The supplied conformation was superimposed on our previous complete
models, and the missing residues were grafted on. Residues 1-5 were
taken from T0288.try2-opt2.repack-nonPC.pdb and 87-end from the first
undertaker-align model (an alignment with 1g9oA).

The resulting chimera was optimized with  undertaker to produce
try6-opt2 (Model 5).

The model was further optimized by undertaker for try7-opt2 (Model 3)
which also had th sidechains repacked by rosetta (Model 4).  This
optimization included alignment insertion, which is almost the same as
starting over with a different initial model, which is not in the
spirit of the refinement experiment. However, try8-opt2 came from an
optimization run with the same starting points and cost function, but
with alignment insertion turned off.  It arrived at a very similar
model to try7-opt2.

try9-opt2 is the optimization of try8-opt2 with break and clash costs
turned up high. It is probably about as good as we can get with the
crude cost functions of undertaker.  It is submitted as model 1, 
and the same backboen with sidechains repacked by rosetta is submitted
as model 2.