[phenixbb] Phenix auto-excluding some reflections

Hi, I'm in the process of depositing coordinates for a few structures and I noticed that the "number of unique reflections (observed)" is different in the "refinement statistics section" (108812) (read automatically from the phenix-refined pdb file) versus the "reflections" section (118749). The "cut- off sigma(F)" value is 0.12 (read automatically from the phenix-refined file). What criteria does phenix use to reject these ~10,000 reflections? Thanks! -Sam