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 50  \
	pred_alpha2k 8 \
	pred_alpha04 8 \
	bonus_constraints 15 \
	hbond_geom 0.2 \
	hbond_geom_backbone 0.8 \
	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	20
HelixConstraint 	E39	L69	10
HelixConstraint 	P76	L107	20
HelixConstraint 	P115	A138	10
HelixConstraint 	V142	M171	10
HelixConstraint 	V177	V208	10


# constraints introduced from the new RR predictions
# specifically the T0198.280.rr.constraints file
 
Constraint D152.CB E191.CB -10. 7.0 12.0 0.824
Constraint F12.CB A63.CB -10. 7.0 12.0 0.819
Constraint G20.CA L134.CB -10. 7.0 12.0 0.817
Constraint D156.CB D195.CB -10. 7.0 12.0 0.745
Constraint A63.CB E185.CB -10. 7.0 12.0 0.741
Constraint L5.CB A63.CB -10. 7.0 12.0 0.732
Constraint L166.CB L183.CB -10. 7.0 12.0 0.729
Constraint N2.CB I73.CB -10. 7.0 12.0 0.722
Constraint D152.CB Y206.CB -10. 7.0 12.0 0.715
Constraint L5.CB L166.CB -10. 7.0 12.0 0.71
Constraint A63.CB E191.CB -10. 7.0 12.0 0.697
Constraint N2.CB P76.CB -10. 7.0 12.0 0.695
Constraint V155.CB D195.CB -10. 7.0 12.0 0.687
Constraint S145.CB V201.CB -10. 7.0 12.0 0.677
# Constraint A19.CB V86.CB -10. 7.0 12.0 0.666
Constraint N2.CB G74.CA -10. 7.0 12.0 0.661
Constraint E191.CB Y206.CB -10. 7.0 12.0 0.642
# Constraint A19.CB A94.CB -10. 7.0 12.0 0.642
Constraint N2.CB S71.CB -10. 7.0 12.0 0.642
Constraint M129.CB E191.CB -10. 7.0 12.0 0.633
Constraint V66.CB E191.CB -10. 7.0 12.0 0.633
Constraint Q60.CB L69.CB -10. 7.0 12.0 0.633
Constraint E49.CB D95.CB -10. 7.0 12.0 0.628
Constraint L77.CB E191.CB -10. 7.0 12.0 0.625
Constraint F12.CB L166.CB -10. 7.0 12.0 0.625
Constraint N2.CB L77.CB -10. 7.0 12.0 0.616
Constraint M129.CB A194.CB -10. 7.0 12.0 0.602


# 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