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I don't understand the meaning of 'out of' in the sentence below:

"We had to make sins out of what they thought were natural actions"

I think that 'out of' means 'what they thought not', but my English book says
that this sentence means "We had to make sins what they thought were natural actions" like 'out of' has no meaning.

The phrase 'out of' can be used to talk about manufacturing or creating something by using one or more ingredients or constituents. We make an omelette out of eggs and butter. We can make a house out of (among other things) bricks, stone blocks, etc. In the 1980s a British insurance company advertised its fuss-free approach to claims with the slogan "We won't make a drama out of a crisis".

You did not state the source of your sentence. It is from a short story called 'Rain' by W Somerset Maugham. A Christian missionary is talking about converting the indigenous inhabitants of a Pacific island to Christianity. One of the central beliefs of the Christian religion is that everyone is a 'sinner'. A 'sin' is an action forbidden by the Christian god, and for which the sinner is required to obtain forgiveness from the god, or else go to a bad place after they die. Since the islanders previously had no idea of 'sin', missionaries tried to make them believe that some natural actions that they did were forbidden by God. Thus 'sins' were manufactured in their minds. The Christian churches often made sins out of natural (e.g. sexual) actions which provided a source of guilty feelings. Maugham is being cynical here.

“Out of” here can be replaced with “from” or “using”.