
#######################################################
#                                                     #
#                        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   29 (  116),  selected   29 , name T0382AL381_1
# Molecule2: number of CA atoms  121 (  929),  selected   29 , name T0382.pdb
# PARAMETERS: T0382AL381_1.T0382.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:    29        87 - 118         3.06     3.06
  LCS_AVERAGE:     23.97

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15        87 - 104         1.98     4.69
  LCS_AVERAGE:     12.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12       105 - 116         0.95     7.82
  LCS_AVERAGE:      8.29

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:  121
LCS_GDT     V      87     V      87     11   15   29     4   10   12   14   17   19   24   26   26   27   28   29   29   29   29   29   29   29   29   29 
LCS_GDT     K      88     K      88     11   15   29     4   10   12   14   17   19   24   26   26   27   28   29   29   29   29   29   29   29   29   29 
LCS_GDT     A      89     A      89     11   15   29     4    6   12   14   17   19   24   26   26   27   28   29   29   29   29   29   29   29   29   29 
LCS_GDT     R      90     R      90     11   15   29     5    8   12   14   17   19   24   26   26   27   28   29   29   29   29   29   29   29   29   29 
LCS_GDT     E      91     E      91     11   15   29     5   10   12   14   17   19   24   26   26   27   28   29   29   29   29   29   29   29   29   29 
LCS_GDT     Q      92     Q      92     11   15   29     6   10   12   14   17   19   24   26   26   27   28   29   29   29   29   29   29   29   29   29 
LCS_GDT     L      93     L      93     11   15   29     6   10   12   14   17   19   24   26   26   27   28   29   29   29   29   29   29   29   29   29 
LCS_GDT     E      94     E      94     11   15   29     6   10   12   14   17   19   24   26   26   27   28   29   29   29   29   29   29   29   29   29 
LCS_GDT     A      95     A      95     11   15   29     6   10   12   14   17   19   24   26   26   27   28   29   29   29   29   29   29   29   29   29 
LCS_GDT     I      96     I      96     11   15   29     6   10   12   14   17   19   24   26   26   27   28   29   29   29   29   29   29   29   29   29 
LCS_GDT     V      97     V      97     11   15   29     6   10   12   12   17   19   24   26   26   27   28   29   29   29   29   29   29   29   29   29 
LCS_GDT     W     101     W     101      3   15   29     2    3    3    4   10   15   22   23   26   27   28   29   29   29   29   29   29   29   29   29 
LCS_GDT     F     102     F     102      3   15   29     0    3    4    6    6    8   22   23   25   26   28   29   29   29   29   29   29   29   29   29 
LCS_GDT     P     103     P     103      3   15   29     2    3    6   11   13   17   22   23   26   27   28   29   29   29   29   29   29   29   29   29 
LCS_GDT     Q     104     Q     104      3   15   29     5   10   12   14   17   19   24   26   26   27   28   29   29   29   29   29   29   29   29   29 
LCS_GDT     A     105     A     105     12   14   29     7   11   11   13   13   13   18   26   26   26   28   29   29   29   29   29   29   29   29   29 
LCS_GDT     G     106     G     106     12   14   29     7   11   12   14   17   19   24   26   26   27   28   29   29   29   29   29   29   29   29   29 
LCS_GDT     D     107     D     107     12   14   29     7   11   12   13   13   17   24   26   26   27   28   29   29   29   29   29   29   29   29   29 
LCS_GDT     A     108     A     108     12   14   29     7   11   12   13   13   13   18   26   26   27   28   29   29   29   29   29   29   29   29   29 
LCS_GDT     G     109     G     109     12   14   29     7   11   12   13   15   19   24   26   26   27   28   29   29   29   29   29   29   29   29   29 
LCS_GDT     M     110     M     110     12   14   29     7   11   12   14   17   19   24   26   26   27   28   29   29   29   29   29   29   29   29   29 
LCS_GDT     C     111     C     111     12   14   29     7   11   12   14   17   19   24   26   26   27   28   29   29   29   29   29   29   29   29   29 
LCS_GDT     L     112     L     112     12   14   29     5   11   12   13   15   19   24   26   26   27   28   29   29   29   29   29   29   29   29   29 
LCS_GDT     D     113     D     113     12   14   29     5   11   12   13   15   18   24   26   26   27   28   29   29   29   29   29   29   29   29   29 
LCS_GDT     L     114     L     114     12   14   29     5   11   12   14   17   19   24   26   26   27   28   29   29   29   29   29   29   29   29   29 
LCS_GDT     L     115     L     115     12   14   29     5   11   12   14   17   19   24   26   26   27   28   29   29   29   29   29   29   29   29   29 
LCS_GDT     D     116     D     116     12   14   29     3    8   12   13   16   19   24   26   26   27   28   29   29   29   29   29   29   29   29   29 
LCS_GDT     D     117     D     117     11   14   29     3    4   12   13   16   19   24   26   26   27   28   29   29   29   29   29   29   29   29   29 
LCS_GDT     G     118     G     118      3   14   29     0    3    3    3    3   15   24   26   26   27   28   29   29   29   29   29   29   29   29   29 
LCS_AVERAGE  LCS_A:  14.75  (   8.29   12.00   23.97 )

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      7     11     12     14     17     19     24     26     26     27     28     29     29     29     29     29     29     29     29     29 
GDT PERCENT_CA   5.79   9.09   9.92  11.57  14.05  15.70  19.83  21.49  21.49  22.31  23.14  23.97  23.97  23.97  23.97  23.97  23.97  23.97  23.97  23.97
GDT RMS_LOCAL    0.28   0.68   0.86   1.36   1.62   1.89   2.34   2.55   2.55   2.76   2.90   3.06   3.06   3.06   3.06   3.06   3.06   3.06   3.06   3.06
GDT RMS_ALL_CA   9.35   8.33   4.87   3.29   3.17   3.10   3.14   3.28   3.28   3.07   3.07   3.06   3.06   3.06   3.06   3.06   3.06   3.06   3.06   3.06

#      Molecule1      Molecule2       DISTANCE
LGA    V      87      V      87          2.452
LGA    K      88      K      88          2.117
LGA    A      89      A      89          2.746
LGA    R      90      R      90          1.316
LGA    E      91      E      91          0.941
LGA    Q      92      Q      92          1.081
LGA    L      93      L      93          1.995
LGA    E      94      E      94          2.442
LGA    A      95      A      95          1.455
LGA    I      96      I      96          1.115
LGA    V      97      V      97          3.488
LGA    W     101      W     101          7.094
LGA    F     102      F     102          7.589
LGA    P     103      P     103          6.818
LGA    Q     104      Q     104          2.866
LGA    A     105      A     105          3.960
LGA    G     106      G     106          1.350
LGA    D     107      D     107          3.466
LGA    A     108      A     108          3.908
LGA    G     109      G     109          2.888
LGA    M     110      M     110          1.471
LGA    C     111      C     111          1.585
LGA    L     112      L     112          3.322
LGA    D     113      D     113          3.393
LGA    L     114      L     114          1.521
LGA    L     115      L     115          2.157
LGA    D     116      D     116          2.954
LGA    D     117      D     117          2.705
LGA    G     118      G     118          3.437

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   29  121    4.0     26    2.55    16.529    16.132     0.980

LGA_LOCAL      RMSD =  2.553  Number of atoms =   26  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.348  Number of atoms =   29 
Std_ALL_ATOMS  RMSD =  3.058  (standard rmsd on all 29 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.417264 * X  +   0.897364 * Y  +  -0.143625 * Z  +  -7.591692
  Y_new =   0.638728 * X  +  -0.402005 * Y  +  -0.656063 * Z  +  67.291077
  Z_new =  -0.646465 * X  +   0.182014 * Y  +  -0.740914 * Z  +  -7.561561 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.900701   -0.240891  [ DEG:   166.1979    -13.8021 ]
  Theta =   0.702942    2.438651  [ DEG:    40.2756    139.7244 ]
  Phi   =   0.992124   -2.149469  [ DEG:    56.8445   -123.1555 ]
 
# 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: T0382AL381_1                                  
REMARK     2: T0382.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0382AL381_1.T0382.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   29  121   4.0   26   2.55  16.132     3.06
REMARK  ---------------------------------------------------------- 
MOLECULE T0382AL381_1
REMARK Aligment from pdb entry: 1zl8B
ATOM      1  N   VAL    87     -21.276  60.969   1.313  1.00  0.00              
ATOM      2  CA  VAL    87     -21.909  60.592   2.566  1.00  0.00              
ATOM      3  C   VAL    87     -22.083  59.074   2.637  1.00  0.00              
ATOM      4  O   VAL    87     -22.012  58.487   3.714  1.00  0.00              
ATOM      5  N   LYS    88     -22.313  58.483   1.474  1.00  0.00              
ATOM      6  CA  LYS    88     -22.501  57.044   1.391  1.00  0.00              
ATOM      7  C   LYS    88     -21.283  56.315   1.962  1.00  0.00              
ATOM      8  O   LYS    88     -21.392  55.179   2.417  1.00  0.00              
ATOM      9  N   ALA    89     -20.150  57.001   1.917  1.00  0.00              
ATOM     10  CA  ALA    89     -18.912  56.434   2.425  1.00  0.00              
ATOM     11  C   ALA    89     -19.052  56.176   3.926  1.00  0.00              
ATOM     12  O   ALA    89     -18.952  55.034   4.375  1.00  0.00              
ATOM     13  N   ARG    90     -19.281  57.253   4.662  1.00  0.00              
ATOM     14  CA  ARG    90     -19.437  57.157   6.103  1.00  0.00              
ATOM     15  C   ARG    90     -20.830  56.615   6.426  1.00  0.00              
ATOM     16  O   ARG    90     -21.063  56.108   7.521  1.00  0.00              
ATOM     17  N   GLU    91     -21.721  56.742   5.453  1.00  0.00              
ATOM     18  CA  GLU    91     -23.084  56.270   5.618  1.00  0.00              
ATOM     19  C   GLU    91     -23.091  54.868   6.233  1.00  0.00              
ATOM     20  O   GLU    91     -23.964  54.543   7.036  1.00  0.00              
ATOM     21  N   GLN    92     -22.110  54.076   5.829  1.00  0.00              
ATOM     22  CA  GLN    92     -21.992  52.717   6.328  1.00  0.00              
ATOM     23  C   GLN    92     -21.845  52.749   7.851  1.00  0.00              
ATOM     24  O   GLN    92     -22.316  51.848   8.542  1.00  0.00              
ATOM     25  N   LEU    93     -21.190  53.797   8.328  1.00  0.00              
ATOM     26  CA  LEU    93     -20.975  53.959   9.757  1.00  0.00              
ATOM     27  C   LEU    93     -22.322  54.182  10.448  1.00  0.00              
ATOM     28  O   LEU    93     -22.502  53.800  11.603  1.00  0.00              
ATOM     29  N   GLU    94     -23.234  54.801   9.711  1.00  0.00              
ATOM     30  CA  GLU    94     -24.559  55.079  10.240  1.00  0.00              
ATOM     31  C   GLU    94     -25.254  53.777  10.644  1.00  0.00              
ATOM     32  O   GLU    94     -25.993  53.744  11.627  1.00  0.00              
ATOM     33  N   ALA    95     -24.992  52.738   9.865  1.00  0.00              
ATOM     34  CA  ALA    95     -25.583  51.436  10.130  1.00  0.00              
ATOM     35  C   ALA    95     -24.783  50.699  11.204  1.00  0.00              
ATOM     36  O   ALA    95     -25.336  49.893  11.951  1.00  0.00              
ATOM     37  N   ILE    96     -23.493  50.998  11.246  1.00  0.00              
ATOM     38  CA  ILE    96     -22.610  50.373  12.216  1.00  0.00              
ATOM     39  C   ILE    96     -22.952  50.885  13.616  1.00  0.00              
ATOM     40  O   ILE    96     -22.497  50.328  14.614  1.00  0.00              
ATOM     41  N   VAL    97     -23.752  51.942  13.645  1.00  0.00              
ATOM     42  CA  VAL    97     -24.161  52.535  14.907  1.00  0.00              
ATOM     43  C   VAL    97     -24.897  51.500  15.759  1.00  0.00              
ATOM     44  O   VAL    97     -24.899  51.588  16.986  1.00  0.00              
ATOM     45  N   TRP   101     -25.504  50.541  15.075  1.00  0.00              
ATOM     46  CA  TRP   101     -26.242  49.489  15.752  1.00  0.00              
ATOM     47  C   TRP   101     -25.302  48.302  15.962  1.00  0.00              
ATOM     48  O   TRP   101     -25.355  47.637  16.996  1.00  0.00              
ATOM     49  N   PHE   102     -24.463  48.067  14.963  1.00  0.00              
ATOM     50  CA  PHE   102     -23.513  46.971  15.023  1.00  0.00              
ATOM     51  C   PHE   102     -22.272  47.364  15.827  1.00  0.00              
ATOM     52  O   PHE   102     -21.545  48.278  15.445  1.00  0.00              
ATOM     53  N   PRO   103     -22.062  46.634  16.955  1.00  0.00              
ATOM     54  CA  PRO   103     -20.921  46.897  17.816  1.00  0.00              
ATOM     55  C   PRO   103     -19.630  46.367  17.191  1.00  0.00              
ATOM     56  O   PRO   103     -19.308  45.187  17.326  1.00  0.00              
ATOM     57  N   GLN   104     -18.924  47.266  16.521  1.00  0.00              
ATOM     58  CA  GLN   104     -17.672  46.905  15.874  1.00  0.00              
ATOM     59  C   GLN   104     -16.492  47.558  16.597  1.00  0.00              
ATOM     60  O   GLN   104     -16.681  48.266  17.584  1.00  0.00              
ATOM     61  N   ALA   105     -15.303  47.297  16.077  1.00  0.00              
ATOM     62  CA  ALA   105     -14.094  47.851  16.660  1.00  0.00              
ATOM     63  C   ALA   105     -14.152  49.378  16.589  1.00  0.00              
ATOM     64  O   ALA   105     -14.157  49.952  15.500  1.00  0.00              
ATOM     65  N   GLY   106     -14.191  49.993  17.760  1.00  0.00              
ATOM     66  CA  GLY   106     -14.248  51.442  17.846  1.00  0.00              
ATOM     67  C   GLY   106     -13.128  52.042  16.994  1.00  0.00              
ATOM     68  O   GLY   106     -13.242  53.172  16.519  1.00  0.00              
ATOM     69  N   ASP   107     -12.073  51.260  16.823  1.00  0.00              
ATOM     70  CA  ASP   107     -10.934  51.700  16.036  1.00  0.00              
ATOM     71  C   ASP   107     -11.278  51.599  14.548  1.00  0.00              
ATOM     72  O   ASP   107     -11.057  52.544  13.790  1.00  0.00              
ATOM     73  N   ALA   108     -11.811  50.446  14.174  1.00  0.00              
ATOM     74  CA  ALA   108     -12.188  50.209  12.791  1.00  0.00              
ATOM     75  C   ALA   108     -13.223  51.251  12.364  1.00  0.00              
ATOM     76  O   ALA   108     -13.035  51.944  11.365  1.00  0.00              
ATOM     77  N   GLY   109     -14.295  51.328  13.139  1.00  0.00              
ATOM     78  CA  GLY   109     -15.359  52.273  12.854  1.00  0.00              
ATOM     79  C   GLY   109     -14.788  53.693  12.851  1.00  0.00              
ATOM     80  O   GLY   109     -15.293  54.568  12.148  1.00  0.00              
ATOM     81  N   MET   110     -13.743  53.878  13.645  1.00  0.00              
ATOM     82  CA  MET   110     -13.098  55.176  13.741  1.00  0.00              
ATOM     83  C   MET   110     -12.299  55.469  12.470  1.00  0.00              
ATOM     84  O   MET   110     -12.090  56.628  12.117  1.00  0.00              
ATOM     85  N   CYS   111     -11.876  54.398  11.815  1.00  0.00              
ATOM     86  CA  CYS   111     -11.105  54.525  10.590  1.00  0.00              
ATOM     87  C   CYS   111     -11.965  55.205   9.522  1.00  0.00              
ATOM     88  O   CYS   111     -11.480  56.065   8.786  1.00  0.00              
ATOM     89  N   LEU   112     -13.222  54.794   9.467  1.00  0.00              
ATOM     90  CA  LEU   112     -14.152  55.351   8.500  1.00  0.00              
ATOM     91  C   LEU   112     -14.463  56.802   8.877  1.00  0.00              
ATOM     92  O   LEU   112     -14.680  57.641   8.004  1.00  0.00              
ATOM     93  N   ASP   113     -14.473  57.052  10.179  1.00  0.00              
ATOM     94  CA  ASP   113     -14.754  58.386  10.680  1.00  0.00              
ATOM     95  C   ASP   113     -13.563  59.312  10.421  1.00  0.00              
ATOM     96  O   ASP   113     -13.730  60.411   9.897  1.00  0.00              
ATOM     97  N   LEU   114     -12.388  58.833  10.802  1.00  0.00              
ATOM     98  CA  LEU   114     -11.170  59.604  10.619  1.00  0.00              
ATOM     99  C   LEU   114     -10.927  59.814   9.122  1.00  0.00              
ATOM    100  O   LEU   114     -10.174  60.705   8.731  1.00  0.00              
ATOM    101  N   LEU   115     -11.576  58.976   8.326  1.00  0.00              
ATOM    102  CA  LEU   115     -11.438  59.060   6.882  1.00  0.00              
ATOM    103  C   LEU   115     -12.097  60.350   6.385  1.00  0.00              
ATOM    104  O   LEU   115     -11.964  60.705   5.214  1.00  0.00              
ATOM    105  N   ASP   116     -12.789  61.012   7.298  1.00  0.00              
ATOM    106  CA  ASP   116     -13.467  62.253   6.966  1.00  0.00              
ATOM    107  C   ASP   116     -12.743  63.443   7.601  1.00  0.00              
ATOM    108  O   ASP   116     -13.111  63.892   8.685  1.00  0.00              
ATOM    109  N   ASP   117     -11.726  63.919   6.897  1.00  0.00              
ATOM    110  CA  ASP   117     -10.948  65.048   7.378  1.00  0.00              
ATOM    111  C   ASP   117     -11.118  66.248   6.444  1.00  0.00              
ATOM    112  O   ASP   117     -11.829  66.163   5.442  1.00  0.00              
ATOM    113  N   GLY   118     -10.438  67.365   6.813  1.00  0.00              
ATOM    114  CA  GLY   118     -10.507  68.581   6.021  1.00  0.00              
ATOM    115  C   GLY   118      -9.670  68.452   4.746  1.00  0.00              
ATOM    116  O   GLY   118      -9.609  69.382   3.943  1.00  0.00              
END
