 0.0997 max: 2.4182 USE_META, weight: 0.4234 cost: 1.5851 min: 0.0997 max: 2.4182 USE_META, weight: 0.4630 cost: 1.4829 min: 0.0997 max: 2.4182 USE_META, weight: 0.4335 cost: 1.5592 min: 0.0997 max: 2.4182 USE_META, weight: 0.4139 cost: 1.6095 min: 0.0997 max: 2.4182 USE_META, weight: 0.1915 cost: 2.1826 min: 0.0997 max: 2.4182 USE_META, weight: 0.8308 cost: 0.5356 min: 0.0997 max: 2.4182 USE_META, weight: 0.2073 cost: 2.1419 min: 0.0997 max: 2.4182 USE_META, weight: 0.4484 cost: 1.5207 min: 0.0997 max: 2.4182 USE_META, weight: 0.2897 cost: 1.9294 min: 0.0997 max: 2.4182 USE_META, weight: 0.3477 cost: 1.7802 min: 0.0997 max: 2.4182 USE_META, weight: 0.2807 cost: 1.9527 min: 0.0997 max: 2.4182 USE_META, weight: 0.4617 cost: 1.4864 min: 0.0997 max: 2.4182 USE_META, weight: 0.4823 cost: 1.4334 min: 0.0997 max: 2.4182 USE_META, weight: 0.5969 cost: 1.1382 min: 0.0997 max: 2.4182 USE_META, weight: 0.7007 cost: 0.8707 min: 0.0997 max: 2.4182 USE_EVALUE, weight: 0.1000 eval: 45.7000 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.1000 eval: 45.7000 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.1000 eval: 45.7000 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.8138 eval: 9.7481 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.8138 eval: 9.7481 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.8138 eval: 9.7481 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.8801 eval: 6.4117 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.8801 eval: 6.4117 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.8801 eval: 6.4117 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.8383 eval: 8.5164 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.8383 eval: 8.5164 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.8383 eval: 8.5164 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.8381 eval: 8.5282 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.8381 eval: 8.5282 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.8381 eval: 8.5282 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.7846 eval: 11.2180 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.7846 eval: 11.2180 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.7846 eval: 11.2180 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.9075 eval: 5.0300 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.9075 eval: 5.0300 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.9075 eval: 5.0300 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.7654 eval: 12.1880 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.7654 eval: 12.1880 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.7654 eval: 12.1880 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.8572 eval: 7.5659 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.8572 eval: 7.5659 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.8572 eval: 7.5659 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.9082 eval: 4.9957 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.9082 eval: 4.9957 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.9082 eval: 4.9957 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.8945 eval: 5.6854 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.8945 eval: 5.6854 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.8945 eval: 5.6854 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 1.0000 eval: 0.3720 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 1.0000 eval: 0.3720 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 1.0000 eval: 0.3720 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.7969 eval: 10.6000 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.7969 eval: 10.6000 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.7969 eval: 10.6000 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.7633 eval: 12.2920 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.7633 eval: 12.2920 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.7633 eval: 12.2920 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.8620 eval: 7.3205 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.8620 eval: 7.3205 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.8620 eval: 7.3205 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.8027 eval: 10.3080 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.8027 eval: 10.3080 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.8027 eval: 10.3080 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.9409 eval: 3.3494 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.9409 eval: 3.3494 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.9409 eval: 3.3494 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.2092 eval: 40.2000 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.2092 eval: 40.2000 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.2092 eval: 40.2000 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.8913 eval: 5.8472 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.8913 eval: 5.8472 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.8913 eval: 5.8472 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.8185 eval: 9.5117 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.8185 eval: 9.5117 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.8185 eval: 9.5117 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.8054 eval: 10.1720 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.8054 eval: 10.1720 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.8054 eval: 10.1720 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.7541 eval: 12.7560 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.7541 eval: 12.7560 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.7541 eval: 12.7560 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.8584 eval: 7.5042 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.8584 eval: 7.5042 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.8584 eval: 7.5042 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.7017 eval: 15.3960 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.7017 eval: 15.3960 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.7017 eval: 15.3960 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.8482 eval: 8.0161 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.8482 eval: 8.0161 min: 0.3720 max: 45.7000 USE_EVALUE, weight: 0.8482 eval: 8.0161 min: 0.3720 max: 45.7000 Number of contacts in models: 252 Number of contacts in alignments: 75 NUMB_ALIGNS: 75 Adding 6323 constraints to all3.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all3.constraints maxweight: 1.0000 Optimizing... Probability sum: -250.3936, CN propb: -250.3936 weights: 0.2667 constraints: 232 # command:Found ConstraintSet # PrintContacts align.constraints_meta03 Number of constraints in align3.constraints 232 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_meta03 Number of constraints in align3.constraints.bonus 232 # command:Found ConstraintSet # PrintContacts rejected.constraints_meta03 Number of constraints in rejected3.constraints 6091 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_meta03 Number of constraints in rejected3.constraints.bonus 6091 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_meta03 Number of constraints in noncontact3.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_meta03 Number of constraints in noncontact3.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_meta03 Number of constraints in all3.constraints 6323 # command: