CreatePredAlphaCost pred_alpha2k alpha11 T0226.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0226.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 10  backbone_clashes 2 \
	break 20  \
	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 1.5

// 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.

StrandConstraint	Y10	V12	6
StrandConstraint	L17	E20	4
StrandConstraint	H39	G43	6
HelixConstraint 	A50	S54	4
StrandConstraint	L65	E69	6
HelixConstraint 	D73	A77	6
HelixConstraint 	A81	A84	3
StrandConstraint	A89	P98	1
StrandConstraint	R90	V94	1
StrandConstraint	V102	I104	5
HelixConstraint 	P111	L119	6
HelixConstraint 	E125	R141	6
HelixConstraint 	P152	L161	6
StrandConstraint	L166	Y168	6
HelixConstraint 	R173	V186	6
StrandConstraint	A217	G222	6
HelixConstraint 	A228	E235	6
StrandConstraint	A242	V244	4
HelixConstraint 	R251	Y273	6
HelixConstraint 	H280	E288	6

# from try1-opt2
SheetConstraint A40 L42  	F66 L68  	hbond A41


# from align1
SheetConstraint A34 G37	A81 A84	hbond Y35
SheetConstraint A41 G43	A84 T86	hbond A41
SheetConstraint L83 T86	E101 I104	hbond A84
SheetConstraint L164 F167	P215 A218	hbond L166
SheetConstraint P165 F167	L190 L192	hbond F167