I have carried out refinement using the latest version of PHENIX, which gives improved molprobity stats. However, these stats still do not match those porvided by the molprobity server:

                                   PHENIX output                                   Molprobity server

                                                                       Existing H-model           Electron-cloud  H-model

All atom clashscore             2.57                           4.2 (81st perc)                 3.25 (88th percentile)

Rotamer outliers                   0.7                              1.14                                     1.14

Overall score                      1.04                         1/24 (89th perc)                   1.16 (93rd percentile)

Given that PHENIX is now giving me the best results and all scenarios give reasonable results I am less inclined to be concerned. However, I still find these inconsistencies rather puzzling and am curious to learn what is causing them.

Thanks in advance.