
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  --------------- 06/2006            #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

# Molecule1: number of CA atoms   57 (   57),  selected   57 , name T0349TS599_2-D1
# Molecule2: number of CA atoms   57 (  873),  selected   57 , name T0349_D1.pdb
# PARAMETERS: T0349TS599_2-D1.T0349_D1.pdb  -3  -ie  -o1  -sda  -d:4  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    31        27 - 72          4.89    14.60
  LCS_AVERAGE:     49.15

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    22         8 - 29          2.00    11.97
  LCS_AVERAGE:     30.47

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    19        10 - 28          0.69    12.11
  LCS_AVERAGE:     20.65

LCS_GDT    MOLECULE-1    MOLECULE-2    LENGTH_OF_THE
LCS_GDT     RESIDUE       RESIDUE         CONTINUOUS
LCS_GDT   NAME NUMBER   NAME NUMBER          SEGMENT     GLOBAL DISTANCE TEST - GDT_DATA_COLUMNS                             NUMBER OF THE RESIDUES:   57
LCS_GDT     M       1     M       1      0    3    8     0    0    0    0    3    3    3    3    5   14   15   17   18   21   23   24   27   28   29   32 
LCS_GDT     R       2     R       2      0    3    8     0    0    3    3    3    3    4    5    6   10   15   20   22   24   26   26   29   30   30   33 
LCS_GDT     E       3     E       3      3    4   22     3    3    3    4    4    4    4    5    6    7    7    8   14   17   19   25   26   27   28   33 
LCS_GDT     L       4     L       4      3    4   26     3    3    3    4    4    4    4    5    6    7    7    8   10   19   21   25   27   29   36   36 
LCS_GDT     L       5     L       5      3    4   26     3    3    3    5    5    5   10   11   14   15   19   24   26   28   32   33   37   40   44   45 
LCS_GDT     R       6     R       6      6    7   26     0    4    6    6    6    8   10   11   14   16   19   24   24   26   28   33   37   40   44   45 
LCS_GDT     T       7     T       7      6    7   26     4    5    6    6    6    8   10   11   14   18   22   24   24   30   32   33   37   40   44   45 
LCS_GDT     N       8     N       8      6   22   26     4    5    6    8   12   19   21   21   22   23   25   27   28   30   32   35   38   40   44   45 
LCS_GDT     D       9     D       9      6   22   26     4    5    6    8   14   20   21   21   22   23   25   27   28   30   32   34   38   40   44   45 
LCS_GDT     A      10     A      10     19   22   26     5   17   19   19   19   20   21   21   22   23   25   27   28   30   32   35   38   40   44   45 
LCS_GDT     V      11     V      11     19   22   26    11   17   19   19   19   20   21   21   22   23   25   27   28   30   32   35   38   40   44   45 
LCS_GDT     L      12     L      12     19   22   26    11   17   19   19   19   20   21   21   22   23   25   27   28   30   32   35   38   40   44   45 
LCS_GDT     L      13     L      13     19   22   26    11   17   19   19   19   20   21   21   22   23   25   27   28   30   32   35   38   40   44   45 
LCS_GDT     S      14     S      14     19   22   26    11   17   19   19   19   20   21   21   22   23   25   27   28   30   32   35   38   40   44   45 
LCS_GDT     A      15     A      15     19   22   26    11   17   19   19   19   20   21   21   22   23   25   27   28   30   32   35   38   40   44   45 
LCS_GDT     V      16     V      16     19   22   26    11   17   19   19   19   20   21   21   22   23   25   27   28   30   32   35   38   40   44   45 
LCS_GDT     G      17     G      17     19   22   26    11   17   19   19   19   20   21   21   22   23   25   27   28   30   32   35   38   40   44   45 
LCS_GDT     A      18     A      18     19   22   26    11   17   19   19   19   20   21   21   22   23   25   27   28   30   32   35   38   40   44   45 
LCS_GDT     L      19     L      19     19   22   26    11   17   19   19   19   20   21   21   22   23   25   27   28   30   32   35   38   40   44   45 
LCS_GDT     L      20     L      20     19   22   26    11   17   19   19   19   20   21   21   22   23   25   27   28   30   32   35   38   40   44   45 
LCS_GDT     D      21     D      21     19   22   26    11   17   19   19   19   20   21   21   22   23   25   27   28   30   32   35   38   40   44   45 
LCS_GDT     G      22     G      22     19   22   26    10   17   19   19   19   20   21   21   22   23   25   27   28   30   32   34   38   40   44   45 
LCS_GDT     A      23     A      23     19   22   26    10   17   19   19   19   20   21   21   22   23   25   27   28   30   32   34   37   40   44   45 
LCS_GDT     D      24     D      24     19   22   26    11   17   19   19   19   20   21   21   22   23   25   27   28   30   32   34   38   40   44   45 
LCS_GDT     I      25     I      25     19   22   26     5   17   19   19   19   20   21   21   22   23   25   27   28   30   32   35   38   40   44   45 
LCS_GDT     G      26     G      26     19   22   26     7   17   19   19   19   20   21   21   22   23   25   27   28   30   32   35   38   40   44   45 
LCS_GDT     H      27     H      27     19   22   31     3   14   19   19   19   20   21   21   22   23   25   27   28   30   32   35   38   40   44   45 
LCS_GDT     L      28     L      28     19   22   31    11   17   19   19   19   20   21   21   22   23   25   27   28   30   32   35   38   40   44   45 
LCS_GDT     V      29     V      29      7   22   31     3    4    7    9   13   20   20   20   20   22   23   23   26   29   32   35   38   40   44   45 
LCS_GDT     P      45     P      45      3    3   31     0    3    4    4    4    5    5    7    8   15   19   22   24   27   28   28   30   31   31   32 
LCS_GDT     R      46     R      46      6   12   31     3    5    6   10   11   11   14   15   16   19   22   23   25   27   28   28   30   31   31   32 
LCS_GDT     R      47     R      47      6   12   31     3    5    6    8   11   11   13   15   16   16   19   22   24   27   28   28   30   31   31   32 
LCS_GDT     V      48     V      48      6   16   31     4    6    9   11   13   16   17   19   21   21   24   25   26   29   32   34   38   40   41   45 
LCS_GDT     L      49     L      49      6   16   31     4    5    7   10   11   14   20   21   22   23   25   27   28   30   32   35   38   40   44   45 
LCS_GDT     V      50     V      50      8   20   31     4    7   10   14   16   18   18   20   21   23   25   27   28   30   32   35   38   40   44   45 
LCS_GDT     H      51     H      51     14   20   31     4   10   13   16   17   18   18   20   21   22   24   25   26   30   32   35   38   40   44   45 
LCS_GDT     E      52     E      52     14   20   31     4    7   12   16   17   18   18   20   21   22   24   25   26   28   32   33   37   40   44   45 
LCS_GDT     D      53     D      53     14   20   31     4    7   13   15   17   18   18   20   21   22   24   25   26   27   28   29   34   37   40   41 
LCS_GDT     D      54     D      54     14   20   31     3   11   13   16   17   18   18   20   21   22   24   25   26   27   28   33   37   40   44   45 
LCS_GDT     L      55     L      55     14   20   31     9   11   13   16   17   18   18   20   21   22   24   26   28   30   32   35   38   40   44   45 
LCS_GDT     A      56     A      56     14   20   31     9   11   13   16   17   18   18   20   21   23   25   27   28   30   32   35   38   40   44   45 
LCS_GDT     G      57     G      57     14   20   31     9   11   13   16   17   18   18   20   21   22   24   25   28   30   32   35   38   40   44   45 
LCS_GDT     A      58     A      58     14   20   31     9   11   13   16   17   18   18   20   21   22   25   27   28   30   32   35   38   40   44   45 
LCS_GDT     R      59     R      59     14   20   31     9   11   13   16   17   18   18   21   22   23   25   27   28   30   32   35   38   40   44   45 
LCS_GDT     R      60     R      60     14   20   31     9   11   13   16   17   18   18   20   21   22   25   27   28   30   32   35   38   40   44   45 
LCS_GDT     L      61     L      61     14   20   31     9   11   13   16   17   18   18   20   21   22   24   25   26   29   32   35   38   40   44   45 
LCS_GDT     L      62     L      62     14   20   31     9   11   13   16   17   18   18   20   21   22   24   25   26   29   32   35   38   40   44   45 
LCS_GDT     T      63     T      63     14   20   31     9   11   13   16   17   18   18   20   21   22   24   25   26   29   32   35   38   40   44   45 
LCS_GDT     D      64     D      64     14   20   31     6   11   13   16   17   18   18   20   21   22   24   25   26   29   32   35   38   40   44   45 
LCS_GDT     A      65     A      65     13   20   31     4    9   13   16   17   18   18   20   20   22   23   25   26   27   30   35   38   40   44   45 
LCS_GDT     G      66     G      66      4   20   31     3    4    4    6   14   18   18   20   21   22   24   25   26   29   32   35   38   40   44   45 
LCS_GDT     L      67     L      67      3   20   31     3    5   13   16   17   18   18   20   21   22   24   25   26   27   30   35   38   40   44   45 
LCS_GDT     A      68     A      68      4   20   31     3    4   12   16   17   18   18   20   21   22   24   25   26   29   32   35   38   40   44   45 
LCS_GDT     H      69     H      69      4   20   31     3    4    6   13   15   18   18   20   21   22   24   25   25   27   28   29   33   35   37   40 
LCS_GDT     E      70     E      70      4    5   31     3    4    4    4    5    8   11   18   20   22   24   25   25   27   28   28   30   31   31   33 
LCS_GDT     L      71     L      71      4    5   31     3    4    4    4    5    8   10   12   20   21   24   25   25   27   28   28   30   31   31   36 
LCS_GDT     R      72     R      72      3    5   31     3    3    3    3    4    6    8   12   14   16   20   21   22   25   27   27   30   31   31   32 
LCS_AVERAGE  LCS_A:  33.43  (  20.65   30.47   49.15 )

GLOBAL_DISTANCE_TEST (the largest set of residues that can fit under specified DISTANCE_CUTOFF)
GDT DIST_CUTOFF  0.50   1.00   1.50   2.00   2.50   3.00   3.50   4.00   4.50   5.00   5.50   6.00   6.50   7.00   7.50   8.00   8.50   9.00   9.50  10.00
GDT NUMBER_CA     11     17     19     19     19     20     21     21     22     23     25     27     28     30     32     35     38     40     44     45 
GDT PERCENT_CA  19.30  29.82  33.33  33.33  33.33  35.09  36.84  36.84  38.60  40.35  43.86  47.37  49.12  52.63  56.14  61.40  66.67  70.18  77.19  78.95
GDT RMS_LOCAL    0.25   0.56   0.69   0.69   0.69   1.10   1.72   1.72   1.96   2.42   3.30   3.80   4.02   4.44   4.77   5.93   6.05   6.15   6.69   6.79
GDT RMS_ALL_CA  12.53  12.18  12.11  12.11  12.11  12.38  11.72  11.72  11.53  11.27  11.03  10.99  10.96  10.92  10.99  10.22  10.44  10.40  10.14  10.16

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1         22.063
LGA    R       2      R       2         17.322
LGA    E       3      E       3         17.845
LGA    L       4      L       4         14.336
LGA    L       5      L       5          9.975
LGA    R       6      R       6         10.209
LGA    T       7      T       7          8.561
LGA    N       8      N       8          3.953
LGA    D       9      D       9          3.239
LGA    A      10      A      10          1.904
LGA    V      11      V      11          2.391
LGA    L      12      L      12          2.086
LGA    L      13      L      13          2.181
LGA    S      14      S      14          1.596
LGA    A      15      A      15          0.582
LGA    V      16      V      16          0.893
LGA    G      17      G      17          0.725
LGA    A      18      A      18          0.304
LGA    L      19      L      19          0.876
LGA    L      20      L      20          0.891
LGA    D      21      D      21          0.938
LGA    G      22      G      22          0.868
LGA    A      23      A      23          0.856
LGA    D      24      D      24          1.281
LGA    I      25      I      25          1.638
LGA    G      26      G      26          1.620
LGA    H      27      H      27          2.560
LGA    L      28      L      28          2.137
LGA    V      29      V      29          5.973
LGA    P      45      P      45         17.981
LGA    R      46      R      46         17.438
LGA    R      47      R      47         14.348
LGA    V      48      V      48          9.463
LGA    L      49      L      49          5.509
LGA    V      50      V      50          9.052
LGA    H      51      H      51         12.867
LGA    E      52      E      52         14.871
LGA    D      53      D      53         19.214
LGA    D      54      D      54         16.568
LGA    L      55      L      55         11.037
LGA    A      56      A      56         11.963
LGA    G      57      G      57         15.202
LGA    A      58      A      58         11.868
LGA    R      59      R      59          9.106
LGA    R      60      R      60         13.581
LGA    L      61      L      61         15.680
LGA    L      62      L      62         12.716
LGA    T      63      T      63         14.198
LGA    D      64      D      64         18.609
LGA    A      65      A      65         18.434
LGA    G      66      G      66         15.983
LGA    L      67      L      67         15.478
LGA    A      68      A      68         11.734
LGA    H      69      H      69         17.282
LGA    E      70      E      70         18.851
LGA    L      71      L      71         13.731
LGA    R      72      R      72         16.233

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   57   57    4.0     21    1.72    40.351    37.242     1.152

LGA_LOCAL      RMSD =  1.723  Number of atoms =   21  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 11.621  Number of atoms =   57 
Std_ALL_ATOMS  RMSD =  9.699  (standard rmsd on all 57 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.992576 * X  +  -0.084795 * Y  +   0.087190 * Z  +  -0.597856
  Y_new =   0.119704 * X  +   0.554253 * Y  +  -0.823696 * Z  +   5.299134
  Z_new =   0.021520 * X  +   0.828018 * Y  +   0.560289 * Z  +   1.089062 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.975905   -2.165687  [ DEG:    55.9153   -124.0847 ]
  Theta =  -0.021521   -3.120071  [ DEG:    -1.2331   -178.7669 ]
  Phi   =   0.120020   -3.021573  [ DEG:     6.8766   -173.1234 ]
 
# END of job
REMARK  ---------------------------------------------------------- 
REMARK   Citing LGA: 
REMARK   Zemla A., LGA - a Method for Finding 3D Similarities in  
REMARK   Protein Structures, Nucleic Acids Research, 2003, V. 31, 
REMARK   No. 13, pp. 3370-3374. 
REMARK  ---------------------------------------------------------- 
REMARK   Superimposed MOLECULES (1=>2)   Output: 1 molecule      
REMARK     1: T0349TS599_2-D1                               
REMARK     2: T0349_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0349TS599_2-D1.T0349_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   57   57   4.0   21   1.72  37.242     9.70
REMARK  ---------------------------------------------------------- 
MOLECULE T0349TS599_2-D1
PFRMAT TS                                                                       
TARGET T0349                                                                    
MODEL  2                                                                        
PARENT N/A                                                                      
ATOM      1  CA  MET     1       0.608  -6.604   7.016  1.00  0.00              
ATOM      2  CA  ARG     2       3.450  -6.031   4.402  1.00  0.00              
ATOM      3  CA  GLU     3       2.392  -9.352   6.751  1.00  0.00              
ATOM      4  CA  LEU     4      -0.358  -8.110   4.814  1.00  0.00              
ATOM      5  CA  LEU     5       1.140  -8.967   1.449  1.00  0.00              
ATOM      6  CA  ARG     6       2.079 -12.502   2.320  1.00  0.00              
ATOM      7  CA  THR     7      -1.253 -13.522   3.723  1.00  0.00              
ATOM      8  CA  ASN     8      -3.594 -11.425   1.598  1.00  0.00              
ATOM      9  CA  ASP     9      -5.260  -9.954   4.631  1.00  0.00              
ATOM     10  CA  ALA    10      -4.718  -6.138   4.756  1.00  0.00              
ATOM     11  CA  VAL    11      -3.115  -5.014   7.995  1.00  0.00              
ATOM     12  CA  LEU    12      -0.242  -2.547   7.299  1.00  0.00              
ATOM     13  CA  LEU    13      -2.163  -0.636   4.610  1.00  0.00              
ATOM     14  CA  SER    14      -5.176  -0.291   6.926  1.00  0.00              
ATOM     15  CA  ALA    15      -3.124   1.017   9.863  1.00  0.00              
ATOM     16  CA  VAL    16      -1.370   3.498   7.575  1.00  0.00              
ATOM     17  CA  GLY    17      -4.692   4.636   6.154  1.00  0.00              
ATOM     18  CA  ALA    18      -6.195   5.423   9.478  1.00  0.00              
ATOM     19  CA  LEU    19      -3.136   7.493  10.497  1.00  0.00              
ATOM     20  CA  LEU    20      -3.200   9.395   7.219  1.00  0.00              
ATOM     21  CA  ASP    21      -6.934  10.224   7.418  1.00  0.00              
ATOM     22  CA  GLY    22      -6.419  11.525  10.944  1.00  0.00              
ATOM     23  CA  ALA    23      -3.843  14.068   9.736  1.00  0.00              
ATOM     24  CA  ASP    24      -6.107  15.355   6.952  1.00  0.00              
ATOM     25  CA  ILE    25      -3.585  14.529   4.204  1.00  0.00              
ATOM     26  CA  GLY    26      -5.166  13.317   1.006  1.00  0.00              
ATOM     27  CA  HIS    27      -2.257  11.399  -0.631  1.00  0.00              
ATOM     28  CA  LEU    28      -2.661   7.899  -1.928  1.00  0.00              
ATOM     29  CA  VAL    29       0.200   5.958  -3.403  1.00  0.00              
ATOM     45  CA  PRO    45      -8.230  10.102  -3.003  1.00  0.00              
ATOM     46  CA  ARG    46      -7.081  13.673  -2.684  1.00  0.00              
ATOM     47  CA  ARG    47      -3.896  13.080  -4.691  1.00  0.00              
ATOM     48  CA  VAL    48      -3.563   9.585  -6.016  1.00  0.00              
ATOM     49  CA  LEU    49      -0.366   8.291  -7.235  1.00  0.00              
ATOM     50  CA  VAL    50      -0.486   5.126  -9.241  1.00  0.00              
ATOM     51  CA  HIS    51       1.738   2.741 -10.765  1.00  0.00              
ATOM     52  CA  GLU    52       4.896   0.980  -9.818  1.00  0.00              
ATOM     53  CA  ASP    53       6.875   2.395 -12.807  1.00  0.00              
ATOM     54  CA  ASP    54       5.840   5.943 -11.737  1.00  0.00              
ATOM     55  CA  LEU    55       6.820   5.584  -8.137  1.00  0.00              
ATOM     56  CA  ALA    56       9.361   8.465  -8.159  1.00  0.00              
ATOM     57  CA  GLY    57       6.678  10.873  -9.431  1.00  0.00              
ATOM     58  CA  ALA    58       4.183   9.707  -6.763  1.00  0.00              
ATOM     59  CA  ARG    59       6.727  10.062  -3.966  1.00  0.00              
ATOM     60  CA  ARG    60       7.522  13.579  -5.233  1.00  0.00              
ATOM     61  CA  LEU    61       3.838  14.555  -5.077  1.00  0.00              
ATOM     62  CA  LEU    62       3.547  13.245  -1.483  1.00  0.00              
ATOM     63  CA  THR    63       6.714  15.157  -0.492  1.00  0.00              
ATOM     64  CA  ASP    64       5.458  18.371  -2.040  1.00  0.00              
ATOM     65  CA  ALA    65       2.209  18.009  -0.070  1.00  0.00              
ATOM     66  CA  GLY    66       4.088  17.347   3.224  1.00  0.00              
ATOM     67  CA  LEU    67       2.676  13.948   3.966  1.00  0.00              
ATOM     68  CA  ALA    68       5.793  12.371   5.572  1.00  0.00              
ATOM     69  CA  HIS    69       6.312  15.293   7.916  1.00  0.00              
ATOM     70  CA  GLU    70       2.645  15.210   9.032  1.00  0.00              
ATOM     71  CA  LEU    71       2.684  11.456   9.719  1.00  0.00              
ATOM     72  CA  ARG    72       6.068  11.341  11.335  1.00  0.00              
TER                                                                             
END
