CreatePredAlphaCost pred_alpha2k alpha11 T0272.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0272.t04.alpha.rdb 2 alpha alpha_prev sum

SetCost wet6.5 5 near_backbone 5 way_back 5 dry5 15 dry6.5 20 dry8 15 dry12 5 \
	phobic_fit 2 \
	sidechain 1 \
	bystroff 5 \
	soft_clashes 10  backbone_clashes 2 \
	break 40  \
	pred_alpha2k 2 \
	pred_alpha04 4 \
	constraints 20 \
	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 T0272.t2k.dssp-ehl2.constraints
# HelixConstraint 	A15	D18	0.7007
# HelixConstraint 	P22	A32	0.6534
# HelixConstraint 	P119	E132	0.7646
# HelixConstraint 	D151	L154	0.6004
# HelixConstraint 	P185	R193	0.8437
# 
# StrandConstraint	L3	V7	0.689
# StrandConstraint	L45	R47	0.7465
# StrandConstraint	V58	Q62	0.8361
# StrandConstraint	Q78	V79	0.6982
# StrandConstraint	R94	A101	0.7432
# StrandConstraint	L168	V182	0.7284

# from T0272.t04.dssp-ehl2.constraints
HelixConstraint 	S12 	D18 	6.372
HelixConstraint 	P22 	V33 	6.279
HelixConstraint 	E121	R129	6.312
HelixConstraint 	W145	Q147	6.048
HelixConstraint 	T152	F153	6.268
HelixConstraint 	P185	R193	8.923

StrandConstraint	W2  	V7  	7.252	# s1
StrandConstraint	L44 	R47 	7.005	# s2
StrandConstraint	V58 	Q62 	8.486	# s3
StrandConstraint	R94 	A101	7.096	# s4
StrandConstraint	K105	L107	6.3  	# s5
StrandConstraint	R113	A115	6.62 	# s6
StrandConstraint	L168	V182	8.2  	# s7
# StrandConstraint	L168	F176	8.143	# s7a
# StrandConstraint	R179	V182	7.871	# s7b
StrandConstraint	L206	S208	6.499	# s8

# some sheets
SheetConstraint V58  Q62 	L95  L99 	hbond V58	10.0 	# s3||s4
SheetConstraint K105 L107	A115 R113	hbond K105	10.0 	# s5^vs6
SheetConstraint R94  A101	A173 L180	hbond L95 	10.0 	# s4||s7	with a bend?

# 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 L29.CB L95.CB -10. 7.0 14.0 0.517 
Constraint V59.CB L99.CB -10. 7.0 14.0 0.361 
Constraint V182.CB L206.CB -10. 7.0 14.0 0.329 bonus
Constraint L99.CB L192.CB -10. 7.0 14.0 0.3 bonus

# another long shot - constraints from thin35
Constraint E132.CB Q147.CB -10. 7.0 12.0 0.661735	bonus
Constraint Y76.CB A109.CB -10. 7.0 12.0 0.640172	bonus
Constraint E39.CB P50.CB -10. 7.0 12.0 0.551715 	bonus
Constraint W145.CB K159.CB -10. 7.0 12.0 0.546168	bonus