
#######################################################
#                                                     #
#                        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 T0299AL381_5-D2
# Molecule2: number of CA atoms   89 (  757),  selected   26 , name T0299_D2.pdb
# PARAMETERS: T0299AL381_5-D2.T0299_D2.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:    15        98 - 112         3.32    15.04
  LCS_AVERAGE:     15.51

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11        79 - 89          0.48    18.98
  LONGEST_CONTINUOUS_SEGMENT:    11        98 - 108         1.51    15.09
  LONGEST_CONTINUOUS_SEGMENT:    11        99 - 109         1.98    15.28
  LCS_AVERAGE:     11.71

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11        79 - 89          0.48    18.98
  LCS_AVERAGE:      9.42

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:   89
LCS_GDT     L      79     L      79     11   11   12     8   11   11   11   11   11   11   11   11   11   11   12   14   18   18   20   20   21   21   22 
LCS_GDT     E      80     E      80     11   11   12     8   11   11   11   11   11   11   11   13   15   16   17   19   19   20   20   21   21   21   22 
LCS_GDT     D      81     D      81     11   11   12     8   11   11   11   11   11   11   11   13   15   16   17   19   19   20   20   21   21   21   22 
LCS_GDT     F      82     F      82     11   11   12     8   11   11   11   11   11   11   11   11   14   16   17   19   19   20   20   21   21   21   22 
LCS_GDT     E      83     E      83     11   11   12     8   11   11   11   11   11   11   11   13   15   16   17   19   19   20   20   21   21   21   22 
LCS_GDT     A      84     A      84     11   11   12     8   11   11   11   11   11   11   11   13   15   16   17   19   19   20   20   21   21   21   22 
LCS_GDT     E      85     E      85     11   11   12     8   11   11   11   11   11   11   11   13   15   16   17   19   19   20   20   21   21   21   22 
LCS_GDT     L      86     L      86     11   11   12     8   11   11   11   11   11   11   11   13   15   16   17   19   19   20   20   21   21   21   22 
LCS_GDT     E      87     E      87     11   11   12     6   11   11   11   11   11   11   11   13   15   16   17   19   19   20   20   21   21   21   22 
LCS_GDT     N      88     N      88     11   11   13     5   11   11   11   11   11   11   11   11   13   14   17   19   19   20   20   21   21   21   22 
LCS_GDT     L      89     L      89     11   11   13     5   11   11   11   11   11   11   11   12   15   16   17   19   19   20   20   21   21   21   22 
LCS_GDT     A      98     A      98      8   11   15     3    3    8   10   10   11   13   13   13   14   14   15   15   15   15   15   15   16   17   20 
LCS_GDT     R      99     R      99      8   11   15     4    7    8   10   10   11   13   13   13   14   14   15   15   15   15   16   20   21   21   22 
LCS_GDT     K     100     K     100      8   11   15     4    7    8   10   10   11   13   13   13   14   14   17   19   19   20   20   21   21   21   22 
LCS_GDT     D     101     D     101      8   11   15     4    7    8   10   10   11   13   13   13   14   14   17   19   19   20   20   21   21   21   22 
LCS_GDT     F     102     F     102      8   11   15     4    7    8   10   10   11   13   13   13   15   16   17   19   19   20   20   21   21   21   22 
LCS_GDT     L     103     L     103      8   11   15     3    7    8   10   10   11   13   13   13   15   16   17   19   19   20   20   21   21   21   22 
LCS_GDT     F     104     F     104      8   11   15     3    7    8   10   10   11   13   13   13   15   16   17   19   19   20   20   21   21   21   22 
LCS_GDT     Y     105     Y     105      8   11   15     3    5    8   10   10   11   13   13   13   15   16   17   19   19   20   20   21   21   21   22 
LCS_GDT     T     106     T     106      8   11   15     3    7    8   10   10   11   13   13   13   15   16   17   19   19   20   20   21   21   21   22 
LCS_GDT     E     107     E     107      5   11   15     3    5    5    9   10   11   13   13   13   15   16   17   19   19   20   20   21   21   21   22 
LCS_GDT     G     108     G     108      5   11   15     3    5    8   10   10   11   13   13   13   15   16   17   19   19   20   20   21   21   21   22 
LCS_GDT     L     109     L     109      4   11   15     3    4    4    6    6    6   13   13   13   14   14   15   17   19   20   20   21   21   21   22 
LCS_GDT     D     110     D     110      4    6   15     3    4    4    6    8   11   13   13   13   14   14   15   15   17   17   20   21   21   21   22 
LCS_GDT     V     111     V     111      4    6   15     3    4    4    6    6    6    7    9   13   14   14   15   15   15   15   17   18   20   21   21 
LCS_GDT     D     112     D     112      3    6   15     3    3    4    6    6    6    7    7    9   10   13   15   15   15   15   17   17   18   18   18 
LCS_AVERAGE  LCS_A:  12.22  (   9.42   11.71   15.51 )

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      8     11     11     11     11     11     13     13     13     15     16     17     19     19     20     20     21     21     21     22 
GDT PERCENT_CA   8.99  12.36  12.36  12.36  12.36  12.36  14.61  14.61  14.61  16.85  17.98  19.10  21.35  21.35  22.47  22.47  23.60  23.60  23.60  24.72
GDT RMS_LOCAL    0.20   0.48   0.48   0.48   0.48   0.48   2.17   2.17   2.17   3.69   3.82   4.02   4.48   4.48   4.89   4.89   5.58   5.16   5.16   5.70
GDT RMS_ALL_CA  18.80  18.98  18.98  18.98  18.98  18.98  15.59  15.59  15.59   9.44   9.52   9.60   9.35   9.35   8.89   8.89   8.44   9.07   9.07   8.90

#      Molecule1      Molecule2       DISTANCE
LGA    L      79      L      79         22.654
LGA    E      80      E      80         25.201
LGA    D      81      D      81         24.821
LGA    F      82      F      82         21.535
LGA    E      83      E      83         22.169
LGA    A      84      A      84         24.748
LGA    E      85      E      85         23.163
LGA    L      86      L      86         20.968
LGA    E      87      E      87         22.430
LGA    N      88      N      88         23.416
LGA    L      89      L      89         20.761
LGA    A      98      A      98          1.293
LGA    R      99      R      99          1.483
LGA    K     100      K     100          2.259
LGA    D     101      D     101          1.579
LGA    F     102      F     102          1.599
LGA    L     103      L     103          1.713
LGA    F     104      F     104          1.827
LGA    Y     105      Y     105          2.548
LGA    T     106      T     106          1.020
LGA    E     107      E     107          2.884
LGA    G     108      G     108          1.839
LGA    L     109      L     109          3.938
LGA    D     110      D     110          3.713
LGA    V     111      V     111          6.069
LGA    D     112      D     112          8.360

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   26   89    4.0     13    2.17    15.449    14.415     0.572

LGA_LOCAL      RMSD =  2.174  Number of atoms =   13  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 15.148  Number of atoms =   26 
Std_ALL_ATOMS  RMSD =  8.009  (standard rmsd on all 26 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.311950 * X  +   0.012051 * Y  +   0.950022 * Z  +   5.830006
  Y_new =  -0.584747 * X  +   0.785670 * Y  +  -0.201974 * Z  +  30.410723
  Z_new =  -0.748838 * X  +  -0.618528 * Y  +  -0.238043 * Z  + 102.182381 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.938178    1.203415  [ DEG:  -111.0494     68.9506 ]
  Theta =   0.846307    2.295286  [ DEG:    48.4898    131.5102 ]
  Phi   =  -2.060867    1.080726  [ DEG:  -118.0790     61.9210 ]
 
# 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: T0299AL381_5-D2                               
REMARK     2: T0299_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0299AL381_5-D2.T0299_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   26   89   4.0   13   2.17  14.415     8.01
REMARK  ---------------------------------------------------------- 
MOLECULE T0299AL381_5-D2
REMARK Aligment from pdb entry: 1z5nA
ATOM    185  N   LEU    79      11.765  53.058   0.718  1.00  0.00              
ATOM    186  CA  LEU    79      11.274  53.786  -0.436  1.00  0.00              
ATOM    187  C   LEU    79      12.288  54.656  -1.187  1.00  0.00              
ATOM    188  O   LEU    79      12.489  54.474  -2.403  1.00  0.00              
ATOM    189  N   GLU    80      12.956  55.570  -0.490  1.00  0.00              
ATOM    190  CA  GLU    80      13.882  56.467  -1.173  1.00  0.00              
ATOM    191  C   GLU    80      15.115  55.795  -1.758  1.00  0.00              
ATOM    192  O   GLU    80      15.664  56.262  -2.766  1.00  0.00              
ATOM    193  N   ASP    81      15.548  54.703  -1.131  1.00  0.00              
ATOM    194  CA  ASP    81      16.687  53.962  -1.618  1.00  0.00              
ATOM    195  C   ASP    81      16.270  53.256  -2.928  1.00  0.00              
ATOM    196  O   ASP    81      17.044  53.171  -3.880  1.00  0.00              
ATOM    197  N   PHE    82      15.050  52.736  -2.964  1.00  0.00              
ATOM    198  CA  PHE    82      14.574  52.061  -4.170  1.00  0.00              
ATOM    199  C   PHE    82      14.423  53.108  -5.287  1.00  0.00              
ATOM    200  O   PHE    82      14.754  52.857  -6.450  1.00  0.00              
ATOM    201  N   GLU    83      13.939  54.292  -4.913  1.00  0.00              
ATOM    202  CA  GLU    83      13.742  55.384  -5.858  1.00  0.00              
ATOM    203  C   GLU    83      15.090  55.866  -6.401  1.00  0.00              
ATOM    204  O   GLU    83      15.234  56.175  -7.582  1.00  0.00              
ATOM    205  N   ALA    84      16.075  55.916  -5.517  1.00  0.00              
ATOM    206  CA  ALA    84      17.420  56.353  -5.869  1.00  0.00              
ATOM    207  C   ALA    84      18.029  55.370  -6.890  1.00  0.00              
ATOM    208  O   ALA    84      18.600  55.793  -7.903  1.00  0.00              
ATOM    209  N   GLU    85      17.897  54.070  -6.622  1.00  0.00              
ATOM    210  CA  GLU    85      18.419  53.064  -7.548  1.00  0.00              
ATOM    211  C   GLU    85      17.688  53.096  -8.894  1.00  0.00              
ATOM    212  O   GLU    85      18.331  53.041  -9.956  1.00  0.00              
ATOM    213  N   LEU    86      16.356  53.207  -8.866  1.00  0.00              
ATOM    214  CA  LEU    86      15.571  53.235 -10.115  1.00  0.00              
ATOM    215  C   LEU    86      15.924  54.469 -10.924  1.00  0.00              
ATOM    216  O   LEU    86      15.934  54.429 -12.173  1.00  0.00              
ATOM    217  N   GLU    87      16.216  55.556 -10.208  1.00  0.00              
ATOM    218  CA  GLU    87      16.590  56.813 -10.834  1.00  0.00              
ATOM    219  C   GLU    87      17.853  56.589 -11.638  1.00  0.00              
ATOM    220  O   GLU    87      18.002  57.119 -12.728  1.00  0.00              
ATOM    221  N   ASN    88      18.768  55.803 -11.080  1.00  0.00              
ATOM    222  CA  ASN    88      20.030  55.513 -11.731  1.00  0.00              
ATOM    223  C   ASN    88      19.862  54.560 -12.897  1.00  0.00              
ATOM    224  O   ASN    88      20.634  54.602 -13.852  1.00  0.00              
ATOM    225  N   LEU    89      18.869  53.681 -12.816  1.00  0.00              
ATOM    226  CA  LEU    89      18.635  52.751 -13.912  1.00  0.00              
ATOM    227  C   LEU    89      17.564  53.296 -14.848  1.00  0.00              
ATOM    228  O   LEU    89      17.196  52.669 -15.838  1.00  0.00              
ATOM    229  N   ALA    98      17.070  54.487 -14.515  1.00  0.00              
ATOM    230  CA  ALA    98      16.056  55.134 -15.330  1.00  0.00              
ATOM    231  C   ALA    98      14.804  54.237 -15.437  1.00  0.00              
ATOM    232  O   ALA    98      14.214  54.090 -16.508  1.00  0.00              
ATOM    233  N   ARG    99      14.405  53.640 -14.306  1.00  0.00              
ATOM    234  CA  ARG    99      13.210  52.779 -14.255  1.00  0.00              
ATOM    235  C   ARG    99      12.087  53.447 -13.444  1.00  0.00              
ATOM    236  O   ARG    99      12.327  54.010 -12.384  1.00  0.00              
ATOM    237  N   LYS   100      10.848  53.425 -13.960  1.00  0.00              
ATOM    238  CA  LYS   100       9.730  54.048 -13.229  1.00  0.00              
ATOM    239  C   LYS   100       9.377  53.318 -11.941  1.00  0.00              
ATOM    240  O   LYS   100       9.349  52.088 -11.916  1.00  0.00              
ATOM    241  N   ASP   101       9.105  54.068 -10.874  1.00  0.00              
ATOM    242  CA  ASP   101       8.716  53.439  -9.613  1.00  0.00              
ATOM    243  C   ASP   101       7.520  54.149  -9.037  1.00  0.00              
ATOM    244  O   ASP   101       7.083  55.166  -9.556  1.00  0.00              
ATOM    245  N   PHE   102       6.976  53.567  -7.978  1.00  0.00              
ATOM    246  CA  PHE   102       5.870  54.129  -7.227  1.00  0.00              
ATOM    247  C   PHE   102       5.843  53.331  -5.931  1.00  0.00              
ATOM    248  O   PHE   102       6.141  52.137  -5.928  1.00  0.00              
ATOM    249  N   LEU   103       5.501  54.013  -4.839  1.00  0.00              
ATOM    250  CA  LEU   103       5.436  53.419  -3.533  1.00  0.00              
ATOM    251  C   LEU   103       3.963  53.327  -3.169  1.00  0.00              
ATOM    252  O   LEU   103       3.230  54.293  -3.336  1.00  0.00              
ATOM    253  N   PHE   104       3.520  52.171  -2.695  1.00  0.00              
ATOM    254  CA  PHE   104       2.133  52.009  -2.304  1.00  0.00              
ATOM    255  C   PHE   104       2.209  51.236  -1.014  1.00  0.00              
ATOM    256  O   PHE   104       2.477  50.039  -1.021  1.00  0.00              
ATOM    257  N   TYR   105       2.019  51.937   0.102  1.00  0.00              
ATOM    258  CA  TYR   105       2.103  51.307   1.409  1.00  0.00              
ATOM    259  C   TYR   105       0.857  51.526   2.274  1.00  0.00              
ATOM    260  O   TYR   105       0.075  52.458   2.057  1.00  0.00              
ATOM    261  N   THR   106       0.670  50.634   3.241  1.00  0.00              
ATOM    262  CA  THR   106      -0.450  50.727   4.167  1.00  0.00              
ATOM    263  C   THR   106       0.082  51.225   5.510  1.00  0.00              
ATOM    264  O   THR   106       1.158  50.832   5.925  1.00  0.00              
ATOM    265  N   GLU   107      -0.696  52.057   6.192  1.00  0.00              
ATOM    266  CA  GLU   107      -0.302  52.628   7.487  1.00  0.00              
ATOM    267  C   GLU   107      -0.433  51.630   8.644  1.00  0.00              
ATOM    268  O   GLU   107      -1.456  50.974   8.812  1.00  0.00              
ATOM    269  N   GLY   108       0.613  51.524   9.450  1.00  0.00              
ATOM    270  CA  GLY   108       0.619  50.602  10.576  1.00  0.00              
ATOM    271  C   GLY   108       0.652  51.310  11.954  1.00  0.00              
ATOM    272  O   GLY   108       0.315  50.711  12.982  1.00  0.00              
ATOM    273  N   LEU   109       1.046  52.578  11.960  1.00  0.00              
ATOM    274  CA  LEU   109       1.163  53.359  13.193  1.00  0.00              
ATOM    275  C   LEU   109       1.266  54.829  12.803  1.00  0.00              
ATOM    276  O   LEU   109       1.159  55.172  11.619  1.00  0.00              
ATOM    277  N   ASP   110       1.459  55.708  13.776  1.00  0.00              
ATOM    278  CA  ASP   110       1.569  57.127  13.453  1.00  0.00              
ATOM    279  C   ASP   110       2.888  57.725  13.912  1.00  0.00              
ATOM    280  O   ASP   110       3.007  58.925  14.157  1.00  0.00              
ATOM    281  N   VAL   111       3.874  56.857  14.056  1.00  0.00              
ATOM    282  CA  VAL   111       5.217  57.251  14.424  1.00  0.00              
ATOM    283  C   VAL   111       5.419  57.976  15.747  1.00  0.00              
ATOM    284  O   VAL   111       6.399  58.700  15.903  1.00  0.00              
ATOM    285  N   ASP   112       4.523  57.786  16.706  1.00  0.00              
ATOM    286  CA  ASP   112       4.685  58.440  18.013  1.00  0.00              
ATOM    287  C   ASP   112       5.272  57.463  19.052  1.00  0.00              
ATOM    288  O   ASP   112       5.814  56.402  18.697  1.00  0.00              
END
