We present the study of copper nanocrystal structure changes caused by transmission of shock waves with varying intensity. Changes of density, mass center velocities, temperature, and meso-volumes potential energy are thoroughly analyzed. We obtain the intervals of shock wave amplitudes where different mechanisms of energy dissipation are observed. The simulation reveals buildup of many structural defects similar to dislocation. It is shown that there is a limit of external load, and the excess of it causes an abrupt change of energy dissipation mechanism. The data obtained demonstrate structure amorphization in a plastic wave.