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ATOM   1489  CA AARG A 181      21.615  11.671  -0.581  0.50 14.29 
ATOM   1490  C  AARG A 181      21.176  11.705   0.880  0.50 13.13 
...
ATOM   1509  NH2BARG A 181      19.926   9.642  -5.944  0.50 24.00

1      2     3  45   6 7        8

my $rx_altloc = qr/
   ^(ATOM.{9}   # match only atom records
...

$file_contents =~ s/$rx_altloc/$1/g;
/xm;

my $rx_altloc_groupByAlt = qr/
   #(?=
...
...

$file_contents =~ s/$rx_altloc_groupByAlt//g;