#CreatePredAlphaCost pred_alpha2k alpha11 T0331.t2k.alpha.rdb 2 alpha alpha_prev sum
#CreatePredAlphaCost pred_alpha04 alpha11 T0331.t04.alpha.rdb 2 alpha alpha_prev sum
#CreatePredAlphaCost pred_alpha06 alpha11 T0331.t06.alpha.rdb 2 alpha alpha_prev sum

SetCost wet6.5 15 near_backbone 5 way_back 5 dry5 15 dry6.5 25 dry8 20 dry12 5 \
	phobic_fit 2 \
	sidechain 5 \
	n_ca_c	5 bad_peptide 10 \
	bystroff 5 \
	soft_clashes 40  backbone_clashes 2 \
	break 100  \
	constraints 10 \
	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.

KnownBreak M150

#include T0331.dssp-ehl2.constraints
#include T0331.undertaker-align.sheets
#include rr.constraints

SheetConstraint (T0331)V15 (T0331)D22	(T0331)H33 (T0331)N26	hbond (T0331)G16	1
SheetConstraint (T0331)G16 (T0331)T20	(T0331)A66 (T0331)V62	hbond (T0331)V17	1
SheetConstraint (T0331)A36 (T0331)N38	(T0331)F43 (T0331)G41	hbond (T0331)N38	1
SheetConstraint (T0331)G41 (T0331)S47	(T0331)Y119 (T0331)M113	hbond (T0331)I42	1
SheetConstraint (T0331)Q60 (T0331)A66	(T0331)A83 (T0331)V77	hbond (T0331)V62	1
SheetConstraint (T0331)I74 (T0331)G81	(T0331)L128 (T0331)G121	hbond (T0331)V76	1
SheetConstraint (T0331)E80 (T0331)V86	(T0331)G121 (T0331)V115	hbond (T0331)R84	1
SheetConstraint (T0331)G121 (T0331)L128	(T0331)I138 (T0331)G131	hbond (T0331)G123	1
SheetConstraint (T0331)K133 (T0331)G139	(T0331)A148 (T0331)E142	hbond (T0331)I135	1

HelixConstraint (T0331)M1	(T0331)M13	1
HelixConstraint (T0331)T50	(T0331)D59	1
HelixConstraint (T0331)E87	(T0331)N98	1