Filing of return incase of search tookplace

The assessee has not filed his return of income for the A.Y. 2016-17. He has time u/s 139(4) upto March 2017.However the Search has taken place on 01-02-2017. But 153A notice is yet to be issued on the assessee. Should he file return u/s 139(4) or straight away can he file return u/s 153A???? In such circumstances, what happens to Penalty later after assessment????