Hello everyone, I am Esra Ayan. I would like to ask you about getting an error in Phenix: *Sorry: Fatal problems interpreting PDB file* *I followed the below command to resolve this issue:* 1. just running "phenix.ready_set MR.1.pdb" 2. then running "phenix.refine MR.1.updated.pdb MR.1.mtz MR.1.ligands.cif refinement.input.xray_data.r_free_flags.generate=True This way, i was able to solve the problem but still getting high Rwork and Rfree values. I still couldn't lower the values even though I tried many ways. What is your recommendation about this issue? i was wondering if I did a mistake by using Step 1 and Step 2 commands. You can find the reference pdb and mtz files in the attachment. Any help would be appreciated. Kind regards, Esra Ayan