For the structure refinement we need to compute the forces on the
atoms that move them into the density.
We derive forces by comparing the target density with a density that
is computed from the coordinates of the model, the model density.
The goal is to minimize the difference between the target and the model
Since experimental density map often contain a significant amount
of noise, we compute a stochastic gradient that is more robust
than an analytical gradient. For this a set of map_probe_n
file) vectors are randomly chosen from within a given search radius (map_probe_sig
The obtained vectors are weighted by the difference density at this point and
then averaged. This averaged vector is used to move the atom.