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