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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Yarrow The inputs are likely telling it to form the bond as it's not an automatic thing. Please send all inputs to Pavel and I, off-line. Cheers Nigel On Mon, Jun 23, 2014 at 6:03 PM, Yarrow Madrona wrote:

Hi again,

So the problem has been solved by adding a bond line into the CIF that explicitely tells phenix that the "bond" should be 4 angstroms instead of 2.1. But I don't understand why Phenix would somehow see that these atoms should be bonded together. This is a phenyl immidazole ligand with two nitrogens, one of which is about 1.9 angstroms from the iron (a real coordination). The other is about 4 angstroms. Why does phenix seem to want to assign a bond between the nitrogen further away?

-Yarrow

On Monday, June 23, 2014, Yarrow Madrona 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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-- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov