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	1
SheetConstraint (T0356)R180 (T0356)I184	(T0356)M191 (T0356)N187	hbond (T0356)Q182	1
SheetConstraint (T0356)L189 (T0356)R192	(T0356)V217 (T0356)A220	hbond (T0356)I190	1
SheetConstraint (T0356)A226 (T0356)T227	(T0356)V219 (T0356)A220	hbond (T0356)A226	1
SheetConstraint (T0356)A226 (T0356)I228	(T0356)A245 (T0356)L247	hbond (T0356)T227	1
SheetConstraint (T0356)T251 (T0356)V255	(T0356)D262 (T0356)C258	hbond (T0356)T253	1
SheetConstraint (T0356)E264 (T0356)S268	(T0356)G275 (T0356)I271	hbond (T0356)V265	1

#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	4
SheetConstraint (T0356)I309 (T0356)F304 (T0356)H318 (T0356)G323	hbond (T0356)V306	4

#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