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 <amadrona@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.