# 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

constraint	V60.CB	I80.CB	4.8	5.14	5.5	0.2
constraint	T61.CB	R81.CB	4.8	5.14	5.5	1.0
constraint	V62.CB	V82.CB	4.8	5.14	5.5	1.0
constraint	C63.CB	V83.CB	4.8	5.14	5.5	1.0
constraint	A64.CB	E84.CB	4.8	5.14	5.5	1.0


constraint	A116.CB	M159.CB	4.8	5.14	5.5	1.0
constraint	G117.CA	I160.CA	4.6	4.84	5.1	1.0
constraint	I118.CB	L161.CB	4.8	5.14	5.5	1.0
constraint	D119.CB	E162.CB	4.8	5.14	5.5	1.0


constraint	V237.CB	Q272.CB	4.8	5.14	5.5	1.0
constraint	L238.CB	V273.CB	4.8	5.14	5.5	1.0
constraint	L239.CB	I274.CB	4.8	5.14	5.5	1.0
constraint	S240.CB	K275.CB	4.8	5.14	5.5	1.0


# antiparallel

constraint	R81.CB	D94.CB	4.8	5.15	5.5	1.0
constraint	V82.CB	R93.CB	4.8	5.15	5.5	1.0
constraint	V83.CB	F92.CB	4.8	5.15	5.5	1.0
constraint	E84.CB	W91.CB	4.8	5.15	5.5	1.0
constraint	M85.CB	S90.CB	4.8	5.15	5.5	1.0
constraint	S86.CB	D89.CB	4.8	5.15	5.5	1.0

constraint	W91.CB	R102.CB	4.8	5.15	5.5	1.0
constraint	F92.CB	V101.CB	4.8	5.15	5.5	1.0
constraint	R93.CB	I100.CB	4.8	5.15	5.5	1.0
constraint	D94.CB	F99.CB	4.8	5.15	5.5	1.0
constraint	S95.CB	T98.CB	4.8	5.15	5.5	1.0