"Missing energy" in output file

In the output file, what does the “missing energy” value indicate?

Don’t worry: the “missing energy” doesn’t mean that something is wrong, it is a honest physical quantity! It is what we call “Q” in nuclear physics. When you have an endoenergetic nuclear reaction, for instance a (n,2n) reaction, you have a positive missing energy (Q<0). It is missing because it has been transformed into mass of the final nucleus. When you have an exoenergetic nuclear reaction, for instance a (n,gamma) or a thermal fission, you have a negative “missing energy” (Q>0). That means, energy is not missing at all, but is created out of nuclear binding energy balance. In the end, FLUKA does its total energy balance, which can be positive or negative. In a pure electromagnetic run, the missing energy is practically zero. In a run with nuclear reactions, it can be positive or negative. With a thermal neutron source or with fissile materials the missing energy can usually have a very large negative value. With Pb and Ta, as in your case, a lot of energy is needed to break the nucleus (think of all reactions having an energy threshold), and the missing energy can be positive. The value you found of 6.3% is not particularly high.