That -$3 is before the Capital Loss carryover is applied.
You have $6995 in capital gains and -$3 in losses for $6992 in net capital gains for 2016.
Then go to line 13 of the Form 1040 and it should be $6,992 less $3,891 for $3,101 that you are being taxed on for 2016.
Go to the Forms mode in the upper right, then click on the Form 1040 in the left side and look at line 13.