
#######################################################
#                                                     #
#                        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 T0349TS393_3-D1
# Molecule2: number of CA atoms   57 (  873),  selected   57 , name T0349_D1.pdb
# PARAMETERS: T0349TS393_3-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:    44         7 - 65          5.00     9.69
  LONGEST_CONTINUOUS_SEGMENT:    44         8 - 66          4.98     9.81
  LCS_AVERAGE:     68.39

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    18        50 - 67          1.98    11.38
  LCS_AVERAGE:     20.99

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13         9 - 21          0.48    12.88
  LCS_AVERAGE:     13.70

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      5    5   15     3    4    5    5    5    5    6    7    8   10   11   14   14   15   15   16   18   22   28   28 
LCS_GDT     R       2     R       2      5    5   15     3    4    5    5    5    5    6    7    8   10   11   14   14   18   19   20   23   25   28   28 
LCS_GDT     E       3     E       3      5    5   15     3    4    5    5    5    5    6    7    8   10   11   14   14   19   22   27   30   31   32   34 
LCS_GDT     L       4     L       4      5    5   15     3    3    5    5    5    5    6    6    8    9   11   14   14   17   19   27   30   31   35   38 
LCS_GDT     L       5     L       5      5    5   25     3    4    5    5    5    5    6    7   10   11   18   19   27   35   37   43   47   48   48   51 
LCS_GDT     R       6     R       6      3    5   29     0    3    3    4    5    7    9   13   25   26   32   36   40   43   45   46   47   48   49   51 
LCS_GDT     T       7     T       7      3    4   44     3    3    3    9   13   16   21   24   28   32   37   39   41   43   45   46   47   48   49   51 
LCS_GDT     N       8     N       8      3   14   44     3    3    4    6   10   14   22   26   30   32   37   39   41   43   45   46   47   48   49   51 
LCS_GDT     D       9     D       9     13   14   44    10   12   14   14   16   17   19   27   29   33   37   39   41   43   45   46   47   48   49   51 
LCS_GDT     A      10     A      10     13   14   44    11   12   14   14   16   17   24   27   31   33   37   39   41   43   45   46   47   48   49   51 
LCS_GDT     V      11     V      11     13   14   44    11   12   14   14   16   17   21   27   31   33   37   39   41   43   45   46   47   48   49   51 
LCS_GDT     L      12     L      12     13   14   44    11   12   14   14   16   17   20   27   31   33   37   39   41   43   45   46   47   48   49   51 
LCS_GDT     L      13     L      13     13   14   44    11   12   14   14   16   20   24   27   31   33   37   39   41   43   45   46   47   48   49   51 
LCS_GDT     S      14     S      14     13   14   44    11   12   14   14   16   20   24   27   31   33   37   39   41   43   45   46   47   48   49   51 
LCS_GDT     A      15     A      15     13   14   44    11   12   14   14   16   20   24   27   31   33   37   39   41   43   45   46   47   48   49   51 
LCS_GDT     V      16     V      16     13   14   44    11   12   14   14   16   20   24   27   31   33   37   39   41   43   45   46   47   48   49   51 
LCS_GDT     G      17     G      17     13   14   44    11   12   14   14   16   20   24   27   31   33   37   39   41   43   45   46   47   48   49   51 
LCS_GDT     A      18     A      18     13   14   44    11   12   14   14   16   20   24   27   31   33   37   39   41   43   45   46   47   48   49   51 
LCS_GDT     L      19     L      19     13   14   44    11   12   14   14   16   20   24   27   31   33   37   39   41   43   45   46   47   48   49   51 
LCS_GDT     L      20     L      20     13   14   44    11   12   14   14   16   20   24   27   31   33   37   39   41   43   45   46   47   48   49   51 
LCS_GDT     D      21     D      21     13   14   44     8   12   14   14   14   16   21   27   31   33   37   39   41   43   45   46   47   48   49   51 
LCS_GDT     G      22     G      22      3   14   44     3    6   10   13   16   17   20   27   30   33   37   39   41   43   45   46   47   48   49   51 
LCS_GDT     A      23     A      23      3    6   44     3    3    3    5    5   12   14   18   20   24   30   33   40   43   45   46   47   48   49   51 
LCS_GDT     D      24     D      24      3    6   44     3    3    6   11   16   17   19   20   28   30   37   39   41   43   45   46   47   48   49   51 
LCS_GDT     I      25     I      25      3    6   44     3    3    6   12   16   17   19   27   28   30   37   39   41   43   45   46   47   48   49   51 
LCS_GDT     G      26     G      26      4    6   44     3    3    4    7   10   13   14   18   21   24   30   33   37   41   44   46   47   48   49   51 
LCS_GDT     H      27     H      27      4    6   44     3    3    4    7   10   14   16   21   25   26   33   36   41   43   45   46   47   48   49   51 
LCS_GDT     L      28     L      28      4    6   44     3    3    6   10   16   17   22   27   31   33   37   39   41   43   45   46   47   48   49   51 
LCS_GDT     V      29     V      29      4    6   44     3    4    8   11   16   20   24   27   31   33   37   39   41   43   45   46   47   48   49   51 
LCS_GDT     P      45     P      45      4    6   44     3    3    4    5    7   12   14   17   17   19   21   22   25   26   34   40   41   42   44   46 
LCS_GDT     R      46     R      46      4    6   44     3    3    4    7   10   13   14   17   18   21   24   28   35   38   41   44   46   48   49   51 
LCS_GDT     R      47     R      47      4    6   44     3    3    4    6   10   14   17   20   22   27   34   37   41   43   45   46   47   48   49   51 
LCS_GDT     V      48     V      48      4    6   44     3    3   14   14   14   16   19   27   31   33   37   39   41   43   45   46   47   48   49   51 
LCS_GDT     L      49     L      49      3   17   44     3    3    4    9   16   20   24   27   31   33   37   39   41   43   45   46   47   48   49   51 
LCS_GDT     V      50     V      50      6   18   44     3    5    8   13   15   17   17   18   29   32   35   38   40   43   45   46   47   48   49   51 
LCS_GDT     H      51     H      51      6   18   44     3    8   13   14   15   18   23   27   30   33   36   39   41   43   45   46   47   48   49   51 
LCS_GDT     E      52     E      52      6   18   44     3    9   13   14   16   20   24   27   31   33   37   39   41   43   45   46   47   48   49   51 
LCS_GDT     D      53     D      53      6   18   44     3    4    7   12   16   20   24   27   31   33   37   39   41   43   45   46   47   48   49   51 
LCS_GDT     D      54     D      54     12   18   44     9   11   13   14   15   20   24   27   31   33   37   39   41   43   45   46   47   48   49   51 
LCS_GDT     L      55     L      55     12   18   44     9   11   12   14   16   20   24   27   31   33   37   39   41   43   45   46   47   48   49   51 
LCS_GDT     A      56     A      56     12   18   44     9   11   13   14   16   20   24   27   31   33   37   39   41   43   45   46   47   48   49   51 
LCS_GDT     G      57     G      57     12   18   44     9   11   13   14   15   20   24   27   31   33   37   39   41   43   45   46   47   48   49   51 
LCS_GDT     A      58     A      58     12   18   44     9   11   13   14   15   20   24   27   31   33   37   39   41   43   45   46   47   48   49   51 
LCS_GDT     R      59     R      59     12   18   44     9   11   13   14   16   20   24   27   31   33   37   39   41   43   45   46   47   48   49   51 
LCS_GDT     R      60     R      60     12   18   44     9   11   13   14   16   20   24   27   31   33   37   39   41   43   45   46   47   48   49   51 
LCS_GDT     L      61     L      61     12   18   44     9   11   13   14   15   20   24   27   31   33   37   39   41   43   45   46   47   48   49   51 
LCS_GDT     L      62     L      62     12   18   44     9   11   13   14   16   20   24   27   31   33   37   39   41   43   45   46   47   48   49   51 
LCS_GDT     T      63     T      63     12   18   44     9   11   13   14   16   20   24   27   31   33   37   39   41   43   45   46   47   48   49   51 
LCS_GDT     D      64     D      64     12   18   44     5   11   13   14   15   17   24   27   31   33   37   39   41   43   45   46   47   48   49   51 
LCS_GDT     A      65     A      65     12   18   44     4    8   13   14   15   17   17   24   31   33   37   39   41   43   45   46   47   48   49   51 
LCS_GDT     G      66     G      66      4   18   44     4    4    4    7   14   17   17   22   31   33   37   39   41   43   45   46   47   48   49   51 
LCS_GDT     L      67     L      67      4   18   24     4    4    4    6    6   12   17   21   29   33   37   39   41   43   45   46   47   48   49   51 
LCS_GDT     A      68     A      68      4    7   24     4    4    4    6    6    7    7    9   10   21   25   28   33   40   45   46   47   48   49   51 
LCS_GDT     H      69     H      69      4    7   24     3    4    4    5    6    7    7    9   11   13   19   28   33   40   45   46   47   48   49   51 
LCS_GDT     E      70     E      70      4    7   23     3    4    4    5    6    6    7    9   10   12   14   15   17   18   19   27   30   35   39   51 
LCS_GDT     L      71     L      71      4    5   19     3    4    4    6    6    7    7    8   10   12   12   15   18   18   26   28   38   39   49   51 
LCS_GDT     R      72     R      72      3    5   14     0    3    4    6    6    7    7    8    8    9   11   15   17   18   18   19   23   25   28   28 
LCS_AVERAGE  LCS_A:  34.36  (  13.70   20.99   68.39 )

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     12     14     14     16     20     24     27     31     33     37     39     41     43     45     46     47     48     49     51 
GDT PERCENT_CA  19.30  21.05  24.56  24.56  28.07  35.09  42.11  47.37  54.39  57.89  64.91  68.42  71.93  75.44  78.95  80.70  82.46  84.21  85.96  89.47
GDT RMS_LOCAL    0.30   0.35   0.77   0.77   1.65   2.19   2.50   2.71   3.06   3.19   3.69   3.87   4.08   4.25   4.75   4.73   4.89   5.11   5.50   5.86
GDT RMS_ALL_CA  12.87  12.76  12.30  12.30  12.84   9.58   9.71   9.80  10.06  10.04   9.72   9.67   9.66   9.55   9.25   9.40   9.32   9.17   9.10   8.95

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1         32.991
LGA    R       2      R       2         27.520
LGA    E       3      E       3         20.862
LGA    L       4      L       4         18.033
LGA    L       5      L       5         10.990
LGA    R       6      R       6          8.491
LGA    T       7      T       7          6.370
LGA    N       8      N       8          5.063
LGA    D       9      D       9          4.364
LGA    A      10      A      10          2.940
LGA    V      11      V      11          3.665
LGA    L      12      L      12          3.812
LGA    L      13      L      13          2.889
LGA    S      14      S      14          2.462
LGA    A      15      A      15          2.775
LGA    V      16      V      16          2.728
LGA    G      17      G      17          3.442
LGA    A      18      A      18          3.649
LGA    L      19      L      19          2.510
LGA    L      20      L      20          3.762
LGA    D      21      D      21          6.061
LGA    G      22      G      22          5.793
LGA    A      23      A      23          9.302
LGA    D      24      D      24          8.108
LGA    I      25      I      25          7.610
LGA    G      26      G      26         10.439
LGA    H      27      H      27          8.973
LGA    L      28      L      28          6.262
LGA    V      29      V      29          2.218
LGA    P      45      P      45         13.879
LGA    R      46      R      46          9.592
LGA    R      47      R      47          6.809
LGA    V      48      V      48          5.264
LGA    L      49      L      49          3.189
LGA    V      50      V      50          5.014
LGA    H      51      H      51          3.209
LGA    E      52      E      52          1.733
LGA    D      53      D      53          2.588
LGA    D      54      D      54          3.191
LGA    L      55      L      55          2.599
LGA    A      56      A      56          2.127
LGA    G      57      G      57          2.954
LGA    A      58      A      58          2.967
LGA    R      59      R      59          1.531
LGA    R      60      R      60          2.094
LGA    L      61      L      61          3.245
LGA    L      62      L      62          2.663
LGA    T      63      T      63          1.209
LGA    D      64      D      64          3.611
LGA    A      65      A      65          5.614
LGA    G      66      G      66          5.841
LGA    L      67      L      67          5.863
LGA    A      68      A      68         10.428
LGA    H      69      H      69         11.507
LGA    E      70      E      70         14.933
LGA    L      71      L      71         15.743
LGA    R      72      R      72         22.383

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   57   57    4.0     27    2.71    43.421    39.027     0.961

LGA_LOCAL      RMSD =  2.711  Number of atoms =   27  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  9.656  Number of atoms =   57 
Std_ALL_ATOMS  RMSD =  8.586  (standard rmsd on all 57 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.349656 * X  +   0.109868 * Y  +   0.930414 * Z  +   0.914926
  Y_new =   0.175714 * X  +   0.967787 * Y  +  -0.180316 * Z  +   2.035417
  Z_new =  -0.920253 * X  +   0.226535 * Y  +   0.319087 * Z  +   5.258061 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.617372   -2.524221  [ DEG:    35.3728   -144.6272 ]
  Theta =   1.168726    1.972866  [ DEG:    66.9631    113.0369 ]
  Phi   =   0.465673   -2.675920  [ DEG:    26.6811   -153.3189 ]
 
# 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: T0349TS393_3-D1                               
REMARK     2: T0349_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0349TS393_3-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   27   2.71  39.027     8.59
REMARK  ---------------------------------------------------------- 
MOLECULE T0349TS393_3-D1
PFRMAT TS
TARGET T0349
MODEL 3
PARENT N/A
ATOM      1  CA  MET     1      -4.372 -19.285   5.697  1.00 25.00           C
ATOM      2  CA  ARG     2      -4.273 -15.588   4.869  1.00 25.00           C
ATOM      3  CA  GLU     3      -3.397 -13.662   1.750  1.00 25.00           C
ATOM      4  CA  LEU     4      -0.344 -12.623   3.815  1.00 25.00           C
ATOM      5  CA  LEU     5       0.373  -9.769   1.364  1.00 25.00           C
ATOM      6  CA  ARG     6      -3.270  -8.612   1.606  1.00 25.00           C
ATOM      7  CA  THR     7      -3.063  -8.680   5.429  1.00 25.00           C
ATOM      8  CA  ASN     8       0.168  -6.625   5.315  1.00 25.00           C
ATOM      9  CA  ASP     9      -1.502  -4.084   2.987  1.00 25.00           C
ATOM     10  CA  ALA    10      -4.493  -3.833   5.366  1.00 25.00           C
ATOM     11  CA  VAL    11      -2.125  -3.273   8.323  1.00 25.00           C
ATOM     12  CA  LEU    12      -0.297  -0.531   6.372  1.00 25.00           C
ATOM     13  CA  LEU    13      -3.640   1.145   5.548  1.00 25.00           C
ATOM     14  CA  SER    14      -4.648   1.008   9.240  1.00 25.00           C
ATOM     15  CA  ALA    15      -1.295   2.568  10.238  1.00 25.00           C
ATOM     16  CA  VAL    16      -1.793   5.351   7.655  1.00 25.00           C
ATOM     17  CA  GLY    17      -5.313   6.013   9.009  1.00 25.00           C
ATOM     18  CA  ALA    18      -3.933   6.188  12.578  1.00 25.00           C
ATOM     19  CA  LEU    19      -1.232   8.653  11.439  1.00 25.00           C
ATOM     20  CA  LEU    20      -3.891  10.810   9.722  1.00 25.00           C
ATOM     21  CA  ASP    21      -6.009  10.783  12.913  1.00 25.00           C
ATOM     22  CA  GLY    22      -7.818   8.905  15.695  1.00 25.00           C
ATOM     23  CA  ALA    23     -10.271   8.116  12.906  1.00 25.00           C
ATOM     24  CA  ASP    24     -11.252  11.374  11.157  1.00 25.00           C
ATOM     25  CA  ILE    25      -8.755  11.590   8.380  1.00 25.00           C
ATOM     26  CA  GLY    26      -9.928   8.126   7.531  1.00 25.00           C
ATOM     27  CA  HIS    27      -9.439   5.291   5.069  1.00 25.00           C
ATOM     28  CA  LEU    28      -8.784   5.605   1.337  1.00 25.00           C
ATOM     29  CA  VAL    29      -6.362   3.353  -0.565  1.00 25.00           C
ATOM     45  CA  PRO    45       6.371   1.102   3.552  1.00 25.00           C
ATOM     46  CA  ARG    46       2.692   2.054   3.176  1.00 25.00           C
ATOM     47  CA  ARG    47       0.027   4.436   1.883  1.00 25.00           C
ATOM     48  CA  VAL    48      -1.260   7.606   0.332  1.00 25.00           C
ATOM     49  CA  LEU    49       0.109   8.864  -2.944  1.00 25.00           C
ATOM     50  CA  VAL    50       2.254   9.101  -6.078  1.00 25.00           C
ATOM     51  CA  HIS    51       2.777  12.779  -5.253  1.00 25.00           C
ATOM     52  CA  GLU    52       5.727  14.551  -3.750  1.00 25.00           C
ATOM     53  CA  ASP    53       4.443  15.996  -0.443  1.00 25.00           C
ATOM     54  CA  ASP    54       1.755  13.272  -0.269  1.00 25.00           C
ATOM     55  CA  LEU    55       4.404  10.582  -0.913  1.00 25.00           C
ATOM     56  CA  ALA    56       6.603  12.049   1.858  1.00 25.00           C
ATOM     57  CA  GLY    57       3.622  12.039   4.263  1.00 25.00           C
ATOM     58  CA  ALA    58       2.890   8.385   3.378  1.00 25.00           C
ATOM     59  CA  ARG    59       6.557   7.474   4.003  1.00 25.00           C
ATOM     60  CA  ARG    60       6.446   9.253   7.393  1.00 25.00           C
ATOM     61  CA  LEU    61       3.249   7.355   8.313  1.00 25.00           C
ATOM     62  CA  LEU    62       4.902   4.044   7.326  1.00 25.00           C
ATOM     63  CA  THR    63       7.956   4.901   9.472  1.00 25.00           C
ATOM     64  CA  ASP    64       5.675   5.723  12.436  1.00 25.00           C
ATOM     65  CA  ALA    65       3.844   2.391  11.983  1.00 25.00           C
ATOM     66  CA  GLY    66       4.962  -1.238  11.375  1.00 25.00           C
ATOM     67  CA  LEU    67       2.368  -3.494  13.064  1.00 25.00           C
ATOM     68  CA  ALA    68       3.369  -3.840  16.762  1.00 25.00           C
ATOM     69  CA  HIS    69       6.459  -3.588  18.918  1.00 25.00           C
ATOM     70  CA  GLU    70      10.098  -4.872  18.845  1.00 25.00           C
ATOM     71  CA  LEU    71       8.606  -7.408  16.385  1.00 25.00           C
ATOM     72  CA  ARG    72       9.147  -9.931  19.103  1.00 25.00           C
TER
END
