CreatePredAlphaCost pred_alpha2k alpha11 T0272.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0272.t04.alpha.rdb 2 alpha alpha_prev sum

SetCost wet6.5 5 near_backbone 5 way_back 5 dry5 15 dry6.5 20 dry8 15 dry12 5 \
	phobic_fit 2 \
	sidechain 1 \
	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 5 \
	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.

StrandConstraint	L3	V7	6.988
HelixConstraint 	S12	D18	16.745
HelixConstraint 	Y23	A32	6.497
StrandConstraint	L45	R47	6.245
StrandConstraint	V58	Q62	8.467
StrandConstraint	Q78	F80	6.383
StrandConstraint	R94	A101	16.478

#include T0272.t04.dssp-ehl2.constraints
include T0272.t04.dssp-ebghstl.constraints
include T0272.t04.stride-ebghtl.constraints
include T0272.t04.str2.constraints
include T0272.t04.alpha.constraints
#include T0272.t04.bys.constraints

# some sheets
SheetConstraint L95  R100	V68  T63 	hbond 
# from t2k.thin-35
Constraint V61.CB F85.CB -10. 7.0 12.0 0.354578	bonus
Constraint E38.CB V61.CB -10. 7.0 12.0 0.346054	bonus
Constraint D18.CB A104.CB -10. 7.0 12.0  0.34441	bonus
Constraint E39.CB L64.CB -10. 7.0 12.0 0.343595	bonus
Constraint Q62.CB V79.CB -10. 7.0 12.0 0.343595	bonus
Constraint V79.CB R98.CB -10. 7.0 12.0 0.341979	bonus
Constraint L37.CB W46.CB -10. 7.0 12.0 0.341178	bonus
Constraint W46.CB L64.CB -10. 7.0 12.0  0.33959	bonus
Constraint R98.CB K105.CB -10. 7.0 12.0  0.33959	bonus
Constraint V59.CB A77.CB -10. 7.0 12.0  0.33802	bonus
Constraint R17.CB R94.CB -10. 7.0 12.0 0.337241	bonus
Constraint D18.CB R94.CB -10. 7.0 12.0 0.337241	bonus
Constraint V79.CB K105.CB -10. 7.0 12.0 0.337241	bonus