[phenixbb] Refinement using data with pseudo translational symmetry

Pavel Afonine pafonine at lbl.gov
Sun Mar 18 08:53:27 PDT 2012

Hi Bret,

if you send me the model (the most current you have) and the data then I 
will have a look.

Did you try to let phenix.refine build and refine water? Given the 
resolution and the fact that you did not add water the R-factors 28 and 
33 seem reasonable (to me).


On 3/18/12 8:37 AM, Bret Wallace wrote:
> To all,
> First I apologize for the long email, but I wont to make sure that I 
> give enough information to describe the problem.
> I have been working on a structure of two proteins in complex with 
> each other (one forms a homodimer, with each monomer bound to 1 
> monomer of the other protein), using data, that according to 
> phenix.xtriage contains pseudo translational symmetry (output pasted 
> below).  I have done a lot of searching of both the phenixBB and 
> ccp4BB regarding solutions to this problem, but unfortunately most 
> responses seem to be directed at resolving issues with MR. I have 
> successfully performed MR using both phenix phaser, ccp4 phaser (the 
> most updated version), as well as molrep.  The issue arises upon 
> structure refinement, where my Rwork and Rfree are essentially stuck 
> at 28 and 33, respectively.  I have built the entire structure, 
> including ligands, except for any solvent molecules.  Here are the 
> details for the data/structure:
> SG: P212121
> Cell: 72 124 175 90 90 90
> Res: 50-2.8
> Patterson analyses
> ------------------
>  Largest Patterson peak with length larger than 15 Angstrom
>  Frac. coord.        :    0.155    0.000    0.500
>  Distance to origin  :   87.222
>  Height (origin=100) :   34.517
>  p_value(height)     :    6.739e-04
>    The reported p_value has the following meaning:
>      The probability that a peak of the specified height
>      or larger is found in a Patterson function of a
>      macro molecule that does not have any translational
>      pseudo symmetry is equal to  6.739e-04.
>      p_values smaller than 0.05 might indicate
>      weak translational pseudo symmetry, or the self vector of
>      a large anomalous scatterer such as Hg, whereas values
>      smaller than 1e-3 are a very strong indication for
>      the presence of translational pseudo symmetry.
> Xtriage notes that the if the PTS is crystallographic, that C2221 is a 
> possible SG (x+1/6, y, z+1/2).  However, neither XDS or HKL picks 
> orthorhombic C, and the indexing/integrating doesn't work if I force it.
> I should also not there is no twinning detected by either xtriage or 
> twinning servers.
> I have done a number of things to try to resolve this:
> -rescaling in lower symmetry (P21 and P1)
> -rescaling in the PG P222 and letting the MR program decide the proper 
> space group
> -shifting origin and re-refining
> -a number of different refinement protocols (TLS, optimized 
> weights/adp, simulated annealing, several cycles of rigid body, etc.)
> I have used HKL2000 and XDS to index/integrate/scale the data, both 
> yield the same results, with slightly different completeness and 
> Rmerge values, but refining with either gives similar R factor values.
> Does any know of any other possible things I should try to refine this 
> data? I am happy to provide additional information upon request.
> Thanks in advance for any help!
> Bret
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