Greetings all, and I hope this little observation helps improve things somehow. I did not expect this result, but there it is. My MolProbity score goes from 0.7 to 1.9 after a run of phenix.geometry_minimization I started with an AMBER-minimized model (based on 1aho), and that got me my best MolProbity score so far (0.7). But, even with hydrogens and waters removed the geometry_minimization run increases the clashscore from 0 to 3.1 and Ramachandran favored drops from 98% to 88% with one residue reaching the outlier level. Just for comparison, with refmac5 in "refi type ideal" mode I see the MolProbity rise to 1.13, but Clashscore remains zero, some Ramas go from favored to allowed, but none rise to the level of outliers. Files and logs here: https://bl831.als.lbl.gov/~jamesh/bugreports/phenixmin_070721.tgz I suspect this might have something to do with library values for main-chain bonds and angles? They do seem to vary between programs. Phenix having the shortest CA-CA distance by up to 0.08 A. After running thorough minimization on a poly-A peptide I get: bond amber refmac phenix shelxl Stryer C-N 1.330 1.339 1.331 1.325 1.32 N-CA 1.462 1.482 1.455 1.454 1.47 CA-C 1.542 1.534 1.521 1.546 1.53 CA-CA 3.862 3.874 3.794 3.854 So, which one is "right" ? Cheers, -James