[phenixbb] Geometry problem with the ligand

Ralf W. Grosse-Kunstleve rwgk at cci.lbl.gov
Sun Mar 29 12:04:59 PDT 2009

Hi John,

> I am working with a 3.0 A dataset, which binds with cAMP. I have refined the
> dataset with phenix (TLS+Group_adp) and followed by weight optimization.
> Though cAMP fit well in the density, validation tools (molprobity, procheck)
> suggest the bond angles and bond lengths of ligand of completely refined
> model is very bad(100% bad). Can anyone suggest what could be the problem
> with model or refinement?  I will appreciate the suggestions.

What is the residue name of the ligand in your pdb file?
Did you check if the corresponding monomer library .cif file is
the correct one for your ligand? -- Sometimes the same 3-character
residue name is used for (slightly) different ligands by different
The next thing to check are the molprobity and procheck definitions
for your ligand. My guess is that the monomer library definition
used by phenix.refine isn't compatible with what molprobity and
procheck expect.
To find the .cif file used by phenix.refine:
This will show a path ending with
If your ligand code is e.g. AMP, look for the file


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