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 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 8  backbone_clashes 2 \
	break 15  \
	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

// 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	0.627
HelixConstraint 	G50	K58	0.674
HelixConstraint 	P81	A91	0.7067
# HelixConstraint 	Y158	F160	0.651

StrandConstraint	A3	Y7	0.6205
StrandConstraint	H12	R15	0.7029
StrandConstraint	F42	S45	0.9165
StrandConstraint	P64	N69	0.6104
StrandConstraint	E96	A107	0.6157
StrandConstraint	A113	V119	0.6461
StrandConstraint	M127	V134	0.685
StrandConstraint	V137	R143	0.6002
StrandConstraint	G146	V149	0.7412
StrandConstraint	C173	I177	0.6447
StrandConstraint	Y189	V191	0.6917
StrandConstraint	K196	A201	0.7313
StrandConstraint	K212	F216	0.6875
StrandConstraint	I220	K224	0.6294
StrandConstraint	A229	N234	0.6836
StrandConstraint	L241	G243	0.6972


#initial hairpin
SheetConstraint A4 K8   	I16 H12	hbond V6	3.0

#parallel strands	(From try6-opt2)
SheetConstraint F42 G47 	P64 N69	hbond I43	5.0


# hairpins
SheetConstraint P101 M108	A118 V111 hbond M108	1.0
SheetConstraint I128 V134	R143 V137	hbond L132	4.0


SheetConstraint Q211 F216	S225 I220		2.0
SheetConstraint E219 E223	K233 A229		2.0


# From mutual information constraints:
# file generated by validate2rr
# using the NN104-40n40all.net network
Constraint P165.CB I175.CB -10. 7.0 12.0 0.534
Constraint D145.CB Y158.CB -10. 7.0 12.0 0.489
Constraint L76.CB P165.CB -10. 7.0 12.0 0.454
Constraint F160.CB V245.CB -10. 7.0 12.0 0.445
Constraint F160.CB F184.CB -10. 7.0 12.0 0.439
Constraint A118.CB Y158.CB -10. 7.0 12.0 0.436
Constraint F160.CB P178.CB -10. 7.0 12.0 0.427
Constraint C144.CB F160.CB -10. 7.0 12.0 0.427
Constraint F160.CB K187.CB -10. 7.0 12.0 0.424
Constraint I52.CB T151.CB -10. 7.0 12.0 0.424
Constraint F160.CB G185.CA -10. 7.0 12.0 0.407
Constraint P165.CB V190.CB -10. 7.0 12.0 0.404
Constraint L75.CB Y158.CB -10. 7.0 12.0 0.404
Constraint L53.CB Y158.CB -10. 7.0 12.0 0.401
Constraint I142.CB F160.CB -10. 7.0 12.0 0.398
Constraint L76.CB F160.CB -10. 7.0 12.0 0.398
Constraint P178.CB K187.CB -10. 7.0 12.0 0.395
Constraint A159.CB I177.CB -10. 7.0 12.0 0.392