CreatePredAlphaCost pred_alpha2k alpha11 T0376.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0376.t04.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha06 alpha11 T0376.t06.alpha.rdb 2 alpha alpha_prev sum

SetCost wet6.5 15 near_backbone 5 way_back 5 dry5 15 dry6.5 20 dry8 15 dry12 5 \
	phobic_fit 2 \
	sidechain 5 \
	n_ca_c	5 bad_peptide 10 \
	bystroff 5 \
	soft_clashes 40  backbone_clashes 2 \
	break 150  \
	pred_alpha2k 2 \
	pred_alpha04 2 \
	pred_alpha06 2 \
	constraints 10 \
	hbond_geom 5 \
	hbond_geom_backbone 10 \
	hbond_geom_beta 50 \
	hbond_geom_beta_pair 100 \
	missing_atoms 1 \
	maybe_metal 0.5 \
	maybe_ssbond 1

// remove maybe_ssbond weight if protein known to be in reducing environment.
// remove maybe_metal weight if protein known to have disulfides or
//	known not to bind metal ions.

// Add the following for extra-cellular proteins:
#	known_ssbond 0.5	# and put ssbond command in constraints file

// 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.

// include T0376.dssp-ehl2.constraints
// include T0376.t06.str2.constraints
// include T0376.undertaker-align.sheets
// include rr.constraints

#sheet constraints from conformation 1 T0376-1o5kA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m:1o5kA
SheetConstraint (T0376)A42 (T0376)Y45	(T0376)P73 (T0376)V76	hbond (T0376)V43	74.3981
SheetConstraint (T0376)I75 (T0376)G77	(T0376)G100 (T0376)M102	hbond (T0376)V76	74.3981
SheetConstraint (T0376)G100 (T0376)I104	(T0376)P132 (T0376)Y136	hbond (T0376)L101	74.3981
SheetConstraint (T0376)G207 (T0376)A208	(T0376)G8 (T0376)V9	hbond (T0376)A208	74.3981

HelixConstraint 	F25	A37	20
StrandConstraint	A42	Y45	20
HelixConstraint 	D57	K69	20
StrandConstraint	P73	G77	20
HelixConstraint 	T83	K95	20
StrandConstraint	G100	V103	20
HelixConstraint 	I114	A127	20
StrandConstraint	A133	Y136	20
HelixConstraint 	A147	E156	20
StrandConstraint	L160	E165	20
HelixConstraint 	M172	T180	20
StrandConstraint	V186	I190	20
HelixConstraint 	T194	N202	20
StrandConstraint	G207	T210	20
HelixConstraint 	P217	A229	20
HelixConstraint 	R238	F254	20
HelixConstraint 	V261	L270	20
HelixConstraint 	D288	F301	20

Hbond	G39.N	I36.O	10
Hbond	M40.N	L35.O	10
Hbond	I72.N	V68.O	10
Hbond	G97.N	Q94.O	10
Hbond	A98.N	A93.O	10
Hbond	A128.N	L125.O	10
Hbond	I131.N	A128.O	10
Hbond	H157.N	R154.O	10
Hbond	L160.N	H157.O	10
Hbond	A205.N	F200.O	10
Hbond	G233.N	A230.O	10
Hbond	L260.N	G257.O	10
Hbond	D273.N	M268.O	10
Hbond	W308.N	Y305.O	10