while (my $line = <INFILE>)
{
    # Do a match against the line, grabbing the number.
    my ($num) = $line =~ /SEQRES\s{2,5}(\d)\s/;

    # This means that the line didn't meet our requirements
    # as defined by the regex. So, go get the next line.
    # (I added this ... you may not want it, depending on
    # what else you're doing in the loop.)
    next unless defined $num;

    # If that number is 2, leave the while loop.
    last if $num == 2;

    # Don't chomp unless there's a possibility we'll use it.
    chomp $line;

    # If the number is 1, print it to two places.
    if ($num == 1)
    {
        print "$line\n";
        print OUTFILE "$line\n";
    }
}