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 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,
//	sheet constraints, ssbonds, hbonds, or just arbitrary pairs of atoms.

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

SheetConstraint V30 Y36  	W125 I119	hbond V32
SheetConstraint V30 R39  	W125 K116	hbond V32

# Not sure how these pair
# SheetConstraint E98 I101  	G123 L120	hbond E99
# SheetConstraint E98 Q100  	G123 V121	hbond E99
# SheetConstraint E98 E99  	S122 V121	hbond E98
# SheetConstraint I101 F103  	V121 I119	hbond S102
# SheetConstraint S102 S105  	V121 K118	hbond F103

# Not sure which the pairing strand is
# SheetConstraint I119 S122  	S321 I324	hbond L120
# SheetConstraint L120 S122  	T270 T272	hbond V121

# no consensus on how these pair
# SheetConstraint V199 N200  	E176 F177	hbond N200
# SheetConstraint S175 G178  	K225 G228	hbond E176
# SheetConstraint G223 V224  	F174 S175	hbond V224
# SheetConstraint R173 F177  	A265 L269	hbond S175
# SheetConstraint I172 S175  	A349 G352	hbond R173
# SheetConstraint F174 E176  	M347 A349	hbond S175

# SheetConstraint K225 I227  	A289 V291	hbond K225

SheetConstraint G266 D271  	V291 D296	hbond D296
SheetConstraint Y290 R294  	I324 D328	hbond V291
SheetConstraint C325 D328  	A349 G352	hbond Y326

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