Briefly, 100 models are generated from the deposited atomic model and EM density using Rosetta, and the resulting models are sorted by Rosetta score, clash score, Ramachandran outliers, and MolProbity score. The top 10 scoring atomic models are refined into the EM density using Phenix real-space refinement and RMSDs of the Cαs are calculated. Regions of well-ordered electron microscopy density will show convergence between models (low RMSD), worse ordered density will have higher RMSD values.
No helical complexes have been processed yet... we're working on it.
More details here: