Re: [phenixbb] Stalled refinement

Given the high TFZ scores in Phaser is does seem unlikely that the search model is dramatically different from the structure in the crystal, however it would be sensible to rule that out. In the absence of other explanations it is possible that there is some issue with the data, but it must have some correctness to it for you to see the difference density for ligands. On Apr 17, 2014, at 8:37 PM, Yarrow Madrona wrote:

I will try this but I performed molecular replacment with the same structure that has a simillar size ligand (Orthorhombic unit cell instead of monoclinic with different lengths and angles). I would be surprised if the changes were this large without any visible fo-fc density showing up.

On Thursday, April 17, 2014, Paul Adams wrote:

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 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 wrote:

What does triage say about translation NCS?

On Thu, Apr 17, 2014 at 4:25 PM, Yarrow Madrona 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 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 [ [email protected] ][ 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 [ [email protected] ][ 1-510-495-2506 ] --