Your SCF shows convergence, but doesn't reach the threshold.
It might be sufficient to increase the number of iterations: MAX_SCF 200
Otherwise you could try different convergence accelerators.
For a geometry optimization you should increase the SCF threshold: EPS_SCF 1.0E-6
otherwise the gradients will be unreliable.
You have a lot of Ru atoms, but only add 10 orbitals in the Fermi smearing, which might also cause problems in the SCF convergence.
VdW correction are described in: