I've never heard it used as a verb, but as a noun it's been "standard operating procedure" for many many years. I suspect it has a military origin. Re the remark "I am not under command," it could mean that the speaker has been given an order re the engines which he thinks is contrary to SOP, and as the person in charge of the engines, he is not required to follow orders which he feels might damage the engines, especially if the orders go against SOP.
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