I am considering various conformations of a given protein and I should compare their corresponding energy values. I have used Pyrosetta to compute the energies using the "scorefxn = create_score_function('standard')" command. I was under the impression that the PDB structure of a protein should have the minimum energy.
However, during my computations I have cases in which the alternative conformations have lower energies according to Pyrosetta. Here is a simple example: I considered the protein with PDB ID 1CQW and one of its alternative conformations. Pyrosetta gives energies -487.858056738 and -488.060045834 for the original and alternative structures, respectively. So my question is whether this is possible, i.e., can an alternative conformation of a protein have energy lower than its PDB structure.