We calculate the small-$x$ evolution of protons with finite size by solving numerically the JIMWLK evolution equation. The initial condition is constrained by the HERA measurements of charm reduced cross section and of exclusive vector meson production. We compute the energy dependence of diffractive cross sections in order to access the energy evolution of the event-by-event fluctuating proton density profile. The fundamental problems arising from the regime sensitive to non-perturbatively large dipoles are also discussed.