I tried to set the occupancy for those atoms 0.8 and refine individually. But obviously occupancies for those atoms are individually refined to different values which I dont think is the right way. Is there a way of how to refine occupancies for those atoms so that they remain identical after refinement (say all have 0.6)?
I'm a little surprised that the atoms within a residue aren't already constrained to be the same occupancy, but that may only apply if they're labeled as an alternate conformer. But I think all you need to do this is to define them as a constrained group, as described here:
(scroll down to Example 4 for the messy details.) If you're using the GUI, you can find the relevant controls by selecting "Occupancy" from the menu labeled "Modify atom selections for" below the strategy choices.
-Nat