
#######################################################
#                                                     #
#                        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 T0372AL333_3-D2
# Molecule2: number of CA atoms  172 ( 1400),  selected   26 , name T0372_D2.pdb
# PARAMETERS: T0372AL333_3-D2.T0372_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       160 - 174         1.43    14.68
  LCS_AVERAGE:      7.74

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15       160 - 174         1.43    14.68
  LCS_AVERAGE:      7.11

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12       163 - 174         0.74    14.50
  LCS_AVERAGE:      4.99

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:  172
LCS_GDT     I     160     I     160      7   15   15     6    6   10   13   15   15   15   15   15   15   15   15   16   17   19   20   20   20   21   21 
LCS_GDT     T     161     T     161      7   15   15     6    6   10   14   15   15   15   15   15   15   18   19   20   20   20   20   20   21   21   21 
LCS_GDT     P     162     P     162      7   15   15     6    6   10   14   15   15   15   15   15   15   18   19   20   20   20   20   20   21   21   21 
LCS_GDT     D     163     D     163     12   15   15     6    6   10   14   15   15   15   15   15   15   18   19   20   20   20   20   20   21   21   21 
LCS_GDT     R     164     R     164     12   15   15    11   11   11   14   15   15   15   15   15   15   18   19   20   20   20   20   20   21   21   21 
LCS_GDT     I     165     I     165     12   15   15    11   11   11   14   15   15   15   15   15   15   18   19   20   20   20   20   20   21   21   21 
LCS_GDT     Q     166     Q     166     12   15   15    11   11   11   14   15   15   15   15   15   15   18   19   20   20   20   20   20   21   21   21 
LCS_GDT     E     167     E     167     12   15   15    11   11   11   14   15   15   15   15   15   15   18   19   20   20   20   20   20   21   21   21 
LCS_GDT     C     168     C     168     12   15   15    11   11   11   14   15   15   15   15   15   15   18   19   20   20   20   20   20   21   21   21 
LCS_GDT     L     169     L     169     12   15   15    11   11   11   14   15   15   15   15   15   15   18   19   20   20   20   20   20   21   21   21 
LCS_GDT     D     170     D     170     12   15   15    11   11   11   14   15   15   15   15   15   15   18   19   20   20   20   20   20   21   21   21 
LCS_GDT     L     171     L     171     12   15   15    11   11   11   14   15   15   15   15   15   15   18   19   20   20   20   20   20   21   21   21 
LCS_GDT     E     172     E     172     12   15   15    11   11   11   14   15   15   15   15   15   15   18   19   20   20   20   20   20   21   21   21 
LCS_GDT     A     173     A     173     12   15   15    11   11   11   14   15   15   15   15   15   15   18   19   20   20   20   20   20   21   21   21 
LCS_GDT     E     174     E     174     12   15   15    11   11   11   14   15   15   15   15   15   15   18   19   20   20   20   20   20   21   21   21 
LCS_GDT     T     207     T     207      0    4   11     0    0    3    3    4    9   11   13   14   14   15   16   17   18   18   18   19   20   21   21 
LCS_GDT     G     208     G     208      3    8   11     1    3    3    4    4    9   11   13   14   14   15   16   17   18   18   18   19   20   21   21 
LCS_GDT     G     209     G     209      7    9   11     4    5    7    7    9    9   11   13   14   14   15   16   17   18   18   18   19   19   21   21 
LCS_GDT     I     210     I     210      7    9   11     4    5    7    7    9    9   11   13   14   14   15   16   17   18   18   18   19   20   21   21 
LCS_GDT     L     211     L     211      7    9   11     4    5    7    7    9    9   11   13   14   14   15   16   17   18   18   18   20   21   21   21 
LCS_GDT     H     212     H     212      7    9   11     4    5    7    7    9    9   11   13   14   14   15   19   20   20   20   20   20   21   21   21 
LCS_GDT     V     213     V     213      7    9   11     3    4    7    7    9    9   11   13   14   14   18   19   20   20   20   20   20   21   21   21 
LCS_GDT     N     214     N     214      7    9   11     3    4    7    7    9    9   11   13   14   15   18   19   20   20   20   20   20   21   21   21 
LCS_GDT     G     215     G     215      7    9   11     3    5    7    7    9    9   11   13   14   15   18   19   20   20   20   20   20   21   21   21 
LCS_GDT     K     216     K     216      3    9   11     3    3    3    6    9    9   11   13   14   15   18   19   20   20   20   20   20   21   21   21 
LCS_GDT     I     217     I     217      3    9   11     0    3    3    5    9    9   11   13   14   14   15   19   20   20   20   20   20   21   21   21 
LCS_AVERAGE  LCS_A:   6.61  (   4.99    7.11    7.74 )

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     11     11     11     14     15     15     15     15     15     15     18     19     20     20     20     20     20     21     21     21 
GDT PERCENT_CA   6.40   6.40   6.40   8.14   8.72   8.72   8.72   8.72   8.72   8.72  10.47  11.05  11.63  11.63  11.63  11.63  11.63  12.21  12.21  12.21
GDT RMS_LOCAL    0.25   0.25   0.25   1.23   1.43   1.43   1.43   1.43   1.43   1.43   4.40   4.55   4.70   4.70   4.70   4.70   4.70   5.23   5.15   5.23
GDT RMS_ALL_CA  14.48  14.48  14.48  14.61  14.68  14.68  14.68  14.68  14.68  14.68   9.64   9.56   9.40   9.40   9.40   9.40   9.40   9.13   9.49   9.13

#      Molecule1      Molecule2       DISTANCE
LGA    I     160      I     160          2.578
LGA    T     161      T     161          1.376
LGA    P     162      P     162          1.727
LGA    D     163      D     163          1.893
LGA    R     164      R     164          1.379
LGA    I     165      I     165          1.696
LGA    Q     166      Q     166          1.146
LGA    E     167      E     167          0.356
LGA    C     168      C     168          1.100
LGA    L     169      L     169          1.257
LGA    D     170      D     170          1.025
LGA    L     171      L     171          1.174
LGA    E     172      E     172          0.804
LGA    A     173      A     173          0.643
LGA    E     174      E     174          1.725
LGA    T     207      T     207         22.160
LGA    G     208      G     208         20.331
LGA    G     209      G     209         17.519
LGA    I     210      I     210         16.549
LGA    L     211      L     211         21.025
LGA    H     212      H     212         21.994
LGA    V     213      V     213         28.058
LGA    N     214      N     214         29.238
LGA    G     215      G     215         24.204
LGA    K     216      K     216         22.756
LGA    I     217      I     217         20.342

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   26  172    4.0     15    1.43     8.721     8.436     0.982

LGA_LOCAL      RMSD =  1.428  Number of atoms =   15  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 14.678  Number of atoms =   26 
Std_ALL_ATOMS  RMSD =  8.108  (standard rmsd on all 26 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.799411 * X  +  -0.169669 * Y  +   0.576328 * Z  +  59.177246
  Y_new =   0.513617 * X  +  -0.690666 * Y  +   0.509096 * Z  +  -2.723650
  Z_new =   0.311672 * X  +   0.702989 * Y  +   0.639271 * Z  +  26.715826 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.832833   -2.308759  [ DEG:    47.7178   -132.2822 ]
  Theta =  -0.316953   -2.824640  [ DEG:   -18.1600   -161.8400 ]
  Phi   =   2.570513   -0.571080  [ DEG:   147.2795    -32.7205 ]
 
# 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: T0372AL333_3-D2                               
REMARK     2: T0372_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0372AL333_3-D2.T0372_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   26  172   4.0   15   1.43   8.436     8.11
REMARK  ---------------------------------------------------------- 
MOLECULE T0372AL333_3-D2
REMARK Aligment from pdb entry: 1lva_A
ATOM    137  N   ILE   160      48.616  46.923  27.459  1.00  0.00              
ATOM    138  CA  ILE   160      49.016  45.890  28.403  1.00  0.00              
ATOM    139  C   ILE   160      50.531  45.851  28.441  1.00  0.00              
ATOM    140  O   ILE   160      51.184  46.260  27.490  1.00  0.00              
ATOM    141  N   THR   161      51.092  45.369  29.542  1.00  0.00              
ATOM    142  CA  THR   161      52.538  45.249  29.645  1.00  0.00              
ATOM    143  C   THR   161      52.932  44.008  28.863  1.00  0.00              
ATOM    144  O   THR   161      52.123  43.092  28.687  1.00  0.00              
ATOM    145  N   PRO   162      54.183  43.956  28.385  1.00  0.00              
ATOM    146  CA  PRO   162      54.657  42.801  27.614  1.00  0.00              
ATOM    147  C   PRO   162      54.365  41.465  28.296  1.00  0.00              
ATOM    148  O   PRO   162      53.878  40.523  27.664  1.00  0.00              
ATOM    149  N   ASP   163      54.679  41.395  29.586  1.00  0.00              
ATOM    150  CA  ASP   163      54.489  40.191  30.391  1.00  0.00              
ATOM    151  C   ASP   163      53.057  39.660  30.342  1.00  0.00              
ATOM    152  O   ASP   163      52.821  38.472  30.100  1.00  0.00              
ATOM    153  N   ARG   164      52.110  40.558  30.576  1.00  0.00              
ATOM    154  CA  ARG   164      50.700  40.215  30.582  1.00  0.00              
ATOM    155  C   ARG   164      50.218  39.739  29.214  1.00  0.00              
ATOM    156  O   ARG   164      49.548  38.706  29.113  1.00  0.00              
ATOM    157  N   ILE   165      50.558  40.477  28.160  1.00  0.00              
ATOM    158  CA  ILE   165      50.119  40.088  26.822  1.00  0.00              
ATOM    159  C   ILE   165      50.673  38.716  26.432  1.00  0.00              
ATOM    160  O   ILE   165      49.936  37.874  25.932  1.00  0.00              
ATOM    161  N   GLN   166      51.960  38.483  26.664  1.00  0.00              
ATOM    162  CA  GLN   166      52.550  37.197  26.304  1.00  0.00              
ATOM    163  C   GLN   166      51.807  36.046  26.965  1.00  0.00              
ATOM    164  O   GLN   166      51.590  34.993  26.356  1.00  0.00              
ATOM    165  N   GLU   167      51.406  36.259  28.213  1.00  0.00              
ATOM    166  CA  GLU   167      50.703  35.230  28.967  1.00  0.00              
ATOM    167  C   GLU   167      49.346  34.912  28.347  1.00  0.00              
ATOM    168  O   GLU   167      48.951  33.749  28.265  1.00  0.00              
ATOM    169  N   CYS   168      48.644  35.951  27.911  1.00  0.00              
ATOM    170  CA  CYS   168      47.334  35.788  27.292  1.00  0.00              
ATOM    171  C   CYS   168      47.476  35.115  25.935  1.00  0.00              
ATOM    172  O   CYS   168      46.726  34.198  25.602  1.00  0.00              
ATOM    173  N   LEU   169      48.446  35.571  25.152  1.00  0.00              
ATOM    174  CA  LEU   169      48.682  35.003  23.830  1.00  0.00              
ATOM    175  C   LEU   169      49.137  33.554  23.909  1.00  0.00              
ATOM    176  O   LEU   169      48.717  32.723  23.103  1.00  0.00              
ATOM    177  N   ASP   170      49.995  33.240  24.876  1.00  0.00              
ATOM    178  CA  ASP   170      50.466  31.876  25.004  1.00  0.00              
ATOM    179  C   ASP   170      49.325  30.977  25.430  1.00  0.00              
ATOM    180  O   ASP   170      49.249  29.821  25.010  1.00  0.00              
ATOM    181  N   LEU   171      48.431  31.505  26.258  1.00  0.00              
ATOM    182  CA  LEU   171      47.281  30.724  26.667  1.00  0.00              
ATOM    183  C   LEU   171      46.407  30.473  25.418  1.00  0.00              
ATOM    184  O   LEU   171      45.897  29.382  25.223  1.00  0.00              
ATOM    185  N   GLU   172      46.227  31.491  24.583  1.00  0.00              
ATOM    186  CA  GLU   172      45.420  31.337  23.365  1.00  0.00              
ATOM    187  C   GLU   172      46.079  30.360  22.396  1.00  0.00              
ATOM    188  O   GLU   172      45.397  29.680  21.636  1.00  0.00              
ATOM    189  N   ALA   173      47.404  30.283  22.421  1.00  0.00              
ATOM    190  CA  ALA   173      48.097  29.338  21.557  1.00  0.00              
ATOM    191  C   ALA   173      47.822  27.906  22.045  1.00  0.00              
ATOM    192  O   ALA   173      47.558  27.010  21.235  1.00  0.00              
ATOM    193  N   GLU   174      47.868  27.690  23.361  1.00  0.00              
ATOM    194  CA  GLU   174      47.607  26.361  23.931  1.00  0.00              
ATOM    195  C   GLU   174      46.176  25.901  23.673  1.00  0.00              
ATOM    196  O   GLU   174      45.922  24.715  23.483  1.00  0.00              
ATOM    197  N   THR   207      45.236  26.834  23.680  1.00  0.00              
ATOM    198  CA  THR   207      43.853  26.479  23.425  1.00  0.00              
ATOM    199  C   THR   207      43.649  26.280  21.931  1.00  0.00              
ATOM    200  O   THR   207      42.593  25.841  21.502  1.00  0.00              
ATOM    201  N   GLY   208      44.663  26.620  21.143  1.00  0.00              
ATOM    202  CA  GLY   208      44.568  26.452  19.701  1.00  0.00              
ATOM    203  C   GLY   208      43.858  27.579  18.980  1.00  0.00              
ATOM    204  O   GLY   208      43.522  27.451  17.812  1.00  0.00              
ATOM    205  N   GLY   209      43.632  28.687  19.673  1.00  0.00              
ATOM    206  CA  GLY   209      42.955  29.838  19.085  1.00  0.00              
ATOM    207  C   GLY   209      43.896  30.613  18.171  1.00  0.00              
ATOM    208  O   GLY   209      43.485  31.153  17.144  1.00  0.00              
ATOM    209  N   ILE   210      45.163  30.667  18.559  1.00  0.00              
ATOM    210  CA  ILE   210      46.182  31.361  17.786  1.00  0.00              
ATOM    211  C   ILE   210      47.347  30.411  17.581  1.00  0.00              
ATOM    212  O   ILE   210      47.479  29.428  18.298  1.00  0.00              
ATOM    213  N   LEU   211      48.181  30.716  16.594  1.00  0.00              
ATOM    214  CA  LEU   211      49.371  29.926  16.295  1.00  0.00              
ATOM    215  C   LEU   211      50.478  30.966  16.193  1.00  0.00              
ATOM    216  O   LEU   211      50.285  32.016  15.575  1.00  0.00              
ATOM    217  N   HIS   212      51.627  30.685  16.805  1.00  0.00              
ATOM    218  CA  HIS   212      52.759  31.617  16.794  1.00  0.00              
ATOM    219  C   HIS   212      53.595  31.417  15.538  1.00  0.00              
ATOM    220  O   HIS   212      54.130  30.329  15.322  1.00  0.00              
ATOM    221  N   VAL   213      53.694  32.458  14.713  1.00  0.00              
ATOM    222  CA  VAL   213      54.469  32.387  13.474  1.00  0.00              
ATOM    223  C   VAL   213      55.915  32.763  13.800  1.00  0.00              
ATOM    224  O   VAL   213      56.856  32.175  13.278  1.00  0.00              
ATOM    225  N   ASN   214      56.075  33.756  14.662  1.00  0.00              
ATOM    226  CA  ASN   214      57.381  34.161  15.157  1.00  0.00              
ATOM    227  C   ASN   214      57.143  34.999  16.410  1.00  0.00              
ATOM    228  O   ASN   214      55.988  35.207  16.814  1.00  0.00              
ATOM    229  N   GLY   215      58.219  35.450  17.046  1.00  0.00              
ATOM    230  CA  GLY   215      58.102  36.228  18.276  1.00  0.00              
ATOM    231  C   GLY   215      57.224  37.460  18.155  1.00  0.00              
ATOM    232  O   GLY   215      56.627  37.902  19.133  1.00  0.00              
ATOM    233  N   LYS   216      57.143  38.010  16.954  1.00  0.00              
ATOM    234  CA  LYS   216      56.355  39.205  16.721  1.00  0.00              
ATOM    235  C   LYS   216      54.931  38.942  16.220  1.00  0.00              
ATOM    236  O   LYS   216      53.995  39.679  16.561  1.00  0.00              
ATOM    237  N   ILE   217      54.755  37.879  15.440  1.00  0.00              
ATOM    238  CA  ILE   217      53.443  37.597  14.874  1.00  0.00              
ATOM    239  C   ILE   217      52.746  36.301  15.219  1.00  0.00              
ATOM    240  O   ILE   217      53.303  35.211  15.063  1.00  0.00              
END
