CreatePredAlphaCost pred_alpha2k alpha11 T0263.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0263.t04.alpha.rdb 2 alpha alpha_prev sum

SetCost wet6.5 10 near_backbone 5 way_back 5 dry5 10 dry6.5 20 dry8 15 dry12 10 \
	phobic_fit 2 \
	sidechain 1 \
	bystroff 5 \
	soft_clashes 10  backbone_clashes 2 \
	break 20  \
	pred_alpha2k 3 \
	pred_alpha04 3 \
	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.

#from  T0263.t04.dssp-ehl2.constraints
HelixConstraint 	G16	N31	0.6339
HelixConstraint 	E59	N75	0.8062

StrandConstraint	L4	F9	0.6147
StrandConstraint	L37	E43	0.6113
StrandConstraint	A50	F56	0.6195
StrandConstraint	V81	D87	0.7319

# from t04.bys.constraints
StrandConstraint        E90     P91     15	#0.684
StrandConstraint        A98     A101    15	#0.635

# hand-picked constraint 
StrandConstraint	E90	A101	15


# from try2-opt2.sheets
SheetConstraint M1 H8	P91 K84		hbond A2	7
SheetConstraint A2 F11	T57 H48		hbond T3	7
SheetConstraint F9 N12	V82 E79		hbond A10	7
SheetConstraint F36 E43	F56 E49		hbond L37	7

# new scaffolding constraints picked by looking at 1lq9A
Constraint G51.CA A101.CA	20.396	22.396	24.396	3
Constraint G51.CA K99.CA	18.370	20.370	22.370	3
Constraint G51.CA N96.CA	15.469	17.469	19.469	3

Constraint I53.CA A101.CA	16.217	18.217	20.217	3
Constraint I53.CA K99.CA	13.661	15.661	17.661	3
Constraint I53.CA N96.CA	10.051	12.051	14.051	3

Constraint L4.CA A101.CA	18.646	20.646	22.646	3
Constraint L4.CA K99.CA		14.956	16.956	18.956	3
Constraint L4.CA N96.CA		9.965	11.965	13.965	3

Constraint P34.CA A101.CA	25.937	27.937	29.937	3
Constraint P34.CA K99.CA	23.087	25.087	27.087	3
Constraint P34.CA N96.CA	17.415	19.415	21.415	3

Constraint G35.CA A101.CA	22.572	24.572	26.472	3
Constraint G35.CA K99.CA	19.418	21.418	23.418	3
Constraint G35.CA N96.CA	13.636	15.636	17.636	3

Constraint L37.CA A101.CA	18.004	20.004	22.004	3
Constraint L37.CA K99.CA	15.869	17.869	19.869	3
Constraint L37.CA N96.CA	11.702	13.702	15.702	3

Constraint T42.CA A101.CA	19.033	21.033	23.033	3
Constraint T42.CA K99.CA	18.453	20.453	22.453	3
Constraint T42.CA N96.CA	17.212	19.212	21.212	3

Constraint L92.CA A101.CA	21.377	23.377	25.377	3
Constraint L92.CA K99.CA	16.680	18.680	20.680	3
Constraint L92.CA N96.CA	10.656	12.656	14.656	3

Constraint P91.CA I95.CA	11.413	13.413	15.413	3

# 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 M1.CB L76.CB -10. 7.0 14.0 0.596 bonus
Constraint A2.CB L76.CB -10. 7.0 14.0 0.531 bonus
Constraint M1.CB S93.CB -10. 7.0 14.0 0.454 bonus
Constraint I30.CB L73.CB -10. 7.0 14.0 0.424 bonus
Constraint Q6.CB A50.CB -10. 7.0 14.0 0.347 bonus
Constraint T42.CB H69.CB -10. 7.0 14.0 0.329 bonus