
#######################################################
#                                                     #
#                        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   19 (   76),  selected   19 , name T0381AL509_1-D1
# Molecule2: number of CA atoms   61 (  477),  selected   19 , name T0381_D1.pdb
# PARAMETERS: T0381AL509_1-D1.T0381_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:    14        42 - 64          4.97     7.63
  LCS_AVERAGE:     21.66

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        59 - 64          0.21     7.80
  LCS_AVERAGE:      7.94

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        59 - 64          0.21     7.80
  LCS_AVERAGE:      7.42

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:   61
LCS_GDT     V      17     V      17      4    4   11     3    3    4    4    4    4    5    7    7    8    9   10   11   14   15   15   17   18   18   18 
LCS_GDT     Q      18     Q      18      4    4   11     3    3    4    4    4    4    5    7    7    8    9   10   11   14   15   15   17   18   18   18 
LCS_GDT     S      19     S      19      4    4   11     3    3    4    4    4    4    5    7    9    9   12   13   13   14   15   15   17   18   18   18 
LCS_GDT     L      20     L      20      4    4   11     0    3    4    4    4    4    4    5    5    8    9   10   10   10   13   15   17   18   18   18 
LCS_GDT     A      21     A      21      3    3   11     0    3    3    3    3    3    4    5    5    6    7    9   10   10   13   15   17   18   18   18 
LCS_GDT     V      42     V      42      4    4   14     4    4    4    6    6    8   10   11   11   11   12   13   13   14   15   15   17   18   18   18 
LCS_GDT     A      43     A      43      4    4   14     4    4    4    4    4    7    9   11   11   11   12   13   13   14   15   15   17   18   18   18 
LCS_GDT     R      44     R      44      4    4   14     4    4    4    4    8    8   10   11   11   11   12   13   13   14   15   15   17   18   18   18 
LCS_GDT     A      45     A      45      4    5   14     4    4    4    6    6    6   10   11   11   11   11   13   13   14   15   15   17   18   18   18 
LCS_GDT     T      46     T      46      4    5   14     3    3    4    6    8    8   10   11   11   11   12   13   13   14   15   15   17   18   18   18 
LCS_GDT     D      47     D      47      4    5   14     3    3    4    6    6    7    8   10   10   11   12   13   13   14   15   15   17   18   18   18 
LCS_GDT     L      48     L      48      4    5   14     3    3    4    6    6    7    8    8    9   10   11   11   13   13   14   15   17   18   18   18 
LCS_GDT     T      49     T      49      3    5   14     3    3    3    6    6    6    6    6    6    7    8   10   10   10   11   12   13   15   15   18 
LCS_GDT     T      59     T      59      6    6   14     6    6    6    6    8    8   10   11   11   11   12   13   13   14   15   15   17   18   18   18 
LCS_GDT     L      60     L      60      6    6   14     6    6    6    6    8    8   10   11   11   11   12   13   13   14   15   15   17   18   18   18 
LCS_GDT     V      61     V      61      6    6   14     6    6    6    6    8    8   10   11   11   11   12   13   13   14   15   15   17   18   18   18 
LCS_GDT     E      62     E      62      6    6   14     6    6    6    6    8    8   10   11   11   11   12   13   13   14   15   15   17   18   18   18 
LCS_GDT     L      63     L      63      6    6   14     6    6    6    6    8    8   10   11   11   11   12   13   13   14   15   15   17   18   18   18 
LCS_GDT     G      64     G      64      6    6   14     6    6    6    6    8    8   10   11   11   11   12   13   13   13   15   15   17   18   18   18 
LCS_AVERAGE  LCS_A:  12.34  (   7.42    7.94   21.66 )

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      6      6      6      6      8      8     10     11     11     11     12     13     13     14     15     15     17     18     18     18 
GDT PERCENT_CA   9.84   9.84   9.84   9.84  13.11  13.11  16.39  18.03  18.03  18.03  19.67  21.31  21.31  22.95  24.59  24.59  27.87  29.51  29.51  29.51
GDT RMS_LOCAL    0.21   0.21   0.21   0.21   1.78   1.78   2.42   2.57   2.57   2.57   3.38   3.60   3.60   5.02   4.99   4.99   5.62   5.87   5.87   5.87
GDT RMS_ALL_CA   7.80   7.80   7.80   7.80   6.88   6.88   7.29   7.27   7.27   7.27   6.94   7.01   7.01   6.62   6.58   6.58   6.52   6.46   6.46   6.46

#      Molecule1      Molecule2       DISTANCE
LGA    V      17      V      17         11.727
LGA    Q      18      Q      18         11.210
LGA    S      19      S      19          8.091
LGA    L      20      L      20         10.642
LGA    A      21      A      21         10.672
LGA    V      42      V      42          2.734
LGA    A      43      A      43          3.586
LGA    R      44      R      44          2.126
LGA    A      45      A      45          3.443
LGA    T      46      T      46          3.211
LGA    D      47      D      47          7.473
LGA    L      48      L      48         10.687
LGA    T      49      T      49         14.341
LGA    T      59      T      59          1.510
LGA    L      60      L      60          2.329
LGA    V      61      V      61          2.220
LGA    E      62      E      62          0.735
LGA    L      63      L      63          2.188
LGA    G      64      G      64          2.806

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   19   61    4.0     11    2.57    15.574    13.906     0.411

LGA_LOCAL      RMSD =  2.573  Number of atoms =   11  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  7.271  Number of atoms =   19 
Std_ALL_ATOMS  RMSD =  6.418  (standard rmsd on all 19 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.092199 * X  +   0.139247 * Y  +  -0.985956 * Z  +  87.799347
  Y_new =   0.875391 * X  +   0.460554 * Y  +   0.146904 * Z  +  23.440338
  Z_new =   0.474542 * X  +  -0.876642 * Y  +  -0.079433 * Z  +  -4.713665 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.661160    1.480433  [ DEG:   -95.1775     84.8225 ]
  Theta =  -0.494444   -2.647149  [ DEG:   -28.3295   -151.6705 ]
  Phi   =   1.465860   -1.675733  [ DEG:    83.9876    -96.0124 ]
 
# 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: T0381AL509_1-D1                               
REMARK     2: T0381_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0381AL509_1-D1.T0381_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   19   61   4.0   11   2.57  13.906     6.42
REMARK  ---------------------------------------------------------- 
MOLECULE T0381AL509_1-D1
REMARK Aligment from pdb entry: 1mkm_A
ATOM     65  N   VAL    17      12.350  60.829  26.552  1.00  0.00              
ATOM     66  CA  VAL    17      12.398  61.098  25.130  1.00  0.00              
ATOM     67  C   VAL    17      12.946  60.007  24.245  1.00  0.00              
ATOM     68  O   VAL    17      13.128  60.252  23.071  1.00  0.00              
ATOM     69  N   GLN    18      13.195  58.823  24.795  1.00  0.00              
ATOM     70  CA  GLN    18      13.726  57.706  24.030  1.00  0.00              
ATOM     71  C   GLN    18      12.624  57.077  23.224  1.00  0.00              
ATOM     72  O   GLN    18      12.870  56.170  22.435  1.00  0.00              
ATOM     73  N   SER    19      11.402  57.548  23.440  1.00  0.00              
ATOM     74  CA  SER    19      10.246  57.023  22.737  1.00  0.00              
ATOM     75  C   SER    19       9.255  58.148  22.442  1.00  0.00              
ATOM     76  O   SER    19       9.211  59.157  23.152  1.00  0.00              
ATOM     77  N   LEU    20       8.495  57.987  21.362  1.00  0.00              
ATOM     78  CA  LEU    20       7.516  58.976  20.950  1.00  0.00              
ATOM     79  C   LEU    20       6.163  58.323  20.736  1.00  0.00              
ATOM     80  O   LEU    20       6.061  57.263  20.108  1.00  0.00              
ATOM     81  N   ALA    21       5.113  58.941  21.255  1.00  0.00              
ATOM     82  CA  ALA    21       3.806  58.359  21.061  1.00  0.00              
ATOM     83  C   ALA    21       3.083  59.133  19.968  1.00  0.00              
ATOM     84  O   ALA    21       2.898  60.350  20.073  1.00  0.00              
ATOM     85  N   VAL    42       2.697  58.419  18.913  1.00  0.00              
ATOM     86  CA  VAL    42       1.998  59.004  17.782  1.00  0.00              
ATOM     87  C   VAL    42       0.529  59.285  18.101  1.00  0.00              
ATOM     88  O   VAL    42      -0.008  58.767  19.075  1.00  0.00              
ATOM     89  N   ALA    43      -0.121  60.097  17.276  1.00  0.00              
ATOM     90  CA  ALA    43      -1.528  60.426  17.491  1.00  0.00              
ATOM     91  C   ALA    43      -2.402  59.178  17.695  1.00  0.00              
ATOM     92  O   ALA    43      -3.298  59.179  18.543  1.00  0.00              
ATOM     93  N   ARG    44      -2.145  58.123  16.922  1.00  0.00              
ATOM     94  CA  ARG    44      -2.915  56.890  17.030  1.00  0.00              
ATOM     95  C   ARG    44      -2.514  56.058  18.253  1.00  0.00              
ATOM     96  O   ARG    44      -2.874  54.882  18.362  1.00  0.00              
ATOM     97  N   ALA    45      -1.758  56.677  19.157  1.00  0.00              
ATOM     98  CA  ALA    45      -1.293  56.056  20.396  1.00  0.00              
ATOM     99  C   ALA    45      -0.150  55.043  20.291  1.00  0.00              
ATOM    100  O   ALA    45       0.496  54.756  21.298  1.00  0.00              
ATOM    101  N   THR    46       0.083  54.482  19.104  1.00  0.00              
ATOM    102  CA  THR    46       1.179  53.527  18.907  1.00  0.00              
ATOM    103  C   THR    46       2.500  54.258  19.130  1.00  0.00              
ATOM    104  O   THR    46       2.604  55.452  18.855  1.00  0.00              
ATOM    105  N   ASP    47       3.507  53.538  19.618  1.00  0.00              
ATOM    106  CA  ASP    47       4.822  54.127  19.878  1.00  0.00              
ATOM    107  C   ASP    47       5.891  53.833  18.824  1.00  0.00              
ATOM    108  O   ASP    47       5.906  52.789  18.169  1.00  0.00              
ATOM    109  N   LEU    48       6.811  54.772  18.700  1.00  0.00              
ATOM    110  CA  LEU    48       7.892  54.661  17.745  1.00  0.00              
ATOM    111  C   LEU    48       9.125  55.232  18.456  1.00  0.00              
ATOM    112  O   LEU    48       8.986  55.933  19.456  1.00  0.00              
ATOM    113  N   THR    49      10.347  54.913  17.983  1.00  0.00              
ATOM    114  CA  THR    49      11.524  55.470  18.673  1.00  0.00              
ATOM    115  C   THR    49      11.607  57.002  18.654  1.00  0.00              
ATOM    116  O   THR    49      11.143  57.651  17.708  1.00  0.00              
ATOM    117  N   THR    59      15.634  61.624  20.863  1.00  0.00              
ATOM    118  CA  THR    59      16.731  61.634  21.819  1.00  0.00              
ATOM    119  C   THR    59      17.796  60.590  21.479  1.00  0.00              
ATOM    120  O   THR    59      18.964  60.809  21.732  1.00  0.00              
ATOM    121  N   LEU    60      17.390  59.450  20.937  1.00  0.00              
ATOM    122  CA  LEU    60      18.343  58.408  20.562  1.00  0.00              
ATOM    123  C   LEU    60      19.308  58.942  19.497  1.00  0.00              
ATOM    124  O   LEU    60      20.464  58.538  19.432  1.00  0.00              
ATOM    125  N   VAL    61      18.834  59.865  18.672  1.00  0.00              
ATOM    126  CA  VAL    61      19.704  60.445  17.659  1.00  0.00              
ATOM    127  C   VAL    61      20.583  61.438  18.378  1.00  0.00              
ATOM    128  O   VAL    61      21.795  61.477  18.173  1.00  0.00              
ATOM    129  N   GLU    62      19.982  62.227  19.258  1.00  0.00              
ATOM    130  CA  GLU    62      20.757  63.233  19.995  1.00  0.00              
ATOM    131  C   GLU    62      21.923  62.591  20.730  1.00  0.00              
ATOM    132  O   GLU    62      23.062  63.070  20.658  1.00  0.00              
ATOM    133  N   LEU    63      21.635  61.495  21.431  1.00  0.00              
ATOM    134  CA  LEU    63      22.650  60.754  22.177  1.00  0.00              
ATOM    135  C   LEU    63      23.627  60.062  21.239  1.00  0.00              
ATOM    136  O   LEU    63      24.826  59.998  21.513  1.00  0.00              
ATOM    137  N   GLY    64      23.084  59.503  20.157  1.00  0.00              
ATOM    138  CA  GLY    64      23.904  58.791  19.197  1.00  0.00              
ATOM    139  C   GLY    64      25.017  59.640  18.627  1.00  0.00              
ATOM    140  O   GLY    64      26.188  59.291  18.699  1.00  0.00              
END
