
#######################################################
#                                                     #
#                        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   31 (  124),  selected   31 , name T0299AL381_4-D2
# Molecule2: number of CA atoms   89 (  757),  selected   31 , name T0299_D2.pdb
# PARAMETERS: T0299AL381_4-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:    17        98 - 114         4.80    14.73
  LCS_AVERAGE:     16.85

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12        98 - 109         1.98    15.36
  LCS_AVERAGE:     11.53

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11        79 - 89          0.53    23.71
  LCS_AVERAGE:      8.66

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   12   13   15   15   17   18   19   19   20   22   22   23   23 
LCS_GDT     E      80     E      80     11   11   12     8   11   11   11   11   11   11   12   13   15   15   17   18   19   19   20   22   22   23   25 
LCS_GDT     D      81     D      81     11   11   12     8   11   11   11   11   11   11   11   13   15   15   17   18   19   19   20   22   22   23   25 
LCS_GDT     F      82     F      82     11   11   12     8   11   11   11   11   11   11   12   13   15   15   17   18   19   19   20   22   22   23   25 
LCS_GDT     E      83     E      83     11   11   12     8   11   11   11   11   11   11   12   13   14   15   17   18   19   19   20   22   22   23   25 
LCS_GDT     A      84     A      84     11   11   12     8   11   11   11   11   11   11   11   11   14   15   17   18   19   19   20   22   22   23   25 
LCS_GDT     E      85     E      85     11   11   12     8   11   11   11   11   11   11   11   11   13   14   17   18   19   19   20   22   22   23   25 
LCS_GDT     L      86     L      86     11   11   12     8   11   11   11   11   11   11   11   11   13   14   17   18   19   19   20   22   22   23   25 
LCS_GDT     E      87     E      87     11   11   12     6   11   11   11   11   11   11   11   11   13   13   16   16   19   19   20   22   22   23   25 
LCS_GDT     N      88     N      88     11   11   13     5   11   11   11   11   11   11   11   11   11   14   17   18   18   19   20   20   22   23   25 
LCS_GDT     L      89     L      89     11   11   13     5   11   11   11   11   11   11   11   11   13   14   17   18   19   19   20   20   22   22   25 
LCS_GDT     A      98     A      98      8   12   17     3    4    8    9   10   11   13   13   14   14   15   15   15   16   18   18   18   18   19   21 
LCS_GDT     R      99     R      99      8   12   17     4    7    8    9   10   11   13   13   14   14   15   15   15   16   18   18   20   21   21   22 
LCS_GDT     K     100     K     100      8   12   17     4    7    8    9   10   11   13   13   14   14   15   17   18   19   19   20   20   22   22   24 
LCS_GDT     D     101     D     101      8   12   17     4    7    8    9   10   11   13   13   14   14   15   17   18   19   19   20   20   22   22   25 
LCS_GDT     F     102     F     102      8   12   17     4    7    8    9   10   11   13   13   14   14   15   17   18   19   19   20   20   22   23   25 
LCS_GDT     L     103     L     103      8   12   17     4    7    8    9   10   11   13   13   14   14   15   17   18   19   19   20   21   22   23   25 
LCS_GDT     F     104     F     104      8   12   17     4    7    8    9   10   11   13   13   14   14   15   17   18   19   19   20   22   22   23   25 
LCS_GDT     Y     105     Y     105      8   12   17     4    5    8    9   10   11   13   13   14   14   15   17   18   19   19   20   22   22   23   25 
LCS_GDT     T     106     T     106      8   12   17     4    7    8    9   10   11   13   13   14   15   15   17   18   19   19   20   22   22   23   25 
LCS_GDT     E     107     E     107      5   12   17     4    5    5    8   10   11   13   13   14   15   15   17   18   19   19   20   22   22   23   25 
LCS_GDT     G     108     G     108      5   12   17     4    5    8    9   10   11   13   13   14   14   15   17   18   19   19   20   22   22   23   24 
LCS_GDT     L     109     L     109      4   12   17     4    4    5    6    6    7   13   13   14   15   15   17   18   19   19   20   22   22   23   25 
LCS_GDT     D     110     D     110      4    7   17     4    4    4    6    8   11   13   13   14   15   15   17   18   19   19   20   22   22   23   25 
LCS_GDT     V     111     V     111      4    7   17     4    4    5    6    6    8    9   12   14   15   15   17   18   19   19   20   22   22   23   25 
LCS_GDT     D     112     D     112      4    7   17     4    4    6    6    6    8    9   12   13   15   15   17   18   19   19   20   22   22   23   25 
LCS_GDT     Q     113     Q     113      4    7   17     4    4    6    6    6    7    9   12   13   15   15   17   18   19   19   20   22   22   23   25 
LCS_GDT     V     114     V     114      4    7   17     4    4    6    6    6    7    9   12   13   15   15   17   18   19   19   20   22   22   23   24 
LCS_GDT     I     115     I     115      4    6   14     4    4    6    6    6    8    9   12   13   15   15   17   18   19   19   20   22   22   23   25 
LCS_GDT     A     116     A     116      4    6   14     4    4    6    6    6    8    9   12   13   15   15   17   18   19   19   20   22   22   23   25 
LCS_GDT     T     117     T     117      4    6   14     4    4    6    6    6    8    9   12   13   15   15   17   18   19   19   20   22   22   23   25 
LCS_AVERAGE  LCS_A:  12.35  (   8.66   11.53   16.85 )

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     14     15     15     17     18     19     19     20     22     22     23     25 
GDT PERCENT_CA   8.99  12.36  12.36  12.36  12.36  12.36  14.61  14.61  15.73  16.85  16.85  19.10  20.22  21.35  21.35  22.47  24.72  24.72  25.84  28.09
GDT RMS_LOCAL    0.17   0.53   0.53   0.53   0.53   0.53   2.13   2.13   2.67   3.41   3.41   3.94   4.08   4.32   4.32   4.96   5.33   5.33   5.67   7.05
GDT RMS_ALL_CA  23.35  23.71  23.71  23.71  23.71  23.71  15.66  15.66  15.09  14.33  14.33  12.93  13.16  13.37  13.37  11.63  11.99  11.99  11.63   9.50

#      Molecule1      Molecule2       DISTANCE
LGA    L      79      L      79         22.745
LGA    E      80      E      80         25.233
LGA    D      81      D      81         24.889
LGA    F      82      F      82         21.602
LGA    E      83      E      83         22.142
LGA    A      84      A      84         24.730
LGA    E      85      E      85         23.186
LGA    L      86      L      86         20.928
LGA    E      87      E      87         22.331
LGA    N      88      N      88         23.292
LGA    L      89      L      89         20.705
LGA    A      98      A      98          1.215
LGA    R      99      R      99          1.336
LGA    K     100      K     100          2.214
LGA    D     101      D     101          1.522
LGA    F     102      F     102          1.546
LGA    L     103      L     103          1.643
LGA    F     104      F     104          1.859
LGA    Y     105      Y     105          2.688
LGA    T     106      T     106          1.066
LGA    E     107      E     107          2.823
LGA    G     108      G     108          1.774
LGA    L     109      L     109          3.815
LGA    D     110      D     110          3.599
LGA    V     111      V     111          5.789
LGA    D     112      D     112          8.008
LGA    Q     113      Q     113         10.465
LGA    V     114      V     114         14.491
LGA    I     115      I     115         13.760
LGA    A     116      A     116         15.648
LGA    T     117      T     117         18.727

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   31   89    4.0     13    2.13    15.449    14.354     0.583

LGA_LOCAL      RMSD =  2.131  Number of atoms =   13  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 15.086  Number of atoms =   31 
Std_ALL_ATOMS  RMSD =  9.022  (standard rmsd on all 31 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.307566 * X  +   0.007675 * Y  +   0.951496 * Z  +   5.950820
  Y_new =  -0.581110 * X  +   0.790311 * Y  +  -0.194216 * Z  +  28.452877
  Z_new =  -0.753468 * X  +  -0.612658 * Y  +  -0.238613 * Z  + 102.319725 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.942194    1.199399  [ DEG:  -111.2795     68.7205 ]
  Theta =   0.853321    2.288271  [ DEG:    48.8917    131.1083 ]
  Phi   =  -2.057588    1.084005  [ DEG:  -117.8911     62.1089 ]
 
# 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_4-D2                               
REMARK     2: T0299_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0299AL381_4-D2.T0299_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   31   89   4.0   13   2.13  14.354     9.02
REMARK  ---------------------------------------------------------- 
MOLECULE T0299AL381_4-D2
REMARK Aligment from pdb entry: 1z5oA
ATOM    185  N   LEU    79      11.800  53.066   0.832  1.00  0.00              
ATOM    186  CA  LEU    79      11.348  53.754  -0.364  1.00  0.00              
ATOM    187  C   LEU    79      12.363  54.636  -1.077  1.00  0.00              
ATOM    188  O   LEU    79      12.600  54.440  -2.266  1.00  0.00              
ATOM    189  N   GLU    80      12.956  55.608  -0.382  1.00  0.00              
ATOM    190  CA  GLU    80      13.907  56.500  -1.047  1.00  0.00              
ATOM    191  C   GLU    80      15.162  55.800  -1.596  1.00  0.00              
ATOM    192  O   GLU    80      15.743  56.266  -2.558  1.00  0.00              
ATOM    193  N   ASP    81      15.580  54.693  -0.980  1.00  0.00              
ATOM    194  CA  ASP    81      16.755  53.955  -1.452  1.00  0.00              
ATOM    195  C   ASP    81      16.382  53.245  -2.757  1.00  0.00              
ATOM    196  O   ASP    81      17.179  53.181  -3.703  1.00  0.00              
ATOM    197  N   PHE    82      15.152  52.737  -2.800  1.00  0.00              
ATOM    198  CA  PHE    82      14.633  52.057  -3.974  1.00  0.00              
ATOM    199  C   PHE    82      14.452  53.073  -5.114  1.00  0.00              
ATOM    200  O   PHE    82      14.819  52.810  -6.267  1.00  0.00              
ATOM    201  N   GLU    83      13.885  54.231  -4.791  1.00  0.00              
ATOM    202  CA  GLU    83      13.681  55.278  -5.787  1.00  0.00              
ATOM    203  C   GLU    83      15.039  55.769  -6.308  1.00  0.00              
ATOM    204  O   GLU    83      15.178  56.069  -7.483  1.00  0.00              
ATOM    205  N   ALA    84      16.032  55.830  -5.426  1.00  0.00              
ATOM    206  CA  ALA    84      17.388  56.290  -5.759  1.00  0.00              
ATOM    207  C   ALA    84      18.004  55.317  -6.773  1.00  0.00              
ATOM    208  O   ALA    84      18.518  55.714  -7.826  1.00  0.00              
ATOM    209  N   GLU    85      17.929  54.032  -6.466  1.00  0.00              
ATOM    210  CA  GLU    85      18.449  53.027  -7.377  1.00  0.00              
ATOM    211  C   GLU    85      17.703  53.110  -8.719  1.00  0.00              
ATOM    212  O   GLU    85      18.330  53.109  -9.768  1.00  0.00              
ATOM    213  N   LEU    86      16.370  53.192  -8.673  1.00  0.00              
ATOM    214  CA  LEU    86      15.551  53.255  -9.888  1.00  0.00              
ATOM    215  C   LEU    86      15.893  54.458 -10.746  1.00  0.00              
ATOM    216  O   LEU    86      15.927  54.370 -11.975  1.00  0.00              
ATOM    217  N   GLU    87      16.127  55.585 -10.088  1.00  0.00              
ATOM    218  CA  GLU    87      16.495  56.826 -10.759  1.00  0.00              
ATOM    219  C   GLU    87      17.794  56.618 -11.545  1.00  0.00              
ATOM    220  O   GLU    87      17.904  57.013 -12.705  1.00  0.00              
ATOM    221  N   ASN    88      18.774  55.983 -10.905  1.00  0.00              
ATOM    222  CA  ASN    88      20.061  55.756 -11.552  1.00  0.00              
ATOM    223  C   ASN    88      20.007  54.805 -12.743  1.00  0.00              
ATOM    224  O   ASN    88      20.907  54.813 -13.582  1.00  0.00              
ATOM    225  N   LEU    89      18.953  53.999 -12.813  1.00  0.00              
ATOM    226  CA  LEU    89      18.771  53.048 -13.906  1.00  0.00              
ATOM    227  C   LEU    89      17.620  53.464 -14.812  1.00  0.00              
ATOM    228  O   LEU    89      17.263  52.760 -15.763  1.00  0.00              
ATOM    229  N   ALA    98      17.028  54.607 -14.495  1.00  0.00              
ATOM    230  CA  ALA    98      15.917  55.130 -15.262  1.00  0.00              
ATOM    231  C   ALA    98      14.718  54.189 -15.323  1.00  0.00              
ATOM    232  O   ALA    98      14.152  53.964 -16.397  1.00  0.00              
ATOM    233  N   ARG    99      14.351  53.633 -14.171  1.00  0.00              
ATOM    234  CA  ARG    99      13.202  52.733 -14.069  1.00  0.00              
ATOM    235  C   ARG    99      12.072  53.428 -13.290  1.00  0.00              
ATOM    236  O   ARG    99      12.293  53.969 -12.192  1.00  0.00              
ATOM    237  N   LYS   100      10.855  53.454 -13.859  1.00  0.00              
ATOM    238  CA  LYS   100       9.709  54.084 -13.192  1.00  0.00              
ATOM    239  C   LYS   100       9.405  53.323 -11.901  1.00  0.00              
ATOM    240  O   LYS   100       9.473  52.083 -11.888  1.00  0.00              
ATOM    241  N   ASP   101       9.060  54.056 -10.840  1.00  0.00              
ATOM    242  CA  ASP   101       8.728  53.451  -9.551  1.00  0.00              
ATOM    243  C   ASP   101       7.576  54.200  -8.898  1.00  0.00              
ATOM    244  O   ASP   101       7.289  55.350  -9.231  1.00  0.00              
ATOM    245  N   PHE   102       6.938  53.543  -7.940  1.00  0.00              
ATOM    246  CA  PHE   102       5.866  54.150  -7.175  1.00  0.00              
ATOM    247  C   PHE   102       5.835  53.384  -5.852  1.00  0.00              
ATOM    248  O   PHE   102       6.087  52.179  -5.819  1.00  0.00              
ATOM    249  N   LEU   103       5.566  54.102  -4.767  1.00  0.00              
ATOM    250  CA  LEU   103       5.476  53.510  -3.445  1.00  0.00              
ATOM    251  C   LEU   103       3.987  53.417  -3.113  1.00  0.00              
ATOM    252  O   LEU   103       3.261  54.403  -3.236  1.00  0.00              
ATOM    253  N   PHE   104       3.531  52.223  -2.739  1.00  0.00              
ATOM    254  CA  PHE   104       2.138  52.018  -2.347  1.00  0.00              
ATOM    255  C   PHE   104       2.166  51.178  -1.074  1.00  0.00              
ATOM    256  O   PHE   104       2.193  49.947  -1.126  1.00  0.00              
ATOM    257  N   TYR   105       2.187  51.849   0.067  1.00  0.00              
ATOM    258  CA  TYR   105       2.226  51.168   1.359  1.00  0.00              
ATOM    259  C   TYR   105       0.950  51.473   2.148  1.00  0.00              
ATOM    260  O   TYR   105       0.139  52.312   1.744  1.00  0.00              
ATOM    261  N   THR   106       0.780  50.780   3.272  1.00  0.00              
ATOM    262  CA  THR   106      -0.378  50.986   4.137  1.00  0.00              
ATOM    263  C   THR   106       0.129  51.377   5.520  1.00  0.00              
ATOM    264  O   THR   106       1.235  51.006   5.905  1.00  0.00              
ATOM    265  N   GLU   107      -0.697  52.109   6.260  1.00  0.00              
ATOM    266  CA  GLU   107      -0.370  52.609   7.594  1.00  0.00              
ATOM    267  C   GLU   107      -0.537  51.575   8.729  1.00  0.00              
ATOM    268  O   GLU   107      -1.594  50.957   8.877  1.00  0.00              
ATOM    269  N   GLY   108       0.508  51.406   9.540  1.00  0.00              
ATOM    270  CA  GLY   108       0.472  50.470  10.664  1.00  0.00              
ATOM    271  C   GLY   108       0.728  51.187  11.987  1.00  0.00              
ATOM    272  O   GLY   108       0.692  50.571  13.046  1.00  0.00              
ATOM    273  N   LEU   109       0.984  52.493  11.916  1.00  0.00              
ATOM    274  CA  LEU   109       1.249  53.309  13.098  1.00  0.00              
ATOM    275  C   LEU   109       1.375  54.759  12.646  1.00  0.00              
ATOM    276  O   LEU   109       1.402  55.020  11.444  1.00  0.00              
ATOM    277  N   ASP   110       1.443  55.691  13.601  1.00  0.00              
ATOM    278  CA  ASP   110       1.581  57.106  13.272  1.00  0.00              
ATOM    279  C   ASP   110       2.897  57.684  13.763  1.00  0.00              
ATOM    280  O   ASP   110       2.999  58.855  14.130  1.00  0.00              
ATOM    281  N   VAL   111       3.908  56.830  13.776  1.00  0.00              
ATOM    282  CA  VAL   111       5.257  57.232  14.136  1.00  0.00              
ATOM    283  C   VAL   111       5.427  58.002  15.432  1.00  0.00              
ATOM    284  O   VAL   111       6.407  58.728  15.576  1.00  0.00              
ATOM    285  N   ASP   112       4.487  57.865  16.367  1.00  0.00              
ATOM    286  CA  ASP   112       4.607  58.563  17.655  1.00  0.00              
ATOM    287  C   ASP   112       5.131  57.579  18.711  1.00  0.00              
ATOM    288  O   ASP   112       5.577  56.478  18.366  1.00  0.00              
ATOM    289  N   GLN   113       5.064  57.950  19.988  1.00  0.00              
ATOM    290  CA  GLN   113       5.582  57.074  21.032  1.00  0.00              
ATOM    291  C   GLN   113       4.867  55.727  21.155  1.00  0.00              
ATOM    292  O   GLN   113       5.373  54.823  21.799  1.00  0.00              
ATOM    293  N   VAL   114       3.709  55.596  20.523  1.00  0.00              
ATOM    294  CA  VAL   114       2.944  54.351  20.539  1.00  0.00              
ATOM    295  C   VAL   114       3.224  53.551  19.266  1.00  0.00              
ATOM    296  O   VAL   114       2.641  52.489  19.053  1.00  0.00              
ATOM    297  N   ILE   115       4.123  54.055  18.423  1.00  0.00              
ATOM    298  CA  ILE   115       4.405  53.395  17.150  1.00  0.00              
ATOM    299  C   ILE   115       4.785  51.911  17.211  1.00  0.00              
ATOM    300  O   ILE   115       4.342  51.140  16.363  1.00  0.00              
ATOM    301  N   ALA   116       5.596  51.501  18.184  1.00  0.00              
ATOM    302  CA  ALA   116       5.975  50.089  18.280  1.00  0.00              
ATOM    303  C   ALA   116       4.755  49.227  18.682  1.00  0.00              
ATOM    304  O   ALA   116       4.497  48.181  18.085  1.00  0.00              
ATOM    305  N   THR   117       4.012  49.667  19.692  1.00  0.00              
ATOM    306  CA  THR   117       2.802  48.954  20.105  1.00  0.00              
ATOM    307  C   THR   117       1.867  48.808  18.893  1.00  0.00              
ATOM    308  O   THR   117       1.357  47.720  18.605  1.00  0.00              
END
