Sets of parameters were identified that consistently achieved high assembly accuracy for ligands up to 50 atoms in size. Some key elements of the approach that enabled assembly of the larger ligands were: 1) long assignment intervals, 2) second-order restraints, and 3) strong ML-Force scales. We found that increasing the strength of the second-order restraints led to instabilities in the integrator, especially when combined with shorter assignment intervals. This could possibly be alleviated with a better assignment algorithm that takes the energy of the second-order assignments into account. Unfortunately, such an assignment algorithm could be far more costly than the Hungarian algorithm. One approach could be to use the Hungarian algorithm as an initial assignment, which is refined by a set of Monte Carlo assignment swaps that are accepted or rejected using the full restraint energy (including the second-order assignments). As this only needs to be run periodically, this could be introduced with a reasonable impact to performance. Another possible improvement would be to learn a set of scaling parameters for the loss function: