To make this model we fussed around a bit with strand pairing to try
to get the alignment to produce a sheet with consistent exposure of
the charged residues.  We also had to tuck the initial and final
helices out of the dimerization interface and what we believed to be
the DNA-binding face.  

We played around mainly with a monomeric model, since undertaker only
understands monomers, but this did not seem to cause much trouble for
us, other than for the initial and final helices.

This is the version output by undertaker, before the dimer repacking
in Rosetta to form model1.