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 10 near_backbone 5 way_back 5 dry5 5 dry6.5 20 dry8 15 dry12 5 \
	phobic_fit 2 \
	sidechain 1 \
	bystroff 5 \
	soft_clashes 10  backbone_clashes 2 \
	break 30  \
	pred_alpha2k 2 \
	pred_alpha04 4 \
	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

# try straightening out that long strand!
# Constraint E67.CA I89.CA 50 60 200 2.0

# 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		# distinct
Constraint F31.CB M61.CB -10. 7.0 14.0 0.817		# distinct
# 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		# distinct
# 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		# distinct
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
# Constraint I44.CB F53.CB -10. 7.0 14.0 0.46 bonus
# Constraint Y14.CB I44.CB -10. 7.0 14.0 0.46 bonus
# Constraint V29.CB I44.CB -10. 7.0 14.0 0.439 bonus
# Constraint P12.CB A60.CB -10. 7.0 14.0 0.412 bonus
Constraint Q11.CB W64.CB -10. 7.0 14.0 0.404 bonus
Constraint Y66.CB V76.CB -10. 7.0 14.0 0.401 bonus
Constraint R65.CB I75.CB -10. 7.0 14.0 0.398 bonus
Constraint F31.CB F53.CB -10. 7.0 14.0 0.398 bonus
Constraint K28.CB I44.CB -10. 7.0 14.0 0.381 bonus
Constraint V39.CB W64.CB -10. 7.0 14.0 0.364 bonus
Constraint L7.CB W64.CB -10. 7.0 14.0 0.358 bonus
Constraint Q11.CB Y66.CB -10. 7.0 14.0 0.356 bonus
Constraint V57.CB T87.CB -10. 7.0 14.0 0.345 bonus
Constraint P49.CB G69.CA -10. 7.0 14.0 0.334 bonus
Constraint P12.CB P71.CB -10. 7.0 14.0 0.323 bonus
Constraint V27.CB A60.CB -10. 7.0 14.0 0.318 bonus
Constraint F31.CB E54.CB -10. 7.0 14.0 0.316 bonus
Constraint A6.CB V39.CB -10. 7.0 14.0 0.31 bonus
Constraint E24.CB I89.CB -10. 7.0 14.0 0.308 bonus
Constraint P12.CB G74.CA -10. 7.0 14.0 0.305 bonus
Constraint V39.CB E56.CB -10. 7.0 14.0 0.303 bonus
Constraint V27.CB V57.CB -10. 7.0 14.0 0.303 bonus
Constraint P4.CB Y66.CB -10. 7.0 14.0 0.303 bonus