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 10 near_backbone 5 way_back 5 dry5 15 dry6.5 30 dry8 15 dry12 5 \
	phobic_fit 2 \
	sidechain 1 \
	bystroff 5 \
	soft_clashes 10  backbone_clashes 2 \
	break 15  \
	pred_alpha2k 1 \
	pred_alpha04 5 \
	constraints 90 \
	hbond_geom 1 \
	hbond_geom_backbone 1 \
	hbond_geom_beta 10 \
	hbond_geom_beta_pair 15

// 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

# sheets from Robetta 6 ( generally matched my designed sheets...)
SheetConstraint Y26  S31 	S39 G34 	hbond Q27	10.0
SheetConstraint V68  S71 	F77 G74 	hbond F69	10.0
SheetConstraint L140 D146	A113 S119	hbond L141	10.0
SheetConstraint V143 P147	V154 R150	hbond D146	10.0

# 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