
#######################################################
#                                                     #
#                        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   32 (  128),  selected   32 , name T0335AL316_4-D1
# Molecule2: number of CA atoms   36 (  584),  selected   32 , name T0335_D1.pdb
# PARAMETERS: T0335AL316_4-D1.T0335_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:    22         5 - 26          4.92    11.85
  LCS_AVERAGE:     55.82

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15         5 - 19          1.99    12.58
  LCS_AVERAGE:     29.95

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11         5 - 15          0.79    12.76
  LCS_AVERAGE:     21.35

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:   36
LCS_GDT     A       5     A       5     11   15   22     8   10   11   11   12   14   15   17   17   18   18   20   20   20   21   21   23   23   25   26 
LCS_GDT     K       6     K       6     11   15   22     9   10   11   11   14   15   15   17   17   18   19   20   20   20   21   21   23   24   25   26 
LCS_GDT     I       7     I       7     11   15   22     9   10   11   11   14   15   15   17   17   18   19   20   20   20   21   22   23   24   25   27 
LCS_GDT     A       8     A       8     11   15   22     9   10   11   11   14   15   15   17   17   18   19   20   20   20   21   22   23   24   25   27 
LCS_GDT     R       9     R       9     11   15   22     9   10   11   11   14   15   15   17   17   18   19   20   20   20   21   22   23   24   25   27 
LCS_GDT     I      10     I      10     11   15   22     9   10   11   11   14   15   15   17   17   18   19   20   20   20   21   22   23   24   25   27 
LCS_GDT     N      11     N      11     11   15   22     9   10   11   11   14   15   15   17   17   18   19   20   20   20   21   22   23   24   25   27 
LCS_GDT     E      12     E      12     11   15   22     9   10   11   11   14   15   15   17   17   18   19   20   20   20   21   22   23   24   25   27 
LCS_GDT     L      13     L      13     11   15   22     9   10   11   11   13   15   15   17   17   18   19   20   20   20   21   22   23   24   25   27 
LCS_GDT     A      14     A      14     11   15   22     9   10   11   11   13   14   15   17   17   18   19   20   20   20   21   22   23   24   25   27 
LCS_GDT     A      15     A      15     11   15   22     7    8   11   11   14   15   15   17   17   18   19   20   20   20   21   22   23   24   25   27 
LCS_GDT     K      16     K      16      8   15   22     7    8    8   11   14   15   15   17   17   18   19   20   20   20   21   22   23   24   25   27 
LCS_GDT     A      17     A      17      8   15   22     7    8    8   11   14   15   15   17   17   18   19   20   20   20   21   22   23   24   25   27 
LCS_GDT     K      18     K      18      8   15   22     7    8    8   11   14   15   15   17   17   18   19   20   20   20   21   22   23   24   25   27 
LCS_GDT     A      19     A      19      8   15   22     7    8    8   11   14   15   15   17   17   18   19   20   20   20   21   22   23   24   25   27 
LCS_GDT     G      20     G      20      8   14   22     7    8    8   10   14   15   15   17   17   18   19   20   20   20   21   22   23   24   25   27 
LCS_GDT     V      21     V      21      8   14   22     3    8    8   10   14   15   15   17   17   18   19   20   20   20   21   22   23   24   25   26 
LCS_GDT     I      22     I      22      3    4   22     3    3    3    4    5    8   14   16   17   18   19   20   20   20   21   22   23   24   25   27 
LCS_GDT     T      23     T      23      3    4   22     3    4    4    4    5    7    9   11   13   15   19   20   20   20   21   22   23   24   25   27 
LCS_GDT     E      24     E      24      3    4   22     3    4    4    4    5    6    9   10   12   15   19   20   20   20   21   22   23   24   25   27 
LCS_GDT     E      25     E      25      3    4   22     3    3    4    4    5    7    8   10   12   12   13   15   17   17   19   22   23   24   25   27 
LCS_GDT     E      26     E      26      4    4   22     4    4    4    4    4    6    8   11   11   12   13   15   16   17   17   18   21   22   24   27 
LCS_GDT     K      27     K      27      4    4   18     4    4    4    4    4    6   10   11   11   12   13   15   16   17   19   22   23   24   25   27 
LCS_GDT     A      28     A      28      4    4   18     4    4    4    4    4    7   10   11   12   12   13   15   17   20   21   22   23   24   25   27 
LCS_GDT     E      29     E      29      4    8   18     4    4    4    4    5    7   10   11   12   12   13   15   16   17   19   22   23   24   25   27 
LCS_GDT     R      34     R      34      7    8   18     7    7    7    7    7    7   10   11   11   11   11   12   12   14   17   18   21   22   24   27 
LCS_GDT     Q      35     Q      35      7    8   18     7    7    7    7    7    7   10   11   11   11   12   15   16   17   19   20   22   24   25   27 
LCS_GDT     E      36     E      36      7    8   17     7    7    7    7    7    7   10   11   11   11   11   14   16   17   18   19   21   24   24   27 
LCS_GDT     Y      37     Y      37      7    8   13     7    7    7    7    7    7   10   11   11   11   11   12   12   14   15   17   19   21   23   25 
LCS_GDT     L      38     L      38      7    8   13     7    7    7    7    7    7   10   11   11   11   11   12   12   13   15   18   19   21   24   27 
LCS_GDT     K      39     K      39      7    8   13     7    7    7    7    7    7   10   11   11   11   11   12   12   14   16   18   21   24   24   27 
LCS_GDT     G      40     G      40      7    8   13     7    7    7    7    7    7   10   11   11   11   11   12   12   12   15   17   19   20   20   22 
LCS_AVERAGE  LCS_A:  35.71  (  21.35   29.95   55.82 )

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      9     10     11     11     14     15     15     17     17     18     19     20     20     20     21     22     23     24     25     27 
GDT PERCENT_CA  25.00  27.78  30.56  30.56  38.89  41.67  41.67  47.22  47.22  50.00  52.78  55.56  55.56  55.56  58.33  61.11  63.89  66.67  69.44  75.00
GDT RMS_LOCAL    0.27   0.33   0.79   0.79   2.00   2.09   1.99   2.38   2.38   2.75   3.70   3.74   3.74   3.74   4.39   5.55   5.18   6.04   6.13   7.19
GDT RMS_ALL_CA  12.71  12.74  12.76  12.76  12.47  12.56  12.58  12.48  12.48  12.30  11.69  11.92  11.92  11.92  10.91   9.64  10.69   9.23   9.44   8.21

#      Molecule1      Molecule2       DISTANCE
LGA    A       5      A       5          3.548
LGA    K       6      K       6          2.325
LGA    I       7      I       7          2.006
LGA    A       8      A       8          0.406
LGA    R       9      R       9          1.123
LGA    I      10      I      10          1.225
LGA    N      11      N      11          2.217
LGA    E      12      E      12          2.519
LGA    L      13      L      13          2.775
LGA    A      14      A      14          3.805
LGA    A      15      A      15          2.099
LGA    K      16      K      16          1.788
LGA    A      17      A      17          1.522
LGA    K      18      K      18          1.353
LGA    A      19      A      19          2.046
LGA    G      20      G      20          3.031
LGA    V      21      V      21          3.597
LGA    I      22      I      22          7.438
LGA    T      23      T      23         12.382
LGA    E      24      E      24         13.355
LGA    E      25      E      25         19.281
LGA    E      26      E      26         18.369
LGA    K      27      K      27         14.633
LGA    A      28      A      28         15.313
LGA    E      29      E      29         18.479
LGA    R      34      R      34         19.497
LGA    Q      35      Q      35         17.586
LGA    E      36      E      36         21.846
LGA    Y      37      Y      37         22.298
LGA    L      38      L      38         18.847
LGA    K      39      K      39         19.931
LGA    G      40      G      40         24.224

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   32   36    4.0     17    2.38    41.667    39.833     0.685

LGA_LOCAL      RMSD =  2.382  Number of atoms =   17  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 12.482  Number of atoms =   32 
Std_ALL_ATOMS  RMSD =  8.093  (standard rmsd on all 32 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.167955 * X  +  -0.966200 * Y  +  -0.195574 * Z  +  25.957022
  Y_new =  -0.323994 * X  +  -0.133268 * Y  +   0.936626 * Z  +  -0.709562
  Z_new =  -0.931031 * X  +   0.220676 * Y  +  -0.290660 * Z  +  -6.679415 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.492214   -0.649378  [ DEG:   142.7934    -37.2066 ]
  Theta =   1.197229    1.944364  [ DEG:    68.5961    111.4039 ]
  Phi   =  -2.049047    1.092546  [ DEG:  -117.4017     62.5983 ]
 
# 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: T0335AL316_4-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0335AL316_4-D1.T0335_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   32   36   4.0   17   2.38  39.833     8.09
REMARK  ---------------------------------------------------------- 
MOLECULE T0335AL316_4-D1
REMARK Aligment from pdb entry: 1e3h_A
ATOM     13  N   ALA     5      -0.798  -7.583  -9.217  1.00  0.00              
ATOM     14  CA  ALA     5      -0.499  -8.288  -7.978  1.00  0.00              
ATOM     15  C   ALA     5      -0.327  -7.337  -6.803  1.00  0.00              
ATOM     16  O   ALA     5      -0.928  -7.540  -5.746  1.00  0.00              
ATOM     17  N   LYS     6       0.469  -6.289  -6.984  1.00  0.00              
ATOM     18  CA  LYS     6       0.689  -5.337  -5.904  1.00  0.00              
ATOM     19  C   LYS     6      -0.583  -4.617  -5.439  1.00  0.00              
ATOM     20  O   LYS     6      -0.756  -4.376  -4.245  1.00  0.00              
ATOM     21  N   ILE     7      -1.483  -4.284  -6.358  1.00  0.00              
ATOM     22  CA  ILE     7      -2.714  -3.604  -5.950  1.00  0.00              
ATOM     23  C   ILE     7      -3.650  -4.535  -5.181  1.00  0.00              
ATOM     24  O   ILE     7      -4.348  -4.105  -4.263  1.00  0.00              
ATOM     25  N   ALA     8      -3.675  -5.806  -5.570  1.00  0.00              
ATOM     26  CA  ALA     8      -4.525  -6.787  -4.902  1.00  0.00              
ATOM     27  C   ALA     8      -3.948  -7.103  -3.522  1.00  0.00              
ATOM     28  O   ALA     8      -4.687  -7.252  -2.546  1.00  0.00              
ATOM     29  N   ARG     9      -2.623  -7.184  -3.448  1.00  0.00              
ATOM     30  CA  ARG     9      -1.943  -7.463  -2.192  1.00  0.00              
ATOM     31  C   ARG     9      -2.234  -6.338  -1.204  1.00  0.00              
ATOM     32  O   ARG     9      -2.811  -6.562  -0.140  1.00  0.00              
ATOM     33  N   ILE    10      -1.835  -5.126  -1.575  1.00  0.00              
ATOM     34  CA  ILE    10      -2.037  -3.949  -0.741  1.00  0.00              
ATOM     35  C   ILE    10      -3.479  -3.782  -0.274  1.00  0.00              
ATOM     36  O   ILE    10      -3.729  -3.480   0.896  1.00  0.00              
ATOM     37  N   ASN    11      -4.427  -3.967  -1.188  1.00  0.00              
ATOM     38  CA  ASN    11      -5.836  -3.824  -0.843  1.00  0.00              
ATOM     39  C   ASN    11      -6.196  -4.795   0.266  1.00  0.00              
ATOM     40  O   ASN    11      -6.694  -4.394   1.315  1.00  0.00              
ATOM     41  N   GLU    12      -5.933  -6.074   0.025  1.00  0.00              
ATOM     42  CA  GLU    12      -6.222  -7.118   1.001  1.00  0.00              
ATOM     43  C   GLU    12      -5.516  -6.848   2.334  1.00  0.00              
ATOM     44  O   GLU    12      -6.014  -7.222   3.396  1.00  0.00              
ATOM     45  N   LEU    13      -4.363  -6.187   2.269  1.00  0.00              
ATOM     46  CA  LEU    13      -3.581  -5.878   3.460  1.00  0.00              
ATOM     47  C   LEU    13      -4.075  -4.688   4.287  1.00  0.00              
ATOM     48  O   LEU    13      -3.995  -4.729   5.515  1.00  0.00              
ATOM     49  N   ALA    14      -4.590  -3.638   3.642  1.00  0.00              
ATOM     50  CA  ALA    14      -5.037  -2.458   4.391  1.00  0.00              
ATOM     51  C   ALA    14      -6.312  -1.763   3.913  1.00  0.00              
ATOM     52  O   ALA    14      -6.609  -0.655   4.349  1.00  0.00              
ATOM     53  N   ALA    15      -7.071  -2.407   3.038  1.00  0.00              
ATOM     54  CA  ALA    15      -8.284  -1.796   2.505  1.00  0.00              
ATOM     55  C   ALA    15      -9.266  -1.280   3.566  1.00  0.00              
ATOM     56  O   ALA    15      -9.791  -0.172   3.444  1.00  0.00              
ATOM     57  N   LYS    16      -9.533  -2.074   4.618  1.00  0.00              
ATOM     58  CA  LYS    16     -10.469  -1.615   5.654  1.00  0.00              
ATOM     59  C   LYS    16      -9.899  -0.508   6.547  1.00  0.00              
ATOM     60  O   LYS    16     -10.625   0.395   6.967  1.00  0.00              
ATOM     61  N   ALA    17      -8.602  -0.590   6.835  1.00  0.00              
ATOM     62  CA  ALA    17      -7.938   0.408   7.669  1.00  0.00              
ATOM     63  C   ALA    17      -7.888   1.738   6.936  1.00  0.00              
ATOM     64  O   ALA    17      -8.288   2.774   7.471  1.00  0.00              
ATOM     65  N   LYS    18      -7.382   1.694   5.708  1.00  0.00              
ATOM     66  CA  LYS    18      -7.271   2.880   4.872  1.00  0.00              
ATOM     67  C   LYS    18      -8.645   3.511   4.694  1.00  0.00              
ATOM     68  O   LYS    18      -8.799   4.730   4.762  1.00  0.00              
ATOM     69  N   ALA    19      -9.643   2.669   4.467  1.00  0.00              
ATOM     70  CA  ALA    19     -11.004   3.143   4.285  1.00  0.00              
ATOM     71  C   ALA    19     -11.480   3.884   5.532  1.00  0.00              
ATOM     72  O   ALA    19     -12.209   4.875   5.441  1.00  0.00              
ATOM     73  N   GLY    20     -11.059   3.397   6.696  1.00  0.00              
ATOM     74  CA  GLY    20     -11.434   3.998   7.972  1.00  0.00              
ATOM     75  C   GLY    20     -10.671   5.298   8.193  1.00  0.00              
ATOM     76  O   GLY    20     -11.245   6.308   8.611  1.00  0.00              
ATOM     77  N   VAL    21      -9.373   5.264   7.908  1.00  0.00              
ATOM     78  CA  VAL    21      -8.519   6.432   8.062  1.00  0.00              
ATOM     79  C   VAL    21      -9.048   7.627   7.261  1.00  0.00              
ATOM     80  O   VAL    21      -9.049   8.757   7.752  1.00  0.00              
ATOM     81  N   ILE    22      -9.507   7.374   6.038  1.00  0.00              
ATOM     82  CA  ILE    22     -10.022   8.440   5.183  1.00  0.00              
ATOM     83  C   ILE    22     -11.332   9.038   5.686  1.00  0.00              
ATOM     84  O   ILE    22     -11.895   9.932   5.048  1.00  0.00              
ATOM     85  N   THR    23     -11.817   8.556   6.827  1.00  0.00              
ATOM     86  CA  THR    23     -13.064   9.071   7.387  1.00  0.00              
ATOM     87  C   THR    23     -12.787  10.195   8.376  1.00  0.00              
ATOM     88  O   THR    23     -13.709  10.875   8.836  1.00  0.00              
ATOM     89  N   GLU    24     -11.510  10.385   8.692  1.00  0.00              
ATOM     90  CA  GLU    24     -11.086  11.422   9.624  1.00  0.00              
ATOM     91  C   GLU    24     -11.006  12.786   8.931  1.00  0.00              
ATOM     92  O   GLU    24     -10.110  13.035   8.120  1.00  0.00              
ATOM     93  N   GLU    25     -11.945  13.666   9.265  1.00  0.00              
ATOM     94  CA  GLU    25     -12.011  15.002   8.681  1.00  0.00              
ATOM     95  C   GLU    25     -10.783  15.868   8.959  1.00  0.00              
ATOM     96  O   GLU    25     -10.282  16.542   8.057  1.00  0.00              
ATOM     97  N   GLU    26     -10.309  15.859  10.204  1.00  0.00              
ATOM     98  CA  GLU    26      -9.145  16.654  10.565  1.00  0.00              
ATOM     99  C   GLU    26      -7.941  16.313   9.711  1.00  0.00              
ATOM    100  O   GLU    26      -7.557  15.149   9.621  1.00  0.00              
ATOM    101  N   LYS    27      -7.336  17.321   9.089  1.00  0.00              
ATOM    102  CA  LYS    27      -6.185  17.092   8.225  1.00  0.00              
ATOM    103  C   LYS    27      -4.994  16.448   8.931  1.00  0.00              
ATOM    104  O   LYS    27      -4.584  15.340   8.585  1.00  0.00              
ATOM    105  N   ALA    28      -4.434  17.142   9.915  1.00  0.00              
ATOM    106  CA  ALA    28      -3.284  16.630  10.650  1.00  0.00              
ATOM    107  C   ALA    28      -3.616  15.384  11.469  1.00  0.00              
ATOM    108  O   ALA    28      -2.745  14.559  11.750  1.00  0.00              
ATOM    109  N   GLU    29      -4.885  15.245  11.837  1.00  0.00              
ATOM    110  CA  GLU    29      -5.329  14.105  12.627  1.00  0.00              
ATOM    111  C   GLU    29      -5.530  12.854  11.760  1.00  0.00              
ATOM    112  O   GLU    29      -5.318  11.728  12.217  1.00  0.00              
ATOM    113  N   ARG    34      -5.944  13.060  10.512  1.00  0.00              
ATOM    114  CA  ARG    34      -6.164  11.965   9.569  1.00  0.00              
ATOM    115  C   ARG    34      -4.850  11.556   8.920  1.00  0.00              
ATOM    116  O   ARG    34      -4.660  10.396   8.556  1.00  0.00              
ATOM    117  N   GLN    35      -3.946  12.517   8.776  1.00  0.00              
ATOM    118  CA  GLN    35      -2.651  12.246   8.171  1.00  0.00              
ATOM    119  C   GLN    35      -1.831  11.375   9.113  1.00  0.00              
ATOM    120  O   GLN    35      -0.807  10.814   8.726  1.00  0.00              
ATOM    121  N   GLU    36      -2.289  11.274  10.356  1.00  0.00              
ATOM    122  CA  GLU    36      -1.620  10.453  11.357  1.00  0.00              
ATOM    123  C   GLU    36      -1.865   9.003  10.970  1.00  0.00              
ATOM    124  O   GLU    36      -0.926   8.242  10.737  1.00  0.00              
ATOM    125  N   TYR    37      -3.142   8.636  10.900  1.00  0.00              
ATOM    126  CA  TYR    37      -3.549   7.289  10.527  1.00  0.00              
ATOM    127  C   TYR    37      -2.909   6.873   9.212  1.00  0.00              
ATOM    128  O   TYR    37      -2.309   5.806   9.113  1.00  0.00              
ATOM    129  N   LEU    38      -3.043   7.728   8.203  1.00  0.00              
ATOM    130  CA  LEU    38      -2.489   7.452   6.885  1.00  0.00              
ATOM    131  C   LEU    38      -1.005   7.085   6.944  1.00  0.00              
ATOM    132  O   LEU    38      -0.587   6.091   6.351  1.00  0.00              
ATOM    133  N   LYS    39      -0.208   7.877   7.658  1.00  0.00              
ATOM    134  CA  LYS    39       1.219   7.582   7.776  1.00  0.00              
ATOM    135  C   LYS    39       1.432   6.264   8.514  1.00  0.00              
ATOM    136  O   LYS    39       2.487   5.638   8.395  1.00  0.00              
ATOM    137  N   GLY    40       0.420   5.848   9.273  1.00  0.00              
ATOM    138  CA  GLY    40       0.483   4.598  10.017  1.00  0.00              
ATOM    139  C   GLY    40       0.089   3.428   9.126  1.00  0.00              
ATOM    140  O   GLY    40       0.851   2.472   8.983  1.00  0.00              
END
