Hello, this means the PDB file that you gave to phenix.refine contains atoms that perfectly (within 0.0001) overlap. If that's what you want, then just follow what phenix.refine suggests to keep going (I think it prints out a keyword that disables this error message). Otherwise edit PDB file and run refinement again. If this does not help please send me PDB file. Pavel On 1/23/14, 12:31 PM, Leonard Thomas wrote:
Hello All,
We are trying to refine a complex that was solved using Phaser. We have run a round of rigid body refinement using Refmac and now want to run a simulated annealing run in Phenix. Visually the complex looks pretty. The resolution we currently are at is 3.6 A. When we go to run phenix.refine the program quits with a Number of non-bonded interactions < 0.0001 error. Is there a way to loosen this up a bit or get around it or should we go about this in a different way?
Best Regard,
Leonard Thomas, Ph.D. Macromolecular Crystallography Laboratory Manager University of Oklahoma Department of Chemistry and Biochemistry Stephenson Life Sciences Research Center 101 Stephenson Parkway Norman, OK 73019-5251 Office: (405)325-1126
[email protected] mailto:[email protected] http://barlywine.chem.ou.edu http://structuralbiology.ou.edu