
#######################################################
#                                                     #
#                        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   30 (  120),  selected   30 , name T0335AL381_1-D1
# Molecule2: number of CA atoms   36 (  584),  selected   30 , name T0335_D1.pdb
# PARAMETERS: T0335AL381_1-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:    29        11 - 40          4.92     5.82
  LCS_AVERAGE:     79.54

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    22        18 - 39          1.89     7.23
  LONGEST_CONTINUOUS_SEGMENT:    22        19 - 40          1.81     7.10
  LCS_AVERAGE:     52.69

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    19        21 - 39          0.64     8.32
  LCS_AVERAGE:     38.61

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     I      10     I      10      3    3   18     0    3    3    3    3    4    8   11   11   12   12   12   12   15   15   17   18   19   19   21 
LCS_GDT     N      11     N      11      5   10   29     3    6    7    8    9   10   10   11   11   13   16   16   18   20   22   22   26   28   29   29 
LCS_GDT     E      12     E      12      5   10   29     3    4    5    8    9   10   10   11   11   13   16   16   19   20   25   28   28   28   29   29 
LCS_GDT     L      13     L      13      5   10   29     3    4    5    7    9   10   10   11   11   13   16   17   22   23   27   28   28   28   29   29 
LCS_GDT     A      14     A      14      5   10   29     3    3    5    7    9   10   10   11   12   14   21   25   26   26   27   28   28   28   29   29 
LCS_GDT     K      16     K      16      6   10   29     4    6    7    8    9   10   10   14   18   23   23   25   26   26   27   28   28   28   29   29 
LCS_GDT     A      17     A      17      6   10   29     4    6    7    8    9   10   10   11   11   13   21   25   26   26   27   28   28   28   29   29 
LCS_GDT     K      18     K      18      6   22   29     4    6    7    8    9   10   17   21   23   23   23   25   26   26   27   28   28   28   29   29 
LCS_GDT     A      19     A      19      6   22   29     4    6    7    8    9   19   21   22   23   23   23   25   26   26   27   28   28   28   29   29 
LCS_GDT     G      20     G      20      6   22   29     3    6    7    8   10   19   21   22   23   23   23   25   26   26   27   28   28   28   29   29 
LCS_GDT     V      21     V      21     19   22   29     6   15   19   19   19   19   21   22   23   23   23   25   26   26   27   28   28   28   29   29 
LCS_GDT     I      22     I      22     19   22   29     6   18   19   19   19   19   21   22   23   23   23   25   26   26   27   28   28   28   29   29 
LCS_GDT     T      23     T      23     19   22   29     8   18   19   19   19   19   21   22   23   23   23   25   26   26   27   28   28   28   29   29 
LCS_GDT     E      24     E      24     19   22   29    14   18   19   19   19   19   21   22   23   23   23   25   26   26   27   28   28   28   29   29 
LCS_GDT     E      25     E      25     19   22   29    12   18   19   19   19   19   21   22   23   23   23   25   26   26   27   28   28   28   29   29 
LCS_GDT     E      26     E      26     19   22   29    14   18   19   19   19   19   21   22   23   23   23   25   26   26   27   28   28   28   29   29 
LCS_GDT     K      27     K      27     19   22   29    14   18   19   19   19   19   21   22   23   23   23   25   26   26   27   28   28   28   29   29 
LCS_GDT     A      28     A      28     19   22   29    14   18   19   19   19   19   21   22   23   23   23   25   26   26   27   28   28   28   29   29 
LCS_GDT     E      29     E      29     19   22   29    14   18   19   19   19   19   21   22   23   23   23   25   26   26   27   28   28   28   29   29 
LCS_GDT     Q      30     Q      30     19   22   29    14   18   19   19   19   19   21   22   23   23   23   25   26   26   27   28   28   28   29   29 
LCS_GDT     Q      31     Q      31     19   22   29    14   18   19   19   19   19   21   22   23   23   23   25   26   26   27   28   28   28   29   29 
LCS_GDT     K      32     K      32     19   22   29    14   18   19   19   19   19   21   22   23   23   23   25   26   26   27   28   28   28   29   29 
LCS_GDT     L      33     L      33     19   22   29    14   18   19   19   19   19   21   22   23   23   23   25   26   26   27   28   28   28   29   29 
LCS_GDT     R      34     R      34     19   22   29    14   18   19   19   19   19   21   22   23   23   23   25   26   26   27   28   28   28   29   29 
LCS_GDT     Q      35     Q      35     19   22   29    14   18   19   19   19   19   21   22   23   23   23   25   26   26   27   28   28   28   29   29 
LCS_GDT     E      36     E      36     19   22   29    14   18   19   19   19   19   21   22   23   23   23   25   26   26   27   28   28   28   29   29 
LCS_GDT     Y      37     Y      37     19   22   29    14   18   19   19   19   19   21   22   23   23   23   25   26   26   27   28   28   28   29   29 
LCS_GDT     L      38     L      38     19   22   29    14   18   19   19   19   19   21   22   23   23   23   25   26   26   27   28   28   28   29   29 
LCS_GDT     K      39     K      39     19   22   29    14   18   19   19   19   19   21   22   23   23   23   25   26   26   27   28   28   28   29   29 
LCS_GDT     G      40     G      40      3   22   29     3    3    4    7   15   19   21   22   23   23   23   25   26   26   27   28   28   28   29   29 
LCS_AVERAGE  LCS_A:  56.94  (  38.61   52.69   79.54 )

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     14     18     19     19     19     19     21     22     23     23     23     25     26     26     27     28     28     28     29     29 
GDT PERCENT_CA  38.89  50.00  52.78  52.78  52.78  52.78  58.33  61.11  63.89  63.89  63.89  69.44  72.22  72.22  75.00  77.78  77.78  77.78  80.56  80.56
GDT RMS_LOCAL    0.34   0.55   0.64   0.64   0.64   0.64   1.64   1.81   2.03   2.03   2.03   3.09   3.44   3.44   3.94   4.45   4.45   4.45   4.92   4.92
GDT RMS_ALL_CA   8.10   8.33   8.32   8.32   8.32   8.32   7.16   7.10   7.17   7.17   7.17   6.45   6.30   6.30   6.08   5.90   5.90   5.90   5.82   5.82

#      Molecule1      Molecule2       DISTANCE
LGA    I      10      I      10         21.494
LGA    N      11      N      11         14.991
LGA    E      12      E      12         14.999
LGA    L      13      L      13         12.615
LGA    A      14      A      14          9.096
LGA    K      16      K      16          9.056
LGA    A      17      A      17          8.680
LGA    K      18      K      18          4.642
LGA    A      19      A      19          3.071
LGA    G      20      G      20          3.834
LGA    V      21      V      21          2.558
LGA    I      22      I      22          2.413
LGA    T      23      T      23          1.189
LGA    E      24      E      24          1.838
LGA    E      25      E      25          1.132
LGA    E      26      E      26          0.543
LGA    K      27      K      27          1.176
LGA    A      28      A      28          0.782
LGA    E      29      E      29          0.662
LGA    Q      30      Q      30          0.558
LGA    Q      31      Q      31          0.790
LGA    K      32      K      32          0.835
LGA    L      33      L      33          1.604
LGA    R      34      R      34          1.669
LGA    Q      35      Q      35          1.042
LGA    E      36      E      36          1.787
LGA    Y      37      Y      37          2.391
LGA    L      38      L      38          1.742
LGA    K      39      K      39          1.392
LGA    G      40      G      40          3.800

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   30   36    4.0     22    1.81    60.417    58.042     1.150

LGA_LOCAL      RMSD =  1.813  Number of atoms =   22  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.866  Number of atoms =   30 
Std_ALL_ATOMS  RMSD =  5.770  (standard rmsd on all 30 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.898914 * X  +   0.125137 * Y  +   0.419875 * Z  +  -1.382992
  Y_new =  -0.247259 * X  +   0.646246 * Y  +  -0.721962 * Z  +  -7.489159
  Z_new =  -0.361686 * X  +  -0.752800 * Y  +  -0.549978 * Z  +  -5.611838 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.201751    0.939842  [ DEG:  -126.1510     53.8490 ]
  Theta =   0.370076    2.771517  [ DEG:    21.2038    158.7962 ]
  Phi   =  -2.873166    0.268426  [ DEG:  -164.6203     15.3797 ]
 
# 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: T0335AL381_1-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0335AL381_1-D1.T0335_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   30   36   4.0   22   1.81  58.042     5.77
REMARK  ---------------------------------------------------------- 
MOLECULE T0335AL381_1-D1
REMARK Aligment from pdb entry: 1r2uA
ATOM      1  N   ILE    10     -23.317   1.945  -3.532  1.00  0.00              
ATOM      2  CA  ILE    10     -22.555   2.784  -2.557  1.00  0.00              
ATOM      3  C   ILE    10     -21.841   1.883  -1.549  1.00  0.00              
ATOM      4  O   ILE    10     -22.367   0.846  -1.139  1.00  0.00              
ATOM      5  N   ASN    11     -20.634   2.297  -1.154  1.00  0.00              
ATOM      6  CA  ASN    11     -19.844   1.527  -0.193  1.00  0.00              
ATOM      7  C   ASN    11     -19.359   2.426   0.944  1.00  0.00              
ATOM      8  O   ASN    11     -18.702   3.443   0.712  1.00  0.00              
ATOM      9  N   GLU    12     -19.689   2.031   2.176  1.00  0.00              
ATOM     10  CA  GLU    12     -19.282   2.801   3.355  1.00  0.00              
ATOM     11  C   GLU    12     -18.238   2.040   4.185  1.00  0.00              
ATOM     12  O   GLU    12     -17.989   2.379   5.345  1.00  0.00              
ATOM     13  N   LEU    13     -17.615   1.020   3.579  1.00  0.00              
ATOM     14  CA  LEU    13     -16.590   0.239   4.278  1.00  0.00              
ATOM     15  C   LEU    13     -15.223   0.918   4.153  1.00  0.00              
ATOM     16  O   LEU    13     -14.356   0.740   5.004  1.00  0.00              
ATOM     17  N   ALA    14     -15.046   1.697   3.078  1.00  0.00              
ATOM     18  CA  ALA    14     -13.785   2.403   2.843  1.00  0.00              
ATOM     19  C   ALA    14     -13.575   3.485   3.897  1.00  0.00              
ATOM     20  O   ALA    14     -12.447   3.775   4.289  1.00  0.00              
ATOM     21  N   LYS    16     -14.683   4.072   4.354  1.00  0.00              
ATOM     22  CA  LYS    16     -14.624   5.125   5.374  1.00  0.00              
ATOM     23  C   LYS    16     -14.433   4.506   6.753  1.00  0.00              
ATOM     24  O   LYS    16     -13.703   5.034   7.593  1.00  0.00              
ATOM     25  N   ALA    17     -15.095   3.371   6.969  1.00  0.00              
ATOM     26  CA  ALA    17     -14.993   2.662   8.244  1.00  0.00              
ATOM     27  C   ALA    17     -13.651   1.928   8.358  1.00  0.00              
ATOM     28  O   ALA    17     -13.158   1.692   9.461  1.00  0.00              
ATOM     29  N   LYS    18     -13.069   1.566   7.206  1.00  0.00              
ATOM     30  CA  LYS    18     -11.790   0.854   7.187  1.00  0.00              
ATOM     31  C   LYS    18     -10.613   1.828   7.221  1.00  0.00              
ATOM     32  O   LYS    18      -9.607   1.564   7.880  1.00  0.00              
ATOM     33  N   ALA    19     -10.743   2.956   6.508  1.00  0.00              
ATOM     34  CA  ALA    19      -9.669   3.956   6.477  1.00  0.00              
ATOM     35  C   ALA    19      -9.362   4.467   7.892  1.00  0.00              
ATOM     36  O   ALA    19      -8.216   4.793   8.208  1.00  0.00              
ATOM     37  N   GLY    20     -10.397   4.518   8.738  1.00  0.00              
ATOM     38  CA  GLY    20     -10.234   4.975  10.120  1.00  0.00              
ATOM     39  C   GLY    20      -9.526   3.910  10.970  1.00  0.00              
ATOM     40  O   GLY    20      -8.933   4.226  12.004  1.00  0.00              
ATOM     41  N   VAL    21      -9.591   2.646  10.525  1.00  0.00              
ATOM     42  CA  VAL    21      -8.948   1.550  11.255  1.00  0.00              
ATOM     43  C   VAL    21      -7.448   1.517  10.961  1.00  0.00              
ATOM     44  O   VAL    21      -6.634   1.280  11.856  1.00  0.00              
ATOM     45  N   ILE    22      -7.096   1.757   9.696  1.00  0.00              
ATOM     46  CA  ILE    22      -5.694   1.755   9.279  1.00  0.00              
ATOM     47  C   ILE    22      -4.936   2.921   9.913  1.00  0.00              
ATOM     48  O   ILE    22      -5.505   3.982  10.182  1.00  0.00              
ATOM     49  N   THR    23      -3.643   2.700  10.149  1.00  0.00              
ATOM     50  CA  THR    23      -2.788   3.723  10.757  1.00  0.00              
ATOM     51  C   THR    23      -1.908   4.389   9.700  1.00  0.00              
ATOM     52  O   THR    23      -1.818   3.926   8.560  1.00  0.00              
ATOM     53  N   GLU    24      -1.245   5.475  10.105  1.00  0.00              
ATOM     54  CA  GLU    24      -0.352   6.203   9.201  1.00  0.00              
ATOM     55  C   GLU    24       0.853   5.333   8.845  1.00  0.00              
ATOM     56  O   GLU    24       1.393   5.420   7.742  1.00  0.00              
ATOM     57  N   GLU    25       1.256   4.485   9.798  1.00  0.00              
ATOM     58  CA  GLU    25       2.390   3.583   9.595  1.00  0.00              
ATOM     59  C   GLU    25       2.101   2.593   8.463  1.00  0.00              
ATOM     60  O   GLU    25       2.973   2.300   7.644  1.00  0.00              
ATOM     61  N   GLU    26       0.862   2.092   8.427  1.00  0.00              
ATOM     62  CA  GLU    26       0.450   1.140   7.391  1.00  0.00              
ATOM     63  C   GLU    26       0.542   1.785   6.011  1.00  0.00              
ATOM     64  O   GLU    26       1.082   1.195   5.074  1.00  0.00              
ATOM     65  N   LYS    27       0.022   3.013   5.901  1.00  0.00              
ATOM     66  CA  LYS    27       0.065   3.742   4.631  1.00  0.00              
ATOM     67  C   LYS    27       1.507   4.115   4.277  1.00  0.00              
ATOM     68  O   LYS    27       1.870   4.172   3.102  1.00  0.00              
ATOM     69  N   ALA    28       2.328   4.352   5.309  1.00  0.00              
ATOM     70  CA  ALA    28       3.737   4.700   5.100  1.00  0.00              
ATOM     71  C   ALA    28       4.468   3.535   4.431  1.00  0.00              
ATOM     72  O   ALA    28       5.212   3.727   3.467  1.00  0.00              
ATOM     73  N   GLU    29       4.229   2.322   4.946  1.00  0.00              
ATOM     74  CA  GLU    29       4.848   1.119   4.381  1.00  0.00              
ATOM     75  C   GLU    29       4.286   0.855   2.987  1.00  0.00              
ATOM     76  O   GLU    29       5.019   0.495   2.068  1.00  0.00              
ATOM     77  N   GLN    30       2.970   1.046   2.851  1.00  0.00              
ATOM     78  CA  GLN    30       2.288   0.839   1.570  1.00  0.00              
ATOM     79  C   GLN    30       2.846   1.785   0.503  1.00  0.00              
ATOM     80  O   GLN    30       3.057   1.385  -0.643  1.00  0.00              
ATOM     81  N   GLN    31       3.085   3.042   0.897  1.00  0.00              
ATOM     82  CA  GLN    31       3.623   4.044  -0.028  1.00  0.00              
ATOM     83  C   GLN    31       5.028   3.650  -0.483  1.00  0.00              
ATOM     84  O   GLN    31       5.341   3.710  -1.671  1.00  0.00              
ATOM     85  N   LYS    32       5.864   3.237   0.475  1.00  0.00              
ATOM     86  CA  LYS    32       7.233   2.820   0.158  1.00  0.00              
ATOM     87  C   LYS    32       7.213   1.547  -0.686  1.00  0.00              
ATOM     88  O   LYS    32       7.943   1.433  -1.672  1.00  0.00              
ATOM     89  N   LEU    33       6.354   0.599  -0.293  1.00  0.00              
ATOM     90  CA  LEU    33       6.217  -0.669  -1.018  1.00  0.00              
ATOM     91  C   LEU    33       5.718  -0.430  -2.446  1.00  0.00              
ATOM     92  O   LEU    33       5.957  -1.242  -3.340  1.00  0.00              
ATOM     93  N   ARG    34       5.026   0.696  -2.651  1.00  0.00              
ATOM     94  CA  ARG    34       4.506   1.038  -3.971  1.00  0.00              
ATOM     95  C   ARG    34       5.576   1.772  -4.783  1.00  0.00              
ATOM     96  O   ARG    34       5.901   1.374  -5.900  1.00  0.00              
ATOM     97  N   GLN    35       6.106   2.853  -4.200  1.00  0.00              
ATOM     98  CA  GLN    35       7.132   3.672  -4.861  1.00  0.00              
ATOM     99  C   GLN    35       8.323   2.842  -5.351  1.00  0.00              
ATOM    100  O   GLN    35       8.857   3.104  -6.430  1.00  0.00              
ATOM    101  N   GLU    36       8.746   1.851  -4.555  1.00  0.00              
ATOM    102  CA  GLU    36       9.890   1.008  -4.944  1.00  0.00              
ATOM    103  C   GLU    36       9.653   0.366  -6.313  1.00  0.00              
ATOM    104  O   GLU    36      10.575   0.247  -7.121  1.00  0.00              
ATOM    105  N   TYR    37       8.403  -0.034  -6.568  1.00  0.00              
ATOM    106  CA  TYR    37       8.047  -0.649  -7.847  1.00  0.00              
ATOM    107  C   TYR    37       7.781   0.428  -8.903  1.00  0.00              
ATOM    108  O   TYR    37       8.007   0.210 -10.094  1.00  0.00              
ATOM    109  N   LEU    38       7.298   1.596  -8.451  1.00  0.00              
ATOM    110  CA  LEU    38       7.004   2.709  -9.361  1.00  0.00              
ATOM    111  C   LEU    38       8.218   3.640  -9.488  1.00  0.00              
ATOM    112  O   LEU    38       8.077   4.863  -9.577  1.00  0.00              
ATOM    113  N   LYS    39       9.415   3.046  -9.511  1.00  0.00              
ATOM    114  CA  LYS    39      10.646   3.830  -9.645  1.00  0.00              
ATOM    115  C   LYS    39      10.791   4.347 -11.080  1.00  0.00              
ATOM    116  O   LYS    39      11.370   5.412 -11.311  1.00  0.00              
ATOM    117  N   GLY    40      10.250   3.585 -12.037  1.00  0.00              
ATOM    118  CA  GLY    40      10.311   3.972 -13.447  1.00  0.00              
ATOM    119  C   GLY    40       9.112   3.403 -14.216  1.00  0.00              
ATOM    120  O   GLY    40       9.252   2.911 -15.340  1.00  0.00              
END
