
#######################################################
#                                                     #
#                        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   31 (  124),  selected   31 , name T0348AL381_4
# Molecule2: number of CA atoms   61 (  465),  selected   31 , name T0348.pdb
# PARAMETERS: T0348AL381_4.T0348.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         9 - 39          2.75     2.75
  LCS_AVERAGE:     50.82

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15        24 - 38          1.93     3.07
  LONGEST_CONTINUOUS_SEGMENT:    15        25 - 39          1.86     3.86
  LCS_AVERAGE:     23.59

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11        26 - 36          0.83     4.24
  LCS_AVERAGE:     12.90

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:   61
LCS_GDT     L       9     L       9      8   12   31     4   10   17   19   21   22   24   28   30   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     V      10     V      10      8   12   31     6   13   18   19   21   22   26   28   30   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     C      11     C      11      8   14   31     6   14   18   19   21   22   26   28   30   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     P      12     P      12      8   14   31     6   14   18   19   21   22   26   28   30   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     L      13     L      13      8   14   31     6    9   18   19   21   22   26   28   30   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     C      14     C      14      8   14   31     6   14   18   19   21   22   26   28   30   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     K      15     K      15      8   14   31     6   14   18   19   21   22   26   28   30   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     G      16     G      16      8   14   31     4   14   18   19   21   22   26   28   30   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     P      17     P      17      7   14   31     4    9   14   19   21   22   26   28   30   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     L      18     L      18      5   14   31     4    4    5   14   17   21   26   28   30   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     V      19     V      19      4   14   31     4    4    5    8   17   20   25   28   30   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     F      20     F      20      4   14   31     4    6   12   17   20   22   26   28   30   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     D      21     D      21      4   14   31     3    4    5    8   12   19   22   25   29   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     K      22     K      22      4   14   31     3    5   12   17   19   22   26   28   30   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     S      23     S      23      4   14   31     3    3    6   10   17   20   25   28   30   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     K      24     K      24      4   15   31     3    3   11   17   19   22   26   28   30   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     D      25     D      25      4   15   31     3    3    6   17   21   22   26   28   30   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     E      26     E      26     11   15   31     5   14   18   19   21   22   26   28   30   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     L      27     L      27     11   15   31     5   14   18   19   21   22   26   28   30   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     I      28     I      28     11   15   31     5   14   18   19   21   22   26   28   30   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     C      29     C      29     11   15   31     6   14   18   19   21   22   26   28   30   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     K      30     K      30     11   15   31     4   11   18   19   21   22   26   28   30   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     G      31     G      31     11   15   31     6   14   18   19   21   22   26   28   30   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     D      32     D      32     11   15   31     6   14   18   19   21   22   26   28   30   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     R      33     R      33     11   15   31     5   12   18   19   21   22   26   28   30   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     L      34     L      34     11   15   31     6   14   18   19   21   22   26   28   30   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     A      35     A      35     11   15   31     6   14   18   19   21   22   26   28   30   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     F      36     F      36     11   15   31     4   14   18   19   21   22   26   28   30   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     P      37     P      37      9   15   31     3    6   13   17   21   22   26   28   30   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     I      38     I      38      5   15   31     3    5    7   10   15   22   26   28   30   31   31   31   31   31   31   31   31   31   31   31 
LCS_GDT     K      39     K      39      5   15   31     3    5    7    8   11   19   23   28   30   31   31   31   31   31   31   31   31   31   31   31 
LCS_AVERAGE  LCS_A:  29.10  (  12.90   23.59   50.82 )

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      6     14     18     19     21     22     26     28     30     31     31     31     31     31     31     31     31     31     31     31 
GDT PERCENT_CA   9.84  22.95  29.51  31.15  34.43  36.07  42.62  45.90  49.18  50.82  50.82  50.82  50.82  50.82  50.82  50.82  50.82  50.82  50.82  50.82
GDT RMS_LOCAL    0.18   0.61   0.89   0.98   1.28   1.43   2.08   2.37   2.57   2.75   2.75   2.75   2.75   2.75   2.75   2.75   2.75   2.75   2.75   2.75
GDT RMS_ALL_CA   4.06   4.15   4.07   4.16   3.84   3.69   2.89   2.78   2.77   2.75   2.75   2.75   2.75   2.75   2.75   2.75   2.75   2.75   2.75   2.75

#      Molecule1      Molecule2       DISTANCE
LGA    L       9      L       9          4.741
LGA    V      10      V      10          3.217
LGA    C      11      C      11          1.198
LGA    P      12      P      12          1.585
LGA    L      13      L      13          2.462
LGA    C      14      C      14          1.501
LGA    K      15      K      15          1.919
LGA    G      16      G      16          1.056
LGA    P      17      P      17          0.766
LGA    L      18      L      18          3.398
LGA    V      19      V      19          3.815
LGA    F      20      F      20          1.596
LGA    D      21      D      21          5.627
LGA    K      22      K      22          1.661
LGA    S      23      S      23          3.869
LGA    K      24      K      24          2.059
LGA    D      25      D      25          3.238
LGA    E      26      E      26          3.985
LGA    L      27      L      27          3.723
LGA    I      28      I      28          3.029
LGA    C      29      C      29          1.378
LGA    K      30      K      30          0.910
LGA    G      31      G      31          0.801
LGA    D      32      D      32          0.865
LGA    R      33      R      33          0.738
LGA    L      34      L      34          1.728
LGA    A      35      A      35          2.485
LGA    F      36      F      36          1.748
LGA    P      37      P      37          1.406
LGA    I      38      I      38          3.746
LGA    K      39      K      39          5.032

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   31   61    4.0     28    2.37    37.705    36.052     1.133

LGA_LOCAL      RMSD =  2.372  Number of atoms =   28  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  2.785  Number of atoms =   31 
Std_ALL_ATOMS  RMSD =  2.752  (standard rmsd on all 31 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.756913 * X  +  -0.336895 * Y  +  -0.559987 * Z  +  11.237266
  Y_new =  -0.361693 * X  +  -0.497721 * Y  +   0.788322 * Z  +  35.429996
  Z_new =  -0.544299 * X  +   0.799234 * Y  +   0.254879 * Z  +  45.675728 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.262088   -1.879505  [ DEG:    72.3123   -107.6877 ]
  Theta =   0.575553    2.566040  [ DEG:    32.9768    147.0232 ]
  Phi   =  -2.695819    0.445774  [ DEG:  -154.4590     25.5410 ]
 
# 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: T0348AL381_4                                  
REMARK     2: T0348.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0348AL381_4.T0348.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   31   61   4.0   28   2.37  36.052     2.75
REMARK  ---------------------------------------------------------- 
MOLECULE T0348AL381_4
REMARK Aligment from pdb entry: 2ct7A
ATOM      1  N   LEU     9      13.466  33.000  55.718  1.00  0.00              
ATOM      2  CA  LEU     9      12.436  31.982  55.540  1.00  0.00              
ATOM      3  C   LEU     9      12.102  31.307  56.865  1.00  0.00              
ATOM      4  O   LEU     9      12.968  30.709  57.504  1.00  0.00              
ATOM      5  N   VAL    10      10.841  31.405  57.272  1.00  0.00              
ATOM      6  CA  VAL    10      10.392  30.801  58.522  1.00  0.00              
ATOM      7  C   VAL    10       8.960  30.296  58.398  1.00  0.00              
ATOM      8  O   VAL    10       8.260  30.611  57.435  1.00  0.00              
ATOM      9  N   CYS    11       8.527  29.510  59.379  1.00  0.00              
ATOM     10  CA  CYS    11       7.177  28.961  59.380  1.00  0.00              
ATOM     11  C   CYS    11       6.136  30.076  59.348  1.00  0.00              
ATOM     12  O   CYS    11       6.477  31.258  59.367  1.00  0.00              
ATOM     13  N   PRO    12       4.864  29.691  59.300  1.00  0.00              
ATOM     14  CA  PRO    12       3.774  30.657  59.269  1.00  0.00              
ATOM     15  C   PRO    12       3.024  30.683  60.597  1.00  0.00              
ATOM     16  O   PRO    12       2.115  31.489  60.789  1.00  0.00              
ATOM     17  N   LEU    13       3.412  29.796  61.507  1.00  0.00              
ATOM     18  CA  LEU    13       2.776  29.718  62.816  1.00  0.00              
ATOM     19  C   LEU    13       3.799  29.900  63.932  1.00  0.00              
ATOM     20  O   LEU    13       3.651  30.772  64.789  1.00  0.00              
ATOM     21  N   CYS    14       4.839  29.072  63.915  1.00  0.00              
ATOM     22  CA  CYS    14       5.888  29.142  64.925  1.00  0.00              
ATOM     23  C   CYS    14       6.844  30.296  64.638  1.00  0.00              
ATOM     24  O   CYS    14       7.396  30.901  65.558  1.00  0.00              
ATOM     25  N   LYS    15       7.034  30.594  63.358  1.00  0.00              
ATOM     26  CA  LYS    15       7.926  31.673  62.949  1.00  0.00              
ATOM     27  C   LYS    15       9.323  31.474  63.531  1.00  0.00              
ATOM     28  O   LYS    15       9.864  32.359  64.193  1.00  0.00              
ATOM     29  N   GLY    16       9.901  30.303  63.280  1.00  0.00              
ATOM     30  CA  GLY    16      11.233  29.986  63.779  1.00  0.00              
ATOM     31  C   GLY    16      12.225  31.087  63.420  1.00  0.00              
ATOM     32  O   GLY    16      12.690  31.827  64.286  1.00  0.00              
ATOM     33  N   PRO    17      12.546  31.190  62.133  1.00  0.00              
ATOM     34  CA  PRO    17      13.482  32.202  61.681  1.00  0.00              
ATOM     35  C   PRO    17      14.826  31.617  61.293  1.00  0.00              
ATOM     36  O   PRO    17      15.746  31.565  62.108  1.00  0.00              
ATOM     37  N   LEU    18      14.939  31.176  60.044  1.00  0.00              
ATOM     38  CA  LEU    18      16.180  30.590  59.550  1.00  0.00              
ATOM     39  C   LEU    18      16.385  30.915  58.074  1.00  0.00              
ATOM     40  O   LEU    18      15.441  30.881  57.283  1.00  0.00              
ATOM     41  N   VAL    19      17.622  31.230  57.710  1.00  0.00              
ATOM     42  CA  VAL    19      17.952  31.561  56.328  1.00  0.00              
ATOM     43  C   VAL    19      18.127  30.302  55.488  1.00  0.00              
ATOM     44  O   VAL    19      18.783  29.348  55.909  1.00  0.00              
ATOM     45  N   PHE    20      17.538  30.304  54.298  1.00  0.00              
ATOM     46  CA  PHE    20      17.628  29.160  53.397  1.00  0.00              
ATOM     47  C   PHE    20      18.317  29.548  52.093  1.00  0.00              
ATOM     48  O   PHE    20      19.110  28.782  51.545  1.00  0.00              
ATOM     49  N   ASP    21      18.007  30.743  51.599  1.00  0.00              
ATOM     50  CA  ASP    21      18.595  31.232  50.359  1.00  0.00              
ATOM     51  C   ASP    21      18.934  30.076  49.423  1.00  0.00              
ATOM     52  O   ASP    21      20.003  30.048  48.813  1.00  0.00              
ATOM     53  N   LYS    22      18.015  29.121  49.316  1.00  0.00              
ATOM     54  CA  LYS    22      18.216  27.960  48.457  1.00  0.00              
ATOM     55  C   LYS    22      17.362  28.063  47.196  1.00  0.00              
ATOM     56  O   LYS    22      16.401  28.829  47.147  1.00  0.00              
ATOM     57  N   SER    23      17.722  27.287  46.178  1.00  0.00              
ATOM     58  CA  SER    23      16.991  27.293  44.918  1.00  0.00              
ATOM     59  C   SER    23      15.994  26.139  44.863  1.00  0.00              
ATOM     60  O   SER    23      15.931  25.406  43.875  1.00  0.00              
ATOM     61  N   LYS    24      15.216  25.985  45.930  1.00  0.00              
ATOM     62  CA  LYS    24      14.223  24.919  46.004  1.00  0.00              
ATOM     63  C   LYS    24      12.969  25.395  46.731  1.00  0.00              
ATOM     64  O   LYS    24      12.945  26.486  47.301  1.00  0.00              
ATOM     65  N   ASP    25      11.930  24.567  46.709  1.00  0.00              
ATOM     66  CA  ASP    25      10.671  24.902  47.367  1.00  0.00              
ATOM     67  C   ASP    25      10.295  23.840  48.394  1.00  0.00              
ATOM     68  O   ASP    25       9.120  23.664  48.715  1.00  0.00              
ATOM     69  N   GLU    26      11.299  23.137  48.907  1.00  0.00              
ATOM     70  CA  GLU    26      11.072  22.093  49.898  1.00  0.00              
ATOM     71  C   GLU    26      11.790  22.418  51.205  1.00  0.00              
ATOM     72  O   GLU    26      12.676  21.682  51.638  1.00  0.00              
ATOM     73  N   LEU    27      11.401  23.526  51.827  1.00  0.00              
ATOM     74  CA  LEU    27      12.008  23.949  53.084  1.00  0.00              
ATOM     75  C   LEU    27      11.426  23.174  54.262  1.00  0.00              
ATOM     76  O   LEU    27      10.239  22.843  54.276  1.00  0.00              
ATOM     77  N   ILE    28      12.268  22.886  55.250  1.00  0.00              
ATOM     78  CA  ILE    28      11.837  22.148  56.430  1.00  0.00              
ATOM     79  C   ILE    28      12.232  22.879  57.709  1.00  0.00              
ATOM     80  O   ILE    28      13.399  23.219  57.907  1.00  0.00              
ATOM     81  N   CYS    29      11.253  23.118  58.574  1.00  0.00              
ATOM     82  CA  CYS    29      11.496  23.808  59.835  1.00  0.00              
ATOM     83  C   CYS    29      12.315  22.937  60.783  1.00  0.00              
ATOM     84  O   CYS    29      12.047  21.748  60.961  1.00  0.00              
ATOM     85  N   LYS    30      13.337  23.540  61.406  1.00  0.00              
ATOM     86  CA  LYS    30      14.215  22.838  62.347  1.00  0.00              
ATOM     87  C   LYS    30      13.505  22.482  63.649  1.00  0.00              
ATOM     88  O   LYS    30      14.109  21.919  64.561  1.00  0.00              
ATOM     89  N   GLY    31      12.221  22.814  63.726  1.00  0.00              
ATOM     90  CA  GLY    31      11.428  22.529  64.916  1.00  0.00              
ATOM     91  C   GLY    31      10.209  21.681  64.568  1.00  0.00              
ATOM     92  O   GLY    31      10.052  20.567  65.066  1.00  0.00              
ATOM     93  N   ASP    32       9.346  22.219  63.711  1.00  0.00              
ATOM     94  CA  ASP    32       8.140  21.514  63.296  1.00  0.00              
ATOM     95  C   ASP    32       8.474  20.394  62.316  1.00  0.00              
ATOM     96  O   ASP    32       7.784  19.376  62.260  1.00  0.00              
ATOM     97  N   ARG    33       9.540  20.588  61.544  1.00  0.00              
ATOM     98  CA  ARG    33       9.967  19.593  60.567  1.00  0.00              
ATOM     99  C   ARG    33       8.876  19.350  59.527  1.00  0.00              
ATOM    100  O   ARG    33       8.711  18.233  59.038  1.00  0.00              
ATOM    101  N   LEU    34       8.135  20.403  59.197  1.00  0.00              
ATOM    102  CA  LEU    34       7.060  20.302  58.218  1.00  0.00              
ATOM    103  C   LEU    34       7.440  21.001  56.917  1.00  0.00              
ATOM    104  O   LEU    34       7.869  22.156  56.922  1.00  0.00              
ATOM    105  N   ALA    35       7.283  20.295  55.801  1.00  0.00              
ATOM    106  CA  ALA    35       7.612  20.847  54.494  1.00  0.00              
ATOM    107  C   ALA    35       6.581  21.883  54.060  1.00  0.00              
ATOM    108  O   ALA    35       5.411  21.560  53.853  1.00  0.00              
ATOM    109  N   PHE    36       7.023  23.128  53.922  1.00  0.00              
ATOM    110  CA  PHE    36       6.137  24.212  53.511  1.00  0.00              
ATOM    111  C   PHE    36       6.816  25.107  52.478  1.00  0.00              
ATOM    112  O   PHE    36       8.010  25.390  52.573  1.00  0.00              
ATOM    113  N   PRO    37       6.045  25.550  51.490  1.00  0.00              
ATOM    114  CA  PRO    37       6.569  26.411  50.438  1.00  0.00              
ATOM    115  C   PRO    37       7.222  27.657  51.029  1.00  0.00              
ATOM    116  O   PRO    37       6.787  28.169  52.060  1.00  0.00              
ATOM    117  N   ILE    38       8.268  28.140  50.367  1.00  0.00              
ATOM    118  CA  ILE    38       8.982  29.327  50.825  1.00  0.00              
ATOM    119  C   ILE    38       8.371  30.594  50.238  1.00  0.00              
ATOM    120  O   ILE    38       8.790  31.705  50.565  1.00  0.00              
ATOM    121  N   LYS    39       7.380  30.422  49.371  1.00  0.00              
ATOM    122  CA  LYS    39       6.711  31.552  48.739  1.00  0.00              
ATOM    123  C   LYS    39       5.338  31.790  49.359  1.00  0.00              
ATOM    124  O   LYS    39       5.133  32.761  50.088  1.00  0.00              
END
