I've built several glucose molecules from my cryosolution into regions of weaker electron density. Attempting to refine the occupancies of the corresponding atoms, I set the value of each to 0.25 in the pdb file. However, after running phenix.refine, most of the atoms still have occupancies of 1.00:

14 atoms with occ = 0.00

5 atoms with 0.00 < occ < 1.00

74 atoms with occ = 1.00

Is this unusual?

Thank you!

Best,

Chris