[phenixbb] Stalled refinement
Yarrow Madrona
amadrona at uci.edu
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
>
> Lawrence Berkeley Laboratory
> 1 Cyclotron Road
> BLDG 64R0121
> Berkeley, CA 94720, USA.
>
> Executive Assistant: Louise Benvenue [ LBenvenue at lbl.gov ][ 1-510-495-2506
> ]
>
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