CreatePredAlphaCost pred_alpha2k alpha11 T0356.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0356.t04.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha06 alpha11 T0356.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 T0356.dssp-ehl2.constraints
#include T0356.undertaker-align.sheets
#sheets taken from try2.sheets

SheetConstraint (T0356)T160 (T0356)H170	(T0356)L183 (T0356)R173	hbond (T0356)T160	10
SheetConstraint (T0356)R180 (T0356)I184	(T0356)M191 (T0356)N187	hbond (T0356)Q182	10
SheetConstraint (T0356)L189 (T0356)R192	(T0356)V217 (T0356)A220	hbond (T0356)I190	10
SheetConstraint (T0356)A226 (T0356)T227	(T0356)V219 (T0356)A220	hbond (T0356)A226	10
SheetConstraint (T0356)A226 (T0356)I228	(T0356)A245 (T0356)L247	hbond (T0356)T227	10
SheetConstraint (T0356)T251 (T0356)V255	(T0356)D262 (T0356)C258	hbond (T0356)T253	10
SheetConstraint (T0356)E264 (T0356)S268	(T0356)G275 (T0356)I271	hbond (T0356)V265	10

#changed last sheet constraint to insert what is currently a helix at 303-310
#to be an anti-parallel strand to try to make a 6 strand anti-parellel sheet

SheetConstraint (T0356)I271 (T0356)Y276	(T0356)I309 (T0356)F304	hbond (T0356)L273	40
SheetConstraint (T0356)I309 (T0356)F304 (T0356)H318 (T0356)G323	hbond (T0356)V306	40

#include rr.constraints

Constraint T164.CB V219.CB -10. 7.0 14.0 2
Constraint V219.CB F304.CB -10. 7.0 14.0 2
Constraint T164.CB L176.CB -10. 7.0 14.0 2
Constraint M191.CB V219.CB -10. 7.0 14.0 0.45184803122 bonus
Constraint V219.CB I228.CB -10. 7.0 14.0 0.355821710887 bonus
Constraint V219.CB A231.CB -10. 7.0 14.0 0.327875402128 bonus
Constraint V219.CB L273.CB -10. 7.0 14.0 0.325646547231 bonus
Constraint V219.CB L229.CB -10. 7.0 14.0 0.312902262544 bonus

Constraint T166.CB G177.CA -10. 7.0 14.0 1
Constraint M191.CB V217.CB -10. 7.0 14.0 1
Constraint Y179.CB M191.CB -10. 7.0 14.0 1