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 40  backbone_clashes 2 \
	break 30  \
	pred_alpha2k 2 \
	pred_alpha04 4 \
	constraints 15 \
	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	3
Constraint D147.OD2	H224.NE2	0	2.943	5.9	3
Constraint H224.NE2	H145.NE2	0	3.233	6.2	3


# 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	5
constraint H224.CA  N294.CA     29.787     32.787	35.787	5
constraint H224.CA  L298.CA     23.850     26.850	29.850	5
constraint H224.CA  S306.CA     29.540     32.540	35.540	5
			                         
constraint T232.CA  K277.CA     31.494     34.494	37.494	5
constraint T232.CA  N294.CA     41.096     44.096	47.096	5
constraint T232.CA  L298.CA     35.485     38.485	41.485	5
constraint T232.CA  S306.CA     45.224     48.224	51.224	5
			                         
constraint G240.CA  K277.CA     16.516     19.516	22.516	5
constraint G240.CA  N294.CA     29.504     32.504	35.504	5
constraint G240.CA  L298.CA     26.294     29.294	32.294	5
constraint G240.CA  S306.CA     36.823     39.823	42.823	5