# command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 1600 examples # computed average trans backbone unit before proline from 52 examples # trans (non-proline) backbone unit: # CA= -2.2097 1.0151 -0.0046 # O= -0.1488 2.2425 0.0020 # C= -0.6903 1.1357 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4580 -0.0000 -0.0000 # cis backbone unit: # CA= -0.1462 2.4515 0.0018 # O= -2.0272 0.9713 0.0022 # C= -0.8006 1.0755 0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4659 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2063 1.0654 0.0002 # O= -0.1193 2.2442 0.0054 # C= -0.6842 1.1479 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4661 -0.0000 0.0000 # After reading cullpdb_pc80_res1.2_R0.2_d070810_chains408.atoms.gz have 408 chains in training database # Count of chains,residues,atoms: 408,82795,639989 # 81291 residues have no bad marker # 565 residues lack atoms needed to compute omega # 313 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 1 # HAS_OXT 265 # TOO_MANY_ATOMS 0 # TOO_FEW_ATOMS 378 # HAS_UNKNOWN_ATOMS 0 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 139 # NON_PLANAR_PEPTIDE 424 # BAD_PEPTIDE 803 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-40pc-3157.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 # command:# Making conformation for sequence T0350 numbered 1 through 117 Created new target T0350 from T0350.a2m # command:CPU_time= 5.159 sec, elapsed time= 5.190 sec. # command:# reading script from file all-templates.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 3proD/T0350-3proD-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3proD expands to /projects/compbio/data/pdb/3pro.pdb.gz 3proD:Skipped atom 4054, because occupancy 0.5 <= existing 0.500 in 3proD Skipped atom 4056, because occupancy 0.500 <= existing 0.500 in 3proD Skipped atom 4058, because occupancy 0.500 <= existing 0.500 in 3proD Skipped atom 4060, because occupancy 0.500 <= existing 0.500 in 3proD Skipped atom 4062, because occupancy 0.500 <= existing 0.500 in 3proD Skipped atom 4064, because occupancy 0.500 <= existing 0.500 in 3proD Skipped atom 4066, because occupancy 0.500 <= existing 0.500 in 3proD Skipped atom 4068, because occupancy 0.500 <= existing 0.500 in 3proD Skipped atom 4070, because occupancy 0.500 <= existing 0.500 in 3proD Skipped atom 4072, because occupancy 0.500 <= existing 0.500 in 3proD Skipped atom 4074, because occupancy 0.500 <= existing 0.500 in 3proD Skipped atom 4229, because occupancy 0.500 <= existing 0.500 in 3proD Skipped atom 4231, because occupancy 0.500 <= existing 0.500 in 3proD Skipped atom 4233, because occupancy 0.500 <= existing 0.500 in 3proD Skipped atom 4235, because occupancy 0.500 <= existing 0.500 in 3proD Skipped atom 4237, because occupancy 0.500 <= existing 0.500 in 3proD Skipped atom 4239, because occupancy 0.500 <= existing 0.500 in 3proD Skipped atom 4241, because occupancy 0.500 <= existing 0.500 in 3proD Skipped atom 4243, because occupancy 0.500 <= existing 0.500 in 3proD Skipped atom 4245, because occupancy 0.500 <= existing 0.500 in 3proD Skipped atom 4247, because occupancy 0.500 <= existing 0.500 in 3proD Skipped atom 4249, because occupancy 0.500 <= existing 0.500 in 3proD Skipped atom 5001, because occupancy 0.500 <= existing 0.500 in 3proD Skipped atom 5003, because occupancy 0.500 <= existing 0.500 in 3proD Skipped atom 5005, because occupancy 0.500 <= existing 0.500 in 3proD Skipped atom 5007, because occupancy 0.500 <= existing 0.500 in 3proD Skipped atom 5009, because occupancy 0.500 <= existing 0.500 in 3proD Skipped atom 5011, because occupancy 0.500 <= existing 0.500 in 3proD # T0350 read from 3proD/T0350-3proD-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3proD read from 3proD/T0350-3proD-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3proD to template set # found chain 3proD in template set Warning: unaligning (T0350)E52 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3proD)L113 T0350 34 :QVSYTNLAEMVGEMNKLL 3proD 85 :RYSLKQLQSAMEQLDAGA # choosing archetypes in rotamer library T0350 59 :KFELHDKLNEYYVKVI 3proD 118 :SWYVDPRSNAVVVKVD T0350 76 :DS 3proD 134 :DG T0350 86 :PPKRWLDFYAA 3proD 136 :ATDAGVDFVAL Number of specific fragments extracted= 4 number of extra gaps= 0 total=4 Will force an alignment to be made, even if fragment is small Number of alignments=1 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3proD/T0350-3proD-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0350 read from 3proD/T0350-3proD-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3proD read from 3proD/T0350-3proD-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3proD in template set Warning: unaligning (T0350)E52 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3proD)L113 T0350 34 :QVSYTNLAEMVGEMNKLL 3proD 85 :RYSLKQLQSAMEQLDAGA T0350 60 :FELHDKLNEYYVKVI 3proD 119 :WYVDPRSNAVVVKVD T0350 76 :DS 3proD 134 :DG T0350 86 :PPKRWLDFYAA 3proD 136 :ATDAGVDFVAL Number of specific fragments extracted= 4 number of extra gaps= 0 total=8 Will force an alignment to be made, even if fragment is small Number of alignments=2 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3proD/T0350-3proD-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0350 read from 3proD/T0350-3proD-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3proD read from 3proD/T0350-3proD-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3proD in template set Warning: unaligning (T0350)E52 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3proD)L113 T0350 34 :QVSYTNLAEMVGEMNKLL 3proD 85 :RYSLKQLQSAMEQLDAGA T0350 60 :FELHDKLNEYYVKVIED 3proD 119 :WYVDPRSNAVVVKVDDG T0350 86 :PPKRWLDFYA 3proD 136 :ATDAGVDFVA Number of specific fragments extracted= 3 number of extra gaps= 0 total=11 Will force an alignment to be made, even if fragment is small Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t6sA/T0350-1t6sA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1t6sA expands to /projects/compbio/data/pdb/1t6s.pdb.gz 1t6sA:# T0350 read from 1t6sA/T0350-1t6sA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t6sA read from 1t6sA/T0350-1t6sA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1t6sA to template set # found chain 1t6sA in template set T0350 32 :VHQVSYTNLAEMVGEMNKLLEPSQVHLKFELHDK 1t6sA 33 :AHKFTPSELQEAVDELNRDYEATGRTFRIHAIAG T0350 70 :YVKVIEDS 1t6sA 67 :GYRFLTEP T0350 87 :PKRWLDFYAAMTEF 1t6sA 93 :SRSMLEVLAVVAWH T0350 101 :LGLF 1t6sA 111 :KGEI Number of specific fragments extracted= 4 number of extra gaps= 0 total=15 Will force an alignment to be made, even if fragment is small Number of alignments=4 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t6sA/T0350-1t6sA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0350 read from 1t6sA/T0350-1t6sA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t6sA read from 1t6sA/T0350-1t6sA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1t6sA in template set T0350 32 :VHQVSYTNLAEMVGEMNKLLEPSQVHLKFELHDK 1t6sA 33 :AHKFTPSELQEAVDELNRDYEATGRTFRIHAIAG T0350 70 :YVKVIEDS 1t6sA 67 :GYRFLTEP T0350 87 :PKRWLDFYAAMTEF 1t6sA 93 :SRSMLEVLAVVAWH T0350 101 :LGLF 1t6sA 111 :KGEI Number of specific fragments extracted= 4 number of extra gaps= 0 total=19 Will force an alignment to be made, even if fragment is small Number of alignments=5 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1t6sA/T0350-1t6sA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0350 read from 1t6sA/T0350-1t6sA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1t6sA read from 1t6sA/T0350-1t6sA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1t6sA in template set T0350 30 :VPVHQVSYTNLAEMVGEMNKLLEPSQVHLKFELHDK 1t6sA 31 :ITAHKFTPSELQEAVDELNRDYEATGRTFRIHAIAG T0350 68 :EYYVK 1t6sA 67 :GYRFL T0350 87 :PKRWLDFYAAMTEF 1t6sA 93 :SRSMLEVLAVVAWH Number of specific fragments extracted= 3 number of extra gaps= 0 total=22 Will force an alignment to be made, even if fragment is small Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cnqA/T0350-2cnqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0350 read from 2cnqA/T0350-2cnqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cnqA read from 2cnqA/T0350-2cnqA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2cnqA in training set Warning: unaligning (T0350)N26 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2cnqA)E169 Warning: unaligning (T0350)D27 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2cnqA)E169 T0350 25 :D 2cnqA 164 :K T0350 31 :PVHQVSYTNLAEMV 2cnqA 170 :HDENISPAQAAELV T0350 45 :GEMNKLL 2cnqA 189 :RRVAELA T0350 56 :VHLKFELHDKLNEYYV 2cnqA 216 :TKFEFGIDEKTNEIIL T0350 73 :VIEDST 2cnqA 243 :FWNGAS T0350 85 :IPPKRWLDFYAAMTEFLGLFVDEKK 2cnqA 280 :MPQDIVDRTRAKYIEAYETLTGSKW Number of specific fragments extracted= 6 number of extra gaps= 1 total=28 Will force an alignment to be made, even if fragment is small Number of alignments=7 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cnqA/T0350-2cnqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0350 read from 2cnqA/T0350-2cnqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cnqA read from 2cnqA/T0350-2cnqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2cnqA in training set Warning: unaligning (T0350)N26 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2cnqA)E169 Warning: unaligning (T0350)D27 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2cnqA)E169 T0350 31 :PVHQVSYTNLAE 2cnqA 170 :HDENISPAQAAE T0350 43 :MVGEMNKLL 2cnqA 187 :LSRRVAELA T0350 55 :QVHLKFELHDKLNEYYV 2cnqA 215 :DTKFEFGIDEKTNEIIL T0350 73 :VIEDST 2cnqA 243 :FWNGAS T0350 85 :IPPKRWLDFYAAMTEFLGLFVDE 2cnqA 280 :MPQDIVDRTRAKYIEAYETLTGS Number of specific fragments extracted= 5 number of extra gaps= 1 total=33 Will force an alignment to be made, even if fragment is small Number of alignments=8 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2cnqA/T0350-2cnqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0350 read from 2cnqA/T0350-2cnqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2cnqA read from 2cnqA/T0350-2cnqA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2cnqA in training set Warning: unaligning (T0350)D27 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2cnqA)E169 T0350 31 :PVHQVSYTNLAEM 2cnqA 170 :HDENISPAQAAEL T0350 44 :VGEMNKLL 2cnqA 188 :SRRVAELA T0350 52 :EPSQV 2cnqA 207 :KEKGI T0350 58 :LKFELHDKLNEYYV 2cnqA 218 :FEFGIDEKTNEIIL Number of specific fragments extracted= 4 number of extra gaps= 0 total=37 Will force an alignment to be made, even if fragment is small Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1obdA/T0350-1obdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1obdA expands to /projects/compbio/data/pdb/1obd.pdb.gz 1obdA:Skipped atom 7, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 22, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 24, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 39, because occupancy 0.300 <= existing 0.700 in 1obdA Skipped atom 41, because occupancy 0.300 <= existing 0.700 in 1obdA Skipped atom 43, because occupancy 0.300 <= existing 0.700 in 1obdA Skipped atom 101, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 103, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 105, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 107, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 125, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 127, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 129, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 131, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 133, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 135, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 137, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 147, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 149, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 151, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 153, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 155, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 179, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 181, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 183, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 185, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 355, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 357, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 359, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 489, because occupancy 0.200 <= existing 0.800 in 1obdA Skipped atom 491, because occupancy 0.200 <= existing 0.800 in 1obdA Skipped atom 599, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 601, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 603, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 605, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 607, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 609, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 611, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 650, because occupancy 0.600 <= existing 0.600 in 1obdA Skipped atom 652, because occupancy 0.600 <= existing 0.600 in 1obdA Skipped atom 654, because occupancy 0.600 <= existing 0.600 in 1obdA Skipped atom 656, because occupancy 0.600 <= existing 0.600 in 1obdA Skipped atom 702, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 704, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 706, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 708, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 765, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 767, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 769, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 771, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 773, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 839, because occupancy 0.400 <= existing 0.600 in 1obdA Skipped atom 841, because occupancy 0.400 <= existing 0.600 in 1obdA Skipped atom 843, because occupancy 0.400 <= existing 0.600 in 1obdA Skipped atom 992, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 994, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 996, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 998, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 1000, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 1136, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 1138, because occupancy 0.000 <= existing 0.500 in 1obdA Skipped atom 1140, because occupancy 0.000 <= existing 0.500 in 1obdA Skipped atom 1142, because occupancy 0.000 <= existing 0.500 in 1obdA Skipped atom 1144, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 1303, because occupancy 0.400 <= existing 0.600 in 1obdA Skipped atom 1305, because occupancy 0.400 <= existing 0.600 in 1obdA Skipped atom 1307, because occupancy 0.400 <= existing 0.600 in 1obdA Skipped atom 1309, because occupancy 0.400 <= existing 0.600 in 1obdA Skipped atom 1311, because occupancy 0.400 <= existing 0.600 in 1obdA Skipped atom 1363, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 1365, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 1367, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 1511, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 1551, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 1553, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 1555, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 1557, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 1559, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 1788, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 1790, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 1792, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 1794, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 1850, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 1852, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 1854, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 1856, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 2100, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 2102, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 2104, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 2106, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 2108, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 2142, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 2144, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 2146, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 2148, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 2150, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 2152, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 2154, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 2227, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 2229, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 2231, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 2233, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 2431, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 2433, because occupancy 0.500 <= existing 0.500 in 1obdA Skipped atom 2435, because occupancy 0.500 <= existing 0.500 in 1obdA # T0350 read from 1obdA/T0350-1obdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1obdA read from 1obdA/T0350-1obdA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1obdA to template set # found chain 1obdA in template set Warning: unaligning (T0350)N26 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1obdA)D171 Warning: unaligning (T0350)V32 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1obdA)D171 Warning: unaligning (T0350)K109 because last residue in template chain is (1obdA)W304 T0350 25 :D 1obdA 164 :K T0350 33 :HQVSYTNLAEMV 1obdA 172 :ENISPAQAAELV T0350 45 :GEMNKLL 1obdA 189 :RRVAELA T0350 56 :VHLKFELHDKLNEYYV 1obdA 216 :TKFEFGIDEKTNEIIL T0350 72 :KVIEDST 1obdA 242 :RFWNGAS T0350 84 :EIPPKRWLDFYAAMTEFLGLFVDEK 1obdA 279 :KMPQDIVDRTRAKYIEAYETLTGSK Number of specific fragments extracted= 6 number of extra gaps= 0 total=43 Will force an alignment to be made, even if fragment is small Number of alignments=10 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1obdA/T0350-1obdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0350 read from 1obdA/T0350-1obdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1obdA read from 1obdA/T0350-1obdA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1obdA in template set Warning: unaligning (T0350)N26 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (1obdA)D171 Warning: unaligning (T0350)V32 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1obdA)D171 T0350 33 :HQVSYTNLAEMV 1obdA 172 :ENISPAQAAELV T0350 45 :GEMNKLL 1obdA 189 :RRVAELA T0350 56 :VHLKFELHDKLNEYYV 1obdA 216 :TKFEFGIDEKTNEIIL T0350 72 :KVIEDST 1obdA 242 :RFWNGAS T0350 84 :EIPPKRWLDFYAAMTEFLGLF 1obdA 279 :KMPQDIVDRTRAKYIEAYETL Number of specific fragments extracted= 5 number of extra gaps= 0 total=48 Will force an alignment to be made, even if fragment is small Number of alignments=11 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1obdA/T0350-1obdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0350 read from 1obdA/T0350-1obdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1obdA read from 1obdA/T0350-1obdA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1obdA in template set Warning: unaligning (T0350)V32 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1obdA)D171 T0350 33 :HQVSYTNLAEMV 1obdA 172 :ENISPAQAAELV T0350 45 :GEMNKLL 1obdA 189 :RRVAELA T0350 52 :EPSQV 1obdA 207 :KEKGI T0350 57 :HLKFELHDKLNEYYV 1obdA 217 :KFEFGIDEKTNEIIL Number of specific fragments extracted= 4 number of extra gaps= 0 total=52 Will force an alignment to be made, even if fragment is small Number of alignments=12 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3proC/T0350-3proC-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 3proC expands to /projects/compbio/data/pdb/3pro.pdb.gz 3proC:Skipped atom 1442, because occupancy 0.500 <= existing 0.500 in 3proC Skipped atom 1444, because occupancy 0.500 <= existing 0.500 in 3proC Skipped atom 1446, because occupancy 0.500 <= existing 0.500 in 3proC Skipped atom 1448, because occupancy 0.500 <= existing 0.500 in 3proC Skipped atom 1450, because occupancy 0.500 <= existing 0.500 in 3proC Skipped atom 1452, because occupancy 0.500 <= existing 0.500 in 3proC Skipped atom 1454, because occupancy 0.500 <= existing 0.500 in 3proC Skipped atom 1456, because occupancy 0.500 <= existing 0.500 in 3proC Skipped atom 1681, because occupancy 0.500 <= existing 0.500 in 3proC Skipped atom 1683, because occupancy 0.500 <= existing 0.500 in 3proC Skipped atom 1685, because occupancy 0.500 <= existing 0.500 in 3proC Skipped atom 1687, because occupancy 0.500 <= existing 0.500 in 3proC Skipped atom 1689, because occupancy 0.500 <= existing 0.500 in 3proC Skipped atom 1691, because occupancy 0.500 <= existing 0.500 in 3proC Skipped atom 1693, because occupancy 0.500 <= existing 0.500 in 3proC Skipped atom 1695, because occupancy 0.500 <= existing 0.500 in 3proC Skipped atom 1697, because occupancy 0.500 <= existing 0.500 in 3proC Skipped atom 1699, because occupancy 0.500 <= existing 0.500 in 3proC Skipped atom 1701, because occupancy 0.500 <= existing 0.500 in 3proC Skipped atom 1703, because occupancy 0.500 <= existing 0.500 in 3proC Skipped atom 1705, because occupancy 0.500 <= existing 0.500 in 3proC Skipped atom 1707, because occupancy 0.500 <= existing 0.500 in 3proC Skipped atom 1709, because occupancy 0.500 <= existing 0.500 in 3proC Skipped atom 1711, because occupancy 0.500 <= existing 0.500 in 3proC Skipped atom 1713, because occupancy 0.500 <= existing 0.500 in 3proC Skipped atom 1715, because occupancy 0.500 <= existing 0.500 in 3proC Skipped atom 1717, because occupancy 0.500 <= existing 0.500 in 3proC Skipped atom 1719, because occupancy 0.500 <= existing 0.500 in 3proC Skipped atom 1939, because occupancy 0.500 <= existing 0.500 in 3proC Skipped atom 1941, because occupancy 0.500 <= existing 0.500 in 3proC Skipped atom 1943, because occupancy 0.500 <= existing 0.500 in 3proC Skipped atom 1945, because occupancy 0.500 <= existing 0.500 in 3proC Skipped atom 1947, because occupancy 0.500 <= existing 0.500 in 3proC Skipped atom 1949, because occupancy 0.500 <= existing 0.500 in 3proC Skipped atom 2003, because occupancy 0.500 <= existing 0.500 in 3proC Skipped atom 2005, because occupancy 0.500 <= existing 0.500 in 3proC Skipped atom 2007, because occupancy 0.500 <= existing 0.500 in 3proC Skipped atom 2009, because occupancy 0.500 <= existing 0.500 in 3proC Skipped atom 2011, because occupancy 0.500 <= existing 0.500 in 3proC Skipped atom 2013, because occupancy 0.500 <= existing 0.500 in 3proC Skipped atom 2015, because occupancy 0.500 <= existing 0.500 in 3proC Skipped atom 2017, because occupancy 0.500 <= existing 0.500 in 3proC Skipped atom 2019, because occupancy 0.500 <= existing 0.500 in 3proC Skipped atom 2021, because occupancy 0.500 <= existing 0.500 in 3proC Skipped atom 2023, because occupancy 0.500 <= existing 0.500 in 3proC Skipped atom 2108, because occupancy 0.500 <= existing 0.500 in 3proC Skipped atom 2110, because occupancy 0.500 <= existing 0.500 in 3proC Skipped atom 2112, because occupancy 0.500 <= existing 0.500 in 3proC Skipped atom 2114, because occupancy 0.500 <= existing 0.500 in 3proC Skipped atom 2116, because occupancy 0.500 <= existing 0.500 in 3proC Skipped atom 2118, because occupancy 0.500 <= existing 0.500 in 3proC # T0350 read from 3proC/T0350-3proC-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3proC read from 3proC/T0350-3proC-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3proC to template set # found chain 3proC in template set Warning: unaligning (T0350)P53 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3proC)L113 T0350 34 :QVSYTNLAEMVGEMNKLLE 3proC 85 :RYSLKQLQSAMEQLDAGAN Number of specific fragments extracted= 1 number of extra gaps= 0 total=53 Will force an alignment to be made, even if fragment is small Number of alignments=13 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3proC/T0350-3proC-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0350 read from 3proC/T0350-3proC-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3proC read from 3proC/T0350-3proC-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3proC in template set Warning: unaligning (T0350)P53 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3proC)L113 T0350 34 :QVSYTNLAEMVGEMNKLLE 3proC 85 :RYSLKQLQSAMEQLDAGAN T0350 60 :FELHDKLNEYYVKVI 3proC 119 :WYVDPRSNAVVVKVD T0350 76 :DS 3proC 134 :DG T0350 86 :PPKRWLDFYA 3proC 136 :ATDAGVDFVA Number of specific fragments extracted= 4 number of extra gaps= 0 total=57 Will force an alignment to be made, even if fragment is small Number of alignments=14 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3proC/T0350-3proC-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0350 read from 3proC/T0350-3proC-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3proC read from 3proC/T0350-3proC-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 3proC in template set Warning: unaligning (T0350)P53 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3proC)L113 T0350 34 :QVSYTNLAEMVGEMNKLLE 3proC 85 :RYSLKQLQSAMEQLDAGAN Number of specific fragments extracted= 1 number of extra gaps= 0 total=58 Will force an alignment to be made, even if fragment is small Number of alignments=15 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1a48/T0350-1a48-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1a48 expands to /projects/compbio/data/pdb/1a48.pdb.gz 1a48:Warning: there is no chain 1a48 will retry with 1a48A Skipped atom 118, because occupancy 0.500 <= existing 0.500 in 1a48 Skipped atom 120, because occupancy 0.500 <= existing 0.500 in 1a48 Skipped atom 122, because occupancy 0.500 <= existing 0.500 in 1a48 Skipped atom 124, because occupancy 0.500 <= existing 0.500 in 1a48 # T0350 read from 1a48/T0350-1a48-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1a48 read from 1a48/T0350-1a48-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1a48 to template set # found chain 1a48 in template set Warning: unaligning (T0350)V32 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1a48)D171 T0350 33 :HQVSYTNLAEMV 1a48 172 :ENISPAQAAELV T0350 45 :GEMNKLL 1a48 189 :RRVAELA T0350 55 :QVHLKFELHDKLNEYYV 1a48 215 :DTKFEFGIDEKTNEIIL T0350 72 :KVIEDST 1a48 242 :RFWNGAS T0350 84 :EIPPKRWLDFYAAMTEFLGLFVDEKK 1a48 279 :KMPQDIVDRTRAKYIEAYETLTGSKW Number of specific fragments extracted= 5 number of extra gaps= 0 total=63 Will force an alignment to be made, even if fragment is small Number of alignments=16 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1a48/T0350-1a48-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0350 read from 1a48/T0350-1a48-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1a48 read from 1a48/T0350-1a48-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1a48 in template set Warning: unaligning (T0350)V32 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1a48)D171 T0350 33 :HQVSYTNLAEMV 1a48 172 :ENISPAQAAELV T0350 45 :GEMNKLL 1a48 189 :RRVAELA T0350 56 :VHLKFELHDKLNEYYV 1a48 216 :TKFEFGIDEKTNEIIL T0350 72 :KVIEDST 1a48 242 :RFWNGAS T0350 84 :EIPPKRWLDFYAAMTEFLGLFV 1a48 279 :KMPQDIVDRTRAKYIEAYETLT Number of specific fragments extracted= 5 number of extra gaps= 0 total=68 Will force an alignment to be made, even if fragment is small Number of alignments=17 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1a48/T0350-1a48-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0350 read from 1a48/T0350-1a48-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1a48 read from 1a48/T0350-1a48-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1a48 in template set Warning: unaligning (T0350)V32 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (1a48)D171 T0350 33 :HQVSYTNLAEMV 1a48 172 :ENISPAQAAELV T0350 45 :GEMNKLL 1a48 189 :RRVAELA T0350 52 :EPSQV 1a48 207 :KEKGI T0350 57 :HLKFELHDKLNEYYV 1a48 217 :KFEFGIDEKTNEIIL Number of specific fragments extracted= 4 number of extra gaps= 0 total=72 Will force an alignment to be made, even if fragment is small Number of alignments=18 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gu3A/T0350-2gu3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 2gu3A expands to /projects/compbio/data/pdb/2gu3.pdb.gz 2gu3A:Skipped atom 159, because occupancy 0.400 <= existing 0.600 in 2gu3A Skipped atom 163, because occupancy 0.400 <= existing 0.600 in 2gu3A Skipped atom 165, because occupancy 0.400 <= existing 0.600 in 2gu3A Skipped atom 167, because occupancy 0.400 <= existing 0.600 in 2gu3A Skipped atom 169, because occupancy 0.400 <= existing 0.600 in 2gu3A Skipped atom 507, because occupancy 0.300 <= existing 0.700 in 2gu3A Skipped atom 511, because occupancy 0.300 <= existing 0.700 in 2gu3A Skipped atom 513, because occupancy 0.300 <= existing 0.700 in 2gu3A Skipped atom 515, because occupancy 0.300 <= existing 0.700 in 2gu3A Skipped atom 517, because occupancy 0.300 <= existing 0.700 in 2gu3A Skipped atom 519, because occupancy 0.300 <= existing 0.700 in 2gu3A # T0350 read from 2gu3A/T0350-2gu3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gu3A read from 2gu3A/T0350-2gu3A-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2gu3A to template set # found chain 2gu3A in template set Warning: unaligning (T0350)P87 because last residue in template chain is (2gu3A)P161 T0350 31 :PVHQ 2gu3A 95 :EAKE T0350 35 :VSYTNLAEMVGEM 2gu3A 100 :ISEDKAAKIIKDE T0350 49 :K 2gu3A 113 :G T0350 52 :EPSQVHL 2gu3A 117 :KQKEVHL T0350 59 :KFELHDKLNEYYVKVIEDSTNEVIREIP 2gu3A 133 :EVTYLDKEGQYSLSYVDFTTGKILKNIT Number of specific fragments extracted= 5 number of extra gaps= 0 total=77 Will force an alignment to be made, even if fragment is small Number of alignments=19 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gu3A/T0350-2gu3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0350 read from 2gu3A/T0350-2gu3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gu3A read from 2gu3A/T0350-2gu3A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gu3A in template set T0350 32 :VHQ 2gu3A 96 :AKE T0350 35 :VSYTNLAEMV 2gu3A 100 :ISEDKAAKII T0350 48 :NKL 2gu3A 110 :KDE T0350 53 :PSQVHLKFELHDK 2gu3A 116 :SKQKEVHLAREGN T0350 66 :LNEYYVKVIEDSTNEVIREI 2gu3A 140 :EGQYSLSYVDFTTGKILKNI Number of specific fragments extracted= 5 number of extra gaps= 0 total=82 Will force an alignment to be made, even if fragment is small Number of alignments=20 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gu3A/T0350-2gu3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0350 read from 2gu3A/T0350-2gu3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gu3A read from 2gu3A/T0350-2gu3A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 2gu3A in template set Warning: unaligning (T0350)P87 because last residue in template chain is (2gu3A)P161 T0350 32 :VHQVSYTNLAEMVGE 2gu3A 97 :KEGISEDKAAKIIKD T0350 53 :PSQVHLKFELHDK 2gu3A 116 :SKQKEVHLAREGN T0350 66 :LNEYYVKVIEDSTNEVIREIP 2gu3A 140 :EGQYSLSYVDFTTGKILKNIT Number of specific fragments extracted= 3 number of extra gaps= 0 total=85 Will force an alignment to be made, even if fragment is small Number of alignments=21 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ospO/T0350-1ospO-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always 1ospO expands to /projects/compbio/data/pdb/1osp.pdb.gz 1ospO:# T0350 read from 1ospO/T0350-1ospO-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ospO read from 1ospO/T0350-1ospO-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ospO to template set # found chain 1ospO in template set T0350 53 :PSQVHLKFELHDKLNEYYVKVIEDSTNEVIRE 1ospO 81 :ADKCKVKLTISDDLGQTTLEVFKEDGKTLVSK Number of specific fragments extracted= 1 number of extra gaps= 0 total=86 Will force an alignment to be made, even if fragment is small Number of alignments=22 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ospO/T0350-1ospO-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0350 read from 1ospO/T0350-1ospO-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ospO read from 1ospO/T0350-1ospO-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ospO in template set T0350 53 :PSQVHLKFELHDKLNEYYVKVIEDSTNEVIRE 1ospO 81 :ADKCKVKLTISDDLGQTTLEVFKEDGKTLVSK Number of specific fragments extracted= 1 number of extra gaps= 0 total=87 Will force an alignment to be made, even if fragment is small Number of alignments=23 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ospO/T0350-1ospO-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library always # T0350 read from 1ospO/T0350-1ospO-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ospO read from 1ospO/T0350-1ospO-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1ospO in template set T0350 53 :PSQVHLKFELHDKLNEYYVKVIEDSTNEVIRE 1ospO 81 :ADKCKVKLTISDDLGQTTLEVFKEDGKTLVSK Number of specific fragments extracted= 1 number of extra gaps= 0 total=88 Will force an alignment to be made, even if fragment is small Number of alignments=24 # command:CPU_time= 8.662 sec, elapsed time= 11.937 sec. # command:Using radius: 8.000 NUMB_ALIGNS: 24 Adding 160 constraints to all_contacts Done adding distance constraints # command:CPU_time= 8.674 sec, elapsed time= 11.950 sec. # command:Reading probabilities from T0350.t06.CB8-sep9.rdb Reading constraints from ConstraintSet all_contacts maxweight: 12.813 Optimizing... Probability sum: -195.251, CN propb: -195.251 weights: 0.265 constraints: 86 # command:CPU_time= 8.699 sec, elapsed time= 11.975 sec. # command:Found ConstraintSet # PrintContacts align.constraints Warning: Couldn't open file align.constraints for output Error: Couldn't open file align.constraints for output Number of constraints in align 86