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_>7->10
SetCost wet6.5 3 near_backbone 10 way_back 10 dry5 5 dry6.5 6 dry8 5 dry12 2 \
	phobic_fit 3 \	#turn back down to 3
	sidechain 3 \
	bystroff 5 \
	soft_clashes 15  backbone_clashes 2 \
	break 30  \
	pred_alpha2k 2 \	#looks more like the str2 predictions (t2k & t04)
	pred_alpha04 2 \	#turn back down to 2
	constraints 20 \	#reduce back to 20 (from 30)
	hbond_geom 5 \		#up 1->5
	hbond_geom_backbone 1 \
	hbond_geom_beta 5 \
	hbond_geom_beta_pair 2	#already formed; drop down, 10->2

#from try3-opt2.scwrl.helices
HelixConstraint I2	H18		5	#turn up the helix weight: 3->5
HelixConstraint S21	H35		5
HelixConstraint F43	K58		5
HelixConstraint A63	A72		5
HelixConstraint V81	N100	5
HelixConstraint A109	Q117	5
HelixConstraint P131	K138	5
HelixConstraint F136	V148	5
HelixConstraint L157	F162	5
HelixConstraint F162	I169	5
HelixConstraint A203	L210	5
HelixConstraint L210	K220	5
HelixConstraint A228	A234	5
HelixConstraint P244	Q250	5
HelixConstraint L248	N265	5
HelixConstraint D272	D287	5
HelixConstraint D287	N294	5

#reduce 5->3
# from T0248.t04.dssp-ehl2.constraints
StrandConstraint	V177	F180	3
StrandConstraint	Q186	L190	3
StrandConstraint	F188	K185	3	bonus	#dubious

#8 is too high; it breaks helices to satisfy these; drop to 4
#doh. forgot to put weights here! trying a weight of 8 each...
# trying to pack the helices! 
# switch distance to "3.0 7.0 5" later
Constraint F172.CB F84.CB -10. 7.0 14.0    4
Constraint I111.CB L190.CB -10. 7.0 14.0   4
Constraint L12.CB L25.CB -10. 7.0 14.0     4
Constraint F8.CB F29.CB -10. 7.0 14.0      4

#drop 10->5; already formed
# from try1-opt2.sheets - satisfied nicely in try4
SheetConstraint K187 L192	Q200 F195	hbond F188	5

# conjectured
SheetConstraint	V177 F180	F188 K185	5	#up 1->5, make bonus


//I'll try putting the rr constraints back in; they were there in try3
# 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