We started out by cleaning up tr366, running it through gromacs and
repacking the sidechains with rosetta.  This improved its score with
undertaker cost functions without moving anything very far.

We then superimposed that model on two different dimers (1tp5 and
1g9o) and did all further optimizations in the dimer context.
The original model was compatible with the 1tp5 dimerization, but had
serious clashes in the 1g9o dimerization, so that the optimization
needed to reshape the C-terminus.

Here is the record of optimizations tried:

try6-opt2:	optimized by undertaker from dimer-tr366-1tp5
try6-opt2.repack-nonPC:	sidechains repacked by Rosetta on backbone of try6-opt2
try6-opt2.unpack.gromacs0:	optimized by gromacs from try6-opt2 dimer
try6-opt2.unpack.gromacs0.repack-nonPC:	sidechains repacked by Rosetta
	on backbone of try6-opt2.unpack.gromacs0

try7-opt2:	optimized by undertaker from try6-opt2.unpack.gromacs0
try7-opt2.repack-nonPC:	sidechains repacked by Rosetta on backbone of try7-opt2
try7-opt2.unpack.gromacs0:	optimized by gromacs from try7-opt2 dimer
try7-opt2.unpack.gromacs0.repack-nonPC:	sidechains repacked by Rosetta
	on backbone of try7-opt2.unpack.gromacs0

try8-opt2:	optimized by undertaker from try7-opt2.unpack.gromacs0.repack-nonPC
try8-opt2.repack-nonPC:	sidechains repacked by Rosetta on backbone of try8-opt2
try8-opt2.unpack.gromacs0:	optimized by gromacs from try8-opt2 dimer
try8-opt2.unpack.gromacs0.repack-nonPC:	sidechains repacked by Rosetta
	on backbone of try8-opt2.unpack.gromacs0
	
try9-opt2:	optimized by undertaker from dimer-tr366-1g9o
try9-opt2.repack-nonPC:	sidechains repacked by Rosetta on backbone of try9-opt2
try9-opt2.unpack.gromacs0:	optimized by gromacs from try9-opt2 dimer
try9-opt2.unpack.gromacs0.repack-nonPC:	sidechains repacked by Rosetta
	on backbone of try9-opt2.unpack.gromacs0

try10-opt2:	optimized by undertaker from try9-opt2.unpack.gromacs0
try10-opt2.repack-nonPC:	sidechains repacked by Rosetta on backbone of try10-opt2
try10-opt2.unpack.gromacs0:	optimized by gromacs from try10-opt2 dimer
try10-opt2.unpack.gromacs0.repack-nonPC:	sidechains repacked by Rosetta
	on backbone of try10-opt2.unpack.gromacs0

try11-opt2:	optimized by undertaker from dimer-tr366-1g9o
try11-opt2.repack-nonPC:	sidechains repacked by Rosetta on backbone of try11-opt2
try11-opt2.unpack.gromacs0:	optimized by gromacs from try11-opt2 dimer
try11-opt2.unpack.gromacs0.repack-nonPC:	sidechains repacked by Rosetta
	on backbone of try11-opt2.unpack.gromacs0

try12-opt2:	optimized by undertaker from try11-opt2
try12-opt2.repack-nonPC:	sidechains repacked by Rosetta on backbone of try12-opt2
try12-opt2.unpack.gromacs0:	optimized by gromacs from try12-opt2 dimer
try12-opt2.unpack.gromacs0.repack-nonPC:	sidechains repacked by Rosetta
	on backbone of try12-opt2.unpack.gromacs0
	
Two of our models came from the 1tp5 dimerization. We put them first
because they are closer to the original that we were refining.

    Refinement 1 is chain A of try8-opt2, the best-scoring of the
	models based on 1tp5 dimerization, at least with cost
	functions with high break penalties. (try7-opt2 does better
	when clashes are more important.)

    Refinement 2 is chain A of try7-opt2.unpack.gromacs0.repack-nonPC,
	the dimer model that rosetta liked best of those it repacked.

Three of our models came from the 1g9o dimerization:

    Refinement 3 is chain A of try12-opt2, which scored the best (in
	several costfcns) of the 1g9o dimerizations.  It may have been
	helped by almost forming an antiparallel sheet between the two
	monomers (L36-P40 to P40-L36).
	
    Refinement 4 is chain A of try9-opt2.unpack.gromacs0.repack-nonPC.
	It was the version of the backbone that rosetta most liked
	repacking among the 1g9o-based dimers.
	
    Refinement 5 is chain A of try10-opt2.  It did not score quite as
	well as some of the other 1g9o dimers, but it provides a
	different N-terminus than any of the others.