CreatePredAlphaCost pred_alpha2k alpha11 T0250.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0250.t04.alpha.rdb 2 alpha alpha_prev sum

SetCost wet6.5 3 near_backbone 3 way_back 3 dry5 5 dry6.5 6 dry8 5 dry12 2 \
	phobic_fit 2 \
	sidechain 6 \
	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.

# Conserved H173, H175, and H186  may be part of a metal-binding site.
# and should probaby be clustered

Constraint H173.NE2 H175.NE2    -10 6 9 1.0
Constraint H173.NE2 H186.NE2    -10 6 9 1.0
Constraint H175.NE2 H186.NE2    -10 6 9 1.0

# The secondary structure patterns seems fairly clear in the t04 predictions:

HelixConstraint         T10     L18     6.018
HelixConstraint         I25     E30     8.218
HelixConstraint         Q92     M103    6.218
HelixConstraint         T134    R141    6.726
HelixConstraint         E162    L163    6.32
HelixConstraint         E214    K218    6.588
HelixConstraint         Y223    A233    7.254

StrandConstraint        L5      Y6      6.084
StrandConstraint        E45     L49     7.068
StrandConstraint        K52     A56     6.802
StrandConstraint        F62     L65     6.814
StrandConstraint        Y73     T77     7.021
StrandConstraint        S110    M125    7.565
# StrandConstraint        H120    M125    7.165
StrandConstraint        G153    F158    6.785
StrandConstraint        I174    F176    6.246
StrandConstraint        H186    V192    6.438
StrandConstraint        V195    Q200    6.065
StrandConstraint        Q206    H208    6.913

# 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 T38.CB P72.CB -10. 7.0 14.0 3.602
Constraint L11.CB F190.CB -10. 7.0 14.0 3.582
Constraint L11.CB A56.CB -10. 7.0 14.0 0.421 bonus
Constraint L5.CB G153.CA -10. 7.0 14.0 0.375 bonus
Constraint L65.CB L90.CB -10. 7.0 14.0 0.37 bonus
Constraint I155.CB V195.CB -10. 7.0 14.0 0.353 bonus
Constraint A56.CB Q92.CB -10. 7.0 14.0 0.345 bonus
Constraint V95.CB V192.CB -10. 7.0 14.0 0.326 bonus
Constraint L11.CB L163.CB -10. 7.0 14.0 0.323 bonus
Constraint M103.CB V192.CB -10. 7.0 14.0 0.321 bonus
Constraint V112.CB I174.CB -10. 7.0 14.0 0.3 bonus


# from try1-opt2.sheets
# for try4, I'm taking this out
# SheetConstraint A37 S42  	F79 A74	hbond L39 	5.0
# adding the next two for try4
SheetConstraint E45 L49 	A56 K52 	5.0	# hbond?
SheetConstraint K52 A56 	L65 E61 	5.0	# hbond?
SheetConstraint E61 K66  	N78 Y73 	4.0	# hbond I63	5.0
SheetConstraint E102 S105	D150 K147	hbond L104	5.0
# WHAT WAS I THINKING?
# SheetConstraint L108 I114	V123 T117	hbond S110	5.0
# For try5, undoing this next one. ~175 is real buried.
# SheetConstraint H175 D179	H186 A182	hbond F176	5.0
# for try5 I'm disconnecting this, yet it might be right...
# SheetConstraint F202 Q207	K220 T215	hbond F202	5.0

# for try5, we'll rework a sheet based on an rr constraint 38-72 (39-71
SheetConstraint I36 T40 	A74 K70 	10.0	# hbond?
# Now to redirect L108-V123, we changed the constraints above
# make a new sheet
SheetConstraint H120 M125	G153 F158	7.0	# hbond?