CreatePredAlphaCost pred_alpha2k alpha11 T0355.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0355.t04.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha06 alpha11 T0355.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 T0355.dssp-ehl2.constraints
//include T0355.undertaker-align.sheets
//include rr.constraints

#sheet constraints from conformation 0 T0355-1rd5A-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m:1rd5A
SheetConstraint (T0355)P32 (T0355)R36	(T0355)G245 (T0355)A249	hbond (T0355)A34	51.8011
SheetConstraint (T0355)I65 (T0355)V66	(T0355)A117 (T0355)I118	hbond (T0355)V66	51.8011
SheetConstraint (T0355)A117 (T0355)K120	(T0355)E144 (T0355)A147	hbond (T0355)I118	51.8011
SheetConstraint (T0355)M143 (T0355)R146	(T0355)I162 (T0355)F165	hbond (T0355)G145	51.8011

#sheet constraints from conformation 1 T0355-1qopA-t04-local-str2+near-backbone-11-0.8+0.6+0.8-adpstyle5.a2m:1qopA
SheetConstraint (T0355)P32 (T0355)R36	(T0355)G245 (T0355)A249	hbond (T0355)A34	51.4648
SheetConstraint (T0355)R36 (T0355)R38	(T0355)I65 (T0355)E67	hbond (T0355)Y37	51.4648
SheetConstraint (T0355)G63 (T0355)E67	(T0355)A115 (T0355)A119	hbond (T0355)L64	51.4648
SheetConstraint (T0355)F116 (T0355)K120	(T0355)M143 (T0355)A147	hbond (T0355)I118	51.4648
SheetConstraint (T0355)E144 (T0355)R146	(T0355)K163 (T0355)F165	hbond (T0355)G145	51.4648
SheetConstraint (T0355)L190 (T0355)F192	(T0355)P224 (T0355)L226	hbond (T0355)A191	51.4648
SheetConstraint (T0355)L225 (T0355)V227	(T0355)S244 (T0355)V246	hbond (T0355)V227	51.4648