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 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 2 \
	pred_alpha04 4 \
	constraints 35 \
	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

# fix two C-terminal helices with respect to strand S14 and conserved binding atom
constraint H224.CA  K277.CA     15.588     18.588	21.588	1.5
constraint H224.CA  N294.CA     29.787     32.787	35.787	1.5
constraint H224.CA  L298.CA     23.850     26.850	29.850	1.5
constraint H224.CA  S306.CA     29.540     32.540	35.540	1.5
			                         
constraint T232.CA  K277.CA     31.494     34.494	37.494	1.5
constraint T232.CA  N294.CA     41.096     44.096	47.096	1.5
constraint T232.CA  L298.CA     35.485     38.485	41.485	1.5
constraint T232.CA  S306.CA     45.224     48.224	51.224	1.5
			                         
constraint G240.CA  K277.CA     16.516     19.516	22.516	1.5
constraint G240.CA  N294.CA     29.504     32.504	35.504	1.5
constraint G240.CA  L298.CA     26.294     29.294	32.294	1.5
constraint G240.CA  S306.CA     36.823     39.823	42.823	1.5