CreatePredAlphaCost pred_alpha2k alpha11 T0356.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0356.t04.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha06 alpha11 T0356.t06.alpha.rdb 2 alpha alpha_prev sum

SetCost wet6.5 15 near_backbone 5 way_back 5 dry5 15 dry6.5 30 dry8 25 dry12 6 \
	phobic_fit 2 \
	sidechain 5 \
	n_ca_c	5 bad_peptide 10 \
	bystroff 5 \
	soft_clashes 60  backbone_clashes 2 \
	break 250  \
	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 T0356.dssp-ehl2.constraints
#include T0356.undertaker-align.sheets
include rr.constraints

#Goal to remove the breaks

#try3-opt2.sheets

SheetConstraint (T0356)E350 (T0356)L356	(T0356)I370 (T0356)R364	hbond (T0356)E350	1
SheetConstraint (T0356)Y363 (T0356)V367	(T0356)A424 (T0356)V428	hbond (T0356)L365	1
SheetConstraint (T0356)F397 (T0356)D402	(T0356)R425 (T0356)V430	hbond (T0356)I399	1
SheetConstraint (T0356)V398 (T0356)D403	(T0356)G448 (T0356)L453	hbond (T0356)V400	1
SheetConstraint (T0356)D402 (T0356)D403	(T0356)E431 (T0356)N432	hbond (T0356)D403	1


#try3-opt2.helices
HelixConstraint (T0356)P326	(T0356)V339
HelixConstraint (T0356)V339	(T0356)F348
HelixConstraint (T0356)Y374	(T0356)Q391
HelixConstraint (T0356)R408	(T0356)D422
#HelixConstraint (T0356)P434	(T0356)S442
#HelixConstraint (T0356)F440	(T0356)S445
HelixConstraint (T0356)D474	(T0356)L488
HelixConstraint (T0356)D486	(T0356)N493