CreatePredAlphaCost pred_alpha2k alpha11 T0198.t2k.alpha.rdb 2 alpha alpha_prev min
CreatePredAlphaCost pred_alpha04 alpha11 T0198.t04.alpha.rdb 2 alpha alpha_prev min


SetCost wet6.5 3 near_backbone 3 way_back 3 dry5 15 dry6.5 10 dry8 10 dry12 10 \
	phobic_fit 4 \
	sidechain 2 \
	bystroff 5 \
	soft_clashes 10  backbone_clashes 2 \
	break 20  \
	pred_alpha2k 8 \
	pred_alpha04 8 \
	constraints 15 \
	hbond_geom 0.2 \
	hbond_geom_backbone 0.5 \
	hbond_geom_beta 0.1 \
	hbond_geom_beta_pair 0.1

# The beta cost functions were down-weighted for this alpha-protein

// 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...

HelixConstraint 	R3	E36	60
HelixConstraint 	E39	L69	30
HelixConstraint 	P76	L107	60
HelixConstraint 	P115	A138	30
HelixConstraint 	V142	M171	30
HelixConstraint 	V177	V208	30


# loose constraints for up-down bundle
# These should be made more specific once the bundles start forming.
constraint	F12.CZ	L69.CG	-10	4	15	1
constraint	L34.CG	V104.CB	-10	4	15	1
constraint	L77.CG	F137.CZ	-10	4	15	1
constraint	I119.CB	M170.CB	-10	4	15	0.5
constraint	F137.CZ	I200.CB	-10	4	15	0.2

# constraints from the robetta best-scoring model
# for the first 4 helices of the bundle

constraint	S33.CB	A42.CB	-7	4	7	1
constraint	L34.CB	L41.CB	-7	4	7	1
constraint	M26.CB	E49.CB	-7	4	7	1

constraint	V66.CB	P76.CB	-7	4	7	1
constraint	A63.CB	V80.CB	-7	4	7	1

constraint	E7.CB	K75.CB	-7	4	7	1
constraint	L5.CB	L78.CB	-7	4	7	1

constraint	A87.CB	S127.CB	-7	4	7	1				


# constraints from George's neural net:
Constraint D152.CB E191.CB -10. 7.0 12.0 0.605
Constraint A63.CB D152.CB -10. 7.0 12.0 0.517
Constraint D152.CB D195.CB -10. 7.0 12.0 0.489
Constraint G68.CA D152.CB -10. 7.0 12.0 0.472
Constraint M129.CB D152.CB -10. 7.0 12.0 0.457
Constraint L77.CB D152.CB -10. 7.0 12.0 0.457
Constraint P72.CB D152.CB -10. 7.0 12.0 0.457

Constraint A63.CB E185.CB -10. 7.0 12.0 0.531
Constraint A63.CB L77.CB -10. 7.0 12.0 0.457

Constraint D156.CB E191.CB -10. 7.0 12.0 0.531


Constraint G20.CA L134.CB -10. 7.0 12.0 0.525
Constraint A82.CB E191.CB -10. 7.0 12.0 0.495
Constraint S71.CB L89.CB -10. 7.0 12.0 0.46