CreatePredAlphaCost pred_alpha2k alpha11 T0386.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0386.t04.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha06 alpha11 T0386.t06.alpha.rdb 2 alpha alpha_prev sum

SetCost wet6.5 15 near_backbone 5 way_back 5 dry5 20 dry6.5 40 dry8 20 dry12 5 \
	phobic_fit 4 \
	sidechain 5 \
	n_ca_c	5 bad_peptide 10 \
	bystroff 5 \
	soft_clashes 50  backbone_clashes 2 \
	break 200  \
	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 T0386.dssp-ehl2.constraints
# include T0386.undertaker-align.sheets
# include rr.constraints

include decoys/try4-opt2.helices

# from decoys/try4-opt2.sheets:
SheetConstraint (T0386)Q183 (T0386)L184 (T0386)D216 (T0386)E215 hbond (T0386)Q183       5
SheetConstraint (T0386)D242 (T0386)P244 (T0386)R238 (T0386)V240 hbond (T0386)R243       5


# Residue constraints from A50-E250/try3.costfcn (to keep our desired
# helix bundle topology together) 
Constraint A180.CB L139.CB -10. 6.5 8.5 0.5
Constraint F173.CB F152.CB -10. 4.9 6.9 0.5
Constraint Q169.CB L155.CB -10. 5.6 7.6 0.5
Constraint T129.CB E147.CB -10. 4.2 6.2 0.5
Constraint L126.CB S154.CB -10. 4.8 6.8 0.5

Constraint N145.CB Q211.CB -10. 5.5 7.5 0.5
Constraint E215.CB R141.CB -10. 6.5 8.5 0.5
Constraint P209.CB A197.CB -10. 4.2 6.2 0.5
Constraint L213.CB R193.CB -10. 5.4 7.4 0.5
Constraint R141.CB E215.CB -10. 6.5 8.5 0.5

Constraint R167.CB F229.CB -10. 5.6 7.6 0.5
Constraint M51.CB L226.CB -10. 5.1 7.1 0.5
Constraint K178.CB K222.CB -10. 11.3 13.3 0.5
Constraint L75.CB R167.CB -10. 6.2 8.2 0.5

Constraint R170.CB F229.CB -10. 5.1 7.1 0.5
Constraint N145.CB Q211.CB -10. 5.5 6.5 0.5
Constraint D127.CB T65.CB -10. 4.8 6.8 0.5
Constraint A180.CB F144.CB -10. 6.4 8.4 0.5
Constraint S218.CB A177.CB -10. 7.3 9.3 0.5

Constraint L158.CB L126.CB -10. 5.5 7.5 0.5
Constraint N175.CB Y67.CB -10. 7.3 9.3 0.5
Constraint Q169.CB L155.CB -10. 5.6 7.6 0.5