# 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/T0377/ # command:# Making conformation for sequence T0377 numbered 1 through 101 Created new target T0377 from T0377.a2m # command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0377/ # command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0377//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0377/manyalignments-good-all.under or /projects/compbio/experiments/protein-predict/casp7/T0377//projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0377/manyalignments-good-all.under.gz for input Trying /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0377/manyalignments-good-all.under # reading script from file /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0377/manyalignments-good-all.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ta9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1ta9A expands to /projects/compbio/data/pdb/1ta9.pdb.gz 1ta9A:# T0377 read from 1ta9A/merged-good-all-a2m # 1ta9A read from 1ta9A/merged-good-all-a2m # adding 1ta9A to template set # found chain 1ta9A in template set T0377 4 :LYLIFYD 1ta9A 93 :SAVVLAD # choosing archetypes in rotamer library T0377 14 :DNLR 1ta9A 100 :QNVW T0377 18 :NRVAEFLKKKGLDRI 1ta9A 108 :NKIVDSLSQNGMTVT T0377 34 :YSVFMGDLNSSRLKDVEAGL 1ta9A 123 :KLVFGGEASLVELDKLRKQC T0377 65 :DERFFI 1ta9A 143 :PDDTQV Number of specific fragments extracted= 5 number of extra gaps= 0 total=5 Number of alignments=1 # 1ta9A read from 1ta9A/merged-good-all-a2m # found chain 1ta9A in template set T0377 4 :LYLIFYD 1ta9A 93 :SAVVLAD T0377 14 :DNLR 1ta9A 100 :QNVW T0377 18 :NRVAEFLKKKGLD 1ta9A 108 :NKIVDSLSQNGMT T0377 32 :IQYSVFMGDLNSSRLKDVEAGLK 1ta9A 121 :VTKLVFGGEASLVELDKLRKQCP T0377 65 :DE 1ta9A 144 :DD T0377 80 :FRERIVIGY 1ta9A 146 :TQVIIGVGG Number of specific fragments extracted= 6 number of extra gaps= 0 total=11 Number of alignments=2 # 1ta9A read from 1ta9A/merged-good-all-a2m # found chain 1ta9A in template set T0377 4 :LYLIFYD 1ta9A 93 :SAVVLAD T0377 14 :DNLR 1ta9A 100 :QNVW T0377 18 :NRVAEFLKKKGLDRIQ 1ta9A 108 :NKIVDSLSQNGMTVTK T0377 35 :SVFMGDLNSSRLKDVEAGLK 1ta9A 124 :LVFGGEASLVELDKLRKQCP T0377 66 :ERFFILI 1ta9A 144 :DDTQVII Number of specific fragments extracted= 5 number of extra gaps= 0 total=16 Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1pm9A/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/T0377/1pm9A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0377/1pm9A/merged-good-all-a2m.gz for input Trying 1pm9A/merged-good-all-a2m Error: Couldn't open file 1pm9A/merged-good-all-a2m or 1pm9A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t8qA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1t8qA expands to /projects/compbio/data/pdb/1t8q.pdb.gz 1t8qA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0377 read from 1t8qA/merged-good-all-a2m # 1t8qA read from 1t8qA/merged-good-all-a2m # adding 1t8qA to template set # found chain 1t8qA in template set T0377 16 :LRNRVAEFLKKKGLD 1t8qA 185 :IAAKTLEVLKKYGYT T0377 36 :VFM 1t8qA 205 :VYL T0377 45 :RLKDVEAGL 1t8qA 214 :ELKRIKNEL T0377 57 :GNRKK 1t8qA 223 :EPKMG T0377 66 :ERFFILIVPITENQFRERIVI 1t8qA 228 :MELNLVQLIAYTDWNETQQKQ T0377 89 :SGS 1t8qA 249 :PDG Number of specific fragments extracted= 6 number of extra gaps= 0 total=22 Number of alignments=4 # 1t8qA read from 1t8qA/merged-good-all-a2m # found chain 1t8qA in template set T0377 16 :LRNRVAEFLKKKGLD 1t8qA 185 :IAAKTLEVLKKYGYT T0377 31 :RIQY 1t8qA 206 :YLQC T0377 45 :RLKDVEAGLK 1t8qA 214 :ELKRIKNELE Number of specific fragments extracted= 3 number of extra gaps= 0 total=25 Number of alignments=5 # 1t8qA read from 1t8qA/merged-good-all-a2m # found chain 1t8qA in template set T0377 16 :LRNRVAEFLKKKGLD 1t8qA 185 :IAAKTLEVLKKYGYT Number of specific fragments extracted= 1 number of extra gaps= 0 total=26 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1fmcA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0377 read from 1fmcA/merged-good-all-a2m # 1fmcA read from 1fmcA/merged-good-all-a2m # found chain 1fmcA in training set T0377 6 :LIFYDI 1fmcA 38 :VVVSDI T0377 13 :DDNLRNRVAEFLKKKGLD 1fmcA 44 :NADAANHVVDEIQQLGGQ T0377 36 :VFMGDL 1fmcA 62 :AFACRC T0377 42 :NSSRLKDVEAGLKII 1fmcA 71 :SEQELSALADFAISK Number of specific fragments extracted= 4 number of extra gaps= 0 total=30 Number of alignments=6 # 1fmcA read from 1fmcA/merged-good-all-a2m # found chain 1fmcA in training set T0377 6 :LIFYDI 1fmcA 38 :VVVSDI T0377 13 :DDNLRNRVAEFLKKKGLD 1fmcA 44 :NADAANHVVDEIQQLGGQ T0377 36 :VFMGDLN 1fmcA 62 :AFACRCD T0377 43 :SSRLKDVEAGLKIIGN 1fmcA 72 :EQELSALADFAISKLG T0377 61 :KL 1fmcA 88 :KV T0377 82 :ERIVI 1fmcA 90 :DILVN Number of specific fragments extracted= 6 number of extra gaps= 0 total=36 Number of alignments=7 # 1fmcA read from 1fmcA/merged-good-all-a2m # found chain 1fmcA in training set T0377 5 :YLIFYDITDD 1fmcA 37 :SVVVSDINAD T0377 16 :LRNRVAEFLKKKGLDR 1fmcA 47 :AANHVVDEIQQLGGQA T0377 37 :FMGDL 1fmcA 63 :FACRC T0377 42 :NSSRLKDVEAGLKIIG 1fmcA 71 :SEQELSALADFAISKL T0377 66 :ERFFILIV 1fmcA 87 :GKVDILVN T0377 75 :ITENQFRERI 1fmcA 106 :MPMADFRRAY Number of specific fragments extracted= 6 number of extra gaps= 0 total=42 Number of alignments=8 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vgjA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vgjA expands to /projects/compbio/data/pdb/1vgj.pdb.gz 1vgjA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0377 read from 1vgjA/merged-good-all-a2m # 1vgjA read from 1vgjA/merged-good-all-a2m # adding 1vgjA to template set # found chain 1vgjA in template set Warning: unaligning (T0377)M3 because first residue in template chain is (1vgjA)M1 T0377 4 :LYLIFYDI 1vgjA 2 :RAFIAIDV T0377 13 :DDNLRNRVAEFLKKKG 1vgjA 10 :NESVRDSLVRAQDYIG T0377 37 :FMGDLNSSRLKDVEAGLKIIGNRKK 1vgjA 45 :FLGEITEEQAEEIKNILKKIAEKYK T0377 65 :DER 1vgjA 70 :KHE T0377 68 :FFILIVP 1vgjA 76 :KGIGVFP T0377 76 :TENQFRERIVI 1vgjA 83 :NPNYIRVIWAG Number of specific fragments extracted= 6 number of extra gaps= 0 total=48 Number of alignments=9 # 1vgjA read from 1vgjA/merged-good-all-a2m # found chain 1vgjA in template set Warning: unaligning (T0377)M3 because first residue in template chain is (1vgjA)M1 T0377 4 :LYLIFYDI 1vgjA 2 :RAFIAIDV T0377 13 :DDNLRNRVAEFLKKKG 1vgjA 10 :NESVRDSLVRAQDYIG T0377 30 :DRIQYSV 1vgjA 37 :ENLHITL T0377 37 :FMGDLNSSRLKDVEAGLKIIGNRKKLQEDERFFILIVP 1vgjA 45 :FLGEITEEQAEEIKNILKKIAEKYKKHEVKVKGIGVFP T0377 76 :TENQFRERIV 1vgjA 83 :NPNYIRVIWA T0377 87 :G 1vgjA 93 :G Number of specific fragments extracted= 6 number of extra gaps= 0 total=54 Number of alignments=10 # 1vgjA read from 1vgjA/merged-good-all-a2m # found chain 1vgjA in template set T0377 4 :LYLIFYDITDD 1vgjA 2 :RAFIAIDVNES T0377 16 :LRNRVAEFLKKKG 1vgjA 13 :VRDSLVRAQDYIG T0377 30 :DRIQYS 1vgjA 37 :ENLHIT T0377 36 :VFMGDLNSSRLKDVEAGLKIIGNRKKLQE 1vgjA 44 :KFLGEITEEQAEEIKNILKKIAEKYKKHE T0377 68 :FFILIVPITE 1vgjA 76 :KGIGVFPNPN Number of specific fragments extracted= 5 number of extra gaps= 0 total=59 Number of alignments=11 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zpwX/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1zpwX expands to /projects/compbio/data/pdb/1zpw.pdb.gz 1zpwX:Skipped atom 88, because occupancy 0.35 <= existing 0.650 in 1zpwX Skipped atom 91, because occupancy 0.350 <= existing 0.650 in 1zpwX Skipped atom 178, because occupancy 0.350 <= existing 0.650 in 1zpwX Skipped atom 180, because occupancy 0.350 <= existing 0.650 in 1zpwX Skipped atom 182, because occupancy 0.350 <= existing 0.650 in 1zpwX Skipped atom 184, because occupancy 0.350 <= existing 0.650 in 1zpwX Skipped atom 421, because occupancy 0.350 <= existing 0.650 in 1zpwX Skipped atom 423, because occupancy 0.350 <= existing 0.650 in 1zpwX Skipped atom 425, because occupancy 0.350 <= existing 0.650 in 1zpwX Skipped atom 427, because occupancy 0.350 <= existing 0.650 in 1zpwX Skipped atom 429, because occupancy 0.350 <= existing 0.650 in 1zpwX Skipped atom 431, because occupancy 0.350 <= existing 0.650 in 1zpwX # T0377 read from 1zpwX/merged-good-all-a2m # 1zpwX read from 1zpwX/merged-good-all-a2m # adding 1zpwX to template set # found chain 1zpwX in template set Warning: unaligning (T0377)N98 because last residue in template chain is (1zpwX)E83 T0377 2 :AMLYLIFYDITDDNLRNRVAEFLKKKG 1zpwX 3 :KRLYAVAYDIPDDTRRVKLANLLKSYG T0377 30 :DRIQYSVFMGDLNSSRLKDVEAGLK 1zpwX 30 :ERVQLSVFECYLDERLLEDLRRRAR T0377 61 :KLQEDERFFILIVPITENQ 1zpwX 55 :RLLDLGQDALRIYPVAGQV T0377 89 :SGSEREEKS 1zpwX 74 :EVLGVGPLP Number of specific fragments extracted= 4 number of extra gaps= 0 total=63 Number of alignments=12 # 1zpwX read from 1zpwX/merged-good-all-a2m # found chain 1zpwX in template set Warning: unaligning (T0377)R93 because last residue in template chain is (1zpwX)E83 T0377 1 :MAMLYLIFYDITDDNLRNRVAEFLKKKG 1zpwX 2 :GKRLYAVAYDIPDDTRRVKLANLLKSYG T0377 30 :DRIQYSVFMGDLNSSRLKDVEAGLK 1zpwX 30 :ERVQLSVFECYLDERLLEDLRRRAR T0377 61 :KLQEDERFFILIVPITENQF 1zpwX 55 :RLLDLGQDALRIYPVAGQVE T0377 85 :VIGYSGSE 1zpwX 75 :VLGVGPLP Number of specific fragments extracted= 4 number of extra gaps= 0 total=67 Number of alignments=13 # 1zpwX read from 1zpwX/merged-good-all-a2m # found chain 1zpwX in template set Warning: unaligning (T0377)K96 because last residue in template chain is (1zpwX)E83 T0377 2 :AMLYLIFYDITDDNLRNRVAEFLKKKG 1zpwX 3 :KRLYAVAYDIPDDTRRVKLANLLKSYG T0377 30 :DRIQYSVFMGDLNSSRLKDVEAGLK 1zpwX 30 :ERVQLSVFECYLDERLLEDLRRRAR T0377 61 :KLQEDERFFILIVPITEN 1zpwX 55 :RLLDLGQDALRIYPVAGQ T0377 86 :IGYSGSEREE 1zpwX 73 :VEVLGVGPLP Number of specific fragments extracted= 4 number of extra gaps= 0 total=71 Number of alignments=14 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1han/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1han expands to /projects/compbio/data/pdb/1han.pdb.gz 1han:Warning: there is no chain 1han will retry with 1hanA # T0377 read from 1han/merged-good-all-a2m # 1han read from 1han/merged-good-all-a2m # adding 1han to template set # found chain 1han in template set T0377 2 :AMLYLIFYDITDDNLRNRVAEFLKKKGLD 1han 58 :DDLAFAGYEVADAAGLAQMADKLKQAGIA T0377 38 :MGDLNSSRLKDV 1han 87 :VTTGDASLARRR T0377 61 :KLQ 1han 99 :GVT T0377 69 :FILIVPITEN 1han 102 :GLITFADPFG T0377 81 :RERIVIGYSGSEREEKS 1han 112 :LPLEIYYGASEVFEKPF Number of specific fragments extracted= 5 number of extra gaps= 0 total=76 Number of alignments=15 # 1han read from 1han/merged-good-all-a2m # found chain 1han in template set T0377 3 :MLYLIFYDITDDNLRNRVAEFLKKKGLD 1han 59 :DLAFAGYEVADAAGLAQMADKLKQAGIA T0377 38 :MGDLNSSRLKDV 1han 87 :VTTGDASLARRR T0377 61 :KLQ 1han 99 :GVT T0377 69 :FILIVPITEN 1han 102 :GLITFADPFG T0377 81 :RERIVI 1han 112 :LPLEIY T0377 87 :GYSGSEREE 1han 119 :GASEVFEKP Number of specific fragments extracted= 6 number of extra gaps= 0 total=82 Number of alignments=16 # 1han read from 1han/merged-good-all-a2m # found chain 1han in template set T0377 4 :LYLIFYDITDDNLRNRVAEFLKKKGLDR 1han 60 :LAFAGYEVADAAGLAQMADKLKQAGIAV T0377 39 :GDLNSSRLKDV 1han 88 :TTGDASLARRR T0377 62 :LQEDERFFILIVP 1han 106 :FADPFGLPLEIYY Number of specific fragments extracted= 3 number of extra gaps= 0 total=85 Number of alignments=17 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lkdA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1lkdA expands to /projects/compbio/data/pdb/1lkd.pdb.gz 1lkdA:# T0377 read from 1lkdA/merged-good-all-a2m # 1lkdA read from 1lkdA/merged-good-all-a2m # adding 1lkdA to template set # found chain 1lkdA in template set T0377 3 :MLYLIFYDITDDNLRNRVAEFLKKKGLD 1lkdA 59 :DLAFAGYEVADAAGLAQMADKLKQAGIA T0377 38 :MGDLNSSRLKDV 1lkdA 87 :VTTGDASLARRR T0377 61 :KLQ 1lkdA 99 :GVT T0377 69 :FILIVPITEN 1lkdA 102 :GLITFADPFG T0377 81 :RERIVIGYSGSEREEKS 1lkdA 112 :LPLEIYYGASEVFEKPF Number of specific fragments extracted= 5 number of extra gaps= 0 total=90 Number of alignments=18 # 1lkdA read from 1lkdA/merged-good-all-a2m # found chain 1lkdA in template set T0377 4 :LYLIFYDITDDNLRNRVAEFLKKKGLD 1lkdA 60 :LAFAGYEVADAAGLAQMADKLKQAGIA T0377 38 :MGDLNSSRLKDV 1lkdA 87 :VTTGDASLARRR T0377 61 :KLQ 1lkdA 99 :GVT T0377 69 :FILIVPITEN 1lkdA 102 :GLITFADPFG T0377 81 :RERIVI 1lkdA 112 :LPLEIY T0377 87 :GYSGSEREE 1lkdA 119 :GASEVFEKP Number of specific fragments extracted= 6 number of extra gaps= 0 total=96 Number of alignments=19 # 1lkdA read from 1lkdA/merged-good-all-a2m # found chain 1lkdA in template set T0377 6 :LIFYDITDDNLRNRVAEFLKKKGLDR 1lkdA 62 :FAGYEVADAAGLAQMADKLKQAGIAV T0377 39 :GDLNSSRLKDV 1lkdA 88 :TTGDASLARRR T0377 62 :LQEDERFFILIVP 1lkdA 106 :FADPFGLPLEIYY Number of specific fragments extracted= 3 number of extra gaps= 0 total=99 Number of alignments=20 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1varA/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/T0377/1varA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0377/1varA/merged-good-all-a2m.gz for input Trying 1varA/merged-good-all-a2m Error: Couldn't open file 1varA/merged-good-all-a2m or 1varA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1zspA/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/T0377/1zspA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0377/1zspA/merged-good-all-a2m.gz for input Trying 1zspA/merged-good-all-a2m Error: Couldn't open file 1zspA/merged-good-all-a2m or 1zspA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1m7bA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1m7bA expands to /projects/compbio/data/pdb/1m7b.pdb.gz 1m7bA:# T0377 read from 1m7bA/merged-good-all-a2m # 1m7bA read from 1m7bA/merged-good-all-a2m # adding 1m7bA to template set # found chain 1m7bA in template set T0377 3 :MLYLIFYDITDDNLRNRVAEFLKKK 1m7bA 96 :DAVLICFDISRPETLDSVLKKWKGE T0377 29 :LD 1m7bA 121 :IQ T0377 51 :AGLK 1m7bA 123 :EFCP T0377 61 :K 1m7bA 127 :N T0377 81 :RERIVIGYSGSERE 1m7bA 128 :TKMLLVGCKSDLRT Number of specific fragments extracted= 5 number of extra gaps= 0 total=104 Number of alignments=21 # 1m7bA read from 1m7bA/merged-good-all-a2m # found chain 1m7bA in template set T0377 4 :LYLIFYDITDDNLRNRVAEFLKKK 1m7bA 97 :AVLICFDISRPETLDSVLKKWKGE T0377 49 :VEAGLK 1m7bA 121 :IQEFCP T0377 61 :KL 1m7bA 127 :NT T0377 82 :ERIVIGYSGSEREE 1m7bA 129 :KMLLVGCKSDLRTD Number of specific fragments extracted= 4 number of extra gaps= 0 total=108 Number of alignments=22 # 1m7bA read from 1m7bA/merged-good-all-a2m # found chain 1m7bA in template set T0377 4 :LYLIFYDITDDNLRNRVAEFLKKKG 1m7bA 97 :AVLICFDISRPETLDSVLKKWKGEI T0377 30 :D 1m7bA 122 :Q T0377 42 :NSSRLKDVE 1m7bA 142 :DVSTLVELS Number of specific fragments extracted= 3 number of extra gaps= 0 total=111 Number of alignments=23 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1oz9A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1oz9A expands to /projects/compbio/data/pdb/1oz9.pdb.gz 1oz9A:# T0377 read from 1oz9A/merged-good-all-a2m # 1oz9A read from 1oz9A/merged-good-all-a2m # adding 1oz9A to template set # found chain 1oz9A in template set T0377 11 :ITDDNLRNRVAEFLKKKGLDRIQYSVF 1oz9A 20 :VRKDKIEKWAELALSALGLNNVELSVY T0377 42 :NSSRLKDVEAGLK 1oz9A 49 :DDQEIRELNKTYR T0377 63 :QEDERFFILIVPITE 1oz9A 62 :KKDKPTDVLSFPMGE T0377 78 :NQFRERIV 1oz9A 79 :GGYKILGD Number of specific fragments extracted= 4 number of extra gaps= 0 total=115 Number of alignments=24 # 1oz9A read from 1oz9A/merged-good-all-a2m # found chain 1oz9A in template set T0377 11 :ITDDNLRNRVAEFLKKKGLDRIQYSVFMG 1oz9A 20 :VRKDKIEKWAELALSALGLNNVELSVYIT T0377 42 :NSSRLKDVEAGLK 1oz9A 49 :DDQEIRELNKTYR T0377 61 :K 1oz9A 62 :K T0377 64 :EDERFFILIVPITE 1oz9A 63 :KDKPTDVLSFPMGE T0377 78 :N 1oz9A 80 :G T0377 79 :QFRERIV 1oz9A 83 :ILGDVVI Number of specific fragments extracted= 6 number of extra gaps= 0 total=121 Number of alignments=25 # 1oz9A read from 1oz9A/merged-good-all-a2m # found chain 1oz9A in template set T0377 11 :ITDDNLRNRVAEFLKKKGLDRIQYSVF 1oz9A 20 :VRKDKIEKWAELALSALGLNNVELSVY T0377 42 :NSSRLKDVEAGLK 1oz9A 49 :DDQEIRELNKTYR T0377 63 :QEDERFFILIVPITE 1oz9A 62 :KKDKPTDVLSFPMGE Number of specific fragments extracted= 3 number of extra gaps= 0 total=124 Number of alignments=26 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1uw1A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1uw1A expands to /projects/compbio/data/pdb/1uw1.pdb.gz 1uw1A:# T0377 read from 1uw1A/merged-good-all-a2m # 1uw1A read from 1uw1A/merged-good-all-a2m # adding 1uw1A to template set # found chain 1uw1A in template set Warning: unaligning (T0377)N42 because first residue in template chain is (1uw1A)D7 T0377 43 :SSRLKDVEAGLK 1uw1A 8 :DKKTNWLKRIYR T0377 57 :GNRKKLQEDERF 1uw1A 20 :VRPCVKCKVAPR T0377 69 :FILIVPITENQFRE 1uw1A 39 :HLRIYNMCKTCFNN Number of specific fragments extracted= 3 number of extra gaps= 0 total=127 Number of alignments=27 # 1uw1A read from 1uw1A/merged-good-all-a2m # found chain 1uw1A in template set Warning: unaligning (T0377)N42 because first residue in template chain is (1uw1A)D7 T0377 43 :SSRLKDVEAGLKII 1uw1A 8 :DKKTNWLKRIYRVR T0377 57 :GNRKKLQEDER 1uw1A 28 :VAPRNWKVKNK T0377 69 :FILIVPITENQFRERIVIGYSGSEREEKSN 1uw1A 39 :HLRIYNMCKTCFNNSIDIGDDTYHGHDDWL Number of specific fragments extracted= 3 number of extra gaps= 0 total=130 Number of alignments=28 # 1uw1A read from 1uw1A/merged-good-all-a2m # found chain 1uw1A in template set Warning: unaligning (T0377)N42 because first residue in template chain is (1uw1A)D7 T0377 43 :SSRLKDVEAGLKI 1uw1A 8 :DKKTNWLKRIYRV T0377 59 :RKKLQEDERFFILIVPITENQFRERIVIGYSGSEREEKS 1uw1A 29 :APRNWKVKNKHLRIYNMCKTCFNNSIDIGDDTYHGHDDW Number of specific fragments extracted= 2 number of extra gaps= 0 total=132 Number of alignments=29 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1szxA/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/T0377/1szxA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0377/1szxA/merged-good-all-a2m.gz for input Trying 1szxA/merged-good-all-a2m Error: Couldn't open file 1szxA/merged-good-all-a2m or 1szxA/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1vdxA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1vdxA expands to /projects/compbio/data/pdb/1vdx.pdb.gz 1vdxA:# T0377 read from 1vdxA/merged-good-all-a2m # 1vdxA read from 1vdxA/merged-good-all-a2m # adding 1vdxA to template set # found chain 1vdxA in template set Warning: unaligning (T0377)M3 because first residue in template chain is (1vdxA)M1 T0377 4 :LYLIFYDI 1vdxA 2 :RAFIAIDV T0377 13 :DDNLRNRVAEFLKKKG 1vdxA 10 :NESVRDSLVRAQDYIG T0377 37 :FMGDLNSSRLKDVEAGLKIIGNRKK 1vdxA 45 :FLGEITEEQAEEIKNILKKIAEKYK T0377 65 :DERFFIL 1vdxA 70 :KHEVKVK T0377 72 :IVP 1vdxA 80 :VFP T0377 76 :TENQFRERIV 1vdxA 83 :NPNYIRVIWA T0377 87 :GYSG 1vdxA 93 :GIEN Number of specific fragments extracted= 7 number of extra gaps= 0 total=139 Number of alignments=30 # 1vdxA read from 1vdxA/merged-good-all-a2m # found chain 1vdxA in template set Warning: unaligning (T0377)M3 because first residue in template chain is (1vdxA)M1 T0377 4 :LYLIFYDI 1vdxA 2 :RAFIAIDV T0377 13 :DDNLRNRVAEFLKKKG 1vdxA 10 :NESVRDSLVRAQDYIG T0377 30 :DRIQYSV 1vdxA 37 :ENLHITL T0377 37 :FMGDLNSSRLKDVEAGLKIIGNRKKL 1vdxA 45 :FLGEITEEQAEEIKNILKKIAEKYKK T0377 66 :ERFFIL 1vdxA 71 :HEVKVK T0377 72 :IVP 1vdxA 80 :VFP T0377 76 :TENQFRERIV 1vdxA 83 :NPNYIRVIWA T0377 87 :GYS 1vdxA 93 :GIE Number of specific fragments extracted= 8 number of extra gaps= 0 total=147 Number of alignments=31 # 1vdxA read from 1vdxA/merged-good-all-a2m # found chain 1vdxA in template set Warning: unaligning (T0377)M3 because first residue in template chain is (1vdxA)M1 T0377 4 :LYLIFYDITDD 1vdxA 2 :RAFIAIDVNES T0377 16 :LRNRVAEFLKKKG 1vdxA 13 :VRDSLVRAQDYIG T0377 30 :DRIQYS 1vdxA 37 :ENLHIT T0377 36 :VFMGDLNSSRLKDVEAGLKIIGNRKKLQE 1vdxA 44 :KFLGEITEEQAEEIKNILKKIAEKYKKHE T0377 68 :FFIL 1vdxA 73 :VKVK T0377 72 :IVPIT 1vdxA 80 :VFPNP Number of specific fragments extracted= 6 number of extra gaps= 0 total=153 Number of alignments=32 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1em1A/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/T0377/1em1A/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0377/1em1A/merged-good-all-a2m.gz for input Trying 1em1A/merged-good-all-a2m Error: Couldn't open file 1em1A/merged-good-all-a2m or 1em1A/merged-good-all-a2m.gz for input # Reading fragments from alignment file # Attempting to read fragment alignments from file 1z08A/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1z08A expands to /projects/compbio/data/pdb/1z08.pdb.gz 1z08A:# T0377 read from 1z08A/merged-good-all-a2m # 1z08A read from 1z08A/merged-good-all-a2m # adding 1z08A to template set # found chain 1z08A in template set T0377 3 :MLYLIFYDITDDNLRNRV 1z08A 93 :NGAILVYDITDEDSFQKV T0377 46 :LKDVEAGLK 1z08A 114 :VKELRKMLG T0377 61 :KLQ 1z08A 123 :NEI T0377 82 :ERIVIGYSGSEREEK 1z08A 126 :CLCIVGNKIDLEKER Number of specific fragments extracted= 4 number of extra gaps= 0 total=157 Number of alignments=33 # 1z08A read from 1z08A/merged-good-all-a2m # found chain 1z08A in template set T0377 4 :LYLIFYDITDDNLRNRVA 1z08A 94 :GAILVYDITDEDSFQKVK T0377 26 :KK 1z08A 112 :NW T0377 46 :LKDVEAGLK 1z08A 114 :VKELRKMLG T0377 61 :KLQ 1z08A 123 :NEI T0377 82 :ERIVIGYSGSEREEKS 1z08A 126 :CLCIVGNKIDLEKERH Number of specific fragments extracted= 5 number of extra gaps= 0 total=162 Number of alignments=34 # 1z08A read from 1z08A/merged-good-all-a2m # found chain 1z08A in template set T0377 4 :LYLIFYDITDDNLRNRV 1z08A 94 :GAILVYDITDEDSFQKV T0377 21 :AEFLKKKG 1z08A 114 :VKELRKML T0377 30 :D 1z08A 122 :G T0377 38 :MGDLNSSRLKDVEAGL 1z08A 139 :ERHVSIQEAESYAESV Number of specific fragments extracted= 4 number of extra gaps= 0 total=166 Number of alignments=35 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1gyxA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0377 read from 1gyxA/merged-good-all-a2m # 1gyxA read from 1gyxA/merged-good-all-a2m # found chain 1gyxA in training set T0377 40 :DLNSSRLKDVEAGLKIIGNRKKLQEDERFFILIVPITENQFR 1gyxA 11 :ELDEQQKAALAADITDVIIRHLNSKDSSISIALQQIQPESWQ Number of specific fragments extracted= 1 number of extra gaps= 0 total=167 Number of alignments=36 # 1gyxA read from 1gyxA/merged-good-all-a2m # found chain 1gyxA in training set T0377 40 :DLNSSRLKDVEAGLKIIGNRKKLQEDERFFILIVPITENQFR 1gyxA 11 :ELDEQQKAALAADITDVIIRHLNSKDSSISIALQQIQPESWQ Number of specific fragments extracted= 1 number of extra gaps= 0 total=168 Number of alignments=37 # 1gyxA read from 1gyxA/merged-good-all-a2m # found chain 1gyxA in training set T0377 39 :GDLNSSRLKDVEAGLKIIGNRKKLQEDERFFILIVPITENQFRERIV 1gyxA 10 :RELDEQQKAALAADITDVIIRHLNSKDSSISIALQQIQPESWQAIWD T0377 86 :IGYSGSEREEKS 1gyxA 61 :PQMEALIKKPGY Number of specific fragments extracted= 2 number of extra gaps= 0 total=170 Number of alignments=38 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1r2qA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0377 read from 1r2qA/merged-good-all-a2m # 1r2qA read from 1r2qA/merged-good-all-a2m # found chain 1r2qA in training set T0377 4 :LYLIFYDITDDNLRNRVA 1r2qA 95 :AAIVVYDITNEESFARAK T0377 22 :EFLKKK 1r2qA 116 :KELQRQ T0377 29 :LD 1r2qA 122 :AS T0377 39 :GDLNSSR 1r2qA 141 :RAVDFQE T0377 49 :VEAGLKI 1r2qA 148 :AQSYADD Number of specific fragments extracted= 5 number of extra gaps= 0 total=175 Number of alignments=39 # 1r2qA read from 1r2qA/merged-good-all-a2m # found chain 1r2qA in training set T0377 4 :LYLIFYDITDDNLRNRVA 1r2qA 95 :AAIVVYDITNEESFARAK T0377 22 :EFLKK 1r2qA 116 :KELQR T0377 52 :GLK 1r2qA 121 :QAS T0377 65 :DE 1r2qA 124 :PN T0377 81 :RERIVIGYSGSEREEK 1r2qA 126 :IVIALSGNKADLANKR Number of specific fragments extracted= 5 number of extra gaps= 0 total=180 Number of alignments=40 # 1r2qA read from 1r2qA/merged-good-all-a2m # found chain 1r2qA in training set T0377 4 :LYLIFYDITDDNLRNRVA 1r2qA 95 :AAIVVYDITNEESFARAK T0377 22 :EFLKK 1r2qA 116 :KELQR T0377 28 :GLDRI 1r2qA 125 :NIVIA T0377 39 :GDLNSSRLKDVEAG 1r2qA 141 :RAVDFQEAQSYADD Number of specific fragments extracted= 4 number of extra gaps= 0 total=184 Number of alignments=41 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ydyA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments # T0377 read from 1ydyA/merged-good-all-a2m # 1ydyA read from 1ydyA/merged-good-all-a2m # found chain 1ydyA in training set T0377 16 :LRNRVAEFLKKKGLD 1ydyA 185 :IAAKTLEVLKKYGYT T0377 36 :VF 1ydyA 205 :VY T0377 45 :RLKDVEAGLKIIG 1ydyA 214 :ELKRIKNELEPKM T0377 61 :KL 1ydyA 227 :GM T0377 67 :RFFILIVPITENQFRERIVIG 1ydyA 229 :ELNLVQLIAYTDWNETQQKQP T0377 89 :SGSE 1ydyA 250 :DGSW Number of specific fragments extracted= 6 number of extra gaps= 0 total=190 Number of alignments=42 # 1ydyA read from 1ydyA/merged-good-all-a2m # found chain 1ydyA in training set T0377 16 :LRNRVAEFLKKKGLD 1ydyA 185 :IAAKTLEVLKKYGYT T0377 31 :RIQY 1ydyA 206 :YLQC T0377 45 :RLKDVEAGLKIIGNR 1ydyA 214 :ELKRIKNELEPKMGM T0377 61 :KL 1ydyA 229 :EL T0377 69 :FILIVPITENQ 1ydyA 231 :NLVQLIAYTDW T0377 95 :EKS 1ydyA 242 :NET Number of specific fragments extracted= 6 number of extra gaps= 0 total=196 Number of alignments=43 # 1ydyA read from 1ydyA/merged-good-all-a2m # found chain 1ydyA in training set T0377 16 :LRNRVAEFLKKKGLD 1ydyA 185 :IAAKTLEVLKKYGYT Number of specific fragments extracted= 1 number of extra gaps= 0 total=197 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1huqA/merged-good-all-a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 1huqA expands to /projects/compbio/data/pdb/1huq.pdb.gz 1huqA:# T0377 read from 1huqA/merged-good-all-a2m # 1huqA read from 1huqA/merged-good-all-a2m # adding 1huqA to template set # found chain 1huqA in template set T0377 4 :LYLIFYDITDDNLRNRVA 1huqA 96 :AAIVVYDITNTDTFARAK T0377 22 :EFLKKK 1huqA 117 :KELQRQ T0377 29 :LD 1huqA 123 :AS T0377 38 :MGDLNSSRLK 1huqA 141 :KRAVEFQEAQ T0377 51 :AGLK 1huqA 151 :AYAD Number of specific fragments extracted= 5 number of extra gaps= 0 total=202 Number of alignments=44 # 1huqA read from 1huqA/merged-good-all-a2m # found chain 1huqA in template set T0377 4 :LYLIFYDITDDNLRNRVAEFL 1huqA 96 :AAIVVYDITNTDTFARAKNWV T0377 47 :KDVEAGLK 1huqA 117 :KELQRQAS T0377 65 :DE 1huqA 125 :PN T0377 81 :RERIVIGYSGSEREEK 1huqA 127 :IVIALAGNKADLASKR Number of specific fragments extracted= 4 number of extra gaps= 0 total=206 Number of alignments=45 # 1huqA read from 1huqA/merged-good-all-a2m # found chain 1huqA in template set T0377 4 :LYLIFYDITDDNLRNRVA 1huqA 96 :AAIVVYDITNTDTFARAK T0377 22 :EFLKK 1huqA 117 :KELQR T0377 28 :GLDRIQ 1huqA 126 :NIVIAL T0377 38 :MGDLNSSRLKDVEAG 1huqA 141 :KRAVEFQEAQAYADD Number of specific fragments extracted= 4 number of extra gaps= 0 total=210 Number of alignments=46 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ivyA/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/T0377/2ivyA/merged-good-all-a2m or /projects/compbio/experiments/protein-predict/casp7/T0377/2ivyA/merged-good-all-a2m.gz for input Trying 2ivyA/merged-good-all-a2m Error: Couldn't open file 2ivyA/merged-good-all-a2m or 2ivyA/merged-good-all-a2m.gz for input # command:Using radius: 8.0000 Alignment mode NUMB_ALIGNS: 46 Adding 805 constraints to all.constraints Done adding distance constraints # command:Reading probabilities from probabilities.dat Reading constraints from ConstraintSet all.constraints maxweight: 1.0000 Optimizing... Probability sum: -178.7185, CN propb: -178.7185 weights: 0.3019 constraints: 272 # command:Found ConstraintSet # PrintContacts align.constraints_v3 Number of constraints in align.constraints 272 # command:Found ConstraintSet # PrintContacts align_bonus.constraints_v3 Number of constraints in align.constraints.bonus 272 # command:Found ConstraintSet # PrintContacts rejected.constraints_v3 Number of constraints in rejected.constraints 533 # command:Found ConstraintSet # PrintContacts rejected_bonus.constraints_v3 Number of constraints in rejected.constraints.bonus 533 # command:Found ConstraintSet # PrintContacts non_contacts.constraints_v3 Number of constraints in noncontact.constraints 0 # command:Found ConstraintSet # PrintContacts non_contacts_bonus.constraints_v3 Number of constraints in noncontact.constraints.bonus 0 # command:Found ConstraintSet # PrintContacts all.constraints_v3 Number of constraints in all.constraints 805 # command: