You should avoid using shift as the name of a subroutine. In this call:

@reduced_protein = shift (\@reduced_protein,($x2-$x1),($y2-$y1),($z2-$
+z1));
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perl thinks you want the built-in shift function which takes an array (not an array ref) as the first argument.

Just rename your subroutine to something else, or qualify it with :::

some_package::shift(\@reduced_protein, ...);
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