On the Excel spreadsheet from LEED, there is no space to put either positive or netative points. The line is shown with a "Y" box, is listed as "prereq." and there is no space listing the number of points possible.

Maybe I am using the wrong spreadsheet, mine is titled on the top "LEED v4 for Homes Design and Construction: Homes and Multifamily Lowrise".
It has colored boxes of green, yellow and tan for the points areas.

Maybe I should be using:
LEED v4 for Homes Design and Construction Checklist.xlsx?

I was reluctant to use the version with macros as I am using the latest version of Open Office.

In our case we have 5980 conditioned floor area actual - 4000 (six bedroom std) = 1980 excess area.

1980 / 3400 = 58.2% = 14.5 point negative! Ouch!