CreatePredAlphaCost pred_alpha2k alpha11 T0375.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0375.t04.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha06 alpha11 T0375.t06.alpha.rdb 2 alpha alpha_prev sum

SetCost wet6.5 15 near_backbone 5 way_back 5 dry5 20 dry6.5 40 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  \
	pred_alpha2k 2 \
	pred_alpha04 2 \
	pred_alpha06 2 \
	constraints 50 \
	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 T0375.dssp-ehl2.constraints
# include T0375.undertaker-align.sheets
# include rr.constraints


#		from	try5	try6	try10
# dry5		15	20	same	same
# dry6.5	20	40	same	same
# dry8		15	20	same	same
# soft_clashes	20	40	same	same
# break		50	100	200	same
# constraints	10	50	same	same

# from monomer try6-opt2
HelixConstraint (T0375)G39	(T0375)G52	1
HelixConstraint (T0375)G64	(T0375)V70	1
HelixConstraint (T0375)F69	(T0375)R75	1
HelixConstraint (T0375)S119	(T0375)T129	1
HelixConstraint (T0375)M147	(T0375)N155	1
HelixConstraint (T0375)V170	(T0375)F181	1
HelixConstraint (T0375)S190	(T0375)H196	1
HelixConstraint (T0375)A202	(T0375)V213	1
HelixConstraint (T0375)G253	(T0375)Q268	1
HelixConstraint (T0375)S271	(T0375)G288	1
SheetConstraint (T0375)Q3 (T0375)V7     (T0375)P54 (T0375)M58   hbond (T0375)I4 1
SheetConstraint (T0375)I4 (T0375)C6     (T0375)W133 (T0375)H135 hbond (T0375)L5 1
SheetConstraint (T0375)V10 (T0375)L17   (T0375)G39 (T0375)S32   hbond (T0375)V11        1
SheetConstraint (T0375)V11 (T0375)L17   (T0375)P93 (T0375)I99   hbond (T0375)L12        1
SheetConstraint (T0375)G59 (T0375)A62   (T0375)T84 (T0375)Q87   hbond (T0375)M61        1
SheetConstraint (T0375)P93 (T0375)I99   (T0375)D112 (T0375)R106 hbond (T0375)I94        1
SheetConstraint (T0375)N100 (T0375)E101 (T0375)S105 (T0375)G104 hbond (T0375)E101       1
SheetConstraint (T0375)I134 (T0375)E137 (T0375)Q158 (T0375)E161 hbond (T0375)I136       1
SheetConstraint (T0375)D185 (T0375)S190 (T0375)A217 (T0375)A222 hbond (T0375)V187       1
SheetConstraint (T0375)D185 (T0375)F188 (T0375)Q158 (T0375)E161 hbond (T0375)F188       1
SheetConstraint (T0375)V218 (T0375)W223 (T0375)G232 (T0375)G227 hbond (T0375)L219       1
SheetConstraint (T0375)G227 (T0375)G232 (T0375)D241 (T0375)K236 hbond (T0375)A228       1