CreatePredAlphaCost pred_alpha2k alpha11 T0273.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0273.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 40  \
	pred_alpha2k 1 \
	pred_alpha04 5 \
	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.

# again these don't seem quite as strong as the t04
# include T0273.t2k.dssp-ehl2.constraints
# include T0273.t2k.dssp-ebghstl.constraints
# include T0273.t2k.stride-ebghtl.constraints
# include T0273.t2k.str2.constraints
# include T0273.t2k.alpha.constraints
# include T0273.t2k.bys.constraints

HelixConstraint 	E13 	L19 	6.757
HelixConstraint 	G46 	E62 	6.024
HelixConstraint 	E96 	A97 	6.288
HelixConstraint 	P124	R136	8.895

StrandConstraint	W28 	R30 	7.516	# s1
StrandConstraint	R35 	W37 	6.152	# s2
StrandConstraint	V67 	F69 	6.64	# s3
StrandConstraint	G74 	K76 	6.211	# s4
StrandConstraint	A87 	E91 	7.546	# s5
StrandConstraint	A113	V117	8.642	# s6
StrandConstraint	L141	V145	8.541	# s7
StrandConstraint	A151	R156	6.586	# s8
StrandConstraint	L162	E165	6.781	# s9
StrandConstraint	A180	L181	6.902

# include T0273.t04.dssp-ebghstl.constraints
# include T0273.t04.stride-ebghtl.constraints
include T0273.t04.str2.constraints
include T0273.t04.alpha.constraints
# include T0273.t04.bys.constraints

# my designed sheets...
SheetConstraint Q27  S31	V38  G34	hbond S31	10.0	# s1^vs2
SheetConstraint V67  D70 	F77  G74	hbond D70	10.0	# s3^vs4
SheetConstraint D86  V90	A113 V117	hbond F89	10.0	# s5||s6
SheetConstraint V114 V117	L141 L144	hbond V143	10.0	# s6||s7
SheetConstraint L141 D146	R156 A151	hbond L144	10.0	# s7^vs8

# file generated by validate2rr
# based on 280 inputs
# using the /projects/compbio/experiments/protein-predict/casp6/networks/NN280-240n300.net.28 network
# limited to score of .30 or greater.
# The score is an approximation of the probability
Constraint V143.CB V154.CB -10. 7.0 14.0 0.91
# Constraint L127.CB L144.CB -10. 7.0 14.0 0.78
# Constraint G42.CA R118.CB -10. 7.0 14.0 0.605
Constraint L16.CB L36.CB -10. 7.0 14.0 0.596 bonus
Constraint R30.CB R92.CB -10. 7.0 14.0 0.585 bonus
Constraint P40.CB S72.CB -10. 7.0 14.0 0.582 bonus
Constraint L56.CB V90.CB -10. 7.0 14.0 0.579 bonus
Constraint L135.CB P157.CB -10. 7.0 14.0 0.567 bonus