//CreatePredAlphaCost pred_alpha2k alpha11 T0368.t2k.alpha.rdb 2 alpha alpha_prev sum
//CreatePredAlphaCost pred_alpha04 alpha11 T0368.t04.alpha.rdb 2 alpha alpha_prev sum
//CreatePredAlphaCost pred_alpha06 alpha11 T0368.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 100  \
	constraints 50	\
	hbond_geom 7 \
	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.

//this is the first residue of the ligand
KnownBreak G175

//these are all the constraints that the ligand has on one side:
//PRO176.CB-LEU99.CB: 4.099
//ILE178.CB-SER102.CA: 5.345
//ILE178.CB-TYR105.CG: 5.974
//VAL181.CB-TYR105.CZ: 4.351
//ASP182.HN-LEU109.CG: 2.842 replaced by ASP182.N-LEU109.CG: 3.779
//LYS98.NZ-GLY175.CA: 3.679
//PRO176.O-LYS98.NZ: 3.377

Constraint P176.CB L99.CB -10.0  4.0 5.0 1
Constraint I178.CB S102.CA -10.0  5.3 6.5 1
Constraint I178.CB Y105.CG -10.0  5.9 7.0 1
Constraint V181.CB Y105.CZ -10.0  4.3 5.7 1
Constraint D182.N L109.CG -10.0  3.7 5.0 1 
Constraint K98.NZ G175.CA -10.0  3.6 5.0 1
Constraint P176.O K98.NZ -10.0  3.3 4.5 1

//the ligand interacts with the other helix:

//GLU179.CG-GLU64.CA: 3.731
//GLU64.CD-THR177.O: 3.245
//ASP182.CG-ALA67.C: 4.672
//PHE57.CD1-THR177.HN: 5.474 replaced by THR177.N-PHE57.CE1: 5.689
//PHE57.CD1-PRO176.CB: 5.675

Constraint E179.CG E64.CA -10.0  3.7 5.0 1
Constraint T177.O E64.CD -10.0  3.2 4.5 1
Constraint D182.CG A67.C -10.0  4.6 6.0 1 
Constraint T177.N F57.CE1 -10.0  5.6 7.0 1 
Constraint P176.CB F57.CD1 -10.0  5.6 7.0 1