# CreatePredAlphaCost pred_alpha2k alpha11 T0223.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0223.t04.alpha.rdb 2 alpha alpha_prev sum

SetCost wet6.5 10 near_backbone 3 way_back 3 dry5 10 dry6.5 20 dry8 10 dry12 5 \
	phobic_fit 2 \
	sidechain 6 \
	bystroff 5 \
	soft_clashes 20  backbone_clashes 2 \
	break 50  \
	pred_alpha04 6 \
	constraints 10 \
	hbond_geom 1 \
	hbond_geom_backbone 1 \
	hbond_geom_beta 4 \
	hbond_geom_beta_pair 10

// 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,
//	sheet constraints, ssbonds, hbonds, or just arbitrary pairs of atoms.

# from T0223.t04.dssp-ehl2.constraints
HelixConstraint 	I3	N9	0.7568
HelixConstraint 	V13	L17	0.6004
HelixConstraint 	E23	E30	0.6851
HelixConstraint 	T38	K40	0.6503
HelixConstraint 	F62	A81	0.6266
HelixConstraint 	P131	L142	0.625
HelixConstraint 	D170	L180	0.6349

StrandConstraint	S52	A56	0.7108
StrandConstraint	T86	M89	0.7093
StrandConstraint	Y99	F103	0.6766
StrandConstraint	W152	Y156	0.6738
StrandConstraint	E160	C162	0.6145
StrandConstraint	T199	L204	0.7256

# from decoys/align2.sheets
SheetConstraint P51 A56	G104 Y99	hbond S52	1.0
SheetConstraint F84 A90	Y105 Y99	hbond G85	1.0

# 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 .30 or greater.
# The score is an approximation of the probability
Constraint V76.CB T86.CB -10. 7.0 14.0 0.619
Constraint V25.CB Y105.CB -10. 7.0 14.0 0.599 
Constraint W88.CB Y99.CB -10. 7.0 14.0 0.489 
Constraint K39.CB R116.CB -10. 7.0 14.0 0.418
Constraint L79.CB F103.CB -10. 7.0 14.0 0.395 bonus
Constraint I75.CB I100.CB -10. 7.0 14.0 0.392 bonus
Constraint L41.CB Y156.CB -10. 7.0 14.0 0.381 bonus
Constraint A56.CB F103.CB -10. 7.0 14.0 0.372 bonus
Constraint A56.CB W88.CB -10. 7.0 14.0 0.356 bonus
Constraint Y68.CB Y99.CB -10. 7.0 14.0 0.353 bonus
Constraint R10.CB W88.CB -10. 7.0 14.0 0.339 bonus
Constraint V76.CB L171.CB -10. 7.0 14.0 0.331 bonus
Constraint V76.CB Y156.CB -10. 7.0 14.0 0.3 bonus
Constraint S52.CB F103.CB -10. 7.0 14.0 0.3 bonus