
#######################################################
#                                                     #
#                        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 T0335AL257_1-D1
# Molecule2: number of CA atoms   36 (  584),  selected   31 , name T0335_D1.pdb
# PARAMETERS: T0335AL257_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:    31         5 - 40          2.74     2.74
  LCS_AVERAGE:     86.11

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15         5 - 19          1.70     3.15
  LCS_AVERAGE:     38.08

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14         5 - 18          0.62     3.73
  LCS_AVERAGE:     30.02

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     A       5     A       5     14   15   31     7   17   20   25   25   25   27   27   28   29   30   31   31   31   31   31   31   31   31   31 
LCS_GDT     K       6     K       6     14   15   31     7   17   20   25   25   25   27   27   28   29   30   31   31   31   31   31   31   31   31   31 
LCS_GDT     I       7     I       7     14   15   31     7   17   20   25   25   25   27   27   28   29   30   31   31   31   31   31   31   31   31   31 
LCS_GDT     A       8     A       8     14   15   31     9   17   20   25   25   25   27   27   28   29   30   31   31   31   31   31   31   31   31   31 
LCS_GDT     R       9     R       9     14   15   31     9   17   20   25   25   25   27   27   28   29   30   31   31   31   31   31   31   31   31   31 
LCS_GDT     I      10     I      10     14   15   31     7   15   20   25   25   25   27   27   28   29   30   31   31   31   31   31   31   31   31   31 
LCS_GDT     N      11     N      11     14   15   31     9   17   20   25   25   25   27   27   28   29   30   31   31   31   31   31   31   31   31   31 
LCS_GDT     E      12     E      12     14   15   31     7   14   20   25   25   25   27   27   28   29   30   31   31   31   31   31   31   31   31   31 
LCS_GDT     L      13     L      13     14   15   31     7   13   20   25   25   25   27   27   28   29   30   31   31   31   31   31   31   31   31   31 
LCS_GDT     A      14     A      14     14   15   31     6   13   15   25   25   25   27   27   28   29   30   31   31   31   31   31   31   31   31   31 
LCS_GDT     A      15     A      15     14   15   31     5   13   14   25   25   25   27   27   28   29   30   31   31   31   31   31   31   31   31   31 
LCS_GDT     K      16     K      16     14   15   31     6   13   15   25   25   25   27   27   28   29   30   31   31   31   31   31   31   31   31   31 
LCS_GDT     A      17     A      17     14   15   31     7   13   15   25   25   25   27   27   28   29   30   31   31   31   31   31   31   31   31   31 
LCS_GDT     K      18     K      18     14   15   31     5   13   15   25   25   25   27   27   28   29   30   31   31   31   31   31   31   31   31   31 
LCS_GDT     A      19     A      19      3   15   31     3    3    3    4   21   23   27   27   27   29   30   31   31   31   31   31   31   31   31   31 
LCS_GDT     G      20     G      20      3   14   31     3    3    3    4    6    9   13   21   24   26   30   31   31   31   31   31   31   31   31   31 
LCS_GDT     V      21     V      21      3   14   31     3    3    3   10   15   23   27   27   27   29   30   31   31   31   31   31   31   31   31   31 
LCS_GDT     T      23     T      23     11   14   31     9   17   20   25   25   25   27   27   28   29   30   31   31   31   31   31   31   31   31   31 
LCS_GDT     E      24     E      24     11   14   31     9   17   20   25   25   25   27   27   28   29   30   31   31   31   31   31   31   31   31   31 
LCS_GDT     E      25     E      25     11   14   31     9   17   20   25   25   25   27   27   28   29   30   31   31   31   31   31   31   31   31   31 
LCS_GDT     E      26     E      26     11   14   31     9   17   20   25   25   25   27   27   28   29   30   31   31   31   31   31   31   31   31   31 
LCS_GDT     K      27     K      27     11   14   31     9   17   20   25   25   25   27   27   28   29   30   31   31   31   31   31   31   31   31   31 
LCS_GDT     A      28     A      28     11   14   31     9   17   20   25   25   25   27   27   28   29   30   31   31   31   31   31   31   31   31   31 
LCS_GDT     E      29     E      29     11   14   31     9   17   20   25   25   25   27   27   28   29   30   31   31   31   31   31   31   31   31   31 
LCS_GDT     Q      30     Q      30     11   14   31     9   17   20   25   25   25   27   27   28   29   30   31   31   31   31   31   31   31   31   31 
LCS_GDT     Q      31     Q      31     11   14   31     9   17   20   25   25   25   27   27   28   29   30   31   31   31   31   31   31   31   31   31 
LCS_GDT     K      32     K      32     11   14   31     5   17   20   25   25   25   27   27   28   29   30   31   31   31   31   31   31   31   31   31 
LCS_GDT     L      33     L      33     11   14   31     6   17   20   25   25   25   27   27   28   29   30   31   31   31   31   31   31   31   31   31 
LCS_GDT     L      38     L      38      3   12   31     3    3    3    3    3    4   19   24   28   29   30   31   31   31   31   31   31   31   31   31 
LCS_GDT     K      39     K      39      3    3   31     3    3    3    3   15   18   23   26   28   29   30   31   31   31   31   31   31   31   31   31 
LCS_GDT     G      40     G      40      3    3   31     3    3    3    3    3    3   17   24   28   28   30   31   31   31   31   31   31   31   31   31 
LCS_AVERAGE  LCS_A:  51.40  (  30.02   38.08   86.11 )

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      9     17     20     25     25     25     27     27     28     29     30     31     31     31     31     31     31     31     31     31 
GDT PERCENT_CA  25.00  47.22  55.56  69.44  69.44  69.44  75.00  75.00  77.78  80.56  83.33  86.11  86.11  86.11  86.11  86.11  86.11  86.11  86.11  86.11
GDT RMS_LOCAL    0.35   0.65   0.81   1.23   1.23   1.23   1.73   1.73   2.14   2.21   2.55   2.74   2.74   2.74   2.74   2.74   2.74   2.74   2.74   2.74
GDT RMS_ALL_CA   3.19   2.91   2.88   2.97   2.97   2.97   2.87   2.87   2.89   2.78   2.76   2.74   2.74   2.74   2.74   2.74   2.74   2.74   2.74   2.74

#      Molecule1      Molecule2       DISTANCE
LGA    A       5      A       5          1.743
LGA    K       6      K       6          1.056
LGA    I       7      I       7          1.406
LGA    A       8      A       8          0.944
LGA    R       9      R       9          0.329
LGA    I      10      I      10          1.083
LGA    N      11      N      11          0.736
LGA    E      12      E      12          1.219
LGA    L      13      L      13          1.450
LGA    A      14      A      14          2.500
LGA    A      15      A      15          3.079
LGA    K      16      K      16          2.669
LGA    A      17      A      17          2.887
LGA    K      18      K      18          2.936
LGA    A      19      A      19          3.565
LGA    G      20      G      20          6.743
LGA    V      21      V      21          3.847
LGA    T      23      T      23          1.239
LGA    E      24      E      24          0.716
LGA    E      25      E      25          0.270
LGA    E      26      E      26          0.726
LGA    K      27      K      27          0.161
LGA    A      28      A      28          0.417
LGA    E      29      E      29          0.548
LGA    Q      30      Q      30          0.416
LGA    Q      31      Q      31          0.387
LGA    K      32      K      32          1.073
LGA    L      33      L      33          1.057
LGA    L      38      L      38          6.192
LGA    K      39      K      39          5.798
LGA    G      40      G      40          7.240

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   31   36    4.0     27    1.73    69.444    63.492     1.475

LGA_LOCAL      RMSD =  1.730  Number of atoms =   27  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  2.870  Number of atoms =   31 
Std_ALL_ATOMS  RMSD =  2.737  (standard rmsd on all 31 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.481445 * X  +   0.131320 * Y  +  -0.866583 * Z  +  26.307337
  Y_new =   0.459274 * X  +   0.879902 * Y  +  -0.121819 * Z  + -31.124479
  Z_new =   0.746511 * X  +  -0.456649 * Y  +  -0.483936 * Z  + -13.428893 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.385197    0.756396  [ DEG:  -136.6617     43.3383 ]
  Theta =  -0.842802   -2.298790  [ DEG:   -48.2890   -131.7110 ]
  Phi   =   2.379758   -0.761835  [ DEG:   136.3501    -43.6499 ]
 
# 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: T0335AL257_1-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0335AL257_1-D1.T0335_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   31   36   4.0   27   1.73  63.492     2.74
REMARK  ---------------------------------------------------------- 
MOLECULE T0335AL257_1-D1
REMARK Aligment from pdb entry: 2c5i_T
ATOM     17  N   ALA     5       0.421  -9.124  -7.795  1.00  0.00              
ATOM     18  CA  ALA     5       0.052  -9.659  -6.464  1.00  0.00              
ATOM     19  C   ALA     5       0.374  -8.719  -5.279  1.00  0.00              
ATOM     20  O   ALA     5      -0.347  -8.676  -4.270  1.00  0.00              
ATOM     21  N   LYS     6       1.460  -7.971  -5.394  1.00  0.00              
ATOM     22  CA  LYS     6       1.789  -6.917  -4.407  1.00  0.00              
ATOM     23  C   LYS     6       0.743  -5.809  -4.418  1.00  0.00              
ATOM     24  O   LYS     6       0.239  -5.408  -3.392  1.00  0.00              
ATOM     25  N   ILE     7       0.417  -5.361  -5.598  1.00  0.00              
ATOM     26  CA  ILE     7      -0.621  -4.369  -5.815  1.00  0.00              
ATOM     27  C   ILE     7      -1.961  -4.815  -5.242  1.00  0.00              
ATOM     28  O   ILE     7      -2.613  -4.031  -4.546  1.00  0.00              
ATOM     29  N   ALA     8      -2.347  -6.058  -5.521  1.00  0.00              
ATOM     30  CA  ALA     8      -3.558  -6.614  -5.007  1.00  0.00              
ATOM     31  C   ALA     8      -3.611  -6.717  -3.530  1.00  0.00              
ATOM     32  O   ALA     8      -4.639  -6.437  -2.932  1.00  0.00              
ATOM     33  N   ARG     9      -2.503  -7.121  -2.923  1.00  0.00              
ATOM     34  CA  ARG     9      -2.383  -7.194  -1.474  1.00  0.00              
ATOM     35  C   ARG     9      -2.694  -5.878  -0.739  1.00  0.00              
ATOM     36  O   ARG     9      -3.246  -5.890   0.370  1.00  0.00              
ATOM     37  N   ILE    10      -2.257  -4.763  -1.334  1.00  0.00              
ATOM     38  CA  ILE    10      -2.435  -3.430  -0.784  1.00  0.00              
ATOM     39  C   ILE    10      -3.850  -2.974  -1.070  1.00  0.00              
ATOM     40  O   ILE    10      -4.492  -2.338  -0.245  1.00  0.00              
ATOM     41  N   ASN    11      -4.350  -3.353  -2.221  1.00  0.00              
ATOM     42  CA  ASN    11      -5.744  -3.125  -2.535  1.00  0.00              
ATOM     43  C   ASN    11      -6.727  -3.761  -1.608  1.00  0.00              
ATOM     44  O   ASN    11      -7.675  -3.142  -1.227  1.00  0.00              
ATOM     45  N   GLU    12      -6.479  -5.017  -1.251  1.00  0.00              
ATOM     46  CA  GLU    12      -7.284  -5.737  -0.292  1.00  0.00              
ATOM     47  C   GLU    12      -7.179  -5.112   1.050  1.00  0.00              
ATOM     48  O   GLU    12      -8.190  -5.028   1.736  1.00  0.00              
ATOM     49  N   LEU    13      -5.986  -4.674   1.446  1.00  0.00              
ATOM     50  CA  LEU    13      -5.814  -4.001   2.725  1.00  0.00              
ATOM     51  C   LEU    13      -6.654  -2.699   2.800  1.00  0.00              
ATOM     52  O   LEU    13      -7.379  -2.462   3.766  1.00  0.00              
ATOM     53  N   ALA    14      -6.526  -1.849   1.790  1.00  0.00              
ATOM     54  CA  ALA    14      -7.365  -0.659   1.704  1.00  0.00              
ATOM     55  C   ALA    14      -8.846  -1.005   1.817  1.00  0.00              
ATOM     56  O   ALA    14      -9.580  -0.306   2.480  1.00  0.00              
ATOM     57  N   ALA    15      -9.295  -2.083   1.186  1.00  0.00              
ATOM     58  CA  ALA    15     -10.681  -2.447   1.316  1.00  0.00              
ATOM     59  C   ALA    15     -11.068  -2.854   2.732  1.00  0.00              
ATOM     60  O   ALA    15     -12.147  -2.498   3.182  1.00  0.00              
ATOM     61  N   LYS    16     -10.206  -3.571   3.441  1.00  0.00              
ATOM     62  CA  LYS    16     -10.526  -3.946   4.818  1.00  0.00              
ATOM     63  C   LYS    16     -10.327  -2.854   5.876  1.00  0.00              
ATOM     64  O   LYS    16     -10.931  -2.926   6.930  1.00  0.00              
ATOM     65  N   ALA    17      -9.464  -1.877   5.638  1.00  0.00              
ATOM     66  CA  ALA    17      -9.193  -0.847   6.623  1.00  0.00              
ATOM     67  C   ALA    17      -9.436   0.521   5.982  1.00  0.00              
ATOM     68  O   ALA    17      -8.567   1.377   5.979  1.00  0.00              
ATOM     69  N   LYS    18     -10.649   0.702   5.440  1.00  0.00              
ATOM     70  CA  LYS    18     -11.195   2.014   4.951  1.00  0.00              
ATOM     71  C   LYS    18     -10.677   3.288   5.620  1.00  0.00              
ATOM     72  O   LYS    18     -10.618   4.364   5.001  1.00  0.00              
ATOM     73  N   ALA    19     -10.356   3.147   6.906  1.00  0.00              
ATOM     74  CA  ALA    19      -9.959   4.245   7.770  1.00  0.00              
ATOM     75  C   ALA    19      -8.470   4.522   7.561  1.00  0.00              
ATOM     76  O   ALA    19      -7.634   3.611   7.664  1.00  0.00              
ATOM     77  N   GLY    20      -8.163   5.785   7.262  1.00  0.00              
ATOM     78  CA  GLY    20      -6.827   6.212   6.833  1.00  0.00              
ATOM     79  C   GLY    20      -5.897   6.408   8.035  1.00  0.00              
ATOM     80  O   GLY    20      -5.334   7.498   8.221  1.00  0.00              
ATOM     81  N   VAL    21      -5.713   5.345   8.829  1.00  0.00              
ATOM     82  CA  VAL    21      -5.122   5.475  10.168  1.00  0.00              
ATOM     83  C   VAL    21      -3.632   5.166  10.343  1.00  0.00              
ATOM     84  O   VAL    21      -2.764   6.038  10.127  1.00  0.00              
ATOM     85  N   THR    23      -3.362   3.930  10.780  1.00  0.00              
ATOM     86  CA  THR    23      -2.024   3.418  11.069  1.00  0.00              
ATOM     87  C   THR    23      -1.029   4.244  10.257  1.00  0.00              
ATOM     88  O   THR    23      -0.949   4.103   9.025  1.00  0.00              
ATOM     89  N   GLU    24      -0.332   5.159  10.937  1.00  0.00              
ATOM     90  CA  GLU    24       0.782   5.898  10.323  1.00  0.00              
ATOM     91  C   GLU    24       1.898   4.957   9.829  1.00  0.00              
ATOM     92  O   GLU    24       2.515   5.209   8.793  1.00  0.00              
ATOM     93  N   GLU    25       2.109   3.871  10.576  1.00  0.00              
ATOM     94  CA  GLU    25       2.962   2.763  10.167  1.00  0.00              
ATOM     95  C   GLU    25       2.568   2.307   8.763  1.00  0.00              
ATOM     96  O   GLU    25       3.310   2.534   7.813  1.00  0.00              
ATOM     97  N   GLU    26       1.385   1.714   8.622  1.00  0.00              
ATOM     98  CA  GLU    26       0.998   1.114   7.341  1.00  0.00              
ATOM     99  C   GLU    26       0.863   2.169   6.255  1.00  0.00              
ATOM    100  O   GLU    26       1.148   1.913   5.104  1.00  0.00              
ATOM    101  N   LYS    27       0.439   3.356   6.614  1.00  0.00              
ATOM    102  CA  LYS    27       0.450   4.451   5.671  1.00  0.00              
ATOM    103  C   LYS    27       1.860   4.672   5.077  1.00  0.00              
ATOM    104  O   LYS    27       2.001   4.959   3.883  1.00  0.00              
ATOM    105  N   ALA    28       2.890   4.556   5.919  1.00  0.00              
ATOM    106  CA  ALA    28       4.285   4.727   5.474  1.00  0.00              
ATOM    107  C   ALA    28       4.688   3.508   4.642  1.00  0.00              
ATOM    108  O   ALA    28       5.227   3.647   3.552  1.00  0.00              
ATOM    109  N   GLU    29       4.412   2.334   5.194  1.00  0.00              
ATOM    110  CA  GLU    29       4.684   1.070   4.561  1.00  0.00              
ATOM    111  C   GLU    29       4.019   0.998   3.176  1.00  0.00              
ATOM    112  O   GLU    29       4.670   0.719   2.204  1.00  0.00              
ATOM    113  N   GLN    30       2.738   1.322   3.089  1.00  0.00              
ATOM    114  CA  GLN    30       2.062   1.420   1.795  1.00  0.00              
ATOM    115  C   GLN    30       2.730   2.413   0.864  1.00  0.00              
ATOM    116  O   GLN    30       2.841   2.188  -0.326  1.00  0.00              
ATOM    117  N   GLN    31       3.170   3.537   1.378  1.00  0.00              
ATOM    118  CA  GLN    31       3.845   4.481   0.518  1.00  0.00              
ATOM    119  C   GLN    31       5.226   3.976   0.035  1.00  0.00              
ATOM    120  O   GLN    31       5.549   4.145  -1.124  1.00  0.00              
ATOM    121  N   LYS    32       5.980   3.317   0.910  1.00  0.00              
ATOM    122  CA  LYS    32       7.211   2.622   0.594  1.00  0.00              
ATOM    123  C   LYS    32       7.052   1.577  -0.523  1.00  0.00              
ATOM    124  O   LYS    32       7.762   1.585  -1.501  1.00  0.00              
ATOM    125  N   LEU    33       6.102   0.667  -0.368  1.00  0.00              
ATOM    126  CA  LEU    33       5.823  -0.388  -1.376  1.00  0.00              
ATOM    127  C   LEU    33       5.419   0.231  -2.721  1.00  0.00              
ATOM    128  O   LEU    33       5.927  -0.122  -3.737  1.00  0.00              
ATOM    129  N   LEU    38       4.569   1.239  -2.709  1.00  0.00              
ATOM    130  CA  LEU    38       4.091   1.831  -3.945  1.00  0.00              
ATOM    131  C   LEU    38       5.235   2.503  -4.727  1.00  0.00              
ATOM    132  O   LEU    38       5.263   2.542  -5.955  1.00  0.00              
ATOM    133  N   LYS    39       6.178   3.051  -3.978  1.00  0.00              
ATOM    134  CA  LYS    39       7.356   3.622  -4.558  1.00  0.00              
ATOM    135  C   LYS    39       8.235   2.538  -5.203  1.00  0.00              
ATOM    136  O   LYS    39       8.738   2.736  -6.284  1.00  0.00              
ATOM    137  N   GLY    40       8.424   1.437  -4.486  1.00  0.00              
ATOM    138  CA  GLY    40       9.138   0.294  -4.937  1.00  0.00              
ATOM    139  C   GLY    40       8.533  -0.203  -6.260  1.00  0.00              
ATOM    140  O   GLY    40       9.271  -0.370  -7.226  1.00  0.00              
END
