You don't mention if your father had other assets that will "go through probate." You can probably disclaim anything that you don't want; however, there are time limits and may be other factors that are relevant. Your decision should be guided by your attorney. I suggest that you call and schedule an appointment with him/her.
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You can file a declination of your inheritance right under the will. If your lawyer is unavailable, talk to the folks at the court for guidance. However, the question will be where will the house then go, which will be determined by Mass. law as to which next relative inherits it, and you might just be passing along a problem. Is the house not economically viable even with renting the two units? If the house is truly under water, another alternative is to talk to the mortgage lender about the whole situation, explaining you are taking this on by inheritance and not voluntarily, and seeking permission for a short sale. Then sell it to someone who will fix it up and make it viable. With an approved short sale, neither you nor the estate will be liable for any shortfall.
I am sorry for your loss and the hardship that you are experiencing.
As mentioned, you most certainly may file a qualified disclaimer so that the house is not devised directly to you as is directed in the Will. Depending on how the Will is written will determine what happens after that. If the devise was to you and, in your absence to your heirs, then the disclaimer will treat you as having predeceased your father and the house will flow to your children if you have any. If you have no children, or if the Will did not address this issue, then the house will likely flow to the residue of the estate. If you have siblings, then you will share with the siblings in receiving the house. The bottom line is that your attorney should be able to advise you surrounding these options. Be aware of the time frames though because a qualified disclaimer needs to be filed within nine months of the date of death.
All this said, as the appointed personal representative of the estate, you do need to deal with the house; you are just not personally liable for the house. If you were paying rent while your father was living, then you need to continue to pay rent to the estate. If you were not paying rent, you need to determine what you plan to do now that you do not want to take on the house. You certainly cannot continue to live there and disregard the loan. As was mentioned, you may be able to enter into negotiations with the bank to purchase the house at a discount where you can then sell the house for a profit in the future. As much as there are a lot of issues that are of a personal and emotional nature, you have to look at this from an objective perspective and a business nature as well.
If your attorney is not able to provide the assistance that you require, you might consider reevaluating your options. I wish you the best of luck.