Hi everyone, I've been working on a low resolution structure (3.6A) which was previously refined with phenix 1.8_1069 (with a reference model, strategy=individual_sites,individual_adp ). I used the same input files and parameters and ended up with significantly different R factors. Start: r_work = 0.2850 r_free = 0.3189 bonds = 0.005 angles = 1.059 Final: r_work = 0.2609 r_free = 0.3160 bonds = 0.003 angles = 0.997 For the old version and Start: r_work = 0.2779 r_free = 0.3183 bonds = 0.006 angles = 1.141 Final: r_work = 0.2889 r_free = 0.3303 bonds = 0.021 angles = 2.737 with the new version 1.8.4 Remarkably it also came with an increased number of C-beta deviation (0 against 16!). Adding tls refinement or ramachandran restrains did not help. Now because I was using the .eff file of an old version of phenix, it came with a long list of unused parameters. These parameters however were all used by default. What should I do? Should I go back to this old phenix, or is there a way to improve the result? Thanks,