
#######################################################
#                                                     #
#                        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 T0372AL044_1-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected   33 , name T0372_D1.pdb
# PARAMETERS: T0372AL044_1-D1.T0372_D1.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:    24        74 - 104         4.68    12.13
  LCS_AVERAGE:     16.26

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8        88 - 95          1.51    13.22
  LCS_AVERAGE:      4.62

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        90 - 94          0.92    13.12
  LONGEST_CONTINUOUS_SEGMENT:     5        91 - 95          0.59    13.56
  LCS_AVERAGE:      2.81

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:  126
LCS_GDT     K      74     K      74      0    0   24     0    3    3    6    8   10   12   15   18   19   20   20   23   23   23   23   24   24   24   24 
LCS_GDT     R      78     R      78      0    0   24     0    0    0    0    0    0    4    5    8    8   14   17   23   23   23   23   24   24   24   24 
LCS_GDT     K      79     K      79      4    7   24     4    4    6    8   11   13   14   17   18   19   20   20   23   23   23   23   24   24   24   24 
LCS_GDT     L      80     L      80      4    7   24     4    4    6    7   11   13   14   17   18   19   20   20   23   23   23   23   24   24   24   25 
LCS_GDT     I      81     I      81      4    7   24     4    4    4    5   10   13   14   17   18   19   20   20   23   23   23   23   24   24   24   25 
LCS_GDT     E      82     E      82      4    7   24     4    4    4    8   11   13   14   17   18   19   20   20   23   23   23   23   24   24   24   25 
LCS_GDT     D      83     D      83      4    7   24     3    3    4    5    9   11   12   15   18   19   20   20   23   23   23   23   24   24   24   25 
LCS_GDT     A      84     A      84      4    7   24     3    3    4    5    7    8    9   10   14   19   19   20   23   23   23   23   24   24   24   25 
LCS_GDT     D      85     D      85      4    7   24     3    4    4    5    7    9   13   17   18   19   20   20   23   23   23   23   24   24   24   25 
LCS_GDT     K      86     K      86      4    7   24     3    4    4    5    6   12   14   17   18   19   20   20   23   23   23   23   24   24   24   25 
LCS_GDT     E      87     E      87      4    7   24     3    4    4    5    6   12   14   17   18   19   20   20   23   23   23   23   24   24   24   25 
LCS_GDT     K      88     K      88      4    8   24     3    4    6    8   11   13   14   17   18   19   20   20   23   23   23   23   24   24   24   25 
LCS_GDT     H      89     H      89      4    8   24     3    4    6    8   11   13   14   17   18   19   20   20   23   23   23   23   24   24   24   25 
LCS_GDT     N      90     N      90      5    8   24     3    4    6    8   11   13   14   17   18   19   20   20   23   23   23   23   24   24   24   25 
LCS_GDT     F      91     F      91      5    8   24     4    5    6    8   11   13   14   17   18   19   20   20   23   23   23   23   24   24   24   25 
LCS_GDT     C      92     C      92      5    8   24     4    5    6    8   11   13   14   17   18   19   20   20   23   23   23   23   24   24   24   25 
LCS_GDT     M      93     M      93      5    8   24     4    5    6    8   11   13   14   17   18   19   20   20   23   23   23   23   24   24   24   25 
LCS_GDT     L      94     L      94      5    8   24     4    5    6    7   11   13   14   17   18   19   20   20   23   23   23   23   24   24   24   24 
LCS_GDT     G      95     G      95      5    8   24     3    5    6    7   11   13   14   17   18   19   20   20   23   23   23   23   24   24   24   25 
LCS_GDT     V      96     V      96      4    6   24     2    4    4    5    7    9   14   17   18   19   20   20   23   23   23   23   24   24   24   25 
LCS_GDT     C      97     C      97      4    6   24     0    4    4    5    7   13   14   17   18   19   20   20   23   23   23   23   24   24   24   25 
LCS_GDT     M     100     M     100      4    6   24     1    4    4    5    6    7    9   11   14   17   20   20   23   23   23   23   24   24   24   25 
LCS_GDT     R     101     R     101      4    6   24     2    4    4    5    6    8    9   11   13   15   18   20   23   23   23   23   24   24   24   25 
LCS_GDT     L     104     L     104      3    5   24     0    3    3    4    5    7    9   11   12   15   16   17   18   20   21   23   24   24   24   25 
LCS_GDT     A     106     A     106      3    4   16     0    3    3    3    4    5    7    7   12   15   16   17   18   18   18   20   21   22   23   25 
LCS_GDT     I     107     I     107      3    4   16     0    3    3    3    4    5    6    7    9   10   11   11   18   18   18   20   21   21   23   25 
LCS_GDT     L     108     L     108      3    3   16     0    3    3    3    4    5    6    7    8   12   13   16   18   18   18   20   21   22   23   25 
LCS_GDT     P     109     P     109      3    5   10     0    3    3    4    5    5    5    5    7    8   10   10   11   13   14   17   18   21   23   23 
LCS_GDT     E     110     E     110      3    5   10     0    3    3    4    5    5    5    5    7    8   10   10   11   13   14   17   18   21   23   25 
LCS_GDT     R     111     R     111      3    5    8     0    3    3    4    5    5    5    5    7    8   10   10   11   13   14   17   17   20   23   25 
LCS_GDT     F     112     F     112      3    5    8     2    3    3    4    5    5    5    5    5    5   10   10   11   11   13   17   17   19   23   23 
LCS_GDT     I     113     I     113      3    5    8     2    3    3    3    5    5    5    5    7    8   10   10   11   13   14   17   17   21   23   23 
LCS_GDT     D     117     D     117      0    0    8     0    0    0    0    0    0    0    0    0    0    0    0    5    9   12   17   17   21   23   23 
LCS_AVERAGE  LCS_A:   7.90  (   2.81    4.62   16.26 )

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      5      6      8     11     13     14     17     18     19     20     20     23     23     23     23     24     24     24     25 
GDT PERCENT_CA   3.17   3.97   4.76   6.35   8.73  10.32  11.11  13.49  14.29  15.08  15.87  15.87  18.25  18.25  18.25  18.25  19.05  19.05  19.05  19.84
GDT RMS_LOCAL    0.18   0.59   1.00   1.31   1.79   2.13   2.25   2.71   2.90   3.17   3.46   3.40   4.16   4.16   4.16   4.16   4.68   4.68   4.68   7.82
GDT RMS_ALL_CA  16.29  13.56  11.80  12.13  12.87  12.78  12.70  12.57  12.62  12.54  12.40  12.54  12.31  12.31  12.31  12.31  12.13  12.13  12.13  10.56

#      Molecule1      Molecule2       DISTANCE
LGA    K      74      K      74          7.633
LGA    R      78      R      78          8.687
LGA    K      79      K      79          3.444
LGA    L      80      L      80          1.505
LGA    I      81      I      81          2.320
LGA    E      82      E      82          2.170
LGA    D      83      D      83          4.705
LGA    A      84      A      84          5.913
LGA    D      85      D      85          3.911
LGA    K      86      K      86          3.444
LGA    E      87      E      87          3.805
LGA    K      88      K      88          1.976
LGA    H      89      H      89          1.593
LGA    N      90      N      90          1.977
LGA    F      91      F      91          2.960
LGA    C      92      C      92          2.186
LGA    M      93      M      93          1.102
LGA    L      94      L      94          2.650
LGA    G      95      G      95          2.574
LGA    V      96      V      96          3.949
LGA    C      97      C      97          3.306
LGA    M     100      M     100          8.847
LGA    R     101      R     101         11.197
LGA    L     104      L     104         15.307
LGA    A     106      A     106         18.870
LGA    I     107      I     107         20.079
LGA    L     108      L     108         17.582
LGA    P     109      P     109         21.650
LGA    E     110      E     110         22.373
LGA    R     111      R     111         21.463
LGA    F     112      F     112         22.691
LGA    I     113      I     113         25.693
LGA    D     117      D     117         28.734

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   33  126    4.0     17    2.71    10.516     9.617     0.604

LGA_LOCAL      RMSD =  2.714  Number of atoms =   17  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 12.624  Number of atoms =   33 
Std_ALL_ATOMS  RMSD =  9.589  (standard rmsd on all 33 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.179437 * X  +   0.770283 * Y  +   0.611936 * Z  +  29.796120
  Y_new =  -0.688170 * X  +  -0.542791 * Y  +   0.481456 * Z  +  50.476906
  Z_new =   0.703011 * X  +  -0.334725 * Y  +   0.627482 * Z  + -28.384098 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.490042    2.651551  [ DEG:   -28.0773    151.9227 ]
  Theta =  -0.779623   -2.361969  [ DEG:   -44.6691   -135.3309 ]
  Phi   =  -1.825862    1.315731  [ DEG:  -104.6142     75.3858 ]
 
# 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: T0372AL044_1-D1                               
REMARK     2: T0372_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0372AL044_1-D1.T0372_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   33  126   4.0   17   2.71   9.617     9.59
REMARK  ---------------------------------------------------------- 
MOLECULE T0372AL044_1-D1
REMARK Aligment from pdb entry: 2go8_A
ATOM      1  N   LYS    74      33.899  60.630   1.162  1.00  0.00              
ATOM      2  CA  LYS    74      32.460  60.799   1.303  1.00  0.00              
ATOM      3  C   LYS    74      31.954  61.053  -0.096  1.00  0.00              
ATOM      4  O   LYS    74      31.453  60.147  -0.763  1.00  0.00              
ATOM      5  N   ARG    78      31.994  62.308  -0.521  1.00  0.00              
ATOM      6  CA  ARG    78      31.669  62.547  -1.902  1.00  0.00              
ATOM      7  C   ARG    78      32.940  61.922  -2.343  1.00  0.00              
ATOM      8  O   ARG    78      32.973  61.210  -3.339  1.00  0.00              
ATOM      9  N   LYS    79      36.835  58.025  -5.556  1.00  0.00              
ATOM     10  CA  LYS    79      37.793  56.961  -5.450  1.00  0.00              
ATOM     11  C   LYS    79      37.210  55.700  -6.068  1.00  0.00              
ATOM     12  O   LYS    79      37.959  54.820  -6.451  1.00  0.00              
ATOM     13  N   LEU    80      35.887  55.609  -6.201  1.00  0.00              
ATOM     14  CA  LEU    80      35.319  54.430  -6.831  1.00  0.00              
ATOM     15  C   LEU    80      35.203  54.519  -8.345  1.00  0.00              
ATOM     16  O   LEU    80      35.407  53.514  -9.008  1.00  0.00              
ATOM     17  N   ILE    81      34.869  55.685  -8.898  1.00  0.00              
ATOM     18  CA  ILE    81      34.724  55.790 -10.345  1.00  0.00              
ATOM     19  C   ILE    81      36.056  55.428 -10.960  1.00  0.00              
ATOM     20  O   ILE    81      36.122  54.797 -12.007  1.00  0.00              
ATOM     21  N   GLU    82      37.105  55.870 -10.285  1.00  0.00              
ATOM     22  CA  GLU    82      38.488  55.671 -10.653  1.00  0.00              
ATOM     23  C   GLU    82      38.865  54.165 -10.690  1.00  0.00              
ATOM     24  O   GLU    82      39.495  53.725 -11.625  1.00  0.00              
ATOM     25  N   ASP    83      36.839  51.608 -11.035  1.00  0.00              
ATOM     26  CA  ASP    83      35.969  51.143 -12.101  1.00  0.00              
ATOM     27  C   ASP    83      36.569  51.393 -13.450  1.00  0.00              
ATOM     28  O   ASP    83      36.395  50.621 -14.405  1.00  0.00              
ATOM     29  N   ALA    84      37.289  52.496 -13.517  1.00  0.00              
ATOM     30  CA  ALA    84      37.868  52.906 -14.773  1.00  0.00              
ATOM     31  C   ALA    84      39.170  52.245 -15.178  1.00  0.00              
ATOM     32  O   ALA    84      39.575  52.282 -16.337  1.00  0.00              
ATOM     33  N   ASP    85      39.836  51.630 -14.222  1.00  0.00              
ATOM     34  CA  ASP    85      41.121  51.036 -14.511  1.00  0.00              
ATOM     35  C   ASP    85      41.177  49.777 -15.337  1.00  0.00              
ATOM     36  O   ASP    85      40.199  49.049 -15.498  1.00  0.00              
ATOM     37  N   LYS    86      42.337  49.549 -15.941  1.00  0.00              
ATOM     38  CA  LYS    86      42.563  48.362 -16.759  1.00  0.00              
ATOM     39  C   LYS    86      42.625  47.232 -15.721  1.00  0.00              
ATOM     40  O   LYS    86      43.212  47.398 -14.646  1.00  0.00              
ATOM     41  N   GLU    87      41.971  46.113 -16.004  1.00  0.00              
ATOM     42  CA  GLU    87      42.013  45.001 -15.078  1.00  0.00              
ATOM     43  C   GLU    87      41.071  45.079 -13.897  1.00  0.00              
ATOM     44  O   GLU    87      41.108  44.216 -13.020  1.00  0.00              
ATOM     45  N   LYS    88      40.267  46.130 -13.829  1.00  0.00              
ATOM     46  CA  LYS    88      39.319  46.233 -12.730  1.00  0.00              
ATOM     47  C   LYS    88      38.188  45.255 -13.018  1.00  0.00              
ATOM     48  O   LYS    88      37.601  45.290 -14.094  1.00  0.00              
ATOM     49  N   HIS    89      37.878  44.392 -12.055  1.00  0.00              
ATOM     50  CA  HIS    89      36.838  43.386 -12.239  1.00  0.00              
ATOM     51  C   HIS    89      35.495  43.711 -11.603  1.00  0.00              
ATOM     52  O   HIS    89      34.478  43.149 -11.993  1.00  0.00              
ATOM     53  N   ASN    90      35.476  44.620 -10.638  1.00  0.00              
ATOM     54  CA  ASN    90      34.215  44.966 -10.001  1.00  0.00              
ATOM     55  C   ASN    90      34.432  45.398  -8.566  1.00  0.00              
ATOM     56  O   ASN    90      35.561  45.368  -8.073  1.00  0.00              
ATOM     57  N   PHE    91      33.360  45.814  -7.892  1.00  0.00              
ATOM     58  CA  PHE    91      33.472  46.242  -6.509  1.00  0.00              
ATOM     59  C   PHE    91      32.197  46.050  -5.717  1.00  0.00              
ATOM     60  O   PHE    91      31.098  46.293  -6.215  1.00  0.00              
ATOM     61  N   CYS    92      32.354  45.622  -4.470  1.00  0.00              
ATOM     62  CA  CYS    92      31.214  45.450  -3.589  1.00  0.00              
ATOM     63  C   CYS    92      31.468  46.371  -2.397  1.00  0.00              
ATOM     64  O   CYS    92      32.487  46.268  -1.708  1.00  0.00              
ATOM     65  N   MET    93      30.567  47.323  -2.197  1.00  0.00              
ATOM     66  CA  MET    93      30.742  48.274  -1.120  1.00  0.00              
ATOM     67  C   MET    93      29.523  48.338  -0.238  1.00  0.00              
ATOM     68  O   MET    93      28.382  48.386  -0.700  1.00  0.00              
ATOM     69  N   LEU    94      29.790  48.345   1.056  1.00  0.00              
ATOM     70  CA  LEU    94      28.736  48.306   2.037  1.00  0.00              
ATOM     71  C   LEU    94      29.201  49.123   3.245  1.00  0.00              
ATOM     72  O   LEU    94      30.359  49.022   3.664  1.00  0.00              
ATOM     73  N   GLY    95      28.313  49.952   3.787  1.00  0.00              
ATOM     74  CA  GLY    95      28.678  50.815   4.909  1.00  0.00              
ATOM     75  C   GLY    95      27.500  50.915   5.853  1.00  0.00              
ATOM     76  O   GLY    95      26.437  51.351   5.443  1.00  0.00              
ATOM     77  N   VAL    96      27.649  50.456   7.096  1.00  0.00              
ATOM     78  CA  VAL    96      26.528  50.562   8.038  1.00  0.00              
ATOM     79  C   VAL    96      26.442  51.948   8.664  1.00  0.00              
ATOM     80  O   VAL    96      27.354  52.784   8.589  1.00  0.00              
ATOM     81  N   CYS    97      25.299  52.134   9.305  1.00  0.00              
ATOM     82  CA  CYS    97      24.915  53.307  10.062  1.00  0.00              
ATOM     83  C   CYS    97      25.996  53.855  10.969  1.00  0.00              
ATOM     84  O   CYS    97      26.396  55.006  10.813  1.00  0.00              
ATOM     85  N   MET   100      26.426  53.010  11.905  1.00  0.00              
ATOM     86  CA  MET   100      27.414  53.308  12.916  1.00  0.00              
ATOM     87  C   MET   100      28.838  53.577  12.448  1.00  0.00              
ATOM     88  O   MET   100      29.705  53.797  13.286  1.00  0.00              
ATOM     89  N   ARG   101      29.089  53.548  11.139  1.00  0.00              
ATOM     90  CA  ARG   101      30.427  53.814  10.641  1.00  0.00              
ATOM     91  C   ARG   101      31.218  52.601  10.197  1.00  0.00              
ATOM     92  O   ARG   101      32.269  52.745   9.583  1.00  0.00              
ATOM     93  N   LEU   104      30.748  51.405  10.524  1.00  0.00              
ATOM     94  CA  LEU   104      31.460  50.203  10.132  1.00  0.00              
ATOM     95  C   LEU   104      31.274  49.896   8.667  1.00  0.00              
ATOM     96  O   LEU   104      30.149  49.936   8.161  1.00  0.00              
ATOM     97  N   ALA   106      32.362  49.527   7.997  1.00  0.00              
ATOM     98  CA  ALA   106      32.253  49.279   6.579  1.00  0.00              
ATOM     99  C   ALA   106      33.268  48.387   5.905  1.00  0.00              
ATOM    100  O   ALA   106      34.437  48.355   6.283  1.00  0.00              
ATOM    101  N   ILE   107      32.807  47.635   4.908  1.00  0.00              
ATOM    102  CA  ILE   107      33.696  46.778   4.145  1.00  0.00              
ATOM    103  C   ILE   107      33.520  47.015   2.638  1.00  0.00              
ATOM    104  O   ILE   107      32.410  46.983   2.088  1.00  0.00              
ATOM    105  N   LEU   108      34.630  47.252   1.961  1.00  0.00              
ATOM    106  CA  LEU   108      34.588  47.447   0.527  1.00  0.00              
ATOM    107  C   LEU   108      35.618  46.524  -0.113  1.00  0.00              
ATOM    108  O   LEU   108      36.796  46.557   0.228  1.00  0.00              
ATOM    109  N   PRO   109      37.328  45.143  -3.693  1.00  0.00              
ATOM    110  CA  PRO   109      37.456  45.384  -5.113  1.00  0.00              
ATOM    111  C   PRO   109      38.201  44.211  -5.707  1.00  0.00              
ATOM    112  O   PRO   109      39.146  43.701  -5.122  1.00  0.00              
ATOM    113  N   GLU   110      37.749  43.779  -6.873  1.00  0.00              
ATOM    114  CA  GLU   110      38.341  42.634  -7.533  1.00  0.00              
ATOM    115  C   GLU   110      39.172  43.048  -8.742  1.00  0.00              
ATOM    116  O   GLU   110      38.772  43.906  -9.530  1.00  0.00              
ATOM    117  N   ARG   111      40.344  42.437  -8.867  1.00  0.00              
ATOM    118  CA  ARG   111      41.285  42.769  -9.922  1.00  0.00              
ATOM    119  C   ARG   111      41.860  41.561 -10.584  1.00  0.00              
ATOM    120  O   ARG   111      42.025  40.526  -9.954  1.00  0.00              
ATOM    121  N   PHE   112      42.198  41.708 -11.857  1.00  0.00              
ATOM    122  CA  PHE   112      42.750  40.603 -12.617  1.00  0.00              
ATOM    123  C   PHE   112      44.200  40.277 -12.358  1.00  0.00              
ATOM    124  O   PHE   112      44.638  39.187 -12.684  1.00  0.00              
ATOM    125  N   ILE   113      44.967  41.195 -11.795  1.00  0.00              
ATOM    126  CA  ILE   113      46.362  40.880 -11.579  1.00  0.00              
ATOM    127  C   ILE   113      46.963  41.744 -10.514  1.00  0.00              
ATOM    128  O   ILE   113      46.475  42.830 -10.220  1.00  0.00              
ATOM    129  N   ASP   117      48.025  41.240  -9.915  1.00  0.00              
ATOM    130  CA  ASP   117      48.725  42.003  -8.910  1.00  0.00              
ATOM    131  C   ASP   117      49.223  43.239  -9.627  1.00  0.00              
ATOM    132  O   ASP   117      49.224  44.320  -9.056  1.00  0.00              
END
