[phenixbb] Worse R factor with newer version of phenix

Tue Oct 8 17:30:21 PDT 2013

Okay, everyone experience problems like this in 1.8.4, could you please
answer the following survey:

1) Are you using secondary structure restraints?
2) If you turn off secondary structure restraints, does that fix the
problem?
3) If you leave secondary structure restraints on, but set the parameter
refinement.secondary_structure.h_bond_restraints.remove_outliers to True,
does that also yield a reasonably correct result?  (GUI users, you should
be able to just do a parameter search for "remove_outliers".)

Jan: using the files you sent me, the fix in (3) does appear to solve the
problem.

Ryan: if you have 1.3Å data and you answered yes to (1), you really
shouldn't use secondary structure restraints at high resolution.  (I'm not
sure there's any fixed cutoff at which they become irrelevant or dangerous,
but my guess would be anything below 2.0Å doesn't need them.)

Anyone else: I'm hoping you all downloaded 1.8.4 before this past weekend
(or if you're using 64-bit Linux, before this morning).  The installers
currently online have been patched to fix the problem (I think) - note
however that using parameters from restored runs will *not* work properly.

thanks,
Nat

On Tue, Oct 8, 2013 at 9:31 AM, Ryan Spencer <rspencer at uci.edu> wrote:

> Hi Nat,****
>
> ** **
>
>                 I’m having a similar issue only in reverse. I’m working
> with a 1.3A data set and halfway during refinement the RMS angles and bonds
> shoot up (0.02/2.3) and the Rfree/Rwork drops by two points (17/15). When I
> don’t use the X-ray/stereochemistry and X-ray/ADP weight optimization the
> Rfree/Rwork values shoot up 10 points on the second run and the RMS
> angles/bonds drop significantly. Any help would be appreciated. I’m running
> the refinement on 1.8.4-1496.****
>
> ** **
>
> Ryan Spencer****
>
> University of California, Irvine****
>
> Nowick Research Group ****
>
> ** **
>
> *From:* phenixbb-bounces at phenix-online.org [mailto:
> phenixbb-bounces at phenix-online.org] *On Behalf Of *Nathaniel Echols
> *Sent:* Tuesday, October 08, 2013 4:24 AM
> *To:* PHENIX user mailing list
> *Subject:* Re: [phenixbb] Worse R factor with newer version of phenix****
>
> ** **
>
> Whenever you see the bond and angle RMSDs blow up like this, it means that
> the weight between the X-ray and geometry restraint terms was not
> calculated correctly.  Probably the quickest solution is to set wxc_scale
> much lower - the default is 0.5 but at this resolution I think 0.1 would be
> more appropriate, and you could try setting it even lower.  (Note that if
> you have weight optimization turned on this will have no effect.)  However,
> the fact that you didn't see this before suggests that there may be a bug
> somewhere that is specific to your data.  Could you please send us input
> files and log file at bugs at phenix-online.org so one of us can take a
> look?  (These will be kept private, obviously.)****
>
> ** **
>
> thanks,****
>
> Nat****
>
> ** **
>
> On Mon, Oct 7, 2013 at 12:46 PM, Jan van Agthoven <janccp4 at gmail.com>
> wrote:****
>
> Hi everyone,
> I've been working on a low resolution structure (3.6A) which was
> previously refined with phenix  1.8_1069 (with a reference model,
> strategy=individual_sites,individual_adp ). I used the same input
> files and parameters and ended up with significantly different R
> factors.
>
> Start: r_work = 0.2850 r_free = 0.3189 bonds = 0.005 angles = 1.059
>
> Final: r_work = 0.2609 r_free = 0.3160 bonds = 0.003 angles = 0.997
>
> For the old version
>
> and
>
> Start: r_work = 0.2779 r_free = 0.3183 bonds = 0.006 angles = 1.141
> Final: r_work = 0.2889 r_free = 0.3303 bonds = 0.021 angles = 2.737
>
> with the new  version 1.8.4
>
> Remarkably it also came with an increased number of C-beta deviation
> (0 against 16!).
>
> Adding tls refinement or ramachandran restrains did not help.
>
> Now because I was using the .eff file of an old version of phenix, it
> came with a long list of unused parameters. These parameters however
> were all used by default.
>
> What should I do? Should I go back to this old phenix, or is there a
> way to improve the result?
>
> Thanks,
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb****
>
> ** **
>
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>
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