
#######################################################
#                                                     #
#                        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   48 (  192),  selected    8 , name T0351AL243_4
# Molecule2: number of CA atoms   56 (  935),  selected    8 , name T0351.pdb
# PARAMETERS: T0351AL243_4.T0351.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:     8        44 - 55          2.86     2.86
  LCS_AVERAGE:     14.29

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        47 - 55          1.99     3.73
  LCS_AVERAGE:      8.26

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4        44 - 47          0.17     4.14
  LONGEST_CONTINUOUS_SEGMENT:     4        52 - 55          0.34     4.27
  LCS_AVERAGE:      7.14

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:   56
LCS_GDT     A      44     A      44      4    4    8     4    4    4    4    4    5    8    8    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     E      45     E      45      4    4    8     4    4    4    4    4    5    8    8    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     L      46     L      46      4    4    8     4    4    4    4    4    6    8    8    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     E      47     E      47      4    5    8     4    4    4    4    4    6    8    8    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     E      52     E      52      4    5    8     4    4    4    4    4    6    8    8    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     L      53     L      53      4    5    8     4    4    4    4    4    6    8    8    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     Q      54     Q      54      4    5    8     4    4    4    4    4    6    8    8    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_GDT     K      55     K      55      4    5    8     4    4    4    4    4    6    8    8    8    8    8    8    8    8    8    8    8    8    8    8 
LCS_AVERAGE  LCS_A:   9.90  (   7.14    8.26   14.29 )

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      4      4      4      4      4      6      8      8      8      8      8      8      8      8      8      8      8      8      8      8 
GDT PERCENT_CA   7.14   7.14   7.14   7.14   7.14  10.71  14.29  14.29  14.29  14.29  14.29  14.29  14.29  14.29  14.29  14.29  14.29  14.29  14.29  14.29
GDT RMS_LOCAL    0.17   0.17   0.17   0.17   0.17   2.46   2.86   2.86   2.86   2.86   2.86   2.86   2.86   2.86   2.86   2.86   2.86   2.86   2.86   2.86
GDT RMS_ALL_CA   4.14   4.14   4.14   4.14   4.14   3.28   2.86   2.86   2.86   2.86   2.86   2.86   2.86   2.86   2.86   2.86   2.86   2.86   2.86   2.86

#      Molecule1      Molecule2       DISTANCE
LGA    A      44      A      44          2.760
LGA    E      45      E      45          3.380
LGA    L      46      L      46          2.693
LGA    E      47      E      47          2.436
LGA    E      52      E      52          3.141
LGA    L      53      L      53          3.141
LGA    Q      54      Q      54          2.710
LGA    K      55      K      55          2.458

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   48   56    4.0      8    2.86    10.714    10.492     0.270

LGA_LOCAL      RMSD =  2.858  Number of atoms =    8  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  2.858  Number of atoms =    8 
Std_ALL_ATOMS  RMSD =  2.858  (standard rmsd on all 8 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.793228 * X  +  -0.155845 * Y  +   0.588643 * Z  + -80.587173
  Y_new =  -0.181914 * X  +  -0.861897 * Y  +  -0.473329 * Z  +  87.875076
  Z_new =   0.581116 * X  +  -0.482540 * Y  +   0.655331 * Z  + -110.363029 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.634695    2.506898  [ DEG:   -36.3653    143.6347 ]
  Theta =  -0.620100   -2.521493  [ DEG:   -35.5291   -144.4709 ]
  Phi   =  -2.916158    0.225435  [ DEG:  -167.0835     12.9165 ]
 
# 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: T0351AL243_4                                  
REMARK     2: T0351.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0351AL243_4.T0351.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   48   56   4.0    8   2.86  10.492     2.86
REMARK  ---------------------------------------------------------- 
MOLECULE T0351AL243_4
REMARK Aligment from pdb entry: 1lwuC
ATOM      1  N   ALA    44      -2.539  -7.852  -6.161  1.00  0.00              
ATOM      2  CA  ALA    44      -2.343  -8.818  -5.043  1.00  0.00              
ATOM      3  C   ALA    44      -1.284  -8.321  -4.069  1.00  0.00              
ATOM      4  O   ALA    44      -0.909  -9.027  -3.138  1.00  0.00              
ATOM      5  N   GLU    45      -0.800  -7.106  -4.295  1.00  0.00              
ATOM      6  CA  GLU    45       0.211  -6.510  -3.430  1.00  0.00              
ATOM      7  C   GLU    45      -0.318  -6.403  -2.003  1.00  0.00              
ATOM      8  O   GLU    45       0.340  -6.834  -1.057  1.00  0.00              
ATOM      9  N   LEU    46      -1.508  -5.827  -1.855  1.00  0.00              
ATOM     10  CA  LEU    46      -2.123  -5.677  -0.542  1.00  0.00              
ATOM     11  C   LEU    46      -2.100  -7.034   0.158  1.00  0.00              
ATOM     12  O   LEU    46      -1.942  -7.121   1.374  1.00  0.00              
ATOM     13  N   GLU    47      -2.252  -8.090  -0.631  1.00  0.00              
ATOM     14  CA  GLU    47      -2.253  -9.452  -0.113  1.00  0.00              
ATOM     15  C   GLU    47      -0.837  -9.982   0.091  1.00  0.00              
ATOM     16  O   GLU    47      -0.621 -10.893   0.885  1.00  0.00              
ATOM     17  N   GLU    52       0.120  -9.424  -0.640  1.00  0.00              
ATOM     18  CA  GLU    52       1.512  -9.846  -0.520  1.00  0.00              
ATOM     19  C   GLU    52       2.211  -9.104   0.612  1.00  0.00              
ATOM     20  O   GLU    52       2.994  -9.695   1.356  1.00  0.00              
ATOM     21  N   LEU    53       1.928  -7.812   0.741  1.00  0.00              
ATOM     22  CA  LEU    53       2.521  -7.011   1.804  1.00  0.00              
ATOM     23  C   LEU    53       2.221  -7.679   3.140  1.00  0.00              
ATOM     24  O   LEU    53       2.723  -7.261   4.174  1.00  0.00              
ATOM     25  N   GLN    54       1.383  -8.712   3.099  1.00  0.00              
ATOM     26  CA  GLN    54       1.009  -9.470   4.285  1.00  0.00              
ATOM     27  C   GLN    54       1.923 -10.676   4.390  1.00  0.00              
ATOM     28  O   GLN    54       2.754 -10.746   5.290  1.00  0.00              
ATOM     29  N   LYS    55       1.763 -11.623   3.468  1.00  0.00              
ATOM     30  CA  LYS    55       2.597 -12.820   3.461  1.00  0.00              
ATOM     31  C   LYS    55       4.032 -12.389   3.713  1.00  0.00              
ATOM     32  O   LYS    55       4.763 -13.035   4.465  1.00  0.00              
ATOM     33  N   GLN    64       4.436 -11.290   3.082  1.00  0.00              
ATOM     34  CA  GLN    64       5.784 -10.786   3.269  1.00  0.00              
ATOM     35  C   GLN    64       6.022 -10.591   4.759  1.00  0.00              
ATOM     36  O   GLN    64       7.036 -11.043   5.294  1.00  0.00              
ATOM     37  N   VAL    65       5.079  -9.936   5.432  1.00  0.00              
ATOM     38  CA  VAL    65       5.210  -9.687   6.865  1.00  0.00              
ATOM     39  C   VAL    65       5.088 -10.953   7.692  1.00  0.00              
ATOM     40  O   VAL    65       5.688 -11.059   8.750  1.00  0.00              
ATOM     41  N   GLU    66       4.311 -11.916   7.218  1.00  0.00              
ATOM     42  CA  GLU    66       4.178 -13.176   7.938  1.00  0.00              
ATOM     43  C   GLU    66       5.552 -13.837   7.940  1.00  0.00              
ATOM     44  O   GLU    66       5.925 -14.531   8.885  1.00  0.00              
ATOM     45  N   LEU    67       6.297 -13.601   6.861  1.00  0.00              
ATOM     46  CA  LEU    67       7.637 -14.148   6.688  1.00  0.00              
ATOM     47  C   LEU    67       8.663 -13.367   7.508  1.00  0.00              
ATOM     48  O   LEU    67       9.475 -13.961   8.221  1.00  0.00              
ATOM     49  N   LEU    68       8.626 -12.039   7.398  1.00  0.00              
ATOM     50  CA  LEU    68       9.556 -11.192   8.134  1.00  0.00              
ATOM     51  C   LEU    68       9.457 -11.409   9.637  1.00  0.00              
ATOM     52  O   LEU    68      10.400 -11.135  10.380  1.00  0.00              
ATOM     53  N   ALA    69       8.307 -11.885  10.094  1.00  0.00              
ATOM     54  CA  ALA    69       8.127 -12.142  11.510  1.00  0.00              
ATOM     55  C   ALA    69       8.820 -13.464  11.830  1.00  0.00              
ATOM     56  O   ALA    69       9.588 -13.556  12.784  1.00  0.00              
ATOM     57  N   GLN    70       8.565 -14.478  11.011  1.00  0.00              
ATOM     58  CA  GLN    70       9.173 -15.787  11.207  1.00  0.00              
ATOM     59  C   GLN    70      10.690 -15.670  11.262  1.00  0.00              
ATOM     60  O   GLN    70      11.342 -16.299  12.095  1.00  0.00              
ATOM     61  N   GLU    71      11.249 -14.866  10.365  1.00  0.00              
ATOM     62  CA  GLU    71      12.690 -14.666  10.325  1.00  0.00              
ATOM     63  C   GLU    71      13.164 -14.007  11.617  1.00  0.00              
ATOM     64  O   GLU    71      13.936 -14.603  12.350  1.00  0.00              
ATOM     65  N   LEU    72      12.691 -12.786  11.880  1.00  0.00              
ATOM     66  CA  LEU    72      13.066 -12.049  13.081  1.00  0.00              
ATOM     67  C   LEU    72      13.179 -12.938  14.306  1.00  0.00              
ATOM     68  O   LEU    72      14.175 -12.895  15.038  1.00  0.00              
ATOM     69  N   SER    73      12.152 -13.756  14.523  1.00  0.00              
ATOM     70  CA  SER    73      12.128 -14.684  15.645  1.00  0.00              
ATOM     71  C   SER    73      13.352 -15.596  15.591  1.00  0.00              
ATOM     72  O   SER    73      14.021 -15.790  16.603  1.00  0.00              
ATOM     73  N   GLN    74      13.649 -16.158  14.424  1.00  0.00              
ATOM     74  CA  GLN    74      14.830 -17.012  14.299  1.00  0.00              
ATOM     75  C   GLN    74      16.080 -16.180  14.593  1.00  0.00              
ATOM     76  O   GLN    74      17.041 -16.657  15.194  1.00  0.00              
ATOM     77  N   GLU    75      16.065 -14.926  14.164  1.00  0.00              
ATOM     78  CA  GLU    75      17.189 -14.062  14.427  1.00  0.00              
ATOM     79  C   GLU    75      17.338 -13.898  15.925  1.00  0.00              
ATOM     80  O   GLU    75      18.452 -13.763  16.428  1.00  0.00              
ATOM     81  N   LYS    76      16.215 -13.923  16.641  1.00  0.00              
ATOM     82  CA  LYS    76      16.245 -13.808  18.096  1.00  0.00              
ATOM     83  C   LYS    76      16.832 -15.087  18.707  1.00  0.00              
ATOM     84  O   LYS    76      17.325 -15.079  19.839  1.00  0.00              
ATOM     85  N   LEU    77      16.778 -16.184  17.956  1.00  0.00              
ATOM     86  CA  LEU    77      17.320 -17.453  18.429  1.00  0.00              
ATOM     87  C   LEU    77      18.793 -17.483  18.100  1.00  0.00              
ATOM     88  O   LEU    77      19.631 -17.828  18.942  1.00  0.00              
ATOM     89  N   ALA    78      19.098 -17.124  16.858  1.00  0.00              
ATOM     90  CA  ALA    78      20.469 -17.114  16.391  1.00  0.00              
ATOM     91  C   ALA    78      21.306 -16.175  17.232  1.00  0.00              
ATOM     92  O   ALA    78      22.481 -16.428  17.470  1.00  0.00              
ATOM     93  N   ARG    79      20.700 -15.090  17.686  1.00  0.00              
ATOM     94  CA  ARG    79      21.422 -14.150  18.518  1.00  0.00              
ATOM     95  C   ARG    79      21.799 -14.836  19.828  1.00  0.00              
ATOM     96  O   ARG    79      22.875 -14.604  20.379  1.00  0.00              
ATOM     97  N   LYS    80      20.916 -15.695  20.321  1.00  0.00              
ATOM     98  CA  LYS    80      21.193 -16.401  21.563  1.00  0.00              
ATOM     99  C   LYS    80      22.220 -17.486  21.318  1.00  0.00              
ATOM    100  O   LYS    80      23.101 -17.721  22.142  1.00  0.00              
ATOM    101  N   GLN    81      22.114 -18.141  20.174  1.00  0.00              
ATOM    102  CA  GLN    81      23.053 -19.189  19.860  1.00  0.00              
ATOM    103  C   GLN    81      24.463 -18.609  19.816  1.00  0.00              
ATOM    104  O   GLN    81      25.446 -19.326  20.021  1.00  0.00              
ATOM    105  N   LEU    82      24.566 -17.308  19.546  1.00  0.00              
ATOM    106  CA  LEU    82      25.875 -16.659  19.487  1.00  0.00              
ATOM    107  C   LEU    82      26.373 -16.315  20.876  1.00  0.00              
ATOM    108  O   LEU    82      27.565 -16.425  21.150  1.00  0.00              
ATOM    109  N   GLU    83      25.466 -15.895  21.752  1.00  0.00              
ATOM    110  CA  GLU    83      25.859 -15.564  23.112  1.00  0.00              
ATOM    111  C   GLU    83      26.273 -16.831  23.838  1.00  0.00              
ATOM    112  O   GLU    83      27.212 -16.822  24.632  1.00  0.00              
ATOM    113  N   GLU    84      25.575 -17.925  23.561  1.00  0.00              
ATOM    114  CA  GLU    84      25.923 -19.197  24.173  1.00  0.00              
ATOM    115  C   GLU    84      27.338 -19.498  23.675  1.00  0.00              
ATOM    116  O   GLU    84      28.264 -19.755  24.456  1.00  0.00              
ATOM    117  N   LEU    85      27.482 -19.422  22.354  1.00  0.00              
ATOM    118  CA  LEU    85      28.741 -19.679  21.672  1.00  0.00              
ATOM    119  C   LEU    85      29.858 -18.808  22.218  1.00  0.00              
ATOM    120  O   LEU    85      31.003 -19.239  22.310  1.00  0.00              
ATOM    121  N   ASN    86      29.527 -17.581  22.587  1.00  0.00              
ATOM    122  CA  ASN    86      30.534 -16.684  23.116  1.00  0.00              
ATOM    123  C   ASN    86      30.921 -17.056  24.540  1.00  0.00              
ATOM    124  O   ASN    86      32.107 -17.065  24.885  1.00  0.00              
ATOM    125  N   LYS    87      29.918 -17.347  25.366  1.00  0.00              
ATOM    126  CA  LYS    87      30.156 -17.725  26.760  1.00  0.00              
ATOM    127  C   LYS    87      31.007 -18.994  26.827  1.00  0.00              
ATOM    128  O   LYS    87      31.941 -19.086  27.620  1.00  0.00              
ATOM    129  N   THR    88      30.679 -19.971  25.993  1.00  0.00              
ATOM    130  CA  THR    88      31.435 -21.208  25.948  1.00  0.00              
ATOM    131  C   THR    88      32.891 -20.872  25.659  1.00  0.00              
ATOM    132  O   THR    88      33.797 -21.303  26.372  1.00  0.00              
ATOM    133  N   LEU    89      33.107 -20.093  24.606  1.00  0.00              
ATOM    134  CA  LEU    89      34.446 -19.686  24.213  1.00  0.00              
ATOM    135  C   LEU    89      35.153 -18.961  25.345  1.00  0.00              
ATOM    136  O   LEU    89      36.282 -19.308  25.696  1.00  0.00              
ATOM    137  N   GLY    90      34.484 -17.968  25.923  1.00  0.00              
ATOM    138  CA  GLY    90      35.082 -17.201  27.006  1.00  0.00              
ATOM    139  C   GLY    90      35.536 -18.121  28.141  1.00  0.00              
ATOM    140  O   GLY    90      36.407 -17.770  28.935  1.00  0.00              
ATOM    141  N   ASN    91      34.942 -19.306  28.209  1.00  0.00              
ATOM    142  CA  ASN    91      35.312 -20.274  29.222  1.00  0.00              
ATOM    143  C   ASN    91      36.529 -21.023  28.709  1.00  0.00              
ATOM    144  O   ASN    91      37.450 -21.323  29.468  1.00  0.00              
ATOM    145  N   GLU    92      36.531 -21.310  27.411  1.00  0.00              
ATOM    146  CA  GLU    92      37.642 -22.006  26.759  1.00  0.00              
ATOM    147  C   GLU    92      38.920 -21.187  26.982  1.00  0.00              
ATOM    148  O   GLU    92      39.986 -21.735  27.276  1.00  0.00              
ATOM    149  N   LEU    93      38.810 -19.869  26.838  1.00  0.00              
ATOM    150  CA  LEU    93      39.952 -18.982  27.034  1.00  0.00              
ATOM    151  C   LEU    93      40.476 -19.115  28.461  1.00  0.00              
ATOM    152  O   LEU    93      41.679 -19.076  28.697  1.00  0.00              
ATOM    153  N   SER    94      39.562 -19.260  29.413  1.00  0.00              
ATOM    154  CA  SER    94      39.943 -19.430  30.808  1.00  0.00              
ATOM    155  C   SER    94      40.696 -20.754  30.923  1.00  0.00              
ATOM    156  O   SER    94      41.837 -20.789  31.368  1.00  0.00              
ATOM    157  N   ASP    95      40.057 -21.843  30.508  1.00  0.00              
ATOM    158  CA  ASP    95      40.690 -23.157  30.565  1.00  0.00              
ATOM    159  C   ASP    95      42.093 -23.124  29.943  1.00  0.00              
ATOM    160  O   ASP    95      43.007 -23.786  30.439  1.00  0.00              
ATOM    161  N   ILE    96      42.273 -22.363  28.863  1.00  0.00              
ATOM    162  CA  ILE    96      43.596 -22.283  28.252  1.00  0.00              
ATOM    163  C   ILE    96      44.466 -21.355  29.089  1.00  0.00              
ATOM    164  O   ILE    96      45.680 -21.533  29.159  1.00  0.00              
ATOM    165  N   LYS    97      43.854 -20.364  29.732  1.00  0.00              
ATOM    166  CA  LYS    97      44.630 -19.462  30.574  1.00  0.00              
ATOM    167  C   LYS    97      45.372 -20.323  31.586  1.00  0.00              
ATOM    168  O   LYS    97      46.593 -20.234  31.709  1.00  0.00              
ATOM    169  N   LEU    98      44.612 -21.169  32.283  1.00  0.00              
ATOM    170  CA  LEU    98      45.127 -22.096  33.294  1.00  0.00              
ATOM    171  C   LEU    98      46.197 -23.032  32.719  1.00  0.00              
ATOM    172  O   LEU    98      47.263 -23.210  33.313  1.00  0.00              
ATOM    173  N   SER    99      45.910 -23.634  31.571  1.00  0.00              
ATOM    174  CA  SER    99      46.861 -24.542  30.929  1.00  0.00              
ATOM    175  C   SER    99      48.191 -23.845  30.607  1.00  0.00              
ATOM    176  O   SER    99      49.268 -24.456  30.663  1.00  0.00              
ATOM    177  N   LEU   100      48.114 -22.557  30.288  1.00  0.00              
ATOM    178  CA  LEU   100      49.307 -21.803  29.965  1.00  0.00              
ATOM    179  C   LEU   100      50.206 -21.659  31.183  1.00  0.00              
ATOM    180  O   LEU   100      51.413 -21.875  31.095  1.00  0.00              
ATOM    181  N   LEU   101      49.638 -21.288  32.324  1.00  0.00              
ATOM    182  CA  LEU   101      50.472 -21.154  33.507  1.00  0.00              
ATOM    183  C   LEU   101      50.983 -22.542  33.882  1.00  0.00              
ATOM    184  O   LEU   101      52.136 -22.701  34.268  1.00  0.00              
ATOM    185  N   SER   102      50.130 -23.547  33.743  1.00  0.00              
ATOM    186  CA  SER   102      50.513 -24.920  34.065  1.00  0.00              
ATOM    187  C   SER   102      51.705 -25.400  33.250  1.00  0.00              
ATOM    188  O   SER   102      52.640 -25.999  33.785  1.00  0.00              
ATOM    189  N   LEU   103      51.667 -25.142  31.948  1.00  0.00              
ATOM    190  CA  LEU   103      52.752 -25.574  31.088  1.00  0.00              
ATOM    191  C   LEU   103      54.000 -24.740  31.378  1.00  0.00              
ATOM    192  O   LEU   103      55.106 -25.292  31.457  1.00  0.00              
END
