
#######################################################
#                                                     #
#                        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   33 (  132),  selected   33 , name T0347AL333_2-D2
# Molecule2: number of CA atoms   71 (  561),  selected   33 , name T0347_D2.pdb
# PARAMETERS: T0347AL333_2-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:    18       140 - 157         3.87    15.02
  LCS_AVERAGE:     23.43

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12       182 - 193         1.96    16.14
  LCS_AVERAGE:     14.26

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11       182 - 192         0.89    15.84
  LCS_AVERAGE:     10.33

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     A     140     A     140      8   11   18     8    8    8    9   10   11   12   13   14   15   16   18   18   18   19   20   21   23   25   26 
LCS_GDT     G     141     G     141      8   11   18     8    8    8    9   10   11   12   13   14   15   16   18   18   18   19   20   21   23   25   26 
LCS_GDT     A     142     A     142      8   11   18     8    8    8    9   10   11   12   13   14   15   16   18   18   18   19   20   21   23   25   26 
LCS_GDT     L     143     L     143      8   11   18     8    8    8    9   10   11   12   13   14   15   16   18   18   18   19   20   21   23   25   26 
LCS_GDT     R     144     R     144      8   11   18     8    8    8    9   10   11   12   13   14   15   16   18   18   18   19   20   21   23   25   26 
LCS_GDT     M     145     M     145      8   11   18     8    8    8    9   10   11   12   13   14   15   16   18   18   18   19   20   21   23   25   26 
LCS_GDT     A     146     A     146      8   11   18     8    8    8    9   10   11   12   13   14   15   16   18   18   18   19   20   21   23   25   26 
LCS_GDT     G     147     G     147      8   11   18     8    8    8    9   10   10   12   13   14   15   16   18   18   18   19   20   21   23   25   26 
LCS_GDT     G     148     G     148      5   11   18     4    5    5    6    9   10   12   13   14   15   16   18   18   18   19   20   20   22   25   26 
LCS_GDT     Y     149     Y     149      5   11   18     4    5    5    8   10   11   12   13   14   15   16   18   18   18   19   20   21   23   25   26 
LCS_GDT     A     150     A     150      5   11   18     4    5    5    8   10   11   12   13   14   15   16   18   18   18   19   20   21   23   25   26 
LCS_GDT     K     151     K     151      5    9   18     4    5    7    9   10   11   12   13   14   15   16   18   18   18   19   20   21   23   25   26 
LCS_GDT     V     152     V     152      5    9   18     3    5    5    6    9   11   12   13   14   15   16   18   18   18   19   20   21   23   25   26 
LCS_GDT     I     153     I     153      4    9   18     3    4    4    5    7    9   11   13   13   15   16   18   18   18   19   20   21   23   25   26 
LCS_GDT     I     154     I     154      4    9   18     3    4    4    6    8    9   11   13   14   15   16   18   18   18   19   20   21   23   25   26 
LCS_GDT     P     155     P     155      4    9   18     3    4    4    6    8    9   11   13   14   15   16   18   18   18   19   20   21   23   25   26 
LCS_GDT     F     156     F     156      4    9   18     3    4    4    6    8    9   11   13   13   15   16   18   18   18   18   19   20   20   23   25 
LCS_GDT     S     157     S     157      4    6   18     3    4    4    6    7    9   11   13   14   15   16   18   18   18   19   20   21   23   25   26 
LCS_GDT     L     182     L     182     11   12   15    10   10   10   10   11   11   12   14   15   15   15   15   16   16   18   18   19   22   22   24 
LCS_GDT     A     183     A     183     11   12   15    10   10   10   10   11   11   12   14   15   15   15   15   16   17   18   18   19   19   20   20 
LCS_GDT     E     184     E     184     11   12   15    10   10   10   10   11   11   12   14   15   15   15   15   16   17   18   20   20   22   23   24 
LCS_GDT     A     185     A     185     11   12   15    10   10   10   10   11   11   12   14   15   15   15   15   16   18   19   20   21   23   25   26 
LCS_GDT     M     186     M     186     11   12   15    10   10   10   10   11   11   12   14   15   15   15   15   16   18   18   20   21   23   24   26 
LCS_GDT     K     187     K     187     11   12   15    10   10   10   10   11   11   12   14   15   15   15   15   16   18   18   20   21   23   25   26 
LCS_GDT     L     188     L     188     11   12   15    10   10   10   10   11   11   12   14   15   15   15   15   16   18   19   20   21   23   25   26 
LCS_GDT     A     189     A     189     11   12   15    10   10   10   10   11   11   12   14   15   15   15   15   16   18   19   20   21   23   25   26 
LCS_GDT     K     190     K     190     11   12   15    10   10   10   10   11   11   12   14   15   15   15   15   16   17   19   20   21   23   25   26 
LCS_GDT     S     191     S     191     11   12   15    10   10   10   10   11   11   12   14   15   15   15   15   16   18   19   20   21   23   25   26 
LCS_GDT     R     192     R     192     11   12   15     3    3    3    9   11   11   12   14   15   15   15   15   16   17   19   19   21   23   25   26 
LCS_GDT     E     193     E     193      3   12   15     3    3    3    4    6    8   11   14   15   15   15   15   16   17   19   20   21   23   25   26 
LCS_GDT     H     196     H     196      3    3   15     3    3    3    3    5    7   12   14   15   15   15   15   16   17   18   18   19   20   21   23 
LCS_GDT     L     197     L     197      3    3   15     3    3    3    4    6    9   12   14   15   15   15   15   16   17   18   18   19   23   23   26 
LCS_GDT     P     198     P     198      3    3   15     3    3    3    3    5    7   11   14   15   15   15   15   16   16   16   17   17   18   19   19 
LCS_AVERAGE  LCS_A:  16.01  (  10.33   14.26   23.43 )

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     10     10     10     10     11     11     12     14     15     15     16     18     18     18     19     20     21     23     25     26 
GDT PERCENT_CA  14.08  14.08  14.08  14.08  15.49  15.49  16.90  19.72  21.13  21.13  22.54  25.35  25.35  25.35  26.76  28.17  29.58  32.39  35.21  36.62
GDT RMS_LOCAL    0.24   0.24   0.24   0.24   0.89   0.89   1.97   2.58   2.82   2.82   3.43   3.87   3.87   3.87   4.76   5.21   5.45   5.93   6.32   6.51
GDT RMS_ALL_CA  16.00  16.00  16.00  16.00  15.84  15.84  13.05  16.77  17.15  17.15  16.20  15.02  15.02  15.02  11.23   8.89   8.96   8.97   8.96   8.94

#      Molecule1      Molecule2       DISTANCE
LGA    A     140      A     140          7.432
LGA    G     141      G     141         12.526
LGA    A     142      A     142         14.762
LGA    L     143      L     143         12.546
LGA    R     144      R     144         17.094
LGA    M     145      M     145         21.307
LGA    A     146      A     146         20.765
LGA    G     147      G     147         21.721
LGA    G     148      G     148         22.754
LGA    Y     149      Y     149         24.322
LGA    A     150      A     150         27.245
LGA    K     151      K     151         25.055
LGA    V     152      V     152         26.125
LGA    I     153      I     153         25.723
LGA    I     154      I     154         26.088
LGA    P     155      P     155         24.085
LGA    F     156      F     156         23.034
LGA    S     157      S     157         18.648
LGA    L     182      L     182          2.080
LGA    A     183      A     183          3.887
LGA    E     184      E     184          2.669
LGA    A     185      A     185          0.374
LGA    M     186      M     186          2.597
LGA    K     187      K     187          2.282
LGA    L     188      L     188          0.947
LGA    A     189      A     189          2.679
LGA    K     190      K     190          2.235
LGA    S     191      S     191          0.557
LGA    R     192      R     192          3.083
LGA    E     193      E     193          3.952
LGA    H     196      H     196          3.823
LGA    L     197      L     197          3.665
LGA    P     198      P     198          5.629

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   33   71    4.0     14    2.58    19.014    17.766     0.523

LGA_LOCAL      RMSD =  2.577  Number of atoms =   14  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 15.894  Number of atoms =   33 
Std_ALL_ATOMS  RMSD =  8.774  (standard rmsd on all 33 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.201004 * X  +   0.798967 * Y  +   0.566788 * Z  +  -6.454471
  Y_new =   0.724135 * X  +   0.268474 * Y  +  -0.635256 * Z  +  39.870338
  Z_new =  -0.659716 * X  +   0.538121 * Y  +  -0.524596 * Z  +  28.844608 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.343469   -0.798124  [ DEG:   134.2709    -45.7291 ]
  Theta =   0.720441    2.421152  [ DEG:    41.2782    138.7218 ]
  Phi   =   1.300035   -1.841558  [ DEG:    74.4865   -105.5135 ]
 
# 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_2-D2                               
REMARK     2: T0347_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0347AL333_2-D2.T0347_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   33   71   4.0   14   2.58  17.766     8.77
REMARK  ---------------------------------------------------------- 
MOLECULE T0347AL333_2-D2
REMARK Aligment from pdb entry: 1bh9_B
ATOM    193  N   ALA   140      14.877  61.696   2.090  1.00  0.00              
ATOM    194  CA  ALA   140      14.855  62.508   0.877  1.00  0.00              
ATOM    195  C   ALA   140      13.558  63.330   0.803  1.00  0.00              
ATOM    196  O   ALA   140      13.557  64.480   0.373  1.00  0.00              
ATOM    197  N   GLY   141      12.457  62.727   1.228  1.00  0.00              
ATOM    198  CA  GLY   141      11.163  63.391   1.223  1.00  0.00              
ATOM    199  C   GLY   141      11.285  64.656   2.060  1.00  0.00              
ATOM    200  O   GLY   141      10.693  65.686   1.743  1.00  0.00              
ATOM    201  N   ALA   142      12.077  64.567   3.123  1.00  0.00              
ATOM    202  CA  ALA   142      12.300  65.686   4.016  1.00  0.00              
ATOM    203  C   ALA   142      13.096  66.798   3.343  1.00  0.00              
ATOM    204  O   ALA   142      12.784  67.974   3.529  1.00  0.00              
ATOM    205  N   LEU   143      14.122  66.428   2.573  1.00  0.00              
ATOM    206  CA  LEU   143      14.965  67.392   1.852  1.00  0.00              
ATOM    207  C   LEU   143      14.131  68.120   0.789  1.00  0.00              
ATOM    208  O   LEU   143      14.171  69.349   0.674  1.00  0.00              
ATOM    209  N   ARG   144      13.376  67.337   0.025  1.00  0.00              
ATOM    210  CA  ARG   144      12.496  67.848  -1.019  1.00  0.00              
ATOM    211  C   ARG   144      11.469  68.801  -0.399  1.00  0.00              
ATOM    212  O   ARG   144      11.104  69.802  -1.000  1.00  0.00              
ATOM    213  N   MET   145      11.020  68.487   0.808  1.00  0.00              
ATOM    214  CA  MET   145      10.066  69.331   1.521  1.00  0.00              
ATOM    215  C   MET   145      10.740  70.655   1.960  1.00  0.00              
ATOM    216  O   MET   145      10.178  71.735   1.782  1.00  0.00              
ATOM    217  N   ALA   146      11.951  70.571   2.514  1.00  0.00              
ATOM    218  CA  ALA   146      12.666  71.767   2.969  1.00  0.00              
ATOM    219  C   ALA   146      13.247  72.652   1.855  1.00  0.00              
ATOM    220  O   ALA   146      13.500  73.834   2.079  1.00  0.00              
ATOM    221  N   GLY   147      13.474  72.095   0.664  1.00  0.00              
ATOM    222  CA  GLY   147      13.998  72.905  -0.435  1.00  0.00              
ATOM    223  C   GLY   147      12.831  73.528  -1.195  1.00  0.00              
ATOM    224  O   GLY   147      12.966  73.987  -2.330  1.00  0.00              
ATOM    225  N   GLY   148      11.679  73.533  -0.534  1.00  0.00              
ATOM    226  CA  GLY   148      10.482  74.101  -1.113  1.00  0.00              
ATOM    227  C   GLY   148       9.949  73.407  -2.347  1.00  0.00              
ATOM    228  O   GLY   148       9.206  74.012  -3.118  1.00  0.00              
ATOM    229  N   TYR   149      10.302  72.143  -2.539  1.00  0.00              
ATOM    230  CA  TYR   149       9.828  71.429  -3.708  1.00  0.00              
ATOM    231  C   TYR   149       8.753  70.409  -3.373  1.00  0.00              
ATOM    232  O   TYR   149       8.398  70.232  -2.218  1.00  0.00              
ATOM    233  N   ALA   150       8.224  69.771  -4.409  1.00  0.00              
ATOM    234  CA  ALA   150       7.179  68.750  -4.294  1.00  0.00              
ATOM    235  C   ALA   150       7.658  67.421  -4.899  1.00  0.00              
ATOM    236  O   ALA   150       8.559  67.384  -5.738  1.00  0.00              
ATOM    237  N   LYS   151       7.063  66.305  -4.471  1.00  0.00              
ATOM    238  CA  LYS   151       7.463  65.016  -5.034  1.00  0.00              
ATOM    239  C   LYS   151       7.101  65.099  -6.532  1.00  0.00              
ATOM    240  O   LYS   151       6.465  66.061  -6.958  1.00  0.00              
ATOM    241  N   VAL   152       7.495  64.114  -7.348  1.00  0.00              
ATOM    242  CA  VAL   152       8.259  62.899  -7.079  1.00  0.00              
ATOM    243  C   VAL   152       9.657  63.272  -6.629  1.00  0.00              
ATOM    244  O   VAL   152      10.136  64.363  -6.932  1.00  0.00              
ATOM    245  N   ILE   153      10.313  62.372  -5.909  1.00  0.00              
ATOM    246  CA  ILE   153      11.674  62.614  -5.459  1.00  0.00              
ATOM    247  C   ILE   153      12.610  62.646  -6.664  1.00  0.00              
ATOM    248  O   ILE   153      12.505  61.810  -7.561  1.00  0.00              
ATOM    249  N   ILE   154      13.514  63.620  -6.682  1.00  0.00              
ATOM    250  CA  ILE   154      14.483  63.759  -7.765  1.00  0.00              
ATOM    251  C   ILE   154      15.825  63.229  -7.273  1.00  0.00              
ATOM    252  O   ILE   154      16.058  63.123  -6.070  1.00  0.00              
ATOM    253  N   PRO   155      16.728  62.893  -8.207  1.00  0.00              
ATOM    254  CA  PRO   155      18.060  62.382  -7.895  1.00  0.00              
ATOM    255  C   PRO   155      18.798  63.243  -6.864  1.00  0.00              
ATOM    256  O   PRO   155      19.441  62.726  -5.954  1.00  0.00              
ATOM    257  N   PHE   156      18.700  64.559  -7.013  1.00  0.00              
ATOM    258  CA  PHE   156      19.374  65.469  -6.099  1.00  0.00              
ATOM    259  C   PHE   156      18.877  65.300  -4.672  1.00  0.00              
ATOM    260  O   PHE   156      19.583  65.651  -3.727  1.00  0.00              
ATOM    261  N   SER   157      17.667  64.766  -4.518  1.00  0.00              
ATOM    262  CA  SER   157      17.085  64.560  -3.194  1.00  0.00              
ATOM    263  C   SER   157      17.645  63.318  -2.525  1.00  0.00              
ATOM    264  O   SER   157      17.858  63.303  -1.313  1.00  0.00              
ATOM    265  N   LEU   182      17.856  62.279  -3.331  1.00  0.00              
ATOM    266  CA  LEU   182      18.354  60.993  -2.862  1.00  0.00              
ATOM    267  C   LEU   182      19.793  61.118  -2.390  1.00  0.00              
ATOM    268  O   LEU   182      20.165  60.652  -1.315  1.00  0.00              
ATOM    269  N   ALA   183      20.611  61.740  -3.219  1.00  0.00              
ATOM    270  CA  ALA   183      21.989  61.889  -2.871  1.00  0.00              
ATOM    271  C   ALA   183      22.178  62.811  -1.698  1.00  0.00              
ATOM    272  O   ALA   183      23.021  62.547  -0.858  1.00  0.00              
ATOM    273  N   GLU   184      21.386  63.874  -1.608  1.00  0.00              
ATOM    274  CA  GLU   184      21.517  64.783  -0.470  1.00  0.00              
ATOM    275  C   GLU   184      21.116  64.065   0.808  1.00  0.00              
ATOM    276  O   GLU   184      21.744  64.237   1.854  1.00  0.00              
ATOM    277  N   ALA   185      20.067  63.252   0.707  1.00  0.00              
ATOM    278  CA  ALA   185      19.567  62.481   1.837  1.00  0.00              
ATOM    279  C   ALA   185      20.634  61.535   2.339  1.00  0.00              
ATOM    280  O   ALA   185      20.821  61.375   3.541  1.00  0.00              
ATOM    281  N   MET   186      21.322  60.904   1.398  1.00  0.00              
ATOM    282  CA  MET   186      22.369  59.962   1.710  1.00  0.00              
ATOM    283  C   MET   186      23.504  60.626   2.469  1.00  0.00              
ATOM    284  O   MET   186      24.090  60.017   3.353  1.00  0.00              
ATOM    285  N   LYS   187      23.801  61.876   2.140  1.00  0.00              
ATOM    286  CA  LYS   187      24.860  62.597   2.833  1.00  0.00              
ATOM    287  C   LYS   187      24.474  62.914   4.270  1.00  0.00              
ATOM    288  O   LYS   187      25.329  62.872   5.154  1.00  0.00              
ATOM    289  N   LEU   188      23.196  63.227   4.501  1.00  0.00              
ATOM    290  CA  LEU   188      22.718  63.547   5.847  1.00  0.00              
ATOM    291  C   LEU   188      22.669  62.292   6.706  1.00  0.00              
ATOM    292  O   LEU   188      23.066  62.315   7.876  1.00  0.00              
ATOM    293  N   ALA   189      22.178  61.198   6.130  1.00  0.00              
ATOM    294  CA  ALA   189      22.116  59.942   6.858  1.00  0.00              
ATOM    295  C   ALA   189      23.522  59.535   7.304  1.00  0.00              
ATOM    296  O   ALA   189      23.704  59.096   8.433  1.00  0.00              
ATOM    297  N   LYS   190      24.510  59.684   6.424  1.00  0.00              
ATOM    298  CA  LYS   190      25.887  59.342   6.776  1.00  0.00              
ATOM    299  C   LYS   190      26.394  60.250   7.893  1.00  0.00              
ATOM    300  O   LYS   190      27.078  59.794   8.795  1.00  0.00              
ATOM    301  N   SER   191      26.052  61.532   7.852  1.00  0.00              
ATOM    302  CA  SER   191      26.476  62.426   8.924  1.00  0.00              
ATOM    303  C   SER   191      25.880  61.960  10.241  1.00  0.00              
ATOM    304  O   SER   191      26.605  61.792  11.221  1.00  0.00              
ATOM    305  N   ARG   192      24.566  61.752  10.265  1.00  0.00              
ATOM    306  CA  ARG   192      23.897  61.272  11.466  1.00  0.00              
ATOM    307  C   ARG   192      24.434  59.885  11.800  1.00  0.00              
ATOM    308  O   ARG   192      24.123  59.318  12.843  1.00  0.00              
ATOM    309  N   GLU   193      25.233  59.341  10.890  1.00  0.00              
ATOM    310  CA  GLU   193      25.807  58.026  11.084  1.00  0.00              
ATOM    311  C   GLU   193      24.775  56.924  11.209  1.00  0.00              
ATOM    312  O   GLU   193      25.066  55.876  11.797  1.00  0.00              
ATOM    313  N   HIS   196      23.574  57.130  10.658  1.00  0.00              
ATOM    314  CA  HIS   196      22.551  56.102  10.763  1.00  0.00              
ATOM    315  C   HIS   196      22.492  55.096   9.622  1.00  0.00              
ATOM    316  O   HIS   196      21.756  54.114   9.708  1.00  0.00              
ATOM    317  N   LEU   197      23.242  55.336   8.549  1.00  0.00              
ATOM    318  CA  LEU   197      23.313  54.365   7.464  1.00  0.00              
ATOM    319  C   LEU   197      24.788  54.152   7.258  1.00  0.00              
ATOM    320  O   LEU   197      25.585  55.032   7.543  1.00  0.00              
ATOM    321  N   PRO   198      25.181  52.955   6.811  1.00  0.00              
ATOM    322  CA  PRO   198      26.594  52.677   6.577  1.00  0.00              
ATOM    323  C   PRO   198      27.144  53.555   5.442  1.00  0.00              
ATOM    324  O   PRO   198      26.438  54.501   5.014  1.00  0.00              
END
