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It’s a known issue that straight-from-the-PDB structures tend to score abysmally poor under the Rosetta score function. The issue is that the Rosetta energy function is sensitive enough that even small (0.1 Ang) movements can result in large scorefunction values. So small differences in atom position which wouldn’t make a difference for electron density do make a difference for Rosetta.
Usually it is recommended to relax the structure with constraints to the starting atom positions (http://www.rosettacommons.org/manuals/archive/rosetta3.2.1_user_guide/preparing_structures.html in the “regular” Rosetta manual) – I’m not sure how best to do it through PyRosetta, though. You could play around with the FastRelax mover (protocols::relax::FastRelax)