[phenixbb] Stalled refinement

Thu Apr 17 18:05:47 PDT 2014

There is no significant peaks for translational NCS. I also didn't see
anything in the patterson map.

However, the Multivariate Z score L-test gives 6.218. Also the observed
Centric reflections are more intense than they should be but I don't
suspect twinning in a monoclinic space group.

-Yarrow

On Thu, Apr 17, 2014 at 4:37 PM, Paul Adams <pdadams at lbl.gov> wrote:

>
> What does triage say about translation NCS?
>
>
> On Thu, Apr 17, 2014 at 4:25 PM, Yarrow Madrona <amadrona at uci.edu> wrote:
>
>> Hello,
>>
>> I using the latest stable build of phenx.refine (1.8.4) I recently
>> collected data, processed and obtained an MR solution using phaser. I am
>> stuck trying to refine with an Rfree sitting at 40%
>>
>> I really want to know if the high Rfree is due to poor data quality or if
>> non-crystallographic symmetry involving a near perfect two fold rotation
>> between the two molecules in the ASU could somehow impede refinement. Stats
>> and other information is below. Thank you for any help you can give.
>>
>> -Yarrow
>>
>>
>> Visually, the quality of the data is marginal at best (streaky/ice rings
>> in many frames) despite good processing stats from XDS. Processing with
>> mosflm or HKL2000 managed to index but failed pretty bad in integration and
>> scaling.
>>
>> Phaser gave high TFZ scores for 2 molecules in the asu (see below).
>>
>> Density for a cholesterol like ligand shows up even though not present in
>> the search model.
>>
>>  MolRep Self rotation shows rotational symmetry.
>> https://www.dropbox.com/s/2zsajl5o091k50r/CYP142A2-032814_21_rf%20copy.pdf
>>
>> The 2 molecules in the ASU are related by almost a 2 fold rotation:
>>
>> Rotation matrix for chain A to chain B:
>>
>> new_ncs_group
>> rota_matrix    1.0000    0.0000    0.0000
>> rota_matrix    0.0000    1.0000    0.0000
>> rota_matrix    0.0000    0.0000    1.0000
>> tran_orth     0.0000    0.0000    0.0000
>>
>> center_orth   15.2016    0.5245   33.7070
>>
>> rota_matrix   -0.9860   -0.1636   -0.0309
>> rota_matrix   -0.1659    0.9511    0.2605
>> rota_matrix   -0.0132    0.2620   -0.9650
>> tran_orth      34.3310  -24.0033  107.0457
>>
>> center_orth   15.7607    7.2426   77.7512
>>
>> RMSD, B onto A = 0.0007 after phaser
>> RMSD, B onto A = 0.347 after one round of refinement in phenix
>>
>>
>> Refinement using aniostropically corrected data (ucla web server:
>> Services.mbi.ucla.edu/anisoscale) did not improve the Rfree in
>> refinement.
>>
>>
>> Statistics are listed below:
>>
>> UNIT CELL: 51.487 88.923 89.592 90 97.15 90 P21
>>
>> RESOLUTION     NUMBER OF REFLECTIONS    COMPLETENESS R-FACTOR  R-FACTOR
>> COMPARED I/SIGMA   R-meas  CC(1/2)  Anomal  SigAno   Nano
>>    LIMIT     OBSERVED  UNIQUE  POSSIBLE     OF DATA   observed  expected
>>                                      Corr
>>
>>      5.99        8280    1927      2087       92.3%       3.1%      3.3%
>>     8246   35.09      3.5%    99.8*    20*   0.909    1296
>>      4.30       14606    3401      3487       97.5%       3.3%      3.5%
>>    14580   33.37      3.8%    99.9*    11*   0.843    2273
>>      3.53       17961    4244      4445       95.5%       3.8%      3.9%
>>    17944   31.11      4.4%    99.8*    -2    0.789    2721
>>      3.06       21954    5068      5221       97.1%       4.9%      5.1%
>>    21933   24.81      5.6%    99.7*    -2    0.780    3455
>>      2.74       25741    5830      5933       98.3%       7.6%      7.6%
>>    25713   18.88      8.6%    99.5*    -2    0.782    4165
>>      2.51       27859    6311      6483       97.3%      10.8%     10.8%
>>    27824   14.06     12.3%    99.1*    -2    0.774    4385
>>      2.32       31336    6979      7084       98.5%      14.9%     15.3%
>>    31296   10.49     16.8%    98.5*    -4    0.748    5095
>>      2.17       32396    7347      7567       97.1%      22.3%     22.7%
>>    32341    7.46     25.4%    97.3*    -7    0.728    5055
>>      2.05       32254    7339      8047       91.2%      33.1%     33.5%
>>    32075    5.06     37.5%    94.8*    -6    0.724    5155
>>     total      212387   48446     50354       96.2%       7.8%      7.9%
>>   211952   16.57      8.8%    99.7*    -3    0.768   33600
>>
>> Processing with mosflm or HKL2000 managed to index but failed pretty bad
>> in integration and scaling.
>>
>>
>> Phaser:
>>
>> SOLU SET RFZ=27.5 TFZ=24.2 PAK=0 LLG=1711 RF++ TFZ=64.6 PAK=0 LLG=3610
>> LLG=4865
>>
>>
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>>
>>
>
>
> --
> Paul Adams
> Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley
> Lab
> Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley
> Lab
> Adjunct Professor, Department of Bioengineering, U.C. Berkeley
> Vice President for Technology, the Joint BioEnergy Institute
> Laboratory Research Manager, ENIGMA Science Focus Area
>
> Building 64, Room 248
> Tel: 1-510-486-4225, Fax: 1-510-486-5909
> http://cci.lbl.gov/paul
>
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>
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>  ]
>
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