[phenixbb] Refinement with new mtz.file
tg at shelx.uni-ac.gwdg.de
Mon Jul 21 07:05:17 PDT 2014
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
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.
Dr Tim Gruene
Institut fuer anorganische Chemie
GPG Key ID = A46BEE1A
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