
#######################################################
#                                                     #
#                        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   34 (  136),  selected   34 , name T0335AL243_1-D1
# Molecule2: number of CA atoms   36 (  584),  selected   34 , name T0335_D1.pdb
# PARAMETERS: T0335AL243_1-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:    34         5 - 40          4.09     4.09
  LCS_AVERAGE:     94.44

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16        24 - 40          1.70     6.55
  LCS_AVERAGE:     41.09

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15         5 - 19          0.70     6.17
  LCS_AVERAGE:     32.76

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     15   15   34     9   14   15   16   16   17   19   19   22   25   28   32   32   33   34   34   34   34   34   34 
LCS_GDT     K       6     K       6     15   15   34     9   14   15   16   16   17   19   20   24   28   30   32   32   33   34   34   34   34   34   34 
LCS_GDT     I       7     I       7     15   15   34     9   14   15   16   16   17   20   24   26   28   30   32   32   33   34   34   34   34   34   34 
LCS_GDT     A       8     A       8     15   15   34     9   14   15   16   16   17   19   23   25   28   30   32   32   33   34   34   34   34   34   34 
LCS_GDT     R       9     R       9     15   15   34     9   14   15   16   16   17   19   21   25   28   30   32   32   33   34   34   34   34   34   34 
LCS_GDT     I      10     I      10     15   15   34     9   14   15   16   16   17   20   24   26   28   30   32   32   33   34   34   34   34   34   34 
LCS_GDT     N      11     N      11     15   15   34     9   14   15   16   16   17   22   24   26   28   30   32   32   33   34   34   34   34   34   34 
LCS_GDT     E      12     E      12     15   15   34     9   14   15   16   16   17   22   24   26   28   30   32   32   33   34   34   34   34   34   34 
LCS_GDT     L      13     L      13     15   15   34     8   14   15   16   16   17   22   24   26   28   30   32   32   33   34   34   34   34   34   34 
LCS_GDT     A      14     A      14     15   15   34     7   14   15   16   17   18   22   24   26   28   30   32   32   33   34   34   34   34   34   34 
LCS_GDT     A      15     A      15     15   15   34     9   14   15   16   17   18   22   24   26   28   30   32   32   33   34   34   34   34   34   34 
LCS_GDT     K      16     K      16     15   15   34     5   14   15   16   17   18   22   24   26   28   30   32   32   33   34   34   34   34   34   34 
LCS_GDT     A      17     A      17     15   15   34     7   14   15   16   16   17   22   24   26   28   30   32   32   33   34   34   34   34   34   34 
LCS_GDT     K      18     K      18     15   15   34     5   14   15   16   17   18   22   24   26   28   30   32   32   33   34   34   34   34   34   34 
LCS_GDT     A      19     A      19     15   15   34     5   11   15   16   16   18   20   23   26   28   30   32   32   33   34   34   34   34   34   34 
LCS_GDT     G      20     G      20      3    4   34     3    3    3   10   14   15   19   20   21   24   25   28   30   33   34   34   34   34   34   34 
LCS_GDT     V      21     V      21      3    4   34     3    3    3    5   15   16   17   21   24   28   30   32   32   33   34   34   34   34   34   34 
LCS_GDT     I      22     I      22      3   14   34     3    3    3    7    9   14   18   20   21   24   28   32   32   33   34   34   34   34   34   34 
LCS_GDT     E      24     E      24      3   16   34     3    3    4    6   12   18   22   24   26   28   30   32   32   33   34   34   34   34   34   34 
LCS_GDT     E      25     E      25     12   16   34     5   13   13   15   17   18   22   24   26   28   30   32   32   33   34   34   34   34   34   34 
LCS_GDT     E      26     E      26     12   16   34     9   13   13   15   17   18   22   24   26   28   30   32   32   33   34   34   34   34   34   34 
LCS_GDT     K      27     K      27     12   16   34     9   13   13   15   17   18   22   24   26   28   30   32   32   33   34   34   34   34   34   34 
LCS_GDT     A      28     A      28     12   16   34     9   13   13   15   17   18   22   24   26   28   30   32   32   33   34   34   34   34   34   34 
LCS_GDT     E      29     E      29     12   16   34     9   13   13   15   17   18   22   24   26   28   30   32   32   33   34   34   34   34   34   34 
LCS_GDT     Q      30     Q      30     12   16   34     9   13   13   15   17   18   22   24   26   28   30   32   32   33   34   34   34   34   34   34 
LCS_GDT     Q      31     Q      31     12   16   34     7   13   13   15   17   18   22   24   26   28   30   32   32   33   34   34   34   34   34   34 
LCS_GDT     K      32     K      32     12   16   34     7   13   13   15   17   18   22   24   26   28   30   32   32   33   34   34   34   34   34   34 
LCS_GDT     L      33     L      33     12   16   34     9   13   13   15   17   18   22   24   26   28   30   32   32   33   34   34   34   34   34   34 
LCS_GDT     R      34     R      34     12   16   34     9   13   13   15   17   18   22   24   26   28   30   32   32   33   34   34   34   34   34   34 
LCS_GDT     Q      35     Q      35     12   16   34     9   13   13   16   17   18   22   24   26   28   30   32   32   33   34   34   34   34   34   34 
LCS_GDT     E      36     E      36     12   16   34     9   13   13   15   17   18   22   24   26   28   30   32   32   33   34   34   34   34   34   34 
LCS_GDT     L      38     L      38     12   16   34     3    4    6   11   13   16   19   20   22   23   26   28   29   33   34   34   34   34   34   34 
LCS_GDT     K      39     K      39      4   16   34     3    3    6   13   16   17   19   21   26   28   30   32   32   33   34   34   34   34   34   34 
LCS_GDT     G      40     G      40      4   16   34     5    7   13   15   17   18   22   24   26   28   30   32   32   33   34   34   34   34   34   34 
LCS_AVERAGE  LCS_A:  56.10  (  32.76   41.09   94.44 )

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     14     15     16     17     18     22     24     26     28     30     32     32     33     34     34     34     34     34     34 
GDT PERCENT_CA  25.00  38.89  41.67  44.44  47.22  50.00  61.11  66.67  72.22  77.78  83.33  88.89  88.89  91.67  94.44  94.44  94.44  94.44  94.44  94.44
GDT RMS_LOCAL    0.26   0.62   0.70   1.06   1.44   1.60   2.34   2.68   2.89   3.16   3.48   3.76   3.76   3.92   4.09   4.09   4.09   4.09   4.09   4.09
GDT RMS_ALL_CA   6.05   6.17   6.17   5.94   5.63   5.74   4.86   4.56   4.50   4.31   4.17   4.12   4.12   4.11   4.09   4.09   4.09   4.09   4.09   4.09

#      Molecule1      Molecule2       DISTANCE
LGA    A       5      A       5          8.063
LGA    K       6      K       6          6.241
LGA    I       7      I       7          3.988
LGA    A       8      A       8          4.773
LGA    R       9      R       9          5.113
LGA    I      10      I      10          3.526
LGA    N      11      N      11          1.583
LGA    E      12      E      12          2.419
LGA    L      13      L      13          3.033
LGA    A      14      A      14          1.854
LGA    A      15      A      15          1.311
LGA    K      16      K      16          2.254
LGA    A      17      A      17          3.426
LGA    K      18      K      18          3.150
LGA    A      19      A      19          4.741
LGA    G      20      G      20          9.088
LGA    V      21      V      21          7.425
LGA    I      22      I      22          7.427
LGA    E      24      E      24          3.499
LGA    E      25      E      25          3.861
LGA    E      26      E      26          3.654
LGA    K      27      K      27          2.530
LGA    A      28      A      28          2.768
LGA    E      29      E      29          3.001
LGA    Q      30      Q      30          1.956
LGA    Q      31      Q      31          0.562
LGA    K      32      K      32          1.858
LGA    L      33      L      33          2.887
LGA    R      34      R      34          2.491
LGA    Q      35      Q      35          1.893
LGA    E      36      E      36          2.793
LGA    L      38      L      38          7.638
LGA    K      39      K      39          5.245
LGA    G      40      G      40          2.992

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   34   36    4.0     24    2.68    61.111    57.398     0.865

LGA_LOCAL      RMSD =  2.676  Number of atoms =   24  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.332  Number of atoms =   34 
Std_ALL_ATOMS  RMSD =  4.089  (standard rmsd on all 34 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.533137 * X  +   0.842644 * Y  +   0.075605 * Z  + -23.249397
  Y_new =   0.836077 * X  +   0.538424 * Y  +  -0.105235 * Z  +  18.746868
  Z_new =  -0.129383 * X  +   0.007107 * Y  +  -0.991569 * Z  + 102.279457 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   3.134426   -0.007167  [ DEG:   179.5894     -0.4106 ]
  Theta =   0.129747    3.011846  [ DEG:     7.4340    172.5660 ]
  Phi   =   2.138452   -1.003141  [ DEG:   122.5242    -57.4757 ]
 
# 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: T0335AL243_1-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0335AL243_1-D1.T0335_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   34   36   4.0   24   2.68  57.398     4.09
REMARK  ---------------------------------------------------------- 
MOLECULE T0335AL243_1-D1
REMARK Aligment from pdb entry: 1dg3A
ATOM      5  N   ALA     5      -6.262  -8.649 -12.114  1.00  0.00              
ATOM      6  CA  ALA     5      -6.589  -9.413 -10.919  1.00  0.00              
ATOM      7  C   ALA     5      -5.617  -9.009  -9.813  1.00  0.00              
ATOM      8  O   ALA     5      -5.940  -9.075  -8.626  1.00  0.00              
ATOM      9  N   LYS     6      -4.423  -8.588 -10.213  1.00  0.00              
ATOM     10  CA  LYS     6      -3.415  -8.157  -9.258  1.00  0.00              
ATOM     11  C   LYS     6      -3.801  -6.799  -8.691  1.00  0.00              
ATOM     12  O   LYS     6      -3.798  -6.603  -7.479  1.00  0.00              
ATOM     13  N   ILE     7      -4.123  -5.858  -9.574  1.00  0.00              
ATOM     14  CA  ILE     7      -4.507  -4.522  -9.136  1.00  0.00              
ATOM     15  C   ILE     7      -5.693  -4.557  -8.180  1.00  0.00              
ATOM     16  O   ILE     7      -5.710  -3.828  -7.189  1.00  0.00              
ATOM     17  N   ALA     8      -6.679  -5.401  -8.466  1.00  0.00              
ATOM     18  CA  ALA     8      -7.851  -5.482  -7.602  1.00  0.00              
ATOM     19  C   ALA     8      -7.497  -6.080  -6.247  1.00  0.00              
ATOM     20  O   ALA     8      -8.017  -5.653  -5.218  1.00  0.00              
ATOM     21  N   ARG     9      -6.618  -7.075  -6.254  1.00  0.00              
ATOM     22  CA  ARG     9      -6.184  -7.717  -5.019  1.00  0.00              
ATOM     23  C   ARG     9      -5.436  -6.676  -4.191  1.00  0.00              
ATOM     24  O   ARG     9      -5.650  -6.541  -2.983  1.00  0.00              
ATOM     25  N   ILE    10      -4.556  -5.943  -4.863  1.00  0.00              
ATOM     26  CA  ILE    10      -3.761  -4.909  -4.223  1.00  0.00              
ATOM     27  C   ILE    10      -4.644  -3.855  -3.564  1.00  0.00              
ATOM     28  O   ILE    10      -4.456  -3.524  -2.391  1.00  0.00              
ATOM     29  N   ASN    11      -5.601  -3.326  -4.322  1.00  0.00              
ATOM     30  CA  ASN    11      -6.510  -2.311  -3.798  1.00  0.00              
ATOM     31  C   ASN    11      -7.251  -2.835  -2.573  1.00  0.00              
ATOM     32  O   ASN    11      -7.417  -2.119  -1.589  1.00  0.00              
ATOM     33  N   GLU    12      -7.689  -4.088  -2.637  1.00  0.00              
ATOM     34  CA  GLU    12      -8.405  -4.708  -1.527  1.00  0.00              
ATOM     35  C   GLU    12      -7.537  -4.791  -0.272  1.00  0.00              
ATOM     36  O   GLU    12      -8.035  -4.641   0.846  1.00  0.00              
ATOM     37  N   LEU    13      -6.243  -5.035  -0.456  1.00  0.00              
ATOM     38  CA  LEU    13      -5.331  -5.141   0.681  1.00  0.00              
ATOM     39  C   LEU    13      -5.024  -3.767   1.264  1.00  0.00              
ATOM     40  O   LEU    13      -4.861  -3.629   2.479  1.00  0.00              
ATOM     41  N   ALA    14      -4.937  -2.752   0.404  1.00  0.00              
ATOM     42  CA  ALA    14      -4.680  -1.395   0.871  1.00  0.00              
ATOM     43  C   ALA    14      -5.856  -1.026   1.760  1.00  0.00              
ATOM     44  O   ALA    14      -5.685  -0.449   2.838  1.00  0.00              
ATOM     45  N   ALA    15      -7.058  -1.359   1.296  1.00  0.00              
ATOM     46  CA  ALA    15      -8.265  -1.075   2.062  1.00  0.00              
ATOM     47  C   ALA    15      -8.176  -1.746   3.433  1.00  0.00              
ATOM     48  O   ALA    15      -8.476  -1.130   4.456  1.00  0.00              
ATOM     49  N   LYS    16      -7.763  -3.010   3.453  1.00  0.00              
ATOM     50  CA  LYS    16      -7.637  -3.731   4.713  1.00  0.00              
ATOM     51  C   LYS    16      -6.639  -3.037   5.641  1.00  0.00              
ATOM     52  O   LYS    16      -6.869  -2.927   6.844  1.00  0.00              
ATOM     53  N   ALA    17      -5.534  -2.567   5.072  1.00  0.00              
ATOM     54  CA  ALA    17      -4.502  -1.872   5.837  1.00  0.00              
ATOM     55  C   ALA    17      -5.089  -0.627   6.501  1.00  0.00              
ATOM     56  O   ALA    17      -4.920  -0.409   7.705  1.00  0.00              
ATOM     57  N   LYS    18      -5.779   0.188   5.708  1.00  0.00              
ATOM     58  CA  LYS    18      -6.387   1.415   6.216  1.00  0.00              
ATOM     59  C   LYS    18      -7.450   1.143   7.272  1.00  0.00              
ATOM     60  O   LYS    18      -7.736   2.002   8.111  1.00  0.00              
ATOM     61  N   ALA    19      -8.027  -0.053   7.235  1.00  0.00              
ATOM     62  CA  ALA    19      -9.062  -0.419   8.192  1.00  0.00              
ATOM     63  C   ALA    19      -8.506  -0.863   9.544  1.00  0.00              
ATOM     64  O   ALA    19      -9.247  -0.936  10.525  1.00  0.00              
ATOM     65  N   GLY    20      -5.800   2.311  15.055  1.00  0.00              
ATOM     66  CA  GLY    20      -4.708   3.022  15.715  1.00  0.00              
ATOM     67  C   GLY    20      -3.329   2.653  15.173  1.00  0.00              
ATOM     68  O   GLY    20      -2.475   2.148  15.905  1.00  0.00              
ATOM     69  N   VAL    21      -3.114   2.893  13.884  1.00  0.00              
ATOM     70  CA  VAL    21      -1.820   2.586  13.283  1.00  0.00              
ATOM     71  C   VAL    21      -0.816   3.684  13.623  1.00  0.00              
ATOM     72  O   VAL    21       0.389   3.448  13.647  1.00  0.00              
ATOM     73  N   ILE    22      -1.315   4.888  13.887  1.00  0.00              
ATOM     74  CA  ILE    22      -0.419   5.978  14.234  1.00  0.00              
ATOM     75  C   ILE    22      -0.034   6.893  13.087  1.00  0.00              
ATOM     76  O   ILE    22      -0.411   6.664  11.937  1.00  0.00              
ATOM     77  N   GLU    24       0.746   7.922  13.410  1.00  0.00              
ATOM     78  CA  GLU    24       1.181   8.926  12.440  1.00  0.00              
ATOM     79  C   GLU    24       2.017   8.460  11.243  1.00  0.00              
ATOM     80  O   GLU    24       2.117   9.180  10.251  1.00  0.00              
ATOM     81  N   GLU    25       2.612   7.271  11.316  1.00  0.00              
ATOM     82  CA  GLU    25       3.451   6.785  10.220  1.00  0.00              
ATOM     83  C   GLU    25       2.717   5.911   9.200  1.00  0.00              
ATOM     84  O   GLU    25       3.326   5.411   8.259  1.00  0.00              
ATOM     85  N   GLU    26       1.416   5.739   9.384  1.00  0.00              
ATOM     86  CA  GLU    26       0.617   4.899   8.496  1.00  0.00              
ATOM     87  C   GLU    26       0.845   5.156   7.006  1.00  0.00              
ATOM     88  O   GLU    26       1.145   4.228   6.251  1.00  0.00              
ATOM     89  N   LYS    27       0.707   6.410   6.586  1.00  0.00              
ATOM     90  CA  LYS    27       0.884   6.772   5.186  1.00  0.00              
ATOM     91  C   LYS    27       2.286   6.586   4.650  1.00  0.00              
ATOM     92  O   LYS    27       2.478   6.004   3.585  1.00  0.00              
ATOM     93  N   ALA    28       3.265   7.098   5.382  1.00  0.00              
ATOM     94  CA  ALA    28       4.660   6.996   4.980  1.00  0.00              
ATOM     95  C   ALA    28       5.082   5.535   4.812  1.00  0.00              
ATOM     96  O   ALA    28       5.739   5.179   3.835  1.00  0.00              
ATOM     97  N   GLU    29       4.694   4.695   5.769  1.00  0.00              
ATOM     98  CA  GLU    29       5.028   3.273   5.737  1.00  0.00              
ATOM     99  C   GLU    29       4.450   2.571   4.496  1.00  0.00              
ATOM    100  O   GLU    29       5.169   1.875   3.783  1.00  0.00              
ATOM    101  N   GLN    30       3.162   2.768   4.234  1.00  0.00              
ATOM    102  CA  GLN    30       2.524   2.138   3.077  1.00  0.00              
ATOM    103  C   GLN    30       3.072   2.631   1.736  1.00  0.00              
ATOM    104  O   GLN    30       3.376   1.830   0.853  1.00  0.00              
ATOM    105  N   GLN    31       3.199   3.945   1.581  1.00  0.00              
ATOM    106  CA  GLN    31       3.695   4.496   0.326  1.00  0.00              
ATOM    107  C   GLN    31       5.122   4.064   0.039  1.00  0.00              
ATOM    108  O   GLN    31       5.481   3.817  -1.111  1.00  0.00              
ATOM    109  N   LYS    32       5.944   3.975   1.076  1.00  0.00              
ATOM    110  CA  LYS    32       7.321   3.545   0.878  1.00  0.00              
ATOM    111  C   LYS    32       7.300   2.091   0.413  1.00  0.00              
ATOM    112  O   LYS    32       8.131   1.670  -0.396  1.00  0.00              
ATOM    113  N   LEU    33       6.346   1.325   0.934  1.00  0.00              
ATOM    114  CA  LEU    33       6.217  -0.074   0.555  1.00  0.00              
ATOM    115  C   LEU    33       5.777  -0.166  -0.900  1.00  0.00              
ATOM    116  O   LEU    33       6.398  -0.853  -1.709  1.00  0.00              
ATOM    117  N   ARG    34       4.694   0.531  -1.218  1.00  0.00              
ATOM    118  CA  ARG    34       4.158   0.527  -2.574  1.00  0.00              
ATOM    119  C   ARG    34       5.191   1.027  -3.579  1.00  0.00              
ATOM    120  O   ARG    34       5.298   0.501  -4.686  1.00  0.00              
ATOM    121  N   GLN    35       5.957   2.038  -3.184  1.00  0.00              
ATOM    122  CA  GLN    35       6.990   2.593  -4.051  1.00  0.00              
ATOM    123  C   GLN    35       7.990   1.511  -4.441  1.00  0.00              
ATOM    124  O   GLN    35       8.417   1.432  -5.591  1.00  0.00              
ATOM    125  N   GLU    36       8.354   0.672  -3.476  1.00  0.00              
ATOM    126  CA  GLU    36       9.314  -0.402  -3.705  1.00  0.00              
ATOM    127  C   GLU    36       8.776  -1.559  -4.551  1.00  0.00              
ATOM    128  O   GLU    36       9.548  -2.394  -5.018  1.00  0.00              
ATOM    129  N   LEU    38       7.462  -1.621  -4.739  1.00  0.00              
ATOM    130  CA  LEU    38       6.871  -2.699  -5.531  1.00  0.00              
ATOM    131  C   LEU    38       6.483  -2.212  -6.925  1.00  0.00              
ATOM    132  O   LEU    38       6.106  -3.000  -7.791  1.00  0.00              
ATOM    133  N   LYS    39       6.585  -0.903  -7.119  1.00  0.00              
ATOM    134  CA  LYS    39       6.248  -0.248  -8.377  1.00  0.00              
ATOM    135  C   LYS    39       6.839  -0.961  -9.594  1.00  0.00              
ATOM    136  O   LYS    39       6.142  -1.217 -10.577  1.00  0.00              
ATOM    137  N   GLY    40       8.123  -1.284  -9.520  1.00  0.00              
ATOM    138  CA  GLY    40       8.796  -1.968 -10.614  1.00  0.00              
ATOM    139  C   GLY    40       8.169  -3.339 -10.851  1.00  0.00              
ATOM    140  O   GLY    40       7.861  -3.707 -11.984  1.00  0.00              
END
