Before revision:  To resolve these ambiguities , we have developed a new Rosetta structure prediction tool (ERRASER: Enumerative Real-space Refinement ASsisted by Electron density under Rosetta ) and coupled it to MolProbity validation and PHENIX diffraction-based refinement.
After revision:  Recent advances in ab initio RNA structure prediction suggest an automated way to resolve these ambiguities , we have developed a new Rosetta structure prediction tool (ERRASER: Enumerative Real-space Refinement ASsisted by Electron density under Rosetta ) and coupled it to MolProbity validation and PHENIX diffraction-based refinement.