For newer versions of Minecraft, there are different permission levels that can be set as a 1-4 value in server settings by editing the op-permission-level option. By default, it is set to 4.
1 - Ops can bypass spawn protection.
2 - Ops can use /clear, /difficulty, /effect, /gamemode, /gamerule, /give, and /tp, and can edit command blocks.
3 - Ops can use /ban, /deop, /kick, and /op.
4 - Ops can use /stop.
As you can see if you want to have OPs to have access to everything, the op-permission-level will need to be set to 4.
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