Dear Nathaniel, dear Pavel, thank you for your fast answers!

currently phenix.refine can add automatically only fully occupied waters (I am not sure it will ever use atomic model for partially occupied waters). If necessary, add partially occupied waters yourself manually. Make sure they have properly set altlocs (alternative location identifiers): non blank (say A and B).

Is it current praxis to let phenix.refine freely refine the occupancy of water molecules (adding partially occupied water molecules in coot and don’t fix the occupancy in phenix)? If I do so, these water molecules are refined by phenix.refine with occupancies between 0.4-0.8. My resolution range was 1.1 – 1.4 Å.

The nightly builds have an option in phenix.refine to place ions automatically based on a variety of criteria (still being tuned). However, what you describe doesn't sound like any ion coordination motif that I've read about. Could you please send us a picture that shows the density in context? Some of the other readers with more experience in "blobology" may recognize it. [if our list server complains about the size of the message, just ignore it, I'll approve it for posting]

Attached you will find the image of the blob. I think it’s easily visible that the density blob is in the middle of the five-ring and that there is also a (smaller) blob in the middle of the six-ring. The water which occupies the blob was not yet refined with phenix, I just put it there to measure the distances to the carbon atoms. Best regards, Stefan