Hi, Ian Tickle has asked the most pertinent question - there are many
reasons for highish FreeR factors. Only some are due to errors or missing
molecules or other problems. How many "Free" reflections are there? When
the sample is very small (< 500 say) you can get different results from a
different Free R set.
And remember that the numbers you quote are overall values,
It is worth looking at the plot of R and Free R against resolution. They
should stay reasonably parallel, but if the data becomes very weak at the
resolution limit the the FreeR can shoot up relative to the overall Rvalue.
I use COOT validation to search the difference maps for peaks and holes.
If there is something missing from your model you should see it in that
list..
Eleanor
On Wed, 13 Jul 2011 20:37:51 +0100, Matthias Zebisch
<[log in to unmask]> wrote:
> Hi Careina,
>
> our lab we once had the problem, that the asymmetric unit contained 8
> molecules,
> whereas 7 had only been modeled. Somehow the 8th monomer had evaded
> detection.
> So be careful not to miss density.
>
> Matthias
>
>
> On 7/13/2011 7:54 PM, Robbie Joosten wrote:
>> Hi Careina,
>>
>>
>>
>> Assuming you don't suffer from a very poor data parameter ratio that
>> would lead to such a large R-free/R, you need to improve your
refinement.
>> If you have NCS you should use local NCS restraints. You could also try
>> jelly-body restraints, although they may not work at your resolution.
>>
>>
>>
>> Cheers,
>>
>> Robbie
>>
>> ________________________________
>>> Date: Wed, 13 Jul 2011 08:38:38 -0700
>>> From: [log in to unmask]
>>> Subject: [ccp4bb] large R-Rfree difference in "final" structure
>>> To: [log in to unmask]
>>>
>>> Dear ccp4 bulletin board
>>>
>>> I just have a slight concern regarding my Rwork Rfree difference. I
>>> have a structure that I have solved. I am reasonably content that it
is
>>> complete because it has refined well, it no longer has bad geometries
>>> and contacts and all the rotamers, ramachandra, bond lengths etc are
>>> good. It gives favourable scores on molprobity and procheck. My only
>>> concern is the R factor difference. The resolution of the structure is
>>> 2.3A. The R factor is 0.24 after refinement but the Rfree is 0.33
which
>>> seems to me to be rather high. Should I be concerned?
>>>
>>> During refinement Rfree only drops from about 0.36 to 0.33 while the R
>>> factor drops from 0.31 to 0.24.. I have removed automatic weighting in
>>> refmac in order to constrain my bond lengths and angles during a
couple
>>> of rounds of refinement. This did not have any effect on the R
factors,
>>> however. I am fairly content that the space group I have chosen is
>>> correct so I am not sure what else could cause the big difference in R
>>> factors? There is no twinning.
>>>
>>> Can I be satisfied that my structure is correct despite the high R
free
>>> or should I be doing other checks/ trying other things before I can
>>> submit this structure?
>>>
>>> Thank you for any help
>>> Careina
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