Dear Silvia, I look at those stats in the log file and worry about your data processing. There are some wild outliers in the measurements Unit cell: (129.59, 129.59, 118.84, 90, 90, 120) Space group: P 61 2 2
>From the log file: outliers Miller Index : Intensity : Sigma : Bin Mean Intensity (1, 0, 47) -28060.000 20530.000 2751.006 (2, -1, 47) -5700.000 29950.000 2751.006 (13, 0, 45) -35490.000 73370.000 2751.006 (18, -9, 44) -35640.000 25140.000 2751.006 (18, 0, 43) -7384.000 30540.000 2751.006 (20, 0, 42) -13600.000 31490.000 2751.006 (41, 0, 18) -27470.000 29190.000 2751.006 (42, -21, 27) 594.400 66990.000 2751.006 (3, -1, 47) 3046.000 44930.000 2751.006 (10, -2, 46) 9610.000 15160.000 2751.006 (11, -5, 46) -42010.000 83820.000 2751.006 (15, -7, 45) 15970.000 34970.000 2751.006 (15, -6, 45) 64660.000 80650.000 2751.006 (16, -1, 44) -3856.000 17690.000 2751.006 (17, -3, 44) 2622.000 25320.000 2751.006 (18, -8, 44) 22440.000 20130.000 2751.006 (18, -7, 44) 6847.000 28640.000 2751.006 (19, -2, 43) -11360.000 88170.000 2751.006 (20, -5, 43) 81040.000 28430.000 2751.006 (21, -2, 42) 54000.000 77760.000 2751.006 (22, -5, 42) 22820.000 22740.000 2751.006 (23, -11, 42) 8416.000 20160.000 2751.006 etc - I note they all have L indices in the range 40-47 and very high Sigmas. That makes me think there is an oddity.. Maybe you have processed your data to too high a resolution? Or is it very anisotropic? If you did the data reduction in CCP4I2 do you have the report? That would analyse data quality.. Then I wouldn't worry too much about the Rfactors yet. They fell satisfactorily in the refinement run. COOT indicates there are quite a few corrections to be made, so the stats will improve. I don't worry too much about ramachandran plots at your stage.. I look for bad residues flagged by the COOT density fit.. and difference map peaks which usually flag errors. Are you using NCS restraints? At this resolution I think that is sensible. Good luck Eleanor On Thu, 6 Aug 2020 at 17:48, Paul Emsley <[email protected]> wrote: > On 06/08/2020 16:39, Silvia Napolitano wrote: > > Dear CCP4BB community, > > > Dear Silvia, > > > > > > I am working on a crystal structure and I am a bit stuck with the > refinement. > > > > To build the model I use Coot and to refine I use Phenix. > > I may be able to offer some insight about the first part. > > > > > > First, I noticed that the geometry analysis of exactly the same files is > quite different between Coot 0.8 and Coot 0.9 (see PowerPoint attached, > slides 1 and 2); isn't that a bit strange? > > > The restraints generation and weighting was completely rewritten between > 0.8 and 0.9. I suspect that what you are seeing is a result of using a > more sensitive scaling. With some experience, I had noticed that the > bars in the geometry analysis as a result of modern refinement were very > often too small - in a non-useful way. So I scaled them up a bit. I > haven't looked at this sort of side by side analysis for many years so > your figures 1 & 2 were a bit of a surprise (that the scaling was so > different), but on the whole I think that the current scaling is better. > > > > Anyway, I tried to fix the Ramachandran outliers, geometry, and > rotamers, obtaining, I think, a decent model (see PowerPoint attached, > slides 3-5). > > > Yes, they look good. > > > > > > However, when I input this model for refinement, the statistics and the > geometry obtained at the end of the refinement cycles are very bad (see > PowerPoint attached, slide 6). > > A useful data point here is how the same analysis looks at the start of > (i.e. before) the refinement. Then one can distinguish between the cases > of the refinement being given a good model and chewing it up and the the > refinement being given what it thinks is a bad model and throwing up its > (metaphorical) hands. > > Also, the underlying data which is used by Coot is different to that > used by Phenix. The Ramachandran plot data is different, the CB > distortion model is different, the non-bonded contact model is different > - and the means to assess "bad contacts" is different. > > FWIW, the rotamer database is much the same (or, at least it used to be > - I haven't updated it in about 10 years). > > > Regards, > > Paul. > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
