[phenixbb] Refinement with new mtz.file

Aleksandar Bijelic aleksandar.bijelic at univie.ac.at
Mon Jul 21 05:32:35 PDT 2014

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 Bijelic, MSc.

Institut für Biophysikalische Chemie
Universität Wien
Althanstrasse 14
A-1090 Wien

Tel: +43 1 4277 52536
e-Mail: aleksandar.bijelic at univie.ac.at


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