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 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.

# 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    16.218	# reenforced
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	# s1a
StrandConstraint	I36	L49	7.0	# s1b	?
StrandConstraint        E45     L49     7.068	# s2
StrandConstraint        K52     A56     6.802	# s3a
StrandConstraint        F62     L65     6.814	# s3b
StrandConstraint        Y73     T77     7.021	# s3c
# I am assuming that s5 is one rather than two strands
StrandConstraint        S110    M125    7.565	# s5
Constraint		S110.CB	M125.CB	40 70 500	10.0	# force straighter
# StrandConstraint        H120    M125    7.165
StrandConstraint        G153    F158    6.785	# s6
StrandConstraint        I174    F176    6.246	# s7
# StrandConstraint        H186    V192    6.438	# s8a
# StrandConstraint        V195    Q200    6.065	# s8b
StrandConstraint	H186	Q200	30.0
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 O.582 bonus
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

SheetConstraint A37 G41 	F48 G44		hbond G41	10.0	# s1, s2
# SheetConstraint G35 L39 	Y73 T77 	10.0	# hbond?	s1||s3c
SheetConstraint A53 N57 	L65 E61 	hbond N57 	10.0 	# s3a,s3b
SheetConstraint E61 K66  	N78 Y73 	hbond E61 	10.0 	# s3b,s3c
# SheetConstraint E102 S105	D150 K147	hbond L104	5.0 	# s?
# SheetConstraint S110 Y115	F172 A177	hbond F176	10.0	# s5a||s7
# SheetConstraint S110 Y115	G153 F158	Hbond A111	10.0	# s5a||s6
SheetConstraint G153 F158	A177 F172	hbond F158	10.0	# s6^vs7
SheetConstraint S110 M125	N201 H186	hbond V112	25.0	# s5^vs8 !!
# for try5 I'm disconnecting this, yet it might be right...
# SheetConstraint F202 Q207	K220 T215	hbond F202	5.0
# SheetConstraint V195 I199	F209 F205	hbond V195	10.0	# s8b^vs9
# for try6, we'll rework a sheet based on an rr constraint 38-72 (39-73
# Now to redirect L108-V123, we changed the constraints above