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 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 T0386.dssp-ehl2.constraints
# include T0386.undertaker-align.sheets
# include rr.constraints

# NO sheets in M1-L75/decoys/try1-opt2
include M1-L75/decoys/try1-opt2.helices


include L225-T299/decoys/try1-opt2.helices
# From L225-T299/try1-opt2.sheets:
SheetConstraint (T0386)R243 (T0386)K249	(T0386)Y258 (T0386)E252	hbond (T0386)V245	5
SheetConstraint (T0386)P244 (T0386)A248	(T0386)L290 (T0386)Q286	hbond (T0386)M246	5
SheetConstraint (T0386)G256 (T0386)R259	(T0386)V270 (T0386)A267	hbond (T0386)T257	5
SheetConstraint (T0386)G260 (T0386)G262	(T0386)A267 (T0386)G265	hbond (T0386)G260	5
SheetConstraint (T0386)E264 (T0386)V270	(T0386)I279 (T0386)A273	hbond (T0386)F266	5
SheetConstraint (T0386)L287 (T0386)K291	(T0386)F298 (T0386)D294	hbond (T0386)L287	5


# From A50-E250/try3-opt2:
SheetConstraint (T0386)T92 (T0386)F93	(T0386)T97 (T0386)G96	hbond (T0386)F93	5
HelixConstraint (T0386)D64	(T0386)F76	2
HelixConstraint (T0386)P102	(T0386)W109	2
HelixConstraint (T0386)L123	(T0386)T140	2
HelixConstraint (T0386)F144	(T0386)L158	2
HelixConstraint (T0386)G164	(T0386)A180	2
HelixConstraint (T0386)K191	(T0386)A202	2
HelixConstraint (T0386)L207	(T0386)D216	2
HelixConstraint (T0386)K222	(T0386)N235	2
HelixConstraint (T0386)G237	(T0386)R243	2
HelixConstraint (T0386)N241	(T0386)E250	2


# 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