CreatePredAlphaCost pred_alpha2k alpha11 T0347.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0347.t04.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha06 alpha11 T0347.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 50 \
	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.

Constraint E4.CB L37.CB -10. 5.0 10.0 1
Constraint E4.CB A87.CB -10. 5.0 10.0 1
Constraint V8.CB I30.CB -10. 5.0 10.0 1
Constraint H11.CB D29.CB -10. 5.0 10.0 1
Constraint R12.CB R98.CB -10. 5.0 10.0 1
Constraint S27.CB R50.CB -10. 5.0 10.0 1
Constraint P31.CB A46.CB -10. 5.0 10.0 1
Constraint P41.CB D78.CB -10. 6.4 10.0 1
Constraint E38.CB F84.CB -10. 5.0 10.0 1
Constraint P41.CB R74.CB -10. 5.2 10.0 1
Constraint L71.CB M92.CB -10. 5.0 10.0 1
Constraint E64.CB E99.CB -10. 5.0 10.0 1
Constraint A56.CB H102.CB -10. 5.0 10.0 1
Constraint V58.CB L103.CB -10. 5.0 10.0 1

# Sheet constraints from try5-opt2.sheets (no sheets in try6-opt2)
SheetConstraint (T0347)H11 (T0347)R12   (T0347)A56 (T0347)K57   hbond (T0347)R12        1

# Helix constraints from try6-opt2.helices.
HelixConstraint (T0347)G1       (T0347)N13	1
HelixConstraint (T0347)D29      (T0347)H35	1
HelixConstraint (T0347)N33      (T0347)D39	1
HelixConstraint (T0347)D39      (T0347)A52	1
HelixConstraint (T0347)V58      (T0347)S63	1
HelixConstraint (T0347)P61      (T0347)R74	1
HelixConstraint (T0347)D82      (T0347)K96	1
HelixConstraint (T0347)A95      (T0347)L103	1
HelixConstraint (T0347)R101     (T0347)G108	1