[phenixbb] Refinement with new mtz.file

Tim Gruene tg at shelx.uni-ac.gwdg.de
Mon Jul 21 07:05:17 PDT 2014

Dear Aleksandar,

the small gap between R and Rfree are indicative that you contaminated
your Rfree set, and very likely you overrefined your structure.

Did you copy the Rfree set from the old mtz-file to the new one? If not,
this would explain the small gap between R and Rfree.

You can add some noise to your PDB file to make it independent from the
Rfree set. Maybe this will also help to reduce the overrefinement a bit.

Do you have many water molecules in the structure? at 3A resolution you
should not see too many of them, and the more you add the lower your
R-value gets.

Also make sure that all atoms have full occupancy. Less experienced
users seem to refine occupancies in a chemically non-realistic way.


On 07/21/2014 02:32 PM, Aleksandar Bijelic wrote:
> Dear CCP4 user and experts,
> I refined (with PHENIX) a 3.0 A dataset obtaining Rfree of about 0.24
> (with good geometry according to Ramachandran, Beta Outliers, etc.) ....
> Everything seems to be ok (especially in relation to the resolution)
> .... because the mtz.file I used was quite old and I cannot find my
> xscale.hkl file, I processed the data set again (this time with
> optimizng and polishing) and received a "better" file according to
> almost everything (resolution limit, I/sigma, CC(1/2), Rmeas), thus I
> used this new mtz.file and put it in my last refinement step (the
> refinement which led to the above mentioned Rfree = 0.24). Suprisingly,
> the refinement starts at Rwork = 0.18 and Rfree = 0.19 but ending up
> with 0.20 and 0.22, respectively. So I wanted to know if this is usual?
> I was expecting my data to become slightlly better but what is
> irritating me is the starting R-values of the refinement and that it get
> worse during refinement. Maybe I did something wrong? Is it reasonable
> to replace the mtz.file with a new one in the last refinement step or
> should I start the refinement from the scratch? In the sake of
> completeness, I deleted the header of the used pdb.file because of the
> R-flag error which occurs, since Phenix reconizes that the pdb.file was
> already used with other Rflags. Sorry, but I am still a beginner in this
> field, so I would be very grateful if somebody could explain me this
> situation and my mistake and if I need to start refinement from the
> beginning. Thank you in advance!
> Best Regards.
> Aleksandar

Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen


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