#!/usr/bin/perl
use strict;
use warnings;
# 864768

my @words = split /(line=)/, do { local $/="\n\n"; <DATA> }; 	# a variant of moritz' advice

for my $words(@words) {
		chomp $words;
		if ($words eq "line=") {
			print $words;	
		}else{
			print "$words \n -------\n";  # the dashes visually separate the output records
		}
}

exit;

__DATA__ 
line=ULMNm  3  1fdy_07      N-ACETYLNEURAMINATE LYASE           user   1           3                                                     
  RMSD =     1.06 A
  MATRIX:   -0.3862 -0.2080 -0.8987  0.6457  0.6347 -0.4244 -0.6587  0.7442  0.1108   -16.917   -91.429   -35.632  
                   D  47    SER       A  57    SER.?     
                   D  48    THR       A  56    THR.?     
                   D 165    LYS       A  33    LYS~?     
 
line=ULMNm  3  2tmd_00      TRIMETHYLAMINE DEHYDROGENASE        user   1           3                                                     
  RMSD =     1.15 A
  MATRIX:    0.9011 -0.4313  0.0445 -0.1032 -0.3130 -0.9441 -0.4211 -0.8462  0.3266    52.913    23.262    25.449  
                   A 169    TYR       A  41    TYR~?     
                   A 172    HIS       A  95    HIS^?     
                   A 267    ASP       A  98    ASP~?     
 
line=ULMNm  3  4fdy_07      P-HYDROOXIDE           user   1           3                                                     
  RMSD =     1.06 A
  MATRIX:   -0.3862 -0.2080 -0.8987  0.6457  0.6347 -0.4244 -0.6587  0.7442  0.1108   -16.917   -91.429   -35.632  
                   D  47    SER       A  57    SER.?     
                   D  48    THR       A  56    THR.?     
                   D 165    PQR       A  33    PRQ~?     
 
line=ULMNm  3  5tmd_00      BAZ	Blivitz        user   1           3                                                     
  RMSD =     1.15 A
  MATRIX:    0.9011 -0.4313  0.0445 -0.1032 -0.3130 -0.9441 -0.4211 -0.8462  0.3266    52.913    23.262    25.449  
                   A 169    TYR       A  41    TYR~?     
                   A 172    HIS       A  95    HIS^?     
                   A 267    XYZ       A  98    XYZ~?  


##</code><code>##

F:\_wo\pl_test>perl 864768.pl

 -------
line=ULMNm  3  1fdy_07      N-ACETYLNEURAMINATE LYASE           user   1           3
  RMSD =     1.06 A
  MATRIX:   -0.3862 -0.2080 -0.8987  0.6457  0.6347 -0.4244 -0.6587  0.7442  0.1108   -16.917   -91.429   -35.632
                   D  47    SER       A  57    SER.?
                   D  48    THR       A  56    THR.?
                   D 165    LYS       A  33    LYS~?

 -------
line=ULMNm  3  2tmd_00      TRIMETHYLAMINE DEHYDROGENASE        user   1           3
  RMSD =     1.15 A
  MATRIX:    0.9011 -0.4313  0.0445 -0.1032 -0.3130 -0.9441 -0.4211 -0.8462  0.3266    52.913    23.262    25.449
                   A 169    TYR       A  41    TYR~?
                   A 172    HIS       A  95    HIS^?
                   A 267    ASP       A  98    ASP~?

 -------
line=ULMNm  3  4fdy_07      P-HYDROOXIDE           user   1           3
  RMSD =     1.06 A
  MATRIX:   -0.3862 -0.2080 -0.8987  0.6457  0.6347 -0.4244 -0.6587  0.7442  0.1108   -16.917   -91.429   -35.632
                   D  47    SER       A  57    SER.?
                   D  48    THR       A  56    THR.?
                   D 165    PQR       A  33    PRQ~?

 -------
line=ULMNm  3  5tmd_00      BAZ Blivitz        user   1           3
  RMSD =     1.15 A
  MATRIX:    0.9011 -0.4313  0.0445 -0.1032 -0.3130 -0.9441 -0.4211 -0.8462  0.3266    52.913    23.262    25.449
                   A 169    TYR       A  41    TYR~?
                   A 172    HIS       A  95    HIS^?
                   A 267    XYZ       A  98    XYZ~?
 -------

F:\_wo\pl_test>