CreatePredAlphaCost pred_alpha2k alpha11 T0379.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0379.t04.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha06 alpha11 T0379.t06.alpha.rdb 2 alpha alpha_prev sum

SetCost wet6.5 15 near_backbone 5 way_back 5 dry5 20 dry6.5 23 dry8 20 dry12 5 \
	phobic_fit 3 \
	sidechain 5 \
	n_ca_c	10 bad_peptide 17 \
	bystroff 5 \
	soft_clashes 60  backbone_clashes 2 \
	break 200  \
	pred_alpha2k 2 \
	pred_alpha04 2 \
	pred_alpha06 2 \
	constraints 12 \
	hbond_geom 4 \
	hbond_geom_backbone 8 \
	hbond_geom_beta 60 \
	hbond_geom_beta_pair 80 \
	missing_atoms 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 T0379.dssp-ehl2.constraints
//include T0379.undertaker-align.sheets
//include rr.constraints


//helix constraints determined from best-models 
HelixConstraint (T0379)N17	(T0379)A31	3
HelixConstraint (T0379)M36	(T0379)E57	3
HelixConstraint (T0379)R60	(T0379)L71	3
HelixConstraint (T0379)Q74	(T0379)L84	3

//helix constriants from try1-opt2
HelixConstraint (T0379)S88	(T0379)L98	1 
HelixConstraint (T0379)V114	(T0379)M119	1
HelixConstraint (T0379)G127	(T0379)F133	1
HelixConstraint (T0379)A139	(T0379)G144	1
HelixConstraint (T0379)E150	(T0379)G161	1
HelixConstraint (T0379)G173	(T0379)R182	1
HelixConstraint (T0379)N195	(T0379)K208	1

//sheet constraints from try1-opt2
SheetConstraint (T0379)R3 (T0379)D8	(T0379)E166 (T0379)D171	hbond (T0379)N4	1
SheetConstraint (T0379)N4 (T0379)D8	(T0379)R103 (T0379)L107	hbond (T0379)I5	1
SheetConstraint (T0379)L13 (T0379)H15	(T0379)L9 (T0379)G11	hbond (T0379)I14	1
SheetConstraint (T0379)L13 (T0379)R18	(T0379)S88 (T0379)F83	hbond (T0379)H15	1
SheetConstraint (T0379)F105 (T0379)N109	(T0379)K136 (T0379)S140	hbond (T0379)L106	1
SheetConstraint (T0379)L168 (T0379)D171	(T0379)H186 (T0379)C189	hbond (T0379)F169	1