Hi everyone, I apologize at the beginning itself as I am new to using PHENIX/X-ray crystallography so this question might not make the most sense but I will try and explain it well. I cut out a part of a map for a PDB fragment using phenix map cut out density resulting in a MTZ file. Now I changed the fragment (changed its phi and psi externally) and want to calculate the RSR [real-space R -factor] for the model based on the old density (to check if I have made things worse or not). how can I go about this? I tried using phenix.refine couldn't get it to work. I have attached the MTZ fragment, the original PDB fragment and the modified PDB fragment. native: nativeFragment.pdb model: modelledFragment.pdb MTZ: cut_out_density.MTZ (I can see mine is worse but I want to quantify that "badness") Thank you, George