[phenixbb] Worse R factor with newer version of phenix

Ryan Spencer rspencer at uci.edu
Tue Oct 8 09:31:16 PDT 2013

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.)





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

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


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?

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