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Dear All， By refinement from a 2.5 A crystal, the Ramachandran favoured is higher than 96%, Ramachandran outlier lower than 0.8%, but the rotamer outlier is about 3% which is relatively high. If I do the auto fit rotamer by coot, for most of the rotamer outliers auto fitted, nearby peptide bonds will be cleft, and if I do real space refine around the cleft bonds, although the cleft bonds can be connected, the rotamer outlier residues are still rotamer outliers. Will you please explain the possible reasons? Smith