# command:# Seed set to 1278313343 # 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 # 493441 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 55 # BAD_PEPTIDE 2680 # HIGH_B_FACTOR 0 # 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:CPU_time= 24.412 sec, elapsed time= 25.047 sec. # command:# Making generic fragment library # fragment library contains # type length num_fragments num_indexes_used # n-terminus 1 1963 20 (100.000%) # n-terminus 2 1934 333 (83.250%) # middle 1 483679 20 (100.000%) # middle 2 477517 400 (100.000%) # middle 3 471578 7988 (99.850%) # middle 4 465793 120683 (75.427%) # c-terminus 1 1917 20 (100.000%) # c-terminus 2 1889 372 (93.000%) # ss-bonds 1052 # command:CPU_time= 37.611 sec, elapsed time= 42.815 sec. # command:# Prefix for input files set to # command:# Making conformation for sequence T0617 numbered 1 through 148 Created new target T0617 from T0617.a2m # command:# command:# No conformations to remove in PopConform # command:CPU_time= 37.613 sec, elapsed time= 42.817 sec. # command:# Prefix for input files set to # command:# reading script from file T0617.undertaker-align.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 3cjnA/T0617-3cjnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 3cjnA expands to /projects/compbio/data/pdb/3cjn.pdb.gz 3cjnA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 408, because occupancy 0.5 <= existing 0.500 in 3cjnA Skipped atom 410, because occupancy 0.500 <= existing 0.500 in 3cjnA Skipped atom 412, because occupancy 0.500 <= existing 0.500 in 3cjnA Skipped atom 414, because occupancy 0.500 <= existing 0.500 in 3cjnA Skipped atom 416, because occupancy 0.500 <= existing 0.500 in 3cjnA Skipped atom 418, because occupancy 0.500 <= existing 0.500 in 3cjnA Skipped atom 420, because occupancy 0.500 <= existing 0.500 in 3cjnA Skipped atom 422, because occupancy 0.500 <= existing 0.500 in 3cjnA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1125, because occupancy 0.500 <= existing 0.500 in 3cjnA Skipped atom 1127, because occupancy 0.500 <= existing 0.500 in 3cjnA Skipped atom 1129, because occupancy 0.500 <= existing 0.500 in 3cjnA Skipped atom 1131, because occupancy 0.500 <= existing 0.500 in 3cjnA Skipped atom 1133, because occupancy 0.500 <= existing 0.500 in 3cjnA Skipped atom 1135, because occupancy 0.500 <= existing 0.500 in 3cjnA Skipped atom 1137, because occupancy 0.500 <= existing 0.500 in 3cjnA Skipped atom 1139, because occupancy 0.500 <= existing 0.500 in 3cjnA Skipped atom 1141, because occupancy 0.500 <= existing 0.500 in 3cjnA # T0617 read from 3cjnA/T0617-3cjnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3cjnA read from 3cjnA/T0617-3cjnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3cjnA to template set # found chain 3cjnA in template set Warning: unaligning (T0617)N2 because first residue in template chain is (3cjnA)R12 Warning: unaligning (T0617)G88 because of BadResidue code BAD_PEPTIDE in next template residue (3cjnA)D98 Warning: unaligning (T0617)H89 because of BadResidue code BAD_PEPTIDE at template residue (3cjnA)D98 Warning: unaligning (T0617)D92 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3cjnA)D101 T0617 3 :AMQKINIDRHATAQINMLANKLMLKSSTA 3cjnA 13 :ELAEIGLEGYAPYLMNRIMGRYNANLRKE # choosing archetypes in rotamer library T0617 33 :TQKFGIGMTEWRIISVLSSASDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVN 3cjnA 42 :MTALGLSTAKMRALAILSAKDGLPIGTLGIFAVVEQSTLSRALDGLQADGLVRRE T0617 93 :KRTYAINLTEMGQELYEVASDFAIEREKQLLEEFEEAEKDQLFILLKKLRNKV 3cjnA 102 :QRSSRVYLTPAGRAVYDRLWPHMRASHDRMFQGITPQERQAFLATLNKMLANI Number of specific fragments extracted= 3 number of extra gaps= 1 total=3 # request to SCWRL produces command: ulimit -t 134 ; scwrl4 -t -i /var/tmp/to_scwrl_1749139433.pdb -s /var/tmp/to_scwrl_1749139433.seq -o /var/tmp/from_scwrl_1749139433.pdb > /var/tmp/scwrl_1749139433.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1749139433.pdb Number of alignments=1 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2nnnA/T0617-2nnnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2nnnA expands to /projects/compbio/data/pdb/2nnn.pdb.gz 2nnnA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0617 read from 2nnnA/T0617-2nnnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2nnnA read from 2nnnA/T0617-2nnnA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2nnnA to template set # found chain 2nnnA in template set Warning: unaligning (T0617)I7 because first residue in template chain is (2nnnA)Y7 T0617 8 :NIDRHATAQINMLANKLMLKSSTA 2nnnA 8 :RLDDQIGFILRQANQRYAALFANG T0617 36 :FGIGMTEWRIISVLSSASDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVNGHSEDKRTYAINLTEMGQELYEVASDFAIEREKQLLEEFEEAEKDQLFILLK 2nnnA 34 :NGLTPTQWAALVRLGETGPCPQNQLGRLTAMDAATIKGVVERLDKRGLIQRSADPDDGRRLLVSLSPAGRAELEAGLAAAREINRQALAPLSLQEQETLRGLLA Number of specific fragments extracted= 2 number of extra gaps= 0 total=5 # request to SCWRL produces command: ulimit -t 134 ; scwrl4 -t -i /var/tmp/to_scwrl_881282393.pdb -s /var/tmp/to_scwrl_881282393.seq -o /var/tmp/from_scwrl_881282393.pdb > /var/tmp/scwrl_881282393.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_881282393.pdb Number of alignments=2 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3bpvA/T0617-3bpvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 3bpvA expands to /projects/compbio/data/pdb/3bpv.pdb.gz 3bpvA:# T0617 read from 3bpvA/T0617-3bpvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3bpvA read from 3bpvA/T0617-3bpvA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3bpvA to template set # found chain 3bpvA in template set T0617 24 :LMLKSSTAYTQKFGIGMTEWRIISVLSSASDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVNGHSEDKRTYAINLTEMGQELYEVASDFAIEREKQLLEEFEEAEKDQLFILLKKLRNKVDQ 3bpvA 17 :SHRVFIGRELGHLNLTDAQVACLLRIHREPGIKQDELATFFHVDKGTIARTLRRLEESGFIEREQDPENRRRYILEVTRRGEEIIPLILKVEERWEDLLFRDFTEDERKLFRKMCRRLAEEAVR Number of specific fragments extracted= 1 number of extra gaps= 0 total=6 # request to SCWRL produces command: ulimit -t 134 ; scwrl4 -t -i /var/tmp/to_scwrl_2035379824.pdb -s /var/tmp/to_scwrl_2035379824.seq -o /var/tmp/from_scwrl_2035379824.pdb > /var/tmp/scwrl_2035379824.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2035379824.pdb Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2a61A/T0617-2a61A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2a61A expands to /projects/compbio/data/pdb/2a61.pdb.gz 2a61A:Skipped atom 654, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 656, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 658, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 660, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 662, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 664, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 666, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 668, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 670, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 672, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 674, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 920, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 922, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 924, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 926, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 928, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 930, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 932, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 934, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 1079, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 1081, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 1083, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 1085, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 1087, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 1089, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 1091, because occupancy 0.500 <= existing 0.500 in 2a61A Skipped atom 1093, because occupancy 0.500 <= existing 0.500 in 2a61A # T0617 read from 2a61A/T0617-2a61A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2a61A read from 2a61A/T0617-2a61A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2a61A to template set # found chain 2a61A in template set T0617 24 :LMLKSSTAYTQKFGIGMTEWRIISVLSSASDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVNGHSEDKRTYAINLTEMGQELYEVASDFAIEREKQLLEEFEEAEKDQLFILLKKLRNKVDQ 2a61A 18 :MVKVEGRKVLRDFGITPAQFDILQKIYFEGPKRPGELSVLLGVAKSTVTGLVKRLEADGYLTRTPDPADRRAYFLVITRKGEEVIEKVIERRENFIEKITSDLGKEKSSKILDYLKELKGVMER Number of specific fragments extracted= 1 number of extra gaps= 0 total=7 # request to SCWRL produces command: ulimit -t 134 ; scwrl4 -t -i /var/tmp/to_scwrl_1482203764.pdb -s /var/tmp/to_scwrl_1482203764.seq -o /var/tmp/from_scwrl_1482203764.pdb > /var/tmp/scwrl_1482203764.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1482203764.pdb Number of alignments=4 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2rdpA/T0617-2rdpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2rdpA expands to /projects/compbio/data/pdb/2rdp.pdb.gz 2rdpA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 89, because occupancy 0.500 <= existing 0.500 in 2rdpA Skipped atom 93, because occupancy 0.500 <= existing 0.500 in 2rdpA Skipped atom 95, because occupancy 0.500 <= existing 0.500 in 2rdpA Skipped atom 97, because occupancy 0.500 <= existing 0.500 in 2rdpA Skipped atom 99, because occupancy 0.500 <= existing 0.500 in 2rdpA Skipped atom 101, because occupancy 0.500 <= existing 0.500 in 2rdpA Skipped atom 130, because occupancy 0.500 <= existing 0.500 in 2rdpA Skipped atom 132, because occupancy 0.500 <= existing 0.500 in 2rdpA Skipped atom 134, because occupancy 0.500 <= existing 0.500 in 2rdpA Skipped atom 136, because occupancy 0.500 <= existing 0.500 in 2rdpA Skipped atom 138, because occupancy 0.500 <= existing 0.500 in 2rdpA Skipped atom 140, because occupancy 0.500 <= existing 0.500 in 2rdpA Skipped atom 142, because occupancy 0.500 <= existing 0.500 in 2rdpA Skipped atom 144, because occupancy 0.500 <= existing 0.500 in 2rdpA Skipped atom 146, because occupancy 0.500 <= existing 0.500 in 2rdpA Skipped atom 148, because occupancy 0.500 <= existing 0.500 in 2rdpA Skipped atom 150, because occupancy 0.500 <= existing 0.500 in 2rdpA Skipped atom 152, because occupancy 0.500 <= existing 0.500 in 2rdpA Skipped atom 399, because occupancy 0.500 <= existing 0.500 in 2rdpA Skipped atom 401, because occupancy 0.500 <= existing 0.500 in 2rdpA Skipped atom 403, because occupancy 0.500 <= existing 0.500 in 2rdpA Skipped atom 405, because occupancy 0.500 <= existing 0.500 in 2rdpA Skipped atom 407, because occupancy 0.500 <= existing 0.500 in 2rdpA Skipped atom 409, because occupancy 0.500 <= existing 0.500 in 2rdpA Skipped atom 411, because occupancy 0.500 <= existing 0.500 in 2rdpA Skipped atom 413, because occupancy 0.500 <= existing 0.500 in 2rdpA Skipped atom 415, because occupancy 0.500 <= existing 0.500 in 2rdpA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 819, because occupancy 0.300 <= existing 0.700 in 2rdpA Skipped atom 821, because occupancy 0.300 <= existing 0.700 in 2rdpA Skipped atom 823, because occupancy 0.300 <= existing 0.700 in 2rdpA Skipped atom 825, because occupancy 0.300 <= existing 0.700 in 2rdpA Skipped atom 827, because occupancy 0.300 <= existing 0.700 in 2rdpA Skipped atom 829, because occupancy 0.300 <= existing 0.700 in 2rdpA Skipped atom 831, because occupancy 0.300 <= existing 0.700 in 2rdpA Skipped atom 833, because occupancy 0.300 <= existing 0.700 in 2rdpA Skipped atom 835, because occupancy 0.300 <= existing 0.700 in 2rdpA Skipped atom 837, because occupancy 0.300 <= existing 0.700 in 2rdpA Skipped atom 839, because occupancy 0.300 <= existing 0.700 in 2rdpA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0617 read from 2rdpA/T0617-2rdpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2rdpA read from 2rdpA/T0617-2rdpA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2rdpA to template set # found chain 2rdpA in template set Warning: unaligning (T0617)E91 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2rdpA)V94 Warning: unaligning (T0617)T95 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2rdpA)V94 T0617 26 :LKSSTAYTQKFGIGMTEWRIISVLSSASDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVNGHS 2rdpA 25 :KQRGREILTNYPITPPQFVALQWLLEEGDLTVGELSNKMYLACSTTTDLVDRMERNGLVARVRDE T0617 96 :YAINLTEMGQELYEVASDFAIEREKQLLEEFEEAEKDQLFILLKKLRNKV 2rdpA 95 :VRIRLLEKGERIIEEVIEKRQRDLANVLESFSDEEIVVFERCLRKLHQEM Number of specific fragments extracted= 2 number of extra gaps= 0 total=9 # request to SCWRL produces command: ulimit -t 134 ; scwrl4 -t -i /var/tmp/to_scwrl_579425247.pdb -s /var/tmp/to_scwrl_579425247.seq -o /var/tmp/from_scwrl_579425247.pdb > /var/tmp/scwrl_579425247.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_579425247.pdb Number of alignments=5 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2pexA/T0617-2pexA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2pexA expands to /projects/compbio/data/pdb/2pex.pdb.gz 2pexA:Skipped atom 867, because occupancy 0.500 <= existing 0.500 in 2pexA Skipped atom 869, because occupancy 0.500 <= existing 0.500 in 2pexA Skipped atom 871, because occupancy 0.500 <= existing 0.500 in 2pexA Skipped atom 873, because occupancy 0.500 <= existing 0.500 in 2pexA Skipped atom 875, because occupancy 0.500 <= existing 0.500 in 2pexA Skipped atom 877, because occupancy 0.500 <= existing 0.500 in 2pexA # T0617 read from 2pexA/T0617-2pexA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2pexA read from 2pexA/T0617-2pexA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2pexA to template set # found chain 2pexA in template set Warning: unaligning (T0617)G88 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2pexA)V103 Warning: unaligning (T0617)Y96 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2pexA)V103 Warning: unaligning (T0617)Q147 because last residue in template chain is (2pexA)A152 T0617 3 :AMQKINIDRHATAQINMLANKLMLKSSTA 2pexA 11 :TDTLLQLDNQLSFALYSANLAMHKLYRGL T0617 33 :TQKFGIGMTEWRIISVLSSASDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVN 2pexA 40 :LKALDLTYPQYLVMLVLWETDERSVSEIGERLYLDSATLTPLLKRLQAAGLVTRT T0617 97 :AINLTEMGQELYEVASDFAIEREKQL 2pexA 104 :IIALTETGRALRSKAGAVPEQVFCAS T0617 125 :EFEEAEKDQLFILLKKLRNKVD 2pexA 130 :ACSLDELRQLKQELEKLRSSLG Number of specific fragments extracted= 4 number of extra gaps= 0 total=13 # request to SCWRL produces command: ulimit -t 134 ; scwrl4 -t -i /var/tmp/to_scwrl_1738191983.pdb -s /var/tmp/to_scwrl_1738191983.seq -o /var/tmp/from_scwrl_1738191983.pdb > /var/tmp/scwrl_1738191983.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1738191983.pdb Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2fa5A/T0617-2fa5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2fa5A expands to /projects/compbio/data/pdb/2fa5.pdb.gz 2fa5A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0617 read from 2fa5A/T0617-2fa5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2fa5A read from 2fa5A/T0617-2fa5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2fa5A to template set # found chain 2fa5A in template set Warning: unaligning (T0617)V86 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2fa5A)S105 Warning: unaligning (T0617)Y96 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2fa5A)S105 T0617 4 :MQKINIDRHATAQINMLANKLMLKSS 2fa5A 16 :LNLEQFLPYRLSVLSNRISGNIAKVY T0617 33 :TQKFGIGMTEWRIISVLSSASDCSVQKISDILGLDKAAVSRTVKKLEEKKYIE 2fa5A 42 :GDRYGMAIPEWRVITILALYPGSSASEVSDRTAMDKVAVSRAVARLLERGFIR T0617 97 :AINLTEMGQELYEVASDFAIEREKQLLEEFEEAEKDQLFILLKKLRN 2fa5A 106 :MLALSPAGRQVYETVAPLVNEMEQRLMSVFSAEEQQTLERLIDRLAK Number of specific fragments extracted= 3 number of extra gaps= 0 total=16 # request to SCWRL produces command: ulimit -t 134 ; scwrl4 -t -i /var/tmp/to_scwrl_292308394.pdb -s /var/tmp/to_scwrl_292308394.seq -o /var/tmp/from_scwrl_292308394.pdb > /var/tmp/scwrl_292308394.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_292308394.pdb Number of alignments=7 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2gxgA/T0617-2gxgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2gxgA expands to /projects/compbio/data/pdb/2gxg.pdb.gz 2gxgA:# T0617 read from 2gxgA/T0617-2gxgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2gxgA read from 2gxgA/T0617-2gxgA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2gxgA to template set # found chain 2gxgA in template set T0617 12 :HATAQINMLANKLMLKSSTAYTQKFGIGMTEWRIISVLS 2gxgA 9 :IQIMSTIAKIYRAMSRELNRRLGELNLSYLDFLVLRATS T0617 53 :SD 2gxgA 48 :DG T0617 55 :CSVQKISDILGLDKAAVSRTVKKLEEKKYIEVNGHSEDKRTYAINLTEMGQELYEVASDFAIEREKQLLEEFEEAEKDQLFILLKKLRNKVDQ 2gxgA 51 :KTMAYLANRYFVTQSAITASVDKLEEMGLVVRVRDREDRRKILIEITEKGLETFNKGIEIYKKLANEVTGDLSEDEVILVLDKISKILKRIEE Number of specific fragments extracted= 3 number of extra gaps= 0 total=19 # request to SCWRL produces command: ulimit -t 134 ; scwrl4 -t -i /var/tmp/to_scwrl_1333772263.pdb -s /var/tmp/to_scwrl_1333772263.seq -o /var/tmp/from_scwrl_1333772263.pdb > /var/tmp/scwrl_1333772263.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1333772263.pdb Number of alignments=8 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3gfmA/T0617-3gfmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 3gfmA expands to /projects/compbio/data/pdb/3gfm.pdb.gz 3gfmA:# T0617 read from 3gfmA/T0617-3gfmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3gfmA read from 3gfmA/T0617-3gfmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3gfmA to template set # found chain 3gfmA in template set T0617 13 :ATAQINMLANKLMLKSSTAYTQKFGIGMTEWRIISVLS 3gfmA 10 :QIMSTIAKIYRAMSRELNRRLGELNLSYLDFLVLRATS T0617 53 :SD 3gfmA 48 :DG T0617 55 :CSVQKISDILGLDKAAVSRTVKKLEEKKYIEVNGHSEDKRTYAINLTEMGQELYEVASDFAIEREKQLLEEFEEAEKDQLFILLKKLRNKVDQ 3gfmA 51 :KTMAYLANRYFVTQSAITASVDKLEEMGLVVRVRDREDRRAILIEITEKGLETFNKGIEIYKKLANEVTGDLSEDEVILVLDKISKILKRIEE Number of specific fragments extracted= 3 number of extra gaps= 0 total=22 # request to SCWRL produces command: ulimit -t 134 ; scwrl4 -t -i /var/tmp/to_scwrl_1963041660.pdb -s /var/tmp/to_scwrl_1963041660.seq -o /var/tmp/from_scwrl_1963041660.pdb > /var/tmp/scwrl_1963041660.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1963041660.pdb Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3ecoA/T0617-3ecoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 3ecoA expands to /projects/compbio/data/pdb/3eco.pdb.gz 3ecoA:# T0617 read from 3ecoA/T0617-3ecoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ecoA read from 3ecoA/T0617-3ecoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3ecoA to template set # found chain 3ecoA in template set Warning: unaligning (T0617)E91 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3ecoA)R87 Warning: unaligning (T0617)R94 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3ecoA)R87 T0617 23 :KLMLKSSTAYTQKFGIGMTEWRIISVLSSASD 3ecoA 14 :HEMKQKADQKLEQFDITNEQGHTLGYLYAHQQ T0617 55 :CSVQKISDILGLDKAAVSRTVKKLEEKKYIEVNGHS 3ecoA 48 :LTQNDIAKALQRTGPTVSNLLRNLERKKLIYRYVDA T0617 95 :TYAINLTEMGQELYEVASDFAIEREKQLLEEFEEAEKDQLFILLKKLRNK 3ecoA 88 :RKNIGLTTSGIKLVEAFTSIFDEMEQTLVSQLSEEENEQMKANLTKMLSS Number of specific fragments extracted= 3 number of extra gaps= 0 total=25 # request to SCWRL produces command: ulimit -t 134 ; scwrl4 -t -i /var/tmp/to_scwrl_165441163.pdb -s /var/tmp/to_scwrl_165441163.seq -o /var/tmp/from_scwrl_165441163.pdb > /var/tmp/scwrl_165441163.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_165441163.pdb Number of alignments=10 # command:Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.389 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 1 total_weight= 10950.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 2 total_weight= 10950.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 3 total_weight= 10950.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 4 total_weight= 10950.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 5 total_weight= 10950.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 1.243 rmsd (weighted)= 3.322 (unweighted)= 28.869 superimposing iter= 1 total_weight= 2155.273 rmsd (weighted)= 2.215 (unweighted)= 28.892 superimposing iter= 2 total_weight= 1085.121 rmsd (weighted)= 2.098 (unweighted)= 28.906 superimposing iter= 3 total_weight= 1020.130 rmsd (weighted)= 2.050 (unweighted)= 28.915 superimposing iter= 4 total_weight= 1014.483 rmsd (weighted)= 2.010 (unweighted)= 28.920 superimposing iter= 5 total_weight= 1007.710 rmsd (weighted)= 1.978 (unweighted)= 28.924 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 1.179 rmsd (weighted)= 3.657 (unweighted)= 35.455 superimposing iter= 1 total_weight= 2333.332 rmsd (weighted)= 2.252 (unweighted)= 35.418 superimposing iter= 2 total_weight= 1194.869 rmsd (weighted)= 1.968 (unweighted)= 35.333 superimposing iter= 3 total_weight= 1013.033 rmsd (weighted)= 1.871 (unweighted)= 35.247 superimposing iter= 4 total_weight= 981.585 rmsd (weighted)= 1.809 (unweighted)= 35.166 superimposing iter= 5 total_weight= 973.760 rmsd (weighted)= 1.757 (unweighted)= 35.087 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 1.179 rmsd (weighted)= 5.711 (unweighted)= 36.025 superimposing iter= 1 total_weight= 2435.431 rmsd (weighted)= 3.405 (unweighted)= 36.120 superimposing iter= 2 total_weight= 1276.710 rmsd (weighted)= 2.850 (unweighted)= 36.349 superimposing iter= 3 total_weight= 1098.550 rmsd (weighted)= 2.561 (unweighted)= 36.683 superimposing iter= 4 total_weight= 1121.499 rmsd (weighted)= 2.257 (unweighted)= 37.108 superimposing iter= 5 total_weight= 1194.297 rmsd (weighted)= 1.912 (unweighted)= 37.554 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 1.126 rmsd (weighted)= 3.344 (unweighted)= 43.520 superimposing iter= 1 total_weight= 2393.740 rmsd (weighted)= 1.980 (unweighted)= 43.593 superimposing iter= 2 total_weight= 1240.446 rmsd (weighted)= 1.654 (unweighted)= 43.573 superimposing iter= 3 total_weight= 1033.975 rmsd (weighted)= 1.518 (unweighted)= 43.535 superimposing iter= 4 total_weight= 962.975 rmsd (weighted)= 1.444 (unweighted)= 43.497 superimposing iter= 5 total_weight= 931.111 rmsd (weighted)= 1.398 (unweighted)= 43.460 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 1.321 rmsd (weighted)= 3.568 (unweighted)= 18.091 superimposing iter= 1 total_weight= 2473.513 rmsd (weighted)= 2.280 (unweighted)= 18.145 superimposing iter= 2 total_weight= 1218.689 rmsd (weighted)= 2.093 (unweighted)= 18.193 superimposing iter= 3 total_weight= 1103.444 rmsd (weighted)= 2.020 (unweighted)= 18.233 superimposing iter= 4 total_weight= 1085.470 rmsd (weighted)= 1.967 (unweighted)= 18.264 superimposing iter= 5 total_weight= 1066.031 rmsd (weighted)= 1.931 (unweighted)= 18.288 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 1.278 rmsd (weighted)= 4.080 (unweighted)= 23.308 superimposing iter= 1 total_weight= 3012.955 rmsd (weighted)= 2.263 (unweighted)= 23.601 superimposing iter= 2 total_weight= 1341.389 rmsd (weighted)= 1.933 (unweighted)= 23.734 superimposing iter= 3 total_weight= 1093.098 rmsd (weighted)= 1.837 (unweighted)= 23.807 superimposing iter= 4 total_weight= 1030.919 rmsd (weighted)= 1.801 (unweighted)= 23.854 superimposing iter= 5 total_weight= 1014.631 rmsd (weighted)= 1.780 (unweighted)= 23.893 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 1.280 rmsd (weighted)= 3.331 (unweighted)= 27.768 superimposing iter= 1 total_weight= 3129.476 rmsd (weighted)= 1.806 (unweighted)= 27.986 superimposing iter= 2 total_weight= 1459.232 rmsd (weighted)= 1.481 (unweighted)= 28.050 superimposing iter= 3 total_weight= 1133.531 rmsd (weighted)= 1.386 (unweighted)= 28.071 superimposing iter= 4 total_weight= 1055.966 rmsd (weighted)= 1.346 (unweighted)= 28.077 superimposing iter= 5 total_weight= 1033.831 rmsd (weighted)= 1.320 (unweighted)= 28.079 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 1.268 rmsd (weighted)= 3.247 (unweighted)= 27.181 superimposing iter= 1 total_weight= 3123.547 rmsd (weighted)= 1.748 (unweighted)= 27.334 superimposing iter= 2 total_weight= 1438.358 rmsd (weighted)= 1.438 (unweighted)= 27.383 superimposing iter= 3 total_weight= 1117.060 rmsd (weighted)= 1.349 (unweighted)= 27.396 superimposing iter= 4 total_weight= 1050.594 rmsd (weighted)= 1.304 (unweighted)= 27.395 superimposing iter= 5 total_weight= 1045.344 rmsd (weighted)= 1.263 (unweighted)= 27.387 Debug: superimposing conformation 9 on the average so far superimposing iter= 0 total_weight= 1.157 rmsd (weighted)= 4.794 (unweighted)= 33.193 superimposing iter= 1 total_weight= 2311.871 rmsd (weighted)= 2.844 (unweighted)= 33.017 superimposing iter= 2 total_weight= 1295.770 rmsd (weighted)= 2.284 (unweighted)= 32.740 superimposing iter= 3 total_weight= 1200.266 rmsd (weighted)= 1.923 (unweighted)= 32.477 superimposing iter= 4 total_weight= 1175.299 rmsd (weighted)= 1.644 (unweighted)= 32.243 superimposing iter= 5 total_weight= 1129.215 rmsd (weighted)= 1.433 (unweighted)= 32.049 Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.389 rmsd (weighted)= 2.844 (unweighted)= 14.417 superimposing iter= 1 total_weight= 2526.693 rmsd (weighted)= 1.817 (unweighted)= 14.489 superimposing iter= 2 total_weight= 1442.108 rmsd (weighted)= 1.558 (unweighted)= 14.517 superimposing iter= 3 total_weight= 1279.550 rmsd (weighted)= 1.424 (unweighted)= 14.530 superimposing iter= 4 total_weight= 1219.148 rmsd (weighted)= 1.336 (unweighted)= 14.541 superimposing iter= 5 total_weight= 1181.863 rmsd (weighted)= 1.275 (unweighted)= 14.550 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 1.292 rmsd (weighted)= 2.493 (unweighted)= 25.416 superimposing iter= 1 total_weight= 2427.276 rmsd (weighted)= 1.569 (unweighted)= 25.430 superimposing iter= 2 total_weight= 1360.724 rmsd (weighted)= 1.336 (unweighted)= 25.444 superimposing iter= 3 total_weight= 1149.264 rmsd (weighted)= 1.240 (unweighted)= 25.451 superimposing iter= 4 total_weight= 1066.492 rmsd (weighted)= 1.196 (unweighted)= 25.455 superimposing iter= 5 total_weight= 1027.537 rmsd (weighted)= 1.176 (unweighted)= 25.457 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 1.262 rmsd (weighted)= 1.903 (unweighted)= 32.254 superimposing iter= 1 total_weight= 2296.487 rmsd (weighted)= 1.227 (unweighted)= 32.267 superimposing iter= 2 total_weight= 1218.218 rmsd (weighted)= 1.100 (unweighted)= 32.266 superimposing iter= 3 total_weight= 1088.812 rmsd (weighted)= 1.046 (unweighted)= 32.255 superimposing iter= 4 total_weight= 1030.783 rmsd (weighted)= 1.024 (unweighted)= 32.244 superimposing iter= 5 total_weight= 1008.077 rmsd (weighted)= 1.013 (unweighted)= 32.234 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 1.262 rmsd (weighted)= 4.006 (unweighted)= 33.451 superimposing iter= 1 total_weight= 2342.903 rmsd (weighted)= 2.551 (unweighted)= 33.548 superimposing iter= 2 total_weight= 1252.131 rmsd (weighted)= 2.249 (unweighted)= 33.646 superimposing iter= 3 total_weight= 1085.940 rmsd (weighted)= 2.131 (unweighted)= 33.743 superimposing iter= 4 total_weight= 1059.977 rmsd (weighted)= 2.040 (unweighted)= 33.848 superimposing iter= 5 total_weight= 1077.045 rmsd (weighted)= 1.930 (unweighted)= 33.971 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 1.167 rmsd (weighted)= 1.838 (unweighted)= 40.582 superimposing iter= 1 total_weight= 2033.405 rmsd (weighted)= 1.213 (unweighted)= 40.585 superimposing iter= 2 total_weight= 1122.463 rmsd (weighted)= 1.087 (unweighted)= 40.555 superimposing iter= 3 total_weight= 982.455 rmsd (weighted)= 1.042 (unweighted)= 40.518 superimposing iter= 4 total_weight= 952.455 rmsd (weighted)= 1.014 (unweighted)= 40.482 superimposing iter= 5 total_weight= 946.342 rmsd (weighted)= 0.989 (unweighted)= 40.447 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 1.331 rmsd (weighted)= 3.034 (unweighted)= 18.788 superimposing iter= 1 total_weight= 2225.177 rmsd (weighted)= 2.055 (unweighted)= 18.778 superimposing iter= 2 total_weight= 1202.948 rmsd (weighted)= 1.907 (unweighted)= 18.777 superimposing iter= 3 total_weight= 1067.659 rmsd (weighted)= 1.881 (unweighted)= 18.781 superimposing iter= 4 total_weight= 1047.159 rmsd (weighted)= 1.873 (unweighted)= 18.788 superimposing iter= 5 total_weight= 1047.840 rmsd (weighted)= 1.863 (unweighted)= 18.798 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 1.278 rmsd (weighted)= 3.049 (unweighted)= 20.688 superimposing iter= 1 total_weight= 2968.456 rmsd (weighted)= 1.683 (unweighted)= 20.739 superimposing iter= 2 total_weight= 1424.655 rmsd (weighted)= 1.395 (unweighted)= 20.744 superimposing iter= 3 total_weight= 1178.215 rmsd (weighted)= 1.277 (unweighted)= 20.739 superimposing iter= 4 total_weight= 1147.070 rmsd (weighted)= 1.185 (unweighted)= 20.735 superimposing iter= 5 total_weight= 1137.253 rmsd (weighted)= 1.104 (unweighted)= 20.741 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 1.363 rmsd (weighted)= 1.851 (unweighted)= 23.615 superimposing iter= 1 total_weight= 3712.810 rmsd (weighted)= 0.953 (unweighted)= 23.702 superimposing iter= 2 total_weight= 1540.612 rmsd (weighted)= 0.783 (unweighted)= 23.751 superimposing iter= 3 total_weight= 1301.163 rmsd (weighted)= 0.702 (unweighted)= 23.794 superimposing iter= 4 total_weight= 1243.156 rmsd (weighted)= 0.646 (unweighted)= 23.828 superimposing iter= 5 total_weight= 1212.971 rmsd (weighted)= 0.603 (unweighted)= 23.856 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 1.351 rmsd (weighted)= 1.726 (unweighted)= 22.895 superimposing iter= 1 total_weight= 3629.036 rmsd (weighted)= 0.893 (unweighted)= 22.897 superimposing iter= 2 total_weight= 1565.645 rmsd (weighted)= 0.725 (unweighted)= 22.899 superimposing iter= 3 total_weight= 1285.833 rmsd (weighted)= 0.651 (unweighted)= 22.907 superimposing iter= 4 total_weight= 1228.355 rmsd (weighted)= 0.600 (unweighted)= 22.917 superimposing iter= 5 total_weight= 1183.022 rmsd (weighted)= 0.564 (unweighted)= 22.929 Debug: superimposing conformation 9 on the average so far superimposing iter= 0 total_weight= 1.198 rmsd (weighted)= 2.913 (unweighted)= 31.003 superimposing iter= 1 total_weight= 2766.255 rmsd (weighted)= 1.492 (unweighted)= 30.828 superimposing iter= 2 total_weight= 1866.616 rmsd (weighted)= 0.983 (unweighted)= 30.737 superimposing iter= 3 total_weight= 1405.545 rmsd (weighted)= 0.783 (unweighted)= 30.712 superimposing iter= 4 total_weight= 1122.766 rmsd (weighted)= 0.706 (unweighted)= 30.697 superimposing iter= 5 total_weight= 1058.072 rmsd (weighted)= 0.659 (unweighted)= 30.680 Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.389 rmsd (weighted)= 2.923 (unweighted)= 14.452 superimposing iter= 1 total_weight= 2500.478 rmsd (weighted)= 1.872 (unweighted)= 14.533 superimposing iter= 2 total_weight= 1451.568 rmsd (weighted)= 1.602 (unweighted)= 14.564 superimposing iter= 3 total_weight= 1273.625 rmsd (weighted)= 1.469 (unweighted)= 14.578 superimposing iter= 4 total_weight= 1217.059 rmsd (weighted)= 1.380 (unweighted)= 14.589 superimposing iter= 5 total_weight= 1178.167 rmsd (weighted)= 1.320 (unweighted)= 14.598 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 1.292 rmsd (weighted)= 2.471 (unweighted)= 25.482 superimposing iter= 1 total_weight= 2459.614 rmsd (weighted)= 1.545 (unweighted)= 25.490 superimposing iter= 2 total_weight= 1389.482 rmsd (weighted)= 1.302 (unweighted)= 25.498 superimposing iter= 3 total_weight= 1156.085 rmsd (weighted)= 1.207 (unweighted)= 25.501 superimposing iter= 4 total_weight= 1067.395 rmsd (weighted)= 1.165 (unweighted)= 25.502 superimposing iter= 5 total_weight= 1025.558 rmsd (weighted)= 1.148 (unweighted)= 25.503 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 1.262 rmsd (weighted)= 1.891 (unweighted)= 32.577 superimposing iter= 1 total_weight= 2252.097 rmsd (weighted)= 1.233 (unweighted)= 32.586 superimposing iter= 2 total_weight= 1214.272 rmsd (weighted)= 1.108 (unweighted)= 32.580 superimposing iter= 3 total_weight= 1084.674 rmsd (weighted)= 1.055 (unweighted)= 32.566 superimposing iter= 4 total_weight= 1028.406 rmsd (weighted)= 1.033 (unweighted)= 32.553 superimposing iter= 5 total_weight= 1007.505 rmsd (weighted)= 1.022 (unweighted)= 32.542 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 1.262 rmsd (weighted)= 3.973 (unweighted)= 33.394 superimposing iter= 1 total_weight= 2329.542 rmsd (weighted)= 2.542 (unweighted)= 33.474 superimposing iter= 2 total_weight= 1231.440 rmsd (weighted)= 2.265 (unweighted)= 33.558 superimposing iter= 3 total_weight= 1068.474 rmsd (weighted)= 2.168 (unweighted)= 33.635 superimposing iter= 4 total_weight= 1044.781 rmsd (weighted)= 2.097 (unweighted)= 33.716 superimposing iter= 5 total_weight= 1055.441 rmsd (weighted)= 2.014 (unweighted)= 33.811 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 1.167 rmsd (weighted)= 1.824 (unweighted)= 40.448 superimposing iter= 1 total_weight= 2029.411 rmsd (weighted)= 1.204 (unweighted)= 40.456 superimposing iter= 2 total_weight= 1128.858 rmsd (weighted)= 1.075 (unweighted)= 40.427 superimposing iter= 3 total_weight= 984.300 rmsd (weighted)= 1.028 (unweighted)= 40.390 superimposing iter= 4 total_weight= 955.823 rmsd (weighted)= 0.997 (unweighted)= 40.352 superimposing iter= 5 total_weight= 948.377 rmsd (weighted)= 0.971 (unweighted)= 40.315 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 1.331 rmsd (weighted)= 3.021 (unweighted)= 18.799 superimposing iter= 1 total_weight= 2298.984 rmsd (weighted)= 2.011 (unweighted)= 18.798 superimposing iter= 2 total_weight= 1210.318 rmsd (weighted)= 1.858 (unweighted)= 18.809 superimposing iter= 3 total_weight= 1076.573 rmsd (weighted)= 1.821 (unweighted)= 18.827 superimposing iter= 4 total_weight= 1068.723 rmsd (weighted)= 1.791 (unweighted)= 18.850 superimposing iter= 5 total_weight= 1074.787 rmsd (weighted)= 1.755 (unweighted)= 18.878 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 1.278 rmsd (weighted)= 2.993 (unweighted)= 20.633 superimposing iter= 1 total_weight= 2990.924 rmsd (weighted)= 1.652 (unweighted)= 20.683 superimposing iter= 2 total_weight= 1421.845 rmsd (weighted)= 1.371 (unweighted)= 20.688 superimposing iter= 3 total_weight= 1194.240 rmsd (weighted)= 1.245 (unweighted)= 20.684 superimposing iter= 4 total_weight= 1167.886 rmsd (weighted)= 1.143 (unweighted)= 20.684 superimposing iter= 5 total_weight= 1166.920 rmsd (weighted)= 1.050 (unweighted)= 20.697 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 1.363 rmsd (weighted)= 1.889 (unweighted)= 23.772 superimposing iter= 1 total_weight= 3762.689 rmsd (weighted)= 0.961 (unweighted)= 23.894 superimposing iter= 2 total_weight= 1563.715 rmsd (weighted)= 0.784 (unweighted)= 23.951 superimposing iter= 3 total_weight= 1289.144 rmsd (weighted)= 0.707 (unweighted)= 23.999 superimposing iter= 4 total_weight= 1241.326 rmsd (weighted)= 0.651 (unweighted)= 24.036 superimposing iter= 5 total_weight= 1213.136 rmsd (weighted)= 0.607 (unweighted)= 24.066 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 1.351 rmsd (weighted)= 1.753 (unweighted)= 22.948 superimposing iter= 1 total_weight= 3641.438 rmsd (weighted)= 0.902 (unweighted)= 22.959 superimposing iter= 2 total_weight= 1595.449 rmsd (weighted)= 0.725 (unweighted)= 22.963 superimposing iter= 3 total_weight= 1293.658 rmsd (weighted)= 0.649 (unweighted)= 22.972 superimposing iter= 4 total_weight= 1231.107 rmsd (weighted)= 0.598 (unweighted)= 22.983 superimposing iter= 5 total_weight= 1181.410 rmsd (weighted)= 0.562 (unweighted)= 22.995 Debug: superimposing conformation 9 on the average so far superimposing iter= 0 total_weight= 1.198 rmsd (weighted)= 2.870 (unweighted)= 31.233 superimposing iter= 1 total_weight= 2742.085 rmsd (weighted)= 1.484 (unweighted)= 31.053 superimposing iter= 2 total_weight= 1808.240 rmsd (weighted)= 0.994 (unweighted)= 30.959 superimposing iter= 3 total_weight= 1406.244 rmsd (weighted)= 0.792 (unweighted)= 30.934 superimposing iter= 4 total_weight= 1132.878 rmsd (weighted)= 0.710 (unweighted)= 30.922 superimposing iter= 5 total_weight= 1062.326 rmsd (weighted)= 0.662 (unweighted)= 30.906 superimposing iter= 0 total_weight= 1.389 rmsd (weighted)= 2.942 (unweighted)= 14.467 superimposing iter= 1 total_weight= 2489.323 rmsd (weighted)= 1.887 (unweighted)= 14.549 superimposing iter= 2 total_weight= 1450.956 rmsd (weighted)= 1.616 (unweighted)= 14.580 superimposing iter= 3 total_weight= 1266.610 rmsd (weighted)= 1.486 (unweighted)= 14.595 superimposing iter= 4 total_weight= 1214.617 rmsd (weighted)= 1.398 (unweighted)= 14.605 superimposing iter= 5 total_weight= 1175.897 rmsd (weighted)= 1.339 (unweighted)= 14.615 superimposing iter= 0 total_weight= 1.292 rmsd (weighted)= 2.468 (unweighted)= 25.549 superimposing iter= 1 total_weight= 2467.038 rmsd (weighted)= 1.541 (unweighted)= 25.557 superimposing iter= 2 total_weight= 1392.472 rmsd (weighted)= 1.297 (unweighted)= 25.566 superimposing iter= 3 total_weight= 1161.112 rmsd (weighted)= 1.200 (unweighted)= 25.570 superimposing iter= 4 total_weight= 1069.945 rmsd (weighted)= 1.157 (unweighted)= 25.572 superimposing iter= 5 total_weight= 1027.676 rmsd (weighted)= 1.140 (unweighted)= 25.574 superimposing iter= 0 total_weight= 1.262 rmsd (weighted)= 1.889 (unweighted)= 32.670 superimposing iter= 1 total_weight= 2251.861 rmsd (weighted)= 1.232 (unweighted)= 32.677 superimposing iter= 2 total_weight= 1215.584 rmsd (weighted)= 1.106 (unweighted)= 32.670 superimposing iter= 3 total_weight= 1083.697 rmsd (weighted)= 1.054 (unweighted)= 32.656 superimposing iter= 4 total_weight= 1028.368 rmsd (weighted)= 1.032 (unweighted)= 32.643 superimposing iter= 5 total_weight= 1007.357 rmsd (weighted)= 1.021 (unweighted)= 32.632 superimposing iter= 0 total_weight= 1.262 rmsd (weighted)= 3.965 (unweighted)= 33.353 superimposing iter= 1 total_weight= 2328.234 rmsd (weighted)= 2.538 (unweighted)= 33.431 superimposing iter= 2 total_weight= 1230.554 rmsd (weighted)= 2.262 (unweighted)= 33.512 superimposing iter= 3 total_weight= 1067.228 rmsd (weighted)= 2.167 (unweighted)= 33.587 superimposing iter= 4 total_weight= 1043.475 rmsd (weighted)= 2.098 (unweighted)= 33.664 superimposing iter= 5 total_weight= 1053.509 rmsd (weighted)= 2.017 (unweighted)= 33.756 superimposing iter= 0 total_weight= 1.167 rmsd (weighted)= 1.820 (unweighted)= 40.410 superimposing iter= 1 total_weight= 2027.621 rmsd (weighted)= 1.201 (unweighted)= 40.418 superimposing iter= 2 total_weight= 1130.119 rmsd (weighted)= 1.072 (unweighted)= 40.388 superimposing iter= 3 total_weight= 985.156 rmsd (weighted)= 1.024 (unweighted)= 40.351 superimposing iter= 4 total_weight= 954.623 rmsd (weighted)= 0.994 (unweighted)= 40.313 superimposing iter= 5 total_weight= 949.377 rmsd (weighted)= 0.967 (unweighted)= 40.275 superimposing iter= 0 total_weight= 1.331 rmsd (weighted)= 3.024 (unweighted)= 18.798 superimposing iter= 1 total_weight= 2320.706 rmsd (weighted)= 2.002 (unweighted)= 18.799 superimposing iter= 2 total_weight= 1214.048 rmsd (weighted)= 1.846 (unweighted)= 18.813 superimposing iter= 3 total_weight= 1080.648 rmsd (weighted)= 1.805 (unweighted)= 18.833 superimposing iter= 4 total_weight= 1074.280 rmsd (weighted)= 1.770 (unweighted)= 18.859 superimposing iter= 5 total_weight= 1079.265 rmsd (weighted)= 1.731 (unweighted)= 18.890 superimposing iter= 0 total_weight= 1.278 rmsd (weighted)= 2.989 (unweighted)= 20.626 superimposing iter= 1 total_weight= 3002.476 rmsd (weighted)= 1.648 (unweighted)= 20.679 superimposing iter= 2 total_weight= 1425.370 rmsd (weighted)= 1.365 (unweighted)= 20.684 superimposing iter= 3 total_weight= 1201.221 rmsd (weighted)= 1.236 (unweighted)= 20.681 superimposing iter= 4 total_weight= 1173.286 rmsd (weighted)= 1.132 (unweighted)= 20.683 superimposing iter= 5 total_weight= 1172.076 rmsd (weighted)= 1.036 (unweighted)= 20.698 superimposing iter= 0 total_weight= 1.363 rmsd (weighted)= 1.904 (unweighted)= 23.881 superimposing iter= 1 total_weight= 3780.032 rmsd (weighted)= 0.965 (unweighted)= 24.008 superimposing iter= 2 total_weight= 1569.181 rmsd (weighted)= 0.787 (unweighted)= 24.065 superimposing iter= 3 total_weight= 1288.856 rmsd (weighted)= 0.709 (unweighted)= 24.114 superimposing iter= 4 total_weight= 1240.732 rmsd (weighted)= 0.653 (unweighted)= 24.151 superimposing iter= 5 total_weight= 1214.262 rmsd (weighted)= 0.608 (unweighted)= 24.182 superimposing iter= 0 total_weight= 1.351 rmsd (weighted)= 1.765 (unweighted)= 22.963 superimposing iter= 1 total_weight= 3651.599 rmsd (weighted)= 0.906 (unweighted)= 22.974 superimposing iter= 2 total_weight= 1601.026 rmsd (weighted)= 0.727 (unweighted)= 22.979 superimposing iter= 3 total_weight= 1293.751 rmsd (weighted)= 0.651 (unweighted)= 22.988 superimposing iter= 4 total_weight= 1230.027 rmsd (weighted)= 0.599 (unweighted)= 22.999 superimposing iter= 5 total_weight= 1182.496 rmsd (weighted)= 0.563 (unweighted)= 23.011 superimposing iter= 0 total_weight= 1.198 rmsd (weighted)= 2.865 (unweighted)= 31.317 superimposing iter= 1 total_weight= 2753.006 rmsd (weighted)= 1.477 (unweighted)= 31.138 superimposing iter= 2 total_weight= 1813.737 rmsd (weighted)= 0.988 (unweighted)= 31.045 superimposing iter= 3 total_weight= 1406.831 rmsd (weighted)= 0.787 (unweighted)= 31.020 superimposing iter= 4 total_weight= 1132.777 rmsd (weighted)= 0.706 (unweighted)= 31.008 superimposing iter= 5 total_weight= 1059.533 rmsd (weighted)= 0.659 (unweighted)= 30.992 # command:# Printing sheets for alignments to T0617.undertaker-align.sheets # command: