#
# 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	(may want to bulge)
Constraint	V4.CB	V13.CB	4.5	5.58	6	1.0
Constraint	T5.CB	E12.CB	4.5	5.02	6	1.0
Constraint	V6.CB	F11.CB	4.5	5.58	6	1.0
Hbond 	T5.N	E12.O	1.0
Hbond 	T5.O	E12.N	1.0
Hbond 	T7.N	F10.O	1.0
Hbond 	T7.O	F10.N	1.0

# make second hairpin
Constraint K44.CB	K55.CB	4.5	5.02	6	1.0
Constraint I45.CB	V54.CB	4.5	5.58	6	1.0
Constraint K46.CB	K53.CB	4.5	5.02	6	1.0
Constraint K47.CB	L52.CB	4.5	5.58	6	1.0
Hbond	K44.N	K55.O	0.5
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	0.5

# 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	H32.NE2		3	4.5	7	1.0
Constraint	H16.NE2	H32.NE2		3	4.5	7	1.0
# Don't force C62 in yet---still questionable
# Constraint	C23.SG	C62.SG		3	4.5	7	1.0
# Constraint	H16.NE2	C62.SG		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


#try forming parallel connection S1-S5

Constraint	I2.CB	I85.CB		4.8	5.14	5.5	1.0
Constraint	K3.CB	R86.CB		4.8	5.14	5.5	1.0
Constraint	V4.CB	V87.CB		4.8	5.14	5.5	1.0
Constraint	T5.CB	E88.CB		4.8	5.14	5.5	1.0
Constraint	V6.CB	V89.CB		4.8	5.14	5.5	1.0


#try forming antiparallel connection S3-S5

Constraint	K47.CB	I85.CB		4.8	5.14	5.5	1.0
Constraint	K46.CB	R86.CB		4.8	5.14	5.5	1.0
Constraint	I45.CB	V87.CB		4.8	5.14	5.5	1.0
Constraint	K44.CB	E88.CB		4.8	5.14	5.5	1.0
Constraint	A43.CB	V89.CB		4.8	5.14	5.5	1.0
Hbond	A43.N	V89.O	1.0
Hbond	A43.O	V89.N	1.0
Hbond	I45.N	V87.O	1.0
Hbond	I45.O	V87.N	1.0