#CreatePredAlphaCost pred_alpha2k alpha11 T0327.t2k.alpha.rdb 2 alpha alpha_prev sum
#CreatePredAlphaCost pred_alpha04 alpha11 T0327.t04.alpha.rdb 2 alpha alpha_prev sum
#CreatePredAlphaCost pred_alpha06 alpha11 T0327.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 10 \
	n_ca_c	5 bad_peptide 10 \
	bystroff 5 \
	soft_clashes 20  backbone_clashes 2 \
	break 50  \
	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

KnownBreak M103

// 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 T0327.dssp-ehl2.constraints
# include T0327.undertaker-align.sheets
# include rr.constraints

#From T0327.dssp-ehl2.constraints:
HelixConstraint 	K3	L11	0.7011
HelixConstraint 	E30	R42	0.6725
StrandConstraint	I46	Y51	0.6763
StrandConstraint	H57	K60	0.6068
HelixConstraint 	E67	E75	0.6288

# increased weighting on the last constraint.
HelixConstraint 	G77	W92	1

# From try1-opt2.sheets
SheetConstraint (T0327)G17 (T0327)L21	(T0327)L61 (T0327)H57	hbond (T0327)T19	1
SheetConstraint (T0327)Y45 (T0327)H50	(T0327)G62 (T0327)H57	hbond (T0327)I47	1

#From T0327.dssp-ehl2.constraints:
HelixConstraint 	K105	L113	0.7011
HelixConstraint 	E132	R144	0.6725
StrandConstraint	I148	Y153	0.6763
StrandConstraint	H159	K162	0.6068
HelixConstraint 	E169	E177	0.6288

# increased weighting on the last constraint.
HelixConstraint 	G179	W194	1

# From try1-opt2.sheets
SheetConstraint (T0327)G119 (T0327)L123	(T0327)L163 (T0327)H159	hbond (T0327)T121	1
SheetConstraint (T0327)Y147 (T0327)H152	(T0327)G164 (T0327)H159	hbond (T0327)I149	1

#To try to keep the helices together.
Constraint L73.CB L175.CB -10. 7.0 14.0	 1