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 20 \
	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 M1-A183/try2.costfcn:
StrandConstraint	R8	M13	0.732
HelixConstraint 	D18	E28	0.7937
StrandConstraint	V33	K39	0.6431
HelixConstraint 	Y56	Q65	0.8878
StrandConstraint	Y70	V73	0.7347
HelixConstraint 	E76	R92	0.7186
HelixConstraint 	F109	T118	0.833
StrandConstraint	Y123	T126	0.6904
HelixConstraint 	P177	L182	0.6971


#New constraints:
Hbond	Y31.N	L26.O	5
Hbond	I68.N	A63.O	5
Hbond	A121.N	A116.O	5

#From A130-I373/try3.costfcn:

# From T0316.dssp-ehl2.constraints:
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	3
StrandConstraint	R131	R134	15
StrandConstraint	V140	V146	15
StrandConstraint	T153	L156	15
HelixConstraint		S160	M168	5
HelixConstraint		K176	G187	5

HelixConstraint		N206	Y214	5



# New sheet constraints:
SheetConstraint (T0316)C307 (T0316)F311	(T0316)H323 (T0316)K319	hbond (T0316)C307	15
SheetConstraint (T0316)K319 (T0316)H323 (T0316)I332 (T0316)K328 hbond (T0316)V320	15
SheetConstraint	(T0316)T329 (T0316)F333 (T0316)Y349 (T0316)A345 hbond (T0316)I332	15


SheetConstraint (T0316)R131 (T0316)R134	(T0316)R144 (T0316)H141 hbond (T0316)R131	15
SheetConstraint	(T0316)H141 (T0316)R144	(T0316)L156 (T0316)T153 hbond (T0316)M142	15
SheetConstraint (T0316)T153 (T0316)L156 (T0316)I202 (T0316)I199 hbond (T0316)Y154	15

# Hbond constraints from o_notor2/n_notor2
Hbond		E184.O	G187.N		3
Hbond		Q218.O	R221.N		3
Hbond		E335.O	R338.N		3
Hbond		L188.N	A183.O		3

#Sheet constraints for the parallel sheet:
SheetConstraint (T0316)Y70 (T0316)N74 (T0316)G35 (T0316)K39 hbond (T0316)Y70	15
SheetConstraint (T0316)V33 (T0316)F37 (T0316)V9  (T0316)M13 hbond (T0316)I34	15
SheetConstraint (T0316)V9  (T0316)G12 (T0316)Y123 (T0316)T126 hbond (T0316)V10	15
SheetConstraint (T0316)V124 (T0316)A125 (T0316)T190 (T0316)A191 hbond (T0316)V124	15