I noticed Phenix refine default settings are using data labels "Imean" and "SigImean" instead of F and SigF. I searched this on the internet and found a post that titled "Phenix.refine Defaults Considered Harmful" ( web link  http://xray0.princeton.edu/~phil/Facility/phenix_fubar.html ). One point in this post shows that "the first thing the program does is ignore that structure factor data and use the IMEAN data instead."  This may force rejecting weak data according to the post. 

The latest Phenix version may be updated from the version the post author used, I wonder if this risk is still in the newest version of Phenix ?