In case the overlap is in between < 0.5, we cannot assume the same pure character of the two states, but we check if the order of the state might be inverted, by looking at the off-diagonal element of the overlap matrix. If any off-diagonal element is larger than the diagonal one, that value is assigned and a change of state will be considered in the next steps of the scoring assignment. If none of the off-diagonal elements is larger than the diagonal element, then the value of the latter is assigned. The same principle is followed if the diagonal element is < 0.2: an off-diagonal state with a similar character is searched and if found, the corresponding value is assigned as a partial score and the corresponding state will be considered in the next steps. Two exceptions are considered, i) if the overlap is larger than 0.9, a maximum value of 0.8 is given to slightly penalize the error in the order of states, and ii) if none of the off-diagonal element is larger than 0.5, this state is considered missing in the reference calculation and a total score of 0 is assigned to that state.