CreatePredAlphaCost pred_alpha2k alpha11 T0216.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0216.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 \
	bonus_constraints 10 \
	hbond_geom 0.1 \
	hbond_geom_backbone 0.1 \
	hbond_geom_beta 0.4 \
	hbond_geom_beta_pair 1

// 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.

include T0216.t2k.dssp-ehl2.constraints
include T0216.t2k.dssp-ebghstl.constraints
include T0216.t2k.stride-ebghtl.constraints
include T0216.t2k.str2.constraints
include T0216.t2k.alpha.constraints
include T0216.t2k.bys.constraints

include T0216.t04.dssp-ehl2.constraints
include T0216.t04.dssp-ebghstl.constraints
include T0216.t04.stride-ebghtl.constraints
include T0216.t04.str2.constraints
include T0216.t04.alpha.constraints
include T0216.t04.bys.constraints

# using the RR constraints and fixing a helix
HelixConstraint	N247 L232	10
# Constraint M236.CB R330.CB 5.0 8.0 12.0	10
# Constraint P241.CB P331.CB 5.0 8.0 12.0	10
# Constraint S374.CB F400.CB 5.0 8.0 14.0	10
# Constraint G361.CA N399.CB 5.0 8.0 14.0	10

# a large set of RR constraints for try4
Constraint L235.CB A245.CB -10. 7.0 12.0 0.926
Constraint G361.CA N399.CB -10. 7.0 12.0 0.91
Constraint D272.CB K295.CB -10. 7.0 12.0 0.883
Constraint R330.CB I421.CB -10. 7.0 12.0 0.862
Constraint M350.CB V382.CB -10. 7.0 12.0 0.85
Constraint P241.CB A422.CB -10. 7.0 12.0 0.847
Constraint E360.CB K378.CB -10. 7.0 12.0 0.841
Constraint E246.CB L375.CB -10. 7.0 12.0 0.841
Constraint F373.CB G398.CA -10. 7.0 12.0 0.837
Constraint G361.CA A377.CB -10. 7.0 12.0 0.834
Constraint E237.CB R330.CB -10. 7.0 12.0 0.831
Constraint E372.CB N399.CB -10. 7.0 12.0 0.815
Constraint P241.CB I421.CB -10. 7.0 12.0 0.811
Constraint S244.CB P331.CB -10. 7.0 12.0 0.809
Constraint A245.CB I329.CB -10. 7.0 12.0 0.808
Constraint F373.CB N399.CB -10. 7.0 12.0 0.79
Constraint P241.CB P331.CB -10. 7.0 12.0 0.788
Constraint P241.CB R330.CB -10. 7.0 12.0 0.782
Constraint M227.CB V359.CB -10. 7.0 12.0 0.78
Constraint M238.CB R330.CB -10. 7.0 12.0 0.778
Constraint E360.CB F376.CB -10. 7.0 12.0 0.772
Constraint E360.CB G398.CA -10. 7.0 12.0 0.765
Constraint I270.CB L334.CB -10. 7.0 12.0 0.759
Constraint M236.CB R330.CB -10. 7.0 12.0 0.752
Constraint I240.CB I421.CB -10. 7.0 12.0 0.75
Constraint S244.CB R330.CB -10. 7.0 12.0 0.743
Constraint A245.CB V332.CB -10. 7.0 12.0 0.736
Constraint E360.CB I369.CB -10. 7.0 12.0 0.729
Constraint E360.CB A377.CB -10. 7.0 12.0 0.727
Constraint L233.CB I396.CB -10. 7.0 12.0 0.724
Constraint K378.CB I394.CB -10. 7.0 12.0 0.722
Constraint A377.CB I394.CB -10. 7.0 12.0 0.72
Constraint G361.CA K378.CB -10. 7.0 12.0 0.717
Constraint L33.CB A377.CB -10. 7.0 12.0 0.71
Constraint I240.CB P331.CB -10. 7.0 12.0 0.7
Constraint M236.CB I421.CB -10. 7.0 12.0 0.7
Constraint I243.CB R330.CB -10. 7.0 12.0 0.695
Constraint D234.CB I396.CB -10. 7.0 12.0 0.695
Constraint N247.CB S374.CB -10. 7.0 12.0 0.69
Constraint I240.CB R330.CB -10. 7.0 12.0 0.687
Constraint V225.CB V359.CB -10. 7.0 12.0 0.682
Constraint I240.CB A422.CB -10. 7.0 12.0 0.679
Constraint E237.CB L375.CB -10. 7.0 12.0 0.679
Constraint E360.CB N399.CB -10. 7.0 12.0 0.671
Constraint I329.CB T420.CB -10. 7.0 12.0 0.671
Constraint E237.CB P331.CB -10. 7.0 12.0 0.671
Constraint M236.CB L334.CB -10. 7.0 12.0 0.671
Constraint L233.CB R330.CB -10. 7.0 12.0 0.671
Constraint G361.CA G398.CA -10. 7.0 12.0 0.669
Constraint G371.CA N399.CB -10. 7.0 12.0 0.666
Constraint M236.CB P331.CB -10. 7.0 12.0 0.666
Constraint L232.CB I396.CB -10. 7.0 12.0 0.666