CreatePredAlphaCost pred_alpha2k alpha11 T0201.t2k.alpha.rdb 2 alpha alpha_prev sum 
CreatePredAlphaCost pred_alpha04 alpha11 T0201.t04.alpha.rdb 2 alpha alpha_prev sum 

#
# 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_alpha2k 5 \
	pred_alpha04 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.

HelixConstraint C23 E40		1.0
HelixConstraint N61 K80		1.0

StrandConstraint M1	T7		1.0
StrandConstraint F10	T14		1.0
StrandConstraint K44 	E48		0.5
StrandConstraint Y51	F56		1.0
StrandConstraint I85	D91		1.0


#
# make his and cys close, to try to form metal-binding site. Also
#  try throwing in D19
#
Constraint      C23.SG  H16.NE2         3       4.5     7       2.0
Constraint      C23.SG  H32.NE2         3       4.5     7       2.0
Constraint      H16.NE2 H32.NE2         3       4.5     7       2.0
Constraint      D19.CG  H16.NE2         3       4.5     7       1.0 
Constraint      D19.CG  C23.SG          3       4.5     7       1.0
Constraint      D19.CG  H32.NE2         3.5     5.0     9       1.0


# constraints to put the helices together
Constraint      L74.CG	L29.CG        -10 4 10       0.1
Constraint      L37.CG  V66.CB        -10 4 10       0.1

# constraints to pack the helices against the sheet
Constraint	V4.CB	V33.CB		-10 4 10	1
Constraint	V13.CB	L29.CB		-10 4 10	0.5

Constraint	L52.CG	M70.CB		-10 4 10	0.5
Constraint	V54.CB	V66.CB		-10 4 10	0.5


# Strand 1 and Strand 2, (Anti-parallel), and first hairpin
SheetConstraint V4 T7     V13 F10   	hbond T5	10

# Strand 1 and Strand 5 (Parallel)
SheetConstraint I2 T7	I85 I90		hbond V6	10

# Strand 3 and Strand 5 (Anti-parallel)
SheetConstraint I45 E48		V89 R86	hbond I45	10

# Strand 3 and Strand 4 (Anti-parallel), and second hairpin
SheetConstraint K44 E48   K55 Y51   hbond K46	10