SetCost wet6.5 5 near_backbone 3 way_back 3 dry5 2 dry6.5 2 dry8 2 dry12 0.2 \
	phobic_fit 0.1 \
	sidechain 6 \
	bystroff 5 \
	soft_clashes 10  backbone_clashes 2 \
	break 20  \
	pred_alpha2 5 \
	constraints 10 \
	hbond_geom 0.1 \
	hbond_geom_backbone 0.1 \
	hbond_geom_beta 0.4 \
	hbond_geom_beta_pair 1

// 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,
//	ssbond, hbond, or just arbitrary pairs of atoms.


#Scaffold constraints: keep domain1 & 2 apart
#weight should be ~1/10 helix/strand constraints
Constraint	VAL22.CB	LEU145.CB	28  38.421  48    0.7	#inner
Constraint	ALA53.CB	LEU284.CB	62  71.987  82    0.7	#outer

#from T0199.1-95.try1-opt2.helices
#I like the ones below better
#HelixConstraint P36	R41
#HelixConstraint R56	G66
#HelixConstraint L84	E89

#from T0199.1-95.try1-opt2.betabonds (.sheets was empty)
#keep the hairpin together
Hbond (T0199)L62.O	(T0199)Y67.N	0.05	# 3.392
Hbond (T0199)Y69.N	(T0199)I78.O	0.05	# 2.88997
Hbond (T0199)Y69.O	(T0199)I78.N	0.05	# 2.86868
Hbond (T0199)Y67.O	(T0199)T80.N	0.05	# 3.02884


#from T0199.t2k.dssp-ehl2.constraints
#HelixConstraint 	R3	K13	0.6117
#HelixConstraint 	D17	E32	0.8383
#HelixConstraint 	Q40	V45	0.7516
#HelixConstraint 	S52	Y64	0.8043
#HelixConstraint 	D81	E90	0.7469
HelixConstraint 	S99	K109	0.7236
HelixConstraint 	P116	L130	0.7398
StrandConstraint	V135	E138	0.7639
StrandConstraint	I147	P154	0.7576
StrandConstraint	Y159	T166	0.6246
StrandConstraint	S171	K177	0.806
HelixConstraint 	W184	L195	0.6434
HelixConstraint 	V200	L223	0.6034
# StrandConstraint	L232	D233	0.6144
HelixConstraint 	L247	L266	0.6901
StrandConstraint	I271	I275	0.6334
StrandConstraint	A288	F295	0.6511
StrandConstraint	P300	F307	0.7671
HelixConstraint 	Y314	T335	0.6403


# From mutual information
#Constraint E90.CB E186.CB -10. 7.0 12.0 0.116795
#Constraint Y24.CB R181.CB -10. 7.0 12.0 0.114953
#Constraint T272.CB P300.CB -10. 7.0 12.0 0.110449
#Constraint N33.CB S299.CB -10. 7.0 12.0 0.105667
#Constraint T80.CB Y134.CB -10. 7.0 12.0 0.106523
#Constraint Q70.CB E90.CB -10. 7.0 12.0 0.109378
#Constraint L191.CB L211.CB -10. 7.0 12.0 0.108783
#Constraint Y294.CB G302.CA -10. 7.0 12.0 0.108672
#Constraint Q19.CB Y87.CB -10. 7.0 12.0 0.108466
#Constraint L127.CB Y294.CB -10. 7.0 12.0 0.108094
#Constraint T80.CB R251.CB -10. 7.0 12.0 0.107916
#Constraint P175.CB K293.CB -10. 7.0 12.0 0.107604
#Constraint D81.CB Y294.CB -10. 7.0 12.0 0.107006
#Constraint Q19.CB D58.CB -10. 7.0 12.0 0.106919
#Constraint G133.CA A234.CB -10. 7.0 12.0 0.106453
#Constraint V45.CB K283.CB -10. 7.0 12.0 0.106429
#Constraint L127.CB G302.CA -10. 7.0 12.0 0.105669


# From alignments and try3-opt2
Hbond Y69.N	I78.O	# 2.84465
Hbond Y69.O	I78.N	# 2.9586

#inserted
Hbond Y134.N	F307.O	0.5
Hbond Y134.O	F307.N	# 3.22055
Hbond L136.N	Y305.O	0.5
Hbond L136.O	Y305.N	0.5
Hbond E138.N	S303.O	0.5
Hbond E138.O	S303.N	0.5
# I don't think P140 Hbonds with I301.

Hbond V135.N	V150.O	0.5
Hbond V135.O	V150.N	0.5
Hbond I137.N	L148.O	0.5
Hbond I137.O	L148.N	# 3.02882
Hbond R139.N	K146.O	# 2.57047
Hbond R139.O	K146.N	# 2.59849
Hbond N141.N	D144.O	# 2.76269
Hbond N141.O	D144.N	0.5

# inserted
Hbond I147.N	S163.O	0.5
Hbond I147.O	S163.N	0.5
Hbond R149.N	I161.O	0.5
Hbond R149.O	I161.N	0.5
Hbond M151.N	Y159.O	0.5
Hbond M151.O	Y159.N	0.5
# Hbond L152.O	E157.N	# 3.477

Hbond L160.N	I176.O	# 2.86407
Hbond L160.O	I176.N	# 2.90507
# bulge?
Hbond F162.O	V173.N	# 3.02822
Hbond I164.N	S171.O	# 2.57769
Hbond I164.O	S171.N	# 2.54847
Hbond T166.N	G169.O	# 2.76246

Hbond I271.O	K293.N	0.5
Hbond V273.N	S291.O	# 2.81224
Hbond V273.O	S291.N	# 2.78349
Hbond I275.N	V289.O	# 2.51394
Hbond I275.O	V289.N	# 3.07124

Hbond A288.N	T308.O	# 2.89553
Hbond A288.O	T308.N	# 2.99127
Hbond F290.N	L306.O	# 3.07227
Hbond F290.O	L306.N	# 2.88703
Hbond G292.N	V304.O	# 2.88172
Hbond G292.O	V304.N	# 2.87363
Hbond Y294.N	G302.O	# 2.66105
Hbond Y294.O	G302.N	# 3.47818
# bulge?
Hbond Y294.O	I301.N	# 3.12304
Hbond K296.N	S299.O	# 2.95503
Hbond K296.O	S299.N	0.5