The RMSD minimization step in regularize for multi-chain PDB files
will go better after this update. Our strategy has been to minimize
individual chains first and then minimize the entire system together.
However, the alignment transformation obtained for each chain was
previously mistakenly applied to the whole system. So, the alignment
for the last chain essentially decided the chain positioning of all
the chains. This meant the final round of RMSD minimization started
at a sub-optimal starting point. Now with the correct application of
the alignment world matrix for each chain, we get much better whole
system RMSD in less time. The change does not involve the energy
minimization part of regularize, but that stage will now start from
different RMSD minimized structures, so the absolute numbers might
be different now.