while (<FILE>) {

#foreach $line = <FILE> {

for ($count = 0; $count < $end; $count++) {

s/^(\s+\S+\s+\S+\s+\S+\s+\S+\s+\S+\s+\S+\s+\S+)\s+(.*)/$1 $array[$count]  $2/;
                                           }
print OUT $_;

}

but the entire array is printed at the substitution point?

# input 
  0.00  1.000  0.00  0.00  1.00  0.00  1.00 0.99
  0.99
  0.710  0.000
  0.22  0.780  0.61  0.39  0.17  0.00  0.50 0.99
  0.99
  0.530  0.753
# output values for residue    1
     0
# input 
  0.00  1.000  1.00  1.00  0.00  0.00  0.00 0.99
  0.99
  0.264  0.000
  0.22  0.780  0.56  0.33  0.22  0.00  0.56 0.99
  0.99
  0.555  0.683
# output values for residue    2
     0