Also note that arguments are passed into subroutines in the array @_ so you need to populate your variables from that. It might also be an idea to change the name of the array reference to avoid confusion.

sub shiftProtein
{
    my (
       $ref_to_reduced_protein,
       $shift_x,
       $shift_y,
       $shift_z
       ) = @_;
    my @reduced_protein = @$ref_to_reduced_protein;
    ...
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I hope this is of use.

Cheers,

JohnGG