# CreatePredAlphaCost pred_alpha2k alpha11 T0203.t2k.alpha.rdb 2 alpha alpha_prev sum 
CreatePredAlphaCost pred_alpha04 alpha11 T0203.t04.alpha.rdb 2 alpha alpha_prev sum 

SetCost wet6.5 3 near_backbone 3 way_back 3 dry5 5 dry6.5 6 dry8 8 dry12 8 \
	phobic_fit 5 \
	sidechain 6 \
	bystroff 5 \
	soft_clashes 10  backbone_clashes 2 \
	break 100  \
	pred_alpha04 5 \
	constraints 10 \
	hbond_geom 0.1 \
	hbond_geom_backbone 0.2 \
	hbond_geom_beta 0.4 \
	hbond_geom_beta_pair 2 

# 	pred_alpha2k 5 \


// Add the following for extra-cellular proteins:
# 	known_ssbond 0.5	# and add SSbond commands
#	maybe_ssbond 0.5

// For comparative modeling, increase weight of break and hbond_geom...

// put any constraints here, such as helix constraints, strand constraints,
//	ssbond, hbond, or just arbitrary pairs of atoms.

include T0203.t04.stride-ebghtl.constraints
include T0203.t04.str2.constraints
# include T0203.t04.alpha.constraints
include T0203.t04.bys.constraints
# include T0203.t04.dssp-ebghstl.constraints
include T0203.t04.dssp-ehl2.constraints

# consensus strand pairing:

# one model made it longer and hbonded with the opposite phase, but
# aligned the same residues
SheetConstraint Y13 M15  	Q371 A373  	hbond Y14	10

SheetConstraint A23 I27  	P372 T368  	hbond W26	10

# disagreement about phase of hbonding, but not about pairing
SheetConstraint D119 A124  	D130 G127			10


SheetConstraint M228 A232  	S240 V236  	hbond C230	10
SheetConstraint F314 A317  	P324 I321  	hbond Y315	10

# two choices of alignment here:
SheetConstraint G320 A323  	H346 V349  	hbond I322	1
# SheetConstraint G320 A323  	S347 G350  	hbond I321	1



# try to force some parallel strands

# SheetConstraint V60 A64		I80 E84		1
# SheetConstraint A116 D119	M159 E162	1
# SheetConstraint	V237 S240	Q272 K275	1

# antiparallel

# SheetConstraint	R81 S86		D94 D89		1
# SheetConstraint W91 S95		R102 T98	1