Dear Tom Peat, Chenghua Shao, Clemens Vonrhein, Nicholas Noinaj, and everyone, Thank you all very much for your helpful advice and for taking the time to respond. I really appreciate your guidance. Based on your suggestions, I understand that the correct approach is to reprocess the diffraction data in P 63 and then carry out the final refinement in that space group. Unfortunately, I do not currently have access to the raw diffraction images. At the moment, I only have the processed files generated during data processing (MTZ, HKL, log, and related files), which are listed below. CORRECT.lp XDS_SCALE.hkl XSCALE (1).lp D1_1_xds.mtz (unmerged) D1_1_xds.log D1_1_aimless.mtz D1_1_aimless.log D1_1_truncate.mtz D1_1_truncate.log D1_1_pointless.log Would it be possible to perform any re-scaling or other processing in Phenix (or another program) using only these files? Thank you again for your time and for sharing your expertise. Your explanations have been extremely helpful in understanding the source of the problem. Best regards, Betul