# command:# Seed set to 1279511059 # 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= 24.242 sec, elapsed time= 26.482 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= 37.670 sec, elapsed time= 44.032 sec. # command:# Prefix for input files set to # command:# Making conformation for sequence T0634 numbered 1 through 140 Created new target T0634 from T0634.a2m # command:# command:# No conformations to remove in PopConform # command:CPU_time= 37.671 sec, elapsed time= 45.445 sec. # command:# Prefix for input files set to # command:# reading script from file T0634.undertaker-align.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 3f6pA/T0634-3f6pA-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 3f6pA expands to /projects/compbio/data/pdb/3f6p.pdb.gz 3f6pA:# T0634 read from 3f6pA/T0634-3f6pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3f6pA read from 3f6pA/T0634-3f6pA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3f6pA to template set # found chain 3f6pA in template set T0634 1 :MSLKKILIIDQQDFSRIELKNFLDSEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRS 3f6pA 1 :MDKKILVVDDEKPIADILEFNLRKEGYEVHCAHDGNEAVEMVEELQPDLILLDIMLPNKDGVEVCREVRKK # choosing archetypes in rotamer library T0634 75 :KNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHL 3f6pA 72 :YDMPIIMLTAKDSEIDKVIGLEIGADDYVTKPFSTRELLARVKANL Number of specific fragments extracted= 2 number of extra gaps= 0 total=2 # request to SCWRL produces command: ulimit -t 126 ; scwrl4 -t -i /var/tmp/to_scwrl_742445813.pdb -s /var/tmp/to_scwrl_742445813.seq -o /var/tmp/from_scwrl_742445813.pdb > /var/tmp/scwrl_742445813.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_742445813.pdb Number of alignments=1 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2zwmA/T0634-2zwmA-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 2zwmA expands to /projects/compbio/data/pdb/2zwm.pdb.gz 2zwmA:# T0634 read from 2zwmA/T0634-2zwmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2zwmA read from 2zwmA/T0634-2zwmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2zwmA to template set # found chain 2zwmA in template set Warning: unaligning (T0634)S2 because first residue in template chain is (2zwmA)D1 T0634 3 :LKKILIIDQQDFSRIELKNFLDSEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRS 2zwmA 2 :KKILVVDDEKPIADILEFNLRKEGYEVHCAHDGNEAVEMVEELQPDLILLDIMLPNKDGVEVCREVRKK T0634 75 :KNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLR 2zwmA 71 :YDMPIIMLTAKDSEIDKVIGLEIGADDYVTKPFSTRELLARVKANLR Number of specific fragments extracted= 2 number of extra gaps= 0 total=4 # request to SCWRL produces command: ulimit -t 126 ; scwrl4 -t -i /var/tmp/to_scwrl_734867206.pdb -s /var/tmp/to_scwrl_734867206.seq -o /var/tmp/from_scwrl_734867206.pdb > /var/tmp/scwrl_734867206.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_734867206.pdb Number of alignments=2 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mvoA/T0634-1mvoA-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 1mvoA expands to /projects/compbio/data/pdb/1mvo.pdb.gz 1mvoA:Skipped atom 611, because occupancy 0.5 <= existing 0.500 in 1mvoA Skipped atom 613, because occupancy 0.500 <= existing 0.500 in 1mvoA Skipped atom 615, because occupancy 0.500 <= existing 0.500 in 1mvoA Skipped atom 617, because occupancy 0.500 <= existing 0.500 in 1mvoA Skipped atom 619, because occupancy 0.500 <= existing 0.500 in 1mvoA Skipped atom 621, because occupancy 0.500 <= existing 0.500 in 1mvoA Skipped atom 623, because occupancy 0.500 <= existing 0.500 in 1mvoA Skipped atom 625, because occupancy 0.500 <= existing 0.500 in 1mvoA # T0634 read from 1mvoA/T0634-1mvoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mvoA read from 1mvoA/T0634-1mvoA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1mvoA to template set # found chain 1mvoA in template set Warning: unaligning (T0634)Q123 because last residue in template chain is (1mvoA)S121 T0634 1 :MSLKKILIIDQQDFSRIELKNFLDSEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSK 1mvoA 1 :MNKKILVVDDEESIVTLLQYNLERSGYDVITASDGEEALKKAETEKPDLIVLDVMLPKLDGIEVCKQLRQQK T0634 75 :KNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRT 1mvoA 73 :LMFPILMLTAKDEEFDKVLGLELGADDYMTKPFSPREVNARVKAILRR Number of specific fragments extracted= 2 number of extra gaps= 0 total=6 # request to SCWRL produces command: ulimit -t 126 ; scwrl4 -t -i /var/tmp/to_scwrl_1196883234.pdb -s /var/tmp/to_scwrl_1196883234.seq -o /var/tmp/from_scwrl_1196883234.pdb > /var/tmp/scwrl_1196883234.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1196883234.pdb Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2jbaA/T0634-2jbaA-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 2jbaA expands to /projects/compbio/data/pdb/2jba.pdb.gz 2jbaA:Skipped atom 132, because occupancy 0.500 <= existing 0.500 in 2jbaA Skipped atom 133, because occupancy 0.500 <= existing 0.500 in 2jbaA Skipped atom 134, because occupancy 0.500 <= existing 0.500 in 2jbaA Skipped atom 135, because occupancy 0.500 <= existing 0.500 in 2jbaA Skipped atom 296, because occupancy 0.500 <= existing 0.500 in 2jbaA Skipped atom 297, because occupancy 0.500 <= existing 0.500 in 2jbaA Skipped atom 455, because occupancy 0.500 <= existing 0.500 in 2jbaA Skipped atom 456, because occupancy 0.500 <= existing 0.500 in 2jbaA Skipped atom 457, because occupancy 0.500 <= existing 0.500 in 2jbaA Skipped atom 458, because occupancy 0.500 <= existing 0.500 in 2jbaA Skipped atom 954, because occupancy 0.500 <= existing 0.500 in 2jbaA Skipped atom 955, because occupancy 0.500 <= existing 0.500 in 2jbaA Skipped atom 956, because occupancy 0.500 <= existing 0.500 in 2jbaA Skipped atom 957, because occupancy 0.500 <= existing 0.500 in 2jbaA # T0634 read from 2jbaA/T0634-2jbaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2jbaA read from 2jbaA/T0634-2jbaA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2jbaA to template set # found chain 2jbaA in template set Warning: unaligning (T0634)S2 because first residue in template chain is (2jbaA)A2 T0634 3 :LKKILIIDQQDFSRIELKNFLDSEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLR 2jbaA 3 :RRILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQLNEPWPDLILLAWMLPGGSGIQFIKHLRRESMTRDIPVVMLTARGEEEDRVRGLETGADDCITKPFSPKELVARIKAVMR Number of specific fragments extracted= 1 number of extra gaps= 0 total=7 # request to SCWRL produces command: ulimit -t 126 ; scwrl4 -t -i /var/tmp/to_scwrl_869573563.pdb -s /var/tmp/to_scwrl_869573563.seq -o /var/tmp/from_scwrl_869573563.pdb > /var/tmp/scwrl_869573563.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_869573563.pdb Number of alignments=4 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1kgsA/T0634-1kgsA-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 # T0634 read from 1kgsA/T0634-1kgsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1kgsA read from 1kgsA/T0634-1kgsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # found chain 1kgsA in training set Warning: unaligning (T0634)S2 because first residue in template chain is (1kgsA)N2 T0634 3 :LKKILIIDQQDFSRIELKNFLDSEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSK 1kgsA 3 :VRVLVVEDERDLADLITEALKKEMFTVDVCYDGEEGMYMALNEPFDVVILDIMLPVHDGWEILKSMRESG T0634 75 :KNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQ 1kgsA 73 :VNTPVLMLTALSDVEYRVKGLNMGADDYLPKPFDLRELIARVRALIRRK Number of specific fragments extracted= 2 number of extra gaps= 0 total=9 # request to SCWRL produces command: ulimit -t 126 ; scwrl4 -t -i /var/tmp/to_scwrl_1250415541.pdb -s /var/tmp/to_scwrl_1250415541.seq -o /var/tmp/from_scwrl_1250415541.pdb > /var/tmp/scwrl_1250415541.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1250415541.pdb Number of alignments=5 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2oqrA/T0634-2oqrA-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 2oqrA expands to /projects/compbio/data/pdb/2oqr.pdb.gz 2oqrA:Skipped atom 782, because occupancy 0.500 <= existing 0.500 in 2oqrA Skipped atom 786, because occupancy 0.500 <= existing 0.500 in 2oqrA Skipped atom 788, because occupancy 0.500 <= existing 0.500 in 2oqrA Skipped atom 790, because occupancy 0.500 <= existing 0.500 in 2oqrA Skipped atom 792, because occupancy 0.500 <= existing 0.500 in 2oqrA Skipped atom 794, because occupancy 0.500 <= existing 0.500 in 2oqrA Skipped atom 796, because occupancy 0.500 <= existing 0.500 in 2oqrA Skipped atom 798, because occupancy 0.500 <= existing 0.500 in 2oqrA # T0634 read from 2oqrA/T0634-2oqrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2oqrA read from 2oqrA/T0634-2oqrA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2oqrA to template set # found chain 2oqrA in template set Warning: unaligning (T0634)L3 because first residue in template chain is (2oqrA)A1 Warning: unaligning (T0634)K105 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2oqrA)P102 Warning: unaligning (T0634)P106 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2oqrA)P102 T0634 4 :KKILIIDQQ 2oqrA 2 :TSVLIVEDE T0634 13 :DFSRIELKNFLDSEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRS 2oqrA 12 :SLADPLAFLLRKEGFEATVVTDGPAALAEFDRAGADIVLLDLMLPGMSGTDVCKQLRAR T0634 75 :KNVPLILL 2oqrA 71 :SSVPVIMV T0634 84 :SSEHKEA 2oqrA 79 :TARDSEI T0634 91 :IVNGLHSGADDYLT 2oqrA 87 :KVVGLELGADDYVT T0634 107 :FNRNDLLSRIEIHLRTQNYYSDLRKNEG 2oqrA 103 :YSARELIARIRAVLRRGGDDDSEMSDGV Number of specific fragments extracted= 6 number of extra gaps= 1 total=15 # request to SCWRL produces command: ulimit -t 126 ; scwrl4 -t -i /var/tmp/to_scwrl_717976983.pdb -s /var/tmp/to_scwrl_717976983.seq -o /var/tmp/from_scwrl_717976983.pdb > /var/tmp/scwrl_717976983.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_717976983.pdb Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1w25A/T0634-1w25A-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 1w25A expands to /projects/compbio/data/pdb/1w25.pdb.gz 1w25A:# T0634 read from 1w25A/T0634-1w25A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1w25A read from 1w25A/T0634-1w25A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1w25A to template set # found chain 1w25A in template set Warning: unaligning (T0634)S2 because first residue in template chain is (1w25A)S2 Warning: unaligning (T0634)H136 because of BadResidue code BAD_PEPTIDE in next template residue (1w25A)R137 Warning: unaligning (T0634)H137 because of BadResidue code BAD_PEPTIDE at template residue (1w25A)R137 T0634 3 :LKKILIIDQQDFSRIELKNFLDSEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHLRTQNYYSDLRKNEGH 1w25A 3 :ARILVVDDIEANVRLLEAKLTAEYYEVSTAMDGPTALAMAARDLPDIILLDVMMPGMDGFTVCRKLKDDPTTRHIPVVLITALDGRGDRIQGLESGASDFLTKPIDDVMLFARVRSLTRFKLVIDELRQREAS Number of specific fragments extracted= 1 number of extra gaps= 1 total=16 # request to SCWRL produces command: ulimit -t 126 ; scwrl4 -t -i /var/tmp/to_scwrl_873689648.pdb -s /var/tmp/to_scwrl_873689648.seq -o /var/tmp/from_scwrl_873689648.pdb > /var/tmp/scwrl_873689648.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_873689648.pdb Number of alignments=7 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3gt7A/T0634-3gt7A-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 3gt7A expands to /projects/compbio/data/pdb/3gt7.pdb.gz 3gt7A:Skipped atom 354, because occupancy 0.500 <= existing 0.500 in 3gt7A Skipped atom 358, because occupancy 0.500 <= existing 0.500 in 3gt7A Skipped atom 360, because occupancy 0.500 <= existing 0.500 in 3gt7A Skipped atom 362, because occupancy 0.500 <= existing 0.500 in 3gt7A Skipped atom 364, because occupancy 0.500 <= existing 0.500 in 3gt7A Skipped atom 366, because occupancy 0.500 <= existing 0.500 in 3gt7A Skipped atom 368, because occupancy 0.500 <= existing 0.500 in 3gt7A Skipped atom 370, because occupancy 0.500 <= existing 0.500 in 3gt7A # T0634 read from 3gt7A/T0634-3gt7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3gt7A read from 3gt7A/T0634-3gt7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3gt7A to template set # found chain 3gt7A in template set Warning: unaligning (T0634)S2 because first residue in template chain is (3gt7A)A11 Warning: unaligning (T0634)K105 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3gt7A)P115 Warning: unaligning (T0634)P106 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3gt7A)P115 Warning: unaligning (T0634)Y126 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3gt7A)E142 Warning: unaligning (T0634)S127 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3gt7A)E142 Warning: unaligning (T0634)H139 because last residue in template chain is (3gt7A)F148 T0634 3 :LKKILIIDQQDFSRIELKNFLDSEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILLFSSEHKEAIVNGLHSGADDYLT 3gt7A 12 :GEILIVEDSPTQAEHLKHILEETGYQTEHVRNGREAVRFLSLTRPDLIISDVLMPEMDGYALCRWLKGQPDLRTIPVILLTILSDPRDVVRSLECGADDFIT T0634 107 :FNRNDLLSRIEIHLRTQNY 3gt7A 116 :CKDVVLASHVKRLLSGVKR T0634 134 :GHHHH 3gt7A 143 :SITLA Number of specific fragments extracted= 3 number of extra gaps= 2 total=19 # request to SCWRL produces command: ulimit -t 126 ; scwrl4 -t -i /var/tmp/to_scwrl_593507848.pdb -s /var/tmp/to_scwrl_593507848.seq -o /var/tmp/from_scwrl_593507848.pdb > /var/tmp/scwrl_593507848.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_593507848.pdb Number of alignments=8 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3dgfC/T0634-3dgfC-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 3dgfC expands to /projects/compbio/data/pdb/3dgf.pdb.gz 3dgfC:Skipped atom 813, because occupancy 0.500 <= existing 0.500 in 3dgfC Skipped atom 817, because occupancy 0.500 <= existing 0.500 in 3dgfC Skipped atom 819, because occupancy 0.500 <= existing 0.500 in 3dgfC Skipped atom 821, because occupancy 0.500 <= existing 0.500 in 3dgfC Skipped atom 823, because occupancy 0.500 <= existing 0.500 in 3dgfC Skipped atom 825, because occupancy 0.500 <= existing 0.500 in 3dgfC # T0634 read from 3dgfC/T0634-3dgfC-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3dgfC read from 3dgfC/T0634-3dgfC-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3dgfC to template set # found chain 3dgfC in template set Warning: unaligning (T0634)S2 because first residue in template chain is (3dgfC)S2 Warning: unaligning (T0634)H96 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3dgfC)L97 Warning: unaligning (T0634)S97 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3dgfC)L97 Warning: unaligning (T0634)G98 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3dgfC)A99 Warning: unaligning (T0634)A99 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3dgfC)A99 Warning: unaligning (T0634)D100 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3dgfC)R100 Warning: unaligning (T0634)D101 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3dgfC)K101 Warning: unaligning (T0634)T104 because of BadResidue code BAD_PEPTIDE in next template residue (3dgfC)K105 Warning: unaligning (T0634)K105 because of BadResidue code BAD_PEPTIDE at template residue (3dgfC)K105 Warning: unaligning (T0634)P106 because of BadResidue code BAD_PEPTIDE at template residue (3dgfC)P106 T0634 3 :LKKILIIDQQDFSRIELKNFLDSEYLVIESKNEKEALEQIDHHHPDLVILDMDIIGENSPNLCLKLKRSKGLKNVPLILLFSSEHKEAIVNGL 3dgfC 3 :KKVLLVDDSAVLRKIVSFNLKKEGYEVIEAENGQIALEKLSEFTPDLIVLDIMMPVMDGFTVLKKLQEKEEWKRIPVIVLTAKGGEEDESLAL T0634 102 :YL 3dgfC 102 :VM T0634 107 :FNRNDLLSRIEIH 3dgfC 107 :FSPSQFIEEVKHL Number of specific fragments extracted= 3 number of extra gaps= 2 total=22 # request to SCWRL produces command: ulimit -t 126 ; scwrl4 -t -i /var/tmp/to_scwrl_1215652479.pdb -s /var/tmp/to_scwrl_1215652479.seq -o /var/tmp/from_scwrl_1215652479.pdb > /var/tmp/scwrl_1215652479.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1215652479.pdb Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3gl9A/T0634-3gl9A-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 3gl9A expands to /projects/compbio/data/pdb/3gl9.pdb.gz 3gl9A:Skipped atom 134, because occupancy 0.500 <= existing 0.500 in 3gl9A Skipped atom 138, because occupancy 0.500 <= existing 0.500 in 3gl9A Skipped atom 140, because occupancy 0.500 <= existing 0.500 in 3gl9A Skipped atom 281, because occupancy 0.500 <= existing 0.500 in 3gl9A Skipped atom 285, because occupancy 0.500 <= existing 0.500 in 3gl9A Skipped atom 287, because occupancy 0.500 <= existing 0.500 in 3gl9A Skipped atom 289, because occupancy 0.500 <= existing 0.500 in 3gl9A Skipped atom 291, because occupancy 0.500 <= existing 0.500 in 3gl9A Skipped atom 333, because occupancy 0.500 <= existing 0.500 in 3gl9A Skipped atom 337, because occupancy 0.500 <= existing 0.500 in 3gl9A Skipped atom 339, because occupancy 0.500 <= existing 0.500 in 3gl9A Bad short name: BE for alphabet: pdb_atoms Bad short name: F1 for alphabet: pdb_atoms Bad short name: F2 for alphabet: pdb_atoms Bad short name: F3 for alphabet: pdb_atoms Skipped atom 817, because occupancy 0.500 <= existing 0.500 in 3gl9A Skipped atom 821, because occupancy 0.500 <= existing 0.500 in 3gl9A Skipped atom 823, because occupancy 0.500 <= existing 0.500 in 3gl9A Skipped atom 825, because occupancy 0.500 <= existing 0.500 in 3gl9A Skipped atom 827, because occupancy 0.500 <= existing 0.500 in 3gl9A Skipped atom 829, because occupancy 0.500 <= existing 0.500 in 3gl9A Skipped atom 831, because occupancy 0.500 <= existing 0.500 in 3gl9A Skipped atom 833, because occupancy 0.500 <= existing 0.500 in 3gl9A # T0634 read from 3gl9A/T0634-3gl9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3gl9A read from 3gl9A/T0634-3gl9A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3gl9A to template set # found chain 3gl9A in template set Warning: unaligning (T0634)S2 because first residue in template chain is (3gl9A)S2 Warning: unaligning (T0634)L52 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3gl9A)I54 Warning: unaligning (T0634)M54 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3gl9A)I54 T0634 3 :LKKILIIDQQDFSRIELKNFLDSEYLVIESKNEKEALEQIDHHHPDLVI 3gl9A 3 :KKVLLVDDSAVLRKIVSFNLKKEGYEVIEAENGQIALEKLSEFTPDLIV T0634 55 :DIIGENSPNLCLKLKRSKGLKNVPLILLFSSEHKEAIVNGLHSGADDYLTKPFNRNDLLSRIEIHL 3gl9A 55 :MMPVMDGFTVLKKLQEKEEWKRIPVIVLTAKGGEEDESLALSLGARKVMRKPFSPSQFIEEVKHLL Number of specific fragments extracted= 2 number of extra gaps= 0 total=24 # request to SCWRL produces command: ulimit -t 126 ; scwrl4 -t -i /var/tmp/to_scwrl_437539077.pdb -s /var/tmp/to_scwrl_437539077.seq -o /var/tmp/from_scwrl_437539077.pdb > /var/tmp/scwrl_437539077.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_437539077.pdb Number of alignments=10 # command:Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.230 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 1 total_weight= 9510.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 2 total_weight= 9510.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 3 total_weight= 9510.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 4 total_weight= 9510.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 5 total_weight= 9510.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 1.211 rmsd (weighted)= 1.350 (unweighted)= 37.645 superimposing iter= 1 total_weight= 7263.649 rmsd (weighted)= 0.343 (unweighted)= 37.659 superimposing iter= 2 total_weight= 3020.086 rmsd (weighted)= 0.184 (unweighted)= 37.657 superimposing iter= 3 total_weight= 1313.498 rmsd (weighted)= 0.154 (unweighted)= 37.657 superimposing iter= 4 total_weight= 1020.851 rmsd (weighted)= 0.147 (unweighted)= 37.658 superimposing iter= 5 total_weight= 961.063 rmsd (weighted)= 0.144 (unweighted)= 37.659 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 1.230 rmsd (weighted)= 2.165 (unweighted)= 31.798 superimposing iter= 1 total_weight= 5069.725 rmsd (weighted)= 0.782 (unweighted)= 32.049 superimposing iter= 2 total_weight= 2203.878 rmsd (weighted)= 0.499 (unweighted)= 31.988 superimposing iter= 3 total_weight= 1290.708 rmsd (weighted)= 0.423 (unweighted)= 31.924 superimposing iter= 4 total_weight= 1083.503 rmsd (weighted)= 0.392 (unweighted)= 31.874 superimposing iter= 5 total_weight= 1004.852 rmsd (weighted)= 0.379 (unweighted)= 31.841 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 1.211 rmsd (weighted)= 2.803 (unweighted)= 31.546 superimposing iter= 1 total_weight= 4936.531 rmsd (weighted)= 1.026 (unweighted)= 31.589 superimposing iter= 2 total_weight= 2289.300 rmsd (weighted)= 0.622 (unweighted)= 31.677 superimposing iter= 3 total_weight= 1438.255 rmsd (weighted)= 0.492 (unweighted)= 31.721 superimposing iter= 4 total_weight= 1111.460 rmsd (weighted)= 0.448 (unweighted)= 31.740 superimposing iter= 5 total_weight= 984.752 rmsd (weighted)= 0.434 (unweighted)= 31.750 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 1.211 rmsd (weighted)= 3.063 (unweighted)= 53.539 superimposing iter= 1 total_weight= 5489.504 rmsd (weighted)= 1.059 (unweighted)= 53.531 superimposing iter= 2 total_weight= 2460.517 rmsd (weighted)= 0.629 (unweighted)= 53.529 superimposing iter= 3 total_weight= 1348.422 rmsd (weighted)= 0.518 (unweighted)= 53.534 superimposing iter= 4 total_weight= 1055.846 rmsd (weighted)= 0.484 (unweighted)= 53.539 superimposing iter= 5 total_weight= 980.252 rmsd (weighted)= 0.470 (unweighted)= 53.543 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 1.166 rmsd (weighted)= 11.672 (unweighted)= 28.097 superimposing iter= 1 total_weight= 3365.836 rmsd (weighted)= 5.016 (unweighted)= 29.232 superimposing iter= 2 total_weight= 2080.083 rmsd (weighted)= 2.814 (unweighted)= 31.012 superimposing iter= 3 total_weight= 2291.677 rmsd (weighted)= 1.546 (unweighted)= 32.104 superimposing iter= 4 total_weight= 2004.173 rmsd (weighted)= 0.990 (unweighted)= 32.389 superimposing iter= 5 total_weight= 1332.972 rmsd (weighted)= 0.804 (unweighted)= 32.443 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 1.211 rmsd (weighted)= 1.861 (unweighted)= 32.401 superimposing iter= 1 total_weight= 4914.261 rmsd (weighted)= 0.712 (unweighted)= 32.340 superimposing iter= 2 total_weight= 2190.173 rmsd (weighted)= 0.455 (unweighted)= 32.316 superimposing iter= 3 total_weight= 1214.314 rmsd (weighted)= 0.396 (unweighted)= 32.299 superimposing iter= 4 total_weight= 1021.343 rmsd (weighted)= 0.377 (unweighted)= 32.287 superimposing iter= 5 total_weight= 969.235 rmsd (weighted)= 0.369 (unweighted)= 32.277 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 1.190 rmsd (weighted)= 2.437 (unweighted)= 25.070 superimposing iter= 1 total_weight= 3687.616 rmsd (weighted)= 1.073 (unweighted)= 24.893 superimposing iter= 2 total_weight= 2011.851 rmsd (weighted)= 0.700 (unweighted)= 24.830 superimposing iter= 3 total_weight= 1280.232 rmsd (weighted)= 0.586 (unweighted)= 24.804 superimposing iter= 4 total_weight= 1034.013 rmsd (weighted)= 0.549 (unweighted)= 24.790 superimposing iter= 5 total_weight= 950.360 rmsd (weighted)= 0.538 (unweighted)= 24.784 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 1.114 rmsd (weighted)= 2.290 (unweighted)= 26.333 superimposing iter= 1 total_weight= 4296.008 rmsd (weighted)= 0.927 (unweighted)= 26.070 superimposing iter= 2 total_weight= 1640.175 rmsd (weighted)= 0.663 (unweighted)= 25.958 superimposing iter= 3 total_weight= 1022.824 rmsd (weighted)= 0.607 (unweighted)= 25.900 superimposing iter= 4 total_weight= 909.733 rmsd (weighted)= 0.589 (unweighted)= 25.866 superimposing iter= 5 total_weight= 886.703 rmsd (weighted)= 0.580 (unweighted)= 25.846 Debug: superimposing conformation 9 on the average so far superimposing iter= 0 total_weight= 1.179 rmsd (weighted)= 2.108 (unweighted)= 20.478 superimposing iter= 1 total_weight= 4363.320 rmsd (weighted)= 0.881 (unweighted)= 20.587 superimposing iter= 2 total_weight= 1671.042 rmsd (weighted)= 0.640 (unweighted)= 20.646 superimposing iter= 3 total_weight= 1088.544 rmsd (weighted)= 0.581 (unweighted)= 20.683 superimposing iter= 4 total_weight= 967.359 rmsd (weighted)= 0.561 (unweighted)= 20.709 superimposing iter= 5 total_weight= 937.066 rmsd (weighted)= 0.550 (unweighted)= 20.728 Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.230 rmsd (weighted)= 1.732 (unweighted)= 19.918 superimposing iter= 1 total_weight= 3052.108 rmsd (weighted)= 0.887 (unweighted)= 19.958 superimposing iter= 2 total_weight= 1787.676 rmsd (weighted)= 0.603 (unweighted)= 19.987 superimposing iter= 3 total_weight= 1617.855 rmsd (weighted)= 0.447 (unweighted)= 20.001 superimposing iter= 4 total_weight= 1243.891 rmsd (weighted)= 0.385 (unweighted)= 20.010 superimposing iter= 5 total_weight= 1101.650 rmsd (weighted)= 0.354 (unweighted)= 20.015 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 1.224 rmsd (weighted)= 1.733 (unweighted)= 23.493 superimposing iter= 1 total_weight= 2689.883 rmsd (weighted)= 0.964 (unweighted)= 23.541 superimposing iter= 2 total_weight= 1506.725 rmsd (weighted)= 0.717 (unweighted)= 23.596 superimposing iter= 3 total_weight= 1534.993 rmsd (weighted)= 0.536 (unweighted)= 23.634 superimposing iter= 4 total_weight= 1462.642 rmsd (weighted)= 0.420 (unweighted)= 23.653 superimposing iter= 5 total_weight= 1259.596 rmsd (weighted)= 0.359 (unweighted)= 23.659 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 1.263 rmsd (weighted)= 2.236 (unweighted)= 33.930 superimposing iter= 1 total_weight= 3588.177 rmsd (weighted)= 1.034 (unweighted)= 34.130 superimposing iter= 2 total_weight= 2156.953 rmsd (weighted)= 0.652 (unweighted)= 34.236 superimposing iter= 3 total_weight= 1648.451 rmsd (weighted)= 0.490 (unweighted)= 34.285 superimposing iter= 4 total_weight= 1226.785 rmsd (weighted)= 0.432 (unweighted)= 34.310 superimposing iter= 5 total_weight= 1066.974 rmsd (weighted)= 0.410 (unweighted)= 34.322 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 1.252 rmsd (weighted)= 2.574 (unweighted)= 24.677 superimposing iter= 1 total_weight= 3434.863 rmsd (weighted)= 1.249 (unweighted)= 24.535 superimposing iter= 2 total_weight= 1698.126 rmsd (weighted)= 0.900 (unweighted)= 24.454 superimposing iter= 3 total_weight= 1508.552 rmsd (weighted)= 0.697 (unweighted)= 24.400 superimposing iter= 4 total_weight= 1308.693 rmsd (weighted)= 0.589 (unweighted)= 24.376 superimposing iter= 5 total_weight= 1108.532 rmsd (weighted)= 0.546 (unweighted)= 24.366 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 1.256 rmsd (weighted)= 2.812 (unweighted)= 38.325 superimposing iter= 1 total_weight= 4464.228 rmsd (weighted)= 1.164 (unweighted)= 38.235 superimposing iter= 2 total_weight= 1943.266 rmsd (weighted)= 0.800 (unweighted)= 38.200 superimposing iter= 3 total_weight= 1280.665 rmsd (weighted)= 0.688 (unweighted)= 38.191 superimposing iter= 4 total_weight= 1094.591 rmsd (weighted)= 0.645 (unweighted)= 38.188 superimposing iter= 5 total_weight= 1012.772 rmsd (weighted)= 0.628 (unweighted)= 38.187 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 1.321 rmsd (weighted)= 13.646 (unweighted)= 24.937 superimposing iter= 1 total_weight= 3160.642 rmsd (weighted)= 6.553 (unweighted)= 25.499 superimposing iter= 2 total_weight= 2366.943 rmsd (weighted)= 3.736 (unweighted)= 26.347 superimposing iter= 3 total_weight= 2224.810 rmsd (weighted)= 2.186 (unweighted)= 27.161 superimposing iter= 4 total_weight= 2507.947 rmsd (weighted)= 1.285 (unweighted)= 27.454 superimposing iter= 5 total_weight= 1772.914 rmsd (weighted)= 0.957 (unweighted)= 27.497 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 1.406 rmsd (weighted)= 8.092 (unweighted)= 34.736 superimposing iter= 1 total_weight= 6495.159 rmsd (weighted)= 2.208 (unweighted)= 34.487 superimposing iter= 2 total_weight= 2931.957 rmsd (weighted)= 1.250 (unweighted)= 34.433 superimposing iter= 3 total_weight= 1554.871 rmsd (weighted)= 0.993 (unweighted)= 34.366 superimposing iter= 4 total_weight= 1573.714 rmsd (weighted)= 0.790 (unweighted)= 34.316 superimposing iter= 5 total_weight= 1522.835 rmsd (weighted)= 0.651 (unweighted)= 34.284 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 1.332 rmsd (weighted)= 3.798 (unweighted)= 17.016 superimposing iter= 1 total_weight= 5888.872 rmsd (weighted)= 1.357 (unweighted)= 16.938 superimposing iter= 2 total_weight= 2356.259 rmsd (weighted)= 0.861 (unweighted)= 16.952 superimposing iter= 3 total_weight= 1526.532 rmsd (weighted)= 0.692 (unweighted)= 16.980 superimposing iter= 4 total_weight= 1261.856 rmsd (weighted)= 0.616 (unweighted)= 17.012 superimposing iter= 5 total_weight= 1181.995 rmsd (weighted)= 0.566 (unweighted)= 17.042 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 1.142 rmsd (weighted)= 2.167 (unweighted)= 25.122 superimposing iter= 1 total_weight= 3739.658 rmsd (weighted)= 0.970 (unweighted)= 25.252 superimposing iter= 2 total_weight= 1654.453 rmsd (weighted)= 0.691 (unweighted)= 25.322 superimposing iter= 3 total_weight= 1124.450 rmsd (weighted)= 0.606 (unweighted)= 25.347 superimposing iter= 4 total_weight= 954.891 rmsd (weighted)= 0.580 (unweighted)= 25.357 superimposing iter= 5 total_weight= 898.734 rmsd (weighted)= 0.573 (unweighted)= 25.362 Debug: superimposing conformation 9 on the average so far superimposing iter= 0 total_weight= 1.208 rmsd (weighted)= 1.871 (unweighted)= 24.287 superimposing iter= 1 total_weight= 3108.575 rmsd (weighted)= 0.947 (unweighted)= 24.352 superimposing iter= 2 total_weight= 1608.872 rmsd (weighted)= 0.695 (unweighted)= 24.403 superimposing iter= 3 total_weight= 1215.614 rmsd (weighted)= 0.597 (unweighted)= 24.443 superimposing iter= 4 total_weight= 1081.263 rmsd (weighted)= 0.549 (unweighted)= 24.468 superimposing iter= 5 total_weight= 1009.696 rmsd (weighted)= 0.524 (unweighted)= 24.483 Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.230 rmsd (weighted)= 1.735 (unweighted)= 19.850 superimposing iter= 1 total_weight= 3058.081 rmsd (weighted)= 0.887 (unweighted)= 19.889 superimposing iter= 2 total_weight= 1801.562 rmsd (weighted)= 0.601 (unweighted)= 19.917 superimposing iter= 3 total_weight= 1612.126 rmsd (weighted)= 0.447 (unweighted)= 19.931 superimposing iter= 4 total_weight= 1233.562 rmsd (weighted)= 0.386 (unweighted)= 19.940 superimposing iter= 5 total_weight= 1095.270 rmsd (weighted)= 0.356 (unweighted)= 19.944 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 1.224 rmsd (weighted)= 1.733 (unweighted)= 23.538 superimposing iter= 1 total_weight= 2689.522 rmsd (weighted)= 0.964 (unweighted)= 23.586 superimposing iter= 2 total_weight= 1513.076 rmsd (weighted)= 0.715 (unweighted)= 23.643 superimposing iter= 3 total_weight= 1534.100 rmsd (weighted)= 0.535 (unweighted)= 23.682 superimposing iter= 4 total_weight= 1458.655 rmsd (weighted)= 0.419 (unweighted)= 23.701 superimposing iter= 5 total_weight= 1257.488 rmsd (weighted)= 0.359 (unweighted)= 23.707 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 1.263 rmsd (weighted)= 2.238 (unweighted)= 33.918 superimposing iter= 1 total_weight= 3580.723 rmsd (weighted)= 1.037 (unweighted)= 34.119 superimposing iter= 2 total_weight= 2150.314 rmsd (weighted)= 0.655 (unweighted)= 34.226 superimposing iter= 3 total_weight= 1634.474 rmsd (weighted)= 0.494 (unweighted)= 34.278 superimposing iter= 4 total_weight= 1221.426 rmsd (weighted)= 0.437 (unweighted)= 34.305 superimposing iter= 5 total_weight= 1070.187 rmsd (weighted)= 0.413 (unweighted)= 34.319 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 1.252 rmsd (weighted)= 2.573 (unweighted)= 24.706 superimposing iter= 1 total_weight= 3447.142 rmsd (weighted)= 1.245 (unweighted)= 24.564 superimposing iter= 2 total_weight= 1711.248 rmsd (weighted)= 0.895 (unweighted)= 24.484 superimposing iter= 3 total_weight= 1498.852 rmsd (weighted)= 0.695 (unweighted)= 24.430 superimposing iter= 4 total_weight= 1306.784 rmsd (weighted)= 0.588 (unweighted)= 24.406 superimposing iter= 5 total_weight= 1109.329 rmsd (weighted)= 0.544 (unweighted)= 24.396 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 1.256 rmsd (weighted)= 2.815 (unweighted)= 38.386 superimposing iter= 1 total_weight= 4450.772 rmsd (weighted)= 1.167 (unweighted)= 38.297 superimposing iter= 2 total_weight= 1949.141 rmsd (weighted)= 0.800 (unweighted)= 38.262 superimposing iter= 3 total_weight= 1284.964 rmsd (weighted)= 0.688 (unweighted)= 38.253 superimposing iter= 4 total_weight= 1095.972 rmsd (weighted)= 0.643 (unweighted)= 38.250 superimposing iter= 5 total_weight= 1013.700 rmsd (weighted)= 0.627 (unweighted)= 38.249 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 1.321 rmsd (weighted)= 13.596 (unweighted)= 24.896 superimposing iter= 1 total_weight= 3165.452 rmsd (weighted)= 6.532 (unweighted)= 25.461 superimposing iter= 2 total_weight= 2351.479 rmsd (weighted)= 3.740 (unweighted)= 26.319 superimposing iter= 3 total_weight= 2205.733 rmsd (weighted)= 2.200 (unweighted)= 27.147 superimposing iter= 4 total_weight= 2506.441 rmsd (weighted)= 1.292 (unweighted)= 27.451 superimposing iter= 5 total_weight= 1783.830 rmsd (weighted)= 0.958 (unweighted)= 27.496 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 1.406 rmsd (weighted)= 8.081 (unweighted)= 34.775 superimposing iter= 1 total_weight= 6457.486 rmsd (weighted)= 2.213 (unweighted)= 34.501 superimposing iter= 2 total_weight= 2919.838 rmsd (weighted)= 1.256 (unweighted)= 34.445 superimposing iter= 3 total_weight= 1544.199 rmsd (weighted)= 1.002 (unweighted)= 34.375 superimposing iter= 4 total_weight= 1576.061 rmsd (weighted)= 0.796 (unweighted)= 34.324 superimposing iter= 5 total_weight= 1524.489 rmsd (weighted)= 0.655 (unweighted)= 34.293 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 1.332 rmsd (weighted)= 3.801 (unweighted)= 16.986 superimposing iter= 1 total_weight= 5876.963 rmsd (weighted)= 1.360 (unweighted)= 16.904 superimposing iter= 2 total_weight= 2384.255 rmsd (weighted)= 0.854 (unweighted)= 16.912 superimposing iter= 3 total_weight= 1603.433 rmsd (weighted)= 0.668 (unweighted)= 16.941 superimposing iter= 4 total_weight= 1306.248 rmsd (weighted)= 0.582 (unweighted)= 16.972 superimposing iter= 5 total_weight= 1171.723 rmsd (weighted)= 0.535 (unweighted)= 16.994 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 1.142 rmsd (weighted)= 2.166 (unweighted)= 25.101 superimposing iter= 1 total_weight= 3739.140 rmsd (weighted)= 0.970 (unweighted)= 25.232 superimposing iter= 2 total_weight= 1655.020 rmsd (weighted)= 0.690 (unweighted)= 25.303 superimposing iter= 3 total_weight= 1123.244 rmsd (weighted)= 0.606 (unweighted)= 25.329 superimposing iter= 4 total_weight= 953.952 rmsd (weighted)= 0.580 (unweighted)= 25.339 superimposing iter= 5 total_weight= 898.532 rmsd (weighted)= 0.573 (unweighted)= 25.345 Debug: superimposing conformation 9 on the average so far superimposing iter= 0 total_weight= 1.208 rmsd (weighted)= 1.870 (unweighted)= 24.260 superimposing iter= 1 total_weight= 3100.208 rmsd (weighted)= 0.948 (unweighted)= 24.326 superimposing iter= 2 total_weight= 1606.086 rmsd (weighted)= 0.696 (unweighted)= 24.377 superimposing iter= 3 total_weight= 1214.360 rmsd (weighted)= 0.598 (unweighted)= 24.418 superimposing iter= 4 total_weight= 1080.591 rmsd (weighted)= 0.550 (unweighted)= 24.443 superimposing iter= 5 total_weight= 1010.438 rmsd (weighted)= 0.526 (unweighted)= 24.458 superimposing iter= 0 total_weight= 1.230 rmsd (weighted)= 1.735 (unweighted)= 19.855 superimposing iter= 1 total_weight= 3058.973 rmsd (weighted)= 0.887 (unweighted)= 19.893 superimposing iter= 2 total_weight= 1803.238 rmsd (weighted)= 0.600 (unweighted)= 19.921 superimposing iter= 3 total_weight= 1612.388 rmsd (weighted)= 0.446 (unweighted)= 19.934 superimposing iter= 4 total_weight= 1232.528 rmsd (weighted)= 0.386 (unweighted)= 19.943 superimposing iter= 5 total_weight= 1094.967 rmsd (weighted)= 0.356 (unweighted)= 19.948 superimposing iter= 0 total_weight= 1.224 rmsd (weighted)= 1.733 (unweighted)= 23.524 superimposing iter= 1 total_weight= 2689.687 rmsd (weighted)= 0.964 (unweighted)= 23.573 superimposing iter= 2 total_weight= 1513.694 rmsd (weighted)= 0.715 (unweighted)= 23.629 superimposing iter= 3 total_weight= 1534.639 rmsd (weighted)= 0.535 (unweighted)= 23.669 superimposing iter= 4 total_weight= 1458.138 rmsd (weighted)= 0.419 (unweighted)= 23.688 superimposing iter= 5 total_weight= 1257.072 rmsd (weighted)= 0.359 (unweighted)= 23.694 superimposing iter= 0 total_weight= 1.263 rmsd (weighted)= 2.238 (unweighted)= 33.914 superimposing iter= 1 total_weight= 3580.788 rmsd (weighted)= 1.037 (unweighted)= 34.115 superimposing iter= 2 total_weight= 2150.592 rmsd (weighted)= 0.655 (unweighted)= 34.222 superimposing iter= 3 total_weight= 1633.173 rmsd (weighted)= 0.495 (unweighted)= 34.273 superimposing iter= 4 total_weight= 1218.825 rmsd (weighted)= 0.437 (unweighted)= 34.300 superimposing iter= 5 total_weight= 1069.629 rmsd (weighted)= 0.414 (unweighted)= 34.314 superimposing iter= 0 total_weight= 1.252 rmsd (weighted)= 2.572 (unweighted)= 24.721 superimposing iter= 1 total_weight= 3447.856 rmsd (weighted)= 1.245 (unweighted)= 24.579 superimposing iter= 2 total_weight= 1714.017 rmsd (weighted)= 0.894 (unweighted)= 24.500 superimposing iter= 3 total_weight= 1497.750 rmsd (weighted)= 0.694 (unweighted)= 24.446 superimposing iter= 4 total_weight= 1306.238 rmsd (weighted)= 0.587 (unweighted)= 24.422 superimposing iter= 5 total_weight= 1109.304 rmsd (weighted)= 0.544 (unweighted)= 24.411 superimposing iter= 0 total_weight= 1.256 rmsd (weighted)= 2.815 (unweighted)= 38.388 superimposing iter= 1 total_weight= 4450.241 rmsd (weighted)= 1.168 (unweighted)= 38.300 superimposing iter= 2 total_weight= 1949.514 rmsd (weighted)= 0.800 (unweighted)= 38.265 superimposing iter= 3 total_weight= 1285.124 rmsd (weighted)= 0.688 (unweighted)= 38.256 superimposing iter= 4 total_weight= 1095.910 rmsd (weighted)= 0.643 (unweighted)= 38.253 superimposing iter= 5 total_weight= 1013.608 rmsd (weighted)= 0.627 (unweighted)= 38.252 superimposing iter= 0 total_weight= 1.321 rmsd (weighted)= 13.594 (unweighted)= 24.886 superimposing iter= 1 total_weight= 3165.687 rmsd (weighted)= 6.531 (unweighted)= 25.457 superimposing iter= 2 total_weight= 2350.625 rmsd (weighted)= 3.741 (unweighted)= 26.321 superimposing iter= 3 total_weight= 2204.957 rmsd (weighted)= 2.200 (unweighted)= 27.152 superimposing iter= 4 total_weight= 2506.517 rmsd (weighted)= 1.292 (unweighted)= 27.457 superimposing iter= 5 total_weight= 1784.407 rmsd (weighted)= 0.958 (unweighted)= 27.503 superimposing iter= 0 total_weight= 1.406 rmsd (weighted)= 8.082 (unweighted)= 34.777 superimposing iter= 1 total_weight= 6457.101 rmsd (weighted)= 2.213 (unweighted)= 34.502 superimposing iter= 2 total_weight= 2919.997 rmsd (weighted)= 1.257 (unweighted)= 34.446 superimposing iter= 3 total_weight= 1543.932 rmsd (weighted)= 1.002 (unweighted)= 34.376 superimposing iter= 4 total_weight= 1577.086 rmsd (weighted)= 0.796 (unweighted)= 34.324 superimposing iter= 5 total_weight= 1524.124 rmsd (weighted)= 0.655 (unweighted)= 34.293 superimposing iter= 0 total_weight= 1.332 rmsd (weighted)= 3.801 (unweighted)= 16.973 superimposing iter= 1 total_weight= 5870.657 rmsd (weighted)= 1.360 (unweighted)= 16.889 superimposing iter= 2 total_weight= 2387.427 rmsd (weighted)= 0.852 (unweighted)= 16.892 superimposing iter= 3 total_weight= 1617.208 rmsd (weighted)= 0.663 (unweighted)= 16.917 superimposing iter= 4 total_weight= 1302.323 rmsd (weighted)= 0.578 (unweighted)= 16.943 superimposing iter= 5 total_weight= 1162.203 rmsd (weighted)= 0.533 (unweighted)= 16.963 superimposing iter= 0 total_weight= 1.142 rmsd (weighted)= 2.166 (unweighted)= 25.081 superimposing iter= 1 total_weight= 3738.654 rmsd (weighted)= 0.970 (unweighted)= 25.212 superimposing iter= 2 total_weight= 1654.987 rmsd (weighted)= 0.690 (unweighted)= 25.283 superimposing iter= 3 total_weight= 1123.011 rmsd (weighted)= 0.606 (unweighted)= 25.309 superimposing iter= 4 total_weight= 953.970 rmsd (weighted)= 0.580 (unweighted)= 25.320 superimposing iter= 5 total_weight= 898.581 rmsd (weighted)= 0.573 (unweighted)= 25.325 superimposing iter= 0 total_weight= 1.208 rmsd (weighted)= 1.870 (unweighted)= 24.259 superimposing iter= 1 total_weight= 3100.079 rmsd (weighted)= 0.948 (unweighted)= 24.325 superimposing iter= 2 total_weight= 1606.237 rmsd (weighted)= 0.696 (unweighted)= 24.376 superimposing iter= 3 total_weight= 1214.460 rmsd (weighted)= 0.598 (unweighted)= 24.416 superimposing iter= 4 total_weight= 1080.529 rmsd (weighted)= 0.550 (unweighted)= 24.441 superimposing iter= 5 total_weight= 1010.076 rmsd (weighted)= 0.526 (unweighted)= 24.456 # command:# Printing sheets for alignments to T0634.undertaker-align.sheets # command: