[phenixbb] Geometry problems

Yarrow Madrona amadrona at uci.edu
Mon Jun 23 17:42:39 PDT 2014

Hello again,

have fixed the CIF and I still get a large overall bond deviation > 0.03,
even when using wxc_scale = 0.02. It does not change much even though the
angle sigmas move from 1.4 to about 0.7.

Is there anyway to set a target of say, .0015 and optimize the R/Rfree
around this? My resolution is 2.5 A. Is it possible I am over parametizing
using isotropic B factor refinement and individual coordinate refinement? I
estitmate my parameter/obs ratio to be ~ 1.5. I have an unusuallyl large
solvent content, about 65%.

On Monday, June 23, 2014, Yarrow Madrona <amadrona at uci.edu> wrote:

> Hello,
> I have a ligand bound to a heme and I have supplied a CIF for phenix in
> refinement. I did not include all atoms just, those close to the iron.
> Unfortunately, I am getting very large reported bond deviations for other
> atoms. For example I get:
> bond pdb="FE   HEM A 410 "
>      pdb=" N3  CPZ A 500 "
>   ideal  model  delta    sigma   weight residual
>   2.100  4.054 -1.954 2.00e-01 2.50e+01 9.54e+01
> N3 and FE are not bonded and not expected to be close to one another. it
> is not supported by the structure. I suspect that this is causing my
> overall bonds deviations to be ~0.03 even if I greatly reduce the weight of
> wxc.
> Is it necessary to enter all of these outliers into the .cif file or is
> there an easier way? Thank you.
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