The PAYG will calculate based on the gross, pay schedule, and tax file declaration of the employee. You can check the ATO tax table for this financial year and the PAYG calculator where you can cross-match the calculations on the pay run.
Also, you can follow these steps on how to adjust PAYG on a pay run.
Open the unlocked pay run and click on the employee name to expand details.
On Actions, select Adjust PAYG.
A new line will show in the dialog box that says PAYG Adjustments.
Enter the amount that you wish the adjustment to be.