# 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



# from T0203.t04-thin35.mi.constraints
# found 10 significant column pairs
#reject: Constraint H11.CB V259.CB -10. 7.0 12.0 0.126744
Constraint A40.CB D79.CB -10. 7.0 12.0 0.117662
Constraint G12.CA F57.CB -10. 7.0 12.0  0.11746
Constraint S90.CB A116.CB -10. 7.0 12.0 0.5	# increased weight
Constraint S65.CB Q75.CB -10. 7.0 12.0 0.108472
Constraint H167.CB V273.CB -10. 7.0 12.0 0.107888
Constraint S263.CB L359.CB -10. 7.0 12.0 0.107875
Constraint E84.CB E374.CB -10. 7.0 12.0 0.107106
#reject: Constraint I115.CB S258.CB -10. 7.0 12.0 0.106724
Constraint V101.CB S158.CB -10. 7.0 12.0 0.106538

# from T0203.t04-thin40.mi.constraints
# found 4 significant column pairs
#reject: Constraint P77.CB T246.CB -10. 7.0 12.0 0.121979
Constraint P77.CB K145.CB -10. 7.0 12.0 0.114233
Constraint N35.CB V46.CB -10. 7.0 12.0 0.112391
Constraint W19.CB V348.CB -10. 7.0 12.0  0.10637

# from T0203.t04-thin50.mi.constraints
# found 7 significant column pairs
Constraint E178.CB K192.CB -10. 7.0 12.0 0.115243
Constraint T242.CB A256.CB -10. 7.0 12.0 0.113317
Constraint V46.CB E84.CB -10. 7.0 12.0 0.110609
Constraint H167.CB C230.CB -10. 7.0 12.0 0.108386
Constraint E178.CB P212.CB -10. 7.0 12.0 0.107768
Constraint A48.CB V236.CB -10. 7.0 12.0 0.106299
#reject: Constraint N35.CB A256.CB -10. 7.0 12.0 0.106031



# from T0203.t2k-thin35.mi.constraints
# found 8 significant column pairs
Constraint G217.CA T242.CB -10. 7.0 12.0  0.11557
Constraint P42.CB R154.CB -10. 7.0 12.0 0.114211
Constraint S65.CB R331.CB -10. 7.0 12.0 0.112225
Constraint R37.CB R267.CB -10. 7.0 12.0 0.110812
Constraint E78.CB I278.CB -10. 7.0 12.0 0.109254
Constraint R306.CB R355.CB -10. 7.0 12.0 0.107355
Constraint W69.CB R267.CB -10. 7.0 12.0 0.107185
Constraint A116.CB E179.CB -10. 7.0 12.0 0.106313



# try to force some parallel strands

SheetConstraint V60 A64		I80 E84		5
SheetConstraint A116 D119	M159 E162	4
SheetConstraint	V237 S240	Q272 K275	4

# antiparallel

SheetConstraint	R81 S86		D94 D89		6
SheetConstraint W91 S95		R102 T98	5