[phenixbb] Rfree doesn't decrease and keeps around 36%, High ramachandran outlier, High RMSD
pafonine at lbl.gov
Fri May 13 12:12:34 PDT 2016
I'm happy to have a closer look at this and try my best to help! Could
you please send me the current model, data and sequence files? Once I
have files I will try a things myself and see what's going on.
On 5/12/16 05:48, chen c wrote:
> Dear all,
> I am solving a structure which diffracted to 2.8 angstrom resolution
> and containes 8 molecules (MW:12 kDa) per ASU. It's noteworthy that
> though the model used for molecular replacement shares 50% sequence
> identity with my protein, however, severe clashes were found as listed
> Packing Table
> Solutions accepted if total number of clashes <= 5% of trace atoms
> i.e. total number of clashes <= 32
> AND if number of clashes <= 5% of trace atoms for each ensemble
> i.e. ensemble1: number of clashes <= 4
> # # #Clash Packs SpaceGroup Annotation
> 1 17 NO C 2 2 21 ... PAK=11 LLG=802 RFZ=3.8 TFZ=9.3
> Only after I changed the packing criteria from 5% to 100%, can I get
> the solution.
> Severe clashes and even coincidence of different molecules were found
> as briefly listed below:
> Molecule A (C-terminal) vs Molecule D (N-terminal) of neighbouring ASU
> Molecule B (C-terminal) vs Molecule C (N-terminal)
> Molecule C (C-terminal) vs Molecule D (C-terminal)
> Molecule E (C-terminal) vs Molecule G (N-terminal)
> Molecule F (C-terminal) vs Molecule H (N-terminal)
> Molecule G (C-terminal) vs Molecule G (C-terminal) of neighbouring ASU
> Molecule H (C-terminal) vs Molecule H (C-terminal) of neighbouring ASU
> Upon this, I manually rebuild the structure in COOT and particularly
> deleted those coincided atoms.
> Then I refined the structure in phenix. However, all the refine gives
> a bad result, namely, RMSD(angle) at 1.8-2.1, RMSD(bond) at
> 0.015-0.02, The Rwork/Rfree at around 0.28/0.36, Ramachandran outlier
> + Rotamer outlier at around 15-20%. I tried a lot of refinement
> strategy and the current status is :
> RMSD(angle)= 1.545, RMSD(bond) = 0.01, Rwork/Rfree = 0.290.36,
> Ramachandran outlier=11.3%,Rotamer outlier =1.5%.
> The data set belonged to C2221 and phenix.xtriage analysis reflects no
> twinning or pseudotranslation problem. In addition, there are two
> beta-turns in each molecule which displays poor electron density and
> geometry. And this two loop are the very residues which appears in
> disallowed regions in ramachandran diagram apart some other residues.
> However, these residues should have little effect on the R factor
> considering of their low contribution to the overall structure due to
> their poor electron density.
> Has anyone has experiences about this? Your help and advice is greatly
> Thank you!
> Cheng Chen, Ph.D. Candidate
> Laboratory of Structural Biology
> Life Science Building,Tsinghua University
> Beijing 100084
> E-mail:chench at xtal.tsinghua.edu.cn
> <mailto:E-mail%3Achench at xtal.tsinghua.edu.cn>
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