My federal refund from the IRS showed up in my checking account as

ACH-A-xxxxxx IRS TREAS 310 (TAX REF)

My federal refund deposit says..... ACH-A-xxxxxx  IRS TREAS 310  (TAX REF)

My California deposit says... ACH-xxxxxxx FRANCHISE TAX BD (CASTTAXRFD)

If you were having the fees deducted from your refund it would show something else.  Maybe like 

TAX PRODUCTS PE4 SBTPG LLC

Was your return Accepted?  When you log into your account you should see the status and if it was Accepted or Rejected, Started, Printed, Ready to Mail, etc.  what does it say?

if you can't find it call  the IRS at 1-800-829-1040.