
#######################################################
#                                                     #
#                        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   26 (  104),  selected   26 , name T0369AL044_2
# Molecule2: number of CA atoms  147 ( 1193),  selected   26 , name T0369.pdb
# PARAMETERS: T0369AL044_2.T0369.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        71 - 99          4.62     7.86
  LONGEST_CONTINUOUS_SEGMENT:    22        72 - 101         4.98     7.50
  LCS_AVERAGE:     14.08

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        78 - 83          1.51    15.99
  LONGEST_CONTINUOUS_SEGMENT:     6        79 - 87          1.99    12.78
  LCS_AVERAGE:      2.83

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4        79 - 82          0.91    16.39
  LCS_AVERAGE:      1.52

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:  147
LCS_GDT     Q      70     Q      70      0    0    0     0    0    0    0    0    0    0    0    0    0    0    0    0    9   11   12   12   12   13   13 
LCS_GDT     F      71     F      71      0    0   22     0    0    0    0    0    1    3    5    5   16   18   19   21   21   22   22   23   23   24   24 
LCS_GDT     Y      72     Y      72      0    0   22     0    0    0    0    0    0    3    5    5    5    6   19   21   21   22   22   23   23   24   24 
LCS_GDT     A      73     A      73      3    3   22     3    3    3    3    4    6    8    9   12   16   17   18   19   20   22   22   22   23   23   23 
LCS_GDT     V      74     V      74      3    3   22     3    3    3    3    6    8    9   13   14   16   17   19   21   21   22   22   23   23   24   24 
LCS_GDT     P      75     P      75      3    3   22     3    3    4    6    7    8   11   13   14   16   18   19   21   21   22   22   23   23   24   24 
LCS_GDT     V      76     V      76      3    4   22     3    3    3    3    4    5    7    9   12   15   18   19   21   21   22   22   23   23   24   24 
LCS_GDT     L      77     L      77      3    4   22     3    3    4    6    7    8   11   13   14   16   18   19   21   21   22   22   23   23   24   24 
LCS_GDT     P      78     P      78      3    6   22     3    4    4    6    7    8   11   13   14   16   18   19   21   21   22   22   23   23   24   24 
LCS_GDT     E      79     E      79      4    6   22     3    4    5    6    6    8    9   12   14   16   18   19   21   21   22   22   23   23   24   24 
LCS_GDT     Q      80     Q      80      4    6   22     3    4    5    6    7    8   10   13   14   16   18   19   21   21   22   22   23   23   24   24 
LCS_GDT     L      81     L      81      4    6   22     3    3    5    6    6    8   10   12   14   16   18   19   21   21   22   22   23   23   24   24 
LCS_GDT     V      82     V      82      4    6   22     3    3    5    6    7    8   11   13   14   16   18   19   21   21   22   22   23   23   24   24 
LCS_GDT     D      83     D      83      3    6   22     3    4    5    6    7    8   11   13   14   16   18   19   21   21   22   22   23   23   24   24 
LCS_GDT     Q      87     Q      87      0    6   22     3    3    4    6    7    8   11   13   14   16   18   19   21   21   22   22   23   23   24   24 
LCS_GDT     W      89     W      89      0    5   22     0    3    4    6    7    8   11   13   14   16   18   19   21   21   22   22   23   23   24   24 
LCS_GDT     Q      90     Q      90      3    5   22     3    3    4    6    7    8   11   13   14   16   18   19   21   21   22   22   23   23   24   24 
LCS_GDT     Y      92     Y      92      3    5   22     2    3    4    5    6    8   10   13   14   16   18   19   21   21   22   22   23   23   24   24 
LCS_GDT     Q      93     Q      93      3    5   22     2    3    4    6    7    8   11   13   14   16   18   19   21   21   22   22   23   23   24   24 
LCS_GDT     L      96     L      96      3    5   22     0    3    3    3    3    6    6   11   11   13   17   19   21   21   22   22   23   23   24   24 
LCS_GDT     M      97     M      97      3    5   22     1    3    3    5    7    8   11   13   14   16   18   19   21   21   22   22   23   23   24   24 
LCS_GDT     A      98     A      98      3    5   22     0    3    4    6    7    8   11   12   14   16   18   19   21   21   22   22   23   23   24   24 
LCS_GDT     D      99     D      99      3    5   22     1    3    3    4    5    6    7   11   13   16   18   19   21   21   22   22   23   23   24   24 
LCS_GDT     S     101     S     101      0    3   22     0    0    0    0    3    4    5    7    9   12   14   16   19   21   22   22   23   23   24   24 
LCS_GDT     T     102     T     102      0    3   20     0    1    2    2    3    4    5    7    9    9   11   14   18   20   22   22   23   23   24   24 
LCS_GDT     E     103     E     103      0    3   12     0    1    2    2    3    4    5    7    9    9   10   13   18   19   22   22   23   23   24   24 
LCS_AVERAGE  LCS_A:   6.14  (   1.52    2.83   14.08 )

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      3      4      5      6      7      8     11     13     14     16     18     19     21     21     22     22     23     23     24     24 
GDT PERCENT_CA   2.04   2.72   3.40   4.08   4.76   5.44   7.48   8.84   9.52  10.88  12.24  12.93  14.29  14.29  14.97  14.97  15.65  15.65  16.33  16.33
GDT RMS_LOCAL    0.02   0.54   1.12   1.51   1.78   1.98   2.76   2.96   3.19   3.48   3.92   4.07   4.37   4.37   4.62   4.62   5.15   5.05   5.49   5.49
GDT RMS_ALL_CA  26.24  23.67  15.33  15.99   8.53   8.58   8.26   8.90   8.47   9.39   7.66   7.62   7.63   7.63   7.86   7.86   7.08   7.45   7.00   7.00

#      Molecule1      Molecule2       DISTANCE
LGA    Q      70      Q      70         25.380
LGA    F      71      F      71          7.735
LGA    Y      72      Y      72          7.696
LGA    A      73      A      73          5.953
LGA    V      74      V      74          3.704
LGA    P      75      P      75          2.450
LGA    V      76      V      76          5.455
LGA    L      77      L      77          3.228
LGA    P      78      P      78          3.486
LGA    E      79      E      79          5.653
LGA    Q      80      Q      80          3.694
LGA    L      81      L      81          5.439
LGA    V      82      V      82          3.852
LGA    D      83      D      83          3.954
LGA    Q      87      Q      87          0.224
LGA    W      89      W      89          2.291
LGA    Q      90      Q      90          1.785
LGA    Y      92      Y      92          3.779
LGA    Q      93      Q      93          2.553
LGA    L      96      L      96          6.889
LGA    M      97      M      97          1.749
LGA    A      98      A      98          5.191
LGA    D      99      D      99          8.430
LGA    S     101      S     101         13.484
LGA    T     102      T     102         15.333
LGA    E     103      E     103         18.146

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   26  147    4.0     13    2.96     7.653     6.695     0.425

LGA_LOCAL      RMSD =  2.956  Number of atoms =   13  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  8.549  Number of atoms =   26 
Std_ALL_ATOMS  RMSD =  6.934  (standard rmsd on all 26 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.419100 * X  +  -0.824901 * Y  +  -0.379334 * Z  +   5.201204
  Y_new =   0.891046 * X  +  -0.293463 * Y  +  -0.346289 * Z  + -12.933183
  Z_new =   0.174334 * X  +  -0.483133 * Y  +   0.858015 * Z  +  -6.375250 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.512832    2.628761  [ DEG:   -29.3831    150.6169 ]
  Theta =  -0.175229   -2.966364  [ DEG:   -10.0399   -169.9601 ]
  Phi   =   2.010440   -1.131153  [ DEG:   115.1897    -64.8103 ]
 
# 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: T0369AL044_2                                  
REMARK     2: T0369.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0369AL044_2.T0369.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   26  147   4.0   13   2.96   6.695     6.93
REMARK  ---------------------------------------------------------- 
MOLECULE T0369AL044_2
REMARK Aligment from pdb entry: 1rxq_A
ATOM      1  N   GLN    70      13.556  21.756 -17.853  1.00  0.00              
ATOM      2  CA  GLN    70      14.263  22.340 -19.001  1.00  0.00              
ATOM      3  C   GLN    70      13.365  23.032 -20.032  1.00  0.00              
ATOM      4  O   GLN    70      13.878  23.569 -20.998  1.00  0.00              
ATOM      5  N   PHE    71       1.850   7.313 -22.620  1.00  0.00              
ATOM      6  CA  PHE    71       2.071   5.985 -23.192  1.00  0.00              
ATOM      7  C   PHE    71       0.872   5.099 -22.827  1.00  0.00              
ATOM      8  O   PHE    71       0.169   5.371 -21.860  1.00  0.00              
ATOM      9  N   TYR    72       0.628   4.057 -23.610  1.00  0.00              
ATOM     10  CA  TYR    72      -0.495   3.148 -23.384  1.00  0.00              
ATOM     11  C   TYR    72      -0.017   2.054 -22.435  1.00  0.00              
ATOM     12  O   TYR    72       0.480   1.032 -22.880  1.00  0.00              
ATOM     13  N   ALA    73       5.272  -9.281 -25.215  1.00  0.00              
ATOM     14  CA  ALA    73       5.806 -10.576 -24.782  1.00  0.00              
ATOM     15  C   ALA    73       6.858 -10.440 -23.679  1.00  0.00              
ATOM     16  O   ALA    73       6.841 -11.168 -22.688  1.00  0.00              
ATOM     17  N   VAL    74       7.769  -9.491 -23.839  1.00  0.00              
ATOM     18  CA  VAL    74       8.784  -9.260 -22.828  1.00  0.00              
ATOM     19  C   VAL    74       8.192  -8.947 -21.443  1.00  0.00              
ATOM     20  O   VAL    74       8.677  -9.450 -20.428  1.00  0.00              
ATOM     21  N   PRO    75       7.166  -8.109 -21.395  1.00  0.00              
ATOM     22  CA  PRO    75       6.531  -7.743 -20.126  1.00  0.00              
ATOM     23  C   PRO    75       5.871  -8.961 -19.451  1.00  0.00              
ATOM     24  O   PRO    75       5.760  -9.052 -18.219  1.00  0.00              
ATOM     25  N   VAL    76       5.412  -9.903 -20.260  1.00  0.00              
ATOM     26  CA  VAL    76       4.752 -11.088 -19.731  1.00  0.00              
ATOM     27  C   VAL    76       5.699 -12.236 -19.356  1.00  0.00              
ATOM     28  O   VAL    76       5.270 -13.169 -18.648  1.00  0.00              
ATOM     29  N   LEU    77       6.952 -12.193 -19.824  1.00  0.00              
ATOM     30  CA  LEU    77       7.882 -13.321 -19.653  1.00  0.00              
ATOM     31  C   LEU    77       9.271 -13.042 -19.044  1.00  0.00              
ATOM     32  O   LEU    77       9.884 -13.956 -18.510  1.00  0.00              
ATOM     33  N   PRO    78      12.275 -12.206 -16.603  1.00  0.00              
ATOM     34  CA  PRO    78      12.527 -12.360 -15.179  1.00  0.00              
ATOM     35  C   PRO    78      12.485 -10.997 -14.498  1.00  0.00              
ATOM     36  O   PRO    78      12.971 -10.015 -15.070  1.00  0.00              
ATOM     37  N   GLU    79      11.899 -10.896 -13.304  1.00  0.00              
ATOM     38  CA  GLU    79      11.861  -9.592 -12.645  1.00  0.00              
ATOM     39  C   GLU    79      13.235  -9.019 -12.317  1.00  0.00              
ATOM     40  O   GLU    79      13.331  -7.807 -12.197  1.00  0.00              
ATOM     41  N   GLN    80      14.264  -9.851 -12.177  1.00  0.00              
ATOM     42  CA  GLN    80      15.563  -9.364 -11.696  1.00  0.00              
ATOM     43  C   GLN    80      16.098  -8.144 -12.460  1.00  0.00              
ATOM     44  O   GLN    80      16.599  -7.219 -11.840  1.00  0.00              
ATOM     45  N   LEU    81      14.455  -5.766 -14.115  1.00  0.00              
ATOM     46  CA  LEU    81      13.651  -4.596 -13.789  1.00  0.00              
ATOM     47  C   LEU    81      13.868  -4.168 -12.364  1.00  0.00              
ATOM     48  O   LEU    81      13.864  -2.988 -12.083  1.00  0.00              
ATOM     49  N   VAL    82      14.042  -5.127 -11.459  1.00  0.00              
ATOM     50  CA  VAL    82      14.333  -4.750 -10.081  1.00  0.00              
ATOM     51  C   VAL    82      15.670  -3.998  -9.976  1.00  0.00              
ATOM     52  O   VAL    82      15.774  -3.003  -9.276  1.00  0.00              
ATOM     53  N   ASP    83      16.676  -4.455 -10.709  1.00  0.00              
ATOM     54  CA  ASP    83      17.981  -3.814 -10.715  1.00  0.00              
ATOM     55  C   ASP    83      17.914  -2.449 -11.391  1.00  0.00              
ATOM     56  O   ASP    83      18.542  -1.490 -10.947  1.00  0.00              
ATOM     57  N   GLN    87      17.162  -2.366 -12.483  1.00  0.00              
ATOM     58  CA  GLN    87      16.987  -1.093 -13.172  1.00  0.00              
ATOM     59  C   GLN    87      16.328  -0.075 -12.241  1.00  0.00              
ATOM     60  O   GLN    87      16.774   1.058 -12.144  1.00  0.00              
ATOM     61  N   TRP    89      15.286  -0.494 -11.534  1.00  0.00              
ATOM     62  CA  TRP    89      14.569   0.382 -10.632  1.00  0.00              
ATOM     63  C   TRP    89      15.455   0.918  -9.513  1.00  0.00              
ATOM     64  O   TRP    89      15.364   2.079  -9.155  1.00  0.00              
ATOM     65  N   GLN    90      18.734   1.374  -9.620  1.00  0.00              
ATOM     66  CA  GLN    90      19.617   2.380 -10.158  1.00  0.00              
ATOM     67  C   GLN    90      18.854   3.632 -10.611  1.00  0.00              
ATOM     68  O   GLN    90      19.339   4.756 -10.448  1.00  0.00              
ATOM     69  N   TYR    92      17.636   3.442 -11.113  1.00  0.00              
ATOM     70  CA  TYR    92      16.852   4.561 -11.618  1.00  0.00              
ATOM     71  C   TYR    92      16.420   5.441 -10.457  1.00  0.00              
ATOM     72  O   TYR    92      16.555   6.643 -10.505  1.00  0.00              
ATOM     73  N   GLN    93      15.917   4.840  -9.396  1.00  0.00              
ATOM     74  CA  GLN    93      15.532   5.624  -8.238  1.00  0.00              
ATOM     75  C   GLN    93      16.745   6.281  -7.582  1.00  0.00              
ATOM     76  O   GLN    93      16.617   7.347  -6.979  1.00  0.00              
ATOM     77  N   LEU    96      17.920   5.664  -7.698  1.00  0.00              
ATOM     78  CA  LEU    96      19.158   6.313  -7.284  1.00  0.00              
ATOM     79  C   LEU    96      19.396   7.636  -8.005  1.00  0.00              
ATOM     80  O   LEU    96      19.621   8.662  -7.374  1.00  0.00              
ATOM     81  N   MET    97      18.758  13.620  -8.549  1.00  0.00              
ATOM     82  CA  MET    97      18.267  14.792  -9.241  1.00  0.00              
ATOM     83  C   MET    97      17.406  15.615  -8.258  1.00  0.00              
ATOM     84  O   MET    97      17.559  16.834  -8.121  1.00  0.00              
ATOM     85  N   ALA    98      16.535  14.927  -7.549  1.00  0.00              
ATOM     86  CA  ALA    98      15.581  15.602  -6.670  1.00  0.00              
ATOM     87  C   ALA    98      16.282  16.389  -5.574  1.00  0.00              
ATOM     88  O   ALA    98      15.832  17.471  -5.171  1.00  0.00              
ATOM     89  N   ASP    99      17.381  15.842  -5.073  1.00  0.00              
ATOM     90  CA  ASP    99      18.131  16.511  -4.018  1.00  0.00              
ATOM     91  C   ASP    99      18.851  17.773  -4.501  1.00  0.00              
ATOM     92  O   ASP    99      19.231  18.605  -3.680  1.00  0.00              
ATOM     93  N   SER   101      19.025  17.942  -5.816  1.00  0.00              
ATOM     94  CA  SER   101      19.642  19.164  -6.335  1.00  0.00              
ATOM     95  C   SER   101      18.654  20.306  -6.537  1.00  0.00              
ATOM     96  O   SER   101      19.079  21.448  -6.742  1.00  0.00              
ATOM     97  N   THR   102      15.985  23.319  -6.295  1.00  0.00              
ATOM     98  CA  THR   102      15.566  24.421  -5.431  1.00  0.00              
ATOM     99  C   THR   102      14.060  24.358  -5.195  1.00  0.00              
ATOM    100  O   THR   102      13.349  23.646  -5.880  1.00  0.00              
ATOM    101  N   GLU   103      13.561  25.149  -4.247  1.00  0.00              
ATOM    102  CA  GLU   103      12.124  25.222  -4.018  1.00  0.00              
ATOM    103  C   GLU   103      11.371  25.677  -5.267  1.00  0.00              
ATOM    104  O   GLU   103      10.284  25.159  -5.559  1.00  0.00              
END
