Quick update:
as @mmclean suggested, I tried increasing the soft padding of my mask (from dilation 5, padding 5, to dilation 10, padding 25): great success!
Resolution is 5.8 Å, but it is pretty clean (before it supposedly was 5.6, but not really interpretable) . I can trace the whole backbone of the protein-of-interest, and I see blobs for larger residues that help adjusting the crystallographic model I am using.
This was done using the minimal map just around the POI, so I will now try to increase map size a bit to include the surrounding ribosomal proteins and RNA.
I’ll follow up once I have more updates (also with respect to @olibclarke suggestion regarding relion).
Thank you very much for the help!
Kind regards,
Luca