//CreatePredAlphaCost 
//CreatePredAlphaCost
//CreatePredAlphaCost 

SetCost wet6.5 15 near_backbone 5 way_back 5 dry5 20 dry6.5 30 dry8 25 dry12 5 \
	phobic_fit 3 \
	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 T0362.dssp-ehl2.constraints
include T0362.undertaker-align.sheets
include rr.constraints


KnownBreak M152 M304 M456


SheetConstraint (T0362)W6 (T0362)V13	(T0362)R90 (T0362)D83	hbond (T0362)L7	1
SheetConstraint (T0362)V64 (T0362)I69	(T0362)N123 (T0362)R118	hbond (T0362)A65	1
SheetConstraint (T0362)H70 (T0362)R76	(T0362)R118 (T0362)A112	hbond (T0362)H70	1
SheetConstraint (T0362)L85 (T0362)E92	(T0362)C107 (T0362)Q100	hbond (T0362)A86	1
SheetConstraint (T0362)R93 (T0362)N95	(T0362)Q100 (T0362)S98	hbond (T0362)R93	1
SheetConstraint (T0362)N97 (T0362)R106	(T0362)A121 (T0362)A112	hbond (T0362)F99	1
SheetConstraint (T0362)A121 (T0362)A124	(T0362)C130 (T0362)R127	hbond (T0362)N123	1


SheetConstraint H70 D74         D225 H221 hbond C71             1