CreatePredAlphaCost pred_alpha2k alpha11 T0226.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0226.t04.alpha.rdb 2 alpha alpha_prev sum

SetCost wet6.5 3 near_backbone 3 way_back 3 dry5 5 dry6.5 6 dry8 5 dry12 2 \
	phobic_fit 2 \
	sidechain 6 \
	bystroff 5 \
	soft_clashes 10  backbone_clashes 2 \
	break 20  \
	pred_alpha2k 3 \
	pred_alpha04 3 \
	constraints 10 \
	hbond_geom 1 \
	hbond_geom_backbone 1 \
	hbond_geom_beta 4 \
	hbond_geom_beta_pair 15

// 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.

StrandConstraint	Y10	V12	6
StrandConstraint	L17	E20	4
StrandConstraint	H39	G43	6
HelixConstraint 	A50	S54	4
StrandConstraint	L65	E69	6
HelixConstraint 	D73	A77	6
HelixConstraint 	A81	A84	3
StrandConstraint	A89	P98	1
StrandConstraint	R90	V94	1
StrandConstraint	E101	I104	5
HelixConstraint 	P111	L119	6
HelixConstraint 	E125	R141	6
HelixConstraint 	P152	L161	6
StrandConstraint	L166	Y168	6
HelixConstraint 	R173	V186	6
StrandConstraint	L216	G222	6
HelixConstraint 	A228	E235	6
StrandConstraint	A242	V244	4
HelixConstraint 	R251	Y273	6
HelixConstraint 	H280	E288	6

# from try1-opt2
# SheetConstraint A40 L42  	F66 L68  	hbond A41

# from align1
# SheetConstraint A34 G37         A81 A84         hbond Y35       5.0
# SheetConstraint A41 G43         A84 T86         hbond A41       5.0
# SheetConstraint L83 T86         E101 I104       hbond A84       5.0
# SheetConstraint L164 F167       P215 A218       hbond L166      5.0
# SheetConstraint P165 F167       L190 L192       hbond F167      5.0
 
# from decoys/try2-opt2.sheets
SheetConstraint R14 G16         L21 L19         hbond G16       5.0
SheetConstraint P38 L42         L65 E69         hbond H39       5.0 
SheetConstraint P38 G43         A89 V94         hbond A40       5.0
# SheetConstraint P215 V219       A242 A246       hbond L216      5.0