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Question about estimating an LTI system matrices using system identification toolbox.

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Hi !
I would like to ask about the the system idintification toolbox.
In my problem I used linear parameter varying model to generate data.
so that I have vector of inputs and outputs.
Then I wanted to build a linear time invatiant system like:
So I used the system identification toolbox, however all the fit estimation error comes out as negative numbers (- 11% , -3, ...)
I use state space model to estimate these matrices with model order=2
is there any other way to estimate A,B, C using the input and output vectors? that might lead to better fit to estimation percentage?
Thanks.

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