CreatePredAlphaCost pred_alpha2k alpha11 T0289.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0289.t04.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha06 alpha11 T0289.t06.alpha.rdb 2 alpha alpha_prev sum

SetCost wet6.5 25 near_backbone 15 way_back 5 dry5 25 dry6.5 30 dry8 25 dry12 15 \
	phobic_fit 2 \
	sidechain 10 \
	n_ca_c	5 bad_peptide 10 \
	bystroff 5 \
	soft_clashes 40  backbone_clashes 2 \
	break 80  \
	pred_alpha2k 2 \
	pred_alpha04 3 \
	pred_alpha06 4 \
	constraints 10 \
	hbond_geom 5 \
	hbond_geom_backbone 10 \
	hbond_geom_beta 50 \
	hbond_geom_beta_pair 100 \
	maybe_metal 0.5  \
	missing_atoms 1

# from decoys/try11-opt2.sheets
#	with weights increased where they agreed with the first
#	undertaker-align alignment
SheetConstraint S1 T2 		V47 E46 	hbond S1 	1
SheetConstraint K11 G17 	Y108 L114 	hbond K12 	3
SheetConstraint K11 G18 	L45 T52 	hbond I13 	3
SheetConstraint D109 N116 	K171 V178 	hbond V111 	3
SheetConstraint C123 L127 	V178 V174 	hbond T124 	3
SheetConstraint T124 L127 	P150 V153 	hbond L125 	3
SheetConstraint L149 V153 	I219 K223 	hbond C151 	3
SheetConstraint V221 M225 	T297 A293 	hbond K223 	1
SheetConstraint M225 V228 	F294 K291 	hbond E226 	1
SheetConstraint A239 H243 	L264 V260 	hbond V241 	1
SheetConstraint W251 L254 	Y278 C275 	hbond K252 	1
SheetConstraint F261 S263 	V268 G266 	hbond S263 	1
SheetConstraint T298 L302 	T310 S306 	hbond L300 	1


# There are disagreements between models about the alignment of the
# strand near Y287-T297, so I removed its sheet constraint and
# put in two strand  constraints in its place.
# SheetConstraint C275 Y278 	A295 E292 	hbond T276 	1
StrandConstraint C275	Y278	1
StrandConstraint E292	A295	1

# from decoys/try11-opt2.helices
# with weights increased where they agreed with T0289.dssp-ehl2.constraints
HelixConstraint L24 	E39		2
HelixConstraint N53 	C60		2
HelixConstraint D73 	S78		2
HelixConstraint D84 	G100		2
HelixConstraint I136 	A147		2
HelixConstraint S160 	S168		2
HelixConstraint L191 	F204		1
HelixConstraint N209 	F214		1
HelixConstraint P231 	G236		1


#  I'm extending this out a little bit
HelixConstraint  	A188 	N209 	3

# New constraints from notor alphabets:
HelixConstraint 	N283 	T297 	1
Hbond		 	H255.O 	D258.N 	0.3
StrandConstraint 	I269 	L271 	1


# New constraints to orient helix L85-F99

Hbond N53.ND2	E88.OE1		0.2
Constraint	A92.CB	F16.CB	0	7	9	1.0
Constraint	A92.CB	F50.CB	0	7	9	1.0
Constraint	I95.CB	F16.CB	0	7	9	1.0
Constraint	I95.CB	F50.CB	0	7	9	1.0