#carbon-copy of try3.costfcn
CreatePredAlphaCost pred_alpha2k alpha11 T0248.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0248.t04.alpha.rdb 2 alpha alpha_prev sum

#trying turning near_back and way_back up, from 3 to 6
SetCost wet6.5 3 near_backbone 6 way_back 6 dry5 5 dry6.5 6 dry8 5 dry12 2 \
	phobic_fit 3 \
	sidechain 4 \
	bystroff 5 \
	soft_clashes 10  backbone_clashes 2 \
	break 20  \
	pred_alpha2k 3 \	#looks more like the str2 predictions (t2k & t04)
	pred_alpha04 2 \
	constraints 20 \
	hbond_geom 1 \
	hbond_geom_backbone 1 \
	hbond_geom_beta 5 \
	hbond_geom_beta_pair 10

# from T0248.t04.dssp-ehl2.constraints, with dubious bits trimmed out
HelixConstraint 	N6	H18	5	#down, to free up this region
HelixConstraint 	Y22	Y32	5
HelixConstraint 	L40	Q57	5
HelixConstraint 	F60	L71	5	
HelixConstraint 	K78	L90	10
HelixConstraint 	H93	A104	10
HelixConstraint 	A108	Q117	10
//HelixConstraint 	M125	K134	10	#uncertain
HelixConstraint 	P139	L145	10	#shortened (V148 -> L145)
HelixConstraint 	S152	N167	10
HelixConstraint 	A203	L219	10
HelixConstraint 	N224	S238	10
HelixConstraint 	L248	L264	10
//HelixConstraint 	E273	L286	10	#uncertain


StrandConstraint	V177	F180	10
StrandConstraint	Q186	L190	10
StrandConstraint	F188	K185	2	#weakly predicted

# from try1-opt2.sheets
SheetConstraint K187 L192	Q200 F195	hbond F188	10

# conjectured
SheetConstraint	V177 F180	F188 K185	1

# file generated by validate2rr
# based on 280 inputs
# using the /projects/compbio/experiments/protein-predict/casp6/networks/NN280-240n300.net.28 network
# limited to score of .35 or greater or
# the best 10 scores
# The score is an approximation of the probability
Constraint L236.CB I262.CB -10. 7.0 12.0 0.752
Constraint I262.CB Y283.CB -10. 7.0 12.0 0.472
Constraint L236.CB Y283.CB -10. 7.0 12.0 0.454
Constraint M125.CB N167.CB -10. 7.0 12.0 0.407
Constraint L217.CB Y283.CB -10. 7.0 12.0 0.378
Constraint A234.CB Y283.CB -10. 7.0 12.0 0.372
Constraint V263.CB L277.CB -10. 7.0 12.0 0.364
Constraint L217.CB I262.CB -10. 7.0 12.0 0.329
Constraint A165.CB F227.CB -10. 7.0 12.0 0.329
Constraint K254.CB Y283.CB -10. 7.0 12.0 0.326