CreatePredAlphaCost pred_alpha2k alpha11 T0228.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0228.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 15 \
	hbond_geom 0.1 \
	hbond_geom_backbone 0.1 \
	hbond_geom_beta 1.2 \
	hbond_geom_beta_pair 2.5

// 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.

HelixConstraint 	E3	F24	4
HelixConstraint 	T44	G61	4
HelixConstraint 	E67	E76	4
HelixConstraint 	S82	S89	4
HelixConstraint 	S124	Y143	4
HelixConstraint 	Y153	D169	4
HelixConstraint 	L185	V199	4
HelixConstraint 	T213	K221	4
HelixConstraint 	V230	S240	4
HelixConstraint 	H247	T259	4
HelixConstraint 	T275	F282	2
HelixConstraint 	P300	L315	4
HelixConstraint 	V332	E344	4
HelixConstraint 	P402	E411	2

StrandConstraint	V30	N38	5
StrandConstraint	E99	E106	5
StrandConstraint	K116	S122	5
StrandConstraint	I172	F177	5
StrandConstraint	A265	D271	5
StrandConstraint	G292	Q295	5
StrandConstraint	K322	S327	5
StrandConstraint	L348	G352	5
StrandConstraint	I376	V383	5
StrandConstraint	N386	S392	5
#StrandConstraint	Y414	S418	5


# N-terminal domain antiparallel sheet    S1-S3-S2
# from try5-opt2.sheets
SheetConstraint T31  Y36 	S124 I119	hbond V32	6
# from undertaker alignments
SheetConstraint S102 E106	S122 K118	hbond S102	6

# C-terminal domain parallel sheet  S5-S6-S7-S8-S4
# from try5-opt2.sheets
SheetConstraint G266 D271	V291 D296	hbond A268	6
# from undertaker alignments
SheetConstraint V291 D296	I323 D328	hbond V293	6
# from try5-opt2.sheets
SheetConstraint I324 S327	L348 F351	hbond C325	6
# from undertaker alignments
SheetConstraint A349 G352	I172 S175	hbond F351	6

# C-terminal domain hairpin   S9-S10
# from try5-opt2.sheets
SheetConstraint L380 V383	I389 N386	hbond L381	6

# todo: C-terminal hairpin hbond to N-terminal antiparllel sheet (S9-S1? S10-S1? S10-S2? S9-S2?)