CreatePredAlphaCost pred_alpha2k alpha11 T0354.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0354.t04.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha06 alpha11 T0354.t06.alpha.rdb 2 alpha alpha_prev sum

SetCost wet6.5 15 near_backbone 5 way_back 5 dry5 15 dry6.5 20 dry8 15 dry12 5 \
	phobic_fit 2 \
	sidechain 5 \
	n_ca_c	5 bad_peptide 10 \
	bystroff 5 \
	soft_clashes 20  backbone_clashes 2 \
	break 50  \
	pred_alpha2k 2 \
	pred_alpha04 2 \
	pred_alpha06 2 \
	constraints 30 \
	hbond_geom 5 \
	hbond_geom_backbone 10 \
	hbond_geom_beta 50 \
	hbond_geom_beta_pair 100 \
	missing_atoms 1 \
	maybe_metal 0.5 \
	maybe_ssbond 1

// remove maybe_ssbond weight if protein known to be in reducing environment.
// remove maybe_metal weight if protein known to have disulfides or
//	known not to bind metal ions.

// Add the following for extra-cellular proteins:
#	known_ssbond 0.5	# and put ssbond command in constraints file

// 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 T0354.dssp-ehl2.constraints

#using str2 T06
HelixConstraint 	I3	I17	0.639
StrandConstraint	I22	D26	0.61
StrandConstraint	R36	A40	0.656
HelixConstraint 	N45	E61	0.682
#strand too short according to costfcn output!
#StrandConstraint	S69	E70	0.647
StrandConstraint	W77	D81	0.788
StrandConstraint	V85	V89	0.64
HelixConstraint 	V94	R95	0.611
HelixConstraint 	Y98	A102	0.633
HelixConstraint 	S120	V122	0.626

#include T0354.undertaker-align.sheets
#use try5's sheets instead
SheetConstraint (T0354)L9 (T0354)E15	(T0354)R36 (T0354)G42	hbond (T0354)I11	1
SheetConstraint (T0354)A10 (T0354)E15	(T0354)G83 (T0354)H88	hbond (T0354)E12	1
SheetConstraint (T0354)R36 (T0354)G42	(T0354)I66 (T0354)H72	hbond (T0354)I38	1
SheetConstraint (T0354)V85 (T0354)V89	(T0354)Q107 (T0354)F111	hbond (T0354)V87	1

#include rr.constraints
#we only include those that occur within the sheets

Constraint L25.CB M37.CB -10. 7.0 14.0 0.807288213983
Constraint M37.CB V86.CB -10. 7.0 14.0 0.770010187903
Constraint I38.CB V78.CB -10. 7.0 14.0 0.767390268185
Constraint I38.CB L79.CB -10. 7.0 14.0 0.764525241634
Constraint V39.CB L79.CB -10. 7.0 14.0 0.761464129615
Constraint V39.CB V86.CB -10. 7.0 14.0 0.746278399529
Constraint V39.CB V87.CB -10. 7.0 14.0 0.745259844462
Constraint I38.CB V86.CB -10. 7.0 14.0 0.737509021681
Constraint I38.CB V87.CB -10. 7.0 14.0 0.726304915947
Constraint V39.CB V85.CB -10. 7.0 14.0 0.713090934171
Constraint I38.CB V80.CB -10. 7.0 14.0 0.708205137942
Constraint L79.CB V89.CB -10. 7.0 14.0 0.699168865986
Constraint I22.CB L79.CB -10. 7.0 14.0 0.679380574234
Constraint M37.CB V80.CB -10. 7.0 14.0 0.657419001885
Constraint V39.CB V80.CB -10. 7.0 14.0 0.65587210542
#Constraint S7.CB V80.CB -10. 7.0 14.0 0.647592941241
Constraint V39.CB V78.CB -10. 7.0 14.0 0.645022042891
Constraint I38.CB V85.CB -10. 7.0 14.0 0.644221360566
Constraint G42.CA V78.CB -10. 7.0 14.0 0.638311562451
#Constraint V48.CB V78.CB -10. 7.0 14.0 0.624008216968
Constraint A40.CB L79.CB -10. 7.0 14.0 0.607564271799
Constraint M37.CB L79.CB -10. 7.0 14.0 0.603136008327
#Constraint L51.CB L79.CB -10. 7.0 14.0 0.598675063943
Constraint V39.CB H88.CB -10. 7.0 14.0 0.577786514847
Constraint V39.CB V89.CB -10. 7.0 14.0 0.574545657816
Constraint L25.CB I38.CB -10. 7.0 14.0 0.568695774705
Constraint F34.CB L79.CB -10. 7.0 14.0 0.56483942718
Constraint L25.CB L79.CB -10. 7.0 14.0 0.563711935742
#Constraint V48.CB L79.CB -10. 7.0 14.0 0.562088783818
#Constraint L9.CB L79.CB -10. 7.0 14.0 0.555574388845
Constraint I38.CB V89.CB -10. 7.0 14.0 0.551593755111
#Constraint I38.CB L51.CB -10. 7.0 14.0 0.550232884296
Constraint V78.CB V87.CB -10. 7.0 14.0 0.537587924511
Constraint W77.CB V86.CB -10. 7.0 14.0 0.536464358571
Constraint L79.CB H88.CB -10. 7.0 14.0 0.534425473826
#Constraint M37.CB V48.CB -10. 7.0 14.0 0.533311593799
Constraint L25.CB V86.CB -10. 7.0 14.0 0.528350849769
Constraint I22.CB I38.CB -10. 7.0 14.0 0.524857434256
#Constraint V55.CB L79.CB -10. 7.0 14.0 0.523339036332
#Constraint A52.CB V86.CB -10. 7.0 14.0 0.522953935409
#Constraint L59.CB L79.CB -10. 7.0 14.0 0.51250669752
Constraint V80.CB V89.CB -10. 7.0 14.0 0.512495694637
Constraint I22.CB M37.CB -10. 7.0 14.0 0.511813515859
#Constraint I38.CB A52.CB -10. 7.0 14.0 0.506575994482
#Constraint I38.CB V55.CB -10. 7.0 14.0 0.505253882506
#Constraint M37.CB L51.CB -10. 7.0 14.0 0.5044028679
Constraint V78.CB H88.CB -10. 7.0 14.0 0.500132598182