CreatePredAlphaCost pred_alpha2k alpha11 T0219.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0219.t04.alpha.rdb 2 alpha alpha_prev sum

SetCost wet6.5 6 near_backbone 6 way_back 6 dry5 8 dry6.5 9 dry8 8 dry12 4 \
	phobic_fit 2 \
	sidechain 6 \
	bystroff 5 \
	soft_clashes 10  backbone_clashes 2 \
	break 5  \
	pred_alpha2k 2 \
	pred_alpha04 4 \
	constraints 40 \
	hbond_geom 1.0 \
	hbond_geom_backbone 1.0 \
	hbond_geom_beta 5.0 \
	hbond_geom_beta_pair 15.0

// 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,
//	sheet constraints, ssbonds, hbonds, or just arbitrary pairs of atoms.

include T0219.t2k.dssp-ehl2.constraints
include T0219.t2k.dssp-ebghstl.constraints
include T0219.t2k.stride-ebghtl.constraints
include T0219.t2k.str2.constraints
include T0219.t2k.alpha.constraints
include T0219.t2k.bys.constraints

include T0219.t04.dssp-ehl2.constraints
include T0219.t04.dssp-ebghstl.constraints
include T0219.t04.stride-ebghtl.constraints
include T0219.t04.str2.constraints
include T0219.t04.alpha.constraints
include T0219.t04.bys.constraints

# for the metal binding site, constrain the strongly conserved residues
# with desired measurements from the 1mzeA template
Constraint D147.OD1	H145.NE2	0	3.824	6.8	1
Constraint D147.OD2	H224.NE2	0	2.943	5.9	1
Constraint H224.NE2	H145.NE2	0	3.233	6.2	1


# Define all the strands, but only emphasize the ones that are having
# trouble forming, since the sheet constraints should get the rest.
StrandConstraint T5   S7   1
StrandConstraint E10  S11  1
StrandConstraint L31  R34  1
StrandConstraint Y59  V66  1
StrandConstraint F81  A88  1
StrandConstraint G95  T103 4	# s6 did not appear spontaneously
StrandConstraint K130 K137 1
StrandConstraint G140 F142 1
StrandConstraint A144 F146 1
StrandConstraint Y149 Q157 1
StrandConstraint E159 K166 1
StrandConstraint A205 T211 1
StrandConstraint T214 P219 1
StrandConstraint W223 S228 1
StrandConstraint T232 G240 1


# Sheet constraints, mostly from 1mzeA alignment, as improved by tries

# from alignment to 1mzeA
SheetConstraint T5  V8		A205 V208	hbond E6  	5	# s1  || s11
SheetConstraint E10 S11		V32  A33	hbond S11 	10	# s2  || s3
SheetConstraint L31 R34		Y217 T214	hbond A33 	10	# s3  ^v s12
# from try1-opt2
SheetConstraint Y59 V66		A88  F81	hbond V63 	10	# s4  ^v s5
# add two constraints to insert one strand (S6) antiparallel between two others (S4,S7)
SheetConstraint Y59  V66 	F102 G95 	hbond M64 	10	# s4  ^v s6
SheetConstraint A96  T103	K137 K130	hbond L98 	5	# s6  ^v s7
# from try1-opt2
SheetConstraint K130 K137	T238 A231	hbond Y134	5	# s7  ^v s14
# from alignment to 1mzeA
# kink not needed in strand without Pro at 143, so combine constraints?
SheetConstraint G140 F142	S228 T226	hbond F142	5	# s8a ^v s13
SheetConstraint A144 F146	S225 W223	hbond H145	5	# s8b ^b s13
# from alignment to 1mzeA
SheetConstraint Y149 Q157	G240 T232	hbond T150	5	# s9  ^v s14
SheetConstraint T150 Q155	P219 T214	hbond N151	5	# s9  ^v s12
SheetConstraint E159 A165	T211 A205	hbond K160	5	# s10 ^v s11
SheetConstraint E159 K166	D229 L222	hbond T161	5	# s10 ^v s13

# attempt to bury some of C-terminal helix to a cleft in the remainder of model
constraint A251.CB 	Y25.CE2     -10 	5.0	10.0	6.5
constraint A251.CB 	Y217.CE2    -10 	5.0	10.0	6.5
constraint F262.CZ	I237.CD1    -10 	5.0	10.0	6.5
constraint F262.CZ	A131.CB     -10 	5.0	10.0	6.5
			                         
# attempt to bury some of C-terminal helix to a cleft in the remainder of model
constraint L280.CD2 	L152.CD1    -10 	5.0	10.0	6.5
constraint L284.CD2 	F154.CZ     -10 	5.0	10.0	6.5
constraint L284.CD2 	I237.CD1    -10 	5.0	10.0	6.5
constraint L291.CD1 	L235.CD2    -10 	5.0	10.0	6.5
constraint L291.CD1 	I156.CD1    -10 	5.0	10.0	6.5

# attempt to bury some of C-terminal helix 
# constraint W244.CH2 	F330.CE     -10 	5.0	10.0	6.5