[phenixbb] Rfree refuse to come down

#HEW KAI LI KELLY# KLHEW1 at e.ntu.edu.sg
Thu Mar 1 23:24:26 PST 2012


This may be a stupid question, but what are the things I should look out for to change if my Rfree goes up?

Kelly

On 2 Mar, 2012, at 3:17 PM, "Vellieux Frederic" <Frederic.Vellieux at ibs.fr> wrote:

> 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.
> 
> Fred.
> 
> 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...
> 
> #HEW KAI LI KELLY# wrote:
>> 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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