I am using PHENIX (http://www.phenix-online.org/) to run MolProbity Analysis and refine a predicted protein structure. PHENIX needs the structure factor data for my protein to start analysis.
Structure factor data provides a topology of the protein such as connected atoms, important torsion angels, etc.
There is almost no structure factor data associated to my protein in the protein data bank and no NOE in biological Magnetic resonance bank.
Does anyone know how to refine my protein structure and fix issues such as poor rotamers, ramachandran outliers, bad bonds and angles?