# command:# Seed set to 1273685656 # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/ # command:# reading dunbrack-2191.atoms # #computed average backbone with maximum peptide_sq_deviance = 0.002 # computed average trans backbone unit from 53157 examples # computed average trans backbone unit before proline from 2010 examples # computed average cis backbone unit from 97 examples # trans (non-proline) backbone unit: # CA= -2.2087 1.0126 -0.0030 # O= -0.1499 2.2440 0.0016 # C= -0.6889 1.1368 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4581 0.0000 0.0000 # cis backbone unit: # CA= -0.1436 2.4534 -0.0002 # O= -2.0284 0.9742 0.0015 # C= -0.8018 1.0771 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4668 0.0000 0.0000 # trans backbone unit before proline: # CA= -2.2100 1.0631 -0.0014 # O= -0.1236 2.2458 0.0075 # C= -0.6872 1.1517 -0.0000 # N+1= 0.0000 0.0000 0.0000 # CA+1= 1.4660 0.0000 0.0000 # After reading dunbrack-2191.atoms have 2191 chains in training database # Count of chains,residues,atoms: 2191,500310,3902258 # 493441 residues have no bad marker # 3226 residues lack atoms needed to compute omega # 1453 residues have cis peptide # number of each bad type: # NON_STANDARD_RESIDUE 4 # HAS_OXT 1167 # TOO_MANY_ATOMS 1 # TOO_FEW_ATOMS 3052 # HAS_UNKNOWN_ATOMS 9 # HAS_DUPLICATE_ATOMS 0 # CHAIN_BREAK_BEFORE 979 # NON_PLANAR_PEPTIDE 55 # BAD_PEPTIDE 2680 # HIGH_B_FACTOR 0 # Note: may sum to more than number of residues, # because one residue may have multiple problems # command:# Reading rotamer library from dunbrack-2191.rot # command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/ # command:# ReadAtomType exp-pdb.types Read AtomType exp-pdb with 49 types. # command:# ReadClashTable exp-pdb-2191-2symm.clash # Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2 # command:# command:CPU_time= 23.803 sec, elapsed time= 25.170 sec. # command:# Making generic fragment library # fragment library contains # type length num_fragments num_indexes_used # n-terminus 1 1963 20 (100.000%) # n-terminus 2 1934 333 (83.250%) # middle 1 483679 20 (100.000%) # middle 2 477517 400 (100.000%) # middle 3 471578 7988 (99.850%) # middle 4 465793 120683 (75.427%) # c-terminus 1 1917 20 (100.000%) # c-terminus 2 1889 372 (93.000%) # ss-bonds 1052 # command:CPU_time= 36.576 sec, elapsed time= 41.464 sec. # command:# Prefix for input files set to # command:# Making conformation for sequence T0532 numbered 1 through 506 Created new target T0532 from T0532.a2m # command:# command:# No conformations to remove in PopConform # command:CPU_time= 36.578 sec, elapsed time= 41.694 sec. # command:# Prefix for input files set to # command:# reading script from file T0532.undertaker-align.under # Reading fragments from alignment file # Attempting to read fragment alignments from file 3cghA/T0532-3cghA-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 3cghA expands to /projects/compbio/data/pdb/3cgh.pdb.gz 3cghA:Skipped atom 107, because occupancy 0.5 <= existing 0.500 in 3cghA Skipped atom 111, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 113, because occupancy 0.500 <= existing 0.500 in 3cghA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 623, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 627, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 629, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 792, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 796, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 798, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 800, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 802, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 804, because occupancy 0.500 <= existing 0.500 in 3cghA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1250, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 1254, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 1256, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 1258, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 1260, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 1262, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 1361, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 1365, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 1367, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 1369, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 1371, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 1605, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 1609, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 1611, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 1613, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 1615, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 1617, because occupancy 0.500 <= existing 0.500 in 3cghA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1723, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 1727, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 1729, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 1942, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 1944, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 1946, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 1948, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 1950, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 1952, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 1954, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 2002, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 2006, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 2008, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 2010, because occupancy 0.500 <= existing 0.500 in 3cghA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 2163, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 2167, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 2169, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 2171, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 2334, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 2336, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 2338, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 2340, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 2342, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 2344, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 2346, because occupancy 0.500 <= existing 0.500 in 3cghA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 2714, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 2718, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 2720, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 2722, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 2724, because occupancy 0.500 <= existing 0.500 in 3cghA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 2772, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 2776, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 2778, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 2780, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 2782, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 2784, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 2970, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 2974, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 2976, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 2978, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 2980, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 3231, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 3235, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 3237, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 3539, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 3543, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 3545, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 3547, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 3549, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 3551, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 3569, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 3571, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 3573, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 3575, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 3577, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 3579, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 3581, because occupancy 0.500 <= existing 0.500 in 3cghA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 4022, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 4026, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 4028, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 4030, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 4032, because occupancy 0.500 <= existing 0.500 in 3cghA Skipped atom 4034, because occupancy 0.500 <= existing 0.500 in 3cghA # T0532 read from 3cghA/T0532-3cghA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3cghA read from 3cghA/T0532-3cghA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3cghA to template set # found chain 3cghA in template set Warning: unaligning (T0532)T34 because of BadResidue code BAD_PEPTIDE in next template residue (3cghA)G41 Warning: unaligning (T0532)K35 because of BadResidue code BAD_PEPTIDE at template residue (3cghA)G41 Warning: unaligning (T0532)G88 because of BadResidue code BAD_PEPTIDE in next template residue (3cghA)V101 Warning: unaligning (T0532)G89 because of BadResidue code BAD_PEPTIDE at template residue (3cghA)V101 Warning: unaligning (T0532)L133 because of BadResidue code BAD_PEPTIDE in next template residue (3cghA)P154 Warning: unaligning (T0532)P134 because of BadResidue code BAD_PEPTIDE at template residue (3cghA)P154 Warning: unaligning (T0532)Y150 because of BadResidue code BAD_PEPTIDE in next template residue (3cghA)D169 Warning: unaligning (T0532)N151 because of BadResidue code BAD_PEPTIDE at template residue (3cghA)D169 Warning: unaligning (T0532)K317 because of BadResidue code BAD_PEPTIDE in next template residue (3cghA)V335 Warning: unaligning (T0532)A318 because of BadResidue code BAD_PEPTIDE at template residue (3cghA)V335 T0532 29 :DPDAT 3cghA 35 :PDLSA # choosing archetypes in rotamer library T0532 36 :VTSSLLATGLLLDITSSSASKSFIYDELLAKQM 3cghA 42 :YALGSAMNNLAGCVVSPDVNTAQFTDCLLGGPL T0532 69 :AWGESMEDYQYNVFGRSGF 3cghA 81 :SNAGFTETISNFNPKDDWS T0532 90 :Y 3cghA 102 :F T0532 91 :TTLINAQKMVESV 3cghA 107 :KIIPTLYSNLTQV T0532 104 :SDDNVNAYDGLAHFIKAYKIFYMSMEMGD 3cghA 124 :QNTNDPVPYAIAQVIKVAAMHRVTDAFGP T0532 135 :YEEALQG 3cghA 155 :YSQIGAN T0532 144 :GLVRPK 3cghA 162 :GEIATP T0532 152 :TQKEVMNFILSDLETAYELFSTA 3cghA 170 :SQEVTYNTFFDELNAAIATLNEN T0532 175 :KDFDGDPILGGSISKWKKATTAFQLKVLMHLSKKESDADLKVKERFAR 3cghA 197 :LVPTADYIYKGDVKKWIRFANSLKLRLAIRIAYANPVKAQQMAEEAVN T0532 224 :VASGSLMESNEDNLQMKYADKANTVYPF 3cghA 245 :PANGGVIESNADNATWNYFETSQNPIYV T0532 252 :HNTNTKHAGYAMLSTMLIDKFKATGDIRMFYYAKPAKAK 3cghA 285 :GGVPCLTGGDTHAAADIICYMNGYKDNRREKFFTKSEWA T0532 307 :DPSLPFEQIE 3cghA 324 :GQDYVGMRRG T0532 319 :YATEQYSGFNARYTDYPSGEPVVRLGYAEQNFILAEAAVRGWIS 3cghA 336 :IPELKTTGHKYSGVNIAPTSPLYWMNAAEVAFLRAEGQAVFNFS T0532 363 :GDASAYYKKAIRAHMEFIASNTPDEEV 3cghA 382 :GTAESFYNQGIRLSFEQWGADGVEDYL T0532 390 :YHHGHPITEEAIAAFLETPAIQLSGEKEADIEKILTQRYLASFM 3cghA 418 :YTDPAGTNTYQNALSNITIKWNDSADKEEKQERIIVQKWIANWQ T0532 435 :HPYDVYYDYRRTGYPVLPINPAT 3cghA 462 :LGNEAWADFRRTGYPKLIPVKEN T0532 458 :NRNTMNDRLPMRWMYPKSESDYNLEHQNEALERQFGGVDDVNKLMWI 3cghA 487 :GGVVDSEKGARRMPYPLDEFVSNKANVEYAIANYLHGADNMATDVWW Number of specific fragments extracted= 18 number of extra gaps= 5 total=18 # request to SCWRL produces command: ulimit -t 456 ; scwrl4 -t -i /var/tmp/to_scwrl_925219575.pdb -s /var/tmp/to_scwrl_925219575.seq -o /var/tmp/from_scwrl_925219575.pdb > /var/tmp/scwrl_925219575.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_925219575.pdb Number of alignments=1 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3gzsA/T0532-3gzsA-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 3gzsA expands to /projects/compbio/data/pdb/3gzs.pdb.gz 3gzsA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 910, because occupancy 0.500 <= existing 0.500 in 3gzsA Skipped atom 914, because occupancy 0.500 <= existing 0.500 in 3gzsA Skipped atom 916, because occupancy 0.500 <= existing 0.500 in 3gzsA Skipped atom 918, because occupancy 0.500 <= existing 0.500 in 3gzsA Skipped atom 920, because occupancy 0.500 <= existing 0.500 in 3gzsA Skipped atom 922, because occupancy 0.500 <= existing 0.500 in 3gzsA Skipped atom 924, because occupancy 0.500 <= existing 0.500 in 3gzsA Skipped atom 926, because occupancy 0.500 <= existing 0.500 in 3gzsA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: OD3 for alphabet: pdb_atoms Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 3710, because occupancy 0.500 <= existing 0.500 in 3gzsA Skipped atom 3714, because occupancy 0.500 <= existing 0.500 in 3gzsA Skipped atom 3716, because occupancy 0.500 <= existing 0.500 in 3gzsA # T0532 read from 3gzsA/T0532-3gzsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3gzsA read from 3gzsA/T0532-3gzsA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3gzsA to template set # found chain 3gzsA in template set Warning: unaligning (T0532)Q348 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3gzsA)F365 Warning: unaligning (T0532)F350 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3gzsA)F365 T0532 36 :VTSSLLATGLLLDITSSSASKSFIYDELLAKQM 3gzsA 49 :VIYGAYLPNLEKSVIPIGTASESTEPVNRYQIG T0532 69 :AWGESMEDYQYNVFGRSGFGGY 3gzsA 103 :SKNFTNYFMYENWVNYVYSFMV T0532 91 :TTLINAQKMVESV 3gzsA 126 :DVYSPWMQIKRIS T0532 104 :SDDNVNAYDGLAHFIKAYKIFYMSMEMGDLPYEEALQG 3gzsA 141 :EGTRNDEIYALAQIIKIAALHRTTDMFGPIPYSQVGKG T0532 145 :LVRPKYNTQKEVMNFILSDLETAYELFS 3gzsA 179 :SFKVAYDSQESVYRSFLKELEEAVQTLD T0532 175 :KDFDGDPILGGSISKWKKATTAFQLKVLMHLSKKESDADLKVKERFAR 3gzsA 215 :VLPAFDIVYNGDVNKWMRFANSLMLRLAIRVRFADAGLAKEYAEKAVK T0532 225 :ASGSLMESNEDNLQMKYADKANTVYPF 3gzsA 263 :HPAGLINSKELAAQMGKGAGLQMKNPL T0532 253 :NTNTKHAGYAMLSTMLIDKFKATGDIRMFYYAKPAKAK 3gzsA 290 :KVINEEYNDTRMGATIYSYLAGYNDARAAVYFVKNNGF T0532 313 :EQIEKAYATEQYSGFNARYTDYPSGEPVVRLGYAE 3gzsA 328 :KAVRCGIAKSGDAYNGFTRPNVHEDDPLYWMKASE T0532 351 :ILAEAAVRGWIS 3gzsA 366 :LKAEGALAGFDM T0532 363 :GDASAYYKKAIRAHMEFIASNTPDEEV 3gzsA 379 :GSAGDFYNAGIRMSFSENGLDNSSAET T0532 390 :YHHGHPITEEAIAAFLETPAIQLSGEKEADIEKILTQRYLASFM 3gzsA 417 :YTDTSNGELSANAPSSITIRWENGATEEEKLERIITQKYLAIFP T0532 435 :HPYDVYYDYRRTGYPVLPINPAT 3gzsA 461 :NGQEAWTEWRRTGYPRQIVVAEN T0532 458 :NRNTMNDRLPMRWMYPKSESDYNLEHQNEALERQFGGVDDVNKLMWI 3gzsA 491 :IGNGYDLGGVRRLPYPRTEYEQNGENLHNAISQYLGGVDNAATKVWW Number of specific fragments extracted= 14 number of extra gaps= 0 total=32 # request to SCWRL produces command: ulimit -t 456 ; scwrl4 -t -i /var/tmp/to_scwrl_601015519.pdb -s /var/tmp/to_scwrl_601015519.seq -o /var/tmp/from_scwrl_601015519.pdb > /var/tmp/scwrl_601015519.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_601015519.pdb Number of alignments=2 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3ehmA/T0532-3ehmA-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 3ehmA expands to /projects/compbio/data/pdb/3ehm.pdb.gz 3ehmA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0532 read from 3ehmA/T0532-3ehmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ehmA read from 3ehmA/T0532-3ehmA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3ehmA to template set # found chain 3ehmA in template set T0532 36 :VTSSLLATGLLLDITSSSASKSFIYDELLAKQM 3ehmA 21 :LKYGARFMNMQQRVIPIGSPSLTTGPGNDLQNT T0532 69 :AWGESMEDYQYNVFGRSGFGGY 3ehmA 69 :NNWGFNNEANWNFTDSRMNYAY T0532 91 :TTLINAQKMVESV 3ehmA 96 :QIFLPWNEIYEIA T0532 104 :SDDNVNAYDGLAHFIKAYKIFYMSMEMGDLPYEEALQG 3ehmA 112 :DSPSEQAILEIANIVRNIAWLRATDVFGPIAYNSAGDG T0532 145 :LVRPKYNTQKEVMNFILSDLETAYELFSTA 3ehmA 150 :SIAPKFDSQEVVYRSMLADLSKSVELLNTI T0532 175 :KDFDGDPILGGSISKWKKATTAFQLKVLMHLSKKESDADLKVKERFAR 3ehmA 183 :VMAQYDLIYNGNVQNWVKLANSLMLRIVVRVHFIDETLAKEYITKALD T0532 224 :VASGSLMESNEDNLQMKYADKANTVYPF 3ehmA 231 :PKNGGVIEDISSEAKIKSSDKMPLLNSM T0532 253 :NTNTKHAGYAMLSTMLIDKFKATGDIRMFYYAKPAKAKLNEGVTADSWDAYIGTDPSLPFE 3ehmA 259 :LASVNEYNETRMGATIWGYLDGYKDPRLSAYFTEGTYGSGSWAQTGYFPVAPTNSKSKSET T0532 323 :QYSGFNARYTDYPSGEPVVRLGYAEQNFILAEAAVRGWISGDASAYYKKAIRAHMEFIASNTPDEEV 3ehmA 320 :SYSAKFASRPKVDSNSPLYWFRASETYFLKAEAALYNLIGGDPKTFYEQGINISFQEQGVSGVATYL T0532 406 :ETPAIQLSGEKEADIEKILTQRYLASFM 3ehmA 418 :WDDYTGNLSKQEEQLQKIITQKYLALYP T0532 435 :HPYDVYYDYRRTGYPVLPINPAT 3ehmA 446 :NAVEAWTEYRRTGFPYLMKPMDE T0532 458 :NRNTMNDRLPMRWMYPKSESDYNL 3ehmA 475 :GASIEDCRVPERFRFAPTAYNSNP T0532 488 :LERQFGGVDDVNKLMWI 3ehmA 503 :IPTLLGGGDIGATKLWW Number of specific fragments extracted= 13 number of extra gaps= 0 total=45 # request to SCWRL produces command: ulimit -t 456 ; scwrl4 -t -i /var/tmp/to_scwrl_833429440.pdb -s /var/tmp/to_scwrl_833429440.seq -o /var/tmp/from_scwrl_833429440.pdb > /var/tmp/scwrl_833429440.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_833429440.pdb Number of alignments=3 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3kezA/T0532-3kezA-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 3kezA expands to /projects/compbio/data/pdb/3kez.pdb.gz 3kezA:Skipped atom 142, because occupancy 0.500 <= existing 0.500 in 3kezA Skipped atom 146, because occupancy 0.500 <= existing 0.500 in 3kezA Skipped atom 148, because occupancy 0.500 <= existing 0.500 in 3kezA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 553, because occupancy 0.500 <= existing 0.500 in 3kezA Skipped atom 557, because occupancy 0.500 <= existing 0.500 in 3kezA Skipped atom 559, because occupancy 0.500 <= existing 0.500 in 3kezA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1666, because occupancy 0.500 <= existing 0.500 in 3kezA Skipped atom 1670, because occupancy 0.500 <= existing 0.500 in 3kezA Skipped atom 1672, because occupancy 0.500 <= existing 0.500 in 3kezA Skipped atom 1674, because occupancy 0.500 <= existing 0.500 in 3kezA Skipped atom 1676, because occupancy 0.500 <= existing 0.500 in 3kezA Skipped atom 1678, because occupancy 0.500 <= existing 0.500 in 3kezA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 2323, because occupancy 0.500 <= existing 0.500 in 3kezA Skipped atom 2327, because occupancy 0.500 <= existing 0.500 in 3kezA Skipped atom 2329, because occupancy 0.500 <= existing 0.500 in 3kezA Skipped atom 2831, because occupancy 0.500 <= existing 0.500 in 3kezA Skipped atom 2835, because occupancy 0.500 <= existing 0.500 in 3kezA Skipped atom 2837, because occupancy 0.500 <= existing 0.500 in 3kezA Skipped atom 2839, because occupancy 0.500 <= existing 0.500 in 3kezA Skipped atom 2841, because occupancy 0.500 <= existing 0.500 in 3kezA Skipped atom 2843, because occupancy 0.500 <= existing 0.500 in 3kezA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 3170, because occupancy 0.500 <= existing 0.500 in 3kezA Skipped atom 3174, because occupancy 0.500 <= existing 0.500 in 3kezA Skipped atom 3176, because occupancy 0.500 <= existing 0.500 in 3kezA Skipped atom 3178, because occupancy 0.500 <= existing 0.500 in 3kezA Skipped atom 3180, because occupancy 0.500 <= existing 0.500 in 3kezA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M # T0532 read from 3kezA/T0532-3kezA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3kezA read from 3kezA/T0532-3kezA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3kezA to template set # found chain 3kezA in template set Warning: unaligning (T0532)D29 because first residue in template chain is (3kezA)E35 Warning: unaligning (T0532)G260 because of BadResidue code BAD_PEPTIDE in next template residue (3kezA)D304 Warning: unaligning (T0532)Y261 because of BadResidue code BAD_PEPTIDE at template residue (3kezA)D304 Warning: unaligning (T0532)Y437 because of BadResidue code BAD_PEPTIDE in next template residue (3kezA)R419 Warning: unaligning (T0532)V439 because of BadResidue code BAD_PEPTIDE at template residue (3kezA)R419 T0532 30 :PDATTKVTSSLLATGLLLDIT 3kezA 36 :TSINVLSDIEFTLNGIYSTMQ T0532 51 :SSSASKSFIYDELLAKQMAWGESMEDYQY 3kezA 59 :DAYSGRLVYYGDVTGDDMQAVSSTKRTGN T0532 80 :NVFGRSGFGG 3kezA 96 :DNGPSSHWSY T0532 90 :YTTLINAQKMVESV 3kezA 107 :YSIIQNCNLILMNV T0532 104 :SDDN 3kezA 126 :DEDE T0532 108 :VNAYDGLAHFIKAYKIFYMSMEMG 3kezA 133 :KNDLKGQALAIRGMALFDLTRIFG T0532 132 :DLPYEEALQG 3kezA 168 :GVPIVKELST T0532 144 :GLVRPKYNTQKEVMNFILSDLETAYELFSTAKD 3kezA 178 :IDSKPARNTVAECYTEIISDLKNSTELLSGDFN T0532 184 :GGSISK 3kezA 211 :KGKVNR T0532 192 :KATTAFQLKVLMHLSKKES 3kezA 217 :WAAMTLLSRVYLYKGEYNE T0532 216 :VKERFARIVA 3kezA 236 :ALTMAENAIK T0532 226 :SG 3kezA 250 :EG T0532 228 :SLM 3kezA 253 :ALW T0532 231 :ESNEDNL 3kezA 258 :EEYPTAW T0532 238 :QMKYADKANTVYPFHNTNTKHA 3kezA 281 :VNLTTDSPGKESMGYLNSYNGY T0532 262 :AMLSTMLIDKFKATG 3kezA 305 :MCITCSFYQLLKKDP T0532 277 :DIRMFYYAKPAK 3kezA 321 :DVRLKILSFDKK T0532 317 :KAYATEQYSGFNAR 3kezA 333 :YYAYVNKYQPQQGE T0532 334 :YPSGEPVVRLGYAEQNFILAEAAVRGWISGDASAYYKK 3kezA 347 :NITDANIPLIRLSEAYLNAAEAAVQTGDNAKAVKYLNS T0532 373 :IRAHMEFIASNTPD 3kezA 385 :IVQRANPENSVEGK T0532 413 :SGE 3kezA 399 :TLT T0532 420 :IEKILTQRYLASF 3kezA 402 :LENVLDERRKELV T0532 434 :QHP 3kezA 415 :AEG T0532 440 :YYDYRRTGYPVLP 3kezA 420 :MYDVIRNGMTVKR T0532 453 :INPATNRNTMNDRLPMRWMYPKSESDYNLEHQNEALE 3kezA 444 :KHNTAYMEYDWNFHKILLPIPKKEMDANPNMKQNPGY Number of specific fragments extracted= 25 number of extra gaps= 2 total=70 # request to SCWRL produces command: ulimit -t 456 ; scwrl4 -t -i /var/tmp/to_scwrl_2002418584.pdb -s /var/tmp/to_scwrl_2002418584.seq -o /var/tmp/from_scwrl_2002418584.pdb > /var/tmp/scwrl_2002418584.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_2002418584.pdb Number of alignments=4 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3i4gA/T0532-3i4gA-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 3i4gA expands to /projects/compbio/data/pdb/3i4g.pdb.gz 3i4gA:Skipped atom 62, because occupancy 0.250 <= existing 0.250 in 3i4gA Skipped atom 65, because occupancy 0.250 <= existing 0.250 in 3i4gA Skipped atom 68, because occupancy 0.250 <= existing 0.250 in 3i4gA Skipped atom 71, because occupancy 0.250 <= existing 0.250 in 3i4gA Skipped atom 74, because occupancy 0.250 <= existing 0.250 in 3i4gA Skipped atom 77, because occupancy 0.250 <= existing 0.250 in 3i4gA Skipped atom 93, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 95, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 97, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 99, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 101, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 103, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 105, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 107, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 109, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 139, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 141, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 143, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 145, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 147, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 149, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 203, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 205, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 207, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 209, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 211, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 213, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 215, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 217, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 272, because occupancy 0.300 <= existing 0.700 in 3i4gA Skipped atom 274, because occupancy 0.300 <= existing 0.700 in 3i4gA Skipped atom 276, because occupancy 0.300 <= existing 0.700 in 3i4gA Skipped atom 278, because occupancy 0.300 <= existing 0.700 in 3i4gA Skipped atom 280, because occupancy 0.300 <= existing 0.700 in 3i4gA Skipped atom 282, because occupancy 0.300 <= existing 0.700 in 3i4gA Skipped atom 284, because occupancy 0.300 <= existing 0.700 in 3i4gA Skipped atom 286, because occupancy 0.300 <= existing 0.700 in 3i4gA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 488, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 490, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 492, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 494, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 496, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 498, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 500, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 502, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 651, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 653, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 655, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 657, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 659, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 661, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 663, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 665, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 667, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 669, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 671, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 699, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 701, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 703, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 705, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 707, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 709, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 711, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 713, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 715, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 799, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 801, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 803, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 805, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 807, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 809, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 811, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 813, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 834, because occupancy 0.300 <= existing 0.700 in 3i4gA Skipped atom 836, because occupancy 0.300 <= existing 0.700 in 3i4gA Skipped atom 838, because occupancy 0.300 <= existing 0.700 in 3i4gA Skipped atom 840, because occupancy 0.300 <= existing 0.700 in 3i4gA Skipped atom 842, because occupancy 0.300 <= existing 0.700 in 3i4gA Skipped atom 844, because occupancy 0.300 <= existing 0.700 in 3i4gA Skipped atom 846, because occupancy 0.300 <= existing 0.700 in 3i4gA Skipped atom 877, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 879, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 881, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 883, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 885, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 887, because occupancy 0.500 <= existing 0.500 in 3i4gA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1223, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 1225, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 1227, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 1229, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 1231, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 1233, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 1235, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 1237, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 1239, because occupancy 0.500 <= existing 0.500 in 3i4gA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1632, because occupancy 0.500 <= existing 0.500 in 3i4gA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1634, because occupancy 0.500 <= existing 0.500 in 3i4gA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1636, because occupancy 0.500 <= existing 0.500 in 3i4gA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1638, because occupancy 0.500 <= existing 0.500 in 3i4gA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1640, because occupancy 0.500 <= existing 0.500 in 3i4gA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1642, because occupancy 0.500 <= existing 0.500 in 3i4gA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1644, because occupancy 0.370 <= existing 0.380 in 3i4gA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1646, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 1665, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 1667, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 1669, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 1671, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 1673, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 1675, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 1677, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 1679, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 1681, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 1754, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 1756, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 1758, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 1760, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 1762, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 1764, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 1766, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 1768, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 1770, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 1772, because occupancy 0.500 <= existing 0.500 in 3i4gA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1798, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 1800, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 1802, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 1804, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 1806, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 1808, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 1810, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 1812, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 1814, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 1946, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 1948, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 1950, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 1952, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 1954, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 1956, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 1976, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 1978, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 1980, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 1982, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 1984, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 1986, because occupancy 0.500 <= existing 0.500 in 3i4gA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 2708, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 2710, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 2712, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 2714, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 2716, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 2718, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 2720, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 2722, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 2724, because occupancy 0.500 <= existing 0.500 in 3i4gA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 2783, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 2785, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 2787, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 2789, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 2791, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 2793, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 2795, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 2797, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 2799, because occupancy 0.500 <= existing 0.500 in 3i4gA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 2999, because occupancy 0.300 <= existing 0.700 in 3i4gA Skipped atom 3001, because occupancy 0.300 <= existing 0.700 in 3i4gA Skipped atom 3003, because occupancy 0.300 <= existing 0.700 in 3i4gA Skipped atom 3005, because occupancy 0.300 <= existing 0.700 in 3i4gA Skipped atom 3007, because occupancy 0.300 <= existing 0.700 in 3i4gA Skipped atom 3009, because occupancy 0.300 <= existing 0.700 in 3i4gA Skipped atom 3056, because occupancy 0.300 <= existing 0.700 in 3i4gA Skipped atom 3058, because occupancy 0.300 <= existing 0.700 in 3i4gA Skipped atom 3060, because occupancy 0.300 <= existing 0.700 in 3i4gA Skipped atom 3062, because occupancy 0.300 <= existing 0.700 in 3i4gA Skipped atom 3064, because occupancy 0.300 <= existing 0.700 in 3i4gA Skipped atom 3066, because occupancy 0.300 <= existing 0.700 in 3i4gA Skipped atom 3068, because occupancy 0.300 <= existing 0.700 in 3i4gA Skipped atom 3070, because occupancy 0.300 <= existing 0.700 in 3i4gA Skipped atom 3072, because occupancy 0.300 <= existing 0.700 in 3i4gA Skipped atom 3265, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 3267, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 3269, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 3271, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 3273, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 3275, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 3277, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 3279, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 3281, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 3283, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 3285, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 3287, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 3289, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 3291, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 3293, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 3295, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 3297, because occupancy 0.500 <= existing 0.500 in 3i4gA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 4267, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 4269, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 4271, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 4273, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 4275, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 4277, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 4279, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 4281, because occupancy 0.500 <= existing 0.500 in 3i4gA Skipped atom 4291, because occupancy 0.300 <= existing 0.700 in 3i4gA Skipped atom 4293, because occupancy 0.300 <= existing 0.700 in 3i4gA Skipped atom 4295, because occupancy 0.300 <= existing 0.700 in 3i4gA Skipped atom 4297, because occupancy 0.300 <= existing 0.700 in 3i4gA Skipped atom 4299, because occupancy 0.300 <= existing 0.700 in 3i4gA Skipped atom 4301, because occupancy 0.300 <= existing 0.700 in 3i4gA Skipped atom 4303, because occupancy 0.300 <= existing 0.700 in 3i4gA # T0532 read from 3i4gA/T0532-3i4gA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3i4gA read from 3i4gA/T0532-3i4gA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3i4gA to template set # found chain 3i4gA in template set Warning: unaligning (T0532)D29 because first residue in template chain is (3i4gA)E33 Warning: unaligning (T0532)Q484 because last residue in template chain is (3i4gA)R545 T0532 30 :PDATTKVTSSLLATGLLL 3i4gA 34 :TFWNSESNAELALTSLYR T0532 48 :DIT 3i4gA 53 :SLT T0532 51 :SSSASKSFIYDELLAKQMAWGESMEDYQY 3i4gA 64 :DWWSYHGMIMMEHLSDNAFDRRGENNPFF T0532 80 :NVFGRSGFGG 3i4gA 103 :NAFIKRYWET T0532 90 :YTTLINAQKMVESV 3i4gA 114 :YKRIGYCNRFLVGI T0532 104 :SDDNVNAYDGLAHFIKAYKIFYMSMEMGDLPYEEALQGELGLVRPKYNTQKEVMNFILSDLETAYELFSTAKDFDGDP 3i4gA 132 :ESEKKTRMIAEARFLRATQYFYLASYFKNVPLVENVLTGEEANNVTKTSQADILKWCVTEFTAAAADLPRFSAIPAGE T0532 184 :GGSISK 3i4gA 210 :AGRACK T0532 192 :KATTAFQLKVLMHLSKKES 3i4gA 216 :QAALAFLGRTCMLQKDWKS T0532 216 :VKERFARIVASG 3i4gA 235 :GAKAFHDIMELG T0532 228 :SLMESNEDNL 3i4gA 249 :AINANYQELF T0532 238 :QMKYADKANTVYPFHNTNTKHAGYAMLSTMLIDKFKATG 3i4gA 275 :YLENYLGTGLPQHALSAKDGGWSLVNPAADLYESYEFKD T0532 277 :DIRMFYYAKPAKAKLNEGVTADSW 3i4gA 334 :DPRLDYTIYYNGAIFMGTEYKMSP T0532 301 :DAYIGTDPSL 3i4gA 364 :KEKLDYTSEA T0532 315 :IEKAYATEQYSGFNARYTDYPSGEP 3i4gA 374 :SRTGFMMRKYFEESTPINDVQSANG T0532 340 :VVRLGYAEQNFILAEAAVRGW 3i4gA 400 :TPVIRYAEVLLGYLECLVEDN T0532 361 :ISGDASAYYKK 3i4gA 424 :TQGILDETINA T0532 373 :IRAH 3i4gA 435 :VRGR T0532 377 :MEFIASN 3i4gA 441 :VNMPPVT T0532 413 :SGEKEADIEKILTQRYLASF 3i4gA 448 :EVTPAKLREIVRHERRIELA T0532 434 :QHPY 3i4gA 468 :MEGI T0532 439 :VYYDYRRTGY 3i4gA 472 :RYWDIMRWGI T0532 449 :PVLP 3i4gA 486 :LSQK T0532 454 :NPATNRNTMN 3i4gA 514 :YRWYVGKRAF T0532 464 :DRLPMRWMYPKSESDYNLEH 3i4gA 525 :NPTDYTWPIPQSEQNINPNL Number of specific fragments extracted= 24 number of extra gaps= 0 total=94 # request to SCWRL produces command: ulimit -t 456 ; scwrl4 -t -i /var/tmp/to_scwrl_734511304.pdb -s /var/tmp/to_scwrl_734511304.seq -o /var/tmp/from_scwrl_734511304.pdb > /var/tmp/scwrl_734511304.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_734511304.pdb Number of alignments=5 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3ihvA/T0532-3ihvA-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 3ihvA expands to /projects/compbio/data/pdb/3ihv.pdb.gz 3ihvA:Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 160, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 164, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 166, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 168, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 170, because occupancy 0.500 <= existing 0.500 in 3ihvA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 467, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 471, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 473, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 475, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 477, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 587, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 591, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 593, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 612, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 616, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 618, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 620, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 622, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 624, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 797, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 801, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 803, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 814, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 818, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 820, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 822, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 824, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 826, because occupancy 0.500 <= existing 0.500 in 3ihvA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1182, because occupancy 0.500 <= existing 0.500 in 3ihvA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1186, because occupancy 0.500 <= existing 0.500 in 3ihvA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1188, because occupancy 0.500 <= existing 0.500 in 3ihvA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1192, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 1195, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 1199, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 1201, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 1260, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 1264, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 1266, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 1268, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 1373, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 1377, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 1379, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 1381, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 1383, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 1852, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 1856, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 1858, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 1860, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 1862, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 1864, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 1866, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 1868, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 2146, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 2150, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 2152, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 2154, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 2156, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 3650, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 3654, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 3656, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 3658, because occupancy 0.500 <= existing 0.500 in 3ihvA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 4320, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 4324, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 4326, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 4328, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 4330, because occupancy 0.500 <= existing 0.500 in 3ihvA Skipped atom 4332, because occupancy 0.500 <= existing 0.500 in 3ihvA # T0532 read from 3ihvA/T0532-3ihvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3ihvA read from 3ihvA/T0532-3ihvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3ihvA to template set # found chain 3ihvA in template set T0532 24 :DEINT 3ihvA 25 :ETRTE T0532 29 :DPDATTKVTSSLLATGLLLDIT 3ihvA 33 :KNYMNNAEEAKDVLLGVYRTNT T0532 51 :SSSASKSFIYDELLAKQMAWGESMEDYQY 3ihvA 57 :AMYGYYLSILFNLGTDISQVEGSGNENFR T0532 80 :NVFGRSGFGG 3ihvA 96 :QSEVQQTWAA T0532 90 :YTTLINAQKMVESV 3ihvA 107 :YTGIYRANDFLERI T0532 104 :SDDNVNA 3ihvA 128 :TTTDKKL T0532 111 :YDGLAHFIKAYKIFYMSMEMGDLPYEEALQG 3ihvA 138 :YIAEARALRGMFYFELVRRFGNVVLMTSTQM T0532 142 :ELGLVRPKYNTQKEVMNFILSDLETAYELFSTAKDFDGDPILGGSISK 3ihvA 170 :NQNPATYVQSAPEKVYEYIEDDLLYACDILPYATDDQYRESNDYRFSK T0532 192 :KATTAFQLKVLMHLSKKESDADL 3ihvA 218 :GAALGLLTKVYATWAGYPVKDES T0532 215 :KVKERFARIVASG 3ihvA 244 :AAAKTARILVESG T0532 228 :SLMESNEDNL 3ihvA 259 :GLLKDYEQLW T0532 238 :QMKYADKANTVYPFHNTNTK 3ihvA 299 :VGRIGKWNGVKTTAIAGVRG T0532 258 :HAGYAMLSTMLIDKF 3ihvA 320 :CAANVKVVHTFVLDW T0532 273 :KATGDIRMFYYAKP 3ihvA 336 :EDVSDIRRDLSIAN T0532 288 :KA 3ihvA 350 :YQ T0532 291 :LNEGVTADSW 3ihvA 352 :YTDTKKSLWV T0532 301 :DAYIG 3ihvA 386 :QNYTP T0532 317 :KAYATEQYSGFNARYTDYPSGEPVVRLGYAEQNFILAEAAVRG 3ihvA 391 :AKWDIQKYVTTNSFINNDKSNVNWYFLRYADVLLLYAEALNEW T0532 360 :WISGDASAYYKK 3ihvA 436 :GPDAEAYNAINA T0532 373 :IRAHMEFIA 3ihvA 448 :VRRRGYGNP T0532 384 :TPDEEVYH 3ihvA 457 :SNTSACDL T0532 411 :QLSGEKEADIEKILTQRYLASF 3ihvA 465 :PQGLDETSFREAVRKERSYELS T0532 434 :QHPY 3ihvA 487 :FEGH T0532 439 :VYYDYRRTGY 3ihvA 491 :RRQDLIRWGI T0532 453 :INPATNRNT 3ihvA 516 :WEGTGSPNY T0532 462 :MNDRLPMRWMYPKSESDYNLEHQNEAL 3ihvA 530 :TEEGKHELFPIPQRDMDLCIQFNQNPK Number of specific fragments extracted= 26 number of extra gaps= 0 total=120 # request to SCWRL produces command: ulimit -t 456 ; scwrl4 -t -i /var/tmp/to_scwrl_1998148612.pdb -s /var/tmp/to_scwrl_1998148612.seq -o /var/tmp/from_scwrl_1998148612.pdb > /var/tmp/scwrl_1998148612.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1998148612.pdb Number of alignments=6 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3fdhA/T0532-3fdhA-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 3fdhA expands to /projects/compbio/data/pdb/3fdh.pdb.gz 3fdhA:Skipped atom 27, because occupancy 0.500 <= existing 0.500 in 3fdhA Skipped atom 31, because occupancy 0.500 <= existing 0.500 in 3fdhA Skipped atom 33, because occupancy 0.500 <= existing 0.500 in 3fdhA Skipped atom 35, because occupancy 0.500 <= existing 0.500 in 3fdhA Skipped atom 37, because occupancy 0.500 <= existing 0.500 in 3fdhA Skipped atom 39, because occupancy 0.500 <= existing 0.500 in 3fdhA Skipped atom 41, because occupancy 0.500 <= existing 0.500 in 3fdhA Skipped atom 43, because occupancy 0.500 <= existing 0.500 in 3fdhA Skipped atom 108, because occupancy 0.300 <= existing 0.700 in 3fdhA Skipped atom 112, because occupancy 0.300 <= existing 0.700 in 3fdhA Skipped atom 114, because occupancy 0.300 <= existing 0.700 in 3fdhA Skipped atom 322, because occupancy 0.500 <= existing 0.500 in 3fdhA Skipped atom 326, because occupancy 0.500 <= existing 0.500 in 3fdhA Skipped atom 328, because occupancy 0.500 <= existing 0.500 in 3fdhA Skipped atom 330, because occupancy 0.500 <= existing 0.500 in 3fdhA Skipped atom 332, because occupancy 0.500 <= existing 0.500 in 3fdhA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1458, because occupancy 0.500 <= existing 0.500 in 3fdhA Skipped atom 1462, because occupancy 0.500 <= existing 0.500 in 3fdhA Skipped atom 1464, because occupancy 0.500 <= existing 0.500 in 3fdhA Skipped atom 1515, because occupancy 0.500 <= existing 0.500 in 3fdhA Skipped atom 1519, because occupancy 0.500 <= existing 0.500 in 3fdhA Skipped atom 1521, because occupancy 0.500 <= existing 0.500 in 3fdhA Skipped atom 1523, because occupancy 0.500 <= existing 0.500 in 3fdhA Skipped atom 1525, because occupancy 0.500 <= existing 0.500 in 3fdhA Skipped atom 1527, because occupancy 0.500 <= existing 0.500 in 3fdhA Skipped atom 1587, because occupancy 0.500 <= existing 0.500 in 3fdhA Skipped atom 1591, because occupancy 0.500 <= existing 0.500 in 3fdhA Skipped atom 1593, because occupancy 0.500 <= existing 0.500 in 3fdhA Skipped atom 1595, because occupancy 0.500 <= existing 0.500 in 3fdhA Skipped atom 1597, because occupancy 0.500 <= existing 0.500 in 3fdhA Skipped atom 1599, because occupancy 0.500 <= existing 0.500 in 3fdhA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 2532, because occupancy 0.500 <= existing 0.500 in 3fdhA Skipped atom 2536, because occupancy 0.500 <= existing 0.500 in 3fdhA Skipped atom 2538, because occupancy 0.500 <= existing 0.500 in 3fdhA Skipped atom 2540, because occupancy 0.500 <= existing 0.500 in 3fdhA Skipped atom 2542, because occupancy 0.500 <= existing 0.500 in 3fdhA Skipped atom 2544, because occupancy 0.500 <= existing 0.500 in 3fdhA Skipped atom 2546, because occupancy 0.500 <= existing 0.500 in 3fdhA Skipped atom 2548, because occupancy 0.500 <= existing 0.500 in 3fdhA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 3271, because occupancy 0.500 <= existing 0.500 in 3fdhA Skipped atom 3275, because occupancy 0.500 <= existing 0.500 in 3fdhA Skipped atom 3277, because occupancy 0.500 <= existing 0.500 in 3fdhA Skipped atom 3279, because occupancy 0.500 <= existing 0.500 in 3fdhA Skipped atom 3281, because occupancy 0.500 <= existing 0.500 in 3fdhA # T0532 read from 3fdhA/T0532-3fdhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3fdhA read from 3fdhA/T0532-3fdhA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3fdhA to template set # found chain 3fdhA in template set Warning: unaligning (T0532)K35 because first residue in template chain is (3fdhA)S39 Warning: unaligning (T0532)L139 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3fdhA)M168 Warning: unaligning (T0532)V146 because of BadResidue code TOO_FEW_ATOMS+CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3fdhA)M168 T0532 36 :VTSSLLATGLLLDITSSSASKSFIYDELLAKQM 3fdhA 40 :VASRFILADVITSTAFSNASGDINTYASSYIEY T0532 69 :AWGESMEDYQYNVFGRSGFGGYTTLINAQKMVESV 3fdhA 83 :AEVRENEPSSSSTFNNSWNGIYSSLKNARIIIDQC T0532 104 :SDDNVNAYDGLAHFIKAYKIFYMSMEMGDLPYEEA 3fdhA 122 :RDHGNDVTRGMAEVMAAYNCALIADFFGDAPCSQA T0532 147 :RPKYNTQKEVMNFILSDLETAYELFSTA 3fdhA 169 :TPKMDTQQEIYTQIISYLDDAIANLQKE T0532 175 :KDFDGDPILGGSISKWKKATTAFQLKVLMHLSKKESDAD 3fdhA 200 :DVTEQDFLYAGDADKWLKFAYGLKARYTMRLINRSSNKS T0532 215 :KVKERFARIVA 3fdhA 239 :ADYEKVLDYVS T0532 228 :SLMESNEDNLQMKYADKANT 3fdhA 250 :KSFTSADDQAAFDIYDSNNI T0532 250 :PFHNTNTKHAGYAMLSTMLIDKFKATGDIRMFYYAKPAKAKLNEG 3fdhA 270 :NPFYGFYNSRAGFGASTSLGTKLLAYNDPRANRAFFTPIVDKKRS T0532 304 :IGTDPSLPFEQIEKAYATEQYSGFNARYTDYPSGEPVVRLGYAEQNFILAEAAVRGWI 3fdhA 315 :QVAANDPSLVPAPNGSPDQSTSKYGISAFVYAKTAPTLLMSYHELMFLKAEALCRLNR T0532 364 :DASAYYKKAIRAHMEFIASNTPDEEV 3fdhA 373 :DAEDALKEAVVAGLLNAENSISIAIK T0532 390 :YHHGHPITEEAIAAFLETP 3fdhA 406 :TNSSEVITETSAGKYFDDV T0532 411 :QLSGEKEADIEKILTQRYLASFMQ 3fdhA 425 :VKAKYAANPLQETMIQKYLAMWGA T0532 436 :P 3fdhA 449 :S T0532 437 :YDVYYDYRRTGYPVLPINPAT 3fdhA 453 :TETYNDFRRMKGLNENFITLT T0532 459 :RNTMNDRLPMRWMYPKSESDYNLE 3fdhA 474 :NPNNSSKFPLRYPYGNSDTAANPE T0532 487 :ALERQFGGVDDVNKLMWI 3fdhA 498 :VKAAYGNGDYVYSEPVWW Number of specific fragments extracted= 16 number of extra gaps= 0 total=136 # request to SCWRL produces command: ulimit -t 456 ; scwrl4 -t -i /var/tmp/to_scwrl_714183798.pdb -s /var/tmp/to_scwrl_714183798.seq -o /var/tmp/from_scwrl_714183798.pdb > /var/tmp/scwrl_714183798.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_714183798.pdb Number of alignments=7 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3jq1A/T0532-3jq1A-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 3jq1A expands to /projects/compbio/data/pdb/3jq1.pdb.gz 3jq1A:Skipped atom 114, because occupancy 0.500 <= existing 0.500 in 3jq1A Skipped atom 118, because occupancy 0.500 <= existing 0.500 in 3jq1A Skipped atom 120, because occupancy 0.500 <= existing 0.500 in 3jq1A Skipped atom 122, because occupancy 0.500 <= existing 0.500 in 3jq1A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 408, because occupancy 0.500 <= existing 0.500 in 3jq1A Skipped atom 412, because occupancy 0.500 <= existing 0.500 in 3jq1A Skipped atom 414, because occupancy 0.500 <= existing 0.500 in 3jq1A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 629, because occupancy 0.500 <= existing 0.500 in 3jq1A Skipped atom 633, because occupancy 0.500 <= existing 0.500 in 3jq1A Skipped atom 635, because occupancy 0.500 <= existing 0.500 in 3jq1A Skipped atom 637, because occupancy 0.500 <= existing 0.500 in 3jq1A Skipped atom 639, because occupancy 0.500 <= existing 0.500 in 3jq1A Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 707, because occupancy 0.300 <= existing 0.700 in 3jq1A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 711, because occupancy 0.300 <= existing 0.700 in 3jq1A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 713, because occupancy 0.300 <= existing 0.700 in 3jq1A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 715, because occupancy 0.230 <= existing 0.520 in 3jq1A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 717, because occupancy 0.300 <= existing 0.700 in 3jq1A Skipped atom 820, because occupancy 0.500 <= existing 0.500 in 3jq1A Skipped atom 824, because occupancy 0.500 <= existing 0.500 in 3jq1A Skipped atom 826, because occupancy 0.500 <= existing 0.500 in 3jq1A Skipped atom 828, because occupancy 0.500 <= existing 0.500 in 3jq1A Skipped atom 830, because occupancy 0.500 <= existing 0.500 in 3jq1A Skipped atom 896, because occupancy 0.300 <= existing 0.700 in 3jq1A Skipped atom 900, because occupancy 0.300 <= existing 0.700 in 3jq1A Skipped atom 902, because occupancy 0.300 <= existing 0.700 in 3jq1A Skipped atom 1040, because occupancy 0.500 <= existing 0.500 in 3jq1A Skipped atom 1044, because occupancy 0.500 <= existing 0.500 in 3jq1A Skipped atom 1046, because occupancy 0.500 <= existing 0.500 in 3jq1A Skipped atom 1048, because occupancy 0.500 <= existing 0.500 in 3jq1A Skipped atom 1050, because occupancy 0.500 <= existing 0.500 in 3jq1A Skipped atom 1052, because occupancy 0.500 <= existing 0.500 in 3jq1A Skipped atom 1397, because occupancy 0.400 <= existing 0.600 in 3jq1A Skipped atom 1401, because occupancy 0.400 <= existing 0.600 in 3jq1A Skipped atom 1403, because occupancy 0.400 <= existing 0.600 in 3jq1A Skipped atom 1405, because occupancy 0.400 <= existing 0.600 in 3jq1A Skipped atom 1407, because occupancy 0.400 <= existing 0.600 in 3jq1A Skipped atom 1409, because occupancy 0.400 <= existing 0.600 in 3jq1A Skipped atom 1625, because occupancy 0.500 <= existing 0.500 in 3jq1A Skipped atom 1629, because occupancy 0.500 <= existing 0.500 in 3jq1A Skipped atom 1631, because occupancy 0.500 <= existing 0.500 in 3jq1A Skipped atom 1633, because occupancy 0.500 <= existing 0.500 in 3jq1A Skipped atom 1635, because occupancy 0.500 <= existing 0.500 in 3jq1A Skipped atom 1637, because occupancy 0.500 <= existing 0.500 in 3jq1A Skipped atom 1662, because occupancy 0.500 <= existing 0.500 in 3jq1A Skipped atom 1666, because occupancy 0.500 <= existing 0.500 in 3jq1A Skipped atom 1668, because occupancy 0.500 <= existing 0.500 in 3jq1A Skipped atom 1670, because occupancy 0.500 <= existing 0.500 in 3jq1A Skipped atom 1672, because occupancy 0.500 <= existing 0.500 in 3jq1A Skipped atom 1674, because occupancy 0.500 <= existing 0.500 in 3jq1A Skipped atom 1723, because occupancy 0.330 <= existing 0.330 in 3jq1A Skipped atom 1728, because occupancy 0.330 <= existing 0.330 in 3jq1A Skipped atom 1731, because occupancy 0.330 <= existing 0.330 in 3jq1A Skipped atom 1734, because occupancy 0.330 <= existing 0.330 in 3jq1A Skipped atom 1737, because occupancy 0.330 <= existing 0.330 in 3jq1A Skipped atom 1740, because occupancy 0.330 <= existing 0.330 in 3jq1A Skipped atom 2102, because occupancy 0.500 <= existing 0.500 in 3jq1A Skipped atom 2106, because occupancy 0.500 <= existing 0.500 in 3jq1A Skipped atom 2108, because occupancy 0.500 <= existing 0.500 in 3jq1A Skipped atom 2110, because occupancy 0.500 <= existing 0.500 in 3jq1A Skipped atom 2112, because occupancy 0.500 <= existing 0.500 in 3jq1A Skipped atom 2114, because occupancy 0.500 <= existing 0.500 in 3jq1A Skipped atom 2116, because occupancy 0.500 <= existing 0.500 in 3jq1A Skipped atom 2118, because occupancy 0.500 <= existing 0.500 in 3jq1A Skipped atom 2120, because occupancy 0.500 <= existing 0.500 in 3jq1A Skipped atom 2122, because occupancy 0.500 <= existing 0.500 in 3jq1A Skipped atom 2124, because occupancy 0.500 <= existing 0.500 in 3jq1A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 2384, because occupancy 0.500 <= existing 0.500 in 3jq1A Skipped atom 2388, because occupancy 0.500 <= existing 0.500 in 3jq1A Skipped atom 2390, because occupancy 0.500 <= existing 0.500 in 3jq1A Skipped atom 2392, because occupancy 0.500 <= existing 0.500 in 3jq1A Skipped atom 2565, because occupancy 0.500 <= existing 0.500 in 3jq1A Skipped atom 2569, because occupancy 0.500 <= existing 0.500 in 3jq1A Skipped atom 2571, because occupancy 0.500 <= existing 0.500 in 3jq1A Skipped atom 2573, because occupancy 0.500 <= existing 0.500 in 3jq1A Skipped atom 2575, because occupancy 0.500 <= existing 0.500 in 3jq1A Skipped atom 2577, because occupancy 0.500 <= existing 0.500 in 3jq1A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 2979, because occupancy 0.500 <= existing 0.500 in 3jq1A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 2983, because occupancy 0.500 <= existing 0.500 in 3jq1A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2985, because occupancy 0.500 <= existing 0.500 in 3jq1A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2987, because occupancy 0.370 <= existing 0.380 in 3jq1A Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 2989, because occupancy 0.500 <= existing 0.500 in 3jq1A Skipped atom 3797, because occupancy 0.500 <= existing 0.500 in 3jq1A Skipped atom 3801, because occupancy 0.500 <= existing 0.500 in 3jq1A Skipped atom 3803, because occupancy 0.500 <= existing 0.500 in 3jq1A Skipped atom 3805, because occupancy 0.500 <= existing 0.500 in 3jq1A Skipped atom 3807, because occupancy 0.500 <= existing 0.500 in 3jq1A # T0532 read from 3jq1A/T0532-3jq1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3jq1A read from 3jq1A/T0532-3jq1A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3jq1A to template set # found chain 3jq1A in template set Warning: unaligning (T0532)P30 because first residue in template chain is (3jq1A)T37 Warning: unaligning (T0532)K244 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3jq1A)S291 Warning: unaligning (T0532)T247 because of BadResidue code BAD_PEPTIDE in next template residue (3jq1A)P295 Warning: unaligning (T0532)V248 because of BadResidue code BAD_PEPTIDE at template residue (3jq1A)P295 Warning: unaligning (T0532)E489 because last residue in template chain is (3jq1A)W513 T0532 31 :DATTKVTSSLLATGLLLDIT 3jq1A 38 :FWKDETDFNLALTSCYTPLK T0532 51 :SSSASKSFIYDELLAKQMAWGESMEDYQY 3jq1A 63 :GYYGTRGVMLRIARADEVDFRNDISDVYT T0532 80 :NVFGRSGFGG 3jq1A 101 :NSLTQGMFYQ T0532 90 :YTTLINAQKMVESV 3jq1A 112 :YNALYRTNSIMQKL T0532 104 :SDDNVNAYDGLAHFIKAYKIFYMSMEMGDLPYEEALQGELGLVRPKYNTQKEVMNFILSDLETAYELFSTAKD 3jq1A 133 :STDFQNSVKGECLFIRGFYLFQLAKEFKDAPLRLTASQSPSTFPLAKSSQADIWAQAKEDLKTAASLLPITNK T0532 184 :GGSISK 3jq1A 206 :IGKPTQ T0532 192 :KATTAFQLKVLMHLSKKES 3jq1A 212 :GAAYAALGKIYVYEENWQE T0532 216 :VKERFARIVASG 3jq1A 231 :AINVLEPLTQNP T0532 228 :SLMESNEDNL 3jq1A 246 :KLVEDFNWNF T0532 245 :AN 3jq1A 292 :NT T0532 249 :YPFHNTNTKHAGYAMLSTMLIDKFKATG 3jq1A 296 :KEYAAAEVGGWYEANPTQQIMDIFWKEK T0532 277 :DIRM 3jq1A 330 :DYRA T0532 281 :FYYAKPAKAKLNEGV 3jq1A 336 :SVAWDYEGCTYYQRP T0532 310 :LPFEQI 3jq1A 355 :FAQDKW T0532 317 :KAYATEQYSGFNAR 3jq1A 361 :KTYWILKYQNWKTQ T0532 331 :YTDYPSGEPVVRLGYAEQNFILAEAAVRGWISGDASAYYKK 3jq1A 378 :PAPPKSFINERAIRYADVLLMLAEAYMNKGALDTSIGYINQ T0532 373 :IRAHMEFIASNT 3jq1A 419 :IRRRANLNDYSG T0532 413 :SGEKEADIEKILTQRYLASF 3jq1A 431 :PITKEGVFEDLVHQRAIEFF T0532 434 :QHPY 3jq1A 451 :VEGE T0532 439 :VYYDYRRTGY 3jq1A 455 :RFYDLRRWGL T0532 458 :NRNTMNDR 3jq1A 480 :YQTGKSDN T0532 466 :LPMRWMYPKSESDYNLEHQNEAL 3jq1A 490 :KFNYFPIPAKELDTNPLCTPSEG Number of specific fragments extracted= 22 number of extra gaps= 1 total=158 # request to SCWRL produces command: ulimit -t 456 ; scwrl4 -t -i /var/tmp/to_scwrl_1388248864.pdb -s /var/tmp/to_scwrl_1388248864.seq -o /var/tmp/from_scwrl_1388248864.pdb > /var/tmp/scwrl_1388248864.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1388248864.pdb Number of alignments=8 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3jysA/T0532-3jysA-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 3jysA expands to /projects/compbio/data/pdb/3jys.pdb.gz 3jysA:Skipped atom 85, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 89, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 91, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 145, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 149, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 151, because occupancy 0.500 <= existing 0.500 in 3jysA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 388, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 392, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 394, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 396, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 398, because occupancy 0.500 <= existing 0.500 in 3jysA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 600, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 604, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 606, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 608, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 610, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 612, because occupancy 0.500 <= existing 0.500 in 3jysA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 775, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 779, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 781, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 783, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 785, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 787, because occupancy 0.500 <= existing 0.500 in 3jysA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 989, because occupancy 0.500 <= existing 0.500 in 3jysA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 993, because occupancy 0.500 <= existing 0.500 in 3jysA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 995, because occupancy 0.500 <= existing 0.500 in 3jysA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 997, because occupancy 0.370 <= existing 0.380 in 3jysA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 999, because occupancy 0.500 <= existing 0.500 in 3jysA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1651, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 1655, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 1657, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 1659, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 1661, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 1663, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 1708, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 1712, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 1714, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 1716, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 1718, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 1720, because occupancy 0.500 <= existing 0.500 in 3jysA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 2392, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 2396, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 2398, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 2400, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 2402, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 2404, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 2705, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 2709, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 2711, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 2713, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 2715, because occupancy 0.500 <= existing 0.500 in 3jysA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 3251, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 3255, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 3257, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 3259, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 3261, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 3264, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 3268, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 3270, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 3272, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 3274, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 3288, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 3292, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 3294, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 3296, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 3298, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 3300, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 3302, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 3304, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 3673, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 3677, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 3679, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 3681, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 3683, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 3839, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 3843, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 3845, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 3847, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 3849, because occupancy 0.500 <= existing 0.500 in 3jysA Skipped atom 3851, because occupancy 0.500 <= existing 0.500 in 3jysA # T0532 read from 3jysA/T0532-3jysA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3jysA read from 3jysA/T0532-3jysA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3jysA to template set # found chain 3jysA in template set Warning: unaligning (T0532)D29 because first residue in template chain is (3jysA)D38 Warning: unaligning (T0532)S51 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3jysA)T79 Warning: unaligning (T0532)T256 because of BadResidue code BAD_PEPTIDE in next template residue (3jysA)Q325 Warning: unaligning (T0532)K257 because of BadResidue code BAD_PEPTIDE at template residue (3jysA)Q325 Warning: unaligning (T0532)G326 because of BadResidue code BAD_PEPTIDE in next template residue (3jysA)L390 Warning: unaligning (T0532)F327 because of BadResidue code BAD_PEPTIDE at template residue (3jysA)L390 Warning: unaligning (T0532)K474 because of BadResidue code BAD_PEPTIDE in next template residue (3jysA)T521 Warning: unaligning (T0532)S475 because of BadResidue code BAD_PEPTIDE at template residue (3jysA)T521 Warning: unaligning (T0532)E489 because last residue in template chain is (3jysA)Y535 T0532 30 :PDATTKVTSSLLATGLLLDIT 3jysA 39 :KAYTDAESYTKGLHKIYSVWA T0532 52 :SSASKSFIYDELLAKQMAWGESMEDYQY 3jysA 80 :ALLRCWWTLQEQPTDEMKNAWNDAWCTE T0532 80 :NVFGRSGFGG 3jysA 118 :VEPIEGVYQR T0532 90 :YTTLINAQKMVESV 3jysA 129 :MYIVALVNEFLKNI T0532 104 :SDD 3jysA 146 :PES T0532 107 :NVNAYDGLAHFIKAYKIFYMSMEMGDLPYEEA 3jysA 150 :DKESYIAQARFNRAFAYYVLMDMFALPPFITE T0532 142 :ELGLVRPKYNTQKEVMNFILSDLETAYELFSTAKDF 3jysA 182 :KNYSIEPAPLSREDLFNWIEAELNEIKPNLPSPRSE T0532 184 :GGSISK 3jysA 218 :YGVADQ T0532 192 :KATTAFQLKVLMHLSKKESDA 3jysA 224 :AVASALLARMYLNAEIYTGKA T0532 213 :DLKVKERFARIVASG 3jysA 246 :YTECINACNEVIKAG T0532 228 :SLMESNEDNL 3jysA 262 :QLADNYADLF T0532 243 :DK 3jysA 319 :AH T0532 253 :NTN 3jysA 321 :SGV T0532 258 :HAGYAMLSTMLIDKF 3jysA 326 :GWAGFRATSNLVHLF T0532 274 :ATG 3jysA 344 :NDE T0532 277 :DIRMFYYAK 3jysA 355 :DKRGIFYDK T0532 301 :DAYIGTDPSLPFEQIEKAYATEQYS 3jysA 364 :GRSIDITSSVSGTFETEGWSVFKFS T0532 328 :NAR 3jysA 391 :NSN T0532 331 :YTDYPSGEPVVRLGYAEQNFILAEAAVRGW 3jysA 398 :KNTLWVDTDFPMFRLGDIYLMYAEAVARGG T0532 361 :ISGDASAYYKK 3jysA 430 :SKASAVEYINA T0532 373 :IRAHMEFIASNTPD 3jysA 441 :LRKRAYGDDKHNIS T0532 387 :EEVY 3jysA 456 :NWLE T0532 413 :SGE 3jysA 460 :ENN T0532 420 :IEKILTQRYLASF 3jysA 463 :FRNLLDERGRELY T0532 434 :QHPY 3jysA 476 :WEGI T0532 439 :VYYDYRRTGYPVLP 3jysA 480 :RRTDLVRFDLLTSG T0532 453 :INPATNRNTMNDRLPMRWMYP 3jysA 499 :FKGGINTGVGVNKRYNVYPIP T0532 476 :ESDYNLEHQNEAL 3jysA 522 :DLTVNGNLQQNEG Number of specific fragments extracted= 28 number of extra gaps= 3 total=186 # request to SCWRL produces command: ulimit -t 456 ; scwrl4 -t -i /var/tmp/to_scwrl_560733388.pdb -s /var/tmp/to_scwrl_560733388.seq -o /var/tmp/from_scwrl_560733388.pdb > /var/tmp/scwrl_560733388.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_560733388.pdb Number of alignments=9 # Reading fragments from alignment file # Attempting to read fragment alignments from file 3hdxA/T0532-3hdxA-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 3hdxA expands to /projects/compbio/data/pdb/3hdx.pdb.gz 3hdxA:Skipped atom 42, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 46, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 48, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 50, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 52, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 54, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 64, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 68, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 70, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 72, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 74, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 77, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 81, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 83, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 85, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 87, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 89, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 107, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 111, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 113, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 115, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 117, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 119, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 121, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 123, because occupancy 0.500 <= existing 0.500 in 3hdxA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 229, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 233, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 235, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 237, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 239, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 410, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 414, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 416, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 478, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 482, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 484, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 486, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 488, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 490, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 501, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 505, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 507, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 509, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 511, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 566, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 570, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 572, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 574, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 576, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 578, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 625, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 629, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 631, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 633, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 635, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 637, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 639, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 641, because occupancy 0.500 <= existing 0.500 in 3hdxA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 748, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 752, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 754, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 756, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 758, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 760, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 763, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 767, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 769, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 771, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 773, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 775, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 840, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 844, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 846, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 848, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 851, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 855, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 857, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 878, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 882, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 884, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 886, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 888, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 890, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 893, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 897, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 899, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 901, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 903, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 905, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 952, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 956, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 958, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 960, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 962, because occupancy 0.500 <= existing 0.500 in 3hdxA Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1077, because occupancy 0.200 <= existing 0.800 in 3hdxA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1081, because occupancy 0.200 <= existing 0.800 in 3hdxA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1083, because occupancy 0.200 <= existing 0.800 in 3hdxA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1085, because occupancy 0.150 <= existing 0.600 in 3hdxA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Skipped atom 1087, because occupancy 0.200 <= existing 0.800 in 3hdxA Skipped atom 1253, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 1257, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 1259, because occupancy 0.500 <= existing 0.500 in 3hdxA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 1295, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 1299, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 1301, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 1303, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 1305, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 1313, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 1317, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 1319, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 1321, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 1323, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 1325, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 1373, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 1377, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 1379, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 1381, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 1383, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 1385, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 1438, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 1442, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 1444, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 1446, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 1448, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 1450, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 1536, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 1540, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 1542, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 1544, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 1546, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 1665, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 1669, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 1671, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 1673, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 1675, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 1677, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 1679, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 1681, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 1732, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 1736, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 1738, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 1817, because occupancy 0.400 <= existing 0.600 in 3hdxA Skipped atom 1821, because occupancy 0.400 <= existing 0.600 in 3hdxA Skipped atom 1823, because occupancy 0.400 <= existing 0.600 in 3hdxA Skipped atom 1825, because occupancy 0.400 <= existing 0.600 in 3hdxA Skipped atom 1827, because occupancy 0.400 <= existing 0.600 in 3hdxA Skipped atom 1889, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 1893, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 1895, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 1959, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 1963, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 1965, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 1967, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 1969, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 1971, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 2071, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 2075, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 2077, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 2079, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 2081, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 2083, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 2128, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 2132, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 2134, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 2137, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 2141, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 2143, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 2145, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 2147, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 2354, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 2356, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 2358, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 2360, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 2362, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 2364, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 2366, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 2368, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 2370, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 2382, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 2386, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 2388, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 2391, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 2395, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 2397, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 2399, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 2401, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 2403, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 2405, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 2407, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 2409, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 2419, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 2423, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 2425, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 2427, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 2429, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 2431, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 2510, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 2514, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 2516, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 2930, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 2934, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 2936, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 2938, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 2940, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 3048, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 3052, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 3054, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 3056, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 3058, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 3078, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 3082, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 3084, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 3086, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 3110, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 3114, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 3116, because occupancy 0.500 <= existing 0.500 in 3hdxA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 3239, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 3243, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 3245, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 3268, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 3272, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 3274, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 3276, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 3278, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 3280, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 3333, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 3337, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 3339, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 3341, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 3343, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 3345, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 3348, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 3352, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 3354, because occupancy 0.500 <= existing 0.500 in 3hdxA Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE with M Bad short name: MSE for alphabet: ExtAA Replacing MSE 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 3855, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 3859, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 3861, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 3863, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 3865, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 3868, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 3872, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 3874, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 3876, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 3878, because occupancy 0.500 <= existing 0.500 in 3hdxA Skipped atom 3880, because occupancy 0.500 <= existing 0.500 in 3hdxA # T0532 read from 3hdxA/T0532-3hdxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # 3hdxA read from 3hdxA/T0532-3hdxA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m # adding 3hdxA to template set # found chain 3hdxA in template set Warning: unaligning (T0532)D29 because first residue in template chain is (3hdxA)T39 Warning: unaligning (T0532)N328 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE in next template residue (3hdxA)G386 Warning: unaligning (T0532)Y334 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE at template residue (3hdxA)G386 T0532 30 :PDATTKVTSSLLATGLLLDIT 3hdxA 40 :QQWKTLEDTRSALMGVYGLTR T0532 53 :SASKSFIYDELLAKQMAWGESMEDYQY 3hdxA 65 :DNNTHWICGDLRKGDFTVYKRSDLQAV T0532 87 :FGG 3hdxA 109 :WRR T0532 90 :YTTLINAQKMVESV 3hdxA 113 :YAVINAASVFMEKA T0532 104 :SDDNVNAYDGLAHFIKAYKIFYMSMEMGDLPYEEALQGELGLVRPKYNTQKEVMNFILSDLETAYELFSTAKDFDG 3hdxA 137 :SEQNLKYDIAQVRALRAFAYFYMVRIWGDVPLVTYSYDNGTFPSMPRTDAQTVLSYAKAELLTAIEDLPYQYGTQT T0532 180 :DPILGGSISK 3hdxA 221 :AQWQGKLFNK T0532 192 :KATTAFQLKVLMHLSKKES 3hdxA 231 :LSAYSVLAHICAWQGNYAE T0532 216 :VKERFARIVASG 3hdxA 250 :AETYSAFIIDHA T0532 228 :SLM 3hdxA 263 :EIN T0532 231 :ESNEDNL 3hdxA 269 :TSIADLT T0532 245 :ANTVYPFHNTNTKHAGYAMLSTM 3hdxA 310 :LEQLTLAYPLVQKSYPEIYISKD T0532 268 :LIDKFKATGDIRMF 3hdxA 334 :LFSIFTNFDDLRFG T0532 294 :GVTADSWDAYIGTDPSL 3hdxA 348 :IIDTIKYSSYYVQNLNE T0532 317 :KAYATEQYSGF 3hdxA 365 :ETPVFSKIKII T0532 335 :PSGEPVVRLGYAEQNFILAEAAVRGWISGDASAYYKK 3hdxA 387 :VFGSSIVFTRLEDITLLRAEALCALNRSTEAVSYLNM T0532 373 :IRAHMEFIASNTPDEE 3hdxA 424 :IRTNRGLREVSFKKDF T0532 413 :SGEKEADIEKILTQRYLASF 3hdxA 440 :GNNRESLIAEIFEERRRELM T0532 434 :QHPY 3hdxA 460 :GEGW T0532 439 :VYYDYRRT 3hdxA 464 :RWYDLVRR T0532 454 :NPATNRNTMNDRLPMRWMYPKSESDYNLEHQNEALE 3hdxA 476 :KDNEAFLRLISSGGIYWPVSEDIITANSQIEQNEFW Number of specific fragments extracted= 20 number of extra gaps= 0 total=206 # request to SCWRL produces command: ulimit -t 456 ; scwrl4 -t -i /var/tmp/to_scwrl_1298657217.pdb -s /var/tmp/to_scwrl_1298657217.seq -o /var/tmp/from_scwrl_1298657217.pdb > /var/tmp/scwrl_1298657217.log # Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1298657217.pdb Number of alignments=10 # command:Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.327 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 1 total_weight= 35690.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 2 total_weight= 35690.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 3 total_weight= 35690.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 4 total_weight= 35690.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 superimposing iter= 5 total_weight= 35690.000 rmsd (weighted)= 0.000 (unweighted)= 0.000 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 1.273 rmsd (weighted)= 4.845 (unweighted)= 68.375 superimposing iter= 1 total_weight= 21170.825 rmsd (weighted)= 1.506 (unweighted)= 68.289 superimposing iter= 2 total_weight= 11430.032 rmsd (weighted)= 0.773 (unweighted)= 68.169 superimposing iter= 3 total_weight= 5704.777 rmsd (weighted)= 0.589 (unweighted)= 68.107 superimposing iter= 4 total_weight= 4077.671 rmsd (weighted)= 0.535 (unweighted)= 68.074 superimposing iter= 5 total_weight= 3655.760 rmsd (weighted)= 0.515 (unweighted)= 68.055 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 1.220 rmsd (weighted)= 5.037 (unweighted)= 67.406 superimposing iter= 1 total_weight= 19854.284 rmsd (weighted)= 1.623 (unweighted)= 66.596 superimposing iter= 2 total_weight= 9706.929 rmsd (weighted)= 0.897 (unweighted)= 66.426 superimposing iter= 3 total_weight= 4935.827 rmsd (weighted)= 0.723 (unweighted)= 66.388 superimposing iter= 4 total_weight= 3662.901 rmsd (weighted)= 0.681 (unweighted)= 66.375 superimposing iter= 5 total_weight= 3364.861 rmsd (weighted)= 0.670 (unweighted)= 66.369 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 1.081 rmsd (weighted)= 8.278 (unweighted)= 64.509 superimposing iter= 1 total_weight= 13894.192 rmsd (weighted)= 3.356 (unweighted)= 65.009 superimposing iter= 2 total_weight= 6508.823 rmsd (weighted)= 2.183 (unweighted)= 65.272 superimposing iter= 3 total_weight= 3860.604 rmsd (weighted)= 1.874 (unweighted)= 65.413 superimposing iter= 4 total_weight= 3211.288 rmsd (weighted)= 1.771 (unweighted)= 65.507 superimposing iter= 5 total_weight= 3018.291 rmsd (weighted)= 1.727 (unweighted)= 65.570 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 1.123 rmsd (weighted)= 8.138 (unweighted)= 69.704 superimposing iter= 1 total_weight= 13692.388 rmsd (weighted)= 3.426 (unweighted)= 70.264 superimposing iter= 2 total_weight= 6163.472 rmsd (weighted)= 2.323 (unweighted)= 70.451 superimposing iter= 3 total_weight= 4000.956 rmsd (weighted)= 1.988 (unweighted)= 70.501 superimposing iter= 4 total_weight= 3309.019 rmsd (weighted)= 1.877 (unweighted)= 70.521 superimposing iter= 5 total_weight= 3084.111 rmsd (weighted)= 1.838 (unweighted)= 70.533 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 1.156 rmsd (weighted)= 8.836 (unweighted)= 58.214 superimposing iter= 1 total_weight= 14288.035 rmsd (weighted)= 3.683 (unweighted)= 57.688 superimposing iter= 2 total_weight= 6846.629 rmsd (weighted)= 2.403 (unweighted)= 57.343 superimposing iter= 3 total_weight= 4376.686 rmsd (weighted)= 2.004 (unweighted)= 57.198 superimposing iter= 4 total_weight= 3544.015 rmsd (weighted)= 1.865 (unweighted)= 57.104 superimposing iter= 5 total_weight= 3305.175 rmsd (weighted)= 1.799 (unweighted)= 57.044 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 1.254 rmsd (weighted)= 8.404 (unweighted)= 56.989 superimposing iter= 1 total_weight= 17648.183 rmsd (weighted)= 2.996 (unweighted)= 57.335 superimposing iter= 2 total_weight= 9804.659 rmsd (weighted)= 1.660 (unweighted)= 57.316 superimposing iter= 3 total_weight= 5702.865 rmsd (weighted)= 1.252 (unweighted)= 57.241 superimposing iter= 4 total_weight= 4210.982 rmsd (weighted)= 1.107 (unweighted)= 57.169 superimposing iter= 5 total_weight= 3691.792 rmsd (weighted)= 1.049 (unweighted)= 57.107 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 1.076 rmsd (weighted)= 7.684 (unweighted)= 75.672 superimposing iter= 1 total_weight= 13794.035 rmsd (weighted)= 3.120 (unweighted)= 75.599 superimposing iter= 2 total_weight= 6620.720 rmsd (weighted)= 2.008 (unweighted)= 75.538 superimposing iter= 3 total_weight= 4024.205 rmsd (weighted)= 1.685 (unweighted)= 75.487 superimposing iter= 4 total_weight= 3352.091 rmsd (weighted)= 1.553 (unweighted)= 75.451 superimposing iter= 5 total_weight= 3114.860 rmsd (weighted)= 1.486 (unweighted)= 75.428 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 1.082 rmsd (weighted)= 8.409 (unweighted)= 112.321 superimposing iter= 1 total_weight= 13970.725 rmsd (weighted)= 3.392 (unweighted)= 112.390 superimposing iter= 2 total_weight= 6742.109 rmsd (weighted)= 2.170 (unweighted)= 112.387 superimposing iter= 3 total_weight= 3977.205 rmsd (weighted)= 1.839 (unweighted)= 112.371 superimposing iter= 4 total_weight= 3230.436 rmsd (weighted)= 1.735 (unweighted)= 112.357 superimposing iter= 5 total_weight= 3031.795 rmsd (weighted)= 1.692 (unweighted)= 112.346 Debug: superimposing conformation 9 on the average so far superimposing iter= 0 total_weight= 1.043 rmsd (weighted)= 7.801 (unweighted)= 84.083 superimposing iter= 1 total_weight= 12691.532 rmsd (weighted)= 3.271 (unweighted)= 83.819 superimposing iter= 2 total_weight= 6208.604 rmsd (weighted)= 2.132 (unweighted)= 83.755 superimposing iter= 3 total_weight= 3804.809 rmsd (weighted)= 1.811 (unweighted)= 83.733 superimposing iter= 4 total_weight= 3041.816 rmsd (weighted)= 1.725 (unweighted)= 83.721 superimposing iter= 5 total_weight= 2857.568 rmsd (weighted)= 1.697 (unweighted)= 83.711 Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.327 rmsd (weighted)= 5.192 (unweighted)= 29.627 superimposing iter= 1 total_weight= 15974.681 rmsd (weighted)= 2.183 (unweighted)= 29.565 superimposing iter= 2 total_weight= 8296.839 rmsd (weighted)= 1.371 (unweighted)= 29.552 superimposing iter= 3 total_weight= 5477.573 rmsd (weighted)= 1.083 (unweighted)= 29.546 superimposing iter= 4 total_weight= 4374.373 rmsd (weighted)= 0.964 (unweighted)= 29.543 superimposing iter= 5 total_weight= 3917.090 rmsd (weighted)= 0.909 (unweighted)= 29.541 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 1.295 rmsd (weighted)= 5.448 (unweighted)= 61.291 superimposing iter= 1 total_weight= 17027.452 rmsd (weighted)= 2.160 (unweighted)= 61.812 superimposing iter= 2 total_weight= 8065.096 rmsd (weighted)= 1.376 (unweighted)= 61.967 superimposing iter= 3 total_weight= 4757.359 rmsd (weighted)= 1.162 (unweighted)= 62.021 superimposing iter= 4 total_weight= 3876.367 rmsd (weighted)= 1.092 (unweighted)= 62.038 superimposing iter= 5 total_weight= 3585.262 rmsd (weighted)= 1.068 (unweighted)= 62.043 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 1.283 rmsd (weighted)= 5.328 (unweighted)= 65.119 superimposing iter= 1 total_weight= 15890.698 rmsd (weighted)= 2.217 (unweighted)= 64.639 superimposing iter= 2 total_weight= 7264.696 rmsd (weighted)= 1.488 (unweighted)= 64.488 superimposing iter= 3 total_weight= 4478.988 rmsd (weighted)= 1.291 (unweighted)= 64.398 superimposing iter= 4 total_weight= 3795.669 rmsd (weighted)= 1.220 (unweighted)= 64.341 superimposing iter= 5 total_weight= 3566.133 rmsd (weighted)= 1.191 (unweighted)= 64.306 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 1.116 rmsd (weighted)= 4.177 (unweighted)= 58.138 superimposing iter= 1 total_weight= 14281.367 rmsd (weighted)= 1.749 (unweighted)= 58.168 superimposing iter= 2 total_weight= 5568.497 rmsd (weighted)= 1.263 (unweighted)= 58.232 superimposing iter= 3 total_weight= 3605.598 rmsd (weighted)= 1.143 (unweighted)= 58.279 superimposing iter= 4 total_weight= 3203.475 rmsd (weighted)= 1.099 (unweighted)= 58.312 superimposing iter= 5 total_weight= 3078.861 rmsd (weighted)= 1.079 (unweighted)= 58.333 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 1.209 rmsd (weighted)= 4.391 (unweighted)= 62.935 superimposing iter= 1 total_weight= 15164.348 rmsd (weighted)= 1.818 (unweighted)= 63.105 superimposing iter= 2 total_weight= 6483.593 rmsd (weighted)= 1.254 (unweighted)= 63.177 superimposing iter= 3 total_weight= 4271.071 rmsd (weighted)= 1.079 (unweighted)= 63.213 superimposing iter= 4 total_weight= 3618.059 rmsd (weighted)= 1.014 (unweighted)= 63.226 superimposing iter= 5 total_weight= 3369.573 rmsd (weighted)= 0.988 (unweighted)= 63.231 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 1.254 rmsd (weighted)= 5.479 (unweighted)= 49.196 superimposing iter= 1 total_weight= 17168.292 rmsd (weighted)= 2.081 (unweighted)= 49.036 superimposing iter= 2 total_weight= 8045.971 rmsd (weighted)= 1.305 (unweighted)= 48.936 superimposing iter= 3 total_weight= 4610.061 rmsd (weighted)= 1.101 (unweighted)= 48.858 superimposing iter= 4 total_weight= 3804.797 rmsd (weighted)= 1.027 (unweighted)= 48.798 superimposing iter= 5 total_weight= 3560.631 rmsd (weighted)= 0.992 (unweighted)= 48.751 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 1.301 rmsd (weighted)= 6.923 (unweighted)= 51.629 superimposing iter= 1 total_weight= 17377.900 rmsd (weighted)= 2.631 (unweighted)= 52.084 superimposing iter= 2 total_weight= 9110.273 rmsd (weighted)= 1.563 (unweighted)= 52.210 superimposing iter= 3 total_weight= 5225.593 rmsd (weighted)= 1.262 (unweighted)= 52.256 superimposing iter= 4 total_weight= 3982.748 rmsd (weighted)= 1.174 (unweighted)= 52.280 superimposing iter= 5 total_weight= 3629.269 rmsd (weighted)= 1.145 (unweighted)= 52.292 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 1.130 rmsd (weighted)= 3.867 (unweighted)= 72.410 superimposing iter= 1 total_weight= 15253.467 rmsd (weighted)= 1.536 (unweighted)= 72.359 superimposing iter= 2 total_weight= 6241.254 rmsd (weighted)= 1.050 (unweighted)= 72.337 superimposing iter= 3 total_weight= 3804.265 rmsd (weighted)= 0.930 (unweighted)= 72.313 superimposing iter= 4 total_weight= 3267.283 rmsd (weighted)= 0.891 (unweighted)= 72.292 superimposing iter= 5 total_weight= 3110.123 rmsd (weighted)= 0.874 (unweighted)= 72.275 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 1.140 rmsd (weighted)= 4.750 (unweighted)= 105.705 superimposing iter= 1 total_weight= 15192.121 rmsd (weighted)= 1.886 (unweighted)= 105.669 superimposing iter= 2 total_weight= 6497.647 rmsd (weighted)= 1.274 (unweighted)= 105.633 superimposing iter= 3 total_weight= 3715.426 rmsd (weighted)= 1.152 (unweighted)= 105.614 superimposing iter= 4 total_weight= 3202.621 rmsd (weighted)= 1.124 (unweighted)= 105.604 superimposing iter= 5 total_weight= 3102.814 rmsd (weighted)= 1.115 (unweighted)= 105.599 Debug: superimposing conformation 9 on the average so far superimposing iter= 0 total_weight= 1.119 rmsd (weighted)= 4.910 (unweighted)= 80.320 superimposing iter= 1 total_weight= 13774.014 rmsd (weighted)= 2.000 (unweighted)= 80.150 superimposing iter= 2 total_weight= 6854.366 rmsd (weighted)= 1.280 (unweighted)= 80.137 superimposing iter= 3 total_weight= 4051.327 rmsd (weighted)= 1.092 (unweighted)= 80.133 superimposing iter= 4 total_weight= 3239.997 rmsd (weighted)= 1.046 (unweighted)= 80.127 superimposing iter= 5 total_weight= 3046.545 rmsd (weighted)= 1.035 (unweighted)= 80.120 Debug: superimposing conformation 0 on the average so far superimposing iter= 0 total_weight= 1.327 rmsd (weighted)= 5.201 (unweighted)= 29.631 superimposing iter= 1 total_weight= 15981.138 rmsd (weighted)= 2.185 (unweighted)= 29.567 superimposing iter= 2 total_weight= 8316.914 rmsd (weighted)= 1.370 (unweighted)= 29.552 superimposing iter= 3 total_weight= 5485.662 rmsd (weighted)= 1.082 (unweighted)= 29.546 superimposing iter= 4 total_weight= 4374.983 rmsd (weighted)= 0.963 (unweighted)= 29.543 superimposing iter= 5 total_weight= 3915.146 rmsd (weighted)= 0.908 (unweighted)= 29.540 Debug: superimposing conformation 1 on the average so far superimposing iter= 0 total_weight= 1.295 rmsd (weighted)= 5.458 (unweighted)= 61.237 superimposing iter= 1 total_weight= 17038.042 rmsd (weighted)= 2.162 (unweighted)= 61.762 superimposing iter= 2 total_weight= 8080.434 rmsd (weighted)= 1.376 (unweighted)= 61.916 superimposing iter= 3 total_weight= 4758.870 rmsd (weighted)= 1.162 (unweighted)= 61.968 superimposing iter= 4 total_weight= 3880.819 rmsd (weighted)= 1.091 (unweighted)= 61.983 superimposing iter= 5 total_weight= 3588.249 rmsd (weighted)= 1.067 (unweighted)= 61.986 Debug: superimposing conformation 2 on the average so far superimposing iter= 0 total_weight= 1.283 rmsd (weighted)= 5.329 (unweighted)= 65.137 superimposing iter= 1 total_weight= 15887.886 rmsd (weighted)= 2.218 (unweighted)= 64.657 superimposing iter= 2 total_weight= 7268.299 rmsd (weighted)= 1.488 (unweighted)= 64.508 superimposing iter= 3 total_weight= 4476.593 rmsd (weighted)= 1.292 (unweighted)= 64.419 superimposing iter= 4 total_weight= 3783.815 rmsd (weighted)= 1.223 (unweighted)= 64.363 superimposing iter= 5 total_weight= 3555.093 rmsd (weighted)= 1.196 (unweighted)= 64.329 Debug: superimposing conformation 3 on the average so far superimposing iter= 0 total_weight= 1.116 rmsd (weighted)= 4.179 (unweighted)= 58.160 superimposing iter= 1 total_weight= 14287.657 rmsd (weighted)= 1.750 (unweighted)= 58.192 superimposing iter= 2 total_weight= 5572.961 rmsd (weighted)= 1.263 (unweighted)= 58.258 superimposing iter= 3 total_weight= 3607.281 rmsd (weighted)= 1.143 (unweighted)= 58.306 superimposing iter= 4 total_weight= 3204.307 rmsd (weighted)= 1.099 (unweighted)= 58.339 superimposing iter= 5 total_weight= 3079.668 rmsd (weighted)= 1.078 (unweighted)= 58.360 Debug: superimposing conformation 4 on the average so far superimposing iter= 0 total_weight= 1.209 rmsd (weighted)= 4.384 (unweighted)= 62.947 superimposing iter= 1 total_weight= 15163.742 rmsd (weighted)= 1.816 (unweighted)= 63.116 superimposing iter= 2 total_weight= 6483.316 rmsd (weighted)= 1.252 (unweighted)= 63.188 superimposing iter= 3 total_weight= 4272.081 rmsd (weighted)= 1.077 (unweighted)= 63.223 superimposing iter= 4 total_weight= 3619.695 rmsd (weighted)= 1.012 (unweighted)= 63.236 superimposing iter= 5 total_weight= 3369.781 rmsd (weighted)= 0.986 (unweighted)= 63.241 Debug: superimposing conformation 5 on the average so far superimposing iter= 0 total_weight= 1.254 rmsd (weighted)= 5.474 (unweighted)= 49.218 superimposing iter= 1 total_weight= 17155.130 rmsd (weighted)= 2.078 (unweighted)= 49.062 superimposing iter= 2 total_weight= 8140.040 rmsd (weighted)= 1.294 (unweighted)= 48.957 superimposing iter= 3 total_weight= 4736.307 rmsd (weighted)= 1.076 (unweighted)= 48.861 superimposing iter= 4 total_weight= 3910.419 rmsd (weighted)= 0.988 (unweighted)= 48.797 superimposing iter= 5 total_weight= 3560.064 rmsd (weighted)= 0.952 (unweighted)= 48.767 Debug: superimposing conformation 6 on the average so far superimposing iter= 0 total_weight= 1.301 rmsd (weighted)= 6.914 (unweighted)= 51.641 superimposing iter= 1 total_weight= 17374.937 rmsd (weighted)= 2.629 (unweighted)= 52.095 superimposing iter= 2 total_weight= 9113.313 rmsd (weighted)= 1.561 (unweighted)= 52.221 superimposing iter= 3 total_weight= 5233.381 rmsd (weighted)= 1.259 (unweighted)= 52.267 superimposing iter= 4 total_weight= 3992.599 rmsd (weighted)= 1.169 (unweighted)= 52.290 superimposing iter= 5 total_weight= 3632.502 rmsd (weighted)= 1.140 (unweighted)= 52.301 Debug: superimposing conformation 7 on the average so far superimposing iter= 0 total_weight= 1.130 rmsd (weighted)= 3.863 (unweighted)= 72.428 superimposing iter= 1 total_weight= 15253.437 rmsd (weighted)= 1.535 (unweighted)= 72.373 superimposing iter= 2 total_weight= 6230.303 rmsd (weighted)= 1.051 (unweighted)= 72.350 superimposing iter= 3 total_weight= 3799.074 rmsd (weighted)= 0.931 (unweighted)= 72.326 superimposing iter= 4 total_weight= 3264.349 rmsd (weighted)= 0.892 (unweighted)= 72.304 superimposing iter= 5 total_weight= 3108.060 rmsd (weighted)= 0.876 (unweighted)= 72.287 Debug: superimposing conformation 8 on the average so far superimposing iter= 0 total_weight= 1.140 rmsd (weighted)= 4.753 (unweighted)= 105.691 superimposing iter= 1 total_weight= 15196.789 rmsd (weighted)= 1.887 (unweighted)= 105.655 superimposing iter= 2 total_weight= 6494.244 rmsd (weighted)= 1.275 (unweighted)= 105.619 superimposing iter= 3 total_weight= 3710.131 rmsd (weighted)= 1.154 (unweighted)= 105.600 superimposing iter= 4 total_weight= 3198.597 rmsd (weighted)= 1.127 (unweighted)= 105.590 superimposing iter= 5 total_weight= 3100.937 rmsd (weighted)= 1.118 (unweighted)= 105.585 Debug: superimposing conformation 9 on the average so far superimposing iter= 0 total_weight= 1.119 rmsd (weighted)= 4.906 (unweighted)= 80.360 superimposing iter= 1 total_weight= 13761.713 rmsd (weighted)= 1.999 (unweighted)= 80.190 superimposing iter= 2 total_weight= 6840.823 rmsd (weighted)= 1.281 (unweighted)= 80.177 superimposing iter= 3 total_weight= 4049.495 rmsd (weighted)= 1.093 (unweighted)= 80.172 superimposing iter= 4 total_weight= 3240.741 rmsd (weighted)= 1.047 (unweighted)= 80.166 superimposing iter= 5 total_weight= 3047.379 rmsd (weighted)= 1.036 (unweighted)= 80.159 superimposing iter= 0 total_weight= 1.327 rmsd (weighted)= 5.201 (unweighted)= 29.634 superimposing iter= 1 total_weight= 15980.801 rmsd (weighted)= 2.185 (unweighted)= 29.568 superimposing iter= 2 total_weight= 8318.897 rmsd (weighted)= 1.370 (unweighted)= 29.552 superimposing iter= 3 total_weight= 5486.869 rmsd (weighted)= 1.081 (unweighted)= 29.546 superimposing iter= 4 total_weight= 4374.673 rmsd (weighted)= 0.962 (unweighted)= 29.542 superimposing iter= 5 total_weight= 3913.717 rmsd (weighted)= 0.908 (unweighted)= 29.539 superimposing iter= 0 total_weight= 1.295 rmsd (weighted)= 5.459 (unweighted)= 61.187 superimposing iter= 1 total_weight= 17037.963 rmsd (weighted)= 2.162 (unweighted)= 61.712 superimposing iter= 2 total_weight= 8081.041 rmsd (weighted)= 1.376 (unweighted)= 61.865 superimposing iter= 3 total_weight= 4758.661 rmsd (weighted)= 1.162 (unweighted)= 61.918 superimposing iter= 4 total_weight= 3880.943 rmsd (weighted)= 1.091 (unweighted)= 61.932 superimposing iter= 5 total_weight= 3588.896 rmsd (weighted)= 1.067 (unweighted)= 61.935 superimposing iter= 0 total_weight= 1.283 rmsd (weighted)= 5.329 (unweighted)= 65.163 superimposing iter= 1 total_weight= 15887.202 rmsd (weighted)= 2.218 (unweighted)= 64.684 superimposing iter= 2 total_weight= 7267.942 rmsd (weighted)= 1.488 (unweighted)= 64.535 superimposing iter= 3 total_weight= 4476.517 rmsd (weighted)= 1.292 (unweighted)= 64.446 superimposing iter= 4 total_weight= 3781.119 rmsd (weighted)= 1.224 (unweighted)= 64.390 superimposing iter= 5 total_weight= 3553.234 rmsd (weighted)= 1.197 (unweighted)= 64.356 superimposing iter= 0 total_weight= 1.116 rmsd (weighted)= 4.180 (unweighted)= 58.177 superimposing iter= 1 total_weight= 14288.380 rmsd (weighted)= 1.750 (unweighted)= 58.209 superimposing iter= 2 total_weight= 5572.950 rmsd (weighted)= 1.263 (unweighted)= 58.275 superimposing iter= 3 total_weight= 3607.261 rmsd (weighted)= 1.143 (unweighted)= 58.323 superimposing iter= 4 total_weight= 3204.314 rmsd (weighted)= 1.099 (unweighted)= 58.356 superimposing iter= 5 total_weight= 3079.667 rmsd (weighted)= 1.078 (unweighted)= 58.377 superimposing iter= 0 total_weight= 1.209 rmsd (weighted)= 4.384 (unweighted)= 62.965 superimposing iter= 1 total_weight= 15163.323 rmsd (weighted)= 1.816 (unweighted)= 63.135 superimposing iter= 2 total_weight= 6483.234 rmsd (weighted)= 1.252 (unweighted)= 63.207 superimposing iter= 3 total_weight= 4272.632 rmsd (weighted)= 1.077 (unweighted)= 63.242 superimposing iter= 4 total_weight= 3619.762 rmsd (weighted)= 1.012 (unweighted)= 63.254 superimposing iter= 5 total_weight= 3369.734 rmsd (weighted)= 0.986 (unweighted)= 63.260 superimposing iter= 0 total_weight= 1.254 rmsd (weighted)= 5.474 (unweighted)= 49.224 superimposing iter= 1 total_weight= 17153.216 rmsd (weighted)= 2.078 (unweighted)= 49.070 superimposing iter= 2 total_weight= 8140.485 rmsd (weighted)= 1.293 (unweighted)= 48.970 superimposing iter= 3 total_weight= 4768.177 rmsd (weighted)= 1.071 (unweighted)= 48.875 superimposing iter= 4 total_weight= 3891.216 rmsd (weighted)= 0.985 (unweighted)= 48.819 superimposing iter= 5 total_weight= 3551.980 rmsd (weighted)= 0.950 (unweighted)= 48.794 superimposing iter= 0 total_weight= 1.301 rmsd (weighted)= 6.913 (unweighted)= 51.645 superimposing iter= 1 total_weight= 17374.550 rmsd (weighted)= 2.628 (unweighted)= 52.102 superimposing iter= 2 total_weight= 9113.756 rmsd (weighted)= 1.561 (unweighted)= 52.228 superimposing iter= 3 total_weight= 5234.224 rmsd (weighted)= 1.258 (unweighted)= 52.274 superimposing iter= 4 total_weight= 3993.136 rmsd (weighted)= 1.168 (unweighted)= 52.297 superimposing iter= 5 total_weight= 3633.872 rmsd (weighted)= 1.139 (unweighted)= 52.309 superimposing iter= 0 total_weight= 1.130 rmsd (weighted)= 3.863 (unweighted)= 72.451 superimposing iter= 1 total_weight= 15254.395 rmsd (weighted)= 1.535 (unweighted)= 72.396 superimposing iter= 2 total_weight= 6230.034 rmsd (weighted)= 1.051 (unweighted)= 72.372 superimposing iter= 3 total_weight= 3796.943 rmsd (weighted)= 0.932 (unweighted)= 72.348 superimposing iter= 4 total_weight= 3264.984 rmsd (weighted)= 0.892 (unweighted)= 72.326 superimposing iter= 5 total_weight= 3108.625 rmsd (weighted)= 0.876 (unweighted)= 72.308 superimposing iter= 0 total_weight= 1.140 rmsd (weighted)= 4.753 (unweighted)= 105.684 superimposing iter= 1 total_weight= 15198.095 rmsd (weighted)= 1.887 (unweighted)= 105.649 superimposing iter= 2 total_weight= 6494.628 rmsd (weighted)= 1.275 (unweighted)= 105.613 superimposing iter= 3 total_weight= 3710.102 rmsd (weighted)= 1.154 (unweighted)= 105.594 superimposing iter= 4 total_weight= 3198.696 rmsd (weighted)= 1.127 (unweighted)= 105.584 superimposing iter= 5 total_weight= 3100.976 rmsd (weighted)= 1.117 (unweighted)= 105.579 superimposing iter= 0 total_weight= 1.119 rmsd (weighted)= 4.906 (unweighted)= 80.388 superimposing iter= 1 total_weight= 13764.024 rmsd (weighted)= 1.999 (unweighted)= 80.218 superimposing iter= 2 total_weight= 6840.779 rmsd (weighted)= 1.281 (unweighted)= 80.206 superimposing iter= 3 total_weight= 4049.485 rmsd (weighted)= 1.093 (unweighted)= 80.201 superimposing iter= 4 total_weight= 3240.437 rmsd (weighted)= 1.047 (unweighted)= 80.195 superimposing iter= 5 total_weight= 3047.093 rmsd (weighted)= 1.036 (unweighted)= 80.189 # command:# Printing sheets for alignments to T0532.undertaker-align.sheets # command: