Parameter estimation in steady state to match measurement data ( for a particular range)

I am trying to implement parameter estimation for full switching model of EV battery charger and fine tune values of L, C components as well as control loop parameters Kp, Ki. I have 10 cycle steady state measurement data @ 50Hz for input current of actual charger (signal length 0.2 sec)
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However, my model simulation has to be done for total of 0.26 sec (13 cycles) to get 10 cycle steady state data, where first 3 cycles are required for the model to stabilize
My question is how I can set the parameter estimation to start at 0.06 sec, i.e after first 3 cycles have passed and do the parameter estimation for next 3-4 cycles. In other words, do the parameter estimation from 0.06 sec to 0.12 sec instead of doing for the whole 10 cycle data.

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Hi Haroon,
Can you please share the Simulink model or MATLAB code so that I could reproduce the graph and work on it?
Thanks Sai. I have attached the model and measurement data. That would be great if you can help me figure this out as I have to develope several of these EV models which seems to be impossible without optimization method.

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