Re: [phenixbb] Geometry problems

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). Pavel 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 mailto:[email protected]> 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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