CreatePredAlphaCost pred_alpha2k alpha11 T0339.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0339.t04.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha06 alpha11 T0339.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 T0339.dssp-ehl2.constraints
//include T0339.undertaker-align.sheets
//include rr.constraints


#sheet constraints from conformation 0 T0339-1eg5A-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m:1eg5A
SheetConstraint (T0339)D63 (T0339)S68	(T0339)I241 (T0339)I236	hbond (T0339)I65	1
SheetConstraint (T0339)P107 (T0339)S112	(T0339)A132 (T0339)V137	hbond (T0339)F109	1
SheetConstraint (T0339)F109 (T0339)T111	(T0339)L161 (T0339)T163	hbond (T0339)I110	1
SheetConstraint (T0339)R160 (T0339)L166	(T0339)I199 (T0339)A205	hbond (T0339)V162	1
SheetConstraint (T0339)V201 (T0339)D204	(T0339)D222 (T0339)T225	hbond (T0339)T203	1
SheetConstraint (T0339)D222 (T0339)H229	(T0339)R242 (T0339)R235	hbond (T0339)L224	1
SheetConstraint (T0339)G310 (T0339)R313	(T0339)I334 (T0339)N331	hbond (T0339)Q311	1
SheetConstraint (T0339)N328 (T0339)S333	(T0339)V389 (T0339)A384	hbond (T0339)C330	1
SheetConstraint (T0339)L351 (T0339)A353	(T0339)V3 (T0339)M5	hbond (T0339)M352	1

#sheet constraints from conformation 1 T0339-1p3wA-t2k-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m:1p3wA
SheetConstraint (T0339)K2 (T0339)M5	(T0339)V350 (T0339)A353	hbond (T0339)V3	1
SheetConstraint (T0339)D63 (T0339)S68	(T0339)I241 (T0339)I236	hbond (T0339)I65	1
SheetConstraint (T0339)P107 (T0339)S112	(T0339)A132 (T0339)V137	hbond (T0339)F109	1
SheetConstraint (T0339)F109 (T0339)T111	(T0339)L161 (T0339)T163	hbond (T0339)I110	1
SheetConstraint (T0339)R160 (T0339)L166	(T0339)I199 (T0339)A205	hbond (T0339)V162	1
SheetConstraint (T0339)V201 (T0339)D204	(T0339)D222 (T0339)T225	hbond (T0339)T203	1
SheetConstraint (T0339)D222 (T0339)H229	(T0339)R242 (T0339)R235	hbond (T0339)L224	1
SheetConstraint (T0339)G310 (T0339)I314	(T0339)R335 (T0339)N331	hbond (T0339)K312	1
SheetConstraint (T0339)N328 (T0339)I334	(T0339)V389 (T0339)N383	hbond (T0339)C330	1
SheetConstraint (T0339)L385 (T0339)R386	(T0339)V355 (T0339)S354	hbond (T0339)R386	1