[phenixbb] Stalled refinement

Thu Apr 17 18:21:33 PDT 2014

Given the resolution you might want to try auto(re)building or morphing to see if there are any unexpected structural changes which explain the high R-factor.

On Apr 17, 2014, at 6:05 PM, Yarrow Madrona <amadrona at UCI.EDU> wrote:

> 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
> 
> Lawrence Berkeley Laboratory
> 1 Cyclotron Road
> BLDG 64R0121
> Berkeley, CA 94720, USA.
> 
> Executive Assistant: Louise Benvenue [ LBenvenue at lbl.gov ][ 1-510-495-2506 ]
> 

-- 
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
Building 80, Room 247
Building 978, Room 4126
Tel: 1-510-486-4225, Fax: 1-510-486-5909
http://cci.lbl.gov/paul

Lawrence Berkeley Laboratory
1 Cyclotron Road
BLDG 64R0121
Berkeley, CA 94720, USA.

Executive Assistant: Louise Benvenue [ LBenvenue at lbl.gov ][ 1-510-495-2506 ]
--