[phenixbb] Stalled refinement
Dale Tronrud
detBB at daletronrud.com
Fri Apr 18 09:34:45 PDT 2014
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Hi,
I don't see how you can not have translational ncs. You are in space
group P21 and have an ncs two-fold parallel to y. Doesn't this
combination have to give rise to translational ncs?
I may have screwed up my paper matrix multiplications but I come up
with a translational ncs of about (0, 0.3, 0.3) in fractional
coordinates. If the translation were 0.3333 you would only see strong
reflections for k+l=3n. This would result in a lot of weak data and
higher than expected free R's.
Of course, xtriage should be screaming bloody murder and you should
be seeing the peak in the Patterson. I'm confused.
Dale Tronrud
On 4/17/2014 6:05 PM, Yarrow Madrona 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
> <mailto: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
> <mailto: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
> <http://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
> <mailto:LBenvenue at lbl.gov> ][ 1-510-495-2506 ]
>
>
>
>
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