Edit: removing for privacy reasons. The advice given still holds! Thanks for the help!
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I don't think you should retake seeing as you have the matriculant average MCAT. Be proud of your score, it's a big achievement! I think a fourth retake after scoring well this time would start to raise questions about whether you are letting perfectionism get in the way of progressing to the next step.
Agree with above advice from MSTPadvocate. Some other MSTPs will consider highly your application with your current 514/513, particularly with a strong research experience as you have. PM me if you have questions that you don't want to disclose publicly.
We consider the MCAT to be binary...ie, we need it to be a certain number for the med school, but once its over that number, it doesn't matter any more. A 516 would hit our threshold. I wouldn't think any better of the applicant if they hit a 521+ - what we are looking for once you hit the threshold is commitment to science, an ability to explain your project, a realistic view of physician scientist training, etc.
We've had great students at the 90th percentile and terrible students at the 100th percentile. The score is just a score.
Agree with above advice from MSTPadvocate. Some other MSTPs will consider highly your application with your current 514/513, particularly with a strong research experience as you have. PM me if you have questions that you don't want to disclose publicly.