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#!/usr/bin/perl -w
use strict;
...
while(<$file>){
print $_;
}

ATOM      5  OE2 GLU A   3
     116.164  67.506  12.993  1.00129.84   8^MATOM      6  C   GLU A  
+ 3     115.793  66.073  17.878  1.00101.37   6^MATOM      7  O   GLU 
+A   3     116.641
...
1.36   6^MATOM     12  CB  GLU A   4     113.440  63.684  18.207  1.00
+ 99.04   6^MATOM     13  CG  GLU A   4     113.897  63.263  19.592  1
+.00118.55   6^MAT
OM     14  CD  GLU A   4     112.731  62.936  20.505  1.00127.23   6^M
+ATOM     15  OE1 GLU A   4     111.851  62.147  20.096  1.00129.74   
+8^MATOM     16  O
E2 GLU A   4     112.699  63.467  21.635  1.00130.22   8^MATOM     17 
+ C   GLU A   4     114.281  63.539  15.867  1.00 84.90   6^M