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.

# from try3-opt2
# HelixConstraint G39	V44
# HelixConstraint W42	G58
HelixConstraint V44	G58	#shrunk

# HelixConstraint D78	G95
HelixConstraint D81	G95	#shrunk

HelixConstraint S127	M138

# HelixConstraint Q139	K152
# HelixConstraint Q150	R155
HelixConstraint P140	R155	#merged

HelixConstraint Q166	M173

# HelixConstraint T178	I194
# HelixConstraint R192	E200
HelixConstraint T178	E199	# merged

HelixConstraint N224	V235
HelixConstraint D256	G265

# HelixConstraint G294	G309
HelixConstraint A299	G309	#shrunk

# HelixConstraint M328	Q354
HelixConstraint L333	Q354	#shrunk

# from T0208.t04.dssp-ehl2.constraints
#	(excluding helices already in try3-opt2)
StrandConstraint	F5	W7	0.6828
HelixConstraint 	L17	R21	0.6347
StrandConstraint	L61	E65	0.6549
StrandConstraint	S100	C103	0.645
StrandConstraint	K203	H207	0.6662
StrandConstraint	I242	F244	0.6575
StrandConstraint	F270	F273	0.7972

# 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	V102 S105	5

SheetConstraint V102 S105	Q150 G153	3
SheetConstraint S151 R155       K203 H207	3

SheetConstraint K203 H207	A239 T243	3
SheetConstraint I242 T246	N269 F273	4
SheetConstraint F270 F273	V313 P316	2

# from try3-opt2.sheets
# SheetConstraint R21 Q22  	I26 G25  	hbond Q22
SheetConstraint F270 F273	V313 P316	hbond V271

#from robetta1.sheets
# SheetConstraint W7 G9   	G28 V30  	hbond Y8
# SheetConstraint T27 T32  	L59 I64  	hbond V29
SheetConstraint S100 V102	G124 L126	hbond V102	#ok
# SheetConstraint E160 R163	I202 G205	hbond E162
SheetConstraint K203 H207	A239 T243	hbond M204	#ok
SheetConstraint T243 C245	F270 H272	hbond F244	#good
SheetConstraint V271 F273	I314 P316	hbond V271	#good

# 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 0.687658
Constraint E285.CB A327.CB -10. 7.0 12.0 0.687658
Constraint Y83.CB P253.CB -10. 7.0 12.0 0.641801
Constraint R187.CB A327.CB -10. 7.0 12.0  0.60583

#from t2k-thin62.mi.constraints
Constraint S66.CB P108.CB -10. 7.0 12.0 0.614792
Constraint E325.CB D335.CB -10. 7.0 12.0  0.56222
Constraint G312.CA Y342.CB -10. 7.0 12.0 0.552067

#from t04-thin30.mi.constraints
Constraint T90.CB I221.CB -10. 7.0 12.0 0.506812

#from t04-thin35.mi.constraints
Constraint K277.CB H289.CB -10. 7.0 12.0 0.638769
Constraint E200.CB V235.CB -10. 7.0 12.0  0.61731
Constraint T243.CB P258.CB -10. 7.0 12.0 0.601764
Constraint K96.CB S105.CB -10. 7.0 12.0 0.556903
Constraint K277.CB A288.CB -10. 7.0 12.0 0.525652

#from t04-thin40.mi.constraints
Constraint K277.CB H289.CB -10. 7.0 12.0 0.745627
Constraint T243.CB H318.CB -10. 7.0 12.0 0.561756
Constraint T243.CB R320.CB -10. 7.0 12.0 0.559147

#from t04-thin50.mi.constraints (>= 0.55)
Constraint F189.CB H318.CB -10. 7.0 12.0 0.731289
Constraint K277.CB H289.CB -10. 7.0 12.0 0.697363
Constraint H289.CB H318.CB -10. 7.0 12.0 0.661792
Constraint F189.CB R220.CB -10. 7.0 12.0 0.624775
Constraint C245.CB D317.CB -10. 7.0 12.0 0.613951
Constraint F189.CB R274.CB -10. 7.0 12.0 0.611381
Constraint K223.CB S248.CB -10. 7.0 12.0 0.601146
Constraint R220.CB H318.CB -10. 7.0 12.0 0.566736
Constraint F270.CB H289.CB -10. 7.0 12.0 0.562201
Constraint R274.CB H289.CB -10. 7.0 12.0 0.556868
Constraint N240.CB D317.CB -10. 7.0 12.0 0.556341


#from t04-thin62.mi.constraints (>=0.7)
Constraint C245.CB D317.CB -10. 7.0 12.0  1.29809
Constraint F189.CB H318.CB -10. 7.0 12.0 0.902121
Constraint F189.CB R274.CB -10. 7.0 12.0 0.887178
Constraint F189.CB R220.CB -10. 7.0 12.0 0.823757
Constraint K223.CB S248.CB -10. 7.0 12.0 0.813292
Constraint C245.CB R274.CB -10. 7.0 12.0 0.804197
Constraint F270.CB R315.CB -10. 7.0 12.0 0.762868
Constraint R274.CB D317.CB -10. 7.0 12.0 0.759125
Constraint D209.CB R274.CB -10. 7.0 12.0 0.716365
Constraint H289.CB P316.CB -10. 7.0 12.0  0.71208
Constraint F189.CB D317.CB -10. 7.0 12.0 0.706078
Constraint K277.CB H289.CB -10. 7.0 12.0 0.702122
Constraint F189.CB R315.CB -10. 7.0 12.0 0.701913