# 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/T0308/
# command:# Making conformation for sequence T0308 numbered 1 through 165
Created new target T0308 from T0308.a2m
# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0308/
# command:Warning: Couldn't open file /projects/compbio/experiments/protein-predict/casp7/T0308//projects/compbio/experiments/protein-predict/casp7/T0308/align.constraints_v3.costfcn or /projects/compbio/experiments/protein-predict/casp7/T0308//projects/compbio/experiments/protein-predict/casp7/T0308/align.constraints_v3.costfcn.gz for input
Trying /projects/compbio/experiments/protein-predict/casp7/T0308/align.constraints_v3.costfcn
# reading script from file /projects/compbio/experiments/protein-predict/casp7/T0308/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((T0308)I18.CB, (T0308)V51.CB) [> 3.4181 = 5.6969 < 7.4060] w=1.0000 to align
# Constraint # added constraint: constraint((T0308)I17.CB, (T0308)A148.CB) [> 2.8683 = 4.7806 < 6.2147] w=1.0000 to align
# Constraint # added constraint: constraint((T0308)I17.CB, (T0308)N114.CB) [> 3.9568 = 6.5947 < 8.5732] w=1.0000 to align
# Constraint # added constraint: constraint((T0308)I17.CB, (T0308)F112.CB) [> 4.3021 = 7.1701 < 9.3212] w=1.0000 to align
# Constraint # added constraint: constraint((T0308)T16.CB, (T0308)A148.CB) [> 2.3463 = 3.9105 < 5.0836] w=1.0000 to align
# Constraint # added constraint: constraint((T0308)G13.CA, (T0308)A148.CB) [> 3.4844 = 5.8074 < 7.5496] w=1.0000 to align
# Constraint # added constraint: constraint((T0308)G13.CA, (T0308)N114.CB) [> 3.2230 = 5.3716 < 6.9831] w=1.0000 to align
# Constraint # added constraint: constraint((T0308)G13.CA, (T0308)D79.CB) [> 4.2592 = 7.0987 < 9.2283] w=1.0000 to align
# Constraint # added constraint: constraint((T0308)G8.CA, (T0308)E92.CB) [> 3.5254 = 5.8757 < 7.6385] w=1.0000 to align
# Constraint # added constraint: constraint((T0308)G8.CA, (T0308)F76.CB) [> 3.6080 = 6.0133 < 7.8173] w=1.0000 to align
# Constraint # added constraint: constraint((T0308)L7.CB, (T0308)F76.CB) [> 3.2066 = 5.3443 < 6.9476] w=1.0000 to align
# Constraint # added constraint: constraint((T0308)L7.CB, (T0308)I75.CB) [> 4.2332 = 7.0553 < 9.1719] w=1.0000 to align
# Constraint # added constraint: constraint((T0308)L7.CB, (T0308)I74.CB) [> 3.6844 = 6.1407 < 7.9829] w=1.0000 to align
# Constraint # added constraint: constraint((T0308)C6.CB, (T0308)I75.CB) [> 2.8509 = 4.7515 < 6.1769] w=1.0000 to align
# Constraint # added constraint: constraint((T0308)C6.CB, (T0308)V51.CB) [> 3.8036 = 6.3394 < 8.2412] w=1.0000 to align
# Constraint # added constraint: constraint((T0308)C6.CB, (T0308)I18.CB) [> 3.8138 = 6.3564 < 8.2633] w=1.0000 to align
# Constraint # added constraint: constraint((T0308)C6.CB, (T0308)I17.CB) [> 4.1292 = 6.8820 < 8.9466] w=1.0000 to align
# Constraint # added constraint: constraint((T0308)L5.CB, (T0308)I75.CB) [> 4.2904 = 7.1506 < 9.2958] w=1.0000 to align
# Constraint # added constraint: constraint((T0308)L5.CB, (T0308)I74.CB) [> 3.0305 = 5.0508 < 6.5660] w=1.0000 to align
# Constraint # added constraint: constraint((T0308)V4.CB, (T0308)I75.CB) [> 3.8769 = 6.4615 < 8.3999] w=1.0000 to align
# Constraint # added constraint: constraint((T0308)V4.CB, (T0308)I74.CB) [> 4.3465 = 7.2442 < 9.4175] w=1.0000 to align
# Constraint # added constraint: constraint((T0308)V4.CB, (T0308)A73.CB) [> 2.9436 = 4.9060 < 6.3778] w=1.0000 to align
# Constraint # added constraint: constraint((T0308)V4.CB, (T0308)Q72.CB) [> 4.0912 = 6.8186 < 8.8642] w=1.0000 to align
# Constraint # added constraint: constraint((T0308)V4.CB, (T0308)G71.CA) [> 4.3021 = 7.1701 < 9.3212] w=1.0000 to align
# Constraint # added constraint: constraint((T0308)V4.CB, (T0308)T50.CB) [> 4.2182 = 7.0303 < 9.1394] w=1.0000 to align
# Constraint # added constraint: constraint((T0308)V4.CB, (T0308)F49.CB) [> 3.3712 = 5.6186 < 7.3042] w=1.0000 to align
# Constraint # added constraint: constraint((T0308)K115.CB, (T0308)A148.CB) [> 4.6002 = 7.6670 < 9.9670] w=1.0000 to align
# Constraint # added constraint: constraint((T0308)N114.CB, (T0308)A148.CB) [> 3.6849 = 6.1415 < 7.9840] w=1.0000 to align
# Constraint # added constraint: constraint((T0308)A113.CB, (T0308)I143.CB) [> 4.1337 = 6.8896 < 8.9564] w=1.0000 to align
# Constraint # added constraint: constraint((T0308)F111.CB, (T0308)I143.CB) [> 2.7614 = 4.6023 < 5.9830] w=1.0000 to align
# Constraint # added constraint: constraint((T0308)L110.CB, (T0308)H142.CB) [> 2.9765 = 4.9608 < 6.4490] w=1.0000 to align
# Constraint # added constraint: constraint((T0308)I109.CB, (T0308)W141.CB) [> 2.8191 = 4.6985 < 6.1081] w=1.0000 to align
# Constraint # added constraint: constraint((T0308)S81.CB, (T0308)K115.CB) [> 3.1679 = 5.2798 < 6.8638] w=1.0000 to align
# Constraint # added constraint: constraint((T0308)S80.CB, (T0308)M116.CB) [> 3.4794 = 5.7990 < 7.5388] w=1.0000 to align
# Constraint # added constraint: constraint((T0308)S80.CB, (T0308)K115.CB) [> 3.2020 = 5.3366 < 6.9376] w=1.0000 to align
# Constraint # added constraint: constraint((T0308)S80.CB, (T0308)N114.CB) [> 3.9375 = 6.5626 < 8.5313] w=1.0000 to align
# Constraint # added constraint: constraint((T0308)S80.CB, (T0308)A113.CB) [> 2.7905 = 4.6508 < 6.0460] w=1.0000 to align
# Constraint # added constraint: constraint((T0308)D79.CB, (T0308)K115.CB) [> 3.1775 = 5.2958 < 6.8846] w=1.0000 to align
# Constraint # added constraint: constraint((T0308)D79.CB, (T0308)N114.CB) [> 3.5310 = 5.8849 < 7.6504] w=1.0000 to align
# Constraint # added constraint: constraint((T0308)K20.CB, (T0308)A148.CB) [> 3.0043 = 5.0072 < 6.5094] w=1.0000 to align
# Constraint # added constraint: constraint((T0308)A73.CB, (T0308)P108.CB) [> 2.5514 = 4.2523 < 5.5280] w=1.0000 to align
# Constraint # added constraint: constraint((T0308)A73.CB, (T0308)I109.CB) [> 4.3203 = 7.2004 < 9.3606] w=1.0000 to align
# Constraint # added constraint: constraint((T0308)A73.CB, (T0308)L161.CB) [> 3.0102 = 5.0170 < 6.5221] w=1.0000 to align
# Constraint # added constraint: constraint((T0308)I74.CB, (T0308)I107.CB) [> 3.5956 = 5.9928 < 7.7906] w=1.0000 to align
# Constraint # added constraint: constraint((T0308)I74.CB, (T0308)I109.CB) [> 2.9941 = 4.9902 < 6.4872] w=1.0000 to align
# Constraint # added constraint: constraint((T0308)I74.CB, (T0308)L110.CB) [> 4.3771 = 7.2952 < 9.4838] w=1.0000 to align
# Constraint # added constraint: constraint((T0308)I75.CB, (T0308)L110.CB) [> 3.0592 = 5.0987 < 6.6284] w=1.0000 to align
# Constraint # added constraint: constraint((T0308)I75.CB, (T0308)F112.CB) [> 3.4952 = 5.8254 < 7.5730] w=1.0000 to align
# Constraint # added constraint: constraint((T0308)F76.CB, (T0308)L93.CB) [> 3.7521 = 6.2536 < 8.1296] w=1.0000 to align
# Constraint # added constraint: constraint((T0308)F76.CB, (T0308)I109.CB) [> 3.7355 = 6.2258 < 8.0936] w=1.0000 to align
# Constraint # added constraint: constraint((T0308)F76.CB, (T0308)L110.CB) [> 4.2567 = 7.0945 < 9.2229] w=1.0000 to align
# Constraint # added constraint: constraint((T0308)F76.CB, (T0308)F111.CB) [> 3.1478 = 5.2463 < 6.8202] w=1.0000 to align
# Constraint # added constraint: constraint((T0308)F76.CB, (T0308)F112.CB) [> 4.1649 = 6.9415 < 9.0239] w=1.0000 to align
# Constraint # added constraint: constraint((T0308)F111.CB, (T0308)H142.CB) [> 4.1464 = 6.9106 < 8.9838] w=0.9939 to align
# Constraint # added constraint: constraint((T0308)L110.CB, (T0308)L161.CB) [> 3.1821 = 5.3035 < 6.8946] w=0.9939 to align
# Constraint # added constraint: constraint((T0308)I74.CB, (T0308)P108.CB) [> 4.3241 = 7.2069 < 9.3689] w=0.9904 to align
# Constraint # added constraint: constraint((T0308)H3.CB, (T0308)T50.CB) [> 3.2540 = 5.4233 < 7.0502] w=0.9818 to align
# Constraint # added constraint: constraint((T0308)H3.CB, (T0308)G71.CA) [> 2.6036 = 4.3393 < 5.6411] w=0.9818 to align
# Constraint # added constraint: constraint((T0308)I74.CB, (T0308)L96.CB) [> 3.5675 = 5.9458 < 7.7295] w=0.9818 to align
# Constraint # added constraint: constraint((T0308)L110.CB, (T0308)G157.CA) [> 3.7418 = 6.2363 < 8.1072] w=0.9818 to align
# Constraint # added constraint: constraint((T0308)F112.CB, (T0308)G157.CA) [> 4.2599 = 7.0998 < 9.2298] w=0.9818 to align
# Constraint # added constraint: constraint((T0308)L5.CB, (T0308)G71.CA) [> 3.5262 = 5.8770 < 7.6402] w=0.9818 to align
# Constraint # added constraint: constraint((T0308)I17.CB, (T0308)L154.CB) [> 3.7596 = 6.2659 < 8.1457] w=0.9818 to align
# Constraint # added constraint: constraint((T0308)H142.CB, (T0308)W160.CB) [> 3.3856 = 5.6427 < 7.3355] w=0.9818 to align
# Constraint # added constraint: constraint((T0308)C6.CB, (T0308)V77.CB) [> 3.8419 = 6.4032 < 8.3241] w=0.9818 to align
# Constraint # added constraint: constraint((T0308)L7.CB, (T0308)V77.CB) [> 4.2105 = 7.0176 < 9.1228] w=0.9818 to align
# Constraint # added constraint: constraint((T0308)G8.CA, (T0308)V77.CB) [> 3.0319 = 5.0531 < 6.5690] w=0.9818 to align
# Constraint # added constraint: constraint((T0308)G8.CA, (T0308)I78.CB) [> 4.1475 = 6.9125 < 8.9862] w=0.9818 to align
# Constraint # added constraint: constraint((T0308)G13.CA, (T0308)V77.CB) [> 3.6389 = 6.0648 < 7.8842] w=0.9818 to align
# Constraint # added constraint: constraint((T0308)K14.CB, (T0308)V77.CB) [> 3.1374 = 5.2291 < 6.7978] w=0.9818 to align
# Constraint # added constraint: constraint((T0308)I17.CB, (T0308)V77.CB) [> 3.9727 = 6.6211 < 8.6075] w=0.9818 to align
# Constraint # added constraint: constraint((T0308)V77.CB, (T0308)F112.CB) [> 2.8560 = 4.7600 < 6.1880] w=0.9818 to align
# Constraint # added constraint: constraint((T0308)V77.CB, (T0308)N114.CB) [> 3.2465 = 5.4109 < 7.0341] w=0.9818 to align
# Constraint # added constraint: constraint((T0308)L5.CB, (T0308)Y68.CB) [> 3.9562 = 6.5937 < 8.5718] w=0.9818 to align
# Constraint # added constraint: constraint((T0308)L110.CB, (T0308)W141.CB) [> 3.9425 = 6.5709 < 8.5422] w=0.9818 to align
# Constraint # added constraint: constraint((T0308)K20.CB, (T0308)L154.CB) [> 3.2144 = 5.3574 < 6.9646] w=0.9818 to align
# Constraint # added constraint: constraint((T0308)L9.CB, (T0308)V88.CB) [> 3.2349 = 5.3915 < 7.0089] w=0.9818 to align
# Constraint # added constraint: constraint((T0308)L9.CB, (T0308)R85.CB) [> 2.7629 = 4.6048 < 5.9862] w=0.9818 to align
# Constraint # added constraint: constraint((T0308)L9.CB, (T0308)D79.CB) [> 4.2919 = 7.1532 < 9.2992] w=0.9818 to align
# Constraint # added constraint: constraint((T0308)G13.CA, (T0308)K115.CB) [> 4.3839 = 7.3065 < 9.4985] w=0.9818 to align
# Constraint # added constraint: constraint((T0308)S12.CB, (T0308)N114.CB) [> 3.5093 = 5.8488 < 7.6034] w=0.9818 to align
# Constraint # added constraint: constraint((T0308)S12.CB, (T0308)D79.CB) [> 2.7001 = 4.5001 < 5.8502] w=0.9818 to align
# Constraint # added constraint: constraint((T0308)N11.CB, (T0308)D79.CB) [> 4.0874 = 6.8123 < 8.8560] w=0.9818 to align
# Constraint # added constraint: constraint((T0308)I78.CB, (T0308)N114.CB) [> 4.0496 = 6.7493 < 8.7741] w=0.9818 to align
# Constraint # added constraint: constraint((T0308)I78.CB, (T0308)A113.CB) [> 3.4404 = 5.7340 < 7.4543] w=0.9818 to align
# Constraint # added constraint: constraint((T0308)I78.CB, (T0308)F112.CB) [> 4.3303 = 7.2171 < 9.3822] w=0.9818 to align
# Constraint # added constraint: constraint((T0308)I78.CB, (T0308)A89.CB) [> 3.2502 = 5.4170 < 7.0421] w=0.9818 to align
# Constraint # added constraint: constraint((T0308)L21.CB, (T0308)L154.CB) [> 3.5132 = 5.8554 < 7.6120] w=0.9722 to align
# Constraint # added constraint: constraint((T0308)L5.CB, (T0308)A73.CB) [> 4.5096 = 7.5161 < 9.7709] w=0.9722 to align
# Constraint # added constraint: constraint((T0308)Q72.CB, (T0308)P108.CB) [> 4.1055 = 6.8425 < 8.8953] w=0.9722 to align
# Constraint # added constraint: constraint((T0308)Y68.CB, (T0308)H99.CB) [> 3.0685 = 5.1141 < 6.6484] w=0.9697 to align
# Constraint # added constraint: constraint((T0308)F111.CB, (T0308)W141.CB) [> 3.3499 = 5.5832 < 7.2582] w=0.9697 to align
# Constraint # added constraint: constraint((T0308)H3.CB, (T0308)Q72.CB) [> 3.1200 = 5.1999 < 6.7599] w=0.9637 to align
# Constraint # added constraint: constraint((T0308)L110.CB, (T0308)C144.CB) [> 3.9353 = 6.5588 < 8.5264] w=0.9637 to align
# Constraint # added constraint: constraint((T0308)F111.CB, (T0308)C144.CB) [> 4.3278 = 7.2130 < 9.3768] w=0.9637 to align
# Constraint # added constraint: constraint((T0308)F112.CB, (T0308)C144.CB) [> 3.2220 = 5.3699 < 6.9809] w=0.9637 to align
# Constraint # added constraint: constraint((T0308)A113.CB, (T0308)C144.CB) [> 4.2440 = 7.0734 < 9.1954] w=0.9637 to align
# Constraint # added constraint: constraint((T0308)A113.CB, (T0308)A145.CB) [> 2.7917 = 4.6528 < 6.0487] w=0.9637 to align
# Constraint # added constraint: constraint((T0308)C144.CB, (T0308)G153.CA) [> 3.8276 = 6.3793 < 8.2931] w=0.9637 to align
# Constraint # added constraint: constraint((T0308)S12.CB, (T0308)V77.CB) [> 2.7410 = 4.5683 < 5.9387] w=0.9637 to align
# Constraint # added constraint: constraint((T0308)S12.CB, (T0308)I78.CB) [> 3.3895 = 5.6492 < 7.3439] w=0.9637 to align
# Constraint # added constraint: constraint((T0308)K20.CB, (T0308)G151.CA) [> 3.4449 = 5.7415 < 7.4640] w=0.9637 to align
# Constraint # added constraint: constraint((T0308)L110.CB, (T0308)W160.CB) [> 3.8395 = 6.3992 < 8.3190] w=0.9576 to align
# Constraint # added constraint: constraint((T0308)A73.CB, (T0308)L110.CB) [> 4.1696 = 6.9494 < 9.0342] w=0.9541 to align
# Constraint # added constraint: constraint((T0308)L7.CB, (T0308)M54.CB) [> 3.4959 = 5.8265 < 7.5745] w=0.9541 to align
# Constraint # added constraint: constraint((T0308)C144.CB, (T0308)G157.CA) [> 2.9993 = 4.9988 < 6.4985] w=0.9455 to align
# Constraint # added constraint: constraint((T0308)H3.CB, (T0308)E70.CB) [> 3.5023 = 5.8372 < 7.5883] w=0.9455 to align
# Constraint # added constraint: constraint((T0308)F112.CB, (T0308)S146.CB) [> 3.1840 = 5.3067 < 6.8987] w=0.9455 to align
# Constraint # added constraint: constraint((T0308)A113.CB, (T0308)S146.CB) [> 4.1746 = 6.9577 < 9.0450] w=0.9455 to align
# Constraint # added constraint: constraint((T0308)N114.CB, (T0308)S146.CB) [> 3.1022 = 5.1703 < 6.7214] w=0.9455 to align
# Constraint # added constraint: constraint((T0308)N114.CB, (T0308)D147.CB) [> 4.1443 = 6.9072 < 8.9793] w=0.9455 to align
# Constraint # added constraint: constraint((T0308)K115.CB, (T0308)D147.CB) [> 3.8253 = 6.3755 < 8.2882] w=0.9455 to align
# Constraint # added constraint: constraint((T0308)M116.CB, (T0308)D147.CB) [> 2.8241 = 4.7069 < 6.1189] w=0.9455 to align
# Constraint # added constraint: constraint((T0308)D117.CB, (T0308)I149.CB) [> 3.3240 = 5.5400 < 7.2020] w=0.9455 to align
# Constraint # added constraint: constraint((T0308)I78.CB, (T0308)F111.CB) [> 4.3945 = 7.3242 < 9.5214] w=0.9455 to align
# Constraint # added constraint: constraint((T0308)M116.CB, (T0308)A145.CB) [> 2.7283 = 4.5471 < 5.9113] w=0.9455 to align
# Constraint # added constraint: constraint((T0308)A73.CB, (T0308)I107.CB) [> 3.8410 = 6.4016 < 8.3221] w=0.9455 to align
# Constraint # added constraint: constraint((T0308)L5.CB, (T0308)Y67.CB) [> 3.6424 = 6.0706 < 7.8918] w=0.9455 to align
# Constraint # added constraint: constraint((T0308)C144.CB, (T0308)E156.CB) [> 3.7976 = 6.3293 < 8.2282] w=0.9455 to align
# Constraint # added constraint: constraint((T0308)S81.CB, (T0308)L118.CB) [> 2.8484 = 4.7474 < 6.1716] w=0.9274 to align
# Constraint # added constraint: constraint((T0308)M116.CB, (T0308)S146.CB) [> 3.5880 = 5.9800 < 7.7740] w=0.9274 to align
# Constraint # added constraint: constraint((T0308)P108.CB, (T0308)L161.CB) [> 3.7834 = 6.3056 < 8.1973] w=0.9274 to align
# Constraint # added constraint: constraint((T0308)T16.CB, (T0308)I149.CB) [> 4.2751 = 7.1252 < 9.2628] w=0.9274 to align
# Constraint # added constraint: constraint((T0308)V2.CB, (T0308)A73.CB) [> 4.0384 = 6.7306 < 8.7498] w=0.9228 to align
# Constraint # added constraint: constraint((T0308)V2.CB, (T0308)Q72.CB) [> 2.9578 = 4.9297 < 6.4086] w=0.9228 to align
# Constraint # added constraint: constraint((T0308)V2.CB, (T0308)S48.CB) [> 4.3412 = 7.2354 < 9.4060] w=0.9228 to align
# Constraint # added constraint: constraint((T0308)V2.CB, (T0308)L47.CB) [> 3.6502 = 6.0836 < 7.9086] w=0.9228 to align
# Constraint # added constraint: constraint((T0308)V4.CB, (T0308)L161.CB) [> 3.9363 = 6.5605 < 8.5286] w=0.9228 to align
# Constraint # added constraint: constraint((T0308)S80.CB, (T0308)L118.CB) [> 4.1525 = 6.9208 < 8.9971] w=0.9177 to align
# Constraint # added constraint: constraint((T0308)I17.CB, (T0308)S146.CB) [> 4.1391 = 6.8985 < 8.9681] w=0.9107 to align
# Constraint # added constraint: constraint((T0308)P108.CB, (T0308)Q164.CB) [> 2.7949 = 4.6582 < 6.0557] w=0.9094 to align
# Constraint # added constraint: constraint((T0308)D117.CB, (T0308)K150.CB) [> 3.2029 = 5.3381 < 6.9395] w=0.9092 to align
# Constraint # added constraint: constraint((T0308)D117.CB, (T0308)D147.CB) [> 2.5691 = 4.2819 < 5.5664] w=0.9092 to align
# Constraint # added constraint: constraint((T0308)L9.CB, (T0308)I78.CB) [> 4.1873 = 6.9789 < 9.0726] w=0.9092 to align
# Constraint # added constraint: constraint((T0308)C6.CB, (T0308)F52.CB) [> 4.0761 = 6.7935 < 8.8315] w=0.9092 to align
# Constraint # added constraint: constraint((T0308)C144.CB, (T0308)W160.CB) [> 4.1842 = 6.9737 < 9.0658] w=0.9034 to align
# Constraint # added constraint: constraint((T0308)S146.CB, (T0308)G157.CA) [> 4.2588 = 7.0980 < 9.2274] w=0.8996 to align
# Constraint # added constraint: constraint((T0308)L7.CB, (T0308)L96.CB) [> 4.2006 = 7.0010 < 9.1013] w=0.8938 to align
# Constraint # added constraint: constraint((T0308)L5.CB, (T0308)F52.CB) [> 2.9767 = 4.9612 < 6.4495] w=0.8910 to align
# Constraint # added constraint: constraint((T0308)S80.CB, (T0308)A145.CB) [> 4.1048 = 6.8414 < 8.8938] w=0.8729 to align
# Constraint # added constraint: constraint((T0308)V4.CB, (T0308)V51.CB) [> 2.9768 = 4.9614 < 6.4498] w=0.8729 to align
# Constraint # added constraint: constraint((T0308)V4.CB, (T0308)F52.CB) [> 4.2277 = 7.0462 < 9.1600] w=0.8729 to align
# Constraint # added constraint: constraint((T0308)C6.CB, (T0308)D53.CB) [> 3.1583 = 5.2638 < 6.8430] w=0.8729 to align
# Constraint # added constraint: constraint((T0308)T15.CB, (T0308)D53.CB) [> 3.3823 = 5.6372 < 7.3284] w=0.8729 to align
# Constraint # added constraint: constraint((T0308)I18.CB, (T0308)D53.CB) [> 3.0319 = 5.0532 < 6.5692] w=0.8729 to align
# Constraint # added constraint: constraint((T0308)F112.CB, (T0308)I143.CB) [> 4.6399 = 7.7331 < 10.0530] w=0.8729 to align
# Constraint # added constraint: constraint((T0308)L110.CB, (T0308)I143.CB) [> 4.5235 = 7.5391 < 9.8009] w=0.8729 to align
# Constraint # added constraint: constraint((T0308)L133.CB, (T0308)I143.CB) [> 3.2900 = 5.4834 < 7.1284] w=0.8698 to align
# Constraint # added constraint: constraint((T0308)F76.CB, (T0308)A89.CB) [> 3.5478 = 5.9130 < 7.6870] w=0.8562 to align
# Constraint # added constraint: constraint((T0308)C6.CB, (T0308)I74.CB) [> 4.6106 = 7.6844 < 9.9897] w=0.8550 to align
# Constraint # added constraint: constraint((T0308)H3.CB, (T0308)F52.CB) [> 4.2551 = 7.0918 < 9.2193] w=0.8547 to align
# Constraint # added constraint: constraint((T0308)H3.CB, (T0308)A73.CB) [> 4.6049 = 7.6749 < 9.9773] w=0.8365 to align
# Constraint # added constraint: constraint((T0308)F52.CB, (T0308)Y67.CB) [> 3.5366 = 5.8943 < 7.6626] w=0.8365 to align
# Constraint # added constraint: constraint((T0308)C6.CB, (T0308)M54.CB) [> 3.8072 = 6.3454 < 8.2490] w=0.8365 to align
# Constraint # added constraint: constraint((T0308)F111.CB, (T0308)I136.CB) [> 3.0462 = 5.0770 < 6.6001] w=0.8301 to align
# Constraint # added constraint: constraint((T0308)I109.CB, (T0308)K139.CB) [> 4.1139 = 6.8565 < 8.9134] w=0.8293 to align
# Constraint # added constraint: constraint((T0308)A73.CB, (T0308)Q164.CB) [> 4.0674 = 6.7790 < 8.8127] w=0.8289 to align
# Constraint # added constraint: constraint((T0308)L47.CB, (T0308)Q162.CB) [> 3.5243 = 5.8739 < 7.6361] w=0.8184 to align
# Constraint # added constraint: constraint((T0308)I39.CB, (T0308)V51.CB) [> 4.2206 = 7.0343 < 9.1446] w=0.8115 to align
# Constraint # added constraint: constraint((T0308)I39.CB, (T0308)T50.CB) [> 3.3448 = 5.5747 < 7.2471] w=0.8115 to align
# Constraint # added constraint: constraint((T0308)L9.CB, (T0308)D82.CB) [> 4.4728 = 7.4547 < 9.6912] w=0.8103 to align
# Constraint # added constraint: constraint((T0308)M54.CB, (T0308)Y67.CB) [> 3.8199 = 6.3665 < 8.2764] w=0.8088 to align
# Constraint # added constraint: constraint((T0308)V2.CB, (T0308)T50.CB) [> 4.2744 = 7.1240 < 9.2612] w=0.8017 to align
# Constraint # added constraint: constraint((T0308)V2.CB, (T0308)F49.CB) [> 3.2477 = 5.4129 < 7.0367] w=0.8017 to align
# Constraint # added constraint: constraint((T0308)Q72.CB, (T0308)I165.CB) [> 3.3109 = 5.5182 < 7.1737] w=0.8015 to align
# Constraint # added constraint: constraint((T0308)D10.CB, (T0308)G56.CA) [> 3.0841 = 5.1401 < 6.6821] w=0.8002 to align
# Constraint # added constraint: constraint((T0308)E40.CB, (T0308)F49.CB) [> 3.3971 = 5.6618 < 7.3604] w=0.7864 to align
# Constraint # added constraint: constraint((T0308)E40.CB, (T0308)V51.CB) [> 3.6911 = 6.1519 < 7.9974] w=0.7775 to align
# Constraint # added constraint: constraint((T0308)L5.CB, (T0308)M54.CB) [> 4.0107 = 6.6845 < 8.6898] w=0.7724 to align
# Constraint # added constraint: constraint((T0308)A73.CB, (T0308)I165.CB) [> 3.3043 = 5.5071 < 7.1592] w=0.7712 to align
# Constraint # added constraint: constraint((T0308)C132.CB, (T0308)I143.CB) [> 3.5508 = 5.9180 < 7.6934] w=0.7701 to align
# Constraint # added constraint: constraint((T0308)P108.CB, (T0308)I165.CB) [> 3.2977 = 5.4962 < 7.1450] w=0.7657 to align
# Constraint # added constraint: constraint((T0308)L5.CB, (T0308)V51.CB) [> 4.6487 = 7.7479 < 10.0723] w=0.7545 to align
# Constraint # added constraint: constraint((T0308)F76.CB, (T0308)L96.CB) [> 4.4771 = 7.4618 < 9.7004] w=0.7543 to align
# Constraint # added constraint: constraint((T0308)Q72.CB, (T0308)I107.CB) [> 3.8935 = 6.4892 < 8.4360] w=0.7543 to align
# Constraint # added constraint: constraint((T0308)L21.CB, (T0308)V51.CB) [> 4.4056 = 7.3427 < 9.5455] w=0.7543 to align
# Constraint # added constraint: constraint((T0308)F37.CB, (T0308)F52.CB) [> 3.2689 = 5.4482 < 7.0826] w=0.7538 to align
# Constraint # added constraint: constraint((T0308)A113.CB, (T0308)C132.CB) [> 3.0112 = 5.0186 < 6.5242] w=0.7487 to align
# Constraint # added constraint: constraint((T0308)M86.CB, (T0308)C132.CB) [> 4.2397 = 7.0662 < 9.1861] w=0.7487 to align
# Constraint # added constraint: constraint((T0308)F112.CB, (T0308)A145.CB) [> 4.4923 = 7.4871 < 9.7332] w=0.7457 to align
# Constraint # added constraint: constraint((T0308)G8.CA, (T0308)M54.CB) [> 4.0964 = 6.8273 < 8.8755] w=0.7376 to align
# Constraint # added constraint: constraint((T0308)G71.CA, (T0308)I107.CB) [> 3.5706 = 5.9510 < 7.7362] w=0.7361 to align
# Constraint # added constraint: constraint((T0308)I17.CB, (T0308)I75.CB) [> 4.4893 = 7.4822 < 9.7269] w=0.7195 to align
# Constraint # added constraint: constraint((T0308)F37.CB, (T0308)V51.CB) [> 4.0331 = 6.7218 < 8.7383] w=0.7138 to align
# Constraint # added constraint: constraint((T0308)V2.CB, (T0308)I165.CB) [> 3.4097 = 5.6828 < 7.3876] w=0.7112 to align
# Constraint # added constraint: constraint((T0308)F49.CB, (T0308)V158.CB) [> 4.1198 = 6.8664 < 8.9263] w=0.7109 to align
# Constraint # added constraint: constraint((T0308)A89.CB, (T0308)F111.CB) [> 4.0895 = 6.8158 < 8.8606] w=0.7109 to align
# Constraint # added constraint: constraint((T0308)F76.CB, (T0308)E92.CB) [> 3.1568 = 5.2614 < 6.8398] w=0.7109 to align
# Constraint # added constraint: constraint((T0308)G8.CA, (T0308)R85.CB) [> 4.2673 = 7.1122 < 9.2459] w=0.7109 to align
# Constraint # added constraint: constraint((T0308)L93.CB, (T0308)I109.CB) [> 4.2787 = 7.1311 < 9.2705] w=0.7109 to align
# Constraint # added constraint: constraint((T0308)F111.CB, (T0308)C132.CB) [> 4.0410 = 6.7350 < 8.7555] w=0.7013 to align
# Constraint # added constraint: constraint((T0308)L21.CB, (T0308)Q155.CB) [> 4.0860 = 6.8100 < 8.8530] w=0.7013 to align
# Constraint # added constraint: constraint((T0308)I39.CB, (T0308)S48.CB) [> 3.5324 = 5.8873 < 7.6535] w=0.6956 to align
# Constraint # added constraint: constraint((T0308)F37.CB, (T0308)T50.CB) [> 3.5298 = 5.8830 < 7.6479] w=0.6956 to align
# Constraint # added constraint: constraint((T0308)L9.CB, (T0308)L84.CB) [> 4.2827 = 7.1378 < 9.2792] w=0.6928 to align
# Constraint # added constraint: constraint((T0308)D79.CB, (T0308)A113.CB) [> 4.5688 = 7.6147 < 9.8991] w=0.6928 to align
# Constraint # added constraint: constraint((T0308)S12.CB, (T0308)R85.CB) [> 3.0512 = 5.0853 < 6.6108] w=0.6928 to align
# Constraint # added constraint: constraint((T0308)I75.CB, (T0308)I109.CB) [> 4.6139 = 7.6899 < 9.9969] w=0.6928 to align
# Constraint # added constraint: constraint((T0308)I78.CB, (T0308)V88.CB) [> 4.3384 = 7.2306 < 9.3998] w=0.6746 to align
# Constraint # added constraint: constraint((T0308)L96.CB, (T0308)I109.CB) [> 4.0373 = 6.7288 < 8.7475] w=0.6731 to align
# Constraint # added constraint: constraint((T0308)S38.CB, (T0308)D53.CB) [> 3.8613 = 6.4354 < 8.3661] w=0.6690 to align
# Constraint # added constraint: constraint((T0308)I109.CB, (T0308)H142.CB) [> 4.3821 = 7.3036 < 9.4946] w=0.6668 to align
# Constraint # added constraint: constraint((T0308)D10.CB, (T0308)S55.CB) [> 4.3389 = 7.2315 < 9.4010] w=0.6665 to align
# Constraint # added constraint: constraint((T0308)P33.CB, (T0308)S55.CB) [> 3.9337 = 6.5561 < 8.5230] w=0.6639 to align
# Constraint # added constraint: constraint((T0308)F37.CB, (T0308)D53.CB) [> 4.1336 = 6.8894 < 8.9562] w=0.6630 to align
# Constraint # added constraint: constraint((T0308)I78.CB, (T0308)C132.CB) [> 4.4717 = 7.4529 < 9.6888] w=0.6622 to align
# Constraint # added constraint: constraint((T0308)M86.CB, (T0308)V127.CB) [> 3.3220 = 5.5367 < 7.1976] w=0.6606 to align
# Constraint # added constraint: constraint((T0308)I39.CB, (T0308)F49.CB) [> 4.1493 = 6.9156 < 8.9902] w=0.6605 to align
# Constraint # added constraint: constraint((T0308)N19.CB, (T0308)A148.CB) [> 4.5112 = 7.5187 < 9.7743] w=0.6592 to align
# Constraint # added constraint: constraint((T0308)V2.CB, (T0308)Q162.CB) [> 3.8098 = 6.3496 < 8.2545] w=0.6589 to align
# Constraint # added constraint: constraint((T0308)L93.CB, (T0308)K139.CB) [> 3.6334 = 6.0556 < 7.8723] w=0.6583 to align
# Constraint # added constraint: constraint((T0308)S12.CB, (T0308)K115.CB) [> 4.6286 = 7.7143 < 10.0286] w=0.6564 to align
# Constraint # added constraint: constraint((T0308)I18.CB, (T0308)S38.CB) [> 3.6047 = 6.0079 < 7.8102] w=0.6480 to align
# Constraint # added constraint: constraint((T0308)I78.CB, (T0308)V127.CB) [> 4.0512 = 6.7520 < 8.7775] w=0.6305 to align
# Constraint # added constraint: constraint((T0308)M86.CB, (T0308)A113.CB) [> 4.5816 = 7.6360 < 9.9268] w=0.6201 to align
# Constraint # added constraint: constraint((T0308)S44.CB, (T0308)Q162.CB) [> 3.6357 = 6.0596 < 7.8774] w=0.6177 to align
# Constraint # added constraint: constraint((T0308)T34.CB, (T0308)S55.CB) [> 3.0665 = 5.1108 < 6.6440] w=0.6146 to align
# Constraint # added constraint: constraint((T0308)G8.CA, (T0308)G56.CA) [> 3.4952 = 5.8253 < 7.5729] w=0.6090 to align
# Constraint # added constraint: constraint((T0308)H142.CB, (T0308)G157.CA) [> 4.4141 = 7.3568 < 9.5638] w=0.6041 to align
# Constraint # added constraint: constraint((T0308)S80.CB, (T0308)C132.CB) [> 4.4691 = 7.4484 < 9.6830] w=0.6038 to align
# Constraint # added constraint: constraint((T0308)I75.CB, (T0308)G157.CA) [> 4.4710 = 7.4517 < 9.6872] w=0.6022 to align
# Constraint # added constraint: constraint((T0308)L96.CB, (T0308)I107.CB) [> 3.8770 = 6.4617 < 8.4002] w=0.6020 to align
# Constraint # added constraint: constraint((T0308)N114.CB, (T0308)A145.CB) [> 4.5724 = 7.6207 < 9.9069] w=0.5923 to align
# Constraint # added constraint: constraint((T0308)L9.CB, (T0308)G56.CA) [> 3.6643 = 6.1072 < 7.9394] w=0.5908 to align
# Constraint # added constraint: constraint((T0308)M86.CB, (T0308)L131.CB) [> 4.4557 = 7.4263 < 9.6541] w=0.5905 to align
# Constraint # added constraint: constraint((T0308)M86.CB, (T0308)N135.CB) [> 4.2239 = 7.0399 < 9.1518] w=0.5805 to align
# Constraint # added constraint: constraint((T0308)I35.CB, (T0308)S55.CB) [> 3.6415 = 6.0692 < 7.8900] w=0.5600 to align
# Constraint # added constraint: constraint((T0308)C132.CB, (T0308)A145.CB) [> 4.4010 = 7.3350 < 9.5355] w=0.5572 to align
# Constraint # added constraint: constraint((T0308)T16.CB, (T0308)N114.CB) [> 4.6668 = 7.7780 < 10.1114] w=0.5379 to align
# Constraint # added constraint: constraint((T0308)K14.CB, (T0308)G56.CA) [> 4.3987 = 7.3311 < 9.5304] w=0.5366 to align
# Constraint # added constraint: constraint((T0308)M54.CB, (T0308)W64.CB) [> 3.5358 = 5.8930 < 7.6609] w=0.5366 to align
# Constraint # added constraint: constraint((T0308)D10.CB, (T0308)Q57.CB) [> 2.7962 = 4.6603 < 6.0584] w=0.5363 to align
# Constraint # added constraint: constraint((T0308)L7.CB, (T0308)G56.CA) [> 4.4790 = 7.4651 < 9.7046] w=0.5231 to align
# Constraint # added constraint: constraint((T0308)I109.CB, (T0308)P140.CB) [> 4.3728 = 7.2879 < 9.4743] w=0.5189 to align
# Constraint # added constraint: constraint((T0308)T34.CB, (T0308)D53.CB) [> 3.4771 = 5.7952 < 7.5338] w=0.5056 to align
# Constraint # added constraint: constraint((T0308)L9.CB, (T0308)V77.CB) [> 4.7040 = 7.8401 < 10.1921] w=0.5030 to align
# Constraint # added constraint: constraint((T0308)G36.CA, (T0308)F52.CB) [> 4.1620 = 6.9366 < 9.0176] w=0.4992 to align
# Constraint # added constraint: constraint((T0308)R83.CB, (T0308)V127.CB) [> 3.6655 = 6.1092 < 7.9420] w=0.4913 to align
# Constraint # added constraint: constraint((T0308)K90.CB, (T0308)N135.CB) [> 4.2403 = 7.0672 < 9.1874] w=0.4877 to align
# Constraint # added constraint: constraint((T0308)F42.CB, (T0308)D159.CB) [> 4.0028 = 6.6714 < 8.6728] w=0.4844 to align
# Constraint # added constraint: constraint((T0308)L21.CB, (T0308)E40.CB) [> 3.9339 = 6.5565 < 8.5234] w=0.4839 to align
# Constraint # added constraint: constraint((T0308)T15.CB, (T0308)T34.CB) [> 3.6904 = 6.1507 < 7.9959] w=0.4813 to align
# Constraint # added constraint: constraint((T0308)K14.CB, (T0308)I75.CB) [> 4.6672 = 7.7787 < 10.1123] w=0.4680 to align
# Constraint # added constraint: constraint((T0308)L9.CB, (T0308)A89.CB) [> 3.7704 = 6.2840 < 8.1692] w=0.4676 to align
# Constraint # added constraint: constraint((T0308)K69.CB, (T0308)H99.CB) [> 3.8407 = 6.4012 < 8.3215] w=0.4609 to align
# Constraint # added constraint: constraint((T0308)N11.CB, (T0308)R85.CB) [> 4.6436 = 7.7393 < 10.0611] w=0.4394 to align
# Constraint # added constraint: constraint((T0308)F76.CB, (T0308)W141.CB) [> 4.5188 = 7.5313 < 9.7907] w=0.4349 to align
# Constraint # added constraint: constraint((T0308)E1.CB, (T0308)S48.CB) [> 3.0432 = 5.0720 < 6.5936] w=0.4338 to align
# Constraint # added constraint: constraint((T0308)L110.CB, (T0308)Q164.CB) [> 4.2130 = 7.0216 < 9.1281] w=0.4273 to align
# Constraint # added constraint: constraint((T0308)E40.CB, (T0308)V158.CB) [> 4.4254 = 7.3757 < 9.5884] w=0.4189 to align
# Constraint # added constraint: constraint((T0308)L7.CB, (T0308)W64.CB) [> 4.0664 = 6.7773 < 8.8105] w=0.4178 to align
# Constraint # added constraint: constraint((T0308)I75.CB, (T0308)V158.CB) [> 4.4804 = 7.4674 < 9.7076] w=0.4110 to align
# Constraint # added constraint: constraint((T0308)I75.CB, (T0308)F111.CB) [> 4.6467 = 7.7445 < 10.0679] w=0.4107 to align
# Constraint # added constraint: constraint((T0308)M54.CB, (T0308)L63.CB) [> 4.2441 = 7.0734 < 9.1955] w=0.4092 to align
# Constraint # added constraint: constraint((T0308)I35.CB, (T0308)D53.CB) [> 4.1440 = 6.9066 < 8.9786] w=0.4070 to align
# Constraint # added constraint: constraint((T0308)Y68.CB, (T0308)T95.CB) [> 4.1777 = 6.9629 < 9.0518] w=0.4004 to align
# Constraint # added constraint: constraint((T0308)T15.CB, (T0308)I31.CB) [> 3.1887 = 5.3146 < 6.9089] w=0.3843 to align
# Constraint # added constraint: constraint((T0308)V2.CB, (T0308)G71.CA) [> 4.6207 = 7.7011 < 10.0114] w=0.3805 to align
# Constraint # added constraint: constraint((T0308)P108.CB, (T0308)W141.CB) [> 4.3144 = 7.1907 < 9.3479] w=0.3799 to align
# Constraint # added constraint: constraint((T0308)L9.CB, (T0308)E92.CB) [> 4.3320 = 7.2199 < 9.3859] w=0.3799 to align
# Constraint # added constraint: constraint((T0308)T34.CB, (T0308)M54.CB) [> 4.2774 = 7.1290 < 9.2677] w=0.3786 to align
# Constraint # added constraint: constraint((T0308)V2.CB, (T0308)L161.CB) [> 4.5550 = 7.5916 < 9.8691] w=0.3740 to align
# Constraint # added constraint: constraint((T0308)D10.CB, (T0308)P33.CB) [> 3.9422 = 6.5703 < 8.5414] w=0.3686 to align
# Constraint # added constraint: constraint((T0308)E1.CB, (T0308)T50.CB) [> 3.7508 = 6.2514 < 8.1268] w=0.3672 to align
# Constraint # added constraint: constraint((T0308)T15.CB, (T0308)L32.CB) [> 4.0773 = 6.7955 < 8.8341] w=0.3641 to align
# Constraint # added constraint: constraint((T0308)E1.CB, (T0308)L47.CB) [> 4.4209 = 7.3681 < 9.5786] w=0.3613 to align
# Constraint # added constraint: constraint((T0308)V77.CB, (T0308)A113.CB) [> 4.7220 = 7.8701 < 10.2311] w=0.3498 to align
# Constraint # added constraint: constraint((T0308)I35.CB, (T0308)F52.CB) [> 3.3401 = 5.5668 < 7.2368] w=0.3465 to align
# Constraint # added constraint: constraint((T0308)S146.CB, (T0308)E156.CB) [> 4.5805 = 7.6342 < 9.9245] w=0.3461 to align
# Constraint # added constraint: constraint((T0308)L97.CB, (T0308)I107.CB) [> 4.2761 = 7.1269 < 9.2650] w=0.3426 to align
# Constraint # added constraint: constraint((T0308)T34.CB, (T0308)G56.CA) [> 4.1926 = 6.9877 < 9.0840] w=0.3417 to align
# Constraint # added constraint: constraint((T0308)E40.CB, (T0308)T50.CB) [> 4.5054 = 7.5090 < 9.7617] w=0.3394 to align
# Constraint # added constraint: constraint((T0308)V77.CB, (T0308)F111.CB) [> 4.6961 = 7.8269 < 10.1749] w=0.3287 to align
# Constraint # added constraint: constraint((T0308)L97.CB, (T0308)I109.CB) [> 4.3735 = 7.2892 < 9.4759] w=0.3272 to align
# Constraint # added constraint: constraint((T0308)I35.CB, (T0308)Y60.CB) [> 4.1169 = 6.8615 < 8.9199] w=0.3185 to align
# Constraint # added constraint: constraint((T0308)L32.CB, (T0308)S55.CB) [> 3.2128 = 5.3547 < 6.9611] w=0.3163 to align
# Constraint # added constraint: constraint((T0308)K41.CB, (T0308)T50.CB) [> 3.1071 = 5.1785 < 6.7321] w=0.3044 to align
# Constraint # added constraint: constraint((T0308)I39.CB, (T0308)F52.CB) [> 2.9598 = 4.9330 < 6.4129] w=0.3044 to align
# Constraint # added constraint: constraint((T0308)K14.CB, (T0308)T34.CB) [> 4.3410 = 7.2350 < 9.4055] w=0.2961 to align
# Constraint # added constraint: constraint((T0308)T16.CB, (T0308)I31.CB) [> 3.6536 = 6.0894 < 7.9162] w=0.2902 to align
# Constraint # added constraint: constraint((T0308)P108.CB, (T0308)H142.CB) [> 4.4812 = 7.4686 < 9.7092] w=0.2897 to align
# Constraint # added constraint: constraint((T0308)H3.CB, (T0308)F49.CB) [> 4.6075 = 7.6791 < 9.9829] w=0.2891 to align
# Constraint # added constraint: constraint((T0308)I18.CB, (T0308)E40.CB) [> 3.6038 = 6.0064 < 7.8083] w=0.2834 to align
# Constraint # added constraint: constraint((T0308)E1.CB, (T0308)F49.CB) [> 4.5410 = 7.5684 < 9.8389] w=0.2787 to align
# Constraint # added constraint: constraint((T0308)Y68.CB, (T0308)I107.CB) [> 4.6374 = 7.7289 < 10.0476] w=0.2742 to align
# Constraint # added constraint: constraint((T0308)K22.CB, (T0308)I39.CB) [> 4.3255 = 7.2092 < 9.3720] w=0.2736 to align
# Constraint # added constraint: constraint((T0308)K41.CB, (T0308)V51.CB) [> 4.4419 = 7.4032 < 9.6242] w=0.2681 to align
# Constraint # added constraint: constraint((T0308)L93.CB, (T0308)F111.CB) [> 4.5042 = 7.5070 < 9.7591] w=0.2543 to align
# Constraint # added constraint: constraint((T0308)L21.CB, (T0308)F49.CB) [> 4.5653 = 7.6088 < 9.8915] w=0.2506 to align
# Constraint # added constraint: constraint((T0308)S80.CB, (T0308)R119.CB) [> 4.2189 = 7.0315 < 9.1410] w=0.2319 to align
# Constraint # added constraint: constraint((T0308)L21.CB, (T0308)F42.CB) [> 3.3631 = 5.6052 < 7.2867] w=0.2317 to align
# Constraint # added constraint: constraint((T0308)I18.CB, (T0308)F42.CB) [> 4.0763 = 6.7938 < 8.8320] w=0.2317 to align
# Constraint # added constraint: constraint((T0308)N11.CB, (T0308)P33.CB) [> 4.4635 = 7.4391 < 9.6708] w=0.2212 to align
# Constraint # added constraint: constraint((T0308)C6.CB, (T0308)F76.CB) [> 4.7281 = 7.8802 < 10.2442] w=0.2179 to align
# Constraint # added constraint: constraint((T0308)G71.CA, (T0308)H104.CB) [> 4.1581 = 6.9302 < 9.0092] w=0.2120 to align
# Constraint # added constraint: constraint((T0308)F52.CB, (T0308)G71.CA) [> 4.5048 = 7.5079 < 9.7603] w=0.2094 to align
# Constraint # added constraint: constraint((T0308)V4.CB, (T0308)I165.CB) [> 4.5605 = 7.6008 < 9.8810] w=0.2037 to align
# Constraint # added constraint: constraint((T0308)T34.CB, (T0308)Y60.CB) [> 3.9015 = 6.5026 < 8.4533] w=0.2004 to align
# Constraint # added constraint: constraint((T0308)L5.CB, (T0308)W64.CB) [> 4.5875 = 7.6458 < 9.9395] w=0.1983 to align
# Constraint # added constraint: constraint((T0308)I39.CB, (T0308)D53.CB) [> 4.3736 = 7.2894 < 9.4762] w=0.1954 to align
# Constraint # added constraint: constraint((T0308)I74.CB, (T0308)E92.CB) [> 4.6214 = 7.7023 < 10.0130] w=0.1940 to align
# Constraint # added constraint: constraint((T0308)L5.CB, (T0308)L96.CB) [> 4.4066 = 7.3444 < 9.5477] w=0.1912 to align
# Constraint # added constraint: constraint((T0308)Q72.CB, (T0308)R106.CB) [> 4.4960 = 7.4933 < 9.7413] w=0.1895 to align
# Constraint # added constraint: constraint((T0308)F37.CB, (T0308)F49.CB) [> 4.1173 = 6.8621 < 8.9208] w=0.1885 to align
# Constraint # added constraint: constraint((T0308)F37.CB, (T0308)S48.CB) [> 3.8097 = 6.3494 < 8.2543] w=0.1885 to align
# Constraint # added constraint: constraint((T0308)I35.CB, (T0308)V51.CB) [> 3.8861 = 6.4768 < 8.4198] w=0.1885 to align
# Constraint # added constraint: constraint((T0308)I35.CB, (T0308)T50.CB) [> 3.6308 = 6.0513 < 7.8667] w=0.1885 to align
# Constraint # added constraint: constraint((T0308)L47.CB, (T0308)I165.CB) [> 4.2926 = 7.1543 < 9.3006] w=0.1829 to align
# Constraint # added constraint: constraint((T0308)S38.CB, (T0308)S48.CB) [> 4.5110 = 7.5183 < 9.7738] w=0.1825 to align
# Constraint # added constraint: constraint((T0308)F112.CB, (T0308)A148.CB) [> 4.6192 = 7.6986 < 10.0082] w=0.1816 to align
# Constraint # added constraint: constraint((T0308)S55.CB, (T0308)W64.CB) [> 3.8720 = 6.4533 < 8.3893] w=0.1816 to align
# Constraint # added constraint: constraint((T0308)Q129.CB, (T0308)I143.CB) [> 4.0268 = 6.7112 < 8.7246] w=0.1816 to align
# Constraint # added constraint: constraint((T0308)S128.CB, (T0308)I143.CB) [> 3.1735 = 5.2892 < 6.8760] w=0.1815 to align
# Constraint # added constraint: constraint((T0308)F112.CB, (T0308)L154.CB) [> 4.3942 = 7.3237 < 9.5209] w=0.1801 to align
# Constraint # added constraint: constraint((T0308)F111.CB, (T0308)L133.CB) [> 4.2926 = 7.1544 < 9.3007] w=0.1756 to align
# Constraint # added constraint: constraint((T0308)I35.CB, (T0308)Q57.CB) [> 4.4524 = 7.4207 < 9.6469] w=0.1755 to align
# Constraint # added constraint: constraint((T0308)V127.CB, (T0308)I143.CB) [> 3.8827 = 6.4711 < 8.4125] w=0.1751 to align
# Constraint # added constraint: constraint((T0308)N11.CB, (T0308)I31.CB) [> 4.1406 = 6.9010 < 8.9713] w=0.1699 to align
# Constraint # added constraint: constraint((T0308)T34.CB, (T0308)L63.CB) [> 3.4755 = 5.7924 < 7.5302] w=0.1641 to align
# Constraint # added constraint: constraint((T0308)I35.CB, (T0308)L63.CB) [> 3.9969 = 6.6616 < 8.6601] w=0.1641 to align
# Constraint # added constraint: constraint((T0308)R83.CB, (T0308)S124.CB) [> 3.4774 = 5.7956 < 7.5343] w=0.1631 to align
# Constraint # added constraint: constraint((T0308)G8.CA, (T0308)L93.CB) [> 4.7293 = 7.8822 < 10.2468] w=0.1619 to align
# Constraint # added constraint: constraint((T0308)S44.CB, (T0308)V158.CB) [> 3.6694 = 6.1156 < 7.9503] w=0.1591 to align
# Constraint # added constraint: constraint((T0308)E40.CB, (T0308)D53.CB) [> 4.4924 = 7.4874 < 9.7336] w=0.1591 to align
# Constraint # added constraint: constraint((T0308)P33.CB, (T0308)M54.CB) [> 3.5462 = 5.9103 < 7.6834] w=0.1560 to align
# Constraint # added constraint: constraint((T0308)S81.CB, (T0308)R119.CB) [> 4.4017 = 7.3362 < 9.5370] w=0.1559 to align
# Constraint # added constraint: constraint((T0308)I35.CB, (T0308)Y67.CB) [> 3.6549 = 6.0915 < 7.9189] w=0.1552 to align
# Constraint # added constraint: constraint((T0308)P33.CB, (T0308)Y60.CB) [> 4.1095 = 6.8492 < 8.9040] w=0.1518 to align
# Constraint # added constraint: constraint((T0308)I78.CB, (T0308)S124.CB) [> 4.2567 = 7.0945 < 9.2228] w=0.1510 to align
# Constraint # added constraint: constraint((T0308)K90.CB, (T0308)I136.CB) [> 3.1509 = 5.2515 < 6.8270] w=0.1498 to align
# Constraint # added constraint: constraint((T0308)L7.CB, (T0308)Y68.CB) [> 4.1778 = 6.9629 < 9.0518] w=0.1469 to align
# Constraint # added constraint: constraint((T0308)D79.CB, (T0308)A89.CB) [> 4.6453 = 7.7422 < 10.0648] w=0.1453 to align
# Constraint # added constraint: constraint((T0308)I78.CB, (T0308)I136.CB) [> 4.4189 = 7.3648 < 9.5742] w=0.1438 to align
# Constraint # added constraint: constraint((T0308)D79.CB, (T0308)V127.CB) [> 4.7090 = 7.8484 < 10.2029] w=0.1396 to align
# Constraint # added constraint: constraint((T0308)S124.CB, (T0308)C144.CB) [> 4.4501 = 7.4169 < 9.6419] w=0.1392 to align
# Constraint # added constraint: constraint((T0308)C6.CB, (T0308)T15.CB) [> 4.7122 = 7.8537 < 10.2098] w=0.1271 to align
# Constraint # added constraint: constraint((T0308)H3.CB, (T0308)S48.CB) [> 3.1182 = 5.1970 < 6.7561] w=0.1271 to align
# Constraint # added constraint: constraint((T0308)V4.CB, (T0308)S48.CB) [> 4.2228 = 7.0379 < 9.1493] w=0.1271 to align
# Constraint # added constraint: constraint((T0308)C6.CB, (T0308)F49.CB) [> 3.5529 = 5.9216 < 7.6981] w=0.1271 to align
# Constraint # added constraint: constraint((T0308)C6.CB, (T0308)T50.CB) [> 4.2665 = 7.1108 < 9.2441] w=0.1271 to align
# Constraint # added constraint: constraint((T0308)L7.CB, (T0308)F52.CB) [> 3.7710 = 6.2849 < 8.1704] w=0.1271 to align
# Constraint # added constraint: constraint((T0308)G8.CA, (T0308)D53.CB) [> 3.8953 = 6.4921 < 8.4398] w=0.1271 to align
# Constraint # added constraint: constraint((T0308)L9.CB, (T0308)D53.CB) [> 3.9925 = 6.6542 < 8.6504] w=0.1271 to align
# Constraint # added constraint: constraint((T0308)L9.CB, (T0308)M54.CB) [> 3.5251 = 5.8752 < 7.6377] w=0.1271 to align
# Constraint # added constraint: constraint((T0308)D10.CB, (T0308)D53.CB) [> 2.7081 = 4.5135 < 5.8676] w=0.1271 to align
# Constraint # added constraint: constraint((T0308)D79.CB, (T0308)L118.CB) [> 4.6367 = 7.7279 < 10.0462] w=0.1271 to align
# Constraint # added constraint: constraint((T0308)L7.CB, (T0308)D53.CB) [> 4.5102 = 7.5170 < 9.7722] w=0.1271 to align
# Constraint # added constraint: constraint((T0308)L21.CB, (T0308)S44.CB) [> 4.1516 = 6.9193 < 8.9950] w=0.1256 to align
# Constraint # added constraint: constraint((T0308)L131.CB, (T0308)I143.CB) [> 4.5057 = 7.5095 < 9.7624] w=0.1214 to align
# Constraint # added constraint: constraint((T0308)G13.CA, (T0308)I31.CB) [> 4.6618 = 7.7697 < 10.1007] w=0.1102 to align
# Constraint # added constraint: constraint((T0308)L9.CB, (T0308)S55.CB) [> 3.2581 = 5.4301 < 7.0592] w=0.1090 to align
# Constraint # added constraint: constraint((T0308)G8.CA, (T0308)S55.CB) [> 4.4207 = 7.3678 < 9.5782] w=0.1090 to align
# Constraint # added constraint: constraint((T0308)L7.CB, (T0308)V51.CB) [> 4.3681 = 7.2802 < 9.4642] w=0.1090 to align
# Constraint # added constraint: constraint((T0308)L5.CB, (T0308)D53.CB) [> 4.6000 = 7.6666 < 9.9666] w=0.1090 to align
# Constraint # added constraint: constraint((T0308)Q72.CB, (T0308)H104.CB) [> 4.4368 = 7.3947 < 9.6131] w=0.1035 to align
# Constraint # added constraint: constraint((T0308)L32.CB, (T0308)Y60.CB) [> 3.7738 = 6.2896 < 8.1765] w=0.1028 to align
# Constraint # added constraint: constraint((T0308)D10.CB, (T0308)R59.CB) [> 2.7502 = 4.5836 < 5.9587] w=0.1004 to align
# Constraint # added constraint: constraint((T0308)H3.CB, (T0308)Y67.CB) [> 4.4023 = 7.3371 < 9.5383] w=0.0908 to align
# Constraint # added constraint: constraint((T0308)I74.CB, (T0308)L93.CB) [> 4.5563 = 7.5938 < 9.8720] w=0.0908 to align
# Constraint # added constraint: constraint((T0308)F49.CB, (T0308)A73.CB) [> 4.7101 = 7.8502 < 10.2052] w=0.0823 to align
# Constraint # added constraint: constraint((T0308)T15.CB, (T0308)G36.CA) [> 4.1394 = 6.8990 < 8.9687] w=0.0793 to align
# Constraint # added constraint: constraint((T0308)E1.CB, (T0308)S46.CB) [> 3.0216 = 5.0360 < 6.5468] w=0.0787 to align
# Constraint # added constraint: constraint((T0308)H3.CB, (T0308)L47.CB) [> 4.6054 = 7.6757 < 9.9784] w=0.0726 to align
# Constraint # added constraint: constraint((T0308)S24.CB, (T0308)K43.CB) [> 3.5833 = 5.9722 < 7.7639] w=0.0726 to align
# Constraint # added constraint: constraint((T0308)I17.CB, (T0308)G151.CA) [> 4.7145 = 7.8574 < 10.2147] w=0.0726 to align
# Constraint # added constraint: constraint((T0308)L118.CB, (T0308)D147.CB) [> 4.4676 = 7.4460 < 9.6797] w=0.0726 to align
# Constraint # added constraint: constraint((T0308)S45.CB, (T0308)V158.CB) [> 4.4462 = 7.4104 < 9.6335] w=0.0711 to align
# Constraint # added constraint: constraint((T0308)V4.CB, (T0308)F42.CB) [> 4.6109 = 7.6849 < 9.9904] w=0.0711 to align
# Constraint # added constraint: constraint((T0308)K115.CB, (T0308)S146.CB) [> 4.6651 = 7.7752 < 10.1078] w=0.0705 to align
# Constraint # added constraint: constraint((T0308)Q129.CB, (T0308)C144.CB) [> 4.4522 = 7.4203 < 9.6464] w=0.0605 to align
# Constraint # added constraint: constraint((T0308)D10.CB, (T0308)L32.CB) [> 4.4952 = 7.4920 < 9.7396] w=0.0551 to align
# Constraint # added constraint: constraint((T0308)F52.CB, (T0308)E70.CB) [> 4.7402 = 7.9003 < 10.2704] w=0.0545 to align
# Constraint # added constraint: constraint((T0308)L5.CB, (T0308)E70.CB) [> 4.6967 = 7.8278 < 10.1762] w=0.0545 to align
# Constraint # added constraint: constraint((T0308)V77.CB, (T0308)S146.CB) [> 4.7409 = 7.9015 < 10.2720] w=0.0545 to align
# Constraint # added constraint: constraint((T0308)C144.CB, (T0308)L154.CB) [> 4.3702 = 7.2837 < 9.4689] w=0.0530 to align
# Constraint # added constraint: constraint((T0308)A113.CB, (T0308)S128.CB) [> 4.5555 = 7.5925 < 9.8702] w=0.0488 to align
# Constraint # added constraint: constraint((T0308)G71.CA, (T0308)R106.CB) [> 4.2006 = 7.0010 < 9.1012] w=0.0484 to align
# Constraint # added constraint: constraint((T0308)I31.CB, (T0308)K41.CB) [> 3.9193 = 6.5321 < 8.4918] w=0.0424 to align
# Constraint # added constraint: constraint((T0308)P33.CB, (T0308)H66.CB) [> 4.6023 = 7.6705 < 9.9717] w=0.0401 to align
# Constraint # added constraint: constraint((T0308)Q72.CB, (T0308)L161.CB) [> 4.5121 = 7.5201 < 9.7761] w=0.0396 to align
# Constraint # added constraint: constraint((T0308)F76.CB, (T0308)K139.CB) [> 4.6374 = 7.7290 < 10.0477] w=0.0363 to align
# Constraint # added constraint: constraint((T0308)L118.CB, (T0308)I149.CB) [> 4.0384 = 6.7306 < 8.7498] w=0.0363 to align
# Constraint # added constraint: constraint((T0308)L7.CB, (T0308)S55.CB) [> 3.6121 = 6.0201 < 7.8261] w=0.0363 to align
# Constraint # added constraint: constraint((T0308)K22.CB, (T0308)K43.CB) [> 3.8085 = 6.3476 < 8.2519] w=0.0363 to align
# Constraint # added constraint: constraint((T0308)K22.CB, (T0308)K41.CB) [> 4.4890 = 7.4817 < 9.7262] w=0.0363 to align
# Constraint # added constraint: constraint((T0308)D10.CB, (T0308)M54.CB) [> 4.6172 = 7.6953 < 10.0039] w=0.0363 to align
# Constraint # added constraint: constraint((T0308)S12.CB, (T0308)F112.CB) [> 4.7073 = 7.8455 < 10.1991] w=0.0363 to align
# Constraint # added constraint: constraint((T0308)F37.CB, (T0308)W64.CB) [> 4.4001 = 7.3335 < 9.5335] w=0.0363 to align
# Constraint # added constraint: constraint((T0308)F37.CB, (T0308)Y60.CB) [> 3.7526 = 6.2544 < 8.1307] w=0.0363 to align
# Constraint # added constraint: constraint((T0308)S81.CB, (T0308)M116.CB) [> 3.7699 = 6.2832 < 8.1681] w=0.0348 to align
# Constraint # added constraint: constraint((T0308)I18.CB, (T0308)F37.CB) [> 4.7103 = 7.8505 < 10.2057] w=0.0303 to align
# Constraint # added constraint: constraint((T0308)V2.CB, (T0308)F42.CB) [> 4.0645 = 6.7742 < 8.8065] w=0.0303 to align
# Constraint # added constraint: constraint((T0308)D79.CB, (T0308)S124.CB) [> 4.6907 = 7.8178 < 10.1632] w=0.0303 to align
# Constraint # added constraint: constraint((T0308)S80.CB, (T0308)V125.CB) [> 3.6882 = 6.1470 < 7.9911] w=0.0303 to align
# Constraint # added constraint: constraint((T0308)A113.CB, (T0308)V125.CB) [> 4.4176 = 7.3626 < 9.5714] w=0.0295 to align
# Constraint # added constraint: constraint((T0308)S128.CB, (T0308)A145.CB) [> 4.0690 = 6.7817 < 8.8162] w=0.0242 to align
# Constraint # added constraint: constraint((T0308)E70.CB, (T0308)R106.CB) [> 4.0515 = 6.7524 < 8.7781] w=0.0242 to align
# Constraint # added constraint: constraint((T0308)A73.CB, (T0308)W141.CB) [> 4.6834 = 7.8056 < 10.1473] w=0.0182 to align
# Constraint # added constraint: constraint((T0308)V2.CB, (T0308)S44.CB) [> 3.7549 = 6.2581 < 8.1355] w=0.0182 to align
# Constraint # added constraint: constraint((T0308)N11.CB, (T0308)M116.CB) [> 4.1846 = 6.9744 < 9.0667] w=0.0182 to align
# Constraint # added constraint: constraint((T0308)D79.CB, (T0308)M116.CB) [> 2.7341 = 4.5568 < 5.9239] w=0.0182 to align
# Constraint # added constraint: constraint((T0308)D79.CB, (T0308)D117.CB) [> 4.5306 = 7.5510 < 9.8163] w=0.0182 to align
# Constraint # added constraint: constraint((T0308)K115.CB, (T0308)A145.CB) [> 4.2518 = 7.0863 < 9.2122] w=0.0182 to align
# Constraint # added constraint: constraint((T0308)L110.CB, (T0308)I136.CB) [> 4.6818 = 7.8030 < 10.1439] w=0.0182 to align
# Constraint # added constraint: constraint((T0308)S38.CB, (T0308)M54.CB) [> 4.7934 = 7.9891 < 10.3858] w=0.0182 to align
# Constraint # added constraint: constraint((T0308)I74.CB, (T0308)L97.CB) [> 4.2446 = 7.0744 < 9.1967] w=0.0182 to align
# Constraint # added constraint: constraint((T0308)M54.CB, (T0308)E65.CB) [> 4.6673 = 7.7789 < 10.1125] w=0.0182 to align
# Constraint # added constraint: constraint((T0308)I18.CB, (T0308)S44.CB) [> 4.5034 = 7.5057 < 9.7573] w=0.0182 to align
# Constraint # added constraint: constraint((T0308)V2.CB, (T0308)E70.CB) [> 3.7777 = 6.2961 < 8.1849] w=0.0182 to align
# Constraint # added constraint: constraint((T0308)L131.CB, (T0308)A145.CB) [> 4.6952 = 7.8254 < 10.1730] w=0.0182 to align
# Constraint # added constraint: constraint((T0308)T16.CB, (T0308)N30.CB) [> 4.4685 = 7.4476 < 9.6818] w=0.0172 to align
# Constraint # added constraint: constraint((T0308)I109.CB, (T0308)L133.CB) [> 4.7059 = 7.8432 < 10.1961] w=0.0121 to align
# Constraint # added constraint: constraint((T0308)L32.CB, (T0308)K43.CB) [> 4.6115 = 7.6859 < 9.9916] w=0.0121 to align
# Constraint # added constraint: constraint((T0308)T16.CB, (T0308)P33.CB) [> 3.0721 = 5.1202 < 6.6563] w=0.0061 to align
# Constraint # added constraint: constraint((T0308)V125.CB, (T0308)I143.CB) [> 4.7276 = 7.8794 < 10.2432] w=0.0053 to align
# SetCost created cost = 
#	( 1.0000 * align )
# command:# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/constraints_v3/T0308/
# command:# reading script from file servers-clean.under
# Prefix for input files set to /projects/compbio/experiments/protein-predict/casp7/T0308/decoys/
# ReadConformPDB reading from PDB file chimera-9-4.pdb.gz looking for model 1
# choosing archetypes in rotamer library
# Found a chain break before 151
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file tr308.pdb.gz looking for model 1
# Found a chain break before 146
# copying to AlignedFragments data structure
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_POPULUS_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0308 can't currently be optimized by undertaker
# 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
# WARNING: incomplete conformation T0308 can't currently be optimized by undertaker
# 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
# WARNING: incomplete conformation T0308 can't currently be optimized by undertaker
# 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 107
# 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
# WARNING: incomplete conformation T0308 can't currently be optimized by undertaker
# 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
# Found a chain break before 139
# copying to AlignedFragments data structure
# naming current conformation 3D-JIGSAW_RECOM_TS1
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS2.pdb.gz looking for model 1
# Found a chain break before 139
# copying to AlignedFragments data structure
# 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 T0308 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation 3D-JIGSAW_RECOM_TS3
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS4.pdb.gz looking for model 1
# Found a chain break before 119
# copying to AlignedFragments data structure
# naming current conformation 3D-JIGSAW_RECOM_TS4
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_RECOM_TS5.pdb.gz looking for model 1
# Found a chain break before 152
# copying to AlignedFragments data structure
# 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 T0308 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation 3D-JIGSAW_TS1
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS2.pdb.gz looking for model 1
# Found a chain break before 148
# 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
# Found a chain break before 135
# copying to AlignedFragments data structure
# naming current conformation 3D-JIGSAW_TS3
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS4.pdb.gz looking for model 1
# Found a chain break before 139
# copying to AlignedFragments data structure
# naming current conformation 3D-JIGSAW_TS4
# ReadConformPDB reading from PDB file servers/3D-JIGSAW_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0308 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# 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 102
# 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 153
# 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 45
# 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 114
# 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 150
# 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 144
# 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 120
# 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 139
# 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 142
# copying to AlignedFragments data structure
# naming current conformation ABIpro_TS5
# ReadConformPDB reading from PDB file servers/BayesHH_TS1.pdb.gz looking for model 1
# Found a chain break before 101
# copying to AlignedFragments data structure
# 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
# Found a chain break before 139
# copying to AlignedFragments data structure
# 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
# Found a chain break before 139
# copying to AlignedFragments data structure
# 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 139
# 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 146
# 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 139
# 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 T0308 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation CIRCLE_TS3
# ReadConformPDB reading from PDB file servers/CIRCLE_TS4.pdb.gz looking for model 1
# Found a chain break before 54
# copying to AlignedFragments data structure
# naming current conformation CIRCLE_TS4
# ReadConformPDB reading from PDB file servers/CIRCLE_TS5.pdb.gz looking for model 1
# Found a chain break before 152
# copying to AlignedFragments data structure
# naming current conformation CIRCLE_TS5
# ReadConformPDB reading from PDB file servers/CPHmodels_TS1.pdb.gz looking for model 1
# Found a chain break before 102
# copying to AlignedFragments data structure
# naming current conformation CPHmodels_TS1
# ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS1.pdb.gz looking for model 1
# Found a chain break before 103
# copying to AlignedFragments data structure
# naming current conformation CaspIta-FOX_TS1
# ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS2.pdb.gz looking for model 1
# Found a chain break before 104
# copying to AlignedFragments data structure
# naming current conformation CaspIta-FOX_TS2
# ReadConformPDB reading from PDB file servers/CaspIta-FOX_TS3.pdb.gz looking for model 1
# Found a chain break before 102
# copying to AlignedFragments data structure
# 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 104
# 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 104
# 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 T0308 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 T0308 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 T0308 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 T0308 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 T0308 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 104
# copying to AlignedFragments data structure
# naming current conformation FAMSD_TS1
# ReadConformPDB reading from PDB file servers/FAMSD_TS2.pdb.gz looking for model 1
# naming current conformation FAMSD_TS2
# ReadConformPDB reading from PDB file servers/FAMSD_TS3.pdb.gz looking for model 1
# Found a chain break before 54
# copying to AlignedFragments data structure
# naming current conformation FAMSD_TS3
# ReadConformPDB reading from PDB file servers/FAMSD_TS4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0308 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation FAMSD_TS4
# ReadConformPDB reading from PDB file servers/FAMSD_TS5.pdb.gz looking for model 1
# naming current conformation FAMSD_TS5
# ReadConformPDB reading from PDB file servers/FAMS_TS1.pdb.gz looking for model 1
# Found a chain break before 139
# copying to AlignedFragments data structure
# naming current conformation FAMS_TS1
# ReadConformPDB reading from PDB file servers/FAMS_TS2.pdb.gz looking for model 1
# Found a chain break before 139
# copying to AlignedFragments data structure
# naming current conformation FAMS_TS2
# ReadConformPDB reading from PDB file servers/FAMS_TS3.pdb.gz looking for model 1
# Found a chain break before 152
# copying to AlignedFragments data structure
# naming current conformation FAMS_TS3
# ReadConformPDB reading from PDB file servers/FAMS_TS4.pdb.gz looking for model 1
# Found a chain break before 157
# copying to AlignedFragments data structure
# naming current conformation FAMS_TS4
# ReadConformPDB reading from PDB file servers/FAMS_TS5.pdb.gz looking for model 1
# naming current conformation FAMS_TS5
# ReadConformPDB reading from PDB file servers/FOLDpro_TS1.pdb.gz looking for model 1
# Found a chain break before 27
# 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 139
# 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 138
# copying to AlignedFragments data structure
# naming current conformation FOLDpro_TS3
# ReadConformPDB reading from PDB file servers/FOLDpro_TS4.pdb.gz looking for model 1
# Found a chain break before 83
# copying to AlignedFragments data structure
# naming current conformation FOLDpro_TS4
# ReadConformPDB reading from PDB file servers/FOLDpro_TS5.pdb.gz looking for model 1
# Found a chain break before 139
# copying to AlignedFragments data structure
# naming current conformation FOLDpro_TS5
# ReadConformPDB reading from PDB file servers/FORTE1_AL1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0308 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation FORTE1_AL1
# ReadConformPDB reading from PDB file servers/FORTE1_AL2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0308 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 T0308 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 T0308 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
# WARNING: incomplete conformation T0308 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
# WARNING: incomplete conformation T0308 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
# WARNING: incomplete conformation T0308 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation FORTE2_AL2
# ReadConformPDB reading from PDB file servers/FORTE2_AL3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0308 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
Skipped atom 94, because occupancy 1 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 96, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 98, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 100, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 114, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 116, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 118, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 120, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 194, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 195, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 197, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 198, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 200, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 201, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 203, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 204, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 298, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 300, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 302, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 304, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 342, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 344, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 346, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
Skipped atom 348, because occupancy 1.000 <= existing 1.000 in servers/FORTE2_AL4.pdb.gz
# WARNING: incomplete conformation T0308 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
# WARNING: incomplete conformation T0308 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 129
# 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 126
# 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 162
# 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 159
# 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 114
# 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
# WARNING: incomplete conformation T0308 can't currently be optimized by undertaker
# 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 146
# copying to AlignedFragments data structure
# naming current conformation FUGMOD_TS2
# ReadConformPDB reading from PDB file servers/FUGMOD_TS3.pdb.gz looking for model 1
# Found a chain break before 156
# copying to AlignedFragments data structure
# naming current conformation FUGMOD_TS3
# ReadConformPDB reading from PDB file servers/FUGMOD_TS4.pdb.gz looking for model 1
# Found a chain break before 77
# copying to AlignedFragments data structure
# naming current conformation FUGMOD_TS4
# ReadConformPDB reading from PDB file servers/FUGMOD_TS5.pdb.gz looking for model 1
# Found a chain break before 66
# copying to AlignedFragments data structure
# naming current conformation FUGMOD_TS5
# ReadConformPDB reading from PDB file servers/FUGUE_AL1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0308 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation FUGUE_AL1
# ReadConformPDB reading from PDB file servers/FUGUE_AL2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0308 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
# WARNING: incomplete conformation T0308 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
# WARNING: incomplete conformation T0308 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 T0308 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 146
# 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 158
# 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 146
# 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 157
# 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 139
# copying to AlignedFragments data structure
# naming current conformation FUNCTION_TS5
# ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS1.pdb.gz looking for model 1
# Found a chain break before 55
# copying to AlignedFragments data structure
# naming current conformation GeneSilicoMetaServer_TS1
# ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS2.pdb.gz looking for model 1
# Found a chain break before 132
# copying to AlignedFragments data structure
# naming current conformation GeneSilicoMetaServer_TS2
# ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS3.pdb.gz looking for model 1
# Found a chain break before 123
# copying to AlignedFragments data structure
# naming current conformation GeneSilicoMetaServer_TS3
# ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS4.pdb.gz looking for model 1
# Found a chain break before 28
# copying to AlignedFragments data structure
# naming current conformation GeneSilicoMetaServer_TS4
# ReadConformPDB reading from PDB file servers/GeneSilicoMetaServer_TS5.pdb.gz looking for model 1
# Found a chain break before 10
# copying to AlignedFragments data structure
# naming current conformation GeneSilicoMetaServer_TS5
# ReadConformPDB reading from PDB file servers/HHpred1_TS1.pdb.gz looking for model 1
# Found a chain break before 57
# copying to AlignedFragments data structure
# naming current conformation HHpred1_TS1
# ReadConformPDB reading from PDB file servers/HHpred2_TS1.pdb.gz looking for model 1
# Found a chain break before 55
# copying to AlignedFragments data structure
# naming current conformation HHpred2_TS1
# ReadConformPDB reading from PDB file servers/HHpred3_TS1.pdb.gz looking for model 1
# naming current conformation HHpred3_TS1
# ReadConformPDB reading from PDB file servers/Huber-Torda-Server_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0308 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# 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 T0308 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# 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 T0308 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# 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 T0308 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 T0308 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation Huber-Torda-Server_TS5
# ReadConformPDB reading from PDB file servers/LOOPP_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0308 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation LOOPP_TS1
# ReadConformPDB reading from PDB file servers/LOOPP_TS2.pdb.gz looking for model 1
# naming current conformation LOOPP_TS2
# ReadConformPDB reading from PDB file servers/LOOPP_TS3.pdb.gz looking for model 1
# naming current conformation LOOPP_TS3
# ReadConformPDB reading from PDB file servers/LOOPP_TS4.pdb.gz looking for model 1
# naming current conformation LOOPP_TS4
# ReadConformPDB reading from PDB file servers/LOOPP_TS5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0308 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation LOOPP_TS5
# ReadConformPDB reading from PDB file servers/Ma-OPUS-server_TS1.pdb.gz looking for model 1
# Found a chain break before 27
# copying to AlignedFragments data structure
# 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 10
# 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
# Found a chain break before 103
# copying to AlignedFragments data structure
# 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 21
# 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 143
# 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 143
# copying to AlignedFragments data structure
# naming current conformation MetaTasser_TS1
# ReadConformPDB reading from PDB file servers/NN_PUT_lab_TS1.pdb.gz looking for model 1
# 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 107
# copying to AlignedFragments data structure
# naming current conformation PROTINFO_TS1
# ReadConformPDB reading from PDB file servers/PROTINFO_TS2.pdb.gz looking for model 1
# naming current conformation PROTINFO_TS2
# ReadConformPDB reading from PDB file servers/PROTINFO_TS3.pdb.gz looking for model 1
# Found a chain break before 107
# copying to AlignedFragments data structure
# naming current conformation PROTINFO_TS3
# ReadConformPDB reading from PDB file servers/PROTINFO_TS4.pdb.gz looking for model 1
# Found a chain break before 106
# copying to AlignedFragments data structure
# 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
# Found a chain break before 135
# copying to AlignedFragments data structure
# naming current conformation Pcons6_TS1
# ReadConformPDB reading from PDB file servers/Pcons6_TS2.pdb.gz looking for model 1
# Found a chain break before 135
# copying to AlignedFragments data structure
# naming current conformation Pcons6_TS2
# ReadConformPDB reading from PDB file servers/Pcons6_TS3.pdb.gz looking for model 1
# Found a chain break before 135
# copying to AlignedFragments data structure
# naming current conformation Pcons6_TS3
# ReadConformPDB reading from PDB file servers/Pcons6_TS4.pdb.gz looking for model 1
# Found a chain break before 135
# copying to AlignedFragments data structure
# naming current conformation Pcons6_TS4
# ReadConformPDB reading from PDB file servers/Pcons6_TS5.pdb.gz looking for model 1
# Found a chain break before 137
# 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 T0308 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation Phyre-1_TS1
# ReadConformPDB reading from PDB file servers/Phyre-2_TS1.pdb.gz looking for model 1
# Found a chain break before 98
# 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 98
# 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 98
# 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 98
# 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 98
# 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 135
# 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 135
# copying to AlignedFragments data structure
# naming current conformation Pmodeller6_TS2
# ReadConformPDB reading from PDB file servers/Pmodeller6_TS3.pdb.gz looking for model 1
# Found a chain break before 135
# copying to AlignedFragments data structure
# naming current conformation Pmodeller6_TS3
# ReadConformPDB reading from PDB file servers/Pmodeller6_TS4.pdb.gz looking for model 1
# Found a chain break before 135
# copying to AlignedFragments data structure
# naming current conformation Pmodeller6_TS4
# ReadConformPDB reading from PDB file servers/Pmodeller6_TS5.pdb.gz looking for model 1
# Found a chain break before 135
# copying to AlignedFragments data structure
# naming current conformation Pmodeller6_TS5
# ReadConformPDB reading from PDB file servers/RAPTOR-ACE_TS1.pdb.gz looking for model 1
# Found a chain break before 105
# 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
# Found a chain break before 105
# 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
# 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 22
# 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 59
# 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
# naming current conformation RAPTORESS_TS2
# ReadConformPDB reading from PDB file servers/RAPTORESS_TS3.pdb.gz looking for model 1
# Found a chain break before 162
# 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 107
# 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 107
# 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 105
# copying to AlignedFragments data structure
# naming current conformation RAPTOR_TS1
# ReadConformPDB reading from PDB file servers/RAPTOR_TS2.pdb.gz looking for model 1
# Found a chain break before 104
# copying to AlignedFragments data structure
# naming current conformation RAPTOR_TS2
# ReadConformPDB reading from PDB file servers/RAPTOR_TS3.pdb.gz looking for model 1
# Found a chain break before 104
# copying to AlignedFragments data structure
# naming current conformation RAPTOR_TS3
# ReadConformPDB reading from PDB file servers/RAPTOR_TS4.pdb.gz looking for model 1
# Found a chain break before 104
# copying to AlignedFragments data structure
# naming current conformation RAPTOR_TS4
# ReadConformPDB reading from PDB file servers/RAPTOR_TS5.pdb.gz looking for model 1
# Found a chain break before 103
# 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 104
# 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 101
# 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 107
# copying to AlignedFragments data structure
# naming current conformation ROBETTA_TS3
# ReadConformPDB reading from PDB file servers/ROBETTA_TS4.pdb.gz looking for model 1
# Found a chain break before 107
# copying to AlignedFragments data structure
# naming current conformation ROBETTA_TS4
# ReadConformPDB reading from PDB file servers/ROBETTA_TS5.pdb.gz looking for model 1
# Found a chain break before 104
# copying to AlignedFragments data structure
# naming current conformation ROBETTA_TS5
# ReadConformPDB reading from PDB file servers/ROKKY_TS1.pdb.gz looking for model 1
# Found a chain break before 103
# 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 102
# 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 41
# 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 102
# copying to AlignedFragments data structure
# naming current conformation ROKKY_TS4
# ReadConformPDB reading from PDB file servers/ROKKY_TS5.pdb.gz looking for model 1
# Found a chain break before 105
# copying to AlignedFragments data structure
# naming current conformation ROKKY_TS5
# ReadConformPDB reading from PDB file servers/SAM-T02_AL1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0308 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation SAM-T02_AL1
# ReadConformPDB reading from PDB file servers/SAM-T02_AL2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0308 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation SAM-T02_AL2
# ReadConformPDB reading from PDB file servers/SAM-T02_AL3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0308 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 54, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 56, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 58, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 60, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 82, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 84, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 86, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 88, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 122, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 124, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 126, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 128, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 134, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 136, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 138, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 140, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 142, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 143, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 145, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 146, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 148, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 149, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 151, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 152, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 178, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 180, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 182, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 184, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 210, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 212, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 214, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 216, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 382, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 384, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 386, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 388, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 426, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 428, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 430, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 432, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 498, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 500, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 502, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 504, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 546, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 548, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 550, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
Skipped atom 552, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL4.pdb.gz
# WARNING: incomplete conformation T0308 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation SAM-T02_AL4
# ReadConformPDB reading from PDB file servers/SAM-T02_AL5.pdb.gz looking for model 1
Skipped atom 142, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz
Skipped atom 144, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz
Skipped atom 146, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz
Skipped atom 148, because occupancy 1.000 <= existing 1.000 in servers/SAM-T02_AL5.pdb.gz
# WARNING: incomplete conformation T0308 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation SAM-T02_AL5
# ReadConformPDB reading from PDB file servers/SAM-T99_AL1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0308 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 T0308 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 T0308 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation SAM-T99_AL3
# ReadConformPDB reading from PDB file servers/SAM-T99_AL4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0308 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation SAM-T99_AL4
# ReadConformPDB reading from PDB file servers/SAM-T99_AL5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0308 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# 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 137
# 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 T0308 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 T0308 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 T0308 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 T0308 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
# naming current conformation SP3_TS1
# ReadConformPDB reading from PDB file servers/SP3_TS2.pdb.gz looking for model 1
# Found a chain break before 105
# 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 104
# copying to AlignedFragments data structure
# naming current conformation SP3_TS3
# ReadConformPDB reading from PDB file servers/SP3_TS4.pdb.gz looking for model 1
# Found a chain break before 102
# copying to AlignedFragments data structure
# naming current conformation SP3_TS4
# ReadConformPDB reading from PDB file servers/SP3_TS5.pdb.gz looking for model 1
# Found a chain break before 22
# copying to AlignedFragments data structure
# naming current conformation SP3_TS5
# ReadConformPDB reading from PDB file servers/SP4_TS1.pdb.gz looking for model 1
# naming current conformation SP4_TS1
# ReadConformPDB reading from PDB file servers/SP4_TS2.pdb.gz looking for model 1
# Found a chain break before 105
# 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 104
# 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 54
# 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 41
# copying to AlignedFragments data structure
# naming current conformation SP4_TS5
# ReadConformPDB reading from PDB file servers/SPARKS2_TS1.pdb.gz looking for model 1
# naming current conformation SPARKS2_TS1
# ReadConformPDB reading from PDB file servers/SPARKS2_TS2.pdb.gz looking for model 1
# Found a chain break before 105
# 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 104
# 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 102
# copying to AlignedFragments data structure
# naming current conformation SPARKS2_TS4
# ReadConformPDB reading from PDB file servers/SPARKS2_TS5.pdb.gz looking for model 1
# naming current conformation SPARKS2_TS5
# ReadConformPDB reading from PDB file servers/UNI-EID_bnmx_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0308 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# 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 T0308 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# 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 T0308 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# 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 T0308 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# 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 T0308 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# 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 T0308 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
# WARNING: incomplete conformation T0308 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation UNI-EID_sfst_AL1
# ReadConformPDB reading from PDB file servers/UNI-EID_sfst_AL2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0308 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# 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 T0308 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# 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 T0308 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# 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 T0308 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# 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 119
# 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 113
# 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
# Found a chain break before 105
# copying to AlignedFragments data structure
# 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 103
# 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 139
# 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 149
# copying to AlignedFragments data structure
# naming current conformation beautshot_TS1
# ReadConformPDB reading from PDB file servers/beautshotbase_TS1.pdb.gz looking for model 1
# Found a chain break before 164
# copying to AlignedFragments data structure
# naming current conformation beautshotbase_TS1
# ReadConformPDB reading from PDB file servers/forecast-s_AL1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0308 can't currently be optimized by undertaker
# naming current conformation forecast-s_AL1
# ReadConformPDB reading from PDB file servers/forecast-s_AL2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0308 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 22, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 23, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 25, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 26, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 28, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 29, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 31, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 32, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 74, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 76, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 78, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 80, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 126, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 128, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 130, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 132, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 134, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 279, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 281, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 283, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
Skipped atom 285, because occupancy 1.000 <= existing 1.000 in servers/forecast-s_AL3.pdb.gz
# WARNING: incomplete conformation T0308 can't currently be optimized by undertaker
# naming current conformation forecast-s_AL3
# ReadConformPDB reading from PDB file servers/forecast-s_AL4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0308 can't currently be optimized by undertaker
# naming current conformation forecast-s_AL4
# ReadConformPDB reading from PDB file servers/forecast-s_AL5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0308 can't currently be optimized by undertaker
# naming current conformation forecast-s_AL5
# ReadConformPDB reading from PDB file servers/gtg_AL1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0308 can't currently be optimized by undertaker
# naming current conformation gtg_AL1
# ReadConformPDB reading from PDB file servers/gtg_AL2.pdb.gz looking for model 1
Skipped atom 639, because occupancy 1.000 <= existing 1.000 in servers/gtg_AL2.pdb.gz
# WARNING: incomplete conformation T0308 can't currently be optimized by undertaker
# naming current conformation gtg_AL2
# ReadConformPDB reading from PDB file servers/gtg_AL3.pdb.gz looking for model 1
# WARNING: incomplete conformation T0308 can't currently be optimized by undertaker
# naming current conformation gtg_AL3
# ReadConformPDB reading from PDB file servers/gtg_AL4.pdb.gz looking for model 1
# WARNING: incomplete conformation T0308 can't currently be optimized by undertaker
# naming current conformation gtg_AL4
# ReadConformPDB reading from PDB file servers/gtg_AL5.pdb.gz looking for model 1
# WARNING: incomplete conformation T0308 can't currently be optimized by undertaker
# naming current conformation gtg_AL5
# ReadConformPDB reading from PDB file servers/karypis.srv.2_TS1.pdb.gz looking for model 1
# Found a chain break before 55
# copying to AlignedFragments data structure
# 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 103
# 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
# Found a chain break before 102
# copying to AlignedFragments data structure
# 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 103
# 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
# Found a chain break before 102
# copying to AlignedFragments data structure
# 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 164
# 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 160
# 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
# Found a chain break before 159
# copying to AlignedFragments data structure
# naming current conformation karypis.srv.4_TS3
# ReadConformPDB reading from PDB file servers/karypis.srv.4_TS5.pdb.gz looking for model 1
# Found a chain break before 162
# 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 T0308 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation karypis.srv_TS1
# ReadConformPDB reading from PDB file servers/karypis.srv_TS2.pdb.gz looking for model 1
# Found a chain break before 101
# copying to AlignedFragments data structure
# naming current conformation karypis.srv_TS2
# ReadConformPDB reading from PDB file servers/karypis.srv_TS3.pdb.gz looking for model 1
# Found a chain break before 104
# copying to AlignedFragments data structure
# naming current conformation karypis.srv_TS3
# ReadConformPDB reading from PDB file servers/karypis.srv_TS4.pdb.gz looking for model 1
# Found a chain break before 103
# copying to AlignedFragments data structure
# naming current conformation karypis.srv_TS4
# ReadConformPDB reading from PDB file servers/karypis.srv_TS5.pdb.gz looking for model 1
# Found a chain break before 102
# copying to AlignedFragments data structure
# naming current conformation karypis.srv_TS5
# ReadConformPDB reading from PDB file servers/mGen-3D_TS1.pdb.gz looking for model 1
# WARNING: incomplete conformation T0308 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 T0308 can't currently be optimized by undertaker
# copying to AlignedFragments data structure
# naming current conformation nFOLD_TS1
# ReadConformPDB reading from PDB file servers/nFOLD_TS2.pdb.gz looking for model 1
# WARNING: incomplete conformation T0308 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 T0308 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 T0308 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 T0308 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
# Found a chain break before 159
# copying to AlignedFragments data structure
# naming current conformation panther2_TS1
# ReadConformPDB reading from PDB file servers/shub_TS1.pdb.gz looking for model 1
# Found a chain break before 164
# copying to AlignedFragments data structure
# naming current conformation shub_TS1
# command:Using radius: 8.0000
Metaserver mode
NUMB_ALIGNS: 250
model score -0.5375
model score -0.5390
model score -0.2142
model score -0.2142
model score -0.2152
model score -0.2208
model score -0.1543
model score -0.2526
model score -0.2522
model score -0.2025
model score -0.2600
model score -0.2490
model score -0.2030
model score -0.2172
model score -0.2308
model score -0.2071
model score -0.2129
model score -0.3106
model score -0.1344
model score 0.6575
model score 1.4928
model score -0.1228
model score 1.4101
model score 1.2807
model score 1.1776
model score 1.3116
model score 1.3898
model score -0.5669
model score -0.5199
model score -0.6455
model score -0.0291
model score -0.6774
model score -0.7023
model score -0.2468
model score -0.2818
model score -0.2232
model score -0.2475
model score -0.2546
model score -0.2516
model score -0.2661
model score -0.2891
model score -0.5155
model score -0.3217
model score -0.2497
model score 1.2741
model score 1.2739
model score 1.2731
model score 1.2747
model score 1.2732
model score -0.2634
model score -0.2580
model score -0.2475
model score -0.2164
model score -0.2795
model score -0.2866
model score -0.2818
model score -0.2546
model score -0.2555
model score -0.2580
model score -0.5404
model score -0.5115
model score 0.3420
model score 1.0898
model score 0.2439
model score 1.2739
model score 1.2713
model score 1.2773
model score 1.2717
model score 1.2758
model score 1.2713
model score 1.2739
model score 1.2758
model score 1.2810
model score 1.2717
model score 2.3035
model score 2.6218
model score 2.3575
model score 2.5840
model score 2.3083
model score -0.4380
model score 0.4561
model score -0.0272
model score -0.1853
model score 1.7402
model score 1.2712
model score 1.2715
model score 1.2770
model score 1.2752
model score 1.2811
model score -0.2425
model score -0.2654
model score -0.2741
model score -0.2555
model score -0.2818
model score -0.5178
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model score -0.5583
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model score -0.5651
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model score -0.2121
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model score -0.2375
model score -0.2807
model score -0.1177
model score -0.4438
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model score -0.2004
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model score -0.4589
model score -0.5399
model score -0.5402
model score -0.5413
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model score -0.5414
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model score -0.5399
model score -0.5437
model score -0.5263
model score -0.5216
model score -0.5402
model score -0.5503
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model score -0.3159
model score -0.3159
model score -0.3159
model score -0.3159
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model score -0.5402
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model score -0.2972
model score -0.5503
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model score -0.3220
model score -0.2767
model score -0.2778
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model score -0.2796
model score -0.2641
model score -0.2060
model score -0.2393
model score -0.2183
model score -0.3242
model score -0.2962
model score -0.2262
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model score -0.2470
model score -0.2808
model score -0.2934
model score -0.3267
model score -0.2928
model score -0.2871
model score -0.2621
model score -0.2874
model score -0.0645
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model score -0.2640
model score 1.2712
model score 1.2739
model score 1.2771
model score 1.2762
model score 1.2713
model score 1.2771
model score 1.2714
model score 1.2765
model score 1.2779
model score 1.2780
model score -0.5460
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model score 1.2717
model score 1.2712
model score 1.2765
model score 1.2715
model score 1.2770
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model score 1.2712
model score 1.2765
model score 1.2715
model score 1.2770
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model score -0.5115
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model score -0.3877
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model score -0.3066
model score 1.2716
model score 1.2771
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model score 1.2717
model score 1.2732
model score 1.2717
model score 1.2745
model score 1.2713
model score 1.2752
model score 1.2755
model score -0.5449
model score -0.5432
model score -0.5514
model score -0.5402
model score -0.5481
model score 2.2307
model score 1.9924
model score 2.1997
model score 1.8254
model score -0.2926
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model score 0.0933
model score -0.4901
model score -0.3101
model score -0.4107
model score -0.5760
model score -0.2359
model score -0.2610
weight: 0.9554 eval: -0.5375 min: -0.7023 max: 2.6218
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weight: 0.4655 eval: 1.2717 min: -0.7023 max: 2.6218
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weight: 0.2143 eval: 2.1997 min: -0.7023 max: 2.6218
weight: 0.3156 eval: 1.8254 min: -0.7023 max: 2.6218
weight: 0.8891 eval: -0.2926 min: -0.7023 max: 2.6218
weight: 0.8855 eval: -0.2793 min: -0.7023 max: 2.6218
weight: 0.8914 eval: -0.3011 min: -0.7023 max: 2.6218
weight: 0.8964 eval: -0.3196 min: -0.7023 max: 2.6218
weight: 0.8850 eval: -0.2776 min: -0.7023 max: 2.6218
weight: 0.9457 eval: -0.5016 min: -0.7023 max: 2.6218
weight: 0.7846 eval: 0.0933 min: -0.7023 max: 2.6218
weight: 0.9425 eval: -0.4901 min: -0.7023 max: 2.6218
weight: 0.8938 eval: -0.3101 min: -0.7023 max: 2.6218
weight: 0.9210 eval: -0.4107 min: -0.7023 max: 2.6218
weight: 0.9658 eval: -0.5760 min: -0.7023 max: 2.6218
weight: 0.8737 eval: -0.2359 min: -0.7023 max: 2.6218
weight: 0.8805 eval: -0.2610 min: -0.7023 max: 2.6218
Adding 3984 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: -266.3738, CN propb: -266.3738 weights: 0.4430 constraints: 513
# command:Found ConstraintSet
# PrintContacts align.constraints_meta02
Number of constraints in align2.constraints 513
# command:Found ConstraintSet
# PrintContacts align_bonus.constraints_meta02
Number of constraints in align2.constraints.bonus 513
# command:Found ConstraintSet
# PrintContacts rejected.constraints_meta02
Number of constraints in rejected2.constraints 3471
# command:Found ConstraintSet
# PrintContacts rejected_bonus.constraints_meta02
Number of constraints in rejected2.constraints.bonus 3471
# 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 3984
# command: