Hi Alex,

While small discrepancies would not be surprising, 2.57 vs. 4.2 is quite different, and indicative that something is not working correctly. Would you be willing to send me the PDB file (offline) from phenix.refine that reports a clashscore of 2.57 so I can look into the behavior directly?

Thanks,
Jeff


On Sat, Apr 27, 2013 at 7:21 PM, Alex Theodossis <alex.theodossis@monash.edu> wrote:
Dear phenixbb,

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.


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