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	# 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    20.0	# s5	was 7.565
# 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	20.0
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	5.0	# s1, s2
# SheetConstraint E45 F48		
SheetConstraint K52 N57 	L65 K60 	hbond N57 	5.0 	# s3a,s3b
SheetConstraint E61 K66  	N78 Y73 	hbond E61 	5.0 	# s3b,s3c
# SheetConstraint E102 S105	D150 K147	hbond L104	5.0 	# s?
# For try6, doing this next one. ~175 is real buried.
SheetConstraint S110 Y115	F172 A177	hbond F176	10.0	# s5a||7
SheetConstraint G153 F158	A177 F172	hbond F158	10.0	# s6^vs7
# for try5 I'm disconnecting this, yet it might be right...
# SheetConstraint F202 Q207	K220 T215	hbond F202	5.0

# for try6, we'll rework a sheet based on an rr constraint 38-72 (39-73
SheetConstraint I36 T40 	L49 E45 	10.0 	# hbond?	s1^vs2
SheetConstraint G35 L39 	Y73 T77 	10.0	# hbond?	s1||s3c
# Now to redirect L108-V123, we changed the constraints above