There is no blue (2fo-fc) density at least at the current contour level
in your difference density.  That probably indicates what you are seeing
is noise rather than a real feature.

I am also seeing more intense (above 7 sigma in some cases) positive
difference density without actual density in my current refmac refined
structure than I am used to.

I ascribed this to being in P1 with significant anisotropy leading to
ripples???, but if this is widespread then there may have been tweaks to
the software.  Anyone else want to comment on this

Best wishes

Nick

--
Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

email     [log in to unmask]
Telephone 020-7631-6852  (Room G54a Office)
           020-7631-6800  (Department Office)
Fax       020-7631-6803
If you want to access me in person you have to come to the crystallography entrance
and ring me or the department office from the internal phone by the door

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