CreatePredAlphaCost pred_alpha2k alpha11 T0241.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0241.t04.alpha.rdb 2 alpha alpha_prev sum

SetCost wet6.5 10 near_backbone 5 way_back 5 dry5 15 dry6.5 20 dry8 10 dry12 7 \
	phobic_fit 4 \
	sidechain 1 \
	bystroff 5 \
	soft_clashes 10  backbone_clashes 2 \
	break 20  \
	pred_alpha2k 1 \
	pred_alpha04 5 \
	constraints 10 \
	hbond_geom 1 \
	hbond_geom_backbone 1 \
	hbond_geom_beta 4 \
	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.

HelixConstraint 	Y8	L16	10
HelixConstraint 	L25	L30	10
HelixConstraint 	Y93	K103	10
HelixConstraint 	Q136	K142	10
HelixConstraint 	Q223	S234	10

StrandConstraint	V4	F6	3
StrandConstraint	E45	M49	10
StrandConstraint	K52	I56	10
StrandConstraint	L62	E64	10
StrandConstraint	F73	H78	10
# StrandConstraint	F110	T126	6.689
StrandConstraint	V109	L115	10
StrandConstraint	M121	T126	10
StrandConstraint	G154	F159	10
StrandConstraint	L175	I178	10
StrandConstraint	H187	D194	10
StrandConstraint	A196	S201	10
StrandConstraint	E205	Q209	10


SheetConstraint M46 M49	Q55 K52	hbond I47	5
SheetConstraint Y54 D57	E64 K61	hbond Q55	5
SheetConstraint H174 I178	L191 H187

# from try1-opt2.sheets
SheetConstraint Y111 T116	T179 H174	hbond A112	7
SheetConstraint Y111 L115	K123 F119 	hbond V113	7
#SheetConstraint G154 Y160 	N169 N163 	hbond L156	7
#SheetConstraint N163 V170	E180 F173 	hbond Y164	7

# hand-picked sheet constraints to insert the predicted strand 186-193
SheetConstraint G154 Y160 	Q192 G186	15
SheetConstraint G186 F193	E180 F173	15

# distance constraints for metal-ion coordination
Constraint H174.CA	H187.CA		2.39	4.39	6.39	5	
Constraint H176.CA	H187.CA		2.44	4.44	6.44	5

# 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 T38.CB P72.CB -10. 7.0 14.0 0.669
Constraint V75.CB F193.CB -10. 7.0 14.0 0.466 bonus
Constraint I11.CB L191.CB -10. 7.0 14.0 0.454 bonus
Constraint I11.CB I56.CB -10. 7.0 14.0 0.424 bonus
Constraint I203.CB D214.CB -10. 7.0 14.0 0.364 bonus
Constraint I11.CB Y164.CB -10. 7.0 14.0 0.345 bonus
Constraint A112.CB L198.CB -10. 7.0 14.0 0.308 bonus
Constraint M34.CB F193.CB -10. 7.0 14.0 0.308 bonus
Constraint I39.CB F193.CB -10. 7.0 14.0 0.3 bonus