#!/usr/bin/perl
use strict;
use warnings;

my @array = qw ( 0.99 0.99 0.99 0.99 );
my $count = 0;
while (<DATA>){
  if (/^(\d\.\d{2,3}\s+)x(\s+\d\.\d{2,3})/){
    print $1, $array[$count++], $2, "\n"
  }
  else {
    print
  }
}

__DATA__
0.00  x  1.000  
0.530 x  0.753
# output values for residue    1
     0
# input   
0.00  x  1.00  
0.555 x  0.683
# output values for residue    2
     0
[download]

0.00  0.99  1.000  
0.530 0.99  0.753
# output values for residue    1
     0
# input   
0.00   0.99  1.00  
0.555  0.99  0.683
# output values for residue    2
     0
[download]