[phenixbb] Geometry problems

Pavel Afonine pafonine at lbl.gov
Mon Jun 23 17:49:06 PDT 2014

Hi Yarrow,

I can have a look if you send me all inputs: data, model and CIF files, 
as well as any parameter files (if used).


On 6/23/14, 5:42 PM, Yarrow Madrona wrote:
> 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 
> <mailto: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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