In the example in Figure , residues indicated by the red arrows were roughly reoriented to their correct positions in the alternative initial model. The residues did not perfectly overlap and still deviated from their correct positions, but they came closer to their correct positions after MD refinement as the region became "refinable" via alternative initial model building. On the other hand, this region could not be refined well when starting from the original initial model because the deviations from the native positions were too large. At the same time, residues that deviated more in the alternative model than in the original initial model but were still within the radius of "refinability" could therefore be improved to a similar degree.