[phenixbb] Geometry problems

[Yarrow Madrona]

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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