CreatePredAlphaCost pred_alpha2k alpha11 T0208.t2k.alpha.rdb 2 alpha alpha_prev sum 
CreatePredAlphaCost pred_alpha04 alpha11 T0208.t04.alpha.rdb 2 alpha alpha_prev sum 

SetCost wet6.5 3 near_backbone 3 way_back 3 dry5 5 dry6.5 6 dry8 5 dry12 2 \
	phobic_fit 2 \
	sidechain 6 \
	bystroff 5 \
	soft_clashes 10  backbone_clashes 2 \
	break 20  \
	pred_alpha2k 3 \
	pred_alpha04 3 \
	constraints 10 \
	hbond_geom 0.1 \
	hbond_geom_backbone 0.1 \
	hbond_geom_beta 0.4 \
	hbond_geom_beta_pair 1

// Add the following for extra-cellular proteins:
#	known_ssbond 0.5	# and put ssbond command in constraints file
#	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 T0208.t2k.dssp-ehl2.constraints
include T0208.t2k.dssp-ebghstl.constraints
include T0208.t2k.stride-ebghtl.constraints
include T0208.t2k.str2.constraints
include T0208.t2k.alpha.constraints
include T0208.t2k.bys.constraints

include T0208.t04.dssp-ehl2.constraints
include T0208.t04.dssp-ebghstl.constraints
include T0208.t04.stride-ebghtl.constraints
include T0208.t04.str2.constraints
include T0208.t04.alpha.constraints
include T0208.t04.bys.constraints


# mi constraints with weight >0.5
#from t2k-thin30.mi.constraints	(only 2 sequences---pretty useless)
#from t2k-thin35.mi.constraints (only 4 sequences)
#from t2k-thin40.mi.constraints (only 5 sequences)
#from t2k-thin50.mi.constraints (only 8 sequences) >=0.6
Constraint N35.CB Q48.CB -10. 7.0 12.0 0.766669
Constraint R187.CB A327.CB -10. 7.0 12.0 0.729521
Constraint N121.CB E200.CB -10. 7.0 12.0 0.646506
Constraint R187.CB E285.CB -10. 7.0 12.0 0.646506
Constraint E285.CB A327.CB -10. 7.0 12.0  0.61191

#from t2k-thin62.mi.constraints
Constraint E325.CB D335.CB -10. 7.0 12.0 0.555341
Constraint S66.CB P108.CB -10. 7.0 12.0 0.535022
Constraint G312.CA Y342.CB -10. 7.0 12.0 0.527208
Constraint S66.CB S248.CB -10. 7.0 12.0  0.50099

#from t04-thin30.mi.constraints
Constraint T90.CB I221.CB -10. 7.0 12.0 0.532454
Constraint K277.CB H289.CB -10. 7.0 12.0 0.479638

#from t04-thin35.mi.constraints
Constraint E200.CB V235.CB -10. 7.0 12.0 0.604006
Constraint K96.CB S105.CB -10. 7.0 12.0 0.586423
Constraint T243.CB P258.CB -10. 7.0 12.0 0.572612
Constraint K277.CB H289.CB -10. 7.0 12.0 0.565897
Constraint K277.CB A288.CB -10. 7.0 12.0 0.506264

#from t04-thin40.mi.constraints
Constraint K277.CB H289.CB -10. 7.0 12.0 0.709731
Constraint T243.CB R320.CB -10. 7.0 12.0  0.52313
Constraint T243.CB H318.CB -10. 7.0 12.0 0.512988

#from t04-thin50.mi.constraints (>= 0.55)
Constraint F189.CB H318.CB -10. 7.0 12.0 0.682278
Constraint K277.CB H289.CB -10. 7.0 12.0 0.673889
Constraint H289.CB H318.CB -10. 7.0 12.0 0.609796
Constraint C245.CB D317.CB -10. 7.0 12.0 0.598091
Constraint F189.CB R274.CB -10. 7.0 12.0 0.592199
Constraint K223.CB S248.CB -10. 7.0 12.0 0.564697
Constraint F189.CB R220.CB -10. 7.0 12.0 0.556846

#from t04-thin62.mi.constraints (>=0.7)
Constraint C245.CB D317.CB -10. 7.0 12.0  1.28852
Constraint F189.CB R274.CB -10. 7.0 12.0 0.827748
Constraint K223.CB S248.CB -10. 7.0 12.0 0.820505
Constraint F189.CB H318.CB -10. 7.0 12.0 0.819495
Constraint F189.CB R220.CB -10. 7.0 12.0 0.803399
Constraint C245.CB R274.CB -10. 7.0 12.0 0.749143
Constraint F270.CB R315.CB -10. 7.0 12.0 0.737382


# try to make a ring of nearest-neighbor connections around the barrel

SheetConstraint	R315 D317	G4 R6		4
SheetConstraint F5   Y8  	L62 E65		3
SheetConstraint L62  E65	S100 C103	5

SheetConstraint V102 S105	Q150 G153	1
SheetConstraint S151 R155       K203 H207	1

SheetConstraint K203 H207	G241 C245	3
SheetConstraint I242 T246	N269 F273	4
SheetConstraint F270 F273	V313 P316	2