CreatePredAlphaCost pred_alpha2k alpha11 T0235.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0235.t04.alpha.rdb 2 alpha alpha_prev sum

SetCost wet6.5 10 near_backbone 3 way_back 3 dry5 10 dry6.5 15 dry8 10 dry12 5 \
	phobic_fit 3 \
	sidechain 6 \
	bystroff 5 \
	soft_clashes 10  backbone_clashes 2 \
	break 30  \
	pred_alpha2k 2 \
	pred_alpha04 6 \
	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... #tried to do this?

// put any constraints here, such as helix constraints, strand constraints,
//	sheet constraints, ssbonds, hbonds, or just arbitrary pairs of atoms.

#from try1-opt2.sheets & .helices
SheetConstraint F6 R11	T20 K15	hbond E7
SheetConstraint F8 R11	T70 L73	hbond F8
SheetConstraint R44 M48	T76 M72	hbond K46
SheetConstraint Y47 V49	S54 G52	hbond V49
SheetConstraint R234 D243	S257 N248	hbond I235
SheetConstraint I235 D243	R305 Y297	hbond K238
SheetConstraint D258 K260	T311 Q313	hbond S259
SheetConstraint K308 Y314	G496 L490	hbond L310
SheetConstraint R316 R321	I329 N324	hbond F318
SheetConstraint V333 F335	T269 F271	hbond V334
SheetConstraint F337 V341	L432 C428	hbond L339
SheetConstraint V429 I433	F497 M493	hbond N431
SheetConstraint I433 I436	Y494 I491	hbond G434
SheetConstraint I433 G440	R453 G446	hbond V435
SheetConstraint Q449 I452	N465 Y462	hbond A450
SheetConstraint W461 N465	V472 K468	hbond K463
HelixConstraint T26	T38
HelixConstraint A96	Q103
HelixConstraint Y119	R129
HelixConstraint V130	N139
HelixConstraint A151	H157
HelixConstraint Q159	N173
HelixConstraint P181	R189
HelixConstraint D209	G226
HelixConstraint D227	F233
HelixConstraint N270	L276
HelixConstraint N274	L280
HelixConstraint N281	K286
HelixConstraint Y349	V354
HelixConstraint V354	E364
HelixConstraint E366	R377
HelixConstraint S382	V387
HelixConstraint P390	L400
HelixConstraint E402	H415
HelixConstraint E473	L480

# constraints to keep first domain docked:
Constraint M72.CE	Q262.CB	 3 4.77 6
Constraint I65.CG2	V253.CG2 3 10 12
Hbond T38.OG1 R321.NH2
Constraint M48.CE	F214.CD2 3 4.75 6