CreatePredAlphaCost pred_alpha2k alpha11 T0289.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0289.t04.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha06 alpha11 T0289.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 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 \
	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 T0289.dssp-ehl2.constraints
# include T0289.undertaker-align.sheets
# include rr.constraints

# From T0289.dssp-ehl2.constraints
StrandConstraint	K12	G17	0.6734
HelixConstraint 	G26	K35	0.7282
StrandConstraint	E46	F50	0.6427
HelixConstraint 	P54	T61	0.6369
HelixConstraint 	L74	N76	0.6065
HelixConstraint 	P86	F99	0.6801
StrandConstraint	D109	D113	0.6332
StrandConstraint	T124	I126	0.6071
HelixConstraint 	F134	C145	0.6388
HelixConstraint 	T166	S168	0.6026
StrandConstraint	V174	V178	0.6754
HelixConstraint 	A188	I205	0.6002

# New constraints
StrandConstraint	A218	V228    0.6000
StrandConstraint	A293	N303    0.6000
StrandConstraint	P259	S263    0.6000
StrandConstraint	K267	L271    0.6000
StrandConstraint	C275	P279    0.6000
HelixConstraint 	E285	K290	0.6002

# From the undertaker-align.sheets
SheetConstraint (T0289)K11 (T0289)G17	(T0289)Y108 (T0289)L114	hbond (T0289)K12	41.5751
SheetConstraint (T0289)K11 (T0289)G18	(T0289)L45 (T0289)T52	hbond (T0289)I13	41.5751
SheetConstraint (T0289)D109 (T0289)N116	(T0289)K171 (T0289)V178	hbond (T0289)V111	41.5751
SheetConstraint (T0289)N116 (T0289)T117	(T0289)G179 (T0289)P180	hbond (T0289)T117	41.5751
SheetConstraint (T0289)C123 (T0289)L127	(T0289)V178 (T0289)V174	hbond (T0289)T124	41.5751
SheetConstraint (T0289)T124 (T0289)L127	(T0289)P150 (T0289)V153	hbond (T0289)L125	41.5751
SheetConstraint (T0289)L149 (T0289)V153	(T0289)I219 (T0289)K223	hbond (T0289)C151	41.5751

# New constraints:
SheetConstraint (T0289)P259 (T0289)S261	(T0289)L271 (T0289)K267	hbond (T0289)V260	20
SheetConstraint (T0289)K267 (T0289)L271	(T0289)P279 (T0289)C275	hbond (T0289)L271	20
SheetConstraint (T0289)A218 (T0289)V228	(T0289)A293 (T0289)N303	hbond (T0289)A218	20