CreatePredAlphaCost pred_alpha2k alpha11 T0316.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0316.t04.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha06 alpha11 T0316.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 \
	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 T0316.dssp-ehl2.constraints
#include T0316.undertaker-align.sheets
#include rr.constraints

# From T0316.dssp-ehl2.constraints:
StrandConstraint	R8	M13	0.7312
HelixConstraint 	V17	E28	0.6201
StrandConstraint	V33	K39	0.6418
HelixConstraint 	Y56	Q65	0.8951
StrandConstraint	Y70	N74	0.624
HelixConstraint 	E76	R92	0.6904
HelixConstraint 	F109	T118	0.8454
StrandConstraint	Y123	T126	0.7185
HelixConstraint 	P177	E185	0.8526
StrandConstraint	D229	E232	0.6788
StrandConstraint	L236	Y239	0.6474
StrandConstraint	L236	Y239	0.6474
StrandConstraint	L305	Y313	0.6061
StrandConstraint	V320	V324	0.8455
StrandConstraint	T329	F333	0.7496
StrandConstraint	A345	Y349	0.8561

# New structure constraints:
HelixConstraint		D281	F295	2

# From T0316.undertaker-align.sheets:
SheetConstraint (T0316)R8 (T0316)M13	(T0316)D32 (T0316)F37	hbond (T0316)V9		1
SheetConstraint (T0316)I34 (T0316)M38	(T0316)P69 (T0316)V73	hbond (T0316)G35	1
SheetConstraint (T0316)R8 (T0316)V11	(T0316)A121 (T0316)V124	hbond (T0316)V10	1

# New sheet constraints:
SheetConstraint (T0316)C307 (T0316)F311	(T0316)H323 (T0316)K319	hbond (T0316)C307	3
SheetConstraint (T0316)K319 (T0316)H323 (T0316)I332 (T0316)K328 hbond (T0316)V320	3
SheetConstraint	(T0316)T329 (T0316)F333 (T0316)Y349 (T0316)A345 hbond (T0316)I332	3


# Hbond constraints from o_notor2/n_notor2
Hbond		K27.O	G30.N	3
Hbond   	D64.O	G67.N	3	
Hbond 		I117.O	G120.N	3
Hbond		E184.O	G187.N	3
Hbond		Q218.O	R221.N	3