CreatePredAlphaCost pred_alpha2k alpha11 T0384.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0384.t04.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha06 alpha11 T0384.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 80  backbone_clashes 2 \
	break 200  \
	pred_alpha2k 2 \
	pred_alpha04 2 \
	pred_alpha06 2 \
	constraints 80 \
	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 T0384.dssp-ehl2.constraints
#include T0384.undertaker-align.sheets
#include rr.constraints



Hbond		N264.O		D260.N		20
Hbond		V266.O		F258.N		20

SheetConstraint (T0384)M1 (T0384)L4	(T0384)E25 (T0384)L28	hbond (T0384)L2	20
SheetConstraint (T0384)K3 (T0384)G8	(T0384)D64 (T0384)A69	hbond (T0384)G5	20
SheetConstraint (T0384)L4 (T0384)I7	(T0384)V29 (T0384)Y32	hbond (T0384)V6	20
SheetConstraint (T0384)L65 (T0384)I68	(T0384)H88 (T0384)L91	hbond (T0384)V66	20
SheetConstraint (T0384)V89 (T0384)E92	(T0384)I116 (T0384)A119	hbond (T0384)V89	20
SheetConstraint (T0384)N146 (T0384)K153	(T0384)Y239 (T0384)S232	hbond (T0384)N146	20
SheetConstraint (T0384)Y147 (T0384)S152	(T0384)V222 (T0384)G227	hbond (T0384)K149	20
SheetConstraint (T0384)D195 (T0384)Q201	(T0384)F216 (T0384)N210	hbond (T0384)D195	20
SheetConstraint (T0384)N210 (T0384)L215	(T0384)G227 (T0384)V222	hbond (T0384)G211	20
SheetConstraint (T0384)P235 (T0384)T240	(T0384)N248 (T0384)G243	hbond (T0384)C236	20
# new
SheetConstraint (T0384)I257 (T0384)D260	(T0384)Q267 (T0384)N264	hbond (T0384)N264	25
SheetConstraint (T0384)T246 (T0384)T249	(T0384)T259 (T0384)A256	hbond (T0384)T249	25


#try15 helix constraints
HelixConstraint (T0384)G10	(T0384)A20
HelixConstraint (T0384)K35	(T0384)Y46
HelixConstraint (T0384)L74	(T0384)A85
HelixConstraint (T0384)Q98	(T0384)N113
HelixConstraint (T0384)E125	(T0384)D137
HelixConstraint (T0384)G173	(T0384)L178
HelixConstraint (T0384)G179	(T0384)G191
HelixConstraint (T0384)H275	(T0384)Q290
HelixConstraint (T0384)D302	(T0384)G318