CreatePredAlphaCost pred_alpha2k alpha11 T0344.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0344.t04.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha06 alpha11 T0344.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 50  backbone_clashes 2 \
	break 200  \
	pred_alpha2k 2 \
	pred_alpha04 2 \
	pred_alpha06 2 \
	constraints 40 \
	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 T0344.dssp-ehl2.constraints
#include T0344.undertaker-align.sheets
#include rr.constraints

# from try15-opt2.sheets
SheetConstraint (T0344)P33 (T0344)R35	(T0344)D75 (T0344)I77	hbond (T0344)Y34	1
SheetConstraint (T0344)Y34 (T0344)R35	(T0344)P47 (T0344)Y48	hbond (T0344)R35	1
SheetConstraint (T0344)V72 (T0344)P74	(T0344)L29 (T0344)E31	hbond (T0344)K73	1
SheetConstraint (T0344)V139 (T0344)A144	(T0344)G169 (T0344)M174	hbond (T0344)V141	1
SheetConstraint (T0344)S187 (T0344)P190	(T0344)Y196 (T0344)G193	hbond (T0344)D189	1

# from try15-opt2.helices
HelixConstraint (T0344)L13 (T0344)E18	1
HelixConstraint (T0344)D51 (T0344)L68	1
HelixConstraint (T0344)G84 (T0344)E93	1
HelixConstraint (T0344)L91 (T0344)L99	1
HelixConstraint (T0344)K104 (T0344)D115	1
HelixConstraint (T0344)L116 (T0344)F123	1

# this one was modified
HelixConstraint (T0344)I129 (T0344)I134	1

HelixConstraint (T0344)Y151 (T0344)I167	1
HelixConstraint (T0344)L195 (T0344)V203	1
HelixConstraint (T0344)P215 (T0344)K228	1

SheetConstraint N177 K179	I184 K182	Hbond N177	1

Hbond I129.N	W124.O	1
Hbond I101.N	I96.O	1

Hbond G194.O	D189.N	1
Hbond E192.N	D189.O	1

Hbond V201.O	K208.N	0.5
Hbond V201.O	W209.N	0.5