[phenixbb] Geometry problems
amadrona at uci.edu
Mon Jun 23 17:42:39 PDT 2014
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:
> 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
> 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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