I'm puzzled about this. If the B's listed by Refmac in the PDB
file are the residuals that are to be added to the values derived
from the TLS model, shouldn't they have a distribution with a mean
value of zero? Why would one what a minimal residual of 2A^2?
Aren't negative residuals not only possible but inevitable?
Dale Tronrud
Eleanor Dodson wrote:
> Two possible points. Could there be a problem with twinning, or
> spacegroup? The Rfactors seem rather high..
>
> You dont say whether you have a non-crystallographic translation, but it
> is faintly possible with 2 molecules that the SG is actually C222 ..
>
> Or that twinning could be present - look at the ctruncate plots - espec
> the L test - for infdications..
>
> But re the TLS. You need to set the overall B to the wilson value more
> or less. All B factors after REFMAC are relative to that initial starting B
>
> If you TLSANL you should get back sensible B values in the PDB slot, but
> of course any which were restricted to the default value of " will be
> corruppted..
>
> Eleanor
>
>
>
>
> Christophe Wirth wrote:
>> Dear CCP Community,
>>
>>
>> We have processed protein scattering data in space group C2221 to a
>> resolution of 2.4 Å. The structure shows two protein molecules (chain
>> A and B) in the asymmetric unit, related by a local two-fold symmetry
>> axis. Initial rigid body refinement and subsequent full refinement of
>> isotropic atomic B-factors (including all water and ligand molecules;
>> using also non-crystallographic symmetry restraints) with the program
>> REFMAC5 yielded R and Rfree values of 32.1and 33.9, respectively.
>>
>> In the next step, after setting the B-factor to 30 Å^2, we carried out
>> 6 cycles of TLS refinement followed by 10 cycles of isotropic atomic
>> B-factor refinement (two TLS-bodies were defined: the two
>> symmetry-related streptavidin chains A and B in the asymmetric unit).
>> As expected, the R and Rfree values droped down by 1-2% to 29.6 and
>> 32.5%, respectively. Checking the residual atomic B-factors their
>> global average had changed from 13 Å^2 (without TLS refinement) to 2
>> Å^2, the lower B-factor boundary. In fact, all atoms in the .pdb file
>> showed B-values of 2 Å^2.
>> Interestingly, when we previously processed the same molecule in C2 we
>> did not have this TLS problem.
>>
>> Does anybody has an explanation why after TLS refinement, individual
>> B-factor refinement is failing? Is this due to wrongly refined (i.e.
>> too large) TLS parameters? Has this been observed before? Any
>> suggestions to solve the problem?
>>
>> Many Thanks,
>>
>>
>> Christophe
>>
>>
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