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 people. 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: phenix.where_mon_lib_list_cif This will show a path ending with .../mon_lib/list/mon_lib_list.cif If your ligand code is e.g. AMP, look for the file .../mon_lib/a/AMP.cif Ralf