CreatePredAlphaCost pred_alpha2k alpha11 T0240.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0240.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 30  \
	pred_alpha2k 1 \
	pred_alpha04 5 \
	constraints 10 \
	hbond_geom 3 \
	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.

# include T0240.t2k.dssp-ehl2.constraints
# include T0240.t2k.dssp-ebghstl.constraints
# include T0240.t2k.stride-ebghtl.constraints
# include T0240.t2k.str2.constraints
# include T0240.t2k.alpha.constraints
# include T0240.t2k.bys.constraints

include T0240.t04.dssp-ehl2.constraints
include T0240.t04.dssp-ebghstl.constraints
include T0240.t04.stride-ebghtl.constraints
include T0240.t04.str2.constraints
include T0240.t04.alpha.constraints
include T0240.t04.bys.constraints

# using the rr constraints for driving the structure towards a 1tolA core

# file generated by validate2rr
# based on 280 inputs
# using the NN280-240n300.net.28 network
# limited to score of .30 or greater.
# The score is an approximation of the probability
Constraint P12.CB Y66.CB -10. 7.0 14.0 0.856
Constraint F31.CB M61.CB -10. 7.0 14.0 0.817
Constraint P12.CB W64.CB -10. 7.0 14.0 0.727
Constraint I23.CB M52.CB -10. 7.0 14.0 0.669
Constraint P15.CB I44.CB -10. 7.0 14.0 0.669
Constraint K30.CB Q43.CB -10. 7.0 14.0 0.596 bonus
Constraint L7.CB Y66.CB -10. 7.0 14.0 0.591 bonus
Constraint Q13.CB R65.CB -10. 7.0 14.0 0.558 bonus
Constraint V29.CB V57.CB -10. 7.0 14.0 0.495 bonus
Constraint A18.CB M52.CB -10. 7.0 14.0 0.489 bonus
Constraint I44.CB V57.CB -10. 7.0 14.0 0.483 bonus