# command:# Prefix for input files set to /projects/compbio/experiments/undertaker/atoms-inputs/
# command:# reading dunbrack-2191.atoms
#
#computed average backbone with maximum peptide_sq_deviance = 0.002
# computed average trans backbone unit from 53157 examples
# computed average trans backbone unit before proline from 2010 examples
# computed average cis backbone unit from 97 examples
# trans (non-proline) backbone unit:
#	  CA= -2.2087 1.0126 -0.0030
#	   O= -0.1499 2.2440 0.0016
#	   C= -0.6889 1.1368 -0.0000
#	 N+1= 0.0000 0.0000 0.0000
#	CA+1= 1.4581 -0.0000 0.0000
# cis backbone unit:
#	  CA= -0.1436 2.4534 -0.0002
#	   O= -2.0284 0.9742 0.0015
#	   C= -0.8018 1.0771 -0.0000
#	 N+1= 0.0000 0.0000 0.0000
#	CA+1= 1.4668 0.0000 0.0000
# trans backbone unit before proline:
#	  CA= -2.2100 1.0631 -0.0014
#	   O= -0.1236 2.2458 0.0075
#	   C= -0.6872 1.1517 -0.0000
#	 N+1= 0.0000 0.0000 0.0000
#	CA+1= 1.4660 0.0000 0.0000


# After reading dunbrack-2191.atoms have 2191 chains in training database
#  Count of chains,residues,atoms: 2191,500310,3902258
#  493341 residues have no bad marker
#  3226 residues lack atoms needed to compute omega
#  1453 residues have cis peptide
#  number of each bad type:
#	NON_STANDARD_RESIDUE	4
#	HAS_OXT	1167
#	TOO_MANY_ATOMS	1
#	TOO_FEW_ATOMS	3052
#	HAS_UNKNOWN_ATOMS	9
#	HAS_DUPLICATE_ATOMS	0
#	CHAIN_BREAK_BEFORE	979
#	NON_PLANAR_PEPTIDE	888
#	BAD_PEPTIDE	2680
#  Note: may sum to more than number of residues, 
#    because one residue may have multiple problems
# command:# Reading rotamer library from dunbrack-2191.rot
# command:# Prefix for input files set to /projects/compbio/experiments/undertaker/spots/
# command:# ReadAtomType exp-pdb.types
Read AtomType exp-pdb with 49 types.
# command:# ReadClashTable exp-pdb-2191-2symm.clash
# Read ClashTable exp-pdb-2191-2symm checking bonds symmetric at MaxSep 2
# command:# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0380/
# command:# Making conformation for sequence T0380 numbered 1 through 145
Created new target T0380 from T0380.a2m
# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0380/
# command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0380//projects/compbio/experiments/protein-predict/casp7/T0380/align.constraints_v3.costfcn or /projects/compbio/experiments/protein-predict/casp7/T0380//projects/compbio/experiments/protein-predict/casp7/T0380/align.constraints_v3.costfcn.gz for input
Trying /projects/compbio/experiments/protein-predict/casp7/T0380/align.constraints_v3.costfcn
# reading script from file /projects/compbio/experiments/protein-predict/casp7/T0380/align.constraints_v3.costfcn
# future Constraint commands -> align
# future HelixConstraint commands -> align
# future StrandConstraint commands -> align
# future SheetConstraint commands -> align
# future Hbond commands -> align
# future SSbond commands -> align
# Constraint # added constraint: constraint((T0380)F47.CB, (T0380)C120.CB) [> 4.2636 = 7.1060 < 9.2378] w=1.0000 to align
# Constraint # added constraint: constraint((T0380)T24.CB, (T0380)I67.CB) [> 3.4458 = 5.7430 < 7.4659] w=1.0000 to align
# Constraint # added constraint: constraint((T0380)G23.CA, (T0380)L69.CB) [> 4.3254 = 7.2091 < 9.3718] w=1.0000 to align
# Constraint # added constraint: constraint((T0380)G23.CA, (T0380)C68.CB) [> 3.0440 = 5.0733 < 6.5953] w=1.0000 to align
# Constraint # added constraint: constraint((T0380)G23.CA, (T0380)I67.CB) [> 3.5946 = 5.9910 < 7.7883] w=1.0000 to align
# Constraint # added constraint: constraint((T0380)G23.CA, (T0380)K34.CB) [> 4.2778 = 7.1297 < 9.2686] w=1.0000 to align
# Constraint # added constraint: constraint((T0380)G23.CA, (T0380)I33.CB) [> 3.0043 = 5.0071 < 6.5092] w=1.0000 to align
# Constraint # added constraint: constraint((T0380)G23.CA, (T0380)N32.CB) [> 3.6697 = 6.1162 < 7.9511] w=1.0000 to align
# Constraint # added constraint: constraint((T0380)V22.CB, (T0380)L69.CB) [> 3.2070 = 5.3450 < 6.9484] w=1.0000 to align
# Constraint # added constraint: constraint((T0380)V22.CB, (T0380)C68.CB) [> 4.4234 = 7.3724 < 9.5841] w=1.0000 to align
# Constraint # added constraint: constraint((T0380)V22.CB, (T0380)I67.CB) [> 3.7099 = 6.1832 < 8.0381] w=1.0000 to align
# Constraint # added constraint: constraint((T0380)V22.CB, (T0380)K34.CB) [> 3.3725 = 5.6208 < 7.3070] w=1.0000 to align
# Constraint # added constraint: constraint((T0380)V22.CB, (T0380)I33.CB) [> 4.2534 = 7.0891 < 9.2158] w=1.0000 to align
# Constraint # added constraint: constraint((T0380)M21.CB, (T0380)Y70.CB) [> 2.7677 = 4.6128 < 5.9966] w=1.0000 to align
# Constraint # added constraint: constraint((T0380)M21.CB, (T0380)L69.CB) [> 4.1367 = 6.8945 < 8.9628] w=1.0000 to align
# Constraint # added constraint: constraint((T0380)M21.CB, (T0380)A35.CB) [> 3.4554 = 5.7590 < 7.4867] w=1.0000 to align
# Constraint # added constraint: constraint((T0380)M21.CB, (T0380)K34.CB) [> 4.2435 = 7.0725 < 9.1943] w=1.0000 to align
# Constraint # added constraint: constraint((T0380)M21.CB, (T0380)I33.CB) [> 3.3388 = 5.5646 < 7.2340] w=1.0000 to align
# Constraint # added constraint: constraint((T0380)V20.CB, (T0380)F71.CB) [> 3.0232 = 5.0387 < 6.5503] w=1.0000 to align
# Constraint # added constraint: constraint((T0380)V20.CB, (T0380)Y70.CB) [> 3.7722 = 6.2869 < 8.1730] w=1.0000 to align
# Constraint # added constraint: constraint((T0380)V20.CB, (T0380)L69.CB) [> 2.9311 = 4.8852 < 6.3508] w=1.0000 to align
# Constraint # added constraint: constraint((T0380)V20.CB, (T0380)A35.CB) [> 4.2592 = 7.0987 < 9.2283] w=1.0000 to align
# Constraint # added constraint: constraint((T0380)I19.CB, (T0380)A35.CB) [> 3.3592 = 5.5986 < 7.2782] w=1.0000 to align
# Constraint # added constraint: constraint((T0380)L89.CB, (T0380)A118.CB) [> 2.5264 = 4.2106 < 5.4738] w=1.0000 to align
# Constraint # added constraint: constraint((T0380)I88.CB, (T0380)L119.CB) [> 3.5454 = 5.9090 < 7.6817] w=1.0000 to align
# Constraint # added constraint: constraint((T0380)I88.CB, (T0380)A118.CB) [> 4.3330 = 7.2216 < 9.3881] w=1.0000 to align
# Constraint # added constraint: constraint((T0380)I88.CB, (T0380)T117.CB) [> 3.4162 = 5.6936 < 7.4017] w=1.0000 to align
# Constraint # added constraint: constraint((T0380)T85.CB, (T0380)F121.CB) [> 4.3672 = 7.2787 < 9.4623] w=1.0000 to align
# Constraint # added constraint: constraint((T0380)G84.CA, (T0380)E124.CB) [> 2.7089 = 4.5149 < 5.8694] w=1.0000 to align
# Constraint # added constraint: constraint((T0380)G84.CA, (T0380)F121.CB) [> 3.4045 = 5.6741 < 7.3764] w=1.0000 to align
# Constraint # added constraint: constraint((T0380)V83.CB, (T0380)E124.CB) [> 3.2888 = 5.4813 < 7.1257] w=1.0000 to align
# Constraint # added constraint: constraint((T0380)M81.CB, (T0380)N127.CB) [> 2.7793 = 4.6321 < 6.0218] w=1.0000 to align
# Constraint # added constraint: constraint((T0380)L80.CB, (T0380)Y128.CB) [> 3.1050 = 5.1751 < 6.7276] w=1.0000 to align
# Constraint # added constraint: constraint((T0380)L80.CB, (T0380)N127.CB) [> 4.2872 = 7.1453 < 9.2889] w=1.0000 to align
# Constraint # added constraint: constraint((T0380)F71.CB, (T0380)L80.CB) [> 2.8466 = 4.7443 < 6.1676] w=1.0000 to align
# Constraint # added constraint: constraint((T0380)Y70.CB, (T0380)M81.CB) [> 3.0538 = 5.0896 < 6.6165] w=1.0000 to align
# Constraint # added constraint: constraint((T0380)Y70.CB, (T0380)L80.CB) [> 4.2317 = 7.0528 < 9.1687] w=1.0000 to align
# Constraint # added constraint: constraint((T0380)L69.CB, (T0380)F121.CB) [> 3.8168 = 6.3613 < 8.2697] w=1.0000 to align
# Constraint # added constraint: constraint((T0380)L69.CB, (T0380)L82.CB) [> 2.7061 = 4.5101 < 5.8632] w=1.0000 to align
# Constraint # added constraint: constraint((T0380)L69.CB, (T0380)M81.CB) [> 4.3022 = 7.1704 < 9.3215] w=1.0000 to align
# Constraint # added constraint: constraint((T0380)C68.CB, (T0380)V83.CB) [> 3.2199 = 5.3665 < 6.9764] w=1.0000 to align
# Constraint # added constraint: constraint((T0380)C68.CB, (T0380)L82.CB) [> 4.0882 = 6.8137 < 8.8578] w=1.0000 to align
# Constraint # added constraint: constraint((T0380)C68.CB, (T0380)M81.CB) [> 3.8077 = 6.3462 < 8.2500] w=1.0000 to align
# Constraint # added constraint: constraint((T0380)I67.CB, (T0380)F121.CB) [> 3.3751 = 5.6252 < 7.3128] w=1.0000 to align
# Constraint # added constraint: constraint((T0380)I67.CB, (T0380)G84.CA) [> 3.4585 = 5.7642 < 7.4935] w=1.0000 to align
# Constraint # added constraint: constraint((T0380)L49.CB, (T0380)L119.CB) [> 3.0751 = 5.1252 < 6.6627] w=1.0000 to align
# Constraint # added constraint: constraint((T0380)L49.CB, (T0380)A118.CB) [> 4.3014 = 7.1691 < 9.3198] w=1.0000 to align
# Constraint # added constraint: constraint((T0380)L80.CB, (T0380)G126.CA) [> 4.1994 = 6.9990 < 9.0987] w=0.9948 to align
# Constraint # added constraint: constraint((T0380)M81.CB, (T0380)G126.CA) [> 3.6496 = 6.0827 < 7.9075] w=0.9948 to align
# Constraint # added constraint: constraint((T0380)L82.CB, (T0380)F121.CB) [> 4.0613 = 6.7687 < 8.7994] w=0.9948 to align
# Constraint # added constraint: constraint((T0380)L82.CB, (T0380)G126.CA) [> 3.2339 = 5.3899 < 7.0068] w=0.9948 to align
# Constraint # added constraint: constraint((T0380)V83.CB, (T0380)W125.CB) [> 2.3744 = 3.9573 < 5.1445] w=0.9948 to align
# Constraint # added constraint: constraint((T0380)V83.CB, (T0380)G126.CA) [> 3.7418 = 6.2363 < 8.1071] w=0.9948 to align
# Constraint # added constraint: constraint((T0380)G84.CA, (T0380)W125.CB) [> 4.1256 = 6.8761 < 8.9389] w=0.9948 to align
# Constraint # added constraint: constraint((T0380)K66.CB, (T0380)T85.CB) [> 3.7097 = 6.1829 < 8.0378] w=0.9825 to align
# Constraint # added constraint: constraint((T0380)K66.CB, (T0380)G84.CA) [> 4.0100 = 6.6832 < 8.6882] w=0.9825 to align
# Constraint # added constraint: constraint((T0380)G79.CA, (T0380)Y128.CB) [> 3.7599 = 6.2665 < 8.1464] w=0.9825 to align
# Constraint # added constraint: constraint((T0380)Y70.CB, (T0380)G79.CA) [> 4.2457 = 7.0762 < 9.1990] w=0.9825 to align
# Constraint # added constraint: constraint((T0380)S50.CB, (T0380)A118.CB) [> 3.2476 = 5.4127 < 7.0366] w=0.9651 to align
# Constraint # added constraint: constraint((T0380)L49.CB, (T0380)F121.CB) [> 4.3986 = 7.3310 < 9.5303] w=0.9651 to align
# Constraint # added constraint: constraint((T0380)T85.CB, (T0380)E124.CB) [> 4.1799 = 6.9665 < 9.0564] w=0.9482 to align
# Constraint # added constraint: constraint((T0380)V22.CB, (T0380)A35.CB) [> 4.5296 = 7.5493 < 9.8141] w=0.9476 to align
# Constraint # added constraint: constraint((T0380)T24.CB, (T0380)R60.CB) [> 2.6257 = 4.3761 < 5.6889] w=0.9476 to align
# Constraint # added constraint: constraint((T0380)N65.CB, (T0380)T85.CB) [> 3.0013 = 5.0022 < 6.5028] w=0.9476 to align
# Constraint # added constraint: constraint((T0380)F47.CB, (T0380)F121.CB) [> 2.8356 = 4.7259 < 6.1437] w=0.9476 to align
# Constraint # added constraint: constraint((T0380)T51.CB, (T0380)T117.CB) [> 3.5740 = 5.9567 < 7.7437] w=0.9476 to align
# Constraint # added constraint: constraint((T0380)C68.CB, (T0380)G84.CA) [> 4.3796 = 7.2994 < 9.4892] w=0.9476 to align
# Constraint # added constraint: constraint((T0380)W48.CB, (T0380)C120.CB) [> 3.3392 = 5.5653 < 7.2349] w=0.9476 to align
# Constraint # added constraint: constraint((T0380)W48.CB, (T0380)L119.CB) [> 4.1223 = 6.8706 < 8.9317] w=0.9476 to align
# Constraint # added constraint: constraint((T0380)W48.CB, (T0380)A118.CB) [> 3.6696 = 6.1160 < 7.9508] w=0.9476 to align
# Constraint # added constraint: constraint((T0380)I67.CB, (T0380)V83.CB) [> 4.5459 = 7.5765 < 9.8494] w=0.9476 to align
# Constraint # added constraint: constraint((T0380)I67.CB, (T0380)T85.CB) [> 4.2204 = 7.0340 < 9.1442] w=0.9476 to align
# Constraint # added constraint: constraint((T0380)I67.CB, (T0380)I86.CB) [> 2.8744 = 4.7906 < 6.2278] w=0.9476 to align
# Constraint # added constraint: constraint((T0380)I86.CB, (T0380)L119.CB) [> 2.9763 = 4.9605 < 6.4487] w=0.9476 to align
# Constraint # added constraint: constraint((T0380)I86.CB, (T0380)C120.CB) [> 4.1503 = 6.9172 < 8.9924] w=0.9476 to align
# Constraint # added constraint: constraint((T0380)I86.CB, (T0380)F121.CB) [> 3.0547 = 5.0911 < 6.6184] w=0.9476 to align
# Constraint # added constraint: constraint((T0380)E87.CB, (T0380)L119.CB) [> 4.1438 = 6.9064 < 8.9783] w=0.9476 to align
# Constraint # added constraint: constraint((T0380)E87.CB, (T0380)C120.CB) [> 3.1354 = 5.2256 < 6.7933] w=0.9476 to align
# Constraint # added constraint: constraint((T0380)L82.CB, (T0380)A123.CB) [> 3.1470 = 5.2449 < 6.8184] w=0.9476 to align
# Constraint # added constraint: constraint((T0380)G84.CA, (T0380)T122.CB) [> 3.5355 = 5.8925 < 7.6603] w=0.9476 to align
# Constraint # added constraint: constraint((T0380)G84.CA, (T0380)A123.CB) [> 3.5165 = 5.8608 < 7.6191] w=0.9476 to align
# Constraint # added constraint: constraint((T0380)T85.CB, (T0380)T122.CB) [> 3.4207 = 5.7011 < 7.4114] w=0.9476 to align
# Constraint # added constraint: constraint((T0380)L89.CB, (T0380)L119.CB) [> 4.2245 = 7.0409 < 9.1532] w=0.9426 to align
# Constraint # added constraint: constraint((T0380)G79.CA, (T0380)Y129.CB) [> 2.9521 = 4.9201 < 6.3962] w=0.9252 to align
# Constraint # added constraint: constraint((T0380)V20.CB, (T0380)R38.CB) [> 3.3594 = 5.5990 < 7.2787] w=0.9251 to align
# Constraint # added constraint: constraint((T0380)V22.CB, (T0380)L49.CB) [> 4.1172 = 6.8621 < 8.9207] w=0.9132 to align
# Constraint # added constraint: constraint((T0380)S50.CB, (T0380)T117.CB) [> 4.1758 = 6.9597 < 9.0477] w=0.9129 to align
# Constraint # added constraint: constraint((T0380)N25.CB, (T0380)K66.CB) [> 3.9312 = 6.5520 < 8.5176] w=0.9127 to align
# Constraint # added constraint: constraint((T0380)N25.CB, (T0380)N64.CB) [> 3.2545 = 5.4242 < 7.0514] w=0.9127 to align
# Constraint # added constraint: constraint((T0380)T51.CB, (T0380)L119.CB) [> 3.8215 = 6.3692 < 8.2800] w=0.9127 to align
# Constraint # added constraint: constraint((T0380)F47.CB, (T0380)L69.CB) [> 3.8175 = 6.3624 < 8.2711] w=0.9127 to align
# Constraint # added constraint: constraint((T0380)S50.CB, (T0380)Y116.CB) [> 3.6530 = 6.0884 < 7.9149] w=0.9076 to align
# Constraint # added constraint: constraint((T0380)F47.CB, (T0380)L82.CB) [> 3.9471 = 6.5786 < 8.5522] w=0.9074 to align
# Constraint # added constraint: constraint((T0380)N32.CB, (T0380)M57.CB) [> 4.1173 = 6.8622 < 8.9209] w=0.8952 to align
# Constraint # added constraint: constraint((T0380)T24.CB, (T0380)L61.CB) [> 3.3998 = 5.6663 < 7.3661] w=0.8952 to align
# Constraint # added constraint: constraint((T0380)N65.CB, (T0380)I86.CB) [> 3.1411 = 5.2352 < 6.8058] w=0.8952 to align
# Constraint # added constraint: constraint((T0380)L61.CB, (T0380)I86.CB) [> 3.1151 = 5.1919 < 6.7495] w=0.8952 to align
# Constraint # added constraint: constraint((T0380)L89.CB, (T0380)C120.CB) [> 3.5602 = 5.9337 < 7.7139] w=0.8952 to align
# Constraint # added constraint: constraint((T0380)V22.CB, (T0380)M36.CB) [> 3.0436 = 5.0726 < 6.5944] w=0.8952 to align
# Constraint # added constraint: constraint((T0380)V20.CB, (T0380)M36.CB) [> 3.3284 = 5.5473 < 7.2115] w=0.8952 to align
# Constraint # added constraint: constraint((T0380)I19.CB, (T0380)M36.CB) [> 4.2298 = 7.0497 < 9.1646] w=0.8952 to align
# Constraint # added constraint: constraint((T0380)L82.CB, (T0380)W125.CB) [> 4.3394 = 7.2323 < 9.4020] w=0.8900 to align
# Constraint # added constraint: constraint((T0380)S50.CB, (T0380)L98.CB) [> 3.9188 = 6.5313 < 8.4907] w=0.8606 to align
# Constraint # added constraint: constraint((T0380)S94.CB, (T0380)A118.CB) [> 3.5945 = 5.9908 < 7.7881] w=0.8605 to align
# Constraint # added constraint: constraint((T0380)M36.CB, (T0380)L49.CB) [> 2.9093 = 4.8489 < 6.3036] w=0.8603 to align
# Constraint # added constraint: constraint((T0380)T53.CB, (T0380)T117.CB) [> 3.2259 = 5.3765 < 6.9895] w=0.8553 to align
# Constraint # added constraint: constraint((T0380)N52.CB, (T0380)Y116.CB) [> 3.6879 = 6.1465 < 7.9904] w=0.8552 to align
# Constraint # added constraint: constraint((T0380)W48.CB, (T0380)F121.CB) [> 4.4941 = 7.4902 < 9.7372] w=0.8434 to align
# Constraint # added constraint: constraint((T0380)K34.CB, (T0380)M57.CB) [> 3.5523 = 5.9205 < 7.6966] w=0.8428 to align
# Constraint # added constraint: constraint((T0380)T24.CB, (T0380)M57.CB) [> 3.2331 = 5.3885 < 7.0051] w=0.8428 to align
# Constraint # added constraint: constraint((T0380)L89.CB, (T0380)T117.CB) [> 3.9237 = 6.5394 < 8.5013] w=0.8428 to align
# Constraint # added constraint: constraint((T0380)T24.CB, (T0380)N64.CB) [> 4.3522 = 7.2537 < 9.4298] w=0.8428 to align
# Constraint # added constraint: constraint((T0380)S50.CB, (T0380)L119.CB) [> 4.4169 = 7.3615 < 9.5699] w=0.8428 to align
# Constraint # added constraint: constraint((T0380)V83.CB, (T0380)A123.CB) [> 4.2613 = 7.1022 < 9.2328] w=0.8428 to align
# Constraint # added constraint: constraint((T0380)T53.CB, (T0380)D115.CB) [> 3.0205 = 5.0341 < 6.5443] w=0.8396 to align
# Constraint # added constraint: constraint((T0380)K45.CB, (T0380)T122.CB) [> 3.7100 = 6.1833 < 8.0383] w=0.8032 to align
# Constraint # added constraint: constraint((T0380)I19.CB, (T0380)R38.CB) [> 4.1156 = 6.8593 < 8.9171] w=0.8031 to align
# Constraint # added constraint: constraint((T0380)M36.CB, (T0380)T51.CB) [> 4.1379 = 6.8965 < 8.9654] w=0.8029 to align
# Constraint # added constraint: constraint((T0380)Y70.CB, (T0380)L82.CB) [> 4.5222 = 7.5370 < 9.7980] w=0.7904 to align
# Constraint # added constraint: constraint((T0380)K46.CB, (T0380)C120.CB) [> 3.4382 = 5.7303 < 7.4494] w=0.7904 to align
# Constraint # added constraint: constraint((T0380)T53.CB, (T0380)Y116.CB) [> 4.2940 = 7.1566 < 9.3036] w=0.7860 to align
# Constraint # added constraint: constraint((T0380)R38.CB, (T0380)F47.CB) [> 3.4321 = 5.7202 < 7.4363] w=0.7856 to align
# Constraint # added constraint: constraint((T0380)L80.CB, (T0380)Y129.CB) [> 4.4457 = 7.4095 < 9.6324] w=0.7854 to align
# Constraint # added constraint: constraint((T0380)N52.CB, (T0380)T117.CB) [> 4.2184 = 7.0307 < 9.1399] w=0.7732 to align
# Constraint # added constraint: constraint((T0380)N52.CB, (T0380)D115.CB) [> 3.4838 = 5.8064 < 7.5483] w=0.7696 to align
# Constraint # added constraint: constraint((T0380)K18.CB, (T0380)R38.CB) [> 3.3171 = 5.5284 < 7.1870] w=0.7681 to align
# Constraint # added constraint: constraint((T0380)K46.CB, (T0380)F121.CB) [> 3.7497 = 6.2495 < 8.1244] w=0.7555 to align
# Constraint # added constraint: constraint((T0380)I19.CB, (T0380)M37.CB) [> 3.6050 = 6.0084 < 7.8109] w=0.7555 to align
# Constraint # added constraint: constraint((T0380)K18.CB, (T0380)M37.CB) [> 3.6062 = 6.0103 < 7.8134] w=0.7555 to align
# Constraint # added constraint: constraint((T0380)L61.CB, (T0380)L119.CB) [> 3.9065 = 6.5108 < 8.4641] w=0.7386 to align
# Constraint # added constraint: constraint((T0380)L98.CB, (T0380)A118.CB) [> 3.1827 = 5.3044 < 6.8957] w=0.7384 to align
# Constraint # added constraint: constraint((T0380)E87.CB, (T0380)T122.CB) [> 4.1532 = 6.9220 < 8.9986] w=0.7380 to align
# Constraint # added constraint: constraint((T0380)S17.CB, (T0380)F71.CB) [> 3.1079 = 5.1798 < 6.7337] w=0.7330 to align
# Constraint # added constraint: constraint((T0380)I19.CB, (T0380)F71.CB) [> 4.5868 = 7.6447 < 9.9381] w=0.7328 to align
# Constraint # added constraint: constraint((T0380)F47.CB, (T0380)A123.CB) [> 4.1659 = 6.9432 < 9.0261] w=0.7211 to align
# Constraint # added constraint: constraint((T0380)T24.CB, (T0380)K66.CB) [> 4.5351 = 7.5585 < 9.8261] w=0.7205 to align
# Constraint # added constraint: constraint((T0380)A78.CB, (T0380)Y129.CB) [> 3.6685 = 6.1142 < 7.9484] w=0.7159 to align
# Constraint # added constraint: constraint((T0380)T51.CB, (T0380)Y116.CB) [> 4.2458 = 7.0763 < 9.1992] w=0.7155 to align
# Constraint # added constraint: constraint((T0380)E27.CB, (T0380)K63.CB) [> 3.6597 = 6.0995 < 7.9294] w=0.7037 to align
# Constraint # added constraint: constraint((T0380)A78.CB, (T0380)Y128.CB) [> 4.4128 = 7.3546 < 9.5610] w=0.7035 to align
# Constraint # added constraint: constraint((T0380)M37.CB, (T0380)L49.CB) [> 4.0837 = 6.8061 < 8.8480] w=0.6981 to align
# Constraint # added constraint: constraint((T0380)V58.CB, (T0380)T117.CB) [> 3.8633 = 6.4387 < 8.3704] w=0.6862 to align
# Constraint # added constraint: constraint((T0380)V14.CB, (T0380)F71.CB) [> 3.7339 = 6.2232 < 8.0901] w=0.6860 to align
# Constraint # added constraint: constraint((T0380)L13.CB, (T0380)L80.CB) [> 3.2057 = 5.3428 < 6.9457] w=0.6685 to align
# Constraint # added constraint: constraint((T0380)M21.CB, (T0380)M36.CB) [> 4.4982 = 7.4970 < 9.7462] w=0.6684 to align
# Constraint # added constraint: constraint((T0380)L13.CB, (T0380)F71.CB) [> 3.6654 = 6.1090 < 7.9416] w=0.6510 to align
# Constraint # added constraint: constraint((T0380)K46.CB, (T0380)T122.CB) [> 3.3269 = 5.5448 < 7.2082] w=0.6338 to align
# Constraint # added constraint: constraint((T0380)F71.CB, (T0380)L82.CB) [> 4.5781 = 7.6302 < 9.9193] w=0.6338 to align
# Constraint # added constraint: constraint((T0380)L13.CB, (T0380)G79.CA) [> 3.8446 = 6.4077 < 8.3301] w=0.6336 to align
# Constraint # added constraint: constraint((T0380)G23.CA, (T0380)M57.CB) [> 4.6069 = 7.6782 < 9.9817] w=0.6332 to align
# Constraint # added constraint: constraint((T0380)K46.CB, (T0380)A123.CB) [> 4.0683 = 6.7805 < 8.8147] w=0.6332 to align
# Constraint # added constraint: constraint((T0380)F71.CB, (T0380)M81.CB) [> 4.5946 = 7.6577 < 9.9550] w=0.6288 to align
# Constraint # added constraint: constraint((T0380)V20.CB, (T0380)F47.CB) [> 4.4007 = 7.3345 < 9.5348] w=0.6282 to align
# Constraint # added constraint: constraint((T0380)M81.CB, (T0380)W125.CB) [> 4.6265 = 7.7109 < 10.0242] w=0.5756 to align
# Constraint # added constraint: constraint((T0380)M21.CB, (T0380)F71.CB) [> 4.5594 = 7.5990 < 9.8787] w=0.5756 to align
# Constraint # added constraint: constraint((T0380)K66.CB, (T0380)I86.CB) [> 4.3443 = 7.2406 < 9.4128] w=0.5639 to align
# Constraint # added constraint: constraint((T0380)F6.CB, (T0380)Y128.CB) [> 3.7614 = 6.2690 < 8.1497] w=0.5586 to align
# Constraint # added constraint: constraint((T0380)V20.CB, (T0380)L49.CB) [> 4.4392 = 7.3987 < 9.6183] w=0.5464 to align
# Constraint # added constraint: constraint((T0380)S17.CB, (T0380)D73.CB) [> 4.1282 = 6.8804 < 8.9445] w=0.5449 to align
# Constraint # added constraint: constraint((T0380)V14.CB, (T0380)L80.CB) [> 3.6868 = 6.1447 < 7.9881] w=0.5413 to align
# Constraint # added constraint: constraint((T0380)G23.CA, (T0380)Y70.CB) [> 4.6193 = 7.6988 < 10.0085] w=0.5292 to align
# Constraint # added constraint: constraint((T0380)I88.CB, (T0380)C120.CB) [> 4.6409 = 7.7348 < 10.0552] w=0.5290 to align
# Constraint # added constraint: constraint((T0380)T24.CB, (T0380)I86.CB) [> 4.5887 = 7.6479 < 9.9422] w=0.5290 to align
# Constraint # added constraint: constraint((T0380)I86.CB, (T0380)T122.CB) [> 4.5795 = 7.6325 < 9.9223] w=0.5284 to align
# Constraint # added constraint: constraint((T0380)L13.CB, (T0380)D73.CB) [> 3.7775 = 6.2958 < 8.1846] w=0.5275 to align
# Constraint # added constraint: constraint((T0380)I67.CB, (T0380)L119.CB) [> 4.5823 = 7.6372 < 9.9284] w=0.5240 to align
# Constraint # added constraint: constraint((T0380)V83.CB, (T0380)N127.CB) [> 4.5206 = 7.5343 < 9.7946] w=0.5234 to align
# Constraint # added constraint: constraint((T0380)S10.CB, (T0380)L80.CB) [> 3.1249 = 5.2081 < 6.7705] w=0.4922 to align
# Constraint # added constraint: constraint((T0380)K95.CB, (T0380)Y116.CB) [> 4.0978 = 6.8296 < 8.8785] w=0.4891 to align
# Constraint # added constraint: constraint((T0380)S10.CB, (T0380)Y128.CB) [> 3.3435 = 5.5726 < 7.2444] w=0.4887 to align
# Constraint # added constraint: constraint((T0380)R38.CB, (T0380)F71.CB) [> 4.5926 = 7.6543 < 9.9506] w=0.4716 to align
# Constraint # added constraint: constraint((T0380)A78.CB, (T0380)H131.CB) [> 3.6438 = 6.0731 < 7.8950] w=0.4714 to align
# Constraint # added constraint: constraint((T0380)M36.CB, (T0380)L69.CB) [> 4.5000 = 7.5001 < 9.7501] w=0.4710 to align
# Constraint # added constraint: constraint((T0380)M37.CB, (T0380)S50.CB) [> 4.2949 = 7.1582 < 9.3057] w=0.4710 to align
# Constraint # added constraint: constraint((T0380)W48.CB, (T0380)L89.CB) [> 4.3993 = 7.3322 < 9.5319] w=0.4536 to align
# Constraint # added constraint: constraint((T0380)S54.CB, (T0380)D115.CB) [> 3.4141 = 5.6902 < 7.3972] w=0.4361 to align
# Constraint # added constraint: constraint((T0380)M81.CB, (T0380)Y128.CB) [> 3.9731 = 6.6218 < 8.6083] w=0.4244 to align
# Constraint # added constraint: constraint((T0380)K62.CB, (T0380)I88.CB) [> 4.0262 = 6.7104 < 8.7235] w=0.4244 to align
# Constraint # added constraint: constraint((T0380)V20.CB, (T0380)M37.CB) [> 4.3882 = 7.3136 < 9.5077] w=0.4242 to align
# Constraint # added constraint: constraint((T0380)M81.CB, (T0380)Y129.CB) [> 4.3612 = 7.2687 < 9.4493] w=0.4192 to align
# Constraint # added constraint: constraint((T0380)M21.CB, (T0380)V72.CB) [> 4.2807 = 7.1345 < 9.2749] w=0.4192 to align
# Constraint # added constraint: constraint((T0380)V14.CB, (T0380)F47.CB) [> 4.2433 = 7.0722 < 9.1938] w=0.4190 to align
# Constraint # added constraint: constraint((T0380)L44.CB, (T0380)T122.CB) [> 4.1539 = 6.9232 < 9.0001] w=0.4067 to align
# Constraint # added constraint: constraint((T0380)S50.CB, (T0380)W99.CB) [> 4.2494 = 7.0822 < 9.2069] w=0.4014 to align
# Constraint # added constraint: constraint((T0380)K45.CB, (T0380)C120.CB) [> 2.9335 = 4.8891 < 6.3559] w=0.3843 to align
# Constraint # added constraint: constraint((T0380)E15.CB, (T0380)K40.CB) [> 3.5861 = 5.9768 < 7.7698] w=0.3841 to align
# Constraint # added constraint: constraint((T0380)S10.CB, (T0380)G126.CA) [> 4.0375 = 6.7292 < 8.7479] w=0.3839 to align
# Constraint # added constraint: constraint((T0380)H90.CB, (T0380)T117.CB) [> 3.6389 = 6.0648 < 7.8842] w=0.3718 to align
# Constraint # added constraint: constraint((T0380)L69.CB, (T0380)G84.CA) [> 4.4632 = 7.4387 < 9.6704] w=0.3718 to align
# Constraint # added constraint: constraint((T0380)T24.CB, (T0380)K34.CB) [> 4.4017 = 7.3361 < 9.5370] w=0.3712 to align
# Constraint # added constraint: constraint((T0380)F6.CB, (T0380)L80.CB) [> 3.7018 = 6.1698 < 8.0207] w=0.3685 to align
# Constraint # added constraint: constraint((T0380)V58.CB, (T0380)L119.CB) [> 4.5319 = 7.5532 < 9.8191] w=0.3668 to align
# Constraint # added constraint: constraint((T0380)K18.CB, (T0380)Y106.CB) [> 3.8211 = 6.3684 < 8.2790] w=0.3664 to align
# Constraint # added constraint: constraint((T0380)K66.CB, (T0380)V83.CB) [> 4.5262 = 7.5436 < 9.8067] w=0.3491 to align
# Constraint # added constraint: constraint((T0380)M36.CB, (T0380)S50.CB) [> 4.5300 = 7.5500 < 9.8150] w=0.3490 to align
# Constraint # added constraint: constraint((T0380)V22.CB, (T0380)Y70.CB) [> 4.6990 = 7.8317 < 10.1812] w=0.3196 to align
# Constraint # added constraint: constraint((T0380)V58.CB, (T0380)I88.CB) [> 3.8020 = 6.3367 < 8.2377] w=0.3194 to align
# Constraint # added constraint: constraint((T0380)T24.CB, (T0380)I33.CB) [> 4.5718 = 7.6197 < 9.9056] w=0.3194 to align
# Constraint # added constraint: constraint((T0380)L69.CB, (T0380)V83.CB) [> 4.7138 = 7.8563 < 10.2132] w=0.3191 to align
# Constraint # added constraint: constraint((T0380)S94.CB, (T0380)T117.CB) [> 3.6874 = 6.1456 < 7.9893] w=0.3144 to align
# Constraint # added constraint: constraint((T0380)S17.CB, (T0380)V72.CB) [> 4.2837 = 7.1395 < 9.2813] w=0.3144 to align
# Constraint # added constraint: constraint((T0380)F77.CB, (T0380)H131.CB) [> 2.4709 = 4.1181 < 5.3535] w=0.3140 to align
# Constraint # added constraint: constraint((T0380)W48.CB, (T0380)G102.CA) [> 3.9080 = 6.5133 < 8.4673] w=0.3140 to align
# Constraint # added constraint: constraint((T0380)K34.CB, (T0380)R56.CB) [> 4.4096 = 7.3493 < 9.5541] w=0.3138 to align
# Constraint # added constraint: constraint((T0380)W99.CB, (T0380)I111.CB) [> 4.0347 = 6.7245 < 8.7419] w=0.3003 to align
# Constraint # added constraint: constraint((T0380)E9.CB, (T0380)Y128.CB) [> 3.9839 = 6.6399 < 8.6318] w=0.3001 to align
# Constraint # added constraint: constraint((T0380)L39.CB, (T0380)A118.CB) [> 4.4780 = 7.4633 < 9.7022] w=0.2969 to align
# Constraint # added constraint: constraint((T0380)K95.CB, (T0380)T117.CB) [> 3.8530 = 6.4217 < 8.3482] w=0.2844 to align
# Constraint # added constraint: constraint((T0380)V14.CB, (T0380)D73.CB) [> 3.5052 = 5.8419 < 7.5945] w=0.2795 to align
# Constraint # added constraint: constraint((T0380)S10.CB, (T0380)K76.CB) [> 3.9267 = 6.5445 < 8.5078] w=0.2795 to align
# Constraint # added constraint: constraint((T0380)L7.CB, (T0380)S17.CB) [> 3.8266 = 6.3776 < 8.2909] w=0.2795 to align
# Constraint # added constraint: constraint((T0380)K45.CB, (T0380)F121.CB) [> 3.1265 = 5.2108 < 6.7741] w=0.2795 to align
# Constraint # added constraint: constraint((T0380)L44.CB, (T0380)C120.CB) [> 3.9549 = 6.5915 < 8.5689] w=0.2794 to align
# Constraint # added constraint: constraint((T0380)F77.CB, (T0380)R130.CB) [> 3.9583 = 6.5971 < 8.5762] w=0.2791 to align
# Constraint # added constraint: constraint((T0380)T51.CB, (T0380)A118.CB) [> 4.3648 = 7.2746 < 9.4570] w=0.2670 to align
# Constraint # added constraint: constraint((T0380)H90.CB, (T0380)A118.CB) [> 4.4960 = 7.4934 < 9.7414] w=0.2670 to align
# Constraint # added constraint: constraint((T0380)L7.CB, (T0380)K18.CB) [> 4.4950 = 7.4917 < 9.7393] w=0.2620 to align
# Constraint # added constraint: constraint((T0380)F6.CB, (T0380)A78.CB) [> 3.8871 = 6.4785 < 8.4221] w=0.2620 to align
# Constraint # added constraint: constraint((T0380)F77.CB, (T0380)Y129.CB) [> 3.9264 = 6.5440 < 8.5072] w=0.2616 to align
# Constraint # added constraint: constraint((T0380)W99.CB, (T0380)Y116.CB) [> 4.0884 = 6.8140 < 8.8582] w=0.2444 to align
# Constraint # added constraint: constraint((T0380)H41.CB, (T0380)D101.CB) [> 3.7530 = 6.2550 < 8.1315] w=0.2443 to align
# Constraint # added constraint: constraint((T0380)K18.CB, (T0380)I105.CB) [> 4.0176 = 6.6960 < 8.7048] w=0.2443 to align
# Constraint # added constraint: constraint((T0380)L39.CB, (T0380)Y106.CB) [> 3.4694 = 5.7824 < 7.5171] w=0.2443 to align
# Constraint # added constraint: constraint((T0380)T53.CB, (T0380)P114.CB) [> 4.4292 = 7.3821 < 9.5967] w=0.2442 to align
# Constraint # added constraint: constraint((T0380)M37.CB, (T0380)Y106.CB) [> 3.6989 = 6.1648 < 8.0143] w=0.2441 to align
# Constraint # added constraint: constraint((T0380)N75.CB, (T0380)L132.CB) [> 4.1696 = 6.9494 < 9.0342] w=0.2271 to align
# Constraint # added constraint: constraint((T0380)N11.CB, (T0380)D42.CB) [> 4.0644 = 6.7739 < 8.8061] w=0.2270 to align
# Constraint # added constraint: constraint((T0380)S50.CB, (T0380)C103.CB) [> 3.9504 = 6.5841 < 8.5593] w=0.2267 to align
# Constraint # added constraint: constraint((T0380)V20.CB, (T0380)V72.CB) [> 4.6502 = 7.7504 < 10.0755] w=0.2148 to align
# Constraint # added constraint: constraint((T0380)V22.CB, (T0380)F121.CB) [> 4.5467 = 7.5779 < 9.8512] w=0.2148 to align
# Constraint # added constraint: constraint((T0380)P31.CB, (T0380)C68.CB) [> 4.5974 = 7.6623 < 9.9610] w=0.2148 to align
# Constraint # added constraint: constraint((T0380)K18.CB, (T0380)F71.CB) [> 4.0037 = 6.6728 < 8.6747] w=0.2146 to align
# Constraint # added constraint: constraint((T0380)N52.CB, (T0380)D113.CB) [> 4.2942 = 7.1570 < 9.3041] w=0.2113 to align
# Constraint # added constraint: constraint((T0380)L82.CB, (T0380)N127.CB) [> 4.6403 = 7.7338 < 10.0540] w=0.2096 to align
# Constraint # added constraint: constraint((T0380)V58.CB, (T0380)D115.CB) [> 4.4742 = 7.4570 < 9.6941] w=0.2096 to align
# Constraint # added constraint: constraint((T0380)W99.CB, (T0380)L109.CB) [> 4.2869 = 7.1448 < 9.2882] w=0.2096 to align
# Constraint # added constraint: constraint((T0380)D74.CB, (T0380)H131.CB) [> 4.3381 = 7.2301 < 9.3991] w=0.2096 to align
# Constraint # added constraint: constraint((T0380)N127.CB, (T0380)T136.CB) [> 3.1492 = 5.2487 < 6.8233] w=0.2092 to align
# Constraint # added constraint: constraint((T0380)L49.CB, (T0380)I86.CB) [> 4.4067 = 7.3445 < 9.5479] w=0.2090 to align
# Constraint # added constraint: constraint((T0380)S10.CB, (T0380)N127.CB) [> 4.4320 = 7.3867 < 9.6027] w=0.1921 to align
# Constraint # added constraint: constraint((T0380)M37.CB, (T0380)G102.CA) [> 4.3317 = 7.2196 < 9.3855] w=0.1919 to align
# Constraint # added constraint: constraint((T0380)S16.CB, (T0380)M37.CB) [> 4.3110 = 7.1850 < 9.3405] w=0.1747 to align
# Constraint # added constraint: constraint((T0380)W99.CB, (T0380)G110.CA) [> 4.2400 = 7.0667 < 9.1867] w=0.1747 to align
# Constraint # added constraint: constraint((T0380)G79.CA, (T0380)H131.CB) [> 4.4874 = 7.4790 < 9.7227] w=0.1747 to align
# Constraint # added constraint: constraint((T0380)L49.CB, (T0380)L69.CB) [> 4.5178 = 7.5297 < 9.7886] w=0.1747 to align
# Constraint # added constraint: constraint((T0380)A78.CB, (T0380)L132.CB) [> 4.2971 = 7.1618 < 9.3103] w=0.1747 to align
# Constraint # added constraint: constraint((T0380)G126.CA, (T0380)T136.CB) [> 3.8248 = 6.3747 < 8.2871] w=0.1745 to align
# Constraint # added constraint: constraint((T0380)H41.CB, (T0380)L98.CB) [> 4.0258 = 6.7098 < 8.7227] w=0.1745 to align
# Constraint # added constraint: constraint((T0380)N127.CB, (T0380)F137.CB) [> 4.2742 = 7.1236 < 9.2607] w=0.1743 to align
# Constraint # added constraint: constraint((T0380)G26.CA, (T0380)E59.CB) [> 4.5545 = 7.5908 < 9.8681] w=0.1624 to align
# Constraint # added constraint: constraint((T0380)I33.CB, (T0380)Y70.CB) [> 4.7633 = 7.9388 < 10.3204] w=0.1624 to align
# Constraint # added constraint: constraint((T0380)S50.CB, (T0380)G110.CA) [> 4.5807 = 7.6344 < 9.9248] w=0.1603 to align
# Constraint # added constraint: constraint((T0380)F6.CB, (T0380)K76.CB) [> 4.7486 = 7.9143 < 10.2886] w=0.1572 to align
# Constraint # added constraint: constraint((T0380)F6.CB, (T0380)D73.CB) [> 4.3697 = 7.2828 < 9.4677] w=0.1572 to align
# Constraint # added constraint: constraint((T0380)W125.CB, (T0380)T136.CB) [> 4.1262 = 6.8770 < 8.9401] w=0.1572 to align
# Constraint # added constraint: constraint((T0380)G79.CA, (T0380)N127.CB) [> 4.7398 = 7.8997 < 10.2696] w=0.1572 to align
# Constraint # added constraint: constraint((T0380)W125.CB, (T0380)F137.CB) [> 4.0953 = 6.8255 < 8.8731] w=0.1572 to align
# Constraint # added constraint: constraint((T0380)T51.CB, (T0380)L61.CB) [> 4.6712 = 7.7854 < 10.1210] w=0.1572 to align
# Constraint # added constraint: constraint((T0380)N65.CB, (T0380)I88.CB) [> 4.1106 = 6.8509 < 8.9062] w=0.1572 to align
# Constraint # added constraint: constraint((T0380)T24.CB, (T0380)C68.CB) [> 4.6028 = 7.6713 < 9.9727] w=0.1572 to align
# Constraint # added constraint: constraint((T0380)V22.CB, (T0380)T51.CB) [> 4.6217 = 7.7028 < 10.0136] w=0.1572 to align
# Constraint # added constraint: constraint((T0380)K34.CB, (T0380)T55.CB) [> 4.4244 = 7.3740 < 9.5862] w=0.1566 to align
# Constraint # added constraint: constraint((T0380)W125.CB, (T0380)K138.CB) [> 3.3075 = 5.5124 < 7.1662] w=0.1397 to align
# Constraint # added constraint: constraint((T0380)F6.CB, (T0380)G126.CA) [> 3.8433 = 6.4056 < 8.3272] w=0.1396 to align
# Constraint # added constraint: constraint((T0380)L98.CB, (T0380)C120.CB) [> 4.1584 = 6.9307 < 9.0099] w=0.1395 to align
# Constraint # added constraint: constraint((T0380)L39.CB, (T0380)C103.CB) [> 4.0006 = 6.6676 < 8.6679] w=0.1394 to align
# Constraint # added constraint: constraint((T0380)F77.CB, (T0380)L132.CB) [> 4.3928 = 7.3213 < 9.5177] w=0.1394 to align
# Constraint # added constraint: constraint((T0380)K45.CB, (T0380)G84.CA) [> 4.7499 = 7.9165 < 10.2915] w=0.1223 to align
# Constraint # added constraint: constraint((T0380)H41.CB, (T0380)C120.CB) [> 4.3639 = 7.2731 < 9.4551] w=0.1222 to align
# Constraint # added constraint: constraint((T0380)R38.CB, (T0380)Y106.CB) [> 4.6511 = 7.7518 < 10.0774] w=0.1222 to align
# Constraint # added constraint: constraint((T0380)G126.CA, (T0380)I142.CB) [> 3.0824 = 5.1374 < 6.6786] w=0.1221 to align
# Constraint # added constraint: constraint((T0380)I19.CB, (T0380)L39.CB) [> 4.3434 = 7.2390 < 9.4108] w=0.1221 to align
# Constraint # added constraint: constraint((T0380)M37.CB, (T0380)I105.CB) [> 4.3579 = 7.2632 < 9.4422] w=0.1221 to align
# Constraint # added constraint: constraint((T0380)F6.CB, (T0380)R130.CB) [> 3.6936 = 6.1560 < 8.0028] w=0.1221 to align
# Constraint # added constraint: constraint((T0380)M37.CB, (T0380)Y107.CB) [> 3.5865 = 5.9775 < 7.7708] w=0.1221 to align
# Constraint # added constraint: constraint((T0380)L49.CB, (T0380)C120.CB) [> 4.3628 = 7.2713 < 9.4527] w=0.1217 to align
# Constraint # added constraint: constraint((T0380)I19.CB, (T0380)V72.CB) [> 4.6395 = 7.7326 < 10.0523] w=0.1100 to align
# Constraint # added constraint: constraint((T0380)G26.CA, (T0380)L61.CB) [> 4.4147 = 7.3578 < 9.5651] w=0.1100 to align
# Constraint # added constraint: constraint((T0380)S16.CB, (T0380)A35.CB) [> 4.6704 = 7.7839 < 10.1191] w=0.1048 to align
# Constraint # added constraint: constraint((T0380)M21.CB, (T0380)C68.CB) [> 4.7293 = 7.8822 < 10.2469] w=0.1048 to align
# Constraint # added constraint: constraint((T0380)W125.CB, (T0380)E141.CB) [> 4.0003 = 6.6671 < 8.6672] w=0.1048 to align
# Constraint # added constraint: constraint((T0380)W125.CB, (T0380)I142.CB) [> 3.9662 = 6.6104 < 8.5935] w=0.1048 to align
# Constraint # added constraint: constraint((T0380)N127.CB, (T0380)I139.CB) [> 3.7923 = 6.3204 < 8.2165] w=0.1048 to align
# Constraint # added constraint: constraint((T0380)N127.CB, (T0380)D140.CB) [> 4.1124 = 6.8540 < 8.9102] w=0.1048 to align
# Constraint # added constraint: constraint((T0380)N127.CB, (T0380)E141.CB) [> 2.6858 = 4.4763 < 5.8192] w=0.1048 to align
# Constraint # added constraint: constraint((T0380)N127.CB, (T0380)I142.CB) [> 4.3998 = 7.3331 < 9.5330] w=0.1048 to align
# Constraint # added constraint: constraint((T0380)L39.CB, (T0380)Y107.CB) [> 3.3153 = 5.5255 < 7.1832] w=0.1048 to align
# Constraint # added constraint: constraint((T0380)R38.CB, (T0380)Y107.CB) [> 4.3502 = 7.2503 < 9.4254] w=0.1048 to align
# Constraint # added constraint: constraint((T0380)T24.CB, (T0380)S54.CB) [> 4.5892 = 7.6487 < 9.9433] w=0.1048 to align
# Constraint # added constraint: constraint((T0380)T24.CB, (T0380)V58.CB) [> 4.1353 = 6.8922 < 8.9598] w=0.1048 to align
# Constraint # added constraint: constraint((T0380)G26.CA, (T0380)V58.CB) [> 3.7701 = 6.2835 < 8.1686] w=0.1048 to align
# Constraint # added constraint: constraint((T0380)N32.CB, (T0380)V58.CB) [> 3.3175 = 5.5291 < 7.1878] w=0.1048 to align
# Constraint # added constraint: constraint((T0380)E124.CB, (T0380)I139.CB) [> 3.3484 = 5.5808 < 7.2550] w=0.1046 to align
# Constraint # added constraint: constraint((T0380)S50.CB, (T0380)Y107.CB) [> 4.6626 = 7.7710 < 10.1023] w=0.1046 to align
# Constraint # added constraint: constraint((T0380)W48.CB, (T0380)C103.CB) [> 3.4997 = 5.8329 < 7.5828] w=0.1046 to align
# Constraint # added constraint: constraint((T0380)C68.CB, (T0380)W125.CB) [> 4.7374 = 7.8957 < 10.2644] w=0.1042 to align
# Constraint # added constraint: constraint((T0380)K95.CB, (T0380)I111.CB) [> 3.7942 = 6.3237 < 8.2208] w=0.0908 to align
# Constraint # added constraint: constraint((T0380)F47.CB, (T0380)A118.CB) [> 3.4142 = 5.6903 < 7.3974] w=0.0873 to align
# Constraint # added constraint: constraint((T0380)C103.CB, (T0380)A118.CB) [> 3.8862 = 6.4770 < 8.4201] w=0.0871 to align
# Constraint # added constraint: constraint((T0380)F6.CB, (T0380)A123.CB) [> 4.1863 = 6.9772 < 9.0704] w=0.0715 to align
# Constraint # added constraint: constraint((T0380)G43.CA, (T0380)A123.CB) [> 3.6440 = 6.0733 < 7.8953] w=0.0699 to align
# Constraint # added constraint: constraint((T0380)Y107.CB, (T0380)Y116.CB) [> 2.9511 = 4.9186 < 6.3941] w=0.0699 to align
# Constraint # added constraint: constraint((T0380)F6.CB, (T0380)I135.CB) [> 2.8869 = 4.8115 < 6.2549] w=0.0699 to align
# Constraint # added constraint: constraint((T0380)I2.CB, (T0380)Y128.CB) [> 3.4564 = 5.7607 < 7.4889] w=0.0699 to align
# Constraint # added constraint: constraint((T0380)I33.CB, (T0380)C68.CB) [> 4.6296 = 7.7160 < 10.0308] w=0.0576 to align
# Constraint # added constraint: constraint((T0380)F47.CB, (T0380)T122.CB) [> 4.7376 = 7.8959 < 10.2647] w=0.0576 to align
# Constraint # added constraint: constraint((T0380)I2.CB, (T0380)A123.CB) [> 4.1652 = 6.9419 < 9.0245] w=0.0541 to align
# Constraint # added constraint: constraint((T0380)N65.CB, (T0380)G84.CA) [> 4.7475 = 7.9126 < 10.2863] w=0.0524 to align
# Constraint # added constraint: constraint((T0380)W125.CB, (T0380)I139.CB) [> 4.1494 = 6.9156 < 8.9903] w=0.0524 to align
# Constraint # added constraint: constraint((T0380)N52.CB, (T0380)Y106.CB) [> 4.4510 = 7.4184 < 9.6439] w=0.0524 to align
# Constraint # added constraint: constraint((T0380)C103.CB, (T0380)Y116.CB) [> 4.2627 = 7.1045 < 9.2359] w=0.0524 to align
# Constraint # added constraint: constraint((T0380)S17.CB, (T0380)Y106.CB) [> 3.5569 = 5.9282 < 7.7067] w=0.0524 to align
# Constraint # added constraint: constraint((T0380)F47.CB, (T0380)I67.CB) [> 4.4937 = 7.4895 < 9.7363] w=0.0524 to align
# Constraint # added constraint: constraint((T0380)F47.CB, (T0380)G84.CA) [> 4.7859 = 7.9765 < 10.3694] w=0.0524 to align
# Constraint # added constraint: constraint((T0380)L49.CB, (T0380)I67.CB) [> 4.7555 = 7.9259 < 10.3037] w=0.0524 to align
# Constraint # added constraint: constraint((T0380)L82.CB, (T0380)E124.CB) [> 4.4852 = 7.4754 < 9.7180] w=0.0524 to align
# Constraint # added constraint: constraint((T0380)V72.CB, (T0380)M81.CB) [> 4.7491 = 7.9152 < 10.2898] w=0.0524 to align
# Constraint # added constraint: constraint((T0380)E124.CB, (T0380)Y143.CB) [> 4.0734 = 6.7890 < 8.8257] w=0.0524 to align
# Constraint # added constraint: constraint((T0380)W125.CB, (T0380)Y143.CB) [> 3.0729 = 5.1214 < 6.6579] w=0.0524 to align
# Constraint # added constraint: constraint((T0380)V20.CB, (T0380)K46.CB) [> 4.5170 = 7.5283 < 9.7868] w=0.0524 to align
# Constraint # added constraint: constraint((T0380)K66.CB, (T0380)E124.CB) [> 4.3526 = 7.2544 < 9.4307] w=0.0524 to align
# Constraint # added constraint: constraint((T0380)N64.CB, (T0380)T85.CB) [> 2.9791 = 4.9652 < 6.4547] w=0.0524 to align
# Constraint # added constraint: constraint((T0380)N25.CB, (T0380)N65.CB) [> 4.0847 = 6.8079 < 8.8503] w=0.0524 to align
# Constraint # added constraint: constraint((T0380)T24.CB, (T0380)N65.CB) [> 4.2847 = 7.1412 < 9.2835] w=0.0524 to align
# Constraint # added constraint: constraint((T0380)F6.CB, (T0380)G79.CA) [> 4.5395 = 7.5658 < 9.8355] w=0.0524 to align
# Constraint # added constraint: constraint((T0380)F6.CB, (T0380)N127.CB) [> 4.3661 = 7.2769 < 9.4599] w=0.0524 to align
# Constraint # added constraint: constraint((T0380)W48.CB, (T0380)Y106.CB) [> 4.4464 = 7.4107 < 9.6339] w=0.0524 to align
# Constraint # added constraint: constraint((T0380)W48.CB, (T0380)I105.CB) [> 4.3772 = 7.2954 < 9.4840] w=0.0524 to align
# Constraint # added constraint: constraint((T0380)Y30.CB, (T0380)R60.CB) [> 4.6080 = 7.6801 < 9.9841] w=0.0524 to align
# Constraint # added constraint: constraint((T0380)C68.CB, (T0380)F121.CB) [> 4.7466 = 7.9110 < 10.2843] w=0.0524 to align
# Constraint # added constraint: constraint((T0380)N25.CB, (T0380)K63.CB) [> 4.3213 = 7.2022 < 9.3629] w=0.0524 to align
# Constraint # added constraint: constraint((T0380)K34.CB, (T0380)T53.CB) [> 3.1489 = 5.2482 < 6.8227] w=0.0524 to align
# Constraint # added constraint: constraint((T0380)K34.CB, (T0380)T51.CB) [> 3.5294 = 5.8824 < 7.6471] w=0.0524 to align
# Constraint # added constraint: constraint((T0380)N32.CB, (T0380)T55.CB) [> 4.1965 = 6.9942 < 9.0925] w=0.0524 to align
# Constraint # added constraint: constraint((T0380)N32.CB, (T0380)T53.CB) [> 4.0876 = 6.8127 < 8.8565] w=0.0524 to align
# Constraint # added constraint: constraint((T0380)V22.CB, (T0380)N32.CB) [> 4.7597 = 7.9328 < 10.3127] w=0.0524 to align
# Constraint # added constraint: constraint((T0380)I2.CB, (T0380)G126.CA) [> 3.7542 = 6.2571 < 8.1342] w=0.0523 to align
# Constraint # added constraint: constraint((T0380)A123.CB, (T0380)I139.CB) [> 3.5009 = 5.8348 < 7.5853] w=0.0522 to align
# Constraint # added constraint: constraint((T0380)A123.CB, (T0380)I142.CB) [> 4.4075 = 7.3458 < 9.5496] w=0.0522 to align
# Constraint # added constraint: constraint((T0380)N52.CB, (T0380)I111.CB) [> 3.4050 = 5.6750 < 7.3774] w=0.0400 to align
# Constraint # added constraint: constraint((T0380)T51.CB, (T0380)D112.CB) [> 3.6348 = 6.0580 < 7.8754] w=0.0382 to align
# Constraint # added constraint: constraint((T0380)L98.CB, (T0380)L109.CB) [> 4.5465 = 7.5774 < 9.8507] w=0.0367 to align
# Constraint # added constraint: constraint((T0380)T51.CB, (T0380)D115.CB) [> 3.0000 = 4.9999 < 6.4999] w=0.0367 to align
# Constraint # added constraint: constraint((T0380)D42.CB, (T0380)T122.CB) [> 4.5189 = 7.5316 < 9.7910] w=0.0349 to align
# Constraint # added constraint: constraint((T0380)K46.CB, (T0380)G84.CA) [> 4.7406 = 7.9010 < 10.2713] w=0.0349 to align
# Constraint # added constraint: constraint((T0380)M81.CB, (T0380)T136.CB) [> 4.5473 = 7.5788 < 9.8524] w=0.0349 to align
# Constraint # added constraint: constraint((T0380)V20.CB, (T0380)W48.CB) [> 4.5142 = 7.5237 < 9.7809] w=0.0349 to align
# Constraint # added constraint: constraint((T0380)V22.CB, (T0380)W48.CB) [> 3.8132 = 6.3553 < 8.2619] w=0.0349 to align
# Constraint # added constraint: constraint((T0380)M36.CB, (T0380)W48.CB) [> 3.1860 = 5.3100 < 6.9030] w=0.0349 to align
# Constraint # added constraint: constraint((T0380)M37.CB, (T0380)W48.CB) [> 4.2954 = 7.1589 < 9.3066] w=0.0349 to align
# Constraint # added constraint: constraint((T0380)M97.CB, (T0380)C120.CB) [> 3.7101 = 6.1834 < 8.0385] w=0.0349 to align
# Constraint # added constraint: constraint((T0380)F6.CB, (T0380)L82.CB) [> 4.4866 = 7.4776 < 9.7209] w=0.0210 to align
# Constraint # added constraint: constraint((T0380)M1.CB, (T0380)K45.CB) [> 3.5576 = 5.9293 < 7.7081] w=0.0209 to align
# Constraint # added constraint: constraint((T0380)I19.CB, (T0380)K40.CB) [> 4.6971 = 7.8285 < 10.1770] w=0.0175 to align
# Constraint # added constraint: constraint((T0380)A78.CB, (T0380)I135.CB) [> 3.5793 = 5.9655 < 7.7552] w=0.0175 to align
# Constraint # added constraint: constraint((T0380)L80.CB, (T0380)I135.CB) [> 3.5887 = 5.9813 < 7.7756] w=0.0175 to align
# Constraint # added constraint: constraint((T0380)E104.CB, (T0380)P114.CB) [> 4.7324 = 7.8873 < 10.2535] w=0.0175 to align
# Constraint # added constraint: constraint((T0380)F6.CB, (T0380)I142.CB) [> 2.3976 = 3.9960 < 5.1948] w=0.0175 to align
# Constraint # added constraint: constraint((T0380)M1.CB, (T0380)W125.CB) [> 4.6238 = 7.7064 < 10.0183] w=0.0174 to align
# Constraint # added constraint: constraint((T0380)D3.CB, (T0380)A78.CB) [> 4.7591 = 7.9319 < 10.3115] w=0.0173 to align
# Constraint # added constraint: constraint((T0380)K46.CB, (T0380)Y143.CB) [> 4.7481 = 7.9134 < 10.2875] w=0.0173 to align
# Constraint # added constraint: constraint((T0380)N25.CB, (T0380)I67.CB) [> 3.9464 = 6.5773 < 8.5505] w=0.0052 to align
# Constraint # added constraint: constraint((T0380)N25.CB, (T0380)C68.CB) [> 4.5891 = 7.6485 < 9.9431] w=0.0052 to align
# Constraint # added constraint: constraint((T0380)P31.CB, (T0380)K66.CB) [> 4.7063 = 7.8438 < 10.1969] w=0.0052 to align
# SetCost created cost = 
#	( 1.0000 * align )
# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0380/
# command:# reading script from file servers-clean.under
# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0380/decoys/
# ReadConformPDB reading from PDB file chimera-4-6.pdb.gz looking for model 1
# choosing archetypes in rotamer library
# Found a chain break before 132
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file chimera-4-8.pdb.gz looking for model 1
# Found a chain break before 132
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file tr380.gromacs0.pdb.gz looking for model 1
# ReadConformPDB reading from PDB file tr380.gromacs0.repack-nonPC.pdb.gz looking for model 1
# ReadConformPDB reading from PDB file tr380.pdb.gz looking for model 1
# ReadConformPDB reading from PDB file tr380.repack-nonPC.pdb.gz looking for model 1
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1
# Found a chain break before 139
# copying to AlignedFragments data structure
# naming current conformation 3D-JIGSAW_POPULUS_TS1
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS2.pdb.gz looking for model 1
# Found a chain break before 139
# copying to AlignedFragments data structure
# naming current conformation 3D-JIGSAW_POPULUS_TS2
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS3.pdb.gz looking for model 1
# Found a chain break before 139
# copying to AlignedFragments data structure
# naming current conformation 3D-JIGSAW_POPULUS_TS3
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS4.pdb.gz looking for model 1
# Found a chain break before 124
# copying to AlignedFragments data structure
# naming current conformation 3D-JIGSAW_POPULUS_TS4
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS5.pdb.gz looking for model 1
# Found a chain break before 139
# copying to AlignedFragments data structure
# naming current conformation 3D-JIGSAW_POPULUS_TS5
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation 3D-JIGSAW_RECOM_TS1
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation 3D-JIGSAW_RECOM_TS2
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation 3D-JIGSAW_RECOM_TS3
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation 3D-JIGSAW_RECOM_TS4
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation 3D-JIGSAW_RECOM_TS5
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation 3D-JIGSAW_TS1
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation 3D-JIGSAW_TS2
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation 3D-JIGSAW_TS3
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation 3D-JIGSAW_TS4
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation 3D-JIGSAW_TS5
# ReadConformPDB reading from PDB file servers/3Dpro_TS1.pdb.gz looking for model 1
# Found a chain break before 106
# copying to AlignedFragments data structure
# naming current conformation 3Dpro_TS1
# ReadConformPDB reading from PDB file servers/3Dpro_TS2.pdb.gz looking for model 1
# Found a chain break before 110
# copying to AlignedFragments data structure
# naming current conformation 3Dpro_TS2
# ReadConformPDB reading from PDB file servers/3Dpro_TS3.pdb.gz looking for model 1
# Found a chain break before 108
# copying to AlignedFragments data structure
# naming current conformation 3Dpro_TS3
# ReadConformPDB reading from PDB file servers/3Dpro_TS4.pdb.gz looking for model 1
# Found a chain break before 130
# copying to AlignedFragments data structure
# naming current conformation 3Dpro_TS4
# ReadConformPDB reading from PDB file servers/3Dpro_TS5.pdb.gz looking for model 1
# Found a chain break before 128
# copying to AlignedFragments data structure
# naming current conformation 3Dpro_TS5
# ReadConformPDB reading from PDB file servers/ABIpro_TS1.pdb.gz looking for model 1
# Found a chain break before 141
# copying to AlignedFragments data structure
# naming current conformation ABIpro_TS1
# ReadConformPDB reading from PDB file servers/ABIpro_TS2.pdb.gz looking for model 1
# Found a chain break before 134
# copying to AlignedFragments data structure
# naming current conformation ABIpro_TS2
# ReadConformPDB reading from PDB file servers/ABIpro_TS3.pdb.gz looking for model 1
# Found a chain break before 128
# copying to AlignedFragments data structure
# naming current conformation ABIpro_TS3
# ReadConformPDB reading from PDB file servers/ABIpro_TS4.pdb.gz looking for model 1
# Found a chain break before 130
# copying to AlignedFragments data structure
# naming current conformation ABIpro_TS4
# ReadConformPDB reading from PDB file servers/ABIpro_TS5.pdb.gz looking for model 1
# Found a chain break before 138
# copying to AlignedFragments data structure
# naming current conformation ABIpro_TS5
# ReadConformPDB reading from PDB file servers/BayesHH_TS1.pdb.gz looking for model 1
# naming current conformation BayesHH_TS1
# ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS1.pdb.gz looking for model 1
# Found a chain break before 136
# copying to AlignedFragments data structure
# naming current conformation Bilab-ENABLE_TS1
# ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS2.pdb.gz looking for model 1
# naming current conformation Bilab-ENABLE_TS2
# ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS3.pdb.gz looking for model 1
# Found a chain break before 143
# copying to AlignedFragments data structure
# naming current conformation Bilab-ENABLE_TS3
# ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS4.pdb.gz looking for model 1
# naming current conformation Bilab-ENABLE_TS4
# ReadConformPDB reading from PDB file servers/Bilab-ENABLE_TS5.pdb.gz looking for model 1
# Found a chain break before 83
# copying to AlignedFragments data structure
# naming current conformation Bilab-ENABLE_TS5
# ReadConformPDB reading from PDB file servers/CIRCLE_TS1.pdb.gz looking for model 1
# Found a chain break before 126
# copying to AlignedFragments data structure
# naming current conformation CIRCLE_TS1
# ReadConformPDB reading from PDB file servers/CIRCLE_TS2.pdb.gz looking for model 1
# Found a chain break before 142
# copying to AlignedFragments data structure
# naming current conformation CIRCLE_TS2
# ReadConformPDB reading from PDB file servers/CIRCLE_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation CIRCLE_TS3
# ReadConformPDB reading from PDB file servers/CIRCLE_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation CIRCLE_TS4
# ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation CIRCLE_TS5
# ReadConformPDB reading from PDB file servers/CPHmodels_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation CPHmodels_TS1
# ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation CaspIta-FOX_TS1
# ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation CaspIta-FOX_TS2
# ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation CaspIta-FOX_TS3
# ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS4.pdb.gz looking for model 1
# Found a chain break before 113
# copying to AlignedFragments data structure
# naming current conformation CaspIta-FOX_TS4
# ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS5.pdb.gz looking for model 1
# Found a chain break before 109
# copying to AlignedFragments data structure
# naming current conformation CaspIta-FOX_TS5
# ReadConformPDB reading from PDB file servers/Distill_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation Distill_TS1
# ReadConformPDB reading from PDB file servers/Distill_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation Distill_TS2
# ReadConformPDB reading from PDB file servers/Distill_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation Distill_TS3
# ReadConformPDB reading from PDB file servers/Distill_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation Distill_TS4
# ReadConformPDB reading from PDB file servers/Distill_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation Distill_TS5
# ReadConformPDB reading from PDB file servers/FAMSD_TS1.pdb.gz looking for model 1
# Found a chain break before 143
# copying to AlignedFragments data structure
# naming current conformation FAMSD_TS1
# ReadConformPDB reading from PDB file servers/FAMSD_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation FAMSD_TS2
# ReadConformPDB reading from PDB file servers/FAMSD_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation FAMSD_TS3
# ReadConformPDB reading from PDB file servers/FAMSD_TS4.pdb.gz looking for model 1
# Found a chain break before 114
# copying to AlignedFragments data structure
# naming current conformation FAMSD_TS4
# ReadConformPDB reading from PDB file servers/FAMSD_TS5.pdb.gz looking for model 1
# Found a chain break before 113
# copying to AlignedFragments data structure
# naming current conformation FAMSD_TS5
# ReadConformPDB reading from PDB file servers/FAMS_TS1.pdb.gz looking for model 1
# Found a chain break before 142
# copying to AlignedFragments data structure
# naming current conformation FAMS_TS1
# ReadConformPDB reading from PDB file servers/FAMS_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation FAMS_TS2
# ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation FAMS_TS3
# ReadConformPDB reading from PDB file servers/FAMS_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation FAMS_TS4
# ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1
# Found a chain break before 142
# copying to AlignedFragments data structure
# naming current conformation FAMS_TS5
# ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1
# Found a chain break before 102
# copying to AlignedFragments data structure
# naming current conformation FOLDpro_TS1
# ReadConformPDB reading from PDB file servers/FOLDpro_TS2.pdb.gz looking for model 1
# Found a chain break before 122
# copying to AlignedFragments data structure
# naming current conformation FOLDpro_TS2
# ReadConformPDB reading from PDB file servers/FOLDpro_TS3.pdb.gz looking for model 1
# Found a chain break before 77
# copying to AlignedFragments data structure
# naming current conformation FOLDpro_TS3
# ReadConformPDB reading from PDB file servers/FOLDpro_TS4.pdb.gz looking for model 1
# naming current conformation FOLDpro_TS4
# ReadConformPDB reading from PDB file servers/FOLDpro_TS5.pdb.gz looking for model 1
# naming current conformation FOLDpro_TS5
# ReadConformPDB reading from PDB file servers/FORTE1_AL1.pdb.gz looking for model 1
Skipped atom 62, because occupancy 1 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz
Skipped atom 64, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz
Skipped atom 66, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz
Skipped atom 68, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz
Skipped atom 318, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz
Skipped atom 320, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz
Skipped atom 322, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz
Skipped atom 324, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz
Skipped atom 374, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz
Skipped atom 376, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz
Skipped atom 378, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz
Skipped atom 380, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz
Skipped atom 490, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz
Skipped atom 492, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz
Skipped atom 494, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz
Skipped atom 496, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL1.pdb.gz
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation FORTE1_AL1
# ReadConformPDB reading from PDB file servers/FORTE1_AL2.pdb.gz looking for model 1
Skipped atom 177, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz
Skipped atom 514, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL2.pdb.gz
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation FORTE1_AL2
# ReadConformPDB reading from PDB file servers/FORTE1_AL3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation FORTE1_AL3
# ReadConformPDB reading from PDB file servers/FORTE1_AL4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation FORTE1_AL4
# ReadConformPDB reading from PDB file servers/FORTE1_AL5.pdb.gz looking for model 1
Skipped atom 126, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz
Skipped atom 128, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz
Skipped atom 130, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz
Skipped atom 132, because occupancy 1.000 <= existing 1.000 in servers/FORTE1_AL5.pdb.gz
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation FORTE1_AL5
# ReadConformPDB reading from PDB file servers/FORTE2_AL1.pdb.gz looking for model 1
Skipped atom 62, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz
Skipped atom 64, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz
Skipped atom 66, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz
Skipped atom 68, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz
Skipped atom 318, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz
Skipped atom 320, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz
Skipped atom 322, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz
Skipped atom 324, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz
Skipped atom 374, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz
Skipped atom 376, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz
Skipped atom 378, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz
Skipped atom 380, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz
Skipped atom 490, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz
Skipped atom 492, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz
Skipped atom 494, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz
Skipped atom 496, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL1.pdb.gz
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation FORTE2_AL1
# ReadConformPDB reading from PDB file servers/FORTE2_AL2.pdb.gz looking for model 1
Skipped atom 177, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz
Skipped atom 514, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL2.pdb.gz
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation FORTE2_AL2
# ReadConformPDB reading from PDB file servers/FORTE2_AL3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation FORTE2_AL3
# ReadConformPDB reading from PDB file servers/FORTE2_AL4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation FORTE2_AL4
# ReadConformPDB reading from PDB file servers/FORTE2_AL5.pdb.gz looking for model 1
Skipped atom 126, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz
Skipped atom 128, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz
Skipped atom 130, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz
Skipped atom 132, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL5.pdb.gz
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation FORTE2_AL5
# ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS1.pdb.gz looking for model 1
# Found a chain break before 117
# copying to AlignedFragments data structure
# naming current conformation FPSOLVER-SERVER_TS1
# ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS2.pdb.gz looking for model 1
# Found a chain break before 124
# copying to AlignedFragments data structure
# naming current conformation FPSOLVER-SERVER_TS2
# ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS3.pdb.gz looking for model 1
# Found a chain break before 46
# copying to AlignedFragments data structure
# naming current conformation FPSOLVER-SERVER_TS3
# ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS4.pdb.gz looking for model 1
# Found a chain break before 133
# copying to AlignedFragments data structure
# naming current conformation FPSOLVER-SERVER_TS4
# ReadConformPDB reading from PDB file servers/FPSOLVER-SERVER_TS5.pdb.gz looking for model 1
# Found a chain break before 144
# copying to AlignedFragments data structure
# naming current conformation FPSOLVER-SERVER_TS5
# ReadConformPDB reading from PDB file servers/FUGMOD_TS1.pdb.gz looking for model 1
# Found a chain break before 44
# copying to AlignedFragments data structure
# naming current conformation FUGMOD_TS1
# ReadConformPDB reading from PDB file servers/FUGMOD_TS2.pdb.gz looking for model 1
# Found a chain break before 107
# copying to AlignedFragments data structure
# naming current conformation FUGMOD_TS2
# ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation FUGMOD_TS3
# ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1
# Found a chain break before 35
# copying to AlignedFragments data structure
# naming current conformation FUGMOD_TS4
# ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation FUGMOD_TS5
# ReadConformPDB reading from PDB file servers/FUGUE_AL1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation FUGUE_AL1
# ReadConformPDB reading from PDB file servers/FUGUE_AL2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation FUGUE_AL2
# ReadConformPDB reading from PDB file servers/FUGUE_AL3.pdb.gz looking for model 1
Skipped atom 58, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL3.pdb.gz
Skipped atom 60, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL3.pdb.gz
Skipped atom 62, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL3.pdb.gz
Skipped atom 64, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL3.pdb.gz
Skipped atom 354, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL3.pdb.gz
Skipped atom 356, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL3.pdb.gz
Skipped atom 358, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL3.pdb.gz
Skipped atom 360, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL3.pdb.gz
Skipped atom 470, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL3.pdb.gz
Skipped atom 472, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL3.pdb.gz
Skipped atom 474, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL3.pdb.gz
Skipped atom 476, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL3.pdb.gz
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation FUGUE_AL3
# ReadConformPDB reading from PDB file servers/FUGUE_AL4.pdb.gz looking for model 1
Skipped atom 126, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL4.pdb.gz
Skipped atom 128, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL4.pdb.gz
Skipped atom 130, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL4.pdb.gz
Skipped atom 132, because occupancy 1.000 <= existing 1.000 in servers/FUGUE_AL4.pdb.gz
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation FUGUE_AL4
# ReadConformPDB reading from PDB file servers/FUGUE_AL5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation FUGUE_AL5
# ReadConformPDB reading from PDB file servers/FUNCTION_TS1.pdb.gz looking for model 1
# Found a chain break before 119
# copying to AlignedFragments data structure
# naming current conformation FUNCTION_TS1
# ReadConformPDB reading from PDB file servers/FUNCTION_TS2.pdb.gz looking for model 1
# Found a chain break before 108
# copying to AlignedFragments data structure
# naming current conformation FUNCTION_TS2
# ReadConformPDB reading from PDB file servers/FUNCTION_TS3.pdb.gz looking for model 1
# Found a chain break before 142
# copying to AlignedFragments data structure
# naming current conformation FUNCTION_TS3
# ReadConformPDB reading from PDB file servers/FUNCTION_TS4.pdb.gz looking for model 1
# Found a chain break before 136
# copying to AlignedFragments data structure
# naming current conformation FUNCTION_TS4
# ReadConformPDB reading from PDB file servers/FUNCTION_TS5.pdb.gz looking for model 1
# Found a chain break before 144
# copying to AlignedFragments data structure
# naming current conformation FUNCTION_TS5
# ReadConformPDB reading from PDB file servers/Frankenstein_TS1.pdb.gz looking for model 1
# naming current conformation Frankenstein_TS1
# ReadConformPDB reading from PDB file servers/Frankenstein_TS2.pdb.gz looking for model 1
# Found a chain break before 120
# copying to AlignedFragments data structure
# naming current conformation Frankenstein_TS2
# ReadConformPDB reading from PDB file servers/Frankenstein_TS3.pdb.gz looking for model 1
# Found a chain break before 130
# copying to AlignedFragments data structure
# naming current conformation Frankenstein_TS3
# ReadConformPDB reading from PDB file servers/Frankenstein_TS4.pdb.gz looking for model 1
# Found a chain break before 12
# copying to AlignedFragments data structure
# naming current conformation Frankenstein_TS4
# ReadConformPDB reading from PDB file servers/Frankenstein_TS5.pdb.gz looking for model 1
# Found a chain break before 84
# copying to AlignedFragments data structure
# naming current conformation Frankenstein_TS5
# ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation GeneSilicoMetaServer_TS1
# ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS2.pdb.gz looking for model 1
# Found a chain break before 138
# copying to AlignedFragments data structure
# naming current conformation GeneSilicoMetaServer_TS2
# ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation GeneSilicoMetaServer_TS3
# ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation GeneSilicoMetaServer_TS4
# ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation GeneSilicoMetaServer_TS5
# ReadConformPDB reading from PDB file servers/HHpred1_TS1.pdb.gz looking for model 1
# naming current conformation HHpred1_TS1
# ReadConformPDB reading from PDB file servers/HHpred2_TS1.pdb.gz looking for model 1
# Found a chain break before 89
# copying to AlignedFragments data structure
# naming current conformation HHpred2_TS1
# ReadConformPDB reading from PDB file servers/HHpred3_TS1.pdb.gz looking for model 1
# Found a chain break before 89
# copying to AlignedFragments data structure
# naming current conformation HHpred3_TS1
# ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation Huber-Torda-Server_TS1
# ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation Huber-Torda-Server_TS2
# ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation Huber-Torda-Server_TS3
# ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation Huber-Torda-Server_TS4
# ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation Huber-Torda-Server_TS5
# ReadConformPDB reading from PDB file servers/LOOPP_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation LOOPP_TS1
# ReadConformPDB reading from PDB file servers/LOOPP_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation LOOPP_TS2
# ReadConformPDB reading from PDB file servers/LOOPP_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation LOOPP_TS3
# ReadConformPDB reading from PDB file servers/LOOPP_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation LOOPP_TS4
# ReadConformPDB reading from PDB file servers/LOOPP_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation LOOPP_TS5
# ReadConformPDB reading from PDB file servers/MIG_FROST_AL1.pdb.gz looking for model 1
Skipped atom 142, because occupancy 1.000 <= existing 1.000 in servers/MIG_FROST_AL1.pdb.gz
Skipped atom 144, because occupancy 1.000 <= existing 1.000 in servers/MIG_FROST_AL1.pdb.gz
Skipped atom 146, because occupancy 1.000 <= existing 1.000 in servers/MIG_FROST_AL1.pdb.gz
Skipped atom 148, because occupancy 1.000 <= existing 1.000 in servers/MIG_FROST_AL1.pdb.gz
Skipped atom 291, because occupancy 1.000 <= existing 1.000 in servers/MIG_FROST_AL1.pdb.gz
Skipped atom 308, because occupancy 1.000 <= existing 1.000 in servers/MIG_FROST_AL1.pdb.gz
Skipped atom 317, because occupancy 1.000 <= existing 1.000 in servers/MIG_FROST_AL1.pdb.gz
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation MIG_FROST_AL1
# ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS1.pdb.gz looking for model 1
# naming current conformation Ma-OPUS-server2_TS1
# ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS2.pdb.gz looking for model 1
# Found a chain break before 73
# copying to AlignedFragments data structure
# naming current conformation Ma-OPUS-server2_TS2
# ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS3.pdb.gz looking for model 1
# Found a chain break before 144
# copying to AlignedFragments data structure
# naming current conformation Ma-OPUS-server2_TS3
# ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS4.pdb.gz looking for model 1
# Found a chain break before 131
# copying to AlignedFragments data structure
# naming current conformation Ma-OPUS-server2_TS4
# ReadConformPDB reading from PDB file servers/Ma-OPUS-server2_TS5.pdb.gz looking for model 1
# naming current conformation Ma-OPUS-server2_TS5
# ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS1.pdb.gz looking for model 1
# naming current conformation Ma-OPUS-server_TS1
# ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS2.pdb.gz looking for model 1
# Found a chain break before 73
# copying to AlignedFragments data structure
# naming current conformation Ma-OPUS-server_TS2
# ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS3.pdb.gz looking for model 1
# naming current conformation Ma-OPUS-server_TS3
# ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS4.pdb.gz looking for model 1
# Found a chain break before 40
# copying to AlignedFragments data structure
# naming current conformation Ma-OPUS-server_TS4
# ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS5.pdb.gz looking for model 1
# Found a chain break before 114
# copying to AlignedFragments data structure
# naming current conformation Ma-OPUS-server_TS5
# ReadConformPDB reading from PDB file servers/MetaTasser_TS1.pdb.gz looking for model 1
# Found a chain break before 144
# copying to AlignedFragments data structure
# naming current conformation MetaTasser_TS1
# ReadConformPDB reading from PDB file servers/MetaTasser_TS2.pdb.gz looking for model 1
# Found a chain break before 144
# copying to AlignedFragments data structure
# naming current conformation MetaTasser_TS2
# ReadConformPDB reading from PDB file servers/MetaTasser_TS3.pdb.gz looking for model 1
# Found a chain break before 144
# copying to AlignedFragments data structure
# naming current conformation MetaTasser_TS3
# ReadConformPDB reading from PDB file servers/MetaTasser_TS4.pdb.gz looking for model 1
# Found a chain break before 144
# copying to AlignedFragments data structure
# naming current conformation MetaTasser_TS4
# ReadConformPDB reading from PDB file servers/MetaTasser_TS5.pdb.gz looking for model 1
# Found a chain break before 144
# copying to AlignedFragments data structure
# naming current conformation MetaTasser_TS5
# ReadConformPDB reading from PDB file servers/NN_PUT_lab_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation NN_PUT_lab_TS1
# ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS1.pdb.gz looking for model 1
# naming current conformation PROTINFO-AB_TS1
# ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS2.pdb.gz looking for model 1
# naming current conformation PROTINFO-AB_TS2
# ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS3.pdb.gz looking for model 1
# naming current conformation PROTINFO-AB_TS3
# ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS4.pdb.gz looking for model 1
# naming current conformation PROTINFO-AB_TS4
# ReadConformPDB reading from PDB file servers/PROTINFO-AB_TS5.pdb.gz looking for model 1
# naming current conformation PROTINFO-AB_TS5
# ReadConformPDB reading from PDB file servers/PROTINFO_TS1.pdb.gz looking for model 1
# Found a chain break before 86
# copying to AlignedFragments data structure
# naming current conformation PROTINFO_TS1
# ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1
# Found a chain break before 109
# copying to AlignedFragments data structure
# naming current conformation PROTINFO_TS2
# ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1
# Found a chain break before 96
# copying to AlignedFragments data structure
# naming current conformation PROTINFO_TS3
# ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1
# naming current conformation PROTINFO_TS4
# ReadConformPDB reading from PDB file servers/PROTINFO_TS5.pdb.gz looking for model 1
# naming current conformation PROTINFO_TS5
# ReadConformPDB reading from PDB file servers/Pcons6_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation Pcons6_TS1
# ReadConformPDB reading from PDB file servers/Pcons6_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation Pcons6_TS2
# ReadConformPDB reading from PDB file servers/Pcons6_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation Pcons6_TS3
# ReadConformPDB reading from PDB file servers/Pcons6_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation Pcons6_TS4
# ReadConformPDB reading from PDB file servers/Pcons6_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation Pcons6_TS5
# ReadConformPDB reading from PDB file servers/Phyre-1_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation Phyre-1_TS1
# ReadConformPDB reading from PDB file servers/Phyre-2_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation Phyre-2_TS1
# ReadConformPDB reading from PDB file servers/Phyre-2_TS2.pdb.gz looking for model 1
# Found a chain break before 131
# copying to AlignedFragments data structure
# naming current conformation Phyre-2_TS2
# ReadConformPDB reading from PDB file servers/Phyre-2_TS3.pdb.gz looking for model 1
# Found a chain break before 131
# copying to AlignedFragments data structure
# naming current conformation Phyre-2_TS3
# ReadConformPDB reading from PDB file servers/Phyre-2_TS4.pdb.gz looking for model 1
# Found a chain break before 131
# copying to AlignedFragments data structure
# naming current conformation Phyre-2_TS4
# ReadConformPDB reading from PDB file servers/Phyre-2_TS5.pdb.gz looking for model 1
# Found a chain break before 137
# copying to AlignedFragments data structure
# naming current conformation Phyre-2_TS5
# ReadConformPDB reading from PDB file servers/Pmodeller6_TS1.pdb.gz looking for model 1
# Found a chain break before 79
# copying to AlignedFragments data structure
# naming current conformation Pmodeller6_TS1
# ReadConformPDB reading from PDB file servers/Pmodeller6_TS2.pdb.gz looking for model 1
# Found a chain break before 75
# copying to AlignedFragments data structure
# naming current conformation Pmodeller6_TS2
# ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1
# naming current conformation Pmodeller6_TS3
# ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1
# Found a chain break before 73
# copying to AlignedFragments data structure
# naming current conformation Pmodeller6_TS4
# ReadConformPDB reading from PDB file servers/Pmodeller6_TS5.pdb.gz looking for model 1
# naming current conformation Pmodeller6_TS5
# ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation RAPTOR-ACE_TS1
# ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation RAPTOR-ACE_TS2
# ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS3.pdb.gz looking for model 1
# Found a chain break before 36
# copying to AlignedFragments data structure
# naming current conformation RAPTOR-ACE_TS3
# ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS4.pdb.gz looking for model 1
# Found a chain break before 11
# copying to AlignedFragments data structure
# naming current conformation RAPTOR-ACE_TS4
# ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS5.pdb.gz looking for model 1
# Found a chain break before 83
# copying to AlignedFragments data structure
# naming current conformation RAPTOR-ACE_TS5
# ReadConformPDB reading from PDB file servers/RAPTORESS_TS1.pdb.gz looking for model 1
# naming current conformation RAPTORESS_TS1
# ReadConformPDB reading from PDB file servers/RAPTORESS_TS2.pdb.gz looking for model 1
# Found a chain break before 140
# copying to AlignedFragments data structure
# naming current conformation RAPTORESS_TS2
# ReadConformPDB reading from PDB file servers/RAPTORESS_TS3.pdb.gz looking for model 1
# Found a chain break before 135
# copying to AlignedFragments data structure
# naming current conformation RAPTORESS_TS3
# ReadConformPDB reading from PDB file servers/RAPTORESS_TS4.pdb.gz looking for model 1
# Found a chain break before 77
# copying to AlignedFragments data structure
# naming current conformation RAPTORESS_TS4
# ReadConformPDB reading from PDB file servers/RAPTORESS_TS5.pdb.gz looking for model 1
# Found a chain break before 144
# copying to AlignedFragments data structure
# naming current conformation RAPTORESS_TS5
# ReadConformPDB reading from PDB file servers/RAPTOR_TS1.pdb.gz looking for model 1
# Found a chain break before 89
# copying to AlignedFragments data structure
# naming current conformation RAPTOR_TS1
# ReadConformPDB reading from PDB file servers/RAPTOR_TS2.pdb.gz looking for model 1
# naming current conformation RAPTOR_TS2
# ReadConformPDB reading from PDB file servers/RAPTOR_TS3.pdb.gz looking for model 1
# naming current conformation RAPTOR_TS3
# ReadConformPDB reading from PDB file servers/RAPTOR_TS4.pdb.gz looking for model 1
# naming current conformation RAPTOR_TS4
# ReadConformPDB reading from PDB file servers/RAPTOR_TS5.pdb.gz looking for model 1
# Found a chain break before 105
# copying to AlignedFragments data structure
# naming current conformation RAPTOR_TS5
# ReadConformPDB reading from PDB file servers/ROBETTA_TS1.pdb.gz looking for model 1
# Found a chain break before 73
# copying to AlignedFragments data structure
# naming current conformation ROBETTA_TS1
# ReadConformPDB reading from PDB file servers/ROBETTA_TS2.pdb.gz looking for model 1
# Found a chain break before 79
# copying to AlignedFragments data structure
# naming current conformation ROBETTA_TS2
# ReadConformPDB reading from PDB file servers/ROBETTA_TS3.pdb.gz looking for model 1
# Found a chain break before 75
# copying to AlignedFragments data structure
# naming current conformation ROBETTA_TS3
# ReadConformPDB reading from PDB file servers/ROBETTA_TS4.pdb.gz looking for model 1
# naming current conformation ROBETTA_TS4
# ReadConformPDB reading from PDB file servers/ROBETTA_TS5.pdb.gz looking for model 1
# naming current conformation ROBETTA_TS5
# ReadConformPDB reading from PDB file servers/ROKKY_TS1.pdb.gz looking for model 1
# Found a chain break before 131
# copying to AlignedFragments data structure
# naming current conformation ROKKY_TS1
# ReadConformPDB reading from PDB file servers/ROKKY_TS2.pdb.gz looking for model 1
# Found a chain break before 112
# copying to AlignedFragments data structure
# naming current conformation ROKKY_TS2
# ReadConformPDB reading from PDB file servers/ROKKY_TS3.pdb.gz looking for model 1
# Found a chain break before 129
# copying to AlignedFragments data structure
# naming current conformation ROKKY_TS3
# ReadConformPDB reading from PDB file servers/ROKKY_TS4.pdb.gz looking for model 1
# Found a chain break before 136
# copying to AlignedFragments data structure
# naming current conformation ROKKY_TS4
# ReadConformPDB reading from PDB file servers/ROKKY_TS5.pdb.gz looking for model 1
# naming current conformation ROKKY_TS5
# ReadConformPDB reading from PDB file servers/SAM-T02_AL1.pdb.gz looking for model 1
Skipped atom 62, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz
Skipped atom 64, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz
Skipped atom 66, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz
Skipped atom 68, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz
Skipped atom 318, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz
Skipped atom 320, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz
Skipped atom 322, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz
Skipped atom 324, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz
Skipped atom 374, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz
Skipped atom 376, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz
Skipped atom 378, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz
Skipped atom 380, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz
Skipped atom 490, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz
Skipped atom 492, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz
Skipped atom 494, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz
Skipped atom 496, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL1.pdb.gz
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation SAM-T02_AL1
# ReadConformPDB reading from PDB file servers/SAM-T02_AL2.pdb.gz looking for model 1
Skipped atom 98, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz
Skipped atom 100, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz
Skipped atom 102, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz
Skipped atom 104, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL2.pdb.gz
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation SAM-T02_AL2
# ReadConformPDB reading from PDB file servers/SAM-T02_AL3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation SAM-T02_AL3
# ReadConformPDB reading from PDB file servers/SAM-T02_AL4.pdb.gz looking for model 1
Skipped atom 222, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 224, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 226, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 228, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 298, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 300, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 302, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 304, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation SAM-T02_AL4
# ReadConformPDB reading from PDB file servers/SAM-T02_AL5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation SAM-T02_AL5
# ReadConformPDB reading from PDB file servers/SAM-T99_AL1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation SAM-T99_AL1
# ReadConformPDB reading from PDB file servers/SAM-T99_AL2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation SAM-T99_AL2
# ReadConformPDB reading from PDB file servers/SAM-T99_AL3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation SAM-T99_AL3
# ReadConformPDB reading from PDB file servers/SAM-T99_AL4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation SAM-T99_AL4
# ReadConformPDB reading from PDB file servers/SAM-T99_AL5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation SAM-T99_AL5
# ReadConformPDB reading from PDB file servers/SAM_T06_server_TS1.pdb.gz looking for model 1
# Found a chain break before 143
# copying to AlignedFragments data structure
# naming current conformation SAM_T06_server_TS1
# ReadConformPDB reading from PDB file servers/SAM_T06_server_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation SAM_T06_server_TS2
# ReadConformPDB reading from PDB file servers/SAM_T06_server_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation SAM_T06_server_TS3
# ReadConformPDB reading from PDB file servers/SAM_T06_server_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation SAM_T06_server_TS4
# ReadConformPDB reading from PDB file servers/SAM_T06_server_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation SAM_T06_server_TS5
# ReadConformPDB reading from PDB file servers/SP3_TS1.pdb.gz looking for model 1
# Found a chain break before 83
# copying to AlignedFragments data structure
# naming current conformation SP3_TS1
# ReadConformPDB reading from PDB file servers/SP3_TS2.pdb.gz looking for model 1
# Found a chain break before 134
# copying to AlignedFragments data structure
# naming current conformation SP3_TS2
# ReadConformPDB reading from PDB file servers/SP3_TS3.pdb.gz looking for model 1
# Found a chain break before 122
# copying to AlignedFragments data structure
# naming current conformation SP3_TS3
# ReadConformPDB reading from PDB file servers/SP3_TS4.pdb.gz looking for model 1
# naming current conformation SP3_TS4
# ReadConformPDB reading from PDB file servers/SP3_TS5.pdb.gz looking for model 1
# Found a chain break before 110
# copying to AlignedFragments data structure
# naming current conformation SP3_TS5
# ReadConformPDB reading from PDB file servers/SP4_TS1.pdb.gz looking for model 1
# Found a chain break before 83
# copying to AlignedFragments data structure
# naming current conformation SP4_TS1
# ReadConformPDB reading from PDB file servers/SP4_TS2.pdb.gz looking for model 1
# Found a chain break before 134
# copying to AlignedFragments data structure
# naming current conformation SP4_TS2
# ReadConformPDB reading from PDB file servers/SP4_TS3.pdb.gz looking for model 1
# Found a chain break before 122
# copying to AlignedFragments data structure
# naming current conformation SP4_TS3
# ReadConformPDB reading from PDB file servers/SP4_TS4.pdb.gz looking for model 1
# Found a chain break before 35
# copying to AlignedFragments data structure
# naming current conformation SP4_TS4
# ReadConformPDB reading from PDB file servers/SP4_TS5.pdb.gz looking for model 1
# Found a chain break before 110
# copying to AlignedFragments data structure
# naming current conformation SP4_TS5
# ReadConformPDB reading from PDB file servers/SPARKS2_TS1.pdb.gz looking for model 1
# Found a chain break before 134
# copying to AlignedFragments data structure
# naming current conformation SPARKS2_TS1
# ReadConformPDB reading from PDB file servers/SPARKS2_TS2.pdb.gz looking for model 1
# Found a chain break before 122
# copying to AlignedFragments data structure
# naming current conformation SPARKS2_TS2
# ReadConformPDB reading from PDB file servers/SPARKS2_TS3.pdb.gz looking for model 1
# Found a chain break before 83
# copying to AlignedFragments data structure
# naming current conformation SPARKS2_TS3
# ReadConformPDB reading from PDB file servers/SPARKS2_TS4.pdb.gz looking for model 1
# Found a chain break before 88
# copying to AlignedFragments data structure
# naming current conformation SPARKS2_TS4
# ReadConformPDB reading from PDB file servers/SPARKS2_TS5.pdb.gz looking for model 1
# Found a chain break before 35
# copying to AlignedFragments data structure
# naming current conformation SPARKS2_TS5
# ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation UNI-EID_bnmx_TS1
# ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation UNI-EID_bnmx_TS2
# ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation UNI-EID_bnmx_TS3
# ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation UNI-EID_bnmx_TS4
# ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation UNI-EID_bnmx_TS5
# ReadConformPDB reading from PDB file servers/UNI-EID_expm_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation UNI-EID_expm_TS1
# ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL1.pdb.gz looking for model 1
Skipped atom 62, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz
Skipped atom 64, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz
Skipped atom 66, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz
Skipped atom 68, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz
Skipped atom 318, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz
Skipped atom 320, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz
Skipped atom 322, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz
Skipped atom 324, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz
Skipped atom 374, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz
Skipped atom 376, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz
Skipped atom 378, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz
Skipped atom 380, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz
Skipped atom 490, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz
Skipped atom 492, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz
Skipped atom 494, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz
Skipped atom 496, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL1.pdb.gz
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation UNI-EID_sfst_AL1
# ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL2.pdb.gz looking for model 1
Skipped atom 98, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz
Skipped atom 100, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz
Skipped atom 102, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz
Skipped atom 104, because occupancy 1.000 <= existing 1.000 in servers/UNI-EID_sfst_AL2.pdb.gz
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation UNI-EID_sfst_AL2
# ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation UNI-EID_sfst_AL3
# ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation UNI-EID_sfst_AL4
# ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation UNI-EID_sfst_AL5
# ReadConformPDB reading from PDB file servers/Zhang-Server_TS1.pdb.gz looking for model 1
# Found a chain break before 83
# copying to AlignedFragments data structure
# naming current conformation Zhang-Server_TS1
# ReadConformPDB reading from PDB file servers/Zhang-Server_TS2.pdb.gz looking for model 1
# Found a chain break before 83
# copying to AlignedFragments data structure
# naming current conformation Zhang-Server_TS2
# ReadConformPDB reading from PDB file servers/Zhang-Server_TS3.pdb.gz looking for model 1
# naming current conformation Zhang-Server_TS3
# ReadConformPDB reading from PDB file servers/Zhang-Server_TS4.pdb.gz looking for model 1
# Found a chain break before 141
# copying to AlignedFragments data structure
# naming current conformation Zhang-Server_TS4
# ReadConformPDB reading from PDB file servers/Zhang-Server_TS5.pdb.gz looking for model 1
# Found a chain break before 137
# copying to AlignedFragments data structure
# naming current conformation Zhang-Server_TS5
# ReadConformPDB reading from PDB file servers/beautshot_TS1.pdb.gz looking for model 1
# Found a chain break before 143
# copying to AlignedFragments data structure
# naming current conformation beautshot_TS1
# ReadConformPDB reading from PDB file servers/beautshotbase_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation beautshotbase_TS1
# ReadConformPDB reading from PDB file servers/forecast-s_AL1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation forecast-s_AL1
# ReadConformPDB reading from PDB file servers/forecast-s_AL2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation forecast-s_AL2
# ReadConformPDB reading from PDB file servers/forecast-s_AL3.pdb.gz looking for model 1
Skipped atom 137, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 138, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 139, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 140, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 525, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 526, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 527, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 528, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 533, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 534, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 535, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 536, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 541, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 542, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 543, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 544, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 549, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 550, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 551, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 552, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 557, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 558, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 559, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 560, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 565, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 566, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 567, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 568, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 573, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 574, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 575, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 576, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 581, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 582, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 583, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 584, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 589, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 590, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 591, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 592, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 597, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 598, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 599, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 600, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 605, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 606, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 607, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 608, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 613, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 614, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 615, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 616, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 621, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 622, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 623, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 624, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation forecast-s_AL3
# ReadConformPDB reading from PDB file servers/forecast-s_AL4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation forecast-s_AL4
# ReadConformPDB reading from PDB file servers/forecast-s_AL5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation forecast-s_AL5
# ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1
# naming current conformation karypis.srv.2_TS1
# ReadConformPDB reading from PDB file servers/karypis.srv.2_TS2.pdb.gz looking for model 1
# Found a chain break before 46
# copying to AlignedFragments data structure
# naming current conformation karypis.srv.2_TS2
# ReadConformPDB reading from PDB file servers/karypis.srv.2_TS3.pdb.gz looking for model 1
# naming current conformation karypis.srv.2_TS3
# ReadConformPDB reading from PDB file servers/karypis.srv.2_TS4.pdb.gz looking for model 1
# Found a chain break before 97
# copying to AlignedFragments data structure
# naming current conformation karypis.srv.2_TS4
# ReadConformPDB reading from PDB file servers/karypis.srv.2_TS5.pdb.gz looking for model 1
# naming current conformation karypis.srv.2_TS5
# ReadConformPDB reading from PDB file servers/karypis.srv.4_TS1.pdb.gz looking for model 1
# Found a chain break before 142
# copying to AlignedFragments data structure
# naming current conformation karypis.srv.4_TS1
# ReadConformPDB reading from PDB file servers/karypis.srv.4_TS2.pdb.gz looking for model 1
# Found a chain break before 142
# copying to AlignedFragments data structure
# naming current conformation karypis.srv.4_TS2
# ReadConformPDB reading from PDB file servers/karypis.srv.4_TS3.pdb.gz looking for model 1
WARNING: atoms too close: (T0380)F121.O and (T0380)T122.N only 0.000 apart, marking (T0380)T122.N as missing
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation karypis.srv.4_TS3
# ReadConformPDB reading from PDB file servers/karypis.srv.4_TS4.pdb.gz looking for model 1
# Found a chain break before 142
# copying to AlignedFragments data structure
# naming current conformation karypis.srv.4_TS4
# ReadConformPDB reading from PDB file servers/karypis.srv.4_TS5.pdb.gz looking for model 1
# Found a chain break before 142
# copying to AlignedFragments data structure
# naming current conformation karypis.srv.4_TS5
# ReadConformPDB reading from PDB file servers/karypis.srv_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation karypis.srv_TS1
# ReadConformPDB reading from PDB file servers/karypis.srv_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation karypis.srv_TS2
# ReadConformPDB reading from PDB file servers/karypis.srv_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation karypis.srv_TS3
# ReadConformPDB reading from PDB file servers/karypis.srv_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation karypis.srv_TS4
# ReadConformPDB reading from PDB file servers/karypis.srv_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation karypis.srv_TS5
# ReadConformPDB reading from PDB file servers/keasar-server_TS1.pdb.gz looking for model 1
# naming current conformation keasar-server_TS1
# ReadConformPDB reading from PDB file servers/keasar-server_TS2.pdb.gz looking for model 1
# Found a chain break before 128
# copying to AlignedFragments data structure
# naming current conformation keasar-server_TS2
# ReadConformPDB reading from PDB file servers/keasar-server_TS3.pdb.gz looking for model 1
# Found a chain break before 144
# copying to AlignedFragments data structure
# naming current conformation keasar-server_TS3
# ReadConformPDB reading from PDB file servers/keasar-server_TS4.pdb.gz looking for model 1
# naming current conformation keasar-server_TS4
# ReadConformPDB reading from PDB file servers/keasar-server_TS5.pdb.gz looking for model 1
# Found a chain break before 84
# copying to AlignedFragments data structure
# naming current conformation keasar-server_TS5
# ReadConformPDB reading from PDB file servers/mGen-3D_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation mGen-3D_TS1
# ReadConformPDB reading from PDB file servers/nFOLD_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation nFOLD_TS1
# ReadConformPDB reading from PDB file servers/nFOLD_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation nFOLD_TS2
# ReadConformPDB reading from PDB file servers/nFOLD_TS3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation nFOLD_TS3
# ReadConformPDB reading from PDB file servers/nFOLD_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation nFOLD_TS4
# ReadConformPDB reading from PDB file servers/nFOLD_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation nFOLD_TS5
# ReadConformPDB reading from PDB file servers/panther2_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation panther2_TS1
# ReadConformPDB reading from PDB file servers/panther3_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# naming current conformation panther3_TS1
# ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0380 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation shub_TS1
# command:Using radius: 8.0000
Metaserver mode
NUMB_ALIGNS: 271
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model score -0.5742
model score -0.5496
model score -0.5504
model score -0.5501
model score -0.5501
model score -0.4084
model score -0.3446
model score 0.2884
model score -0.3414
model score -0.3181
model score 0.3202
model score 0.3193
model score 0.3202
model score 0.3226
model score 0.3322
model score 0.3582
model score -0.3866
model score 0.3324
model score 0.3799
model score 0.3464
model score -0.4677
model score -0.2269
model score -0.5410
model score -0.4740
model score -0.5219
model score 1.2536
model score 1.3936
model score 1.5540
model score 1.3756
model score 1.3562
model score -0.6330
model score -0.5841
model score -0.6106
model score -0.6097
model score -0.5543
model score -0.2944
model score -0.5600
model score -0.5594
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model score -0.5289
model score -0.5339
model score -0.0944
model score -0.5523
model score -0.4572
model score -0.4596
model score -0.4141
model score -0.5151
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score -0.5593
model score -0.5303
model score -0.5289
model score -0.4818
model score -0.4863
model score -0.5825
model score -0.5059
model score -0.5289
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model score -0.5594
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model score -0.1215
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model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score 2.0213
model score 2.2301
model score 2.0646
model score 1.8460
model score 2.3115
model score -0.4742
model score -0.5090
model score -0.2633
model score -0.4566
model score -0.4654
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score -0.4346
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model score -0.4710
model score -0.5907
model score -0.3783
model score 0.4809
model score 0.9865
model score 0.9409
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model score -0.4894
model score -0.2835
model score -0.5952
model score -0.6369
model score -0.6369
model score -0.5182
model score 0.7840
model score 1.0785
model score 2.0155
model score 1.6484
model score -0.3146
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model score -0.2691
model score -0.4228
model score -0.3431
model score 1.2771
model score -0.6116
model score -0.6017
model score 0.9022
model score -0.5589
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model score -0.6116
model score -0.6017
model score -0.5501
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model score -0.4471
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model score -0.6035
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model score -0.4796
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model score -0.3936
model score -0.4764
model score -0.4741
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model score -0.5411
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model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score -0.5542
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model score -0.4751
model score -0.4942
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score -0.6202
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score -0.5654
model score -0.5815
model score -0.5325
model score -0.5429
model score -0.5851
model score -0.5694
model score -0.4813
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score 1.2771
model score -0.4952
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model score -0.5147
model score -0.3109
model score -0.5097
model score 2.1480
model score 2.0226
model score 1.9693
model score 1.9666
model score 1.5020
model score -0.4800
model score -0.3742
model score -0.3335
model score -0.3221
model score 1.3318
model score -0.4140
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model score -0.4116
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model score -0.4520
model score 0.7949
model score -0.4950
model score 0.7848
model score 0.0357
model score 0.5605
model score 1.1851
model score -0.5778
weight: 0.9442 eval: -0.4542 min: -0.6369 max: 2.3115
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Adding 4306 constraints to all2.constraints
Done adding distance constraints
# command:Reading probabilities from probabilities.dat
Reading constraints from ConstraintSet all2.constraints
maxweight: 1.0000
Optimizing...
 Probability sum: -248.9018, CN propb: -248.9018 weights: 0.3495 constraints: 551
# command:Found ConstraintSet
# PrintContacts align.constraints_meta02
Number of constraints in align2.constraints 551
# command:Found ConstraintSet
# PrintContacts align_bonus.constraints_meta02
Number of constraints in align2.constraints.bonus 551
# command:Found ConstraintSet
# PrintContacts rejected.constraints_meta02
Number of constraints in rejected2.constraints 3755
# command:Found ConstraintSet
# PrintContacts rejected_bonus.constraints_meta02
Number of constraints in rejected2.constraints.bonus 3755
# command:Found ConstraintSet
# PrintContacts non_contacts.constraints_meta02
Number of constraints in noncontact2.constraints 0
# command:Found ConstraintSet
# PrintContacts non_contacts_bonus.constraints_meta02
Number of constraints in noncontact2.constraints.bonus 0
# command:Found ConstraintSet
# PrintContacts all.constraints_meta02
Number of constraints in all2.constraints 4306
# command: