The most significant error (shift as a sub) has been already mentioned. (Put a large 'S' as the first char if you need to name it that way).

I'd like to make a comment to other aspects of your code. If you give a reference to something into a sub, this (referenced) object will be modified, so you won't need to copy it back and forth.

 ...
 # the array will be modified 'in place', so theres
 # no necessity to copy stuff around
 Shift( \@reduced_protein, $x2-$x1, $y2-$y1, $z2-$z1 ); 
 
 ...

 sub Shift
{
 my ($rp_ref, $x, $y, $z) = @_;   # traditional way to  feed a sub
 my $index1;                      
 # the expression @$array_ref expands a reference to a list
 my $protein_length = findColumnLength(@$rp_ref);
 for (shifting operation) {
    ...
    # instead of:   $reduced_protein[i], 
    # you say:      $rp_ref->[i]
    ...
 }
 # no need to return anything, the original array is
 # already modified
}
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Regards

mwa