Pavel,
Thanks a lot! I found my situation in the letter you wrote:
4. Overlapping chains: It may happen
that stretches of two or more chains overlap in space such
that when one is present the other one isn’t . This
situation is not recognized automatically by phenix.refine
but can be dealt with successfully. This requires two
actions. Firstly, overlapping atoms of both chains need to
be assigned different altloc ; this will ensure that these
atoms will not be pushed apart by non-‐bonded repulsion.
Secondly, one needs to compose a parameter file telling
phenix.refine what occupancies need to be coupled; this will
override any default behavior applicable to these groups of
atoms.
But I feel I do not need to compose a
parameter file telling phenix.refine what occupancies need
to be couples as in your letter. I just edit it by Phenix
PDB Editor set two chains with different ID and set Atloc
for each chain, then set 0.5 occupancy for each chain and
run Phenix.Refine, it seems Phenix.Refine can handle it well
and not asking me to provide a parameter file about
occupancies.