In the default Rosetta structure setup, the first chain doesn’t have a “jump” to control rigid body orientations — it’s assumed that the rest of the chains will move around it.
If you’re doing ligand docking, the way to fix it would be to set up your input structures such that the protein comes first and the ligand comes second. That way the protein will be chain 1 (and without a jump) and the ligand will be chain 2 (or 3 or … depending on how your protein is set up), and thus will be movable by the jump.
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