[phenixbb] Stalled refinement
Yarrow Madrona
amadrona at uci.edu
Fri Apr 18 13:59:55 PDT 2014
Thanks Kay,
XDS kicked out a lot of reflections. There were about 23,000 rejected
reflections out of ~ 190,000 collected. I can clearly see another minor
lattice in many frames and I presume that the rejections are coming from
the minor lattice that was not selected. I was thinking of processing with
EVAL15 to see if I get better results. Thanks for your help. Maybe respond
off-line as this is a discussion maybe more suited for another mailing list
(CCP4?).
-Yarrow
On Fri, Apr 18, 2014 at 7:11 AM, Kay Diederichs <
kay.diederichs at uni-konstanz.de> wrote:
> Hi Yarrow,
>
> the problem is that during structure solution, many wrong paths may have
> to be followed until finally identifying the correct path.
>
> So the general answer to this kind of problem is: in some way, your
> parameterization of the experiment is wrong or incomplete.
>
> From what you write, data quality does not seem to be the problem. But:
> did XDS really integrate _all_ the reflections, or only a subset (say,
> every second reflection)?
>
> Check out http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.
> php/Refinement#what_can_go_wrong_in_refinement.3F
>
> If, after thorough attempts, you fail to find the solution, upload your
> current model, sequence and raw data frames to a Dropbox folder and post
> the link here - there may be people who succeed in processing the data
> nicely, or otherwise can identify the problem based on the data (rather
> than based on your description only).
>
> HTH,
>
> Kay
>
> Am 18.04.14 01:25, schrieb phenixbb-request at phenix-online.org:
>
>> Date: Thu, 17 Apr 2014 16:25:00 -0700
>> From: Yarrow Madrona<amadrona at uci.edu>
>> To: PHENIX user mailing list<phenixbb at phenix-online.org>
>> Subject: [phenixbb] Stalled refinement
>> Message-ID:
>> <CAMHjG6bPE4q1xWidpE2VwFMJ9qLSqjtLRuLMM1ef9vWBHBfZKg at mail.
>> gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>>
>> 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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