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[ccp4bb]: sigmaa weighted fo-fc omit map

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Dear all,

I would like to have some help to figure out what is going on difference
maps. The apo structure was solved at 1.8 A and well refined. A ligand
from a co-crystal was easily located by fo-fc omit map using the
apo-structure.  The fo-fc map is very clean and good enough to fit the
ligand. After all the refinement of the ligand into the co-crystal
structure, the sigmaa weighted fo-fc omit map was calculated, but it
is much worse that the starting fo-fc omit map.

I was always understood that the sigmma weighted fo-fc map should
be better.  Is is true?

Thank you in advance.
Youngsoo Kim