CreatePredAlphaCost pred_alpha2k alpha11 T0241.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0241.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

// 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.

HelixConstraint 	Y8	L16	1
HelixConstraint 	L25	L30	1
HelixConstraint 	Y93	K103	1
HelixConstraint 	Q136	K142	1
HelixConstraint 	Q223	S234	1

StrandConstraint	V4	F6	0.3
StrandConstraint	E45	M49	1
StrandConstraint	K52	I56	1
StrandConstraint	L62	E64	1
StrandConstraint	F73	H78	1
# StrandConstraint	F110	T126	0.6689
StrandConstraint	V109	L115	1
StrandConstraint	M121	T126	1
StrandConstraint	G154	F159	1
StrandConstraint	L175	I178	0.5
StrandConstraint	H187	D194	01
StrandConstraint	A196	S201	1
StrandConstraint	E205	Q209	1


SheetConstraint M46 M49	Q55 K52	hbond I47
SheetConstraint Y54 D57	E64 K61	hbond Q55


SheetConstraint H174 I178	L191 H187