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CCTBX, which powers this version of MolProbity (4.2), requires stricter adherence to PDB format. If you are having trouble with version 4.2 try using MolProbity4 legacy version 4.02 at http://rutile.biochem.duke.edu. Note that not all features are supported on legacy 4.02 and we suggest repairing your PDB format instead.
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