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Rosetta 3.2 includes some crystallographic tools, but I don’t know if they are compatible with the data you have. Look for the cryoEM or molecular replacement tutorials in the manual/download.
If those won’t help, but you have a vague idea of where domain E goes from the weak density, then you can bias docking by playing E next to CD/cat in the correct location, but only use the -spin flag on domain E in docking, and do perturbative rather than global docking. This should try all orientations of E, but leave it in approximately the same place on the CD/cat surface.
You could also write constraints to get the same effect.