CreatePredAlphaCost pred_alpha2k alpha11 T0356.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0356.t04.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha06 alpha11 T0356.t06.alpha.rdb 2 alpha alpha_prev sum

SetCost wet6.5 15 near_backbone 5 way_back 5 dry5 20 dry6.5 30 dry8 20 dry12 8.5 \
	phobic_fit 2 \
	sidechain 5 \
	n_ca_c	5 bad_peptide 10 \
	bystroff 5 \
	soft_clashes 20  backbone_clashes 2 \
	break 50  \
	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 T0356.dssp-ehl2.constraints
//include T0356.undertaker-align.sheets
include rr.constraints

//  T0356.dssp-ehl2.constraints
HelixConstraint 	A330	L332	0.6013
HelixConstraint 	V334	K346	0.7181
StrandConstraint	I351	Y355	0.6505
StrandConstraint	L365	I370	0.7272
HelixConstraint 	G376	L389	0.6358
StrandConstraint	F397	C401	0.8535
HelixConstraint 	W410	T419	0.7032
StrandConstraint	T427	V430	0.6541
StrandConstraint	M451	D454	0.7899
HelixConstraint 	P475	L488	0.626


//Sheet Constraints

#sheet constraints from conformation 0 T0356-1wqaA-t06-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m:1wqaA
SheetConstraint (T0356)T395 (T0356)V400	(T0356)R425 (T0356)V430	hbond (T0356)F397	0.512245
SheetConstraint (T0356)F397 (T0356)C401	(T0356)S449 (T0356)L453	hbond (T0356)V398	0.512245
SheetConstraint (T0356)V400 (T0356)C401	(T0356)E431 (T0356)N432	hbond (T0356)C401	0.512245