CreatePredAlphaCost pred_alpha2k alpha11 T0225.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0225.t04.alpha.rdb 2 alpha alpha_prev sum

SetCost wet6.5 3 near_backbone 3 way_back 3 dry5 5 dry6.5 6 dry8 5 dry12 2 \
	phobic_fit 2 \
	sidechain 6 \
	bystroff 5 \
	soft_clashes 20  backbone_clashes 2 \
	break 50  \
	pred_alpha2k 3 \
	pred_alpha04 3 \
	constraints 10 \
	hbond_geom 0.1 \
	hbond_geom_backbone 0.1 \
	hbond_geom_beta 0.4 \
	hbond_geom_beta_pair 1

// Add the following for extra-cellular proteins:
#	known_ssbond 0.5	# and put ssbond command in constraints file
#	maybe_ssbond 0.5

// For comparative modeling, increase weight of break and hbond_geom...

// put any constraints here, such as helix constraints, strand constraints,
//	sheet constraints, ssbonds, hbonds, or just arbitrary pairs of atoms.

# Helices from try1-opt2, trimmed back to predicted helices

HelixConstraint	Q11 G22
HelixConstraint V40 E49
HelixConstraint Y71 S91
HelixConstraint A124 L139
HelixConstraint F158 K167
HelixConstraint T185 D197
HelixConstraint W214 T225
HelixConstraint Y254 T260
HelixConstraint W267 Q279

# added manually
SheetConstraint K2 T6   	E26 T30		hbond I5
# from try1-opt2:
SheetConstraint K2 G7   	N53 C58 	hbond L4
SheetConstraint N53 N57 	A94 Q98 	hbond V55
SheetConstraint I96 T101 	Y143 T148 	hbond Q98
SheetConstraint P112 I113 	V250 L251 	hbond I113
SheetConstraint Y144 T148 	G202 C206 	hbond I145
SheetConstraint E171 V175 	K230 C234 	hbond L172
SheetConstraint Q178 G180 	K247 S249 	hbond V179
SheetConstraint V179 T181 	S213 I211 	hbond G180
SheetConstraint P182 T183 	W150 L151 	hbond T183