
#######################################################
#                                                     #
#                        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 T0378AL257_4-D1
# Molecule2: number of CA atoms   89 (  716),  selected   19 , name T0378_D1.pdb
# PARAMETERS: T0378AL257_4-D1.T0378_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:    11        10 - 20          3.36    14.73
  LCS_AVERAGE:     10.94

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8        33 - 40          0.93    19.40
  LCS_AVERAGE:      8.10

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8        33 - 40          0.93    19.40
  LCS_AVERAGE:      7.39

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      10     L      10      5    6   11     4    4    5    6    6    7    8   10   11   11   11   11   12   12   13   15   16   16   18   19 
LCS_GDT     R      11     R      11      5    6   11     4    4    5    6    6    7    8   10   11   11   11   11   12   14   14   15   16   16   18   19 
LCS_GDT     S      12     S      12      5    6   11     4    4    5    6    6    7    8   10   11   11   11   11   12   14   14   15   16   16   18   19 
LCS_GDT     L      13     L      13      5    6   11     4    4    5    6    6    7    7   10   11   11   11   11   12   14   14   15   16   16   18   19 
LCS_GDT     R      14     R      14      5    7   11     3    4    5    6    6    7    7    9   11   11   11   11   12   14   14   15   16   16   18   19 
LCS_GDT     E      15     E      15      6    7   11     0    4    6    6    6    7    8   10   11   11   11   11   12   14   14   15   16   16   18   19 
LCS_GDT     R      16     R      16      6    7   11     5    5    6    6    6    7    8   10   11   11   11   11   12   14   14   15   16   16   18   19 
LCS_GDT     K      17     K      17      6    7   11     5    5    6    6    6    7    8   10   11   11   11   11   12   14   14   15   16   16   18   19 
LCS_GDT     Y      18     Y      18      6    7   11     5    5    6    6    6    7    8   10   11   11   11   11   12   14   14   15   16   16   18   19 
LCS_GDT     R      19     R      19      6    7   11     5    5    6    6    6    7    8   10   11   11   11   11   12   14   14   15   16   16   18   19 
LCS_GDT     L      20     L      20      6    7   11     5    5    6    6    6    7    7   10   11   11   11   11   12   14   14   15   16   16   18   19 
LCS_GDT     V      33     V      33      8    8    8     4    5    8    8    8    8    8    8    8    8    8    8   10   11   13   14   15   16   18   19 
LCS_GDT     G      34     G      34      8    8    8     4    5    8    8    8    8    8    8    8    8    8    8   10   11   13   14   15   16   18   19 
LCS_GDT     E      35     E      35      8    8    8     4    5    8    8    8    8    8    8    8    8    8    8   10   11   12   14   15   16   18   19 
LCS_GDT     M      36     M      36      8    8    8     4    5    8    8    8    8    8    8    8    8   11   11   12   12   14   15   16   16   18   19 
LCS_GDT     L      37     L      37      8    8    8     4    5    8    8    8    8    8    8    8    9   11   11   12   14   14   15   16   16   18   19 
LCS_GDT     P      38     P      38      8    8    8     3    5    8    8    8    8    8    8    8    8   11   11   12   14   14   15   16   16   18   19 
LCS_GDT     F      39     F      39      8    8    8     3    5    8    8    8    8    8    8    8    9   11   11   12   14   14   15   16   16   18   19 
LCS_GDT     Y      40     Y      40      8    8    8     3    5    8    8    8    8    8    8    8    9   11   11   12   14   14   15   16   16   18   19 
LCS_AVERAGE  LCS_A:   8.81  (   7.39    8.10   10.94 )

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      5      5      8      8      8      8      8     10     11     11     11     11     12     14     14     15     16     16     18     19 
GDT PERCENT_CA   5.62   5.62   8.99   8.99   8.99   8.99   8.99  11.24  12.36  12.36  12.36  12.36  13.48  15.73  15.73  16.85  17.98  17.98  20.22  21.35
GDT RMS_LOCAL    0.32   0.32   0.93   0.93   0.93   0.93   0.93   3.12   3.36   3.36   3.36   3.36   4.64   5.18   5.18   5.48   5.73   5.73   6.41   6.68
GDT RMS_ALL_CA  14.31  14.31  19.40  19.40  19.40  19.40  19.40  15.15  14.73  14.73  14.73  14.73   6.74   7.31   7.31   7.06   6.94   6.94   6.72   6.68

#      Molecule1      Molecule2       DISTANCE
LGA    L      10      L      10          2.899
LGA    R      11      R      11          3.324
LGA    S      12      S      12          1.997
LGA    L      13      L      13          3.736
LGA    R      14      R      14          4.681
LGA    E      15      E      15          2.710
LGA    R      16      R      16          3.433
LGA    K      17      K      17          3.326
LGA    Y      18      Y      18          3.454
LGA    R      19      R      19          2.988
LGA    L      20      L      20          3.759
LGA    V      33      V      33         22.142
LGA    G      34      G      34         22.881
LGA    E      35      E      35         23.510
LGA    M      36      M      36         23.049
LGA    L      37      L      37         22.164
LGA    P      38      P      38         22.106
LGA    F      39      F      39         22.169
LGA    Y      40      Y      40         20.654

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   19   89    4.0     10    3.12    10.674    10.029     0.311

LGA_LOCAL      RMSD =  3.116  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 14.726  Number of atoms =   19 
Std_ALL_ATOMS  RMSD =  6.683  (standard rmsd on all 19 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.679516 * X  +   0.200470 * Y  +  -0.705741 * Z  +  44.435921
  Y_new =   0.322674 * X  +  -0.782249 * Y  +  -0.532886 * Z  +  19.952261
  Z_new =  -0.658893 * X  +  -0.589829 * Y  +   0.466864 * Z  +  67.936668 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.901244    2.240348  [ DEG:   -51.6375    128.3625 ]
  Theta =   0.719346    2.422246  [ DEG:    41.2155    138.7845 ]
  Phi   =   2.698260   -0.443332  [ DEG:   154.5989    -25.4011 ]
 
# 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: T0378AL257_4-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0378AL257_4-D1.T0378_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   19   89   4.0   10   3.12  10.029     6.68
REMARK  ---------------------------------------------------------- 
MOLECULE T0378AL257_4-D1
REMARK Aligment from pdb entry: 1v2x_A
ATOM      1  N   LEU    10      12.065  31.521  48.290  1.00  0.00              
ATOM      2  CA  LEU    10      11.599  30.112  48.458  1.00  0.00              
ATOM      3  C   LEU    10      12.735  29.098  48.380  1.00  0.00              
ATOM      4  O   LEU    10      12.817  28.187  49.207  1.00  0.00              
ATOM      5  N   ARG    11      13.603  29.239  47.381  1.00  0.00              
ATOM      6  CA  ARG    11      14.709  28.304  47.245  1.00  0.00              
ATOM      7  C   ARG    11      15.850  28.742  48.162  1.00  0.00              
ATOM      8  O   ARG    11      16.738  27.960  48.492  1.00  0.00              
ATOM      9  N   SER    12      15.824  29.998  48.584  1.00  0.00              
ATOM     10  CA  SER    12      16.854  30.493  49.484  1.00  0.00              
ATOM     11  C   SER    12      16.568  29.833  50.839  1.00  0.00              
ATOM     12  O   SER    12      17.470  29.465  51.597  1.00  0.00              
ATOM     13  N   LEU    13      15.278  29.672  51.105  1.00  0.00              
ATOM     14  CA  LEU    13      14.767  29.068  52.324  1.00  0.00              
ATOM     15  C   LEU    13      14.951  27.550  52.317  1.00  0.00              
ATOM     16  O   LEU    13      15.227  26.931  53.346  1.00  0.00              
ATOM     17  N   ARG    14      14.818  26.953  51.141  1.00  0.00              
ATOM     18  CA  ARG    14      14.919  25.511  51.032  1.00  0.00              
ATOM     19  C   ARG    14      16.214  25.061  50.335  1.00  0.00              
ATOM     20  O   ARG    14      17.000  24.302  50.901  1.00  0.00              
ATOM     21  N   GLU    15      16.453  25.558  49.130  1.00  0.00              
ATOM     22  CA  GLU    15      17.642  25.179  48.374  1.00  0.00              
ATOM     23  C   GLU    15      18.924  25.449  49.143  1.00  0.00              
ATOM     24  O   GLU    15      19.926  24.780  48.927  1.00  0.00              
ATOM     25  N   ARG    16      18.897  26.409  50.055  1.00  0.00              
ATOM     26  CA  ARG    16      20.105  26.728  50.800  1.00  0.00              
ATOM     27  C   ARG    16      20.139  26.178  52.220  1.00  0.00              
ATOM     28  O   ARG    16      20.659  25.092  52.464  1.00  0.00              
ATOM     29  N   LYS    17      19.592  26.952  53.151  1.00  0.00              
ATOM     30  CA  LYS    17      19.563  26.585  54.552  1.00  0.00              
ATOM     31  C   LYS    17      19.167  25.123  54.717  1.00  0.00              
ATOM     32  O   LYS    17      19.916  24.327  55.278  1.00  0.00              
ATOM     33  N   TYR    18      17.988  24.785  54.205  1.00  0.00              
ATOM     34  CA  TYR    18      17.438  23.442  54.282  1.00  0.00              
ATOM     35  C   TYR    18      18.401  22.344  53.808  1.00  0.00              
ATOM     36  O   TYR    18      18.670  21.398  54.543  1.00  0.00              
ATOM     37  N   ARG    19      18.915  22.487  52.591  1.00  0.00              
ATOM     38  CA  ARG    19      19.834  21.517  51.983  1.00  0.00              
ATOM     39  C   ARG    19      21.195  21.415  52.676  1.00  0.00              
ATOM     40  O   ARG    19      21.684  20.304  52.899  1.00  0.00              
ATOM     41  N   LEU    20      21.817  22.543  53.019  1.00  0.00              
ATOM     42  CA  LEU    20      23.117  22.470  53.682  1.00  0.00              
ATOM     43  C   LEU    20      23.017  21.855  55.084  1.00  0.00              
ATOM     44  O   LEU    20      23.890  21.100  55.497  1.00  0.00              
ATOM     45  N   VAL    33      21.956  22.174  55.819  1.00  0.00              
ATOM     46  CA  VAL    33      21.789  21.625  57.156  1.00  0.00              
ATOM     47  C   VAL    33      21.604  20.096  57.134  1.00  0.00              
ATOM     48  O   VAL    33      22.108  19.370  58.004  1.00  0.00              
ATOM     49  N   GLY    34      20.864  19.602  56.151  1.00  0.00              
ATOM     50  CA  GLY    34      20.626  18.172  56.102  1.00  0.00              
ATOM     51  C   GLY    34      21.906  17.521  55.666  1.00  0.00              
ATOM     52  O   GLY    34      22.237  16.442  56.140  1.00  0.00              
ATOM     53  N   GLU    35      22.619  18.165  54.757  1.00  0.00              
ATOM     54  CA  GLU    35      23.881  17.602  54.285  1.00  0.00              
ATOM     55  C   GLU    35      24.783  17.312  55.474  1.00  0.00              
ATOM     56  O   GLU    35      25.395  16.247  55.562  1.00  0.00              
ATOM     57  N   MET    36      24.864  18.265  56.390  1.00  0.00              
ATOM     58  CA  MET    36      25.668  18.111  57.585  1.00  0.00              
ATOM     59  C   MET    36      25.077  17.106  58.576  1.00  0.00              
ATOM     60  O   MET    36      25.803  16.333  59.217  1.00  0.00              
ATOM     61  N   LEU    37      23.745  17.093  58.694  1.00  0.00              
ATOM     62  CA  LEU    37      23.100  16.173  59.603  1.00  0.00              
ATOM     63  C   LEU    37      23.389  14.743  59.158  1.00  0.00              
ATOM     64  O   LEU    37      23.470  13.819  59.975  1.00  0.00              
ATOM     65  N   PRO    38      23.545  14.582  57.853  1.00  0.00              
ATOM     66  CA  PRO    38      23.809  13.264  57.267  1.00  0.00              
ATOM     67  C   PRO    38      25.204  12.731  57.570  1.00  0.00              
ATOM     68  O   PRO    38      25.491  11.552  57.341  1.00  0.00              
ATOM     69  N   PHE    39      26.083  13.589  58.082  1.00  0.00              
ATOM     70  CA  PHE    39      27.421  13.157  58.449  1.00  0.00              
ATOM     71  C   PHE    39      27.537  13.032  59.984  1.00  0.00              
ATOM     72  O   PHE    39      28.592  12.707  60.482  1.00  0.00              
ATOM     73  N   TYR    40      26.471  13.284  60.733  1.00  0.00              
ATOM     74  CA  TYR    40      26.573  13.179  62.188  1.00  0.00              
ATOM     75  C   TYR    40      26.784  11.743  62.658  1.00  0.00              
ATOM     76  O   TYR    40      26.128  10.830  62.154  1.00  0.00              
END
