CreatePredAlphaCost pred_alpha2k alpha11 T0283.t2k.alpha.rdb 2 alpha alpha_prev sum
CreatePredAlphaCost pred_alpha04 alpha11 T0283.t04.alpha.rdb 2 alpha alpha_prev sum

SetCost wet6.5 15 near_backbone 5 way_back 5 dry5 20 dry6.5 25 dry8 15 	dry12 10 \
	phobic_fit 4 \
	sidechain 5 \
	n_ca_c	5 bad_peptide 10 \
	bystroff 5 \
	soft_clashes 20  backbone_clashes 2 \
	break 60  \
	pred_alpha2k 4 \
	pred_alpha04 4 \
	constraints 10 \
	hbond_geom 5 \
	hbond_geom_backbone 10 

# No reward for beta sheets in THIS protein
#	hbond_geom_beta 50 \
#	hbond_geom_beta_pair 100 

# from T0283.dssp-ehl2.constraints
# HelixConstraint 	F3	K25	0.682
# HelixConstraint 	K29	T44	0.7839
# HelixConstraint 	W51	A70	0.7193
# HelixConstraint 	T76	D77	0.6175
# HelixConstraint 	V83	D93	0.7024
# HelixConstraint 	M98	L105	0.6139

# split the first helix constraint
HelixConstraint 	F3	L11	07.00
HelixConstraint 	K14	K25	08.17

# shrink the second helix to higher-confidence region
HelixConstraint 	K29	W43	08.574

HelixConstraint 	W51	A70	07.193

# eliminate tiny 3-10 helix (V75-D77)
# HelixConstraint 	T76	D77	06.175

# shrink next helix to high-confidence region
HelixConstraint 	V83	K92	08.259

# shrink last helix to high-confidence region
HelixConstraint 	K100	L105	07.202


# 3-10 predictions
# from n_notor2
Hbond L27.N A24.O	0.54

Hbond G72.N A69.O	0.49
Hbond G72.N G68.O	0.31

# Hbond S10.N M7.O	0.32	alpha helix stronger
# Hbond Y31.N P28.O	0.31	alpha helix stronger


# from o_notor2
Hbond A24.O L27.N	0.52
Hbond A69.O G72.N	0.75
Hbond A70.O K73.N	0.34

Hbond M91.O T94.N	0.30


# packing the final helix
Constraint L105.CB V83.CB -10. 7.0 14.0	1
Constraint Y101.CB C87.CB -10. 7.0 14.0	1





# Constraints from rr.constraints, selected for conserved residues
#	that look like they ought to pair
Constraint F65.CB F86.CB -10. 7.0 14.0 3
Constraint L62.CB L90.CB -10. 7.0 14.0 3

# file generated by validate2rr
# Neural Net:
# logseploglen.5xt04_ent.5xnearNS_str2.miRpz_entR_pplR.n45.net
#
Constraint I61.CB V83.CB -10. 7.0 14.0 0.628027969049
Constraint I38.CB C87.CB -10. 7.0 14.0 0.548024496068
Constraint M42.CB L90.CB -10. 7.0 14.0 0.530248847174
Constraint M42.CB F58.CB -10. 7.0 14.0 0.478340422052 bonus
Constraint I38.CB I57.CB -10. 7.0 14.0 0.451668950804 bonus
Constraint I38.CB F65.CB -10. 7.0 14.0 0.43878890557 bonus
Constraint M42.CB I57.CB -10. 7.0 14.0 0.430372667619 bonus
Constraint L64.CB V83.CB -10. 7.0 14.0 0.429544348943 bonus
Constraint I38.CB I61.CB -10. 7.0 14.0 0.42798412964 bonus
Constraint I38.CB L90.CB -10. 7.0 14.0 0.424936352976 bonus
Constraint M7.CB A24.CB -10. 7.0 14.0 0.424118698291 bonus
Constraint I38.CB L62.CB -10. 7.0 14.0 0.380591509331 bonus
Constraint M42.CB I61.CB -10. 7.0 14.0 0.379896327948 bonus
Constraint F65.CB L90.CB -10. 7.0 14.0 0.376371371567 bonus
Constraint L62.CB L105.CB -10. 7.0 14.0 0.372840043725 bonus
Constraint F65.CB C87.CB -10. 7.0 14.0 0.36838849577 bonus
Constraint I38.CB L64.CB -10. 7.0 14.0 0.360996071233 bonus
Constraint I4.CB S45.CB -10. 7.0 14.0 0.357480344704 bonus
Constraint W43.CB A70.CB -10. 7.0 14.0 0.34840412127 bonus
Constraint W43.CB I61.CB -10. 7.0 14.0 0.342941125373 bonus
Constraint A24.CB M42.CB -10. 7.0 14.0 0.334186947808 bonus
Constraint I57.CB L105.CB -10. 7.0 14.0 0.320735779796 bonus
Constraint W43.CB L62.CB -10. 7.0 14.0 0.320495972758 bonus
Constraint W17.CB I38.CB -10. 7.0 14.0 0.320243203178 bonus
Constraint Y35.CB I61.CB -10. 7.0 14.0 0.315820623608 bonus
Constraint M42.CB F65.CB -10. 7.0 14.0 0.313379246208 bonus
Constraint W43.CB I57.CB -10. 7.0 14.0 0.307639380552 bonus
Constraint L62.CB V75.CB -10. 7.0 14.0 0.307261635054 bonus
Constraint I57.CB L90.CB -10. 7.0 14.0 0.303977259976 bonus
Constraint Y31.CB M42.CB -10. 7.0 14.0 0.302898762999 bonus