I checked the “ Get your refund status” on the IRS website and I saw the amount it was going to get deposit after they deducted but bank deposit was less. Why?

Know that your Federal and State refunds will come separately. Your refund could also be offset.

The IRS and State Governments have the ability to offset a refund to pay for certain past due debts.  You generally will receive a letter stating what the offset was for.   

The IRS provides a toll-free number, (800) 304-3107, to call for information about tax offsets.

The amount on the IRS Where's my Refund is the total BEFORE they take the fees out.  And then there is an Extra $40 Refund Processing Service charge  ($45 in California).

How to review your fees
https://ttlc.intuit.com/community/charges-and-fees/help/how-do-i-review-my-fees-in-turbotax-online/00/26353