# command:# Seed set to 1216893562 # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading dunbrack-2191.atoms # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 53157 examples # computed average trans backbone unit before proline from 2010 examples # computed average cis backbone unit from 97 examples # trans (non-proline) backbone unit: # CA= -2.2087 1.0126 -0.0030 # O= -0.1499 2.2440 0.0016 # C= -0.6889 1.1368 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4581 -0.0000 0.0000 # cis backbone unit: # CA= -0.1436 2.4534 -0.0002 # O= -2.0284 0.9742 0.0015 # C= -0.8018 1.0771 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4668 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2100 1.0631 -0.0014 # O= -0.1236 2.2458 0.0075 # C= -0.6872 1.1517 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4660 0.0000 0.0000 # After reading dunbrack-2191.atoms have 2191 chains in training database # Count of chains,residues,atoms: 2191,500310,3902258 # 493341 residues have no bad marker # 3226 residues lack atoms needed to compute omega # 1453 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 4 # HAS_OXT 1167 # TOO_MANY_ATOMS 1 # TOO_FEW_ATOMS 3052 # HAS_UNKNOWN_ATOMS 9 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 979 # NON_PLANAR_PEPTIDE 888 # BAD_PEPTIDE 2680 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-2191.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:CPU_time= 26.308 sec, elapsed time= 26.524 sec. # command:# Prefix for input files set to # command:# Making conformation for sequence T0507 numbered 1 through 148 Created new target T0507 from T0507.a2m # command:# command:# No conformations to remove in PopConform # command:CPU_time= 36.585 sec, elapsed time= 36.959 sec. # command:# Making generic fragment library # fragment library contains # type length num_fragments num_indexes_used # n-terminus 1 1957 20 (100.000%) # n-terminus 2 1932 333 (83.250%) # middle 1 481122 20 (100.000%) # middle 2 474896 400 (100.000%) # middle 3 468898 7988 (99.850%) # middle 4 463038 120397 (75.248%) # c-terminus 1 1914 20 (100.000%) # c-terminus 2 1887 372 (93.000%) # ss-bonds 1042 # command:CPU_time= 46.370 sec, elapsed time= 46.756 sec. # command:# Prefix for input files set to # command:# reading script from file T0507.undertaker-align.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 1qjcA/T0507-1qjcA-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 1qjcA expands to /projects/compbio/data/pdb/1qjc.pdb.gz 1qjcA:# T0507 read from 1qjcA/T0507-1qjcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1qjcA read from 1qjcA/T0507-1qjcA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1qjcA to template set # found chain 1qjcA in template set Warning: unaligning (T0507)I45 because of BadResidue code BAD_PEPTIDE in next template residue (1qjcA)K43 Warning: unaligning (T0507)R46 because of BadResidue code BAD_PEPTIDE at template residue (1qjcA)K43 T0507 2 :KVALGGTFEPLHEGHKKLIDVAIKLG 1qjcA 4 :RAIYPGTFDPITNGHIDIVTRATQMF # choosing archetypes in rotamer library T0507 30 :DITI 1qjcA 30 :DHVI T0507 34 :GVTSDRM 1qjcA 35 :AIAASPS T0507 47 :SVLPFAIRAENVKRYVMRKYGFEPEIVKIT 1qjcA 44 :PMFTLEERVALAQQATAHLGNVEVVGFSDL T0507 78 :PYGKTLDVDFEYLVVSPETYEMALKINQKREELGKR 1qjcA 74 :MANFARNQHATVLIRGLRAVADFEYEMQLAHMNRHL T0507 114 :KITIVKV 1qjcA 112 :ELESVFL T0507 123 :MMAEDGKPISSTRIKRGEIDRYG 1qjcA 119 :MPSKEWSFISSSLVKEVARHQGD Number of specific fragments extracted= 7 number of extra gaps= 1 total=7 # request to SCWRL produces command: ulimit -t 134 ; scwrl3 -i /var/tmp/to_scwrl_614871894.pdb -s /var/tmp/to_scwrl_614871894.seq -o /var/tmp/from_scwrl_614871894.pdb > /var/tmp/scwrl_614871894.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_614871894.pdb Number of alignments=1 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1cozA/T0507-1cozA-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 1cozA expands to /projects/compbio/data/pdb/1coz.pdb.gz 1cozA:# T0507 read from 1cozA/T0507-1cozA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1cozA read from 1cozA/T0507-1cozA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1cozA to template set # found chain 1cozA in template set T0507 1 :M 1cozA 1 :M T0507 2 :KVALGGTFEPLHEGHKKLIDVAIKLG 1cozA 3 :KVITYGTFDLLHWGHIKLLERAKQLG T0507 30 :DITI 1cozA 29 :DYLV T0507 34 :GVTSDRMA 1cozA 34 :AISTDEFN T0507 42 :RARIRSVLPFAIRAENV 1cozA 43 :QKQKKAYHSYEHRKLIL T0507 63 :MRKYGF 1cozA 60 :ETIRYV T0507 69 :EPEIVKIT 1cozA 67 :EVIPEKNW T0507 77 :NPYGKTLDVDFEYLVVSPETYEMALKI 1cozA 76 :QKKQDIIDHNIDVFVMGDDWEGKFDFL T0507 110 :LGKRK 1cozA 103 :KDQCE T0507 116 :TIVK 1cozA 108 :VVYL T0507 126 :EDGKPISSTRIKR 1cozA 112 :PRTEGISTTKIKE Number of specific fragments extracted= 11 number of extra gaps= 0 total=18 # request to SCWRL produces command: ulimit -t 134 ; scwrl3 -i /var/tmp/to_scwrl_524024036.pdb -s /var/tmp/to_scwrl_524024036.seq -o /var/tmp/from_scwrl_524024036.pdb > /var/tmp/scwrl_524024036.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_524024036.pdb Number of alignments=2 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1yumA/T0507-1yumA-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 1yumA expands to /projects/compbio/data/pdb/1yum.pdb.gz 1yumA:Skipped atom 69, because occupancy 0.43 <= existing 0.570 in 1yumA Skipped atom 71, because occupancy 0.430 <= existing 0.570 in 1yumA Skipped atom 73, because occupancy 0.430 <= existing 0.570 in 1yumA Skipped atom 612, because occupancy 0.330 <= existing 0.330 in 1yumA Skipped atom 613, because occupancy 0.330 <= existing 0.330 in 1yumA Skipped atom 615, because occupancy 0.330 <= existing 0.330 in 1yumA Skipped atom 616, because occupancy 0.330 <= existing 0.330 in 1yumA Skipped atom 618, because occupancy 0.330 <= existing 0.330 in 1yumA Skipped atom 619, because occupancy 0.330 <= existing 0.330 in 1yumA Skipped atom 621, because occupancy 0.330 <= existing 0.330 in 1yumA Skipped atom 622, because occupancy 0.330 <= existing 0.330 in 1yumA Skipped atom 624, because occupancy 0.330 <= existing 0.330 in 1yumA Skipped atom 625, because occupancy 0.330 <= existing 0.330 in 1yumA Skipped atom 627, because occupancy 0.330 <= existing 0.330 in 1yumA Skipped atom 628, because occupancy 0.330 <= existing 0.330 in 1yumA Skipped atom 630, because occupancy 0.330 <= existing 0.330 in 1yumA Skipped atom 631, because occupancy 0.330 <= existing 0.330 in 1yumA Skipped atom 868, because occupancy 0.330 <= existing 0.670 in 1yumA Skipped atom 870, because occupancy 0.330 <= existing 0.670 in 1yumA Skipped atom 872, because occupancy 0.330 <= existing 0.670 in 1yumA Skipped atom 874, because occupancy 0.330 <= existing 0.670 in 1yumA Skipped atom 1216, because occupancy 0.330 <= existing 0.670 in 1yumA Skipped atom 1218, because occupancy 0.330 <= existing 0.670 in 1yumA Skipped atom 1220, because occupancy 0.330 <= existing 0.670 in 1yumA Skipped atom 1222, because occupancy 0.330 <= existing 0.670 in 1yumA Skipped atom 1224, because occupancy 0.330 <= existing 0.670 in 1yumA Skipped atom 1226, because occupancy 0.330 <= existing 0.670 in 1yumA Skipped atom 1228, because occupancy 0.330 <= existing 0.670 in 1yumA # T0507 read from 1yumA/T0507-1yumA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1yumA read from 1yumA/T0507-1yumA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1yumA to template set # found chain 1yumA in template set Warning: unaligning (T0507)V22 because of BadResidue code BAD_PEPTIDE in next template residue (1yumA)M26 Warning: unaligning (T0507)A23 because of BadResidue code BAD_PEPTIDE at template residue (1yumA)M26 Warning: unaligning (T0507)A41 because of BadResidue code BAD_PEPTIDE in next template residue (1yumA)H45 Warning: unaligning (T0507)R42 because of BadResidue code BAD_PEPTIDE at template residue (1yumA)H45 Warning: unaligning (T0507)S47 because of BadResidue code BAD_PEPTIDE in next template residue (1yumA)Q50 Warning: unaligning (T0507)V48 because of BadResidue code BAD_PEPTIDE at template residue (1yumA)Q50 Warning: unaligning (T0507)I117 because of BadResidue code BAD_PEPTIDE in next template residue (1yumA)L132 Warning: unaligning (T0507)V118 because of BadResidue code BAD_PEPTIDE at template residue (1yumA)L132 T0507 2 :KVALGGTFEPLHEGHKKLID 1yumA 5 :IGLFGGTFDPVHIGHMRSAV T0507 24 :IKLGGRDITIGVTSDRM 1yumA 27 :AEQFALDELRLLPNARP T0507 43 :A 1yumA 46 :R T0507 45 :IR 1yumA 47 :ET T0507 49 :LPFAIRAENVKRYVMRKYGFEPEIVK 1yumA 51 :VSAAQRLAMVERAVAGVERLTVDPRE T0507 77 :NPYGKTLDV 1yumA 84 :YTIDTLESV T0507 89 :YLVVSPETYEMALKINQKREELGKRKIT 1yumA 103 :FMLIGWDAFCGLPTWHRWEALLDHCHIV T0507 119 :KVDWMMAED 1yumA 133 :QRPDADSEP T0507 128 :GKPISSTRIKRGEIDRYG 1yumA 174 :PLAVSATQIRALLGAGRS Number of specific fragments extracted= 9 number of extra gaps= 4 total=27 # request to SCWRL produces command: ulimit -t 134 ; scwrl3 -i /var/tmp/to_scwrl_1077213548.pdb -s /var/tmp/to_scwrl_1077213548.seq -o /var/tmp/from_scwrl_1077213548.pdb > /var/tmp/scwrl_1077213548.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1077213548.pdb Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2h29A/T0507-2h29A-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 2h29A expands to /projects/compbio/data/pdb/2h29.pdb.gz 2h29A:# T0507 read from 2h29A/T0507-2h29A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2h29A read from 2h29A/T0507-2h29A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2h29A to template set # found chain 2h29A in template set Warning: unaligning (T0507)P11 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2h29A)I14 Warning: unaligning (T0507)L12 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2h29A)I14 T0507 1 :M 2h29A 1 :M T0507 2 :KVALGGTFE 2h29A 4 :IVLYGGQFN T0507 13 :HEGHKKLIDVAIKLGGRDITIGVTSDRMARARIRSVLPFAIRAENVKRYVMRKYGFEP 2h29A 15 :HTAHMIVASEVFHELQPDEFYFLPSFMSPLKKHHDFIDVQHRLTMIQMIIDELGFGDI T0507 73 :V 2h29A 73 :C T0507 76 :T 2h29A 74 :D T0507 77 :NPYGKTLDV 2h29A 84 :YTYDTIKAF T0507 86 :DFE 2h29A 98 :DSE T0507 89 :YLVVSPETYEMALKINQKREELGKRKITIVKVDWMMAED 2h29A 102 :YFVIGTDQYNQLEKWYQIEYLKEMVTFVVVNRDKNSQNV T0507 128 :GKPISSTRIKRGEIDRY 2h29A 151 :RVDISSTMIRQRVSEGK Number of specific fragments extracted= 9 number of extra gaps= 1 total=36 # request to SCWRL produces command: ulimit -t 134 ; scwrl3 -i /var/tmp/to_scwrl_835916541.pdb -s /var/tmp/to_scwrl_835916541.seq -o /var/tmp/from_scwrl_835916541.pdb > /var/tmp/scwrl_835916541.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_835916541.pdb Number of alignments=4 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2b7lA/T0507-2b7lA-t2k-global-adpstyle1.a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2b7lA expands to /projects/compbio/data/pdb/2b7l.pdb.gz 2b7lA:# T0507 read from 2b7lA/T0507-2b7lA-t2k-global-adpstyle1.a2m # 2b7lA read from 2b7lA/T0507-2b7lA-t2k-global-adpstyle1.a2m # adding 2b7lA to template set # found chain 2b7lA in template set Warning: unaligning (T0507)T116 because last residue in template chain is (2b7lA)E115 T0507 1 :MKVALGGTFEPLHEGHKKLIDVAIKLGGRDITIGVTSDRMARARIRSVLPFAIRAENVKRYVMRKYGFE 2b7lA 2 :KRVITYGTYDLLHYGHIELLRRAREMGDYLIVALSTDEFNQIKHKKSYYDYEQRKMMLESIRYVDLVIP T0507 72 :IVKITNPYGKTLDVDFEYLVVSPETYEMALKINQKREELGKRKI 2b7lA 71 :EKGWGQKEDDVEKFDVDVFVMGHDWEGEFDFLKDKCEVIYLKRT Number of specific fragments extracted= 2 number of extra gaps= 0 total=38 # request to SCWRL produces command: ulimit -t 134 ; scwrl3 -i /var/tmp/to_scwrl_1133420659.pdb -s /var/tmp/to_scwrl_1133420659.seq -o /var/tmp/from_scwrl_1133420659.pdb > /var/tmp/scwrl_1133420659.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1133420659.pdb Number of alignments=5 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1mrzA/T0507-1mrzA-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 1mrzA expands to /projects/compbio/data/pdb/1mrz.pdb.gz 1mrzA:# T0507 read from 1mrzA/T0507-1mrzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1mrzA read from 1mrzA/T0507-1mrzA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1mrzA to template set # found chain 1mrzA in template set Warning: unaligning (T0507)V3 because first residue in template chain is (1mrzA)V2 T0507 4 :ALGGTFEPLHEGHKKLIDVAIKLG 1mrzA 3 :VSIGVFDGVHIGHQKVLRTMKEIA T0507 28 :GRDITI 1mrzA 30 :KDDSLI T0507 34 :GVTSDRMARA 1mrzA 37 :TISYPPEYFL T0507 44 :RIRSVLPFAIRAENV 1mrzA 49 :FPGLLMTVESRVEML T0507 63 :MRKYGFEP 1mrzA 64 :SRYARTVV T0507 73 :VKIT 1mrzA 72 :LDFF T0507 77 :NPYGKT 1mrzA 80 :LTPEGF T0507 83 :LDV 1mrzA 88 :RYL T0507 86 :DFEYLVVSPETYEMALKINQ 1mrzA 92 :GVSAVVVGRDFRFGKNASGN T0507 107 :REELGKRKITIVKVDWMMA 1mrzA 112 :ASFLRKKGVEVYEIEDVVV T0507 127 :DGKPISSTRIKRGEIDRY 1mrzA 131 :QGKRVSSSLIRNLVQEGR T0507 146 :GI 1mrzA 158 :RY Number of specific fragments extracted= 12 number of extra gaps= 0 total=50 # request to SCWRL produces command: ulimit -t 134 ; scwrl3 -i /var/tmp/to_scwrl_1035519453.pdb -s /var/tmp/to_scwrl_1035519453.seq -o /var/tmp/from_scwrl_1035519453.pdb > /var/tmp/scwrl_1035519453.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1035519453.pdb Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1lw7A/T0507-1lw7A-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 1lw7A expands to /projects/compbio/data/pdb/1lw7.pdb.gz 1lw7A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0507 read from 1lw7A/T0507-1lw7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1lw7A read from 1lw7A/T0507-1lw7A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1lw7A to template set # found chain 1lw7A in template set T0507 2 :KVALGGTFEPLHEGHKKLIDVAIKLG 1lw7A 60 :VGVIFGKFYPVHTGHINMIYEAFSKV T0507 30 :DITI 1lw7A 86 :DELH T0507 34 :GVTSDRMA 1lw7A 91 :IVCSDTVR T0507 44 :RIRSVLPFAIRAENVKRYVMRK 1lw7A 107 :KMKRMPTVQDRLRWMQQIFKYQ T0507 66 :YGFEPEIVKIT 1lw7A 130 :NQIFIHHLVED T0507 78 :PYGKT 1lw7A 155 :AVKTL T0507 83 :LDVDFEYLVVSPET 1lw7A 163 :KHFEPSIVFSSEPQ T0507 98 :E 1lw7A 177 :D T0507 106 :KREELGKRKITIVKVDWM 1lw7A 178 :KAPYEKYLGLEVSLVDPD T0507 126 :EDGKPISSTRIKR 1lw7A 196 :RTFFNVSATKIRT Number of specific fragments extracted= 10 number of extra gaps= 0 total=60 # request to SCWRL produces command: ulimit -t 134 ; scwrl3 -i /var/tmp/to_scwrl_1855628940.pdb -s /var/tmp/to_scwrl_1855628940.seq -o /var/tmp/from_scwrl_1855628940.pdb > /var/tmp/scwrl_1855628940.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1855628940.pdb Number of alignments=7 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2qjoA/T0507-2qjoA-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 2qjoA expands to /projects/compbio/data/pdb/2qjo.pdb.gz 2qjoA:# T0507 read from 2qjoA/T0507-2qjoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qjoA read from 2qjoA/T0507-2qjoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2qjoA to template set # found chain 2qjoA in template set Warning: unaligning (T0507)K129 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2qjoA)D136 Warning: unaligning (T0507)P130 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2qjoA)D136 T0507 2 :KVALGGTFEPLHEGHKKLIDVAIKLG 2qjoA 7 :YGIYIGRFQPFHLGHLRTLNLALEKA T0507 30 :DITIGVTSDRMARARIRSVLPFAIRAENV 2qjoA 33 :EQVIIILGSHRVAADTRNPWRSPERMAMI T0507 60 :RYV 2qjoA 62 :EAC T0507 64 :RKYGFEPEIVKIT 2qjoA 69 :ILKRVHFLTVRDW T0507 77 :NPYGK 2qjoA 83 :YSDNL T0507 98 :EMALKINQKREELGKRKITIVKVDWMMAED 2qjoA 88 :WLAAVQQQVLKITGGSNSVVVLGHRKDASS T0507 128 :G 2qjoA 134 :Y T0507 131 :ISSTRIKRGEIDRY 2qjoA 137 :FSSTAIRGAYFEGK Number of specific fragments extracted= 8 number of extra gaps= 1 total=68 # request to SCWRL produces command: ulimit -t 134 ; scwrl3 -i /var/tmp/to_scwrl_1395837607.pdb -s /var/tmp/to_scwrl_1395837607.seq -o /var/tmp/from_scwrl_1395837607.pdb > /var/tmp/scwrl_1395837607.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1395837607.pdb Number of alignments=8 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2qjtA/T0507-2qjtA-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 2qjtA expands to /projects/compbio/data/pdb/2qjt.pdb.gz 2qjtA:# T0507 read from 2qjtA/T0507-2qjtA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qjtA read from 2qjtA/T0507-2qjtA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2qjtA to template set # found chain 2qjtA in template set Warning: unaligning (T0507)D86 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2qjtA)N102 Warning: unaligning (T0507)S93 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2qjtA)S114 Warning: unaligning (T0507)E98 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2qjtA)S114 T0507 1 :M 2qjtA 1 :M T0507 2 :KVALGGTFEPLHEGHKKLIDVAIKLG 2qjtA 4 :ISVFIGRFQPFHKGHLHNIIIALQNS T0507 30 :DITI 2qjtA 30 :KKVI T0507 34 :GVTSDRMAR 2qjtA 35 :NIGSCFNTP T0507 44 :RIRSVLPFAIRAENVKRYVM 2qjtA 44 :NIKNPFSFEQRKQMIESDLQ T0507 64 :RKYGFEPEIVKIT 2qjtA 68 :DLDTVVIEPLADY T0507 79 :YGKTLDV 2qjtA 88 :QDELRKN T0507 87 :FEYLVV 2qjtA 103 :NSIAIV T0507 105 :QKREELGKRKITIVKV 2qjtA 115 :SSYYIRSFPEWDYIGV T0507 126 :EDGKPISSTRIKRGEIDRY 2qjtA 131 :DNYKNFNATEFRQKFYNGI Number of specific fragments extracted= 10 number of extra gaps= 1 total=78 # request to SCWRL produces command: ulimit -t 134 ; scwrl3 -i /var/tmp/to_scwrl_2117928320.pdb -s /var/tmp/to_scwrl_2117928320.seq -o /var/tmp/from_scwrl_2117928320.pdb > /var/tmp/scwrl_2117928320.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2117928320.pdb Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 1ihoA/T0507-1ihoA-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 1ihoA expands to /projects/compbio/data/pdb/1iho.pdb.gz 1ihoA:Skipped atom 636, because occupancy 0.500 <= existing 0.500 in 1ihoA Skipped atom 638, because occupancy 0.500 <= existing 0.500 in 1ihoA Skipped atom 640, because occupancy 0.500 <= existing 0.500 in 1ihoA Skipped atom 642, because occupancy 0.500 <= existing 0.500 in 1ihoA Skipped atom 2108, because occupancy 0.500 <= existing 0.500 in 1ihoA Skipped atom 2110, because occupancy 0.500 <= existing 0.500 in 1ihoA Skipped atom 2112, because occupancy 0.500 <= existing 0.500 in 1ihoA Skipped atom 2114, because occupancy 0.500 <= existing 0.500 in 1ihoA # T0507 read from 1ihoA/T0507-1ihoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 1ihoA read from 1ihoA/T0507-1ihoA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 1ihoA to template set # found chain 1ihoA in template set Warning: unaligning (T0507)L12 because of BadResidue code BAD_PEPTIDE in next template residue (1ihoA)H34 Warning: unaligning (T0507)H13 because of BadResidue code BAD_PEPTIDE at template residue (1ihoA)H34 Warning: unaligning (T0507)E14 because of BadResidue code BAD_PEPTIDE in next template residue (1ihoA)G36 Warning: unaligning (T0507)G15 because of BadResidue code BAD_PEPTIDE at template residue (1ihoA)G36 T0507 2 :KVALGGTFEP 1ihoA 23 :RVALVPTMGN T0507 16 :HKKLIDVAIKLG 1ihoA 37 :HMKLVDEAKARA T0507 30 :DITI 1ihoA 49 :DVVV T0507 34 :GVTSDRMA 1ihoA 54 :SIFVNPMQ T0507 48 :VLPFAIRAENVKRY 1ihoA 72 :PRTLQEDCEKLNKR T0507 64 :RKYGF 1ihoA 86 :KVDLV T0507 73 :VKIT 1ihoA 91 :FAPS T0507 77 :NPYGKTLDVDFEYLVVSPETYEMALKINQKREELG 1ihoA 133 :IVSKLFNLVQPDIACFGEKDFQQLALIRKMVADMG T0507 113 :RKITIVKVDWMMAED 1ihoA 168 :FDIEIVGVPIMRAKD T0507 134 :TRIKRGEIDRY 1ihoA 209 :SSIADKLQAGE Number of specific fragments extracted= 10 number of extra gaps= 1 total=88 # request to SCWRL produces command: ulimit -t 134 ; scwrl3 -i /var/tmp/to_scwrl_934924769.pdb -s /var/tmp/to_scwrl_934924769.seq -o /var/tmp/from_scwrl_934924769.pdb > /var/tmp/scwrl_934924769.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_934924769.pdb Number of alignments=10 # command:Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.344 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 1 total_weight= 10610.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 2 total_weight= 10610.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 3 total_weight= 10610.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 4 total_weight= 10610.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 5 total_weight= 10610.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 1.113 rmsd (weighted)= 5.021 (unweighted)= 27.726 superimposing iter= 1 total_weight= 3499.286 rmsd (weighted)= 2.164 (unweighted)= 28.051 superimposing iter= 2 total_weight= 1710.805 rmsd (weighted)= 1.507 (unweighted)= 28.161 superimposing iter= 3 total_weight= 1035.190 rmsd (weighted)= 1.370 (unweighted)= 28.233 superimposing iter= 4 total_weight= 914.955 rmsd (weighted)= 1.328 (unweighted)= 28.291 superimposing iter= 5 total_weight= 901.850 rmsd (weighted)= 1.299 (unweighted)= 28.338 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 1.237 rmsd (weighted)= 6.301 (unweighted)= 43.214 superimposing iter= 1 total_weight= 3885.732 rmsd (weighted)= 2.784 (unweighted)= 42.598 superimposing iter= 2 total_weight= 2067.938 rmsd (weighted)= 1.816 (unweighted)= 42.306 superimposing iter= 3 total_weight= 1421.345 rmsd (weighted)= 1.469 (unweighted)= 42.120 superimposing iter= 4 total_weight= 1181.671 rmsd (weighted)= 1.315 (unweighted)= 41.989 superimposing iter= 5 total_weight= 1091.719 rmsd (weighted)= 1.229 (unweighted)= 41.902 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 1.276 rmsd (weighted)= 5.803 (unweighted)= 26.581 superimposing iter= 1 total_weight= 4115.258 rmsd (weighted)= 2.556 (unweighted)= 26.578 superimposing iter= 2 total_weight= 2425.672 rmsd (weighted)= 1.551 (unweighted)= 26.567 superimposing iter= 3 total_weight= 1679.936 rmsd (weighted)= 1.169 (unweighted)= 26.562 superimposing iter= 4 total_weight= 1286.744 rmsd (weighted)= 1.019 (unweighted)= 26.561 superimposing iter= 5 total_weight= 1111.680 rmsd (weighted)= 0.960 (unweighted)= 26.561 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 1.046 rmsd (weighted)= 8.012 (unweighted)= 32.267 superimposing iter= 1 total_weight= 3962.693 rmsd (weighted)= 3.093 (unweighted)= 32.154 superimposing iter= 2 total_weight= 2088.133 rmsd (weighted)= 1.851 (unweighted)= 32.124 superimposing iter= 3 total_weight= 1251.975 rmsd (weighted)= 1.481 (unweighted)= 32.142 superimposing iter= 4 total_weight= 941.043 rmsd (weighted)= 1.376 (unweighted)= 32.167 superimposing iter= 5 total_weight= 861.417 rmsd (weighted)= 1.339 (unweighted)= 32.194 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 1.228 rmsd (weighted)= 5.955 (unweighted)= 24.333 superimposing iter= 1 total_weight= 3816.446 rmsd (weighted)= 2.700 (unweighted)= 24.203 superimposing iter= 2 total_weight= 1843.435 rmsd (weighted)= 1.914 (unweighted)= 24.194 superimposing iter= 3 total_weight= 1196.676 rmsd (weighted)= 1.707 (unweighted)= 24.200 superimposing iter= 4 total_weight= 1035.366 rmsd (weighted)= 1.641 (unweighted)= 24.206 superimposing iter= 5 total_weight= 987.733 rmsd (weighted)= 1.615 (unweighted)= 24.210 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 1.172 rmsd (weighted)= 4.092 (unweighted)= 32.716 superimposing iter= 1 total_weight= 4711.330 rmsd (weighted)= 1.532 (unweighted)= 32.564 superimposing iter= 2 total_weight= 2156.635 rmsd (weighted)= 0.976 (unweighted)= 32.506 superimposing iter= 3 total_weight= 1227.940 rmsd (weighted)= 0.839 (unweighted)= 32.465 superimposing iter= 4 total_weight= 1010.495 rmsd (weighted)= 0.799 (unweighted)= 32.440 superimposing iter= 5 total_weight= 955.365 rmsd (weighted)= 0.782 (unweighted)= 32.427 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 1.130 rmsd (weighted)= 8.365 (unweighted)= 51.935 superimposing iter= 1 total_weight= 3603.366 rmsd (weighted)= 3.430 (unweighted)= 51.213 superimposing iter= 2 total_weight= 2435.282 rmsd (weighted)= 1.828 (unweighted)= 50.877 superimposing iter= 3 total_weight= 1695.995 rmsd (weighted)= 1.278 (unweighted)= 50.781 superimposing iter= 4 total_weight= 1137.257 rmsd (weighted)= 1.118 (unweighted)= 50.743 superimposing iter= 5 total_weight= 967.680 rmsd (weighted)= 1.065 (unweighted)= 50.720 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 1.169 rmsd (weighted)= 4.145 (unweighted)= 30.492 superimposing iter= 1 total_weight= 4557.556 rmsd (weighted)= 1.677 (unweighted)= 30.514 superimposing iter= 2 total_weight= 1760.791 rmsd (weighted)= 1.193 (unweighted)= 30.532 superimposing iter= 3 total_weight= 1169.120 rmsd (weighted)= 1.049 (unweighted)= 30.547 superimposing iter= 4 total_weight= 1049.285 rmsd (weighted)= 0.976 (unweighted)= 30.557 superimposing iter= 5 total_weight= 992.523 rmsd (weighted)= 0.934 (unweighted)= 30.562 Debug: superimposing conformation 9 on the average so far superimposing iter= 0 total_weight= 1.164 rmsd (weighted)= 10.231 (unweighted)= 34.329 superimposing iter= 1 total_weight= 3091.964 rmsd (weighted)= 4.523 (unweighted)= 35.210 superimposing iter= 2 total_weight= 1657.925 rmsd (weighted)= 3.199 (unweighted)= 35.616 superimposing iter= 3 total_weight= 1254.450 rmsd (weighted)= 2.655 (unweighted)= 35.820 superimposing iter= 4 total_weight= 1133.020 rmsd (weighted)= 2.343 (unweighted)= 35.907 superimposing iter= 5 total_weight= 1071.283 rmsd (weighted)= 2.143 (unweighted)= 35.944 Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.344 rmsd (weighted)= 3.980 (unweighted)= 19.809 superimposing iter= 1 total_weight= 4156.427 rmsd (weighted)= 1.790 (unweighted)= 19.815 superimposing iter= 2 total_weight= 2120.874 rmsd (weighted)= 1.214 (unweighted)= 19.846 superimposing iter= 3 total_weight= 1500.283 rmsd (weighted)= 1.005 (unweighted)= 19.868 superimposing iter= 4 total_weight= 1235.216 rmsd (weighted)= 0.923 (unweighted)= 19.883 superimposing iter= 5 total_weight= 1133.426 rmsd (weighted)= 0.888 (unweighted)= 19.893 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 1.197 rmsd (weighted)= 2.841 (unweighted)= 23.529 superimposing iter= 1 total_weight= 3069.873 rmsd (weighted)= 1.490 (unweighted)= 23.548 superimposing iter= 2 total_weight= 1489.046 rmsd (weighted)= 1.166 (unweighted)= 23.554 superimposing iter= 3 total_weight= 1095.253 rmsd (weighted)= 1.073 (unweighted)= 23.556 superimposing iter= 4 total_weight= 982.972 rmsd (weighted)= 1.044 (unweighted)= 23.558 superimposing iter= 5 total_weight= 957.764 rmsd (weighted)= 1.030 (unweighted)= 23.561 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 1.322 rmsd (weighted)= 4.287 (unweighted)= 39.932 superimposing iter= 1 total_weight= 3674.958 rmsd (weighted)= 2.158 (unweighted)= 39.959 superimposing iter= 2 total_weight= 1608.553 rmsd (weighted)= 1.724 (unweighted)= 39.965 superimposing iter= 3 total_weight= 1154.629 rmsd (weighted)= 1.635 (unweighted)= 39.961 superimposing iter= 4 total_weight= 1079.253 rmsd (weighted)= 1.605 (unweighted)= 39.956 superimposing iter= 5 total_weight= 1061.020 rmsd (weighted)= 1.589 (unweighted)= 39.949 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 1.404 rmsd (weighted)= 4.391 (unweighted)= 16.926 superimposing iter= 1 total_weight= 4498.463 rmsd (weighted)= 2.032 (unweighted)= 16.928 superimposing iter= 2 total_weight= 1929.687 rmsd (weighted)= 1.526 (unweighted)= 16.924 superimposing iter= 3 total_weight= 1264.825 rmsd (weighted)= 1.423 (unweighted)= 16.927 superimposing iter= 4 total_weight= 1146.283 rmsd (weighted)= 1.395 (unweighted)= 16.930 superimposing iter= 5 total_weight= 1117.266 rmsd (weighted)= 1.384 (unweighted)= 16.932 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 1.149 rmsd (weighted)= 5.550 (unweighted)= 27.149 superimposing iter= 1 total_weight= 3994.073 rmsd (weighted)= 2.343 (unweighted)= 27.135 superimposing iter= 2 total_weight= 1858.923 rmsd (weighted)= 1.581 (unweighted)= 27.114 superimposing iter= 3 total_weight= 1283.516 rmsd (weighted)= 1.304 (unweighted)= 27.120 superimposing iter= 4 total_weight= 1107.779 rmsd (weighted)= 1.165 (unweighted)= 27.129 superimposing iter= 5 total_weight= 1014.050 rmsd (weighted)= 1.092 (unweighted)= 27.134 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 1.363 rmsd (weighted)= 4.182 (unweighted)= 11.134 superimposing iter= 1 total_weight= 3429.651 rmsd (weighted)= 2.232 (unweighted)= 11.115 superimposing iter= 2 total_weight= 1653.088 rmsd (weighted)= 1.762 (unweighted)= 11.117 superimposing iter= 3 total_weight= 1340.476 rmsd (weighted)= 1.559 (unweighted)= 11.128 superimposing iter= 4 total_weight= 1214.082 rmsd (weighted)= 1.452 (unweighted)= 11.137 superimposing iter= 5 total_weight= 1144.155 rmsd (weighted)= 1.394 (unweighted)= 11.143 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 1.241 rmsd (weighted)= 3.598 (unweighted)= 33.750 superimposing iter= 1 total_weight= 3916.069 rmsd (weighted)= 1.621 (unweighted)= 33.709 superimposing iter= 2 total_weight= 1941.055 rmsd (weighted)= 1.116 (unweighted)= 33.677 superimposing iter= 3 total_weight= 1351.785 rmsd (weighted)= 0.936 (unweighted)= 33.661 superimposing iter= 4 total_weight= 1157.084 rmsd (weighted)= 0.854 (unweighted)= 33.653 superimposing iter= 5 total_weight= 1051.896 rmsd (weighted)= 0.819 (unweighted)= 33.649 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 1.229 rmsd (weighted)= 5.970 (unweighted)= 47.782 superimposing iter= 1 total_weight= 3495.402 rmsd (weighted)= 2.865 (unweighted)= 47.546 superimposing iter= 2 total_weight= 1966.641 rmsd (weighted)= 1.889 (unweighted)= 47.413 superimposing iter= 3 total_weight= 1549.793 rmsd (weighted)= 1.438 (unweighted)= 47.339 superimposing iter= 4 total_weight= 1302.446 rmsd (weighted)= 1.211 (unweighted)= 47.297 superimposing iter= 5 total_weight= 1167.795 rmsd (weighted)= 1.084 (unweighted)= 47.272 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 1.235 rmsd (weighted)= 3.776 (unweighted)= 23.123 superimposing iter= 1 total_weight= 3817.864 rmsd (weighted)= 1.770 (unweighted)= 23.100 superimposing iter= 2 total_weight= 1778.902 rmsd (weighted)= 1.266 (unweighted)= 23.133 superimposing iter= 3 total_weight= 1359.339 rmsd (weighted)= 1.055 (unweighted)= 23.149 superimposing iter= 4 total_weight= 1158.284 rmsd (weighted)= 0.960 (unweighted)= 23.154 superimposing iter= 5 total_weight= 1084.007 rmsd (weighted)= 0.906 (unweighted)= 23.158 Debug: superimposing conformation 9 on the average so far superimposing iter= 0 total_weight= 1.207 rmsd (weighted)= 9.472 (unweighted)= 23.764 superimposing iter= 1 total_weight= 3633.154 rmsd (weighted)= 3.768 (unweighted)= 23.676 superimposing iter= 2 total_weight= 1983.113 rmsd (weighted)= 2.510 (unweighted)= 23.729 superimposing iter= 3 total_weight= 1221.764 rmsd (weighted)= 2.197 (unweighted)= 23.780 superimposing iter= 4 total_weight= 1050.490 rmsd (weighted)= 2.088 (unweighted)= 23.819 superimposing iter= 5 total_weight= 1009.088 rmsd (weighted)= 2.029 (unweighted)= 23.850 Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.344 rmsd (weighted)= 4.010 (unweighted)= 19.838 superimposing iter= 1 total_weight= 4133.747 rmsd (weighted)= 1.805 (unweighted)= 19.843 superimposing iter= 2 total_weight= 2116.825 rmsd (weighted)= 1.227 (unweighted)= 19.872 superimposing iter= 3 total_weight= 1489.222 rmsd (weighted)= 1.020 (unweighted)= 19.892 superimposing iter= 4 total_weight= 1231.749 rmsd (weighted)= 0.940 (unweighted)= 19.905 superimposing iter= 5 total_weight= 1132.502 rmsd (weighted)= 0.905 (unweighted)= 19.914 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 1.197 rmsd (weighted)= 2.839 (unweighted)= 23.496 superimposing iter= 1 total_weight= 3080.406 rmsd (weighted)= 1.482 (unweighted)= 23.527 superimposing iter= 2 total_weight= 1514.483 rmsd (weighted)= 1.148 (unweighted)= 23.539 superimposing iter= 3 total_weight= 1110.360 rmsd (weighted)= 1.048 (unweighted)= 23.544 superimposing iter= 4 total_weight= 989.355 rmsd (weighted)= 1.017 (unweighted)= 23.547 superimposing iter= 5 total_weight= 958.967 rmsd (weighted)= 1.002 (unweighted)= 23.549 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 1.322 rmsd (weighted)= 4.253 (unweighted)= 39.962 superimposing iter= 1 total_weight= 3715.786 rmsd (weighted)= 2.133 (unweighted)= 39.983 superimposing iter= 2 total_weight= 1591.467 rmsd (weighted)= 1.713 (unweighted)= 39.987 superimposing iter= 3 total_weight= 1151.330 rmsd (weighted)= 1.626 (unweighted)= 39.982 superimposing iter= 4 total_weight= 1083.274 rmsd (weighted)= 1.592 (unweighted)= 39.974 superimposing iter= 5 total_weight= 1065.039 rmsd (weighted)= 1.573 (unweighted)= 39.966 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 1.404 rmsd (weighted)= 4.400 (unweighted)= 16.941 superimposing iter= 1 total_weight= 4550.193 rmsd (weighted)= 2.021 (unweighted)= 16.946 superimposing iter= 2 total_weight= 1925.019 rmsd (weighted)= 1.519 (unweighted)= 16.943 superimposing iter= 3 total_weight= 1260.651 rmsd (weighted)= 1.418 (unweighted)= 16.947 superimposing iter= 4 total_weight= 1147.502 rmsd (weighted)= 1.388 (unweighted)= 16.950 superimposing iter= 5 total_weight= 1120.856 rmsd (weighted)= 1.374 (unweighted)= 16.953 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 1.149 rmsd (weighted)= 5.537 (unweighted)= 27.129 superimposing iter= 1 total_weight= 3965.949 rmsd (weighted)= 2.348 (unweighted)= 27.120 superimposing iter= 2 total_weight= 1859.401 rmsd (weighted)= 1.586 (unweighted)= 27.103 superimposing iter= 3 total_weight= 1287.410 rmsd (weighted)= 1.305 (unweighted)= 27.113 superimposing iter= 4 total_weight= 1118.228 rmsd (weighted)= 1.160 (unweighted)= 27.126 superimposing iter= 5 total_weight= 1020.577 rmsd (weighted)= 1.084 (unweighted)= 27.133 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 1.363 rmsd (weighted)= 4.182 (unweighted)= 11.135 superimposing iter= 1 total_weight= 3381.127 rmsd (weighted)= 2.253 (unweighted)= 11.114 superimposing iter= 2 total_weight= 1609.486 rmsd (weighted)= 1.805 (unweighted)= 11.114 superimposing iter= 3 total_weight= 1291.872 rmsd (weighted)= 1.629 (unweighted)= 11.123 superimposing iter= 4 total_weight= 1218.600 rmsd (weighted)= 1.517 (unweighted)= 11.133 superimposing iter= 5 total_weight= 1153.656 rmsd (weighted)= 1.451 (unweighted)= 11.141 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 1.241 rmsd (weighted)= 3.567 (unweighted)= 33.766 superimposing iter= 1 total_weight= 3884.260 rmsd (weighted)= 1.621 (unweighted)= 33.728 superimposing iter= 2 total_weight= 1911.603 rmsd (weighted)= 1.127 (unweighted)= 33.701 superimposing iter= 3 total_weight= 1322.675 rmsd (weighted)= 0.958 (unweighted)= 33.687 superimposing iter= 4 total_weight= 1133.978 rmsd (weighted)= 0.884 (unweighted)= 33.680 superimposing iter= 5 total_weight= 1038.664 rmsd (weighted)= 0.853 (unweighted)= 33.675 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 1.229 rmsd (weighted)= 5.955 (unweighted)= 47.819 superimposing iter= 1 total_weight= 3511.483 rmsd (weighted)= 2.850 (unweighted)= 47.585 superimposing iter= 2 total_weight= 1976.754 rmsd (weighted)= 1.877 (unweighted)= 47.452 superimposing iter= 3 total_weight= 1543.415 rmsd (weighted)= 1.434 (unweighted)= 47.381 superimposing iter= 4 total_weight= 1289.060 rmsd (weighted)= 1.216 (unweighted)= 47.339 superimposing iter= 5 total_weight= 1153.346 rmsd (weighted)= 1.098 (unweighted)= 47.317 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 1.235 rmsd (weighted)= 3.777 (unweighted)= 23.108 superimposing iter= 1 total_weight= 3828.270 rmsd (weighted)= 1.771 (unweighted)= 23.078 superimposing iter= 2 total_weight= 1744.146 rmsd (weighted)= 1.283 (unweighted)= 23.103 superimposing iter= 3 total_weight= 1313.416 rmsd (weighted)= 1.089 (unweighted)= 23.114 superimposing iter= 4 total_weight= 1133.855 rmsd (weighted)= 1.002 (unweighted)= 23.117 superimposing iter= 5 total_weight= 1059.777 rmsd (weighted)= 0.956 (unweighted)= 23.119 Debug: superimposing conformation 9 on the average so far superimposing iter= 0 total_weight= 1.207 rmsd (weighted)= 9.498 (unweighted)= 23.713 superimposing iter= 1 total_weight= 3645.702 rmsd (weighted)= 3.771 (unweighted)= 23.623 superimposing iter= 2 total_weight= 1985.579 rmsd (weighted)= 2.514 (unweighted)= 23.673 superimposing iter= 3 total_weight= 1205.893 rmsd (weighted)= 2.216 (unweighted)= 23.722 superimposing iter= 4 total_weight= 1040.622 rmsd (weighted)= 2.117 (unweighted)= 23.760 superimposing iter= 5 total_weight= 1004.179 rmsd (weighted)= 2.063 (unweighted)= 23.791 superimposing iter= 0 total_weight= 1.344 rmsd (weighted)= 4.016 (unweighted)= 19.839 superimposing iter= 1 total_weight= 4140.336 rmsd (weighted)= 1.806 (unweighted)= 19.844 superimposing iter= 2 total_weight= 2120.730 rmsd (weighted)= 1.227 (unweighted)= 19.873 superimposing iter= 3 total_weight= 1488.059 rmsd (weighted)= 1.020 (unweighted)= 19.893 superimposing iter= 4 total_weight= 1229.889 rmsd (weighted)= 0.941 (unweighted)= 19.906 superimposing iter= 5 total_weight= 1131.738 rmsd (weighted)= 0.906 (unweighted)= 19.914 superimposing iter= 0 total_weight= 1.197 rmsd (weighted)= 2.838 (unweighted)= 23.496 superimposing iter= 1 total_weight= 3082.776 rmsd (weighted)= 1.481 (unweighted)= 23.528 superimposing iter= 2 total_weight= 1514.578 rmsd (weighted)= 1.147 (unweighted)= 23.541 superimposing iter= 3 total_weight= 1110.175 rmsd (weighted)= 1.047 (unweighted)= 23.546 superimposing iter= 4 total_weight= 989.832 rmsd (weighted)= 1.015 (unweighted)= 23.549 superimposing iter= 5 total_weight= 959.041 rmsd (weighted)= 1.000 (unweighted)= 23.552 superimposing iter= 0 total_weight= 1.322 rmsd (weighted)= 4.250 (unweighted)= 39.964 superimposing iter= 1 total_weight= 3719.401 rmsd (weighted)= 2.131 (unweighted)= 39.985 superimposing iter= 2 total_weight= 1589.124 rmsd (weighted)= 1.713 (unweighted)= 39.988 superimposing iter= 3 total_weight= 1151.580 rmsd (weighted)= 1.625 (unweighted)= 39.983 superimposing iter= 4 total_weight= 1084.286 rmsd (weighted)= 1.590 (unweighted)= 39.975 superimposing iter= 5 total_weight= 1065.528 rmsd (weighted)= 1.570 (unweighted)= 39.968 superimposing iter= 0 total_weight= 1.404 rmsd (weighted)= 4.400 (unweighted)= 16.950 superimposing iter= 1 total_weight= 4551.865 rmsd (weighted)= 2.021 (unweighted)= 16.956 superimposing iter= 2 total_weight= 1923.507 rmsd (weighted)= 1.519 (unweighted)= 16.953 superimposing iter= 3 total_weight= 1259.837 rmsd (weighted)= 1.419 (unweighted)= 16.957 superimposing iter= 4 total_weight= 1147.736 rmsd (weighted)= 1.388 (unweighted)= 16.960 superimposing iter= 5 total_weight= 1121.517 rmsd (weighted)= 1.374 (unweighted)= 16.963 superimposing iter= 0 total_weight= 1.149 rmsd (weighted)= 5.534 (unweighted)= 27.122 superimposing iter= 1 total_weight= 3964.864 rmsd (weighted)= 2.348 (unweighted)= 27.115 superimposing iter= 2 total_weight= 1857.885 rmsd (weighted)= 1.586 (unweighted)= 27.098 superimposing iter= 3 total_weight= 1287.670 rmsd (weighted)= 1.305 (unweighted)= 27.109 superimposing iter= 4 total_weight= 1118.628 rmsd (weighted)= 1.160 (unweighted)= 27.122 superimposing iter= 5 total_weight= 1021.129 rmsd (weighted)= 1.083 (unweighted)= 27.130 superimposing iter= 0 total_weight= 1.363 rmsd (weighted)= 4.181 (unweighted)= 11.139 superimposing iter= 1 total_weight= 3368.576 rmsd (weighted)= 2.257 (unweighted)= 11.117 superimposing iter= 2 total_weight= 1603.757 rmsd (weighted)= 1.813 (unweighted)= 11.116 superimposing iter= 3 total_weight= 1277.136 rmsd (weighted)= 1.646 (unweighted)= 11.124 superimposing iter= 4 total_weight= 1192.549 rmsd (weighted)= 1.550 (unweighted)= 11.134 superimposing iter= 5 total_weight= 1174.440 rmsd (weighted)= 1.472 (unweighted)= 11.144 superimposing iter= 0 total_weight= 1.241 rmsd (weighted)= 3.565 (unweighted)= 33.778 superimposing iter= 1 total_weight= 3880.327 rmsd (weighted)= 1.621 (unweighted)= 33.740 superimposing iter= 2 total_weight= 1907.617 rmsd (weighted)= 1.129 (unweighted)= 33.713 superimposing iter= 3 total_weight= 1321.942 rmsd (weighted)= 0.959 (unweighted)= 33.699 superimposing iter= 4 total_weight= 1133.890 rmsd (weighted)= 0.885 (unweighted)= 33.692 superimposing iter= 5 total_weight= 1038.741 rmsd (weighted)= 0.854 (unweighted)= 33.687 superimposing iter= 0 total_weight= 1.229 rmsd (weighted)= 5.951 (unweighted)= 47.831 superimposing iter= 1 total_weight= 3510.556 rmsd (weighted)= 2.848 (unweighted)= 47.598 superimposing iter= 2 total_weight= 1976.657 rmsd (weighted)= 1.876 (unweighted)= 47.465 superimposing iter= 3 total_weight= 1543.574 rmsd (weighted)= 1.433 (unweighted)= 47.393 superimposing iter= 4 total_weight= 1289.417 rmsd (weighted)= 1.215 (unweighted)= 47.351 superimposing iter= 5 total_weight= 1154.418 rmsd (weighted)= 1.097 (unweighted)= 47.329 superimposing iter= 0 total_weight= 1.235 rmsd (weighted)= 3.776 (unweighted)= 23.102 superimposing iter= 1 total_weight= 3830.087 rmsd (weighted)= 1.770 (unweighted)= 23.073 superimposing iter= 2 total_weight= 1744.231 rmsd (weighted)= 1.282 (unweighted)= 23.097 superimposing iter= 3 total_weight= 1311.592 rmsd (weighted)= 1.089 (unweighted)= 23.108 superimposing iter= 4 total_weight= 1132.852 rmsd (weighted)= 1.003 (unweighted)= 23.111 superimposing iter= 5 total_weight= 1059.083 rmsd (weighted)= 0.957 (unweighted)= 23.113 superimposing iter= 0 total_weight= 1.207 rmsd (weighted)= 9.503 (unweighted)= 23.710 superimposing iter= 1 total_weight= 3646.743 rmsd (weighted)= 3.772 (unweighted)= 23.619 superimposing iter= 2 total_weight= 1985.127 rmsd (weighted)= 2.516 (unweighted)= 23.669 superimposing iter= 3 total_weight= 1202.864 rmsd (weighted)= 2.221 (unweighted)= 23.718 superimposing iter= 4 total_weight= 1038.827 rmsd (weighted)= 2.124 (unweighted)= 23.757 superimposing iter= 5 total_weight= 1003.572 rmsd (weighted)= 2.069 (unweighted)= 23.787 # command:# Printing sheets for alignments to T0507.undertaker-align.sheets # command: