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    There is nothing wrong here.

    First, physics. The crystal structure is the lowest energy structure if it has been solved to infinitesimal resolution with no errors. This has never happened and probably never will.

    Also, a crystal structure is a static (and usually mostly desolvated) image, but actual proteins are dynamic and solvated, so they will occupy an ensemble of structures in any real situation. We assume the crystal is representative of that ensemble, but it might not be for many reasons (crystal packing, most importantly).

    Second, Rosetta’s scorefunction is not a perfect match for actual physics, it has errors. So whatever Rosetta thinks is best is likely to be at least slightly different from what real physics thinks is best.

    In fact, most straight-from-the-PDB structures have horrible Rosetta energies; we relax them into Rosetta’s energy function before using them. This generally gives them a small RMSD from the crystal structure, but makes their energies reasonable. Both the crystal structure and the Rosetta-relaxed structure are likely to be representative of the real physical ensemble, so, it’s good enough.

    Finally, the two energies you quote are trivially different. On the protein scale energy differences like that (one energy unit) are meaningless.