Do not withdraw from the waitlist unless you would rather not be a doctor than go there.
Almost everybody gets secondaries from CA schools.
Your Master's gpa is incidental to the evaluation of your academic prowess.
Your gpa is quite low for MD and the average of your MCAT's is also below average.
Even a much better third MCAT will be considered in the context of your previous scores.
A similar or worse one will close even more doors.
You may well get the opportunity to incur the stigma of becoming a re-applicant, avoid it if possible.
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