[phenixbb] Rfree refuse to come down

Vellieux Frederic Frederic.Vellieux at ibs.fr
Thu Mar 1 23:16:14 PST 2012

A couple of things:

TFZ of 9 is on the lowish side therefore one could question the validity 
of the MR solution, are all protein molecules correctly positioned for 
example. Are there domains and subdomains that have moved in your 
structure relative to your search model?

with 4-fold NCS you can use the redundancy to 1) improve the maps by 
iterative NCS averaging; 2- use NCS contraints (then restraints later 
on) during refinement.


PS refinement of a model does not mean "bring R-free down", the R-free 
going up is a symptom that should be investigated and the causes of it 
then treated...

> HI,
> I have a few questions about a dataset that I am working on currently.
> So I ran Xtraige and it tells me that other than pseudoNCS, there is 
> no other problems like twinning etc. And then I used autoMR and Phaser 
> from Phenix to run molecular replacement with a the structure of the 
> same protein (but that is with DNA bound). The TFZ is more than 9 
> after from both the runs. Autobuild managed to build the 4 molecules 
> in my ASU (Rfactor/Rfree = 28/32 for a resolution of 2.4A). But 
> because there are some clashes and outliers in the Ramachandran Plot 
> etc, I started to manually refine them in coot. In addition, there is 
> a loop that is unable to fit into the density, so I chopped about 10 
> residues off each molecule in the ASU.
> However, as I started to refine the model from AutoBuild, my Rfree 
> begins to climb. So currently, I am at Rfactor/Rfree=27/36. I don't 
> know if there is anything wrong with I had done. So many thanks in 
> advance for your advices on this!!
> Warmest Regards,
> Kelly Hew
> Nanyang Technogical University
> School of Biological Sciences
> Division of Structural Biology & Biochemistry
> Address : #07-01, IMCB, 61 Biopolis Drive, Proteos, Singapore 138673 
> Telephone (O): +65 65869673
> Telephone (HP): +65 98713553
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