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

include decoys/try1-opt2.helices
include decoys/try1-opt2.sheets


# Distance constraints to attempt to make helix bundle.  Taken from 
# model 1 of T0386.undertaker-align.pdb

Constraint R55.CB L225.CB -10. 4.8 6 0.5
Constraint F229.CB I52.CB -10. 6.7 8 0.5
Constraint F229.CB M51.CB -10. 4.9 6 0.5
Constraint Q74.CB L54.CB  -10. 5.2 6.5 0.5
Constraint L54.CB L75.CB -10. 7.3 9 0.5


Constraint D64.CB D127.CB -10. 5.7 7 0.5
Constraint D127.CB T65.CB -10. 5.7 7 0.5
Constraint T65.CB L123.CB -10. 5.1 6.5 0.5
Constraint I119.CB L158.CB -10. 6.8 8 0.5

Constraint T129.CB S146.CB -10. 6.7 8 0.5
Constraint R141.CB E215.CB -10. 6.5 8 0.5
Constraint R141.CB Q211.CB -10. 7.7 9 0.5
Constraint T211.CB N145.CB -10. 5.2 7 0.5

Constraint A202.CB Q157.CB -10. 5.9 7.1 0.5
Constraint Q157.CB V201.CB -10. 8 9 0.5
Constraint V201.CB N153.CB -10. 4.8 6 0.5
Constraint A197.CB P209.CB -10. 4.0 5 0.5
Constraint A197.CB L213.CB -10. 4.9 6 0.5

Constraint R193.CB L213.CB -10. 5.9 7 0.5
Constraint N145.CB L207.CB -10. 6.5 8 0.5
Constraint N145.CB Q211.CB -10. 5.2 6.5 0.5
Constraint L126.CB S154.CB -10. 4.7 6 0.5
Constraint S154.CB T129.CB -10. 6.6 8 0.5
Constraint L123.CB L158.CB -10. 6.3 8 0.5
Constraint D127.CB D64.CB -10. 5.7 7 0.5
Constraint D117.CB T65.CB -10. 5.7 7 0.5

Constraint L176.CB A131.CB -10. 6 7 0.5
Constraint N175.CB I71.CB -10. 8.2 9.5 0.5
Constraint A177.CB H182.CB -10. 4.8 6 0.5
Constraint Q169.CB N156.CB -10. 5.9 7 0.5
Constraint R167.CB T232.CB -10. 5.3 6.5 0.5
Constraint H72.CB T168.CB -10. 4.3 5.5 0.5