#
# Need to adjust this part, not optimized yet
#
SetCost wet6.5 3 near_backbone 3 way_back 3 dry5 5 dry6.5 6 dry8 5 dry12 2 \
	phobic_fit 4 \
	sidechain 6 \
	bystroff 5 \
	soft_clashes 10  backbone_clashes 2 \
	break 10  \
	pred_alpha2 5 \
	constraints 10 \
	hbond_geom 0.1 \
	hbond_geom_backbone 0.1 \
	hbond_geom_beta 1 \
	hbond_geom_beta_pair 2

// 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,
//	ssbond, hbond, or just arbitrary pairs of atoms.

# From T0201.t04.dssp-ehl2.constraints
StrandConstraint	K3	V4	0.7391
StrandConstraint	F10	T14	0.6307
HelixConstraint 	C23	E40	0.6964
StrandConstraint	Y51	F56	0.6428
HelixConstraint 	N61	K80	0.6419
StrandConstraint	I85	I90	0.7018

#From T0204.t04.str2.constraints
StrandConstraint	K3	V4	0.795
StrandConstraint	F10	V13	0.709
HelixConstraint 	C23	A39	0.719
StrandConstraint	Y51	F56	0.713
HelixConstraint 	C62	K80	0.613
StrandConstraint	R86	I90	0.624

# make first hairpin
Constraint	K3.CB	E12.CB	4.5	5.25	6	1.0
Constraint	V4.CB	F11.CB	4.5	5.25	6	1.0
Constraint	T5.CB	F10.CB	4.5	5.25	6	1.0
# Hbond	I2.O	V13.N	1.0
# Hbond	V4.N	F11.O	1.0
# Hbond	V4.O	F11.N	1.0
# Hbond	V6.N	S9.O	1.0
# Hbond	V6.O	S9.N	1.0

# make second hairpin
Constraint K44.CB	K55.CB	4.5	5.25	6	1.0
Constraint I45.CB	V54.CB	4.5	5.25	6	1.0
Constraint K46.CB	K53.CB	4.5	5.25	6	1.0
Constraint K47.CB	L52.CB	4.5	5.25	6	1.0
# Hbond	K44.N	K55.O	1.0
# Hbond	K44.O	K55.N	1.0
# Hbond	K46.N	K53.O	1.0
# Hbond	K46.O	K53.N	1.0
# Hbond	E48.N	Y51.O	1.0
# Hbond	E48.O	Y51.N	1.0

# make his and cys close, to try to form metal-binding site.

Constraint	C23.SG	H16.NE2		3	4.5	7	4.0
Constraint	C23.SG	C62.SG		3	4.5	7	1.0
Constraint	C23.SG	H32.NE2		3	4.5	7	1.0

Constraint	H16.NE2	C62.SG		3	4.5	7	1.0
Constraint	H16.NE2	H32.NE2		3	4.5	7	1.0

Constraint	C62.SG	H32.NE2		3	4.5	7	0.5


# cluster conserved hydrophobics

Constraint	I2.CD1	L77.CG		0	4	8	1.0
Constraint	I2.CD1	F81.CZ		0	4	8	1.0
Constraint	L77.CG	F81.CZ		0	4	8	1.0