Not to be dismissive, but please read How do I post a question effectively?. It would assist us terribly if you provided both some sample text that one would find in a PDB file as well as the code you've written that counts your lines.

Barring additional information, you're probably best off using a hash to index captured values. Something like:

use strict;
use warnings;

my %matches = ();
while (<DATA>) {
    if (/Good\s(\d)/) {
        $matches{$1}++;
    }
}

foreach my $key (keys %matches) {
    print "$key: $matches{$key}\n";
}

__DATA__
Good 1
Good 2
Good 3
Bad 1
Bad 2
Bad 1
Good 3
Good 1
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