Hi,
the user defined bonds have nothing to do with the error message.
Either you have entered Angstrom values as coordinates instead of atomic units, so that all distances are unreasonable, or you have changed the symmetry group by hand without letting define adapt the coordinates to that symmetry.
Please check that your coordinates are in atomic units, and rerun define: enter the geometry section and say 'desy' to let define determine the symmetry.
Regards,
Uwe