Ask for more in salary. They may say no. You can still take the job.
I've said something like, "I was expecting an offer of closer to $65,000 a year. Do you have any more room?" if you don't have other offers to play off of. Of course your salary is below average, because you are substantially less experienced than the "average" worker. But, try to get up above $60!
This first salary is the salary on which all future raises will likely be based. (3%, 10% raise) If you move companies they will ask this salary and base your offer on it. So, even a slight increase here, will pay off over your lifetime. Also, paycheck wise, $3,000 a year is $250 a month. $5,000 would get you close to maxing a Roth just with the negotiated raise.