> the sum of the left two balances is minus five, and the sum of right three balances is 505.

Recheck your math the left two balances is actually 505.

5,000

-4,495

=====

  0505

its (4,495) not (4,995)

So it all balances out, which is what accountant actually do but intstead of choosing any two disjoint sets. Specific nodes are grouped into either Assets or Liablities+Equity. Essentially group all the accounts with negative balances and all the accounts with positive balances into another set. Which in this case is 5008 and -5008.