 file1 = small_1muc.pdb
 prot1->Compound = MOL_ID: 1;                                                   MOLECULE: MUCONATE LACTONIZING ENZYME;                      CHAIN: A, B;                                                SYNONYM: CIC, CIS MUCONATE CYCLOISOMERASE;                  EC: 5.5.1.1                                                
 file2 = small_2mnr.pdb
 prot2->Compound = MANDELATE RACEMASE (E.C.5.1.2.2)                            
ARNDCQEGHILKMFPSTWYVBZX
matrix constant = 8
Cycle 1, 15 residues selected
Cycle 2, 20 residues selected
Cycle 3, 25 residues selected
Cycle 4, 30 residues selected
Cycle 5, 35 residues selected

 score = 5385.266113

Percent sel on aln =  100.00
Percent aln in sel =   38.89
 *V    2  77.8   1 A* 
**L    3 231.2   2 L* 
**I    4 281.2   3 I**
 *T    5 269.0   4 E  
  G    6 218.0   5 R* 
 *L    7 191.9   6 I**
 *R    8 200.8   7 D* 
 *T    9 185.0   8 A* 
 *R   10 115.4   9 I* 
 *A   11  98.3  10 I* 
  V   12  63.3  11 V* 
 *N   13  79.1  12 D* 
 *V   14  49.8  13 L* 
 *P   15  28.7  14 P  
 *L   16  16.8  15 T**
  A   17   4.1  16 I  
  Y   18   0.3  17 R  
 *G   28   1.1  18 Q  
 *T   29   7.3  19 Q**
**A   30  40.3  20 Q**
**P   31  73.4  21 T**
**L   32  88.3  22 L* 
**V   33 148.2  23 V**
 *L   34 188.9  24 V* 
 *I   35 211.6  25 L**
 *D   36 195.0  26 R* 
 *L   37 202.1  27 V* 
 *A   38 162.3  28 R* 
**T   39 201.0  29 C**
  S   40 158.4  30 S  
  A   41 116.0  31 D  
  G   42 126.5  32 G  
  V   43  58.1  33 V  
 *V   44 118.7  34 E* 
 *G   45 150.7  35 G* 
 *H   46 143.5  36 I* 
  S   47  34.9  37 G* 
 *Y   48  18.5  38 E* 
 *L   49 147.2  39 A* 
 *F   50   3.9  40 T* 
 *A   51   1.1  41 T* 
  Y   52  41.9  42 I* 
 *T   53   0.3  43 G  
 *P   54   7.9  44 G  
  V   55   0.1  45 L  
 *A   56   0.4  51 S**
 *L   57  69.3  52 P**
 *K   58  39.0  53 E  
  S   59  91.3  54 G  
**L   60 109.2  55 I**
**K   61  94.5  56 K**
  Q   62  68.9  57 A  
 *L   63 136.1  58 N* 
 *L   64 184.0  59 I**
 *D   65  86.6  60 D* 
  D   66  49.7  61 A  
 *M   67  16.3  63 L**
**A   68 128.2  64 A* 
  A   69 119.8  65 P* 
  M   70 140.0  66 A* 
**I   71 180.0  67 L**
 *V   72 194.6  68 I* 
  N   73 159.5  69 G  
  E   74 163.8  70 L  
 *P   75 104.8  71 A* 
 *L   76  11.1  72 A* 
 *A   77   1.2  74 N* 
  P   78  39.1  75 I* 
  V   79  38.2  76 N  
  S   80  65.2  77 A  
**L   81  69.4  78 A**
  E   82  92.8  79 M* 
  A   83  84.5  80 L* 
  M   84 154.4  81 K* 
 *L   85 162.7  82 L**
 *A   86 148.1  83 D* 
 *K   87 105.6  84 K  
  R   88  26.3  85 L  
 *F   89   2.6  86 A* 
 *C   90   0.1  87 K* 
  L   91   0.1  88 G  
  A   92   5.8  89 N**
  G   93   0.0  90 T* 
 *Y   94   0.1  91 F* 
 *T   95   0.1  92 A**
  G   96   0.1  93 K**
 *L   97   0.1  94 S* 
**I   98   0.1  95 G**
 *R   99   0.3  96 I* 
**M  100   0.0  97 E* 
small_2mnr.pdb Weighted RMSd =   0.851 over weighted 90 atoms ( 7901.511230  16.7 )
small_2mnr.pdb Un-weighted RMSd =   0.831 over best 53 atoms ( 7901.511230   16.7 )
small_2mnr.pdb Un-weighted RMSd =   1.597 over all 76 atoms ( 7901.511230   16.7 )
