# command:# Seed set to 1214707370 # 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= 27.828 sec, elapsed time= 27.962 sec. # command:# Prefix for input files set to # command:# Making conformation for sequence T0470 numbered 1 through 223 Created new target T0470 from T0470.a2m # command:# command:# No conformations to remove in PopConform # command:CPU_time= 38.380 sec, elapsed time= 38.529 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= 48.345 sec, elapsed time= 48.507 sec. # command:# Prefix for input files set to # command:# reading script from file T0470.undertaker-align.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 2qgsA/T0470-2qgsA-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 2qgsA expands to /projects/compbio/data/pdb/2qgs.pdb.gz 2qgsA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0470 read from 2qgsA/T0470-2qgsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2qgsA read from 2qgsA/T0470-2qgsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2qgsA to template set # found chain 2qgsA in template set Warning: unaligning (T0470)S101 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2qgsA)H109 Warning: unaligning (T0470)G108 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2qgsA)H109 Warning: unaligning (T0470)I215 because last residue in template chain is (2qgsA)K216 T0470 1 :MTKQEKIEKTITFVKHILEKDASGHDWYHIRRVHKMAISLSEQEG 2qgsA 1 :MNSRMKIKKAYEYMKSFHQHDTTGHDIAHVERVYNNACYIAKREN # choosing archetypes in rotamer library T0470 46 :GNRFIIEMAALLHDVADEKLNE 2qgsA 47 :TDTLVIELSSLLHDTVDSKLTD T0470 69 :EEAGMKKVSDWLEELHVEEEESKHVLHIIANM 2qgsA 69 :EILAYDQLKQFLSTLDLSSEISQQVLYIIKHM T0470 109 :KVESIEGKLVQDADRLDALGAIGIARTFAYGGAKGRLMYDPTIPPREVMTKDEYRKNNDPSLNHFYEKLLKLKDLMNTNAAKQEAEVRHRYMEQFIEQFMKEWNAQ 2qgsA 110 :VKLSIDGEIVRDADRLDAIGAIGIARTFQFSGHFGEPMWTETKLSNEELHTSLVEELDNSAIKHFYEKLFKLKDLMHTPTAKKLAEERHQFMIQYLKQFMSEWNFN Number of specific fragments extracted= 4 number of extra gaps= 0 total=4 # request to SCWRL produces command: ulimit -t 201 ; scwrl3 -i /var/tmp/to_scwrl_22712338.pdb -s /var/tmp/to_scwrl_22712338.seq -o /var/tmp/from_scwrl_22712338.pdb > /var/tmp/scwrl_22712338.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_22712338.pdb Number of alignments=1 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3b57A/T0470-3b57A-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 3b57A expands to /projects/compbio/data/pdb/3b57.pdb.gz 3b57A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0470 read from 3b57A/T0470-3b57A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3b57A read from 3b57A/T0470-3b57A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3b57A to template set # found chain 3b57A in template set Warning: unaligning (T0470)L18 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3b57A)H25 Warning: unaligning (T0470)H25 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3b57A)H25 Warning: unaligning (T0470)D62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3b57A)Q70 Warning: unaligning (T0470)E70 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3b57A)Q70 Warning: unaligning (T0470)S101 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3b57A)A111 Warning: unaligning (T0470)V110 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3b57A)A111 Warning: unaligning (T0470)T150 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3b57A)P153 Warning: unaligning (T0470)N165 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3b57A)P153 T0470 1 :MTKQEKIEKTITFVKHI 3b57A 1 :MNKEEIILSAKNWMHSH T0470 26 :DWYHIRRVHKMAISLSEQEGGNRFIIEMAALLHDVA 3b57A 26 :DWSHIKRVWKLSKEIQSKEGGDLFTIELAALFHDYS T0470 71 :AGMKKVSDWLEELHVEEEESKHVLHIIANM 3b57A 71 :EATKTLINWMETKEIPSELIKKIIRIIQSV T0470 111 :ESIEGKLVQDADRLDALGAIGIARTFAYGGAKGRLMYDP 3b57A 112 :LTIEEKIVQDADRLDAIGAIGIARTFTYGGAHNREIANQ T0470 166 :NDPSLNHFYEKLLKLKDLMNTNAAKQEAEVRHRYMEQFIEQFMKEWNA 3b57A 154 :KNTTLQHFYDKLLLIKDQLNTETAKTIAKEKQKIMQDFIQALEKELKV Number of specific fragments extracted= 5 number of extra gaps= 0 total=9 # request to SCWRL produces command: ulimit -t 201 ; scwrl3 -i /var/tmp/to_scwrl_1506890924.pdb -s /var/tmp/to_scwrl_1506890924.seq -o /var/tmp/from_scwrl_1506890924.pdb > /var/tmp/scwrl_1506890924.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1506890924.pdb Number of alignments=2 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2pq7A/T0470-2pq7A-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 2pq7A expands to /projects/compbio/data/pdb/2pq7.pdb.gz 2pq7A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2, because occupancy 0.5 <= existing 0.500 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 4, because occupancy 0.500 <= existing 0.500 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 6, because occupancy 0.500 <= existing 0.500 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 8, because occupancy 0.500 <= existing 0.500 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 10, because occupancy 0.500 <= existing 0.500 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 12, because occupancy 0.500 <= existing 0.500 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 14, because occupancy 0.370 <= existing 0.370 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 16, because occupancy 0.500 <= existing 0.500 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 56, because occupancy 0.500 <= existing 0.500 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 58, because occupancy 0.500 <= existing 0.500 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 60, because occupancy 0.500 <= existing 0.500 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 62, because occupancy 0.500 <= existing 0.500 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 64, because occupancy 0.500 <= existing 0.500 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 66, because occupancy 0.500 <= existing 0.500 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 68, because occupancy 0.370 <= existing 0.370 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 70, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 145, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 147, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 149, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 151, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 153, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 155, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 157, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 159, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 161, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 163, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 165, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 167, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 169, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 171, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 173, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 175, because occupancy 0.500 <= existing 0.500 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 352, because occupancy 0.500 <= existing 0.500 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 354, because occupancy 0.500 <= existing 0.500 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 356, because occupancy 0.500 <= existing 0.500 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 358, because occupancy 0.500 <= existing 0.500 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 360, because occupancy 0.500 <= existing 0.500 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 362, because occupancy 0.500 <= existing 0.500 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 364, because occupancy 0.370 <= existing 0.370 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 366, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 396, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 398, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 400, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 402, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 404, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 406, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 498, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 500, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 502, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 504, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 506, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 508, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 510, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 512, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 674, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 676, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 678, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 680, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 682, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 684, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 686, because occupancy 0.250 <= existing 0.250 in 2pq7A Skipped atom 689, because occupancy 0.250 <= existing 0.250 in 2pq7A Skipped atom 692, because occupancy 0.250 <= existing 0.250 in 2pq7A Skipped atom 695, because occupancy 0.250 <= existing 0.250 in 2pq7A Skipped atom 698, because occupancy 0.250 <= existing 0.250 in 2pq7A Skipped atom 701, because occupancy 0.250 <= existing 0.250 in 2pq7A Skipped atom 739, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 741, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 743, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 745, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 747, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 749, because occupancy 0.500 <= existing 0.500 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 870, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 874, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 876, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 909, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 911, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 913, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 915, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 917, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 919, because occupancy 0.500 <= existing 0.500 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1253, because occupancy 0.500 <= existing 0.500 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1255, because occupancy 0.500 <= existing 0.500 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1257, because occupancy 0.500 <= existing 0.500 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1259, because occupancy 0.500 <= existing 0.500 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1261, because occupancy 0.500 <= existing 0.500 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1263, because occupancy 0.500 <= existing 0.500 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1265, because occupancy 0.370 <= existing 0.370 in 2pq7A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1267, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 1311, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 1313, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 1315, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 1317, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 1319, because occupancy 0.500 <= existing 0.500 in 2pq7A Skipped atom 1321, because occupancy 0.500 <= existing 0.500 in 2pq7A # T0470 read from 2pq7A/T0470-2pq7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2pq7A read from 2pq7A/T0470-2pq7A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2pq7A to template set # found chain 2pq7A in template set Warning: unaligning (T0470)S101 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2pq7A)T118 Warning: unaligning (T0470)G107 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2pq7A)T118 Warning: unaligning (T0470)Y138 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2pq7A)P186 Warning: unaligning (T0470)K181 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2pq7A)P186 T0470 1 :MTKQEKIE 2pq7A 1 :MNLTELME T0470 9 :KTITFVKHILEKDA 2pq7A 15 :EILNIVREAFKDYD T0470 23 :SGHDWYHIRRVHKMAISLSEQEGGNRFIIEMAALLHDVADE 2pq7A 30 :PAHDISHTFRVMENASEIASREKCDLQKAIIAALLHDIKRP T0470 64 :KLNESEEAGMKKVSDWLEELHVEEEESKHVLHIIANM 2pq7A 75 :TGVDHAESGAEYASGLLPTMGFDISFVAEVSKAIRSH T0470 110 :VESIEGKLVQDADRLDALGAIGIARTFA 2pq7A 119 :PTSLTGKILQDADRLDAIGAVAIARVFS T0470 182 :DLMNTNAAKQEAEVRHRYMEQFIEQFMKEW 2pq7A 187 :ETFWTETARKMAEDRYSFVVEFVQRFLAEW Number of specific fragments extracted= 6 number of extra gaps= 0 total=15 # request to SCWRL produces command: ulimit -t 201 ; scwrl3 -i /var/tmp/to_scwrl_1960355930.pdb -s /var/tmp/to_scwrl_1960355930.seq -o /var/tmp/from_scwrl_1960355930.pdb > /var/tmp/scwrl_1960355930.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1960355930.pdb Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2pjqA/T0470-2pjqA-t2k-global-adpstyle1.a2m with NO bystroff filtering # adding to alignment library if long or multiple fragments 2pjqA expands to /projects/compbio/data/pdb/2pjq.pdb.gz 2pjqA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0470 read from 2pjqA/T0470-2pjqA-t2k-global-adpstyle1.a2m # 2pjqA read from 2pjqA/T0470-2pjqA-t2k-global-adpstyle1.a2m # adding 2pjqA to template set # found chain 2pjqA in template set Warning: unaligning (T0470)D62 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (2pjqA)A72 Warning: unaligning (T0470)G72 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2pjqA)A72 Warning: unaligning (T0470)Q214 because last residue in template chain is (2pjqA)D215 T0470 3 :KQEKIEKTITFVKHILEKDASGHDWYHIRRVHKMAISLSEQEGGNRFIIEMAALLHDVA 2pjqA 3 :TETQLTAIQTYALQKLAHDHSGHGRDHLQRVNRLARRLAKDEGANLNLTLAAAWLHDVI T0470 73 :MKKVSDWLEELHVEEEESKHVLHIIANMSYKGGHG 2pjqA 73 :HQDLIVQLNAQNVTADDQTAIFAIIDHMSFSKSFN T0470 108 :GKVESIEGKLVQDADRLDALGAIGIARTFAYGGAKGRLMYDPTIPPREVMTKDEYRKNNDPSLNHFYEKLLKLKDLMNTNAAKQEAEVRHRYMEQFIEQFMKEWNA 2pjqA 109 :PQKLSLEGQVVQDADRLDAIGAIGIARALYYSGHVGEKIYDPAIAPREHMTREQYRHQPGTAINHFYEKLFKLAALMNTDTAKALAAHRTAVMHEFVDQFKAEWTA Number of specific fragments extracted= 3 number of extra gaps= 0 total=18 # request to SCWRL produces command: ulimit -t 201 ; scwrl3 -i /var/tmp/to_scwrl_1571435198.pdb -s /var/tmp/to_scwrl_1571435198.seq -o /var/tmp/from_scwrl_1571435198.pdb > /var/tmp/scwrl_1571435198.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1571435198.pdb Number of alignments=4 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2o08A/T0470-2o08A-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 2o08A expands to /projects/compbio/data/pdb/2o08.pdb.gz 2o08A:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 270, because occupancy 0.500 <= existing 0.500 in 2o08A Skipped atom 274, because occupancy 0.500 <= existing 0.500 in 2o08A Skipped atom 276, because occupancy 0.500 <= existing 0.500 in 2o08A Skipped atom 278, because occupancy 0.500 <= existing 0.500 in 2o08A Skipped atom 280, because occupancy 0.500 <= existing 0.500 in 2o08A Skipped atom 282, because occupancy 0.500 <= existing 0.500 in 2o08A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 743, because occupancy 0.500 <= existing 0.500 in 2o08A Skipped atom 747, because occupancy 0.500 <= existing 0.500 in 2o08A Skipped atom 749, because occupancy 0.500 <= existing 0.500 in 2o08A Skipped atom 751, because occupancy 0.500 <= existing 0.500 in 2o08A Skipped atom 753, because occupancy 0.500 <= existing 0.500 in 2o08A Skipped atom 755, because occupancy 0.500 <= existing 0.500 in 2o08A Skipped atom 757, because occupancy 0.500 <= existing 0.500 in 2o08A Skipped atom 759, because occupancy 0.500 <= existing 0.500 in 2o08A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1106, because occupancy 0.500 <= existing 0.500 in 2o08A Skipped atom 1110, because occupancy 0.500 <= existing 0.500 in 2o08A Skipped atom 1112, because occupancy 0.500 <= existing 0.500 in 2o08A Skipped atom 1114, because occupancy 0.500 <= existing 0.500 in 2o08A Skipped atom 1116, because occupancy 0.500 <= existing 0.500 in 2o08A Skipped atom 1118, because occupancy 0.500 <= existing 0.500 in 2o08A Skipped atom 1120, because occupancy 0.500 <= existing 0.500 in 2o08A Skipped atom 1122, because occupancy 0.500 <= existing 0.500 in 2o08A Skipped atom 1267, because occupancy 0.500 <= existing 0.500 in 2o08A Skipped atom 1271, because occupancy 0.500 <= existing 0.500 in 2o08A Skipped atom 1273, because occupancy 0.500 <= existing 0.500 in 2o08A Skipped atom 1291, because occupancy 0.500 <= existing 0.500 in 2o08A Skipped atom 1295, because occupancy 0.500 <= existing 0.500 in 2o08A Skipped atom 1297, because occupancy 0.500 <= existing 0.500 in 2o08A Skipped atom 1299, because occupancy 0.500 <= existing 0.500 in 2o08A Skipped atom 1301, because occupancy 0.500 <= existing 0.500 in 2o08A # T0470 read from 2o08A/T0470-2o08A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2o08A read from 2o08A/T0470-2o08A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2o08A to template set # found chain 2o08A in template set T0470 1 :MTKQ 2o08A 1 :MNRG T0470 9 :KTITFV 2o08A 5 :KALQLV T0470 19 :EKDASGHDWYHIRRVHKMAISLSEQEGGNRFIIEMAALLHDVADEKLNESEE 2o08A 11 :KPHLTEHRYQHTIGVMETAIDLAKLYGADQQKAELAAIFHDYAKFRDKNEMR T0470 71 :AGMKKVSDWLE 2o08A 82 :LHAPCGAYYVR T0470 82 :ELHVEEEE 2o08A 94 :EVGIEDED T0470 93 :VLHIIANMS 2o08A 102 :VLQAIRFHT T0470 104 :GGHGGK 2o08A 111 :TGRPNM T0470 112 :SIEGKLVQDADRLDAL 2o08A 117 :SLLEKIIFLADYIEPN T0470 151 :IPPRE 2o08A 133 :RQFPG T0470 159 :KDEYRKNNDPSLNHFYEKLLK 2o08A 138 :VEKVRTQAKTDLNGAIISSLV T0470 191 :QEAEVRHR 2o08A 159 :NTITFLLK T0470 199 :YMEQFIEQFMKE 2o08A 174 :DTLATYNQLLLE Number of specific fragments extracted= 12 number of extra gaps= 0 total=30 # request to SCWRL produces command: ulimit -t 201 ; scwrl3 -i /var/tmp/to_scwrl_530709127.pdb -s /var/tmp/to_scwrl_530709127.seq -o /var/tmp/from_scwrl_530709127.pdb > /var/tmp/scwrl_530709127.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_530709127.pdb Number of alignments=5 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2ogiA/T0470-2ogiA-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 2ogiA expands to /projects/compbio/data/pdb/2ogi.pdb.gz 2ogiA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 827, because occupancy 0.500 <= existing 0.500 in 2ogiA Skipped atom 829, because occupancy 0.500 <= existing 0.500 in 2ogiA Skipped atom 831, because occupancy 0.500 <= existing 0.500 in 2ogiA Skipped atom 833, because occupancy 0.500 <= existing 0.500 in 2ogiA Skipped atom 835, because occupancy 0.500 <= existing 0.500 in 2ogiA Skipped atom 837, because occupancy 0.500 <= existing 0.500 in 2ogiA Skipped atom 839, because occupancy 0.500 <= existing 0.500 in 2ogiA Skipped atom 841, because occupancy 0.500 <= existing 0.500 in 2ogiA Skipped atom 953, because occupancy 0.500 <= existing 0.500 in 2ogiA Skipped atom 955, because occupancy 0.500 <= existing 0.500 in 2ogiA Skipped atom 957, because occupancy 0.500 <= existing 0.500 in 2ogiA Skipped atom 959, because occupancy 0.500 <= existing 0.500 in 2ogiA Skipped atom 961, because occupancy 0.500 <= existing 0.500 in 2ogiA Skipped atom 963, because occupancy 0.500 <= existing 0.500 in 2ogiA Skipped atom 965, because occupancy 0.500 <= existing 0.500 in 2ogiA Skipped atom 967, because occupancy 0.500 <= existing 0.500 in 2ogiA Skipped atom 969, because occupancy 0.500 <= existing 0.500 in 2ogiA Skipped atom 971, because occupancy 0.500 <= existing 0.500 in 2ogiA Skipped atom 973, because occupancy 0.500 <= existing 0.500 in 2ogiA Skipped atom 975, because occupancy 0.500 <= existing 0.500 in 2ogiA Skipped atom 977, because occupancy 0.500 <= existing 0.500 in 2ogiA Skipped atom 979, because occupancy 0.500 <= existing 0.500 in 2ogiA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0470 read from 2ogiA/T0470-2ogiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2ogiA read from 2ogiA/T0470-2ogiA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2ogiA to template set # found chain 2ogiA in template set Warning: unaligning (T0470)L57 because of BadResidue code NON_PLANAR_PEPTIDE in next template residue (2ogiA)H58 Warning: unaligning (T0470)H58 because of BadResidue code NON_PLANAR_PEPTIDE at template residue (2ogiA)H58 Warning: unaligning (T0470)H106 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE in next template residue (2ogiA)A122 Warning: unaligning (T0470)G107 because of BadResidue code NON_PLANAR_PEPTIDE+BAD_PEPTIDE at template residue (2ogiA)A122 Warning: unaligning (T0470)D125 because of BadResidue code BAD_PEPTIDE in next template residue (2ogiA)H139 Warning: unaligning (T0470)A126 because of BadResidue code BAD_PEPTIDE at template residue (2ogiA)H139 T0470 2 :TKQEK 2ogiA 10 :DRTEL T0470 15 :KHILEKDASGHDWYHIRRVHKMAISLSEQEGGNRFIIEMAAL 2ogiA 15 :LSKVRHMMSDKRFNHVLGVERAAIELAERYGYDKEKAGLAAL T0470 59 :DVADEKLNESEE 2ogiA 59 :DYAKELSDDEFL T0470 71 :AGMKKVSDWLEEL 2ogiA 90 :WHGLVGIYKIQED T0470 84 :HVEEEE 2ogiA 104 :AIKDQD T0470 93 :VLHIIANMS 2ogiA 110 :ILAAIAKHT T0470 104 :GG 2ogiA 119 :VG T0470 108 :GK 2ogiA 123 :QM T0470 112 :SIEGKLVQDADRL 2ogiA 125 :STLDKIVYVADYI T0470 164 :KNNDPSLNHFYEKLLKLKDLMNTNAAKQEAEVRHR 2ogiA 140 :NRDFPGVEEARELAKVDLNKAVAYETARTVAFLAS T0470 199 :YMEQFIEQF 2ogiA 182 :KTIETYNAY Number of specific fragments extracted= 11 number of extra gaps= 3 total=41 # request to SCWRL produces command: ulimit -t 201 ; scwrl3 -i /var/tmp/to_scwrl_2004382503.pdb -s /var/tmp/to_scwrl_2004382503.seq -o /var/tmp/from_scwrl_2004382503.pdb > /var/tmp/scwrl_2004382503.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2004382503.pdb Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3ccgA/T0470-3ccgA-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 3ccgA expands to /projects/compbio/data/pdb/3ccg.pdb.gz 3ccgA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 34, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 36, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 38, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 40, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 42, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 44, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 46, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 48, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 50, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 52, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 54, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 56, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 90, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 92, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 94, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 96, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 98, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 100, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 102, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 104, because occupancy 0.500 <= existing 0.500 in 3ccgA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 126, because occupancy 0.300 <= existing 0.700 in 3ccgA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 128, because occupancy 0.300 <= existing 0.700 in 3ccgA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 130, because occupancy 0.300 <= existing 0.700 in 3ccgA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 132, because occupancy 0.300 <= existing 0.700 in 3ccgA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 134, because occupancy 0.300 <= existing 0.700 in 3ccgA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 136, because occupancy 0.300 <= existing 0.700 in 3ccgA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 138, because occupancy 0.250 <= existing 0.500 in 3ccgA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 140, because occupancy 0.300 <= existing 0.700 in 3ccgA Skipped atom 142, because occupancy 0.300 <= existing 0.700 in 3ccgA Skipped atom 144, because occupancy 0.300 <= existing 0.700 in 3ccgA Skipped atom 146, because occupancy 0.300 <= existing 0.700 in 3ccgA Skipped atom 148, because occupancy 0.300 <= existing 0.700 in 3ccgA Skipped atom 150, because occupancy 0.300 <= existing 0.700 in 3ccgA Skipped atom 152, because occupancy 0.300 <= existing 0.700 in 3ccgA Skipped atom 154, because occupancy 0.300 <= existing 0.700 in 3ccgA Skipped atom 156, because occupancy 0.300 <= existing 0.700 in 3ccgA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 337, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 339, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 341, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 343, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 345, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 347, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 349, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 351, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 400, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 402, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 404, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 406, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 408, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 410, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 412, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 414, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 416, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 418, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 420, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 554, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 556, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 558, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 560, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 562, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 564, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 566, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 568, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 570, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 673, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 675, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 677, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 679, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 681, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 683, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 685, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 687, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 689, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 691, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 693, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 706, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 708, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 710, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 712, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 714, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 716, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 718, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 720, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 722, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 724, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 726, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 728, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 869, because occupancy 0.300 <= existing 0.700 in 3ccgA Skipped atom 871, because occupancy 0.300 <= existing 0.700 in 3ccgA Skipped atom 873, because occupancy 0.300 <= existing 0.700 in 3ccgA Skipped atom 875, because occupancy 0.300 <= existing 0.700 in 3ccgA Skipped atom 877, because occupancy 0.300 <= existing 0.700 in 3ccgA Skipped atom 879, because occupancy 0.300 <= existing 0.700 in 3ccgA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1289, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 1291, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 1293, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 1295, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 1297, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 1299, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 1301, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 1303, because occupancy 0.500 <= existing 0.500 in 3ccgA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1313, because occupancy 0.500 <= existing 0.500 in 3ccgA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1315, because occupancy 0.500 <= existing 0.500 in 3ccgA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1317, because occupancy 0.500 <= existing 0.500 in 3ccgA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1319, because occupancy 0.500 <= existing 0.500 in 3ccgA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1321, because occupancy 0.500 <= existing 0.500 in 3ccgA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1323, because occupancy 0.500 <= existing 0.500 in 3ccgA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1325, because occupancy 0.370 <= existing 0.380 in 3ccgA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1327, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 1354, because occupancy 0.300 <= existing 0.700 in 3ccgA Skipped atom 1356, because occupancy 0.300 <= existing 0.700 in 3ccgA Skipped atom 1358, because occupancy 0.300 <= existing 0.700 in 3ccgA Skipped atom 1360, because occupancy 0.300 <= existing 0.700 in 3ccgA Skipped atom 1362, because occupancy 0.300 <= existing 0.700 in 3ccgA Skipped atom 1364, because occupancy 0.300 <= existing 0.700 in 3ccgA Skipped atom 1366, because occupancy 0.300 <= existing 0.700 in 3ccgA Skipped atom 1368, because occupancy 0.300 <= existing 0.700 in 3ccgA Skipped atom 1420, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 1422, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 1424, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 1426, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 1428, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 1430, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 1432, because occupancy 0.500 <= existing 0.500 in 3ccgA Skipped atom 1434, because occupancy 0.500 <= existing 0.500 in 3ccgA # T0470 read from 3ccgA/T0470-3ccgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ccgA read from 3ccgA/T0470-3ccgA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3ccgA to template set # found chain 3ccgA in template set Warning: unaligning (T0470)A71 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3ccgA)L84 Warning: unaligning (T0470)G72 because of BadResidue code BAD_PEPTIDE at template residue (3ccgA)H85 T0470 8 :EKTITFVKHILEKDA 3ccgA 5 :DKITDYLMNNLGEKR T0470 27 :WYHIRRVHKMAISLSEQEGGNRFIIEMAALLHDVADE 3ccgA 20 :YKHSLGVMDTAVRLAGIYNEDTEKARIAGLVHDCAKK T0470 64 :KLNESEE 3ccgA 72 :ELGDEDI T0470 73 :MKKVSDWLE 3ccgA 86 :GLAGRILAK T0470 82 :ELHVEEEE 3ccgA 96 :VIGIDDED T0470 93 :VLHIIANMS 3ccgA 104 :VLNAIEFHT T0470 104 :GGHGGK 3ccgA 113 :TGRPNM T0470 112 :SIEGKLVQDADRLD 3ccgA 119 :SLLEKIIYIADYIE T0470 149 :P 3ccgA 133 :P T0470 164 :KNNDPSLNHFYEKLLKLKDLMNTNAAKQEAEVRHR 3ccgA 134 :GREFKGVDELRKAADEDLNKALLMSFDNTIKFVID T0470 199 :YMEQFIEQFMKE 3ccgA 176 :NTIEARNYLISR Number of specific fragments extracted= 11 number of extra gaps= 1 total=52 # request to SCWRL produces command: ulimit -t 201 ; scwrl3 -i /var/tmp/to_scwrl_970590851.pdb -s /var/tmp/to_scwrl_970590851.seq -o /var/tmp/from_scwrl_970590851.pdb > /var/tmp/scwrl_970590851.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_970590851.pdb Number of alignments=7 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2hekA/T0470-2hekA-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 2hekA expands to /projects/compbio/data/pdb/2hek.pdb.gz 2hekA:# T0470 read from 2hekA/T0470-2hekA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2hekA read from 2hekA/T0470-2hekA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2hekA to template set # found chain 2hekA in template set T0470 20 :KDASGHDWYHIRRVHKMAISLSEQEGG 2hekA 45 :PSAQHTRFEHSLGVYHITERICESLKV T0470 47 :NRFIIEMAALLHDVADEKLNESEE 2hekA 73 :EKELVKLAGLLHDLGHPPFSHTTE T0470 75 :KVSDWLEEL 2hekA 117 :EIYEILKQD T0470 85 :VEEEESKHVLHIIA 2hekA 126 :YSHEDIERLVRITL T0470 104 :GGHGGKVESIEGKLVQ 2hekA 140 :GKPEDEEEKLLSEIIT T0470 120 :DADRLDALGAIGIA 2hekA 159 :GSDRMDYLRRDAYF T0470 135 :TFAYGGAKGRLMYDPT 2hekA 186 :ISTLRVYENKVVVDES T0470 166 :NDPSLNHFYEKLLKLKDLMN 2hekA 202 :GLRALENFLISRYFMYVQVY T0470 186 :TNAAKQEAEVRHRYMEQF 2hekA 223 :HKVVRILSIHLVEFLKKL T0470 204 :IEQFMKEWN 2hekA 257 :DAFVISELF T0470 213 :AQILEHHHHHH 2hekA 271 :REDFERIFQRK Number of specific fragments extracted= 11 number of extra gaps= 0 total=63 # request to SCWRL produces command: ulimit -t 201 ; scwrl3 -i /var/tmp/to_scwrl_203220355.pdb -s /var/tmp/to_scwrl_203220355.seq -o /var/tmp/from_scwrl_203220355.pdb > /var/tmp/scwrl_203220355.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_203220355.pdb Number of alignments=8 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2dqbA/T0470-2dqbA-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 2dqbA expands to /projects/compbio/data/pdb/2dqb.pdb.gz 2dqbA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0470 read from 2dqbA/T0470-2dqbA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2dqbA read from 2dqbA/T0470-2dqbA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2dqbA to template set # found chain 2dqbA in template set Warning: unaligning (T0470)A22 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2dqbA)Y72 Warning: unaligning (T0470)K109 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (2dqbA)G183 T0470 23 :SGHDWYHIRRVHKMAISLSEQEGGNRFIIEMAALLHDVADEKLNESEE 2dqbA 73 :YRTRLTHTLEVAQVSRSIARALGLNEDLTEAIALSHDLGHPPFGHTGE T0470 71 :AGMKKVSDWLEEL 2dqbA 134 :EHNAQALRILTHL T0470 84 :H 2dqbA 151 :P T0470 85 :VEEE 2dqbA 158 :LTYE T0470 93 :VLHIIANMS 2dqbA 162 :VLEGIATHE T0470 110 :VESIEGKLVQDADRLDA 2dqbA 184 :QGTLEAQVVDLSDAIAY T0470 127 :LGAIGIAR 2dqbA 203 :HDLDDGFR T0470 135 :TFAYGGAKG 2dqbA 266 :RVEEAGVQS T0470 159 :KDEYRKNN 2dqbA 275 :AEAVRRHP T0470 167 :DPSLNHFYEKLLKLK 2dqbA 289 :GEEAEKALKALKAFL T0470 182 :DLMN 2dqbA 305 :ERFY T0470 186 :TNAAKQEAEVRHRYMEQFIEQFMK 2dqbA 310 :HPEVLRERRKAEAVLEGLFAAYTR Number of specific fragments extracted= 12 number of extra gaps= 0 total=75 # request to SCWRL produces command: ulimit -t 201 ; scwrl3 -i /var/tmp/to_scwrl_1275884680.pdb -s /var/tmp/to_scwrl_1275884680.seq -o /var/tmp/from_scwrl_1275884680.pdb > /var/tmp/scwrl_1275884680.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1275884680.pdb Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 2hd1A/T0470-2hd1A-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 2hd1A expands to /projects/compbio/data/pdb/2hd1.pdb.gz 2hd1A:# T0470 read from 2hd1A/T0470-2hd1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 2hd1A read from 2hd1A/T0470-2hd1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 2hd1A to template set # found chain 2hd1A in template set T0470 4 :QEKIEKTITFVKHILEKDA 2hd1A 232 :PVTLRRWLFCVHDNYRNNP T0470 24 :GHDWYHIRRVHKMAISLSEQEGG 2hd1A 251 :FHNFRHCFCVAQMMYSMVWLCSL T0470 47 :NRFI 2hd1A 278 :SQTD T0470 51 :IEMAALLHDVADEKLNESEE 2hd1A 285 :LMTAAICHDLDHPGYNNTYQ T0470 71 :AGMKKVSDWLE 2hd1A 324 :HHCAVAFQILA T0470 84 :HVEEEESKHVLHIIANMS 2hd1A 343 :NIPPDGFKQIRQGMITLI T0470 102 :YKGGHGGKVESIEGKLVQDADRLDA 2hd1A 379 :MENFDYSNEEHMTLLKMILIKCCDI T0470 129 :AIGIAR 2hd1A 404 :SNEVRP T0470 135 :TFAYGGAKGRLMYDPTIPPREVMTKDEYRK 2hd1A 430 :REKSEGLPVAPFMDRDKVTKATAQIGFIKF T0470 169 :SLNHFYEKLLKLKDLMN 2hd1A 460 :VLIPMFETVTKLFPMVE T0470 194 :EVRHRYMEQFIEQFMKEWNAQILEHHHHHH 2hd1A 477 :EIMLQPLWESRDRYEELKRIDDAMKELQKK Number of specific fragments extracted= 11 number of extra gaps= 0 total=86 # request to SCWRL produces command: ulimit -t 201 ; scwrl3 -i /var/tmp/to_scwrl_1920183506.pdb -s /var/tmp/to_scwrl_1920183506.seq -o /var/tmp/from_scwrl_1920183506.pdb > /var/tmp/scwrl_1920183506.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1920183506.pdb Number of alignments=10 # command:Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.371 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 1 total_weight= 16770.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 2 total_weight= 16770.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 3 total_weight= 16770.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 4 total_weight= 16770.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 5 total_weight= 16770.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 1.135 rmsd (weighted)= 2.029 (unweighted)= 63.941 superimposing iter= 1 total_weight= 6188.617 rmsd (weighted)= 0.894 (unweighted)= 63.839 superimposing iter= 2 total_weight= 2414.127 rmsd (weighted)= 0.666 (unweighted)= 63.776 superimposing iter= 3 total_weight= 1682.686 rmsd (weighted)= 0.600 (unweighted)= 63.726 superimposing iter= 4 total_weight= 1534.630 rmsd (weighted)= 0.566 (unweighted)= 63.685 superimposing iter= 5 total_weight= 1483.661 rmsd (weighted)= 0.543 (unweighted)= 63.653 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 1.047 rmsd (weighted)= 4.329 (unweighted)= 59.819 superimposing iter= 1 total_weight= 6176.787 rmsd (weighted)= 1.677 (unweighted)= 59.642 superimposing iter= 2 total_weight= 2601.221 rmsd (weighted)= 1.157 (unweighted)= 59.530 superimposing iter= 3 total_weight= 1522.843 rmsd (weighted)= 1.052 (unweighted)= 59.452 superimposing iter= 4 total_weight= 1404.105 rmsd (weighted)= 0.998 (unweighted)= 59.383 superimposing iter= 5 total_weight= 1407.368 rmsd (weighted)= 0.946 (unweighted)= 59.318 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 1.287 rmsd (weighted)= 4.685 (unweighted)= 58.727 superimposing iter= 1 total_weight= 6393.578 rmsd (weighted)= 2.015 (unweighted)= 58.904 superimposing iter= 2 total_weight= 2612.254 rmsd (weighted)= 1.517 (unweighted)= 58.926 superimposing iter= 3 total_weight= 1873.979 rmsd (weighted)= 1.369 (unweighted)= 58.995 superimposing iter= 4 total_weight= 1758.114 rmsd (weighted)= 1.279 (unweighted)= 59.083 superimposing iter= 5 total_weight= 1786.722 rmsd (weighted)= 1.189 (unweighted)= 59.175 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 1.023 rmsd (weighted)= 13.683 (unweighted)= 59.493 superimposing iter= 1 total_weight= 5455.050 rmsd (weighted)= 5.411 (unweighted)= 61.612 superimposing iter= 2 total_weight= 3899.649 rmsd (weighted)= 2.775 (unweighted)= 62.260 superimposing iter= 3 total_weight= 2706.504 rmsd (weighted)= 1.801 (unweighted)= 62.373 superimposing iter= 4 total_weight= 2101.028 rmsd (weighted)= 1.354 (unweighted)= 62.383 superimposing iter= 5 total_weight= 1731.061 rmsd (weighted)= 1.135 (unweighted)= 62.384 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 0.963 rmsd (weighted)= 11.919 (unweighted)= 48.243 superimposing iter= 1 total_weight= 5287.254 rmsd (weighted)= 4.642 (unweighted)= 47.214 superimposing iter= 2 total_weight= 3702.277 rmsd (weighted)= 2.381 (unweighted)= 46.849 superimposing iter= 3 total_weight= 2626.658 rmsd (weighted)= 1.522 (unweighted)= 46.747 superimposing iter= 4 total_weight= 1923.491 rmsd (weighted)= 1.160 (unweighted)= 46.709 superimposing iter= 5 total_weight= 1537.694 rmsd (weighted)= 0.997 (unweighted)= 46.690 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 0.990 rmsd (weighted)= 13.314 (unweighted)= 40.024 superimposing iter= 1 total_weight= 5735.168 rmsd (weighted)= 4.959 (unweighted)= 42.924 superimposing iter= 2 total_weight= 3543.323 rmsd (weighted)= 2.723 (unweighted)= 43.411 superimposing iter= 3 total_weight= 2122.795 rmsd (weighted)= 2.024 (unweighted)= 43.514 superimposing iter= 4 total_weight= 1659.729 rmsd (weighted)= 1.709 (unweighted)= 43.597 superimposing iter= 5 total_weight= 1603.734 rmsd (weighted)= 1.467 (unweighted)= 43.634 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 1.085 rmsd (weighted)= 19.346 (unweighted)= 37.357 superimposing iter= 1 total_weight= 5042.024 rmsd (weighted)= 7.875 (unweighted)= 38.511 superimposing iter= 2 total_weight= 5006.084 rmsd (weighted)= 3.528 (unweighted)= 38.958 superimposing iter= 3 total_weight= 3212.439 rmsd (weighted)= 2.147 (unweighted)= 39.105 superimposing iter= 4 total_weight= 2295.334 rmsd (weighted)= 1.580 (unweighted)= 39.158 superimposing iter= 5 total_weight= 1837.715 rmsd (weighted)= 1.313 (unweighted)= 39.169 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 1.051 rmsd (weighted)= 19.501 (unweighted)= 41.243 superimposing iter= 1 total_weight= 3541.017 rmsd (weighted)= 9.783 (unweighted)= 43.169 superimposing iter= 2 total_weight= 4135.119 rmsd (weighted)= 4.538 (unweighted)= 43.512 superimposing iter= 3 total_weight= 3741.875 rmsd (weighted)= 2.437 (unweighted)= 43.524 superimposing iter= 4 total_weight= 2671.823 rmsd (weighted)= 1.611 (unweighted)= 43.515 superimposing iter= 5 total_weight= 2040.464 rmsd (weighted)= 1.239 (unweighted)= 43.531 Debug: superimposing conformation 9 on the average so far superimposing iter= 0 total_weight= 1.247 rmsd (weighted)= 8.707 (unweighted)= 40.188 superimposing iter= 1 total_weight= 6056.957 rmsd (weighted)= 4.050 (unweighted)= 40.002 superimposing iter= 2 total_weight= 2470.359 rmsd (weighted)= 3.147 (unweighted)= 40.005 superimposing iter= 3 total_weight= 1737.111 rmsd (weighted)= 2.938 (unweighted)= 40.026 superimposing iter= 4 total_weight= 1595.739 rmsd (weighted)= 2.864 (unweighted)= 40.044 superimposing iter= 5 total_weight= 1560.853 rmsd (weighted)= 2.825 (unweighted)= 40.057 Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.371 rmsd (weighted)= 7.633 (unweighted)= 22.524 superimposing iter= 1 total_weight= 7264.648 rmsd (weighted)= 3.077 (unweighted)= 23.216 superimposing iter= 2 total_weight= 4759.904 rmsd (weighted)= 1.711 (unweighted)= 23.422 superimposing iter= 3 total_weight= 2932.951 rmsd (weighted)= 1.246 (unweighted)= 23.504 superimposing iter= 4 total_weight= 2382.300 rmsd (weighted)= 1.015 (unweighted)= 23.550 superimposing iter= 5 total_weight= 2094.246 rmsd (weighted)= 0.887 (unweighted)= 23.570 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 1.135 rmsd (weighted)= 6.818 (unweighted)= 58.584 superimposing iter= 1 total_weight= 6824.183 rmsd (weighted)= 2.471 (unweighted)= 58.549 superimposing iter= 2 total_weight= 4367.086 rmsd (weighted)= 1.302 (unweighted)= 58.500 superimposing iter= 3 total_weight= 2501.959 rmsd (weighted)= 0.947 (unweighted)= 58.492 superimposing iter= 4 total_weight= 1844.752 rmsd (weighted)= 0.811 (unweighted)= 58.487 superimposing iter= 5 total_weight= 1579.222 rmsd (weighted)= 0.754 (unweighted)= 58.486 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 1.053 rmsd (weighted)= 6.371 (unweighted)= 45.729 superimposing iter= 1 total_weight= 4605.687 rmsd (weighted)= 2.696 (unweighted)= 44.503 superimposing iter= 2 total_weight= 3924.918 rmsd (weighted)= 1.381 (unweighted)= 44.207 superimposing iter= 3 total_weight= 2839.409 rmsd (weighted)= 0.882 (unweighted)= 44.096 superimposing iter= 4 total_weight= 2047.152 rmsd (weighted)= 0.685 (unweighted)= 44.049 superimposing iter= 5 total_weight= 1553.546 rmsd (weighted)= 0.616 (unweighted)= 44.021 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 1.333 rmsd (weighted)= 7.218 (unweighted)= 42.717 superimposing iter= 1 total_weight= 7715.038 rmsd (weighted)= 2.953 (unweighted)= 42.454 superimposing iter= 2 total_weight= 3360.388 rmsd (weighted)= 1.983 (unweighted)= 42.606 superimposing iter= 3 total_weight= 2378.111 rmsd (weighted)= 1.604 (unweighted)= 42.736 superimposing iter= 4 total_weight= 2097.852 rmsd (weighted)= 1.392 (unweighted)= 42.826 superimposing iter= 5 total_weight= 1905.344 rmsd (weighted)= 1.274 (unweighted)= 42.874 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 1.059 rmsd (weighted)= 7.857 (unweighted)= 46.152 superimposing iter= 1 total_weight= 5381.155 rmsd (weighted)= 3.224 (unweighted)= 47.276 superimposing iter= 2 total_weight= 3780.668 rmsd (weighted)= 1.698 (unweighted)= 47.649 superimposing iter= 3 total_weight= 2772.876 rmsd (weighted)= 1.123 (unweighted)= 47.716 superimposing iter= 4 total_weight= 1803.657 rmsd (weighted)= 0.941 (unweighted)= 47.728 superimposing iter= 5 total_weight= 1435.692 rmsd (weighted)= 0.888 (unweighted)= 47.731 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 0.987 rmsd (weighted)= 6.666 (unweighted)= 36.351 superimposing iter= 1 total_weight= 4924.752 rmsd (weighted)= 2.817 (unweighted)= 36.061 superimposing iter= 2 total_weight= 3493.598 rmsd (weighted)= 1.497 (unweighted)= 35.777 superimposing iter= 3 total_weight= 2644.020 rmsd (weighted)= 0.975 (unweighted)= 35.676 superimposing iter= 4 total_weight= 1732.417 rmsd (weighted)= 0.805 (unweighted)= 35.645 superimposing iter= 5 total_weight= 1339.813 rmsd (weighted)= 0.758 (unweighted)= 35.630 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 1.026 rmsd (weighted)= 7.637 (unweighted)= 24.912 superimposing iter= 1 total_weight= 5312.581 rmsd (weighted)= 3.192 (unweighted)= 26.284 superimposing iter= 2 total_weight= 2637.825 rmsd (weighted)= 2.079 (unweighted)= 26.871 superimposing iter= 3 total_weight= 1872.862 rmsd (weighted)= 1.660 (unweighted)= 27.130 superimposing iter= 4 total_weight= 1612.634 rmsd (weighted)= 1.442 (unweighted)= 27.272 superimposing iter= 5 total_weight= 1564.363 rmsd (weighted)= 1.274 (unweighted)= 27.345 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 1.182 rmsd (weighted)= 13.504 (unweighted)= 28.078 superimposing iter= 1 total_weight= 7623.108 rmsd (weighted)= 5.018 (unweighted)= 28.143 superimposing iter= 2 total_weight= 3854.264 rmsd (weighted)= 2.882 (unweighted)= 28.151 superimposing iter= 3 total_weight= 2601.627 rmsd (weighted)= 2.046 (unweighted)= 28.157 superimposing iter= 4 total_weight= 2246.921 rmsd (weighted)= 1.577 (unweighted)= 28.170 superimposing iter= 5 total_weight= 2044.892 rmsd (weighted)= 1.286 (unweighted)= 28.177 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 1.062 rmsd (weighted)= 14.451 (unweighted)= 29.578 superimposing iter= 1 total_weight= 6710.330 rmsd (weighted)= 4.867 (unweighted)= 29.577 superimposing iter= 2 total_weight= 4459.930 rmsd (weighted)= 2.332 (unweighted)= 29.564 superimposing iter= 3 total_weight= 3084.889 rmsd (weighted)= 1.440 (unweighted)= 29.558 superimposing iter= 4 total_weight= 2063.709 rmsd (weighted)= 1.115 (unweighted)= 29.559 superimposing iter= 5 total_weight= 1591.030 rmsd (weighted)= 0.989 (unweighted)= 29.560 Debug: superimposing conformation 9 on the average so far superimposing iter= 0 total_weight= 1.365 rmsd (weighted)= 8.589 (unweighted)= 33.841 superimposing iter= 1 total_weight= 6414.943 rmsd (weighted)= 4.086 (unweighted)= 33.807 superimposing iter= 2 total_weight= 2781.035 rmsd (weighted)= 3.127 (unweighted)= 33.803 superimposing iter= 3 total_weight= 1951.446 rmsd (weighted)= 2.878 (unweighted)= 33.803 superimposing iter= 4 total_weight= 1791.831 rmsd (weighted)= 2.769 (unweighted)= 33.804 superimposing iter= 5 total_weight= 1742.842 rmsd (weighted)= 2.703 (unweighted)= 33.806 Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.371 rmsd (weighted)= 7.669 (unweighted)= 22.530 superimposing iter= 1 total_weight= 7193.109 rmsd (weighted)= 3.117 (unweighted)= 23.245 superimposing iter= 2 total_weight= 4759.138 rmsd (weighted)= 1.730 (unweighted)= 23.473 superimposing iter= 3 total_weight= 2956.907 rmsd (weighted)= 1.255 (unweighted)= 23.553 superimposing iter= 4 total_weight= 2369.968 rmsd (weighted)= 1.026 (unweighted)= 23.592 superimposing iter= 5 total_weight= 2081.748 rmsd (weighted)= 0.899 (unweighted)= 23.612 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 1.135 rmsd (weighted)= 6.825 (unweighted)= 58.423 superimposing iter= 1 total_weight= 6770.784 rmsd (weighted)= 2.495 (unweighted)= 58.419 superimposing iter= 2 total_weight= 4339.257 rmsd (weighted)= 1.318 (unweighted)= 58.384 superimposing iter= 3 total_weight= 2536.640 rmsd (weighted)= 0.952 (unweighted)= 58.377 superimposing iter= 4 total_weight= 1876.059 rmsd (weighted)= 0.808 (unweighted)= 58.372 superimposing iter= 5 total_weight= 1602.671 rmsd (weighted)= 0.745 (unweighted)= 58.370 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 1.053 rmsd (weighted)= 6.429 (unweighted)= 45.558 superimposing iter= 1 total_weight= 4667.136 rmsd (weighted)= 2.698 (unweighted)= 44.340 superimposing iter= 2 total_weight= 4039.825 rmsd (weighted)= 1.357 (unweighted)= 44.055 superimposing iter= 3 total_weight= 2870.374 rmsd (weighted)= 0.863 (unweighted)= 43.944 superimposing iter= 4 total_weight= 2026.538 rmsd (weighted)= 0.674 (unweighted)= 43.892 superimposing iter= 5 total_weight= 1558.406 rmsd (weighted)= 0.605 (unweighted)= 43.860 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 1.333 rmsd (weighted)= 7.186 (unweighted)= 42.878 superimposing iter= 1 total_weight= 7513.744 rmsd (weighted)= 2.975 (unweighted)= 42.536 superimposing iter= 2 total_weight= 3391.177 rmsd (weighted)= 1.986 (unweighted)= 42.671 superimposing iter= 3 total_weight= 2398.213 rmsd (weighted)= 1.600 (unweighted)= 42.795 superimposing iter= 4 total_weight= 2118.351 rmsd (weighted)= 1.382 (unweighted)= 42.883 superimposing iter= 5 total_weight= 1919.846 rmsd (weighted)= 1.261 (unweighted)= 42.931 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 1.059 rmsd (weighted)= 7.921 (unweighted)= 46.020 superimposing iter= 1 total_weight= 5435.094 rmsd (weighted)= 3.233 (unweighted)= 47.146 superimposing iter= 2 total_weight= 3775.562 rmsd (weighted)= 1.706 (unweighted)= 47.521 superimposing iter= 3 total_weight= 2758.155 rmsd (weighted)= 1.131 (unweighted)= 47.588 superimposing iter= 4 total_weight= 1803.750 rmsd (weighted)= 0.948 (unweighted)= 47.599 superimposing iter= 5 total_weight= 1436.220 rmsd (weighted)= 0.894 (unweighted)= 47.601 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 0.987 rmsd (weighted)= 6.713 (unweighted)= 36.298 superimposing iter= 1 total_weight= 4919.863 rmsd (weighted)= 2.844 (unweighted)= 36.017 superimposing iter= 2 total_weight= 3477.407 rmsd (weighted)= 1.515 (unweighted)= 35.727 superimposing iter= 3 total_weight= 2653.280 rmsd (weighted)= 0.984 (unweighted)= 35.622 superimposing iter= 4 total_weight= 1744.382 rmsd (weighted)= 0.810 (unweighted)= 35.590 superimposing iter= 5 total_weight= 1344.743 rmsd (weighted)= 0.761 (unweighted)= 35.573 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 1.026 rmsd (weighted)= 7.679 (unweighted)= 24.787 superimposing iter= 1 total_weight= 5286.759 rmsd (weighted)= 3.224 (unweighted)= 26.126 superimposing iter= 2 total_weight= 2624.843 rmsd (weighted)= 2.103 (unweighted)= 26.742 superimposing iter= 3 total_weight= 1875.160 rmsd (weighted)= 1.678 (unweighted)= 27.015 superimposing iter= 4 total_weight= 1598.679 rmsd (weighted)= 1.464 (unweighted)= 27.158 superimposing iter= 5 total_weight= 1554.936 rmsd (weighted)= 1.298 (unweighted)= 27.236 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 1.182 rmsd (weighted)= 13.412 (unweighted)= 28.081 superimposing iter= 1 total_weight= 7605.367 rmsd (weighted)= 4.998 (unweighted)= 28.159 superimposing iter= 2 total_weight= 3817.326 rmsd (weighted)= 2.888 (unweighted)= 28.172 superimposing iter= 3 total_weight= 2563.392 rmsd (weighted)= 2.068 (unweighted)= 28.179 superimposing iter= 4 total_weight= 2231.884 rmsd (weighted)= 1.598 (unweighted)= 28.192 superimposing iter= 5 total_weight= 2059.637 rmsd (weighted)= 1.296 (unweighted)= 28.200 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 1.062 rmsd (weighted)= 14.318 (unweighted)= 29.467 superimposing iter= 1 total_weight= 6664.655 rmsd (weighted)= 4.838 (unweighted)= 29.476 superimposing iter= 2 total_weight= 4459.799 rmsd (weighted)= 2.319 (unweighted)= 29.468 superimposing iter= 3 total_weight= 3073.052 rmsd (weighted)= 1.436 (unweighted)= 29.464 superimposing iter= 4 total_weight= 2057.559 rmsd (weighted)= 1.114 (unweighted)= 29.465 superimposing iter= 5 total_weight= 1589.973 rmsd (weighted)= 0.989 (unweighted)= 29.467 Debug: superimposing conformation 9 on the average so far superimposing iter= 0 total_weight= 1.365 rmsd (weighted)= 8.543 (unweighted)= 33.825 superimposing iter= 1 total_weight= 6403.398 rmsd (weighted)= 4.068 (unweighted)= 33.798 superimposing iter= 2 total_weight= 2795.446 rmsd (weighted)= 3.105 (unweighted)= 33.795 superimposing iter= 3 total_weight= 1959.840 rmsd (weighted)= 2.850 (unweighted)= 33.797 superimposing iter= 4 total_weight= 1807.088 rmsd (weighted)= 2.729 (unweighted)= 33.799 superimposing iter= 5 total_weight= 1757.236 rmsd (weighted)= 2.652 (unweighted)= 33.801 superimposing iter= 0 total_weight= 1.371 rmsd (weighted)= 7.668 (unweighted)= 22.519 superimposing iter= 1 total_weight= 7185.136 rmsd (weighted)= 3.120 (unweighted)= 23.235 superimposing iter= 2 total_weight= 4758.296 rmsd (weighted)= 1.732 (unweighted)= 23.465 superimposing iter= 3 total_weight= 2958.073 rmsd (weighted)= 1.256 (unweighted)= 23.545 superimposing iter= 4 total_weight= 2369.130 rmsd (weighted)= 1.027 (unweighted)= 23.584 superimposing iter= 5 total_weight= 2078.505 rmsd (weighted)= 0.901 (unweighted)= 23.605 superimposing iter= 0 total_weight= 1.135 rmsd (weighted)= 6.823 (unweighted)= 58.402 superimposing iter= 1 total_weight= 6763.287 rmsd (weighted)= 2.498 (unweighted)= 58.400 superimposing iter= 2 total_weight= 4337.414 rmsd (weighted)= 1.320 (unweighted)= 58.366 superimposing iter= 3 total_weight= 2537.437 rmsd (weighted)= 0.953 (unweighted)= 58.360 superimposing iter= 4 total_weight= 1878.794 rmsd (weighted)= 0.808 (unweighted)= 58.355 superimposing iter= 5 total_weight= 1606.622 rmsd (weighted)= 0.744 (unweighted)= 58.353 superimposing iter= 0 total_weight= 1.053 rmsd (weighted)= 6.432 (unweighted)= 45.548 superimposing iter= 1 total_weight= 4671.005 rmsd (weighted)= 2.699 (unweighted)= 44.332 superimposing iter= 2 total_weight= 4042.117 rmsd (weighted)= 1.356 (unweighted)= 44.047 superimposing iter= 3 total_weight= 2872.909 rmsd (weighted)= 0.863 (unweighted)= 43.935 superimposing iter= 4 total_weight= 2026.186 rmsd (weighted)= 0.673 (unweighted)= 43.882 superimposing iter= 5 total_weight= 1559.411 rmsd (weighted)= 0.605 (unweighted)= 43.849 superimposing iter= 0 total_weight= 1.333 rmsd (weighted)= 7.180 (unweighted)= 42.905 superimposing iter= 1 total_weight= 7492.417 rmsd (weighted)= 2.977 (unweighted)= 42.557 superimposing iter= 2 total_weight= 3393.084 rmsd (weighted)= 1.986 (unweighted)= 42.689 superimposing iter= 3 total_weight= 2401.541 rmsd (weighted)= 1.599 (unweighted)= 42.813 superimposing iter= 4 total_weight= 2119.733 rmsd (weighted)= 1.381 (unweighted)= 42.899 superimposing iter= 5 total_weight= 1917.680 rmsd (weighted)= 1.260 (unweighted)= 42.947 superimposing iter= 0 total_weight= 1.059 rmsd (weighted)= 7.928 (unweighted)= 46.009 superimposing iter= 1 total_weight= 5439.629 rmsd (weighted)= 3.235 (unweighted)= 47.135 superimposing iter= 2 total_weight= 3776.902 rmsd (weighted)= 1.706 (unweighted)= 47.511 superimposing iter= 3 total_weight= 2757.780 rmsd (weighted)= 1.132 (unweighted)= 47.579 superimposing iter= 4 total_weight= 1803.576 rmsd (weighted)= 0.949 (unweighted)= 47.590 superimposing iter= 5 total_weight= 1435.761 rmsd (weighted)= 0.895 (unweighted)= 47.591 superimposing iter= 0 total_weight= 0.987 rmsd (weighted)= 6.717 (unweighted)= 36.310 superimposing iter= 1 total_weight= 4917.405 rmsd (weighted)= 2.847 (unweighted)= 36.031 superimposing iter= 2 total_weight= 3475.539 rmsd (weighted)= 1.517 (unweighted)= 35.741 superimposing iter= 3 total_weight= 2654.947 rmsd (weighted)= 0.985 (unweighted)= 35.636 superimposing iter= 4 total_weight= 1746.941 rmsd (weighted)= 0.810 (unweighted)= 35.604 superimposing iter= 5 total_weight= 1345.305 rmsd (weighted)= 0.761 (unweighted)= 35.587 superimposing iter= 0 total_weight= 1.026 rmsd (weighted)= 7.681 (unweighted)= 24.773 superimposing iter= 1 total_weight= 5283.723 rmsd (weighted)= 3.227 (unweighted)= 26.108 superimposing iter= 2 total_weight= 2622.480 rmsd (weighted)= 2.105 (unweighted)= 26.727 superimposing iter= 3 total_weight= 1875.264 rmsd (weighted)= 1.680 (unweighted)= 27.001 superimposing iter= 4 total_weight= 1597.840 rmsd (weighted)= 1.466 (unweighted)= 27.145 superimposing iter= 5 total_weight= 1554.493 rmsd (weighted)= 1.300 (unweighted)= 27.223 superimposing iter= 0 total_weight= 1.182 rmsd (weighted)= 13.405 (unweighted)= 28.086 superimposing iter= 1 total_weight= 7597.483 rmsd (weighted)= 5.001 (unweighted)= 28.165 superimposing iter= 2 total_weight= 3802.953 rmsd (weighted)= 2.897 (unweighted)= 28.179 superimposing iter= 3 total_weight= 2553.564 rmsd (weighted)= 2.078 (unweighted)= 28.186 superimposing iter= 4 total_weight= 2228.878 rmsd (weighted)= 1.607 (unweighted)= 28.201 superimposing iter= 5 total_weight= 2065.285 rmsd (weighted)= 1.301 (unweighted)= 28.209 superimposing iter= 0 total_weight= 1.062 rmsd (weighted)= 14.306 (unweighted)= 29.459 superimposing iter= 1 total_weight= 6658.062 rmsd (weighted)= 4.837 (unweighted)= 29.468 superimposing iter= 2 total_weight= 4459.018 rmsd (weighted)= 2.319 (unweighted)= 29.460 superimposing iter= 3 total_weight= 3072.039 rmsd (weighted)= 1.436 (unweighted)= 29.456 superimposing iter= 4 total_weight= 2057.293 rmsd (weighted)= 1.114 (unweighted)= 29.457 superimposing iter= 5 total_weight= 1589.516 rmsd (weighted)= 0.989 (unweighted)= 29.459 superimposing iter= 0 total_weight= 1.365 rmsd (weighted)= 8.534 (unweighted)= 33.826 superimposing iter= 1 total_weight= 6401.457 rmsd (weighted)= 4.065 (unweighted)= 33.798 superimposing iter= 2 total_weight= 2798.035 rmsd (weighted)= 3.100 (unweighted)= 33.795 superimposing iter= 3 total_weight= 1961.051 rmsd (weighted)= 2.845 (unweighted)= 33.796 superimposing iter= 4 total_weight= 1808.571 rmsd (weighted)= 2.723 (unweighted)= 33.798 superimposing iter= 5 total_weight= 1758.535 rmsd (weighted)= 2.645 (unweighted)= 33.800 # command:# Printing sheets for alignments to T0470.undertaker-align.sheets # command: