In my experience, the most common cause of this is the "locally correct,
globally wrong" issue. You could be in the wrong space group (i.e P21212 when
you should be in P212121). Another possibility is missing some element of
local symmetry. Is the packing in the unit cell appropriate or are you
underpacked? Do you have pseudosymmetry, which can mask the effects of
merohedral twinning on certain measures?
Adrian.
On 14 Jul 2011, at 04:54, 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: careinaedgo...@yahoo.com
>> Subject: [ccp4bb] large R-Rfree difference in "final" structure
>> To: CCP4BB@JISCMAIL.AC.UK
>>
>> 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
