
#######################################################
#                                                     #
#                        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   33 (  132),  selected   33 , name T0335TS307_4u-D1
# Molecule2: number of CA atoms   36 (  584),  selected   33 , name T0335_D1.pdb
# PARAMETERS: T0335TS307_4u-D1.T0335_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:    22        11 - 34          4.85     9.14
  LCS_AVERAGE:     56.31

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14         8 - 23          1.95    13.54
  LCS_AVERAGE:     31.73

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12         8 - 19          0.81    14.48
  LCS_AVERAGE:     23.82

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:   36
LCS_GDT     K       6     K       6      3    4   17     0    3    3    3    4    4    4    6    9   11   14   15   16   20   22   22   25   25   26   27 
LCS_GDT     I       7     I       7      3   13   18     3    3    3    7   12   12   13   15   15   16   17   19   22   23   25   26   26   27   28   29 
LCS_GDT     A       8     A       8     12   14   18     4    6   12   12   12   12   13   15   15   16   18   20   22   23   25   26   26   27   28   29 
LCS_GDT     R       9     R       9     12   14   18     4   11   12   12   12   12   13   15   15   15   15   16   22   23   25   26   26   27   28   29 
LCS_GDT     I      10     I      10     12   14   18     8   11   12   12   12   12   13   15   15   15   15   16   22   23   25   26   26   27   28   29 
LCS_GDT     N      11     N      11     12   14   22     8   11   12   12   12   12   13   15   15   17   18   20   22   23   25   26   26   27   28   29 
LCS_GDT     E      12     E      12     12   14   22     8   11   12   12   12   12   13   15   15   17   18   20   22   23   25   26   26   27   28   29 
LCS_GDT     L      13     L      13     12   14   22     8   11   12   12   12   12   13   15   15   17   18   20   22   23   25   26   26   27   28   29 
LCS_GDT     A      14     A      14     12   14   22     8   11   12   12   12   12   13   15   15   17   18   20   22   23   25   26   26   27   28   29 
LCS_GDT     A      15     A      15     12   14   22     8   11   12   12   12   12   13   15   15   17   18   20   22   23   25   26   26   27   28   29 
LCS_GDT     K      16     K      16     12   14   22     8   11   12   12   12   12   13   15   15   17   18   20   22   23   25   26   26   27   28   29 
LCS_GDT     A      17     A      17     12   14   22     8   11   12   12   12   12   13   15   15   17   18   20   22   23   25   26   26   27   28   29 
LCS_GDT     K      18     K      18     12   14   22     7   11   12   12   12   12   13   15   15   15   15   18   19   21   22   25   25   27   28   28 
LCS_GDT     A      19     A      19     12   14   22     7   11   12   12   12   12   13   15   15   15   15   15   16   17   18   20   20   23   27   28 
LCS_GDT     I      22     I      22      3   14   22     1    3    4    8   10   12   13   15   15   17   18   20   22   23   25   26   26   27   28   29 
LCS_GDT     T      23     T      23      3   14   22     3    3    5    8   11   12   13   15   15   17   18   20   22   23   25   26   26   27   28   29 
LCS_GDT     E      24     E      24      3    4   22     3    3    4    5    7    8    9   11   15   17   18   20   22   23   25   26   26   27   28   29 
LCS_GDT     E      25     E      25      3    4   22     3    3    5    6    7    9   10   11   15   17   18   20   22   23   25   26   26   27   28   29 
LCS_GDT     E      26     E      26      3    4   22     3    3    5    5    7    9   10   10   12   14   18   20   22   23   25   26   26   27   28   29 
LCS_GDT     K      27     K      27      3    4   22     3    3    5    5    6    7   10   11   15   17   18   20   22   23   25   26   26   27   28   29 
LCS_GDT     A      28     A      28      3    4   22     3    3    5    5    7    9   10   11   15   17   18   20   22   23   25   26   26   27   28   29 
LCS_GDT     E      29     E      29      6   12   22     5    5    9   11   12   12   12   12   12   16   17   19   20   21   24   25   25   27   28   29 
LCS_GDT     Q      30     Q      30      6   12   22     5    5    9   11   12   12   12   12   13   16   17   19   20   21   24   25   26   27   28   29 
LCS_GDT     Q      31     Q      31     10   12   22     5    5    9   11   12   12   12   12   15   17   18   20   22   23   25   26   26   27   28   29 
LCS_GDT     K      32     K      32     10   12   22     8    9    9   11   12   12   12   12   15   17   18   20   22   23   25   26   26   27   28   29 
LCS_GDT     L      33     L      33     10   12   22     8    9    9   11   12   12   12   12   15   17   18   20   22   23   25   26   26   27   28   29 
LCS_GDT     R      34     R      34     10   12   22     8    9    9   11   12   12   12   12   15   17   18   20   22   23   25   26   26   27   28   29 
LCS_GDT     Q      35     Q      35     10   12   16     8    9    9   11   12   12   12   12   12   15   18   20   22   23   25   26   26   27   28   29 
LCS_GDT     E      36     E      36     10   12   16     8    9    9   11   12   12   12   12   12   14   14   18   21   23   25   26   26   27   28   29 
LCS_GDT     Y      37     Y      37     10   12   16     8    9    9   11   12   12   12   12   12   14   14   16   19   22   25   26   26   27   28   29 
LCS_GDT     L      38     L      38     10   12   16     8    9    9   11   12   12   12   12   12   14   14   16   18   22   24   26   26   27   28   29 
LCS_GDT     K      39     K      39     10   12   16     8    9    9   11   12   12   12   12   12   14   14   16   18   19   21   24   26   27   28   29 
LCS_GDT     G      40     G      40     10   12   16     3    9    9   11   12   12   12   12   12   13   14   16   17   18   21   22   23   23   26   26 
LCS_AVERAGE  LCS_A:  37.29  (  23.82   31.73   56.31 )

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      8     11     12     12     12     12     13     15     15     17     18     20     22     23     25     26     26     27     28     29 
GDT PERCENT_CA  22.22  30.56  33.33  33.33  33.33  33.33  36.11  41.67  41.67  47.22  50.00  55.56  61.11  63.89  69.44  72.22  72.22  75.00  77.78  80.56
GDT RMS_LOCAL    0.20   0.57   0.81   0.81   0.81   0.81   1.42   2.43   2.43   3.73   3.90   4.28   4.66   4.78   5.22   5.49   5.37   5.57   5.79   6.15
GDT RMS_ALL_CA  14.17  14.46  14.48  14.48  14.48  14.48  14.33  13.24  13.24   8.51   8.40   7.98   8.00   7.92   7.57   7.42   7.62   7.99   7.76   7.41

#      Molecule1      Molecule2       DISTANCE
LGA    K       6      K       6          9.378
LGA    I       7      I       7          3.439
LGA    A       8      A       8          3.103
LGA    R       9      R       9          1.012
LGA    I      10      I      10          2.827
LGA    N      11      N      11          2.956
LGA    E      12      E      12          1.434
LGA    L      13      L      13          1.235
LGA    A      14      A      14          2.740
LGA    A      15      A      15          2.895
LGA    K      16      K      16          1.934
LGA    A      17      A      17          2.338
LGA    K      18      K      18          3.775
LGA    A      19      A      19          3.980
LGA    I      22      I      22          3.164
LGA    T      23      T      23          3.276
LGA    E      24      E      24          9.462
LGA    E      25      E      25         14.068
LGA    E      26      E      26         13.085
LGA    K      27      K      27         14.515
LGA    A      28      A      28         17.164
LGA    E      29      E      29         20.695
LGA    Q      30      Q      30         16.957
LGA    Q      31      Q      31         17.531
LGA    K      32      K      32         18.691
LGA    L      33      L      33         15.414
LGA    R      34      R      34         10.590
LGA    Q      35      Q      35         12.880
LGA    E      36      E      36         16.985
LGA    Y      37      Y      37         14.021
LGA    L      38      L      38         11.919
LGA    K      39      K      39         17.168
LGA    G      40      G      40         20.938

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   33   36    4.0     15    2.43    44.444    39.963     0.594

LGA_LOCAL      RMSD =  2.426  Number of atoms =   15  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 11.572  Number of atoms =   33 
Std_ALL_ATOMS  RMSD =  7.344  (standard rmsd on all 33 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.216948 * X  +   0.872309 * Y  +  -0.438191 * Z  +  -6.963006
  Y_new =   0.922215 * X  +   0.035960 * Y  +  -0.385003 * Z  +   0.034912
  Z_new =  -0.320084 * X  +  -0.487632 * Y  +  -0.812257 * Z  +   3.694767 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.600922    0.540671  [ DEG:  -149.0219     30.9782 ]
  Theta =   0.325818    2.815774  [ DEG:    18.6680    161.3320 ]
  Phi   =   1.801842   -1.339750  [ DEG:   103.2380    -76.7620 ]
 
# 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: T0335TS307_4u-D1                              
REMARK     2: T0335_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0335TS307_4u-D1.T0335_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   33   36   4.0   15   2.43  39.963     7.34
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS307_4u-D1
PFRMAT   TS
TARGET   T0335
MODEL    4  UNREFINED
PARENT   2co5_A
ATOM      1  N   LYS     6      -7.943  -8.681 -10.339  1.00 53.96           N  
ATOM      2  CA  LYS     6      -7.333  -8.655  -8.983  1.00 50.66           C  
ATOM      3  C   LYS     6      -6.042  -7.846  -9.012  1.00 51.97           C  
ATOM      4  O   LYS     6      -5.453  -7.598 -10.068  1.00 48.63           O  
ATOM     10  N   ILE     7      -5.625  -7.415  -7.832  1.00 51.68           N  
ATOM     11  CA  ILE     7      -4.468  -6.557  -7.690  1.00 52.65           C  
ATOM     12  C   ILE     7      -3.525  -7.191  -6.693  1.00 53.43           C  
ATOM     13  O   ILE     7      -3.900  -8.134  -5.987  1.00 53.07           O  
ATOM     22  N   ALA     8      -2.296  -6.689  -6.655  1.00 53.82           N  
ATOM     23  CA  ALA     8      -1.329  -7.112  -5.641  1.00 53.49           C  
ATOM     24  C   ALA     8      -1.921  -6.837  -4.250  1.00 52.16           C  
ATOM     25  O   ALA     8      -2.464  -5.753  -4.019  1.00 52.39           O  
ATOM     30  N   ARG     9      -1.827  -7.824  -3.351  1.00 52.09           N  
ATOM     31  C   ARG     9      -2.022  -6.606  -1.189  1.00 51.76           C  
ATOM     32  O   ARG     9      -2.778  -6.068  -0.383  1.00 51.79           O  
ATOM     33  CA  ARG     9      -2.509  -7.765  -2.045  1.00 50.86           C  
ATOM     41  N   ILE    10      -0.764  -6.216  -1.347  1.00 53.16           N  
ATOM     42  CA  ILE    10      -0.234  -5.140  -0.528  1.00 52.78           C  
ATOM     43  C   ILE    10      -1.104  -3.873  -0.642  1.00 49.11           C  
ATOM     44  O   ILE    10      -1.196  -3.112   0.314  1.00 51.83           O  
ATOM     49  N   ASN    11      -1.748  -3.673  -1.798  1.00 51.58           N  
ATOM     50  CA  ASN    11      -2.663  -2.538  -2.010  1.00 50.11           C  
ATOM     51  C   ASN    11      -3.856  -2.600  -1.059  1.00 49.61           C  
ATOM     52  O   ASN    11      -4.276  -1.595  -0.488  1.00 47.67           O  
ATOM     57  N   GLU    12      -4.403  -3.800  -0.910  1.00 50.83           N  
ATOM     58  CA  GLU    12      -5.499  -4.065   0.013  1.00 49.80           C  
ATOM     59  C   GLU    12      -5.109  -3.665   1.448  1.00 49.90           C  
ATOM     60  O   GLU    12      -5.856  -2.959   2.133  1.00 48.82           O  
ATOM     69  N   LEU    13      -3.924  -4.081   1.874  1.00 48.95           N  
ATOM     70  CA  LEU    13      -3.434  -3.779   3.218  1.00 49.96           C  
ATOM     71  C   LEU    13      -3.277  -2.264   3.442  1.00 49.87           C  
ATOM     72  O   LEU    13      -3.668  -1.743   4.492  1.00 45.50           O  
ATOM     81  N   ALA    14      -2.706  -1.574   2.454  1.00 48.10           N  
ATOM     82  CA  ALA    14      -2.449  -0.137   2.548  1.00 47.53           C  
ATOM     83  C   ALA    14      -3.763   0.634   2.641  1.00 48.65           C  
ATOM     84  O   ALA    14      -3.878   1.564   3.432  1.00 48.76           O  
ATOM     89  N   ALA    15      -4.750   0.238   1.842  1.00 49.61           N  
ATOM     90  CA  ALA    15      -6.078   0.854   1.881  1.00 49.59           C  
ATOM     91  C   ALA    15      -6.719   0.743   3.274  1.00 49.41           C  
ATOM     92  O   ALA    15      -7.141   1.742   3.858  1.00 49.54           O  
ATOM     97  N   LYS    16      -6.768  -0.471   3.802  1.00 49.25           N  
ATOM     98  CA  LYS    16      -7.334  -0.706   5.136  1.00 50.40           C  
ATOM     99  C   LYS    16      -6.555   0.034   6.224  1.00 48.60           C  
ATOM    100  O   LYS    16      -7.150   0.595   7.140  1.00 51.30           O  
ATOM    105  N   ALA    17      -5.231   0.048   6.111  1.00 48.53           N  
ATOM    106  CA  ALA    17      -4.371   0.737   7.079  1.00 50.04           C  
ATOM    107  C   ALA    17      -4.649   2.239   7.097  1.00 49.75           C  
ATOM    108  O   ALA    17      -4.762   2.831   8.164  1.00 50.10           O  
ATOM    114  N   LYS    18      -4.752   2.849   5.919  1.00 50.95           N  
ATOM    115  CA  LYS    18      -5.022   4.288   5.821  1.00 49.73           C  
ATOM    116  C   LYS    18      -6.388   4.632   6.414  1.00 48.61           C  
ATOM    117  O   LYS    18      -6.553   5.688   7.026  1.00 47.69           O  
ATOM    121  N   ALA    19      -7.357   3.736   6.239  1.00 49.00           N  
ATOM    122  CA  ALA    19      -8.672   3.903   6.858  1.00 48.54           C  
ATOM    123  C   ALA    19      -8.584   3.780   8.374  1.00 49.31           C  
ATOM    124  O   ALA    19      -9.153   4.606   9.093  1.00 50.44           O  
ATOM    129  N   ILE    22      -7.863   2.772   8.860  1.00 46.84           N  
ATOM    130  CA  ILE    22      -7.703   2.591  10.306  1.00 49.92           C  
ATOM    131  C   ILE    22      -7.016   3.804  10.943  1.00 49.84           C  
ATOM    132  O   ILE    22      -7.501   4.341  11.938  1.00 54.63           O  
ATOM    136  N   THR    23      -5.904   4.239  10.358  1.00 52.28           N  
ATOM    137  CA  THR    23      -5.207   5.455  10.803  1.00 51.93           C  
ATOM    138  C   THR    23      -6.139   6.671  10.856  1.00 51.02           C  
ATOM    139  O   THR    23      -5.970   7.538  11.705  1.00 48.78           O  
ATOM    144  N   GLU    24      -7.115   6.732   9.953  1.00 51.55           N  
ATOM    145  CA  GLU    24      -8.080   7.840   9.921  1.00 52.06           C  
ATOM    146  C   GLU    24      -9.391   7.563  10.667  1.00 50.28           C  
ATOM    147  O   GLU    24     -10.425   8.149  10.348  1.00 51.23           O  
ATOM    152  N   GLU    25      -9.346   6.685  11.666  1.00 50.18           N  
ATOM    153  CA  GLU    25     -10.528   6.379  12.476  1.00 51.62           C  
ATOM    154  C   GLU    25     -11.612   5.609  11.736  1.00 50.43           C  
ATOM    155  O   GLU    25     -12.803   5.781  12.013  1.00 50.25           O  
ATOM    156  N   GLU    26     -11.190   4.768  10.795  1.00 49.98           N  
ATOM    157  CA  GLU    26     -12.081   3.893  10.010  1.00 51.82           C  
ATOM    158  C   GLU    26     -13.082   4.628   9.106  1.00 50.73           C  
ATOM    159  O   GLU    26     -14.033   4.021   8.606  1.00 48.95           O  
ATOM    162  N   LYS    27     -12.844   5.920   8.881  1.00 52.63           N  
ATOM    163  CA  LYS    27     -13.668   6.740   7.992  1.00 52.01           C  
ATOM    164  C   LYS    27     -12.750   7.640   7.168  1.00 52.71           C  
ATOM    165  O   LYS    27     -11.750   8.151   7.679  1.00 53.25           O  
ATOM    173  N   ALA    28     -13.093   7.832   5.896  1.00 51.74           N  
ATOM    174  CA  ALA    28     -12.328   8.718   5.022  1.00 51.34           C  
ATOM    175  C   ALA    28     -13.117   9.023   3.759  1.00 49.56           C  
ATOM    176  O   ALA    28     -13.786   8.148   3.216  1.00 48.42           O  
ATOM    181  N   GLU    29     -13.047  10.270   3.304  1.00 51.34           N  
ATOM    182  CA  GLU    29     -13.664  10.653   2.036  1.00 51.18           C  
ATOM    183  C   GLU    29     -12.953   9.906   0.916  1.00 50.08           C  
ATOM    184  O   GLU    29     -11.725   9.877   0.876  1.00 50.71           O  
ATOM    190  N   GLN    30     -13.732   9.297   0.026  1.00 50.16           N  
ATOM    191  CA  GLN    30     -13.198   8.499  -1.081  1.00 50.00           C  
ATOM    192  C   GLN    30     -12.154   9.256  -1.907  1.00 49.71           C  
ATOM    193  O   GLN    30     -11.136   8.684  -2.292  1.00 51.42           O  
ATOM    199  N   GLN    31     -12.400  10.540  -2.156  1.00 47.68           N  
ATOM    200  CA  GLN    31     -11.492  11.370  -2.960  1.00 49.76           C  
ATOM    201  C   GLN    31     -10.139  11.615  -2.302  1.00 49.97           C  
ATOM    202  O   GLN    31      -9.166  11.901  -2.992  1.00 51.13           O  
ATOM    208  N   LYS    32     -10.080  11.516  -0.977  1.00 51.68           N  
ATOM    209  CA  LYS    32      -8.841  11.778  -0.238  1.00 51.08           C  
ATOM    210  C   LYS    32      -7.962  10.539  -0.036  1.00 51.76           C  
ATOM    211  O   LYS    32      -6.870  10.644   0.530  1.00 53.61           O  
ATOM    219  N   LEU    33      -8.417   9.375  -0.488  1.00 51.21           N  
ATOM    220  CA  LEU    33      -7.686   8.128  -0.233  1.00 51.41           C  
ATOM    221  C   LEU    33      -6.293   8.141  -0.883  1.00 51.24           C  
ATOM    222  O   LEU    33      -5.287   7.841  -0.235  1.00 49.47           O  
ATOM    227  N   ARG    34      -6.246   8.513  -2.155  1.00 48.07           N  
ATOM    228  CA  ARG    34      -4.999   8.558  -2.892  1.00 47.57           C  
ATOM    229  C   ARG    34      -3.987   9.509  -2.256  1.00 50.03           C  
ATOM    230  O   ARG    34      -2.825   9.141  -2.068  1.00 52.26           O  
ATOM    238  N   GLN    35      -4.438  10.728  -1.940  1.00 48.45           N  
ATOM    239  CA  GLN    35      -3.618  11.736  -1.259  1.00 47.82           C  
ATOM    240  C   GLN    35      -3.146  11.283   0.118  1.00 47.42           C  
ATOM    241  O   GLN    35      -1.999  11.522   0.493  1.00 48.18           O  
ATOM    244  N   GLU    36      -4.045  10.664   0.881  1.00 48.49           N  
ATOM    245  CA  GLU    36      -3.710  10.163   2.216  1.00 50.08           C  
ATOM    246  C   GLU    36      -2.619   9.102   2.181  1.00 48.26           C  
ATOM    247  O   GLU    36      -1.686   9.148   2.982  1.00 51.10           O  
ATOM    253  N   TYR    37      -2.734   8.154   1.258  1.00 51.65           N  
ATOM    254  CA  TYR    37      -1.724   7.109   1.098  1.00 49.13           C  
ATOM    255  C   TYR    37      -0.347   7.716   0.795  1.00 50.61           C  
ATOM    256  O   TYR    37       0.671   7.270   1.331  1.00 50.62           O  
ATOM    261  N   LEU    38      -0.337   8.735  -0.058  1.00 51.37           N  
ATOM    262  CA  LEU    38       0.890   9.430  -0.451  1.00 51.21           C  
ATOM    263  C   LEU    38       1.450  10.225   0.742  1.00 52.28           C  
ATOM    264  O   LEU    38       2.653  10.222   0.985  1.00 48.55           O  
ATOM    269  N   LYS    39       0.562  10.897   1.472  1.00 50.29           N  
ATOM    270  CA  LYS    39       0.929  11.665   2.662  1.00 50.84           C  
ATOM    271  C   LYS    39       1.508  10.766   3.756  1.00 50.37           C  
ATOM    272  O   LYS    39       2.601  11.028   4.265  1.00 48.57           O  
ATOM    278  N   GLY    40       0.784   9.702   4.096  1.00 48.06           N  
ATOM    279  CA  GLY    40       1.142   8.842   5.225  1.00 48.79           C  
ATOM    280  C   GLY    40       2.335   7.937   4.951  1.00 48.76           C  
ATOM    281  O   GLY    40       3.134   7.693   5.853  1.00 45.36           O  
TER
END
