in some of my macromolecular crystal structures with resolutions between 1.1 - 1.4 Å, several round positive Fo-Fc electron density blobs are detectable which show after assignment of a water molecule to these blobs and subsequent refinement with Phenix.refine a good-looking 2Fo-Fc electron density. However, there also occurs a small negative Fo-Fc electron density detectable inside the 2Fo-Fc density blob. The negative Fo-Fc electron density disappears if the occupancy of the water molecule is automatically refined by Phenix.refine (occupancy manually set to a value below 100% followed by refinement) or manually set to 50% and fixed for this value (Fix occupancy option in phenix.refine). Therefore, I think these positions are partly occupied by water molecules, but I am not sure how I should handle it/how it is generally handled. Which one of the two options described above is the better one? I would be thankful for any advice and/or literature about this topic.

When I had to deal with this in the past, I followed this advice (from Thomas Schneider):

http://www.embl-hamburg.de/~tschneider/shelxl/shelxl_faq/shelxlfaq.html#Q16

This is especially true at the resolutions you're working with; even with subatomic resolution data I believe that the observation in the FAQ (that refining the occupancies doesn't improve R-factors and may even make them worse) will be true in most cases - and regardless of program used, btw. (I can't remember if I ever tried comparing the outcomes myself, though.)

-Nat