[phenixbb] Worse R factor with newer version of phenix

Jan van Agthoven janccp4 at gmail.com
Mon Oct 7 12:46:59 PDT 2013

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

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


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?


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