
#######################################################
#                                                     #
#                        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   32 (  128),  selected   32 , name T0347AL333_4-D2
# Molecule2: number of CA atoms   71 (  561),  selected   32 , name T0347_D2.pdb
# PARAMETERS: T0347AL333_4-D2.T0347_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:    12       144 - 155         4.79    12.64
  LONGEST_CONTINUOUS_SEGMENT:    12       145 - 156         3.72    12.43
  LONGEST_CONTINUOUS_SEGMENT:    12       146 - 157         4.83    12.70
  LONGEST_CONTINUOUS_SEGMENT:    12       150 - 161         4.96    23.47
  LCS_AVERAGE:     14.92

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8       146 - 153         1.57    13.56
  LCS_AVERAGE:      7.17

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       139 - 142         0.72    18.44
  LONGEST_CONTINUOUS_SEGMENT:     4       146 - 149         0.97    13.11
  LONGEST_CONTINUOUS_SEGMENT:     4       148 - 151         0.54    15.68
  LONGEST_CONTINUOUS_SEGMENT:     4       150 - 153         0.57    20.59
  LONGEST_CONTINUOUS_SEGMENT:     4       153 - 156         0.31    27.51
  LONGEST_CONTINUOUS_SEGMENT:     4       156 - 159         0.19    27.45
  LCS_AVERAGE:      4.89

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:   71
LCS_GDT     D     134     D     134      0    0    9     0    0    0    0    1    2    5    8    8    8   10   11   11   13   14   16   17   17   17   19 
LCS_GDT     L     139     L     139      4    6   10     1    4    4    7    8    9    9   10   11   11   13   14   14   16   16   16   17   17   17   19 
LCS_GDT     A     140     A     140      4    6   10     3    4    4    5    6    6    7    9   10   11   13   14   14   16   16   16   17   17   17   19 
LCS_GDT     G     141     G     141      4    6   10     3    4    4    5    6    6    8    8    9    9   10   12   13   16   16   16   17   17   17   19 
LCS_GDT     A     142     A     142      4    6   10     3    4    4    5    6    6    8    8   10   11   13   14   14   16   16   16   17   17   17   19 
LCS_GDT     L     143     L     143      3    6   10     3    3    4    5    6    6    8    8    9    9   10   10   13   16   16   16   17   17   17   19 
LCS_GDT     R     144     R     144      3    6   12     0    3    4    4    6    6    8    8    9    9   10   10   10   11   12   12   14   14   15   15 
LCS_GDT     M     145     M     145      3    5   12     3    3    3    4    4    5    6    7    7    9   12   14   14   16   16   16   17   17   17   19 
LCS_GDT     A     146     A     146      4    8   12     3    6    6    7    8    9   10   10   11   11   13   14   14   16   16   16   17   17   18   19 
LCS_GDT     G     147     G     147      4    8   12     3    3    4    7    8    9   10   10   11   11   13   14   14   16   16   16   17   17   18   19 
LCS_GDT     G     148     G     148      4    8   12     3    6    6    7    8    9   10   10   11   11   13   14   14   16   16   16   17   17   18   19 
LCS_GDT     Y     149     Y     149      4    8   12     3    6    6    7    8    9   10   10   11   11   13   14   14   16   16   16   17   17   18   19 
LCS_GDT     A     150     A     150      4    8   12     3    6    6    7    8    9   10   10   11   11   13   14   14   16   16   16   17   17   18   19 
LCS_GDT     K     151     K     151      4    8   12     3    4    4    5    8    9   10   10   11   11   13   14   14   16   16   16   17   17   18   19 
LCS_GDT     V     152     V     152      4    8   12     3    6    6    7    8    9   10   10   11   11   13   14   14   16   16   16   17   17   18   19 
LCS_GDT     I     153     I     153      4    8   12     4    6    6    7    8    9   10   10   11   11   13   14   14   16   16   16   17   17   18   19 
LCS_GDT     I     154     I     154      4    5   12     4    4    4    5    7    9   10   10   11   11   13   14   14   16   16   16   17   17   18   19 
LCS_GDT     P     155     P     155      4    5   12     4    4    4    5    7    9   10   10   11   11   13   14   14   16   16   16   17   17   18   19 
LCS_GDT     F     156     F     156      4    4   12     4    4    4    4    4    5    6    7    7    8   11   11   11   13   14   15   16   17   18   19 
LCS_GDT     S     157     S     157      4    4   12     4    4    4    4    4    4    5    7    8    8    9   11   11   11   12   12   13   13   16   17 
LCS_GDT     E     158     E     158      4    4   12     4    4    4    4    4    5    5    7    8    8    9   11   11   11   12   12   13   15   16   17 
LCS_GDT     F     159     F     159      4    4   12     4    4    4    4    4    4    6    7    8    8    9   11   11   13   14   14   15   17   18   18 
LCS_GDT     G     160     G     160      3    4   12     3    3    3    3    4    4    6    7    8    8    9   11   11   13   14   14   15   17   18   18 
LCS_GDT     W     161     W     161      3    4   12     1    3    3    3    4    4    5    7    8    8    9   11   11   13   14   14   15   17   18   18 
LCS_GDT     A     162     A     162      3    3   11     0    3    3    3    4    4    5    7    8    8    9   11   11   13   14   14   15   17   18   18 
LCS_GDT     D     163     D     163      3    3   11     0    3    3    3    3    4    6    7    8    8    9   11   11   11   12   13   15   17   18   18 
LCS_GDT     F     164     F     164      3    3   11     0    3    3    3    4    5    8    8    9    9   10   11   11   11   14   14   15   17   18   18 
LCS_GDT     L     165     L     165      3    3   11     1    3    3    3    4    5    8    8    9    9   10   11   11   11   12   13   15   16   18   19 
LCS_GDT     R     166     R     166      3    3   11     2    3    3    4    5    6    8    8    9    9   10   11   11   11   12   13   14   14   17   19 
LCS_GDT     R     167     R     167      3    3    3     3    3    3    3    3    3    3    3    3    3    3    3    5    6    9   14   14   15   16   16 
LCS_GDT     R     168     R     168      3    3    3     3    3    3    3    3    3    3    3    3    3    3    3    5    6   12   14   14   15   16   16 
LCS_GDT     I     169     I     169      3    3    3     3    3    3    3    3    3    3    3    3    3    3    3    3    3   12   14   14   15   16   16 
LCS_AVERAGE  LCS_A:   8.99  (   4.89    7.17   14.92 )

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      6      6      7      8      9     10     10     11     11     13     14     14     16     16     16     17     17     18     19 
GDT PERCENT_CA   5.63   8.45   8.45   9.86  11.27  12.68  14.08  14.08  15.49  15.49  18.31  19.72  19.72  22.54  22.54  22.54  23.94  23.94  25.35  26.76
GDT RMS_LOCAL    0.19   0.82   0.82   1.05   1.31   1.62   2.35   2.35   2.69   2.69   3.58   3.80   3.80   4.65   4.65   4.65   5.18   5.18   6.94   6.40
GDT RMS_ALL_CA  27.45  13.33  13.33  13.55  13.62  13.72  12.38  12.38  12.95  12.95  13.23  13.16  13.16  13.34  13.34  13.34  13.47  13.47  14.69  12.88

#      Molecule1      Molecule2       DISTANCE
LGA    D     134      D     134         16.999
LGA    L     139      L     139          7.757
LGA    A     140      A     140          8.040
LGA    G     141      G     141         11.910
LGA    A     142      A     142          9.671
LGA    L     143      L     143          9.053
LGA    R     144      R     144         14.374
LGA    M     145      M     145          6.570
LGA    A     146      A     146          1.422
LGA    G     147      G     147          2.553
LGA    G     148      G     148          1.739
LGA    Y     149      Y     149          2.389
LGA    A     150      A     150          0.961
LGA    K     151      K     151          3.244
LGA    V     152      V     152          0.573
LGA    I     153      I     153          3.035
LGA    I     154      I     154          2.918
LGA    P     155      P     155          2.884
LGA    F     156      F     156          8.524
LGA    S     157      S     157         14.563
LGA    E     158      E     158         16.300
LGA    F     159      F     159         16.838
LGA    G     160      G     160         16.728
LGA    W     161      W     161         16.141
LGA    A     162      A     162         15.786
LGA    D     163      D     163         16.943
LGA    F     164      F     164         14.344
LGA    L     165      L     165         13.191
LGA    R     166      R     166         13.748
LGA    R     167      R     167         21.520
LGA    R     168      R     168         21.158
LGA    I     169      I     169         21.949

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   32   71    4.0     10    2.35    13.732    12.413     0.409

LGA_LOCAL      RMSD =  2.347  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 12.384  Number of atoms =   32 
Std_ALL_ATOMS  RMSD = 11.318  (standard rmsd on all 32 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.297732 * X  +  -0.771651 * Y  +   0.562059 * Z  +  71.215912
  Y_new =   0.923175 * X  +  -0.382659 * Y  +  -0.036331 * Z  +  75.092590
  Z_new =   0.243112 * X  +   0.508062 * Y  +   0.826299 * Z  + -66.463348 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.551278   -2.590314  [ DEG:    31.5859   -148.4141 ]
  Theta =  -0.245573   -2.896020  [ DEG:   -14.0703   -165.9297 ]
  Phi   =   1.882773   -1.258820  [ DEG:   107.8750    -72.1250 ]
 
# 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: T0347AL333_4-D2                               
REMARK     2: T0347_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0347AL333_4-D2.T0347_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   32   71   4.0   10   2.35  12.413    11.32
REMARK  ---------------------------------------------------------- 
MOLECULE T0347AL333_4-D2
REMARK Aligment from pdb entry: 1ltl_A
ATOM    529  N   ASP   134      17.764  65.152   5.132  1.00  0.00              
ATOM    530  CA  ASP   134      17.413  66.127   4.104  1.00  0.00              
ATOM    531  C   ASP   134      17.311  65.601   2.693  1.00  0.00              
ATOM    532  O   ASP   134      16.836  66.312   1.806  1.00  0.00              
ATOM    533  N   LEU   139      17.749  64.366   2.479  1.00  0.00              
ATOM    534  CA  LEU   139      17.661  63.764   1.163  1.00  0.00              
ATOM    535  C   LEU   139      16.284  63.205   0.963  1.00  0.00              
ATOM    536  O   LEU   139      15.950  62.706  -0.105  1.00  0.00              
ATOM    537  N   ALA   140      15.472  63.274   1.996  1.00  0.00              
ATOM    538  CA  ALA   140      14.132  62.745   1.892  1.00  0.00              
ATOM    539  C   ALA   140      13.334  63.574   0.906  1.00  0.00              
ATOM    540  O   ALA   140      13.560  64.770   0.779  1.00  0.00              
ATOM    541  N   GLY   141      12.413  62.928   0.201  1.00  0.00              
ATOM    542  CA  GLY   141      11.535  63.607  -0.755  1.00  0.00              
ATOM    543  C   GLY   141      12.336  64.510  -1.673  1.00  0.00              
ATOM    544  O   GLY   141      12.029  65.690  -1.815  1.00  0.00              
ATOM    545  N   ALA   142      13.361  63.934  -2.296  1.00  0.00              
ATOM    546  CA  ALA   142      14.253  64.648  -3.191  1.00  0.00              
ATOM    547  C   ALA   142      14.123  64.131  -4.620  1.00  0.00              
ATOM    548  O   ALA   142      14.292  64.881  -5.571  1.00  0.00              
ATOM    549  N   LEU   143      13.813  62.850  -4.768  1.00  0.00              
ATOM    550  CA  LEU   143      13.684  62.268  -6.088  1.00  0.00              
ATOM    551  C   LEU   143      12.277  61.803  -6.365  1.00  0.00              
ATOM    552  O   LEU   143      11.469  61.654  -5.451  1.00  0.00              
ATOM    553  N   ARG   144      11.987  61.575  -7.642  1.00  0.00              
ATOM    554  CA  ARG   144      10.667  61.103  -8.067  1.00  0.00              
ATOM    555  C   ARG   144      10.735  60.241  -9.315  1.00  0.00              
ATOM    556  O   ARG   144      11.664  60.348 -10.103  1.00  0.00              
ATOM    557  N   MET   145      22.278  59.460 -10.447  1.00  0.00              
ATOM    558  CA  MET   145      23.521  58.805 -10.137  1.00  0.00              
ATOM    559  C   MET   145      23.670  58.801  -8.626  1.00  0.00              
ATOM    560  O   MET   145      24.368  59.661  -8.040  1.00  0.00              
ATOM    561  N   ALA   146      22.990  57.829  -8.012  1.00  0.00              
ATOM    562  CA  ALA   146      22.982  57.613  -6.568  1.00  0.00              
ATOM    563  C   ALA   146      24.349  57.239  -6.028  1.00  0.00              
ATOM    564  O   ALA   146      24.945  56.284  -6.478  1.00  0.00              
ATOM    565  N   GLY   147      24.847  57.995  -5.069  1.00  0.00              
ATOM    566  CA  GLY   147      26.135  57.675  -4.469  1.00  0.00              
ATOM    567  C   GLY   147      25.872  57.298  -3.003  1.00  0.00              
ATOM    568  O   GLY   147      25.208  58.043  -2.271  1.00  0.00              
ATOM    569  N   GLY   148      26.397  56.161  -2.563  1.00  0.00              
ATOM    570  CA  GLY   148      26.171  55.778  -1.189  1.00  0.00              
ATOM    571  C   GLY   148      26.852  54.498  -0.771  1.00  0.00              
ATOM    572  O   GLY   148      27.578  53.880  -1.548  1.00  0.00              
ATOM    573  N   TYR   149      26.616  54.088   0.466  1.00  0.00              
ATOM    574  CA  TYR   149      27.229  52.868   0.963  1.00  0.00              
ATOM    575  C   TYR   149      26.384  51.652   0.616  1.00  0.00              
ATOM    576  O   TYR   149      25.159  51.676   0.744  1.00  0.00              
ATOM    577  N   ALA   150      27.015  50.585   0.148  1.00  0.00              
ATOM    578  CA  ALA   150      26.214  49.411  -0.167  1.00  0.00              
ATOM    579  C   ALA   150      26.066  48.603   1.111  1.00  0.00              
ATOM    580  O   ALA   150      27.042  48.207   1.747  1.00  0.00              
ATOM    581  N   LYS   151      24.826  48.382   1.501  1.00  0.00              
ATOM    582  CA  LYS   151      24.571  47.658   2.718  1.00  0.00              
ATOM    583  C   LYS   151      23.785  46.401   2.389  1.00  0.00              
ATOM    584  O   LYS   151      23.205  46.250   1.299  1.00  0.00              
ATOM    585  N   VAL   152      23.786  45.468   3.320  1.00  0.00              
ATOM    586  CA  VAL   152      23.011  44.285   3.071  1.00  0.00              
ATOM    587  C   VAL   152      22.162  43.975   4.292  1.00  0.00              
ATOM    588  O   VAL   152      22.491  44.359   5.419  1.00  0.00              
ATOM    589  N   ILE   153      21.061  43.282   4.047  1.00  0.00              
ATOM    590  CA  ILE   153      20.164  42.920   5.109  1.00  0.00              
ATOM    591  C   ILE   153      19.421  41.637   4.825  1.00  0.00              
ATOM    592  O   ILE   153      18.946  41.420   3.711  1.00  0.00              
ATOM    593  N   ILE   154      19.319  40.790   5.850  1.00  0.00              
ATOM    594  CA  ILE   154      18.619  39.519   5.738  1.00  0.00              
ATOM    595  C   ILE   154      17.123  39.718   5.866  1.00  0.00              
ATOM    596  O   ILE   154      16.633  40.314   6.825  1.00  0.00              
ATOM    597  N   PRO   155      16.409  39.216   4.873  1.00  0.00              
ATOM    598  CA  PRO   155      14.961  39.297   4.829  1.00  0.00              
ATOM    599  C   PRO   155      14.350  38.271   5.766  1.00  0.00              
ATOM    600  O   PRO   155      14.515  37.070   5.567  1.00  0.00              
ATOM    601  N   PHE   156      13.629  38.750   6.776  1.00  0.00              
ATOM    602  CA  PHE   156      12.982  37.883   7.763  1.00  0.00              
ATOM    603  C   PHE   156      12.050  36.861   7.112  1.00  0.00              
ATOM    604  O   PHE   156      11.324  37.172   6.159  1.00  0.00              
ATOM    605  N   SER   157      12.073  35.645   7.649  1.00  0.00              
ATOM    606  CA  SER   157      11.245  34.549   7.152  1.00  0.00              
ATOM    607  C   SER   157      11.848  33.867   5.912  1.00  0.00              
ATOM    608  O   SER   157      11.608  32.679   5.675  1.00  0.00              
ATOM    609  N   GLU   158      12.621  34.610   5.123  1.00  0.00              
ATOM    610  CA  GLU   158      13.270  34.043   3.933  1.00  0.00              
ATOM    611  C   GLU   158      14.676  33.608   4.314  1.00  0.00              
ATOM    612  O   GLU   158      15.196  32.625   3.792  1.00  0.00              
ATOM    613  N   PHE   159      15.271  34.347   5.245  1.00  0.00              
ATOM    614  CA  PHE   159      16.617  34.063   5.729  1.00  0.00              
ATOM    615  C   PHE   159      17.700  34.420   4.692  1.00  0.00              
ATOM    616  O   PHE   159      18.889  34.189   4.920  1.00  0.00              
ATOM    617  N   GLY   160      17.277  35.014   3.574  1.00  0.00              
ATOM    618  CA  GLY   160      18.193  35.407   2.510  1.00  0.00              
ATOM    619  C   GLY   160      18.587  36.888   2.546  1.00  0.00              
ATOM    620  O   GLY   160      17.742  37.756   2.712  1.00  0.00              
ATOM    621  N   TRP   161      19.880  37.169   2.412  1.00  0.00              
ATOM    622  CA  TRP   161      20.333  38.540   2.394  1.00  0.00              
ATOM    623  C   TRP   161      19.970  39.165   1.064  1.00  0.00              
ATOM    624  O   TRP   161      19.716  38.467   0.100  1.00  0.00              
ATOM    625  N   ALA   162      19.949  40.492   1.024  1.00  0.00              
ATOM    626  CA  ALA   162      19.598  41.264  -0.170  1.00  0.00              
ATOM    627  C   ALA   162      20.388  42.548  -0.069  1.00  0.00              
ATOM    628  O   ALA   162      20.556  43.065   1.029  1.00  0.00              
ATOM    629  N   ASP   163      20.878  43.089  -1.178  1.00  0.00              
ATOM    630  CA  ASP   163      21.648  44.328  -1.051  1.00  0.00              
ATOM    631  C   ASP   163      20.838  45.565  -1.356  1.00  0.00              
ATOM    632  O   ASP   163      19.905  45.526  -2.150  1.00  0.00              
ATOM    633  N   PHE   164      21.184  46.669  -0.709  1.00  0.00              
ATOM    634  CA  PHE   164      20.487  47.926  -0.966  1.00  0.00              
ATOM    635  C   PHE   164      21.490  49.058  -0.833  1.00  0.00              
ATOM    636  O   PHE   164      22.555  48.882  -0.241  1.00  0.00              
ATOM    637  N   LEU   165      21.176  50.213  -1.399  1.00  0.00              
ATOM    638  CA  LEU   165      22.104  51.325  -1.259  1.00  0.00              
ATOM    639  C   LEU   165      21.608  52.348  -0.265  1.00  0.00              
ATOM    640  O   LEU   165      20.451  52.780  -0.309  1.00  0.00              
ATOM    641  N   ARG   166      22.506  52.727   0.634  1.00  0.00              
ATOM    642  CA  ARG   166      22.226  53.739   1.638  1.00  0.00              
ATOM    643  C   ARG   166      22.767  55.014   0.999  1.00  0.00              
ATOM    644  O   ARG   166      23.981  55.264   0.975  1.00  0.00              
ATOM    645  N   ARG   167      22.605  63.074  -7.584  1.00  0.00              
ATOM    646  CA  ARG   167      22.893  63.979  -8.684  1.00  0.00              
ATOM    647  C   ARG   167      22.125  63.538  -9.924  1.00  0.00              
ATOM    648  O   ARG   167      21.914  62.347 -10.153  1.00  0.00              
ATOM    649  N   ARG   168      21.702  64.495 -10.732  1.00  0.00              
ATOM    650  CA  ARG   168      20.986  64.131 -11.934  1.00  0.00              
ATOM    651  C   ARG   168      21.943  64.024 -13.114  1.00  0.00              
ATOM    652  O   ARG   168      23.025  64.617 -13.116  1.00  0.00              
ATOM    653  N   ILE   169      21.543  63.248 -14.113  1.00  0.00              
ATOM    654  CA  ILE   169      22.365  63.054 -15.292  1.00  0.00              
ATOM    655  C   ILE   169      21.731  63.736 -16.491  1.00  0.00              
ATOM    656  O   ILE   169      22.486  64.284 -17.332  1.00  0.00              
END
