CreatePredAlphaCost pred_alpha2k alpha11 T0202.t2k.alpha.rdb 2 alpha alpha_prev sum 
CreatePredAlphaCost pred_alpha04 alpha11 T0202.t04.alpha.rdb 2 alpha alpha_prev sum 

SetCost wet6.5 9 near_backbone 3 way_back 3 dry5 10 dry6.5 10 dry8 10 dry12 5 \
	phobic_fit 4 \
	sidechain 6 \
	bystroff 5 \
	soft_clashes 8  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 0.4 \
	hbond_geom_beta_pair 1.2

// 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 T0202.t2k.dssp-ehl2.constraints
HelixConstraint 	K21	V27	10
HelixConstraint 	G50	K58	10
HelixConstraint 	P81	A91	10
HelixConstraint 	Y158	F160	0.1

StrandConstraint	A3	Y7	8
StrandConstraint	H12	R15	8
StrandConstraint	F42	S45	8
StrandConstraint	P64	N69	8
StrandConstraint	E96	F100	8
StrandConstraint	V103	A107	8
StrandConstraint	A113	V119	8
StrandConstraint	M127	V134	8
StrandConstraint	V137	R143	8
StrandConstraint	G146	V149	8
StrandConstraint	C173	I177	8
StrandConstraint	Y189	V191	8
StrandConstraint	K196	A201	8
StrandConstraint	I205	A208	1
StrandConstraint	K212	F216	8
StrandConstraint	I220	K224	8
StrandConstraint	A229	N234	8
StrandConstraint	L241	G243	8


#initial hairpin
SheetConstraint A3 Y7   	I16 H12	hbond V5	6	#s1 ^v s2

SheetConstraint P101 M108	A118 V111 hbond M108	4	# s6 ^v s7

SheetConstraint I128 V134	R143 V137 hbond L132	4	# s8 ^v s9

SheetConstraint E219 E223	K233 A229 hbond F232	6	# s16 ^v s17
SheetConstraint Q211 F216	S225 I220 hbond D215	6	# s15 ^v s16
SheetConstraint Q211 F216	F42 G47   hbond V44	5	# s15 || s3
SheetConstraint F42 G47 	P64 N69	  hbond I43	6	# s3 || s4
SheetConstraint	P64 N69		Q152 F147 hbond I65	5	# s4 ^v s10
SheetConstraint F147 T151	F174 P178 hbond A150	6	# s10 || s11

# From mutual information constraints:
# file generated by validate2rr
# using the /projects/compbio/experiments/protein-predict/casp6/networks/NN134-90n70err.net.6 network
Constraint P165.CB I175.CB -10. 7.0 12.0	0.1
Constraint D145.CB Y158.CB -10. 7.0 12.0 	0.1
Constraint L76.CB P165.CB -10. 7.0 12.0 	0.1
Constraint F160.CB V245.CB -10. 7.0 12.0 	0.1
Constraint F160.CB F184.CB -10. 7.0 12.0 	0.1
Constraint A118.CB Y158.CB -10. 7.0 12.0 	0.1
Constraint F160.CB P178.CB -10. 7.0 12.0 	0.1
Constraint C144.CB F160.CB -10. 7.0 12.0 	0.1
Constraint F160.CB K187.CB -10. 7.0 12.0 	0.08
Constraint I52.CB T151.CB -10. 7.0 12.0 	0.08
Constraint F160.CB G185.CA -10. 7.0 12.0 	0.08
Constraint P165.CB V190.CB -10. 7.0 12.0 	0.08
Constraint L75.CB Y158.CB -10. 7.0 12.0 	0.08
Constraint L53.CB Y158.CB -10. 7.0 12.0 	0.08
Constraint I142.CB F160.CB -10. 7.0 12.0 	0.07
Constraint L76.CB F160.CB -10. 7.0 12.0 	0.07
Constraint P178.CB K187.CB -10. 7.0 12.0 	0.07
Constraint A159.CB I177.CB -10. 7.0 12.0 	0.07


# bring conserved ASP together (catalytic triad??)

Constraint D49.CG	D217.CG		-10 6.0	9.0	5
Constraint D145.CG	D217.CG		-10 6.0	9.0	5
Constraint D49.CG	D145.CG		-10 6.0	9.0	5