# command:# Seed set to 1279904651
# 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= 23.018 sec, elapsed time= 26.765 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= 36.201 sec, elapsed time= 43.581 sec.
# command:# Prefix for input files set to 
# command:# Making conformation for sequence T0642 numbered 1 through 387
Created new target T0642 from T0642.a2m
# command:# command:# No conformations to remove in PopConform
# command:CPU_time= 36.203 sec, elapsed time= 43.584 sec.
# command:# Prefix for input files set to 
# command:# reading script from file T0642.undertaker-align.under
# Reading fragments from alignment file
# Attempting to read fragment alignments from file 2r5jA/T0642-2r5jA-simplesw-adpstyle1.a2m with NO bystroff filtering
# adding to alignment library if long or multiple fragments
2r5jA expands to /projects/compbio/data/pdb/2r5j.pdb.gz
2r5jA:# T0642 read from 2r5jA/T0642-2r5jA-simplesw-adpstyle1.a2m
# 2r5jA read from 2r5jA/T0642-2r5jA-simplesw-adpstyle1.a2m
# adding 2r5jA to template set
# found chain 2r5jA in template set
Warning: unaligning (T0642)E128 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2r5jA)R336
Warning: unaligning (T0642)R129 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2r5jA)R336
Warning: unaligning (T0642)S134 because of BadResidue code CHAIN_BREAK_BEFORE in next template residue (2r5jA)V342
Warning: unaligning (T0642)T135 because of BadResidue code CHAIN_BREAK_BEFORE at template residue (2r5jA)V342
       T0642    115 :CIENTIFICCENT
       2r5jA    322 :CWSNQLFVTVVDT
# choosing archetypes in rotamer library
       T0642    130 :STHI
       2r5jA    337 :STNM
       T0642    136 :ARGETISDIFFERENTANDHASVERYSPECIF
       2r5jA    343 :CSAVSSSDSTYKNDNFKEYLRHGEEYDLQFIF
       T0642    180 :HECKITATTHEM
       2r5jA    375 :QLCKITLTADVM
Number of specific fragments extracted= 4 number of extra gaps= 2 total=4
# request to SCWRL produces command: ulimit -t 349 ; scwrl4 -t -i /var/tmp/to_scwrl_1417271934.pdb -s /var/tmp/to_scwrl_1417271934.seq -o /var/tmp/from_scwrl_1417271934.pdb > /var/tmp/scwrl_1417271934.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1417271934.pdb
  Number of alignments=1
# Reading fragments from alignment file
# Attempting to read fragment alignments from file 1e3dB/T0642-1e3dB-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
1e3dB expands to /projects/compbio/data/pdb/1e3d.pdb.gz
1e3dB:Skipped atom 4486, because occupancy 0.4 <= existing 0.600 in 1e3dB
Skipped atom 4487, because occupancy 0.400 <= existing 0.600 in 1e3dB
Skipped atom 5538, because occupancy 0.450 <= existing 0.550 in 1e3dB
Skipped atom 5539, because occupancy 0.450 <= existing 0.550 in 1e3dB
Skipped atom 5540, because occupancy 0.450 <= existing 0.550 in 1e3dB
Skipped atom 5541, because occupancy 0.450 <= existing 0.550 in 1e3dB
Skipped atom 10524, because occupancy 0.450 <= existing 0.550 in 1e3dB
Skipped atom 10525, because occupancy 0.450 <= existing 0.550 in 1e3dB
Skipped atom 10526, because occupancy 0.450 <= existing 0.550 in 1e3dB
Skipped atom 10527, because occupancy 0.450 <= existing 0.550 in 1e3dB
Skipped atom 12122, because occupancy 0.160 <= existing 0.700 in 1e3dB
Skipped atom 12123, because occupancy 0.160 <= existing 0.700 in 1e3dB
Skipped atom 12126, because occupancy 0.140 <= existing 0.700 in 1e3dB
Skipped atom 12127, because occupancy 0.140 <= existing 0.700 in 1e3dB
# T0642 read from 1e3dB/T0642-1e3dB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m
# 1e3dB read from 1e3dB/T0642-1e3dB-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m
# adding 1e3dB to template set
# found chain 1e3dB in template set
Warning: unaligning (T0642)D357 because of BadResidue code BAD_PEPTIDE in next template residue (1e3dB)H225
Warning: unaligning (T0642)H358 because of BadResidue code BAD_PEPTIDE at template residue (1e3dB)H225
       T0642    178 :LCHECKITATT
       1e3dB     37 :VIKEARSCATL
       T0642    189 :HEMEETINGINPACIF
       1e3dB     49 :RGIETILKGRDPRDAQ
       T0642    205 :ICGRVEHAHALASTWCFINAL
       1e3dB     70 :TCGVCTYTHALASTRCLEDAI
       T0642    226 :ISTSITALYANDFRANCE
       1e3dB    111 :MHDHLVHFYHLHALDFVD
       T0642    252 :INATEDINPRELIMINARY
       1e3dB    129 :VTSALLADPAKAAKLANSI
       T0642    290 :NSTNETHERLANDS
       1e3dB    148 :SPRKATTEEFAAVQ
       T0642    305 :NFINALINTERESTINGENDINGH
       1e3dB    162 :AKLKTFVASGQLGPFTNAYFLGGH
       T0642    330 :VEAN
       1e3dB    192 :PEAN
       T0642    334 :ICEFALLMERRYCHRIST
       1e3dB    197 :VCTAHYLQALRAQVEVAK
       T0642    352 :MASAN
       1e3dB    219 :FGAKN
       T0642    359 :AP
       1e3dB    226 :TQ
       T0642    361 :PYNEWYEARTAKEITEA
       1e3dB    235 :TCYEALTPERIKQFREL
Number of specific fragments extracted= 12 number of extra gaps= 1 total=16
# request to SCWRL produces command: ulimit -t 349 ; scwrl4 -t -i /var/tmp/to_scwrl_1276680966.pdb -s /var/tmp/to_scwrl_1276680966.seq -o /var/tmp/from_scwrl_1276680966.pdb > /var/tmp/scwrl_1276680966.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1276680966.pdb
  Number of alignments=2
# Reading fragments from alignment file
# Attempting to read fragment alignments from file 2i53A/T0642-2i53A-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
2i53A expands to /projects/compbio/data/pdb/2i53.pdb.gz
2i53A:# T0642 read from 2i53A/T0642-2i53A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m
# 2i53A read from 2i53A/T0642-2i53A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m
# adding 2i53A to template set
# found chain 2i53A in template set
       T0642    201 :ACIFICGRV
       2i53A     98 :CCLFLAGKV
       T0642    210 :EHAHALASTWCFINALISTSITALYANDFRANCEWEREELIM
       2i53A    108 :ETPKKCKDIIKTARSLLNDVQFGQFGDDPKEEVMVLERILLQ
       T0642    253 :NATEDINPRELIMINAR
       2i53A    150 :TIKFDLQVEHPYQFLLK
       T0642    285 :NAGAINSTNETHERLANDSINFINALINT
       2i53A    167 :YAKQLKGDKNKIQKLVQMAWTFVNDSLCT
       T0642    329 :AVEAN
       2i53A    200 :QWEPE
       T0642    334 :ICEFALLMERRYCH
       2i53A    206 :IAVAVMYLAGRLCK
       T0642    348 :RISTMAS
       2i53A    221 :EIQEWTS
       T0642    359 :APPYNEWYE
       2i53A    228 :KPMYRRWWE
       T0642    368 :ARTAKEITE
       2i53A    241 :DVPVDVLED
Number of specific fragments extracted= 9 number of extra gaps= 0 total=25
# request to SCWRL produces command: ulimit -t 349 ; scwrl4 -t -i /var/tmp/to_scwrl_306619267.pdb -s /var/tmp/to_scwrl_306619267.seq -o /var/tmp/from_scwrl_306619267.pdb > /var/tmp/scwrl_306619267.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_306619267.pdb
  Number of alignments=3
# Reading fragments from alignment file
# Attempting to read fragment alignments from file 2fmyA/T0642-2fmyA-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
2fmyA expands to /projects/compbio/data/pdb/2fmy.pdb.gz
2fmyA:# T0642 read from 2fmyA/T0642-2fmyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m
# 2fmyA read from 2fmyA/T0642-2fmyA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m
# adding 2fmyA to template set
# found chain 2fmyA in template set
       T0642     89 :ASSESSMENTDET
       2fmyA     16 :LNSEEYSGVLKEF
       T0642    102 :ERMINETH
       2fmyA     30 :EQRYSKKA
       T0642    112 :STSCIENTIFICCEN
       2fmyA     41 :TPNTERNLVFLVKSG
       T0642    130 :STHISTARGETI
       2fmyA     56 :RVRVYLAYEDKE
       T0642    156 :ASVERYSPECIF
       2fmyA     68 :FTLAILEAGDIF
       T0642    169 :CSHAPEWILLCHECKITATTHEMEETINGINPACIFICGRVEHAHALASTWCFINALISTS
       2fmyA     80 :CTHTRAFIQAMEDTTILYTDIRNFQNIVVEFPAFSLNMVKVLGDLLKNSLTIINGLVFKDA
       T0642    230 :ITALYANDFRANCE
       2fmyA    144 :LAEFLVQAAMDTGL
       T0642    245 :EREELIMINA
       2fmyA    158 :KVPQGIKLEL
       T0642    257 :DINPRELIMI
       2fmyA    168 :GLNTEEIALM
       T0642    289 :INSTNETHERLANDSIN
       2fmyA    178 :LGTTRQTVSVLLNDFKK
Number of specific fragments extracted= 10 number of extra gaps= 0 total=35
# request to SCWRL produces command: ulimit -t 349 ; scwrl4 -t -i /var/tmp/to_scwrl_1970725061.pdb -s /var/tmp/to_scwrl_1970725061.seq -o /var/tmp/from_scwrl_1970725061.pdb > /var/tmp/scwrl_1970725061.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1970725061.pdb
  Number of alignments=4
# Reading fragments from alignment file
# Attempting to read fragment alignments from file 2fxqA/T0642-2fxqA-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
2fxqA expands to /projects/compbio/data/pdb/2fxq.pdb.gz
2fxqA:# T0642 read from 2fxqA/T0642-2fxqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m
# 2fxqA read from 2fxqA/T0642-2fxqA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m
# adding 2fxqA to template set
# found chain 2fxqA in template set
Warning: unaligning (T0642)I122 because of BadResidue code BAD_PEPTIDE in next template residue (2fxqA)I11
Warning: unaligning (T0642)C123 because of BadResidue code BAD_PEPTIDE at template residue (2fxqA)I11
Warning: unaligning (T0642)E149 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2fxqA)D38
Warning: unaligning (T0642)N150 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (2fxqA)D38
Warning: unaligning (T0642)I205 because of BadResidue code BAD_PEPTIDE in next template residue (2fxqA)E79
Warning: unaligning (T0642)C206 because of BadResidue code BAD_PEPTIDE at template residue (2fxqA)E79
Warning: unaligning (T0642)A212 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (2fxqA)S95
       T0642    117 :ENTIF
       2fxqA      5 :LNQVF
       T0642    124 :CENTERSTHISTARGETISDIFFER
       2fxqA     12 :GTLTARPDMRYTPGGLAILDLNLAG
       T0642    151 :TANDHASVERY
       2fxqA     39 :AFTDESGQERE
       T0642    178 :LCHECKITATTHEMEETINGINPA
       2fxqA     50 :VPWYHRVRLLGRQAEMWGDLLEKG
       T0642    202 :CIF
       2fxqA     75 :LIF
       T0642    207 :GRVEH
       2fxqA     80 :GRLEY
Number of specific fragments extracted= 6 number of extra gaps= 3 total=41
# request to SCWRL produces command: ulimit -t 349 ; scwrl4 -t -i /var/tmp/to_scwrl_621138666.pdb -s /var/tmp/to_scwrl_621138666.seq -o /var/tmp/from_scwrl_621138666.pdb > /var/tmp/scwrl_621138666.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_621138666.pdb
  Number of alignments=5
# Reading fragments from alignment file
# Attempting to read fragment alignments from file 1dzlA/T0642-1dzlA-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
1dzlA expands to /projects/compbio/data/pdb/1dzl.pdb.gz
1dzlA:# T0642 read from 1dzlA/T0642-1dzlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m
# 1dzlA read from 1dzlA/T0642-1dzlA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m
# adding 1dzlA to template set
# found chain 1dzlA in template set
       T0642     15 :RRIFICNEWSYESTERDAY
       1dzlA    258 :RHLFNRAGTVGENVPDDLY
       T0642     38 :LEASEDTHELASTS
       1dzlA    277 :IKGSGSTANLASSN
       T0642     62 :THCASP
       1dzlA    293 :PTPSGS
       T0642     78 :ESTEDANDLET
       1dzlA    299 :MVTSDAQIFNK
       T0642    115 :CIENTIFICCENTERSTHISTARGET
       1dzlA    324 :CWGNQLFVTVVDTTRSTNMSLCAAIS
       T0642    148 :RENTANDHASVERY
       1dzlA    350 :TSETTYKNTNFKEY
       T0642    165 :CIFICS
       1dzlA    364 :LRHGEE
       T0642    174 :EWILLCHECKITATT
       1dzlA    371 :DLQFIFQLCKITLTA
       T0642    190 :EMEETINGIN
       1dzlA    386 :DVMTYIHSMN
       T0642    227 :STSI
       1dzlA    396 :STIL
       T0642    236 :NDFRAN
       1dzlA    400 :EDWNFG
       T0642    252 :INATEDINPRELIMINARYMATCHESSPAI
       1dzlA    406 :LQPPPGGTLEDTYRFVTSQAIACQKHTPPA
       T0642    294 :ETHERLANDS
       1dzlA    436 :PKEDPLKKYT
       T0642    316 :ESTINGENDINGHAVEANICEFALL
       1dzlA    446 :FWEVNLKEKFSADLDQFPLGRKFLL
Number of specific fragments extracted= 14 number of extra gaps= 0 total=55
# request to SCWRL produces command: ulimit -t 349 ; scwrl4 -t -i /var/tmp/to_scwrl_1047453136.pdb -s /var/tmp/to_scwrl_1047453136.seq -o /var/tmp/from_scwrl_1047453136.pdb > /var/tmp/scwrl_1047453136.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_1047453136.pdb
  Number of alignments=6
# Reading fragments from alignment file
# Attempting to read fragment alignments from file 2koeA/T0642-2koeA-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
2koeA expands to /projects/compbio/data/pdb/2koe.pdb.gz
2koeA:# T0642 read from 2koeA/T0642-2koeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m
# 2koeA read from 2koeA/T0642-2koeA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m
# adding 2koeA to template set
# found chain 2koeA in template set
       T0642    214 :ALASTWCFINA
       2koeA      4 :AFASMLCLLNS
       T0642    351 :TMASAN
       2koeA     15 :TVNPII
Number of specific fragments extracted= 2 number of extra gaps= 0 total=57
# request to SCWRL produces command: ulimit -t 349 ; scwrl4 -t -i /var/tmp/to_scwrl_944605058.pdb -s /var/tmp/to_scwrl_944605058.seq -o /var/tmp/from_scwrl_944605058.pdb > /var/tmp/scwrl_944605058.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_944605058.pdb
  Number of alignments=7
# Reading fragments from alignment file
# Attempting to read fragment alignments from file 1x7aL/T0642-1x7aL-t04-global-adpstyle1.a2m with NO bystroff filtering
# adding to alignment library if long or multiple fragments
1x7aL expands to /projects/compbio/data/pdb/1x7a.pdb.gz
1x7aL:# T0642 read from 1x7aL/T0642-1x7aL-t04-global-adpstyle1.a2m
# 1x7aL read from 1x7aL/T0642-1x7aL-t04-global-adpstyle1.a2m
# adding 1x7aL to template set
# found chain 1x7aL in template set
Warning: unaligning (T0642)H109 because first residue in template chain is (1x7aL)Q50
Warning: unaligning (T0642)E110 because of BadResidue code BAD_PEPTIDE at template residue (1x7aL)C51
Warning: unaligning (T0642)E111 because of BadResidue code BAD_PEPTIDE in next template residue (1x7aL)P53
Warning: unaligning (T0642)S112 because of BadResidue code BAD_PEPTIDE at template residue (1x7aL)P53
Warning: unaligning (T0642)T119 because of BadResidue code BAD_PEPTIDE in next template residue (1x7aL)L61
Warning: unaligning (T0642)I120 because of BadResidue code BAD_PEPTIDE at template residue (1x7aL)L61
Warning: unaligning (T0642)T127 because of BadResidue code BAD_PEPTIDE in next template residue (1x7aL)I66
Warning: unaligning (T0642)E128 because of BadResidue code BAD_PEPTIDE at template residue (1x7aL)I66
Warning: unaligning (T0642)I141 because of BadResidue code BAD_PEPTIDE in next template residue (1x7aL)C73
Warning: unaligning (T0642)S142 because of BadResidue code BAD_PEPTIDE at template residue (1x7aL)C73
Warning: unaligning (T0642)F145 because of BadResidue code BAD_PEPTIDE in next template residue (1x7aL)F77
Warning: unaligning (T0642)F146 because of BadResidue code BAD_PEPTIDE at template residue (1x7aL)F77
Warning: unaligning (T0642)R148 because of BadResidue code BAD_PEPTIDE in next template residue (1x7aL)K80
Warning: unaligning (T0642)E149 because of BadResidue code BAD_PEPTIDE at template residue (1x7aL)K80
Warning: unaligning (T0642)P173 because of BadResidue code BAD_PEPTIDE in next template residue (1x7aL)D104
Warning: unaligning (T0642)E174 because of BadResidue code BAD_PEPTIDE at template residue (1x7aL)D104
Warning: unaligning (T0642)H180 because of BadResidue code BAD_PEPTIDE in next template residue (1x7aL)C111
Warning: unaligning (T0642)T185 because of BadResidue code BAD_PEPTIDE at template residue (1x7aL)C111
Warning: unaligning (T0642)A186 because of BadResidue code BAD_PEPTIDE in next template residue (1x7aL)T113
Warning: unaligning (T0642)T187 because of BadResidue code BAD_PEPTIDE at template residue (1x7aL)T113
Warning: unaligning (T0642)T194 because of BadResidue code BAD_PEPTIDE in next template residue (1x7aL)Q121
Warning: unaligning (T0642)I195 because of BadResidue code BAD_PEPTIDE at template residue (1x7aL)Q121
Warning: unaligning (T0642)F204 because of BadResidue code BAD_PEPTIDE in next template residue (1x7aL)P131
Warning: unaligning (T0642)I205 because of BadResidue code BAD_PEPTIDE at template residue (1x7aL)P131
Warning: unaligning (T0642)N381 because of BadResidue code BAD_PEPTIDE in next template residue (1x7aL)P141
Warning: unaligning (T0642)D382 because of BadResidue code BAD_PEPTIDE at template residue (1x7aL)P141
       T0642    113 :TSCIEN
       1x7aL     54 :NPCLNG
       T0642    124 :CEN
       1x7aL     62 :CKD
       T0642    129 :RST
       1x7aL     67 :NSY
       T0642    139 :ET
       1x7aL     70 :EC
       T0642    143 :DI
       1x7aL     74 :QV
       T0642    147 :E
       1x7aL     78 :E
       T0642    150 :NTAND
       1x7aL     81 :NCELD
       T0642    156 :ASVERYSPECIFICSHA
       1x7aL     86 :ATCNIKNGRCKQFCKTG
       T0642    175 :WILLC
       1x7aL    105 :SKVLC
       T0642    188 :THEMEE
       1x7aL    114 :GYRLAP
       T0642    196 :NGINPACI
       1x7aL    122 :KSCKPAVP
       T0642    206 :CGRVEHAH
       1x7aL    132 :CGRVSVSH
       T0642    383 :SMILE
       1x7aL    142 :TTLTR
Number of specific fragments extracted= 13 number of extra gaps= 10 total=70
# request to SCWRL produces command: ulimit -t 349 ; scwrl4 -t -i /var/tmp/to_scwrl_991677442.pdb -s /var/tmp/to_scwrl_991677442.seq -o /var/tmp/from_scwrl_991677442.pdb > /var/tmp/scwrl_991677442.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_991677442.pdb
  Number of alignments=8
# Reading fragments from alignment file
# Attempting to read fragment alignments from file 1jlvA/T0642-1jlvA-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
# T0642 read from 1jlvA/T0642-1jlvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m
# 1jlvA read from 1jlvA/T0642-1jlvA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m
# found chain 1jlvA in training set
       T0642    188 :THEMEETINGINPACIFICGRVE
       1jlvA     40 :KPEFLKINPQHCIPTLVDNGFAL
       T0642    216 :ASTWCFINALIS
       1jlvA     63 :WESRAICTYLAE
       T0642    233 :LYANDFRANC
       1jlvA     75 :KYGKDDKLYP
       T0642    258 :INPRELIMINARY
       1jlvA     85 :KDPQKRAVVNQRL
       T0642    271 :MATCHESSPAINWINAGAINSTNETHERLANDSINFINALINTER
       1jlvA    101 :MGTLYQRFADYYYPQIFAKQPANAENEKKMKDAVDFLNTFLDGHK
       T0642    324 :DINGHA
       1jlvA    146 :YVAGDS
       T0642    332 :ANICEFALLMERRYCH
       1jlvA    152 :LTIADLTVLATVSTYD
       T0642    349 :IST
       1jlvA    168 :VAG
       T0642    354 :SANDHAPPYNEWYE
       1jlvA    171 :FELAKYPHVAAWYE
       T0642    369 :RTAKEI
       1jlvA    185 :RTRKEA
Number of specific fragments extracted= 10 number of extra gaps= 0 total=80
# request to SCWRL produces command: ulimit -t 349 ; scwrl4 -t -i /var/tmp/to_scwrl_363964257.pdb -s /var/tmp/to_scwrl_363964257.seq -o /var/tmp/from_scwrl_363964257.pdb > /var/tmp/scwrl_363964257.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_363964257.pdb
  Number of alignments=9
# Reading fragments from alignment file
# Attempting to read fragment alignments from file 3lqaG/T0642-3lqaG-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
3lqaG expands to /projects/compbio/data/pdb/3lqa.pdb.gz
3lqaG:# T0642 read from 3lqaG/T0642-3lqaG-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m
# 3lqaG read from 3lqaG/T0642-3lqaG-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m
# adding 3lqaG to template set
# found chain 3lqaG in template set
Warning: unaligning (T0642)T119 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3lqaG)N193
Warning: unaligning (T0642)E128 because of BadResidue code CHAIN_BREAK_BEFORE+BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3lqaG)N193
Warning: unaligning (T0642)D154 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR in next template residue (3lqaG)P208
Warning: unaligning (T0642)H155 because of BadResidue code BAD_PEPTIDE+HIGH_B_FACTOR at template residue (3lqaG)P208
       T0642    118 :N
       3lqaG    122 :T
       T0642    129 :RSTHISTARGETI
       3lqaG    194 :TSTIAQACPKVSF
       T0642    156 :ASVERYSPE
       3lqaG    209 :IPIHYCAPA
       T0642    165 :CIFICSHAP
       3lqaG    220 :AILKCNDKT
       T0642    174 :EWILLCHECKITATTHE
       3lqaG    230 :NGIGPCNNVSTVQCTHG
       T0642    198 :INPAC
       3lqaG    247 :IKPVV
Number of specific fragments extracted= 6 number of extra gaps= 1 total=86
# request to SCWRL produces command: ulimit -t 349 ; scwrl4 -t -i /var/tmp/to_scwrl_767788961.pdb -s /var/tmp/to_scwrl_767788961.seq -o /var/tmp/from_scwrl_767788961.pdb > /var/tmp/scwrl_767788961.log
# Trying to read SCWRLed conformation from /var/tmp/from_scwrl_767788961.pdb
  Number of alignments=10
# command:Debug: superimposing conformation 0 on the average so far
superimposing iter= 0 total_weight= 0.238 rmsd (weighted)= 0.000 (unweighted)= 0.000
superimposing iter= 1 total_weight= 4870.000 rmsd (weighted)= 0.000 (unweighted)= 0.000
superimposing iter= 2 total_weight= 4870.000 rmsd (weighted)= 0.000 (unweighted)= 0.000
superimposing iter= 3 total_weight= 4870.000 rmsd (weighted)= 0.000 (unweighted)= 0.000
superimposing iter= 4 total_weight= 4870.000 rmsd (weighted)= 0.000 (unweighted)= 0.000
superimposing iter= 5 total_weight= 4870.000 rmsd (weighted)= 0.000 (unweighted)= 0.000
Debug: superimposing conformation 1 on the average so far
superimposing iter= 0 total_weight= 0.047 rmsd (weighted)= 5.827 (unweighted)= 102.329
superimposing iter= 1 total_weight= 232.019 rmsd (weighted)= 3.179 (unweighted)= 102.787
superimposing iter= 2 total_weight= 247.894 rmsd (weighted)= 1.760 (unweighted)= 104.512
superimposing iter= 3 total_weight= 176.260 rmsd (weighted)= 1.203 (unweighted)= 106.142
superimposing iter= 4 total_weight= 138.861 rmsd (weighted)= 0.968 (unweighted)= 106.776
superimposing iter= 5 total_weight= 113.687 rmsd (weighted)= 0.872 (unweighted)= 107.077
Debug: superimposing conformation 2 on the average so far
superimposing iter= 0 total_weight= 0.000 rmsd (weighted)= nan (unweighted)= 58.093
superimposing iter= 1 total_weight= 0.000 rmsd (weighted)= nan (unweighted)= 58.093
superimposing iter= 2 total_weight= 0.000 rmsd (weighted)= nan (unweighted)= 58.093
superimposing iter= 3 total_weight= 0.000 rmsd (weighted)= nan (unweighted)= 58.093
superimposing iter= 4 total_weight= 0.000 rmsd (weighted)= nan (unweighted)= 58.093
superimposing iter= 5 total_weight= 0.000 rmsd (weighted)= nan (unweighted)= 58.093
Debug: superimposing conformation 3 on the average so far
superimposing iter= 0 total_weight= 0.178 rmsd (weighted)= 15.882 (unweighted)= 104.937
superimposing iter= 1 total_weight= 820.871 rmsd (weighted)= 10.073 (unweighted)= 97.117
superimposing iter= 2 total_weight= 585.744 rmsd (weighted)= 7.692 (unweighted)= 92.024
superimposing iter= 3 total_weight= 545.412 rmsd (weighted)= 6.113 (unweighted)= 90.063
superimposing iter= 4 total_weight= 466.240 rmsd (weighted)= 5.254 (unweighted)= 89.392
superimposing iter= 5 total_weight= 436.347 rmsd (weighted)= 4.663 (unweighted)= 89.051
Debug: superimposing conformation 4 on the average so far
superimposing iter= 0 total_weight= 0.193 rmsd (weighted)= 29.190 (unweighted)= 118.601
superimposing iter= 1 total_weight= 778.293 rmsd (weighted)= 19.650 (unweighted)= 122.495
superimposing iter= 2 total_weight= 759.337 rmsd (weighted)= 13.551 (unweighted)= 123.479
superimposing iter= 3 total_weight= 613.456 rmsd (weighted)= 10.567 (unweighted)= 124.036
superimposing iter= 4 total_weight= 499.675 rmsd (weighted)= 9.220 (unweighted)= 124.556
superimposing iter= 5 total_weight= 431.969 rmsd (weighted)= 8.682 (unweighted)= 125.023
Debug: superimposing conformation 5 on the average so far
superimposing iter= 0 total_weight= 0.193 rmsd (weighted)= 11.585 (unweighted)= 161.827
superimposing iter= 1 total_weight= 995.869 rmsd (weighted)= 5.837 (unweighted)= 156.593
superimposing iter= 2 total_weight= 1579.498 rmsd (weighted)= 2.227 (unweighted)= 155.116
superimposing iter= 3 total_weight= 1734.752 rmsd (weighted)= 0.914 (unweighted)= 154.834
superimposing iter= 4 total_weight= 992.639 rmsd (weighted)= 0.558 (unweighted)= 154.760
superimposing iter= 5 total_weight= 549.551 rmsd (weighted)= 0.467 (unweighted)= 154.743
Debug: superimposing conformation 6 on the average so far
superimposing iter= 0 total_weight= 0.000 rmsd (weighted)= nan (unweighted)= 46.687
superimposing iter= 1 total_weight= 0.000 rmsd (weighted)= nan (unweighted)= 46.687
superimposing iter= 2 total_weight= 0.000 rmsd (weighted)= nan (unweighted)= 46.687
superimposing iter= 3 total_weight= 0.000 rmsd (weighted)= nan (unweighted)= 46.687
superimposing iter= 4 total_weight= 0.000 rmsd (weighted)= nan (unweighted)= 46.687
superimposing iter= 5 total_weight= 0.000 rmsd (weighted)= nan (unweighted)= 46.687
Debug: superimposing conformation 7 on the average so far
superimposing iter= 0 total_weight= 0.135 rmsd (weighted)= 21.291 (unweighted)= 55.785
superimposing iter= 1 total_weight= 863.666 rmsd (weighted)= 11.239 (unweighted)= 59.633
superimposing iter= 2 total_weight= 460.098 rmsd (weighted)= 8.553 (unweighted)= 58.608
superimposing iter= 3 total_weight= 317.213 rmsd (weighted)= 7.913 (unweighted)= 58.594
superimposing iter= 4 total_weight= 283.367 rmsd (weighted)= 7.756 (unweighted)= 58.627
superimposing iter= 5 total_weight= 275.751 rmsd (weighted)= 7.712 (unweighted)= 58.611
Debug: superimposing conformation 8 on the average so far
superimposing iter= 0 total_weight= 0.016 rmsd (weighted)= 1.733 (unweighted)= 189.377
superimposing iter= 1 total_weight= 167.115 rmsd (weighted)= 0.566 (unweighted)= 186.180
superimposing iter= 2 total_weight= 145.174 rmsd (weighted)= 0.241 (unweighted)= 185.698
superimposing iter= 3 total_weight= 67.666 rmsd (weighted)= 0.166 (unweighted)= 185.630
superimposing iter= 4 total_weight= 44.050 rmsd (weighted)= 0.142 (unweighted)= 185.653
superimposing iter= 5 total_weight= 39.026 rmsd (weighted)= 0.130 (unweighted)= 185.691
Debug: superimposing conformation 9 on the average so far
superimposing iter= 0 total_weight= 0.131 rmsd (weighted)= 18.094 (unweighted)= 97.574
superimposing iter= 1 total_weight= 746.194 rmsd (weighted)= 10.454 (unweighted)= 102.917
superimposing iter= 2 total_weight= 358.737 rmsd (weighted)= 8.911 (unweighted)= 105.683
superimposing iter= 3 total_weight= 297.106 rmsd (weighted)= 8.407 (unweighted)= 107.041
superimposing iter= 4 total_weight= 271.975 rmsd (weighted)= 8.299 (unweighted)= 107.809
superimposing iter= 5 total_weight= 265.420 rmsd (weighted)= 8.295 (unweighted)= 108.222
Debug: superimposing conformation 0 on the average so far
superimposing iter= 0 total_weight= 0.238 rmsd (weighted)= 12.612 (unweighted)= 94.416
superimposing iter= 1 total_weight= 1657.094 rmsd (weighted)= 6.209 (unweighted)= 93.607
superimposing iter= 2 total_weight= 923.443 rmsd (weighted)= 4.390 (unweighted)= 93.721
superimposing iter= 3 total_weight= 613.613 rmsd (weighted)= 3.866 (unweighted)= 93.900
superimposing iter= 4 total_weight= 530.300 rmsd (weighted)= 3.674 (unweighted)= 94.101
superimposing iter= 5 total_weight= 504.686 rmsd (weighted)= 3.586 (unweighted)= 94.275
Debug: superimposing conformation 1 on the average so far
superimposing iter= 0 total_weight= 0.654 rmsd (weighted)= 22.456 (unweighted)= 51.440
superimposing iter= 1 total_weight= 3746.229 rmsd (weighted)= 12.638 (unweighted)= 48.951
superimposing iter= 2 total_weight= 1993.682 rmsd (weighted)= 10.111 (unweighted)= 48.447
superimposing iter= 3 total_weight= 1614.954 rmsd (weighted)= 9.075 (unweighted)= 48.299
superimposing iter= 4 total_weight= 1481.656 rmsd (weighted)= 8.533 (unweighted)= 48.261
superimposing iter= 5 total_weight= 1398.544 rmsd (weighted)= 8.271 (unweighted)= 48.253
Debug: superimposing conformation 2 on the average so far
superimposing iter= 0 total_weight= 0.549 rmsd (weighted)= 16.684 (unweighted)= 60.659
superimposing iter= 1 total_weight= 2808.455 rmsd (weighted)= 10.195 (unweighted)= 59.846
superimposing iter= 2 total_weight= 1313.297 rmsd (weighted)= 9.356 (unweighted)= 59.551
superimposing iter= 3 total_weight= 1159.429 rmsd (weighted)= 9.158 (unweighted)= 59.394
superimposing iter= 4 total_weight= 1149.403 rmsd (weighted)= 9.009 (unweighted)= 59.314
superimposing iter= 5 total_weight= 1156.146 rmsd (weighted)= 8.839 (unweighted)= 59.281
Debug: superimposing conformation 3 on the average so far
superimposing iter= 0 total_weight= 0.661 rmsd (weighted)= 15.201 (unweighted)= 76.056
superimposing iter= 1 total_weight= 3404.170 rmsd (weighted)= 9.290 (unweighted)= 74.568
superimposing iter= 2 total_weight= 1686.093 rmsd (weighted)= 8.192 (unweighted)= 73.747
superimposing iter= 3 total_weight= 1484.374 rmsd (weighted)= 7.743 (unweighted)= 73.350
superimposing iter= 4 total_weight= 1406.878 rmsd (weighted)= 7.533 (unweighted)= 73.122
superimposing iter= 5 total_weight= 1376.345 rmsd (weighted)= 7.413 (unweighted)= 72.942
Debug: superimposing conformation 4 on the average so far
superimposing iter= 0 total_weight= 0.284 rmsd (weighted)= 18.559 (unweighted)= 73.857
superimposing iter= 1 total_weight= 1168.895 rmsd (weighted)= 12.624 (unweighted)= 74.822
superimposing iter= 2 total_weight= 726.013 rmsd (weighted)= 11.097 (unweighted)= 75.573
superimposing iter= 3 total_weight= 637.532 rmsd (weighted)= 10.442 (unweighted)= 76.466
superimposing iter= 4 total_weight= 631.473 rmsd (weighted)= 9.881 (unweighted)= 77.362
superimposing iter= 5 total_weight= 624.103 rmsd (weighted)= 9.422 (unweighted)= 78.096
Debug: superimposing conformation 5 on the average so far
superimposing iter= 0 total_weight= 0.756 rmsd (weighted)= 20.855 (unweighted)= 103.542
superimposing iter= 1 total_weight= 4175.696 rmsd (weighted)= 10.722 (unweighted)= 107.262
superimposing iter= 2 total_weight= 4870.835 rmsd (weighted)= 5.327 (unweighted)= 108.198
superimposing iter= 3 total_weight= 4393.710 rmsd (weighted)= 2.807 (unweighted)= 108.466
superimposing iter= 4 total_weight= 4129.913 rmsd (weighted)= 1.492 (unweighted)= 108.561
superimposing iter= 5 total_weight= 4038.047 rmsd (weighted)= 0.794 (unweighted)= 108.585
Debug: superimposing conformation 6 on the average so far
superimposing iter= 0 total_weight= 0.062 rmsd (weighted)= 9.648 (unweighted)= 63.484
superimposing iter= 1 total_weight= 362.893 rmsd (weighted)= 5.366 (unweighted)= 63.097
superimposing iter= 2 total_weight= 164.390 rmsd (weighted)= 4.567 (unweighted)= 62.830
superimposing iter= 3 total_weight= 132.324 rmsd (weighted)= 4.358 (unweighted)= 62.698
superimposing iter= 4 total_weight= 125.435 rmsd (weighted)= 4.277 (unweighted)= 62.642
superimposing iter= 5 total_weight= 123.580 rmsd (weighted)= 4.234 (unweighted)= 62.620
Debug: superimposing conformation 7 on the average so far
superimposing iter= 0 total_weight= 0.272 rmsd (weighted)= 11.401 (unweighted)= 83.884
superimposing iter= 1 total_weight= 1060.720 rmsd (weighted)= 8.123 (unweighted)= 84.515
superimposing iter= 2 total_weight= 624.553 rmsd (weighted)= 7.572 (unweighted)= 85.079
superimposing iter= 3 total_weight= 622.861 rmsd (weighted)= 7.064 (unweighted)= 85.634
superimposing iter= 4 total_weight= 678.347 rmsd (weighted)= 6.301 (unweighted)= 86.116
superimposing iter= 5 total_weight= 755.128 rmsd (weighted)= 5.300 (unweighted)= 86.289
Debug: superimposing conformation 8 on the average so far
superimposing iter= 0 total_weight= 0.576 rmsd (weighted)= 21.720 (unweighted)= 101.889
superimposing iter= 1 total_weight= 2703.398 rmsd (weighted)= 13.903 (unweighted)= 100.822
superimposing iter= 2 total_weight= 1471.640 rmsd (weighted)= 12.245 (unweighted)= 99.253
superimposing iter= 3 total_weight= 1375.232 rmsd (weighted)= 11.193 (unweighted)= 97.903
superimposing iter= 4 total_weight= 1328.900 rmsd (weighted)= 10.440 (unweighted)= 96.978
superimposing iter= 5 total_weight= 1274.179 rmsd (weighted)= 9.966 (unweighted)= 96.436
Debug: superimposing conformation 9 on the average so far
superimposing iter= 0 total_weight= 0.207 rmsd (weighted)= 14.305 (unweighted)= 83.334
superimposing iter= 1 total_weight= 914.976 rmsd (weighted)= 9.426 (unweighted)= 85.551
superimposing iter= 2 total_weight= 550.808 rmsd (weighted)= 8.113 (unweighted)= 86.470
superimposing iter= 3 total_weight= 478.488 rmsd (weighted)= 7.518 (unweighted)= 87.023
superimposing iter= 4 total_weight= 446.362 rmsd (weighted)= 7.216 (unweighted)= 87.442
superimposing iter= 5 total_weight= 424.154 rmsd (weighted)= 7.104 (unweighted)= 87.804
Debug: superimposing conformation 0 on the average so far
superimposing iter= 0 total_weight= 0.238 rmsd (weighted)= 13.474 (unweighted)= 91.691
superimposing iter= 1 total_weight= 1790.657 rmsd (weighted)= 6.350 (unweighted)= 91.316
superimposing iter= 2 total_weight= 990.910 rmsd (weighted)= 4.355 (unweighted)= 91.379
superimposing iter= 3 total_weight= 595.847 rmsd (weighted)= 3.908 (unweighted)= 91.508
superimposing iter= 4 total_weight= 508.406 rmsd (weighted)= 3.803 (unweighted)= 91.593
superimposing iter= 5 total_weight= 491.328 rmsd (weighted)= 3.766 (unweighted)= 91.646
Debug: superimposing conformation 1 on the average so far
superimposing iter= 0 total_weight= 0.654 rmsd (weighted)= 16.749 (unweighted)= 45.791
superimposing iter= 1 total_weight= 3243.062 rmsd (weighted)= 10.562 (unweighted)= 45.698
superimposing iter= 2 total_weight= 1505.217 rmsd (weighted)= 9.920 (unweighted)= 45.681
superimposing iter= 3 total_weight= 1361.861 rmsd (weighted)= 9.798 (unweighted)= 45.662
superimposing iter= 4 total_weight= 1343.963 rmsd (weighted)= 9.735 (unweighted)= 45.643
superimposing iter= 5 total_weight= 1340.714 rmsd (weighted)= 9.676 (unweighted)= 45.627
Debug: superimposing conformation 2 on the average so far
superimposing iter= 0 total_weight= 0.549 rmsd (weighted)= 13.697 (unweighted)= 57.362
superimposing iter= 1 total_weight= 1901.484 rmsd (weighted)= 10.340 (unweighted)= 57.832
superimposing iter= 2 total_weight= 1284.216 rmsd (weighted)= 9.568 (unweighted)= 58.488
superimposing iter= 3 total_weight= 1210.260 rmsd (weighted)= 9.131 (unweighted)= 58.939
superimposing iter= 4 total_weight= 1223.163 rmsd (weighted)= 8.676 (unweighted)= 59.264
superimposing iter= 5 total_weight= 1206.777 rmsd (weighted)= 8.309 (unweighted)= 59.510
Debug: superimposing conformation 3 on the average so far
superimposing iter= 0 total_weight= 0.661 rmsd (weighted)= 12.707 (unweighted)= 78.805
superimposing iter= 1 total_weight= 3760.735 rmsd (weighted)= 7.226 (unweighted)= 77.749
superimposing iter= 2 total_weight= 1796.424 rmsd (weighted)= 6.129 (unweighted)= 77.385
superimposing iter= 3 total_weight= 1515.112 rmsd (weighted)= 5.703 (unweighted)= 77.153
superimposing iter= 4 total_weight= 1500.738 rmsd (weighted)= 5.349 (unweighted)= 77.001
superimposing iter= 5 total_weight= 1531.670 rmsd (weighted)= 4.971 (unweighted)= 76.868
Debug: superimposing conformation 4 on the average so far
superimposing iter= 0 total_weight= 0.284 rmsd (weighted)= 17.319 (unweighted)= 73.486
superimposing iter= 1 total_weight= 1191.170 rmsd (weighted)= 11.537 (unweighted)= 74.945
superimposing iter= 2 total_weight= 756.819 rmsd (weighted)= 9.842 (unweighted)= 76.082
superimposing iter= 3 total_weight= 674.302 rmsd (weighted)= 8.943 (unweighted)= 76.992
superimposing iter= 4 total_weight= 657.505 rmsd (weighted)= 8.303 (unweighted)= 77.555
superimposing iter= 5 total_weight= 621.680 rmsd (weighted)= 7.967 (unweighted)= 77.907
Debug: superimposing conformation 5 on the average so far
superimposing iter= 0 total_weight= 0.756 rmsd (weighted)= 19.471 (unweighted)= 102.788
superimposing iter= 1 total_weight= 3723.526 rmsd (weighted)= 11.499 (unweighted)= 105.822
superimposing iter= 2 total_weight= 3110.286 rmsd (weighted)= 7.377 (unweighted)= 107.466
superimposing iter= 3 total_weight= 4173.915 rmsd (weighted)= 3.948 (unweighted)= 108.166
superimposing iter= 4 total_weight= 4154.116 rmsd (weighted)= 2.078 (unweighted)= 108.424
superimposing iter= 5 total_weight= 4055.282 rmsd (weighted)= 1.102 (unweighted)= 108.496
Debug: superimposing conformation 6 on the average so far
superimposing iter= 0 total_weight= 0.062 rmsd (weighted)= 5.212 (unweighted)= 62.203
superimposing iter= 1 total_weight= 275.418 rmsd (weighted)= 3.355 (unweighted)= 62.957
superimposing iter= 2 total_weight= 166.533 rmsd (weighted)= 2.830 (unweighted)= 63.171
superimposing iter= 3 total_weight= 148.048 rmsd (weighted)= 2.550 (unweighted)= 63.230
superimposing iter= 4 total_weight= 133.799 rmsd (weighted)= 2.424 (unweighted)= 63.234
superimposing iter= 5 total_weight= 126.819 rmsd (weighted)= 2.368 (unweighted)= 63.217
Debug: superimposing conformation 7 on the average so far
superimposing iter= 0 total_weight= 0.272 rmsd (weighted)= 11.505 (unweighted)= 82.808
superimposing iter= 1 total_weight= 1298.134 rmsd (weighted)= 7.285 (unweighted)= 84.168
superimposing iter= 2 total_weight= 832.434 rmsd (weighted)= 5.760 (unweighted)= 84.865
superimposing iter= 3 total_weight= 695.373 rmsd (weighted)= 4.970 (unweighted)= 85.242
superimposing iter= 4 total_weight= 637.779 rmsd (weighted)= 4.476 (unweighted)= 85.505
superimposing iter= 5 total_weight= 604.582 rmsd (weighted)= 4.139 (unweighted)= 85.680
Debug: superimposing conformation 8 on the average so far
superimposing iter= 0 total_weight= 0.576 rmsd (weighted)= 13.366 (unweighted)= 95.154
superimposing iter= 1 total_weight= 2951.328 rmsd (weighted)= 8.016 (unweighted)= 94.519
superimposing iter= 2 total_weight= 1823.636 rmsd (weighted)= 6.314 (unweighted)= 94.413
superimposing iter= 3 total_weight= 1460.176 rmsd (weighted)= 5.602 (unweighted)= 94.462
superimposing iter= 4 total_weight= 1301.486 rmsd (weighted)= 5.262 (unweighted)= 94.507
superimposing iter= 5 total_weight= 1216.344 rmsd (weighted)= 5.105 (unweighted)= 94.533
Debug: superimposing conformation 9 on the average so far
superimposing iter= 0 total_weight= 0.207 rmsd (weighted)= 14.289 (unweighted)= 84.079
superimposing iter= 1 total_weight= 801.066 rmsd (weighted)= 10.042 (unweighted)= 86.422
superimposing iter= 2 total_weight= 556.477 rmsd (weighted)= 8.610 (unweighted)= 87.395
superimposing iter= 3 total_weight= 466.367 rmsd (weighted)= 8.098 (unweighted)= 87.905
superimposing iter= 4 total_weight= 433.462 rmsd (weighted)= 7.897 (unweighted)= 88.323
superimposing iter= 5 total_weight= 426.076 rmsd (weighted)= 7.751 (unweighted)= 88.743
superimposing iter= 0 total_weight= 0.238 rmsd (weighted)= 13.585 (unweighted)= 90.764
superimposing iter= 1 total_weight= 1807.164 rmsd (weighted)= 6.381 (unweighted)= 90.696
superimposing iter= 2 total_weight= 974.245 rmsd (weighted)= 4.423 (unweighted)= 90.764
superimposing iter= 3 total_weight= 591.533 rmsd (weighted)= 3.984 (unweighted)= 90.852
superimposing iter= 4 total_weight= 513.950 rmsd (weighted)= 3.856 (unweighted)= 90.926
superimposing iter= 5 total_weight= 498.655 rmsd (weighted)= 3.792 (unweighted)= 90.979
superimposing iter= 0 total_weight= 0.654 rmsd (weighted)= 16.099 (unweighted)= 45.711
superimposing iter= 1 total_weight= 3238.466 rmsd (weighted)= 10.149 (unweighted)= 45.672
superimposing iter= 2 total_weight= 1520.616 rmsd (weighted)= 9.462 (unweighted)= 45.669
superimposing iter= 3 total_weight= 1371.577 rmsd (weighted)= 9.295 (unweighted)= 45.665
superimposing iter= 4 total_weight= 1341.810 rmsd (weighted)= 9.229 (unweighted)= 45.657
superimposing iter= 5 total_weight= 1332.099 rmsd (weighted)= 9.194 (unweighted)= 45.647
superimposing iter= 0 total_weight= 0.549 rmsd (weighted)= 13.622 (unweighted)= 60.846
superimposing iter= 1 total_weight= 1974.764 rmsd (weighted)= 10.012 (unweighted)= 60.750
superimposing iter= 2 total_weight= 1358.562 rmsd (weighted)= 8.945 (unweighted)= 61.390
superimposing iter= 3 total_weight= 1265.142 rmsd (weighted)= 8.296 (unweighted)= 61.838
superimposing iter= 4 total_weight= 1301.342 rmsd (weighted)= 7.608 (unweighted)= 62.128
superimposing iter= 5 total_weight= 1304.604 rmsd (weighted)= 6.986 (unweighted)= 62.317
superimposing iter= 0 total_weight= 0.661 rmsd (weighted)= 12.483 (unweighted)= 79.632
superimposing iter= 1 total_weight= 3824.927 rmsd (weighted)= 7.040 (unweighted)= 78.199
superimposing iter= 2 total_weight= 1776.379 rmsd (weighted)= 5.967 (unweighted)= 77.542
superimposing iter= 3 total_weight= 1664.274 rmsd (weighted)= 5.243 (unweighted)= 77.231
superimposing iter= 4 total_weight= 1865.880 rmsd (weighted)= 4.352 (unweighted)= 77.136
superimposing iter= 5 total_weight= 2232.935 rmsd (weighted)= 3.272 (unweighted)= 77.085
superimposing iter= 0 total_weight= 0.284 rmsd (weighted)= 17.167 (unweighted)= 73.834
superimposing iter= 1 total_weight= 1225.891 rmsd (weighted)= 11.236 (unweighted)= 75.406
superimposing iter= 2 total_weight= 782.435 rmsd (weighted)= 9.387 (unweighted)= 76.494
superimposing iter= 3 total_weight= 699.048 rmsd (weighted)= 8.371 (unweighted)= 77.212
superimposing iter= 4 total_weight= 658.091 rmsd (weighted)= 7.771 (unweighted)= 77.614
superimposing iter= 5 total_weight= 612.750 rmsd (weighted)= 7.511 (unweighted)= 77.837
superimposing iter= 0 total_weight= 0.756 rmsd (weighted)= 19.430 (unweighted)= 102.778
superimposing iter= 1 total_weight= 3812.563 rmsd (weighted)= 11.357 (unweighted)= 105.848
superimposing iter= 2 total_weight= 3182.335 rmsd (weighted)= 7.211 (unweighted)= 107.468
superimposing iter= 3 total_weight= 4132.868 rmsd (weighted)= 3.869 (unweighted)= 108.164
superimposing iter= 4 total_weight= 4118.871 rmsd (weighted)= 2.042 (unweighted)= 108.405
superimposing iter= 5 total_weight= 4033.324 rmsd (weighted)= 1.085 (unweighted)= 108.460
superimposing iter= 0 total_weight= 0.062 rmsd (weighted)= 5.454 (unweighted)= 64.682
superimposing iter= 1 total_weight= 323.286 rmsd (weighted)= 3.213 (unweighted)= 65.765
superimposing iter= 2 total_weight= 176.113 rmsd (weighted)= 2.645 (unweighted)= 66.159
superimposing iter= 3 total_weight= 140.969 rmsd (weighted)= 2.452 (unweighted)= 66.239
superimposing iter= 4 total_weight= 128.126 rmsd (weighted)= 2.385 (unweighted)= 66.276
superimposing iter= 5 total_weight= 124.295 rmsd (weighted)= 2.354 (unweighted)= 66.308
superimposing iter= 0 total_weight= 0.272 rmsd (weighted)= 11.621 (unweighted)= 82.537
superimposing iter= 1 total_weight= 1338.775 rmsd (weighted)= 7.224 (unweighted)= 83.575
superimposing iter= 2 total_weight= 823.552 rmsd (weighted)= 5.722 (unweighted)= 84.154
superimposing iter= 3 total_weight= 694.798 rmsd (weighted)= 4.928 (unweighted)= 84.589
superimposing iter= 4 total_weight= 637.690 rmsd (weighted)= 4.429 (unweighted)= 84.934
superimposing iter= 5 total_weight= 605.775 rmsd (weighted)= 4.085 (unweighted)= 85.184
superimposing iter= 0 total_weight= 0.576 rmsd (weighted)= 12.615 (unweighted)= 94.642
superimposing iter= 1 total_weight= 2993.916 rmsd (weighted)= 7.552 (unweighted)= 93.989
superimposing iter= 2 total_weight= 1807.848 rmsd (weighted)= 5.964 (unweighted)= 93.818
superimposing iter= 3 total_weight= 1449.448 rmsd (weighted)= 5.295 (unweighted)= 93.899
superimposing iter= 4 total_weight= 1282.444 rmsd (weighted)= 4.998 (unweighted)= 94.001
superimposing iter= 5 total_weight= 1203.100 rmsd (weighted)= 4.865 (unweighted)= 94.067
superimposing iter= 0 total_weight= 0.207 rmsd (weighted)= 14.388 (unweighted)= 85.143
superimposing iter= 1 total_weight= 793.067 rmsd (weighted)= 10.157 (unweighted)= 87.527
superimposing iter= 2 total_weight= 555.628 rmsd (weighted)= 8.714 (unweighted)= 88.571
superimposing iter= 3 total_weight= 463.772 rmsd (weighted)= 8.218 (unweighted)= 89.096
superimposing iter= 4 total_weight= 433.397 rmsd (weighted)= 8.019 (unweighted)= 89.495
superimposing iter= 5 total_weight= 424.738 rmsd (weighted)= 7.892 (unweighted)= 89.882
# command:# Printing sheets for alignments to T0642.undertaker-align.sheets
# command: