Maybe I'm getting senile before my time here, but I am not sure what you are asking.

Looking at the regex you are the first change I would propose would be the use of s/\s+(.*)$/$z3leu $z$leu $z1leu $1/ in your substitution. I set up a quick test that looks like:

$done=0;
while (<DATA>){
    $_ =~ s/\s+(.*)$/$1/ unless $done;
    print;
    $done=1;
}
 
__END__
     0.123  0.654   - so write before these values only
     0.987  0.678
[download]

just to prove out the regex. However, I don't know what those other variables are about.

Note that I have a "flag" set to make it only act on the first line.

I hope this helps, but I'm not 100% sure what you are after...