Found the solution after a few days.
The new takeoff mass of the takeoff configuration needs to be modified in Procedure.py
Under def weight(nexus):
weights = nexus.analyses.takeoff.weights.evaluate(method="SUAVE")
nexus.vehicle_configurations.takeoff.mass_properties.breakdown = weights
then change the takeoff mass of the takeoff configuration
nexus.vehicle_configurations.takeoff.mass_properties.takeoff = vehicle.mass_properties.breakdown.zero_fuel_weight + float(mat_data['aircraft']['Wf'])