
#######################################################
#                                                     #
#                        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 T0335AL333_5-D1
# Molecule2: number of CA atoms   36 (  584),  selected   32 , name T0335_D1.pdb
# PARAMETERS: T0335AL333_5-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:    17        24 - 40          4.93    10.58
  LCS_AVERAGE:     44.62

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13        26 - 38          1.87    14.05
  LCS_AVERAGE:     22.48

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8        31 - 38          0.25    12.22
  LCS_AVERAGE:     13.89

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      0    0   15     0    0    1    1    6    7    7    7    8    9    9   14   15   19   23   26   27   30   31   31 
LCS_GDT     K       6     K       6      6    7   15     6    6    6    6    6    9   13   13   15   16   18   19   20   21   23   26   28   30   31   31 
LCS_GDT     I       7     I       7      6    7   15     6    6    6    6    6    6    8   14   16   17   18   19   20   21   24   26   28   30   31   31 
LCS_GDT     A       8     A       8      6    7   15     6    6    6    6    8   10   12   14   16   17   18   19   20   21   24   26   28   30   31   31 
LCS_GDT     R       9     R       9      6    7   15     6    6    6    6    8   10   12   14   16   17   18   19   20   21   24   26   28   30   31   31 
LCS_GDT     I      10     I      10      6    7   15     6    6    6    6    6    9   12   14   16   17   18   19   20   21   24   26   28   30   31   31 
LCS_GDT     N      11     N      11      6    7   15     6    6    6    6    6    6    8    9   12   15   17   18   20   21   24   26   28   30   31   31 
LCS_GDT     K      16     K      16      3    7   15     3    3    3    4    5    5    8    9   11   12   14   18   20   21   24   26   28   30   31   31 
LCS_GDT     A      17     A      17      3    5   15     3    3    3    4    5    5    8    9   11   14   17   18   20   21   24   26   28   30   31   31 
LCS_GDT     K      18     K      18      3    5   15     3    3    3    4    6    7    7    8    9   10   12   15   17   19   22   25   27   30   31   31 
LCS_GDT     A      19     A      19      3    5   15     3    3    4    5    5    7    7    8    9   10   11   14   17   18   22   23   26   28   31   31 
LCS_GDT     G      20     G      20      3    5   15     3    3    4    5    6    7    7    8    9   10   11   15   17   21   24   26   28   30   31   31 
LCS_GDT     V      21     V      21      3    5   15     3    3    4    5    6    7    7    8    9   10   13   16   20   21   24   26   28   30   31   31 
LCS_GDT     I      22     I      22      3    5   15     3    3    4    4    6    7    7    8    9   10   12   15   20   21   24   26   28   30   31   31 
LCS_GDT     T      23     T      23      3    5   15     3    3    3    4    6    7    7    8    9    9   11   14   15   15   17   19   24   24   24   25 
LCS_GDT     E      24     E      24      3    3   17     3    4    4    4   10   11   13   13   16   17   18   19   20   21   24   26   28   30   31   31 
LCS_GDT     E      25     E      25      3    3   17     3    4    4    5    5    6    7   13   15   17   18   19   20   21   24   26   28   30   31   31 
LCS_GDT     E      26     E      26      6   13   17     4    5    6    8   10   13   13   13   14   16   16   19   20   21   23   26   28   30   31   31 
LCS_GDT     K      27     K      27      6   13   17     4    5    6    8   11   13   13   13   15   16   16   19   20   21   24   26   28   30   31   31 
LCS_GDT     A      28     A      28      6   13   17     4    5    8    9   11   13   13   14   16   17   18   19   20   21   24   26   28   30   31   31 
LCS_GDT     E      29     E      29      6   13   17     4    5    7   10   11   13   13   14   16   17   18   19   20   21   24   26   28   30   31   31 
LCS_GDT     Q      30     Q      30      6   13   17     3    5    6   10   11   13   13   13   16   17   18   19   20   21   24   26   28   30   31   31 
LCS_GDT     Q      31     Q      31      8   13   17     8    8    8   10   11   13   13   14   16   17   18   19   20   21   24   26   28   30   31   31 
LCS_GDT     K      32     K      32      8   13   17     8    8    8   10   11   13   13   14   16   17   18   19   20   21   24   26   28   30   31   31 
LCS_GDT     L      33     L      33      8   13   17     8    8    8   10   11   13   13   14   16   17   18   19   20   21   24   26   28   30   31   31 
LCS_GDT     R      34     R      34      8   13   17     8    8    8   10   11   13   13   14   16   17   18   19   20   21   24   26   28   30   31   31 
LCS_GDT     Q      35     Q      35      8   13   17     8    8    8   10   11   13   13   14   16   17   18   19   20   21   24   26   28   30   31   31 
LCS_GDT     E      36     E      36      8   13   17     8    8    8   10   11   13   13   14   16   17   18   19   20   21   24   26   28   30   31   31 
LCS_GDT     Y      37     Y      37      8   13   17     8    8    8   10   11   13   13   14   16   17   18   19   20   21   24   26   28   30   31   31 
LCS_GDT     L      38     L      38      8   13   17     8    8    8   10   11   13   13   14   16   17   18   19   20   21   24   26   28   30   31   31 
LCS_GDT     K      39     K      39      0    0   17     0    0    0    0    0    0    0    4    4   14   17   18   19   21   23   26   28   30   31   31 
LCS_GDT     G      40     G      40      0    0   17     0    1    2    2    2    2    3    5    8   14   17   18   19   20   23   26   28   30   31   31 
LCS_AVERAGE  LCS_A:  27.00  (  13.89   22.48   44.62 )

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      8      8      8     10     11     13     13     14     16     17     18     19     20     21     24     26     28     30     31     31 
GDT PERCENT_CA  22.22  22.22  22.22  27.78  30.56  36.11  36.11  38.89  44.44  47.22  50.00  52.78  55.56  58.33  66.67  72.22  77.78  83.33  86.11  86.11
GDT RMS_LOCAL    0.25   0.25   0.25   1.26   1.43   1.87   1.87   2.78   3.09   3.33   3.51   3.78   3.93   4.86   5.41   5.66   6.05   6.38   6.53   6.53
GDT RMS_ALL_CA  12.22  12.22  12.22  12.45  12.72  14.05  14.05   8.10   8.45   8.77   8.89   9.60   9.09   7.41   7.22   7.23   6.96   6.84   6.84   6.84

#      Molecule1      Molecule2       DISTANCE
LGA    A       5      A       5         14.242
LGA    K       6      K       6          5.899
LGA    I       7      I       7          3.819
LGA    A       8      A       8          3.071
LGA    R       9      R       9          3.132
LGA    I      10      I      10          3.187
LGA    N      11      N      11          7.303
LGA    K      16      K      16         12.449
LGA    A      17      A      17         10.426
LGA    K      18      K      18         14.471
LGA    A      19      A      19         14.418
LGA    G      20      G      20         11.500
LGA    V      21      V      21          8.365
LGA    I      22      I      22          9.052
LGA    T      23      T      23         12.955
LGA    E      24      E      24          5.544
LGA    E      25      E      25          8.279
LGA    E      26      E      26          9.348
LGA    K      27      K      27          8.251
LGA    A      28      A      28          3.868
LGA    E      29      E      29          3.571
LGA    Q      30      Q      30          5.273
LGA    Q      31      Q      31          1.361
LGA    K      32      K      32          1.941
LGA    L      33      L      33          2.934
LGA    R      34      R      34          2.332
LGA    Q      35      Q      35          1.637
LGA    E      36      E      36          2.533
LGA    Y      37      Y      37          1.430
LGA    L      38      L      38          2.373
LGA    K      39      K      39         11.524
LGA    G      40      G      40         12.403

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   32   36    4.0     14    2.78    40.278    35.457     0.486

LGA_LOCAL      RMSD =  2.779  Number of atoms =   14  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  8.103  Number of atoms =   32 
Std_ALL_ATOMS  RMSD =  6.810  (standard rmsd on all 32 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.986263 * X  +  -0.114277 * Y  +   0.119277 * Z  + -34.529865
  Y_new =   0.158086 * X  +   0.443559 * Y  +  -0.882193 * Z  +  21.018705
  Z_new =   0.047908 * X  +   0.888930 * Y  +   0.455531 * Z  + -151.506546 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.097239   -2.044353  [ DEG:    62.8672   -117.1328 ]
  Theta =  -0.047927   -3.093666  [ DEG:    -2.7460   -177.2540 ]
  Phi   =   0.158936   -2.982657  [ DEG:     9.1063   -170.8937 ]
 
# 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: T0335AL333_5-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0335AL333_5-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   14   2.78  35.457     6.81
REMARK  ---------------------------------------------------------- 
MOLECULE T0335AL333_5-D1
REMARK Aligment from pdb entry: 2irf_G
ATOM      1  N   ALA     5       5.862  -5.775 -16.425  1.00  0.00              
ATOM      2  CA  ALA     5       4.930  -6.057 -17.558  1.00  0.00              
ATOM      3  C   ALA     5       3.483  -6.186 -17.076  1.00  0.00              
ATOM      4  O   ALA     5       2.547  -5.933 -17.838  1.00  0.00              
ATOM      5  N   LYS     6      -2.218  -4.351  -8.645  1.00  0.00              
ATOM      6  CA  LYS     6      -2.822  -3.750  -7.463  1.00  0.00              
ATOM      7  C   LYS     6      -3.561  -4.789  -6.637  1.00  0.00              
ATOM      8  O   LYS     6      -3.472  -4.782  -5.413  1.00  0.00              
ATOM      9  N   ILE     7      -4.311  -5.668  -7.299  1.00  0.00              
ATOM     10  CA  ILE     7      -5.041  -6.712  -6.587  1.00  0.00              
ATOM     11  C   ILE     7      -4.056  -7.571  -5.812  1.00  0.00              
ATOM     12  O   ILE     7      -4.292  -7.904  -4.659  1.00  0.00              
ATOM     13  N   ALA     8      -2.939  -7.896  -6.453  1.00  0.00              
ATOM     14  CA  ALA     8      -1.887  -8.703  -5.848  1.00  0.00              
ATOM     15  C   ALA     8      -1.278  -7.986  -4.634  1.00  0.00              
ATOM     16  O   ALA     8      -0.903  -8.627  -3.653  1.00  0.00              
ATOM     17  N   ARG     9      -1.189  -6.657  -4.707  1.00  0.00              
ATOM     18  CA  ARG     9      -0.648  -5.846  -3.616  1.00  0.00              
ATOM     19  C   ARG     9      -1.606  -5.844  -2.437  1.00  0.00              
ATOM     20  O   ARG     9      -1.181  -5.954  -1.290  1.00  0.00              
ATOM     21  N   ILE    10      -2.899  -5.719  -2.727  1.00  0.00              
ATOM     22  CA  ILE    10      -3.929  -5.708  -1.693  1.00  0.00              
ATOM     23  C   ILE    10      -4.000  -7.073  -1.022  1.00  0.00              
ATOM     24  O   ILE    10      -3.956  -7.177   0.205  1.00  0.00              
ATOM     25  N   ASN    11      -4.078  -8.113  -1.847  1.00  0.00              
ATOM     26  CA  ASN    11      -4.177  -9.486  -1.376  1.00  0.00              
ATOM     27  C   ASN    11      -2.974  -9.960  -0.569  1.00  0.00              
ATOM     28  O   ASN    11      -3.106 -10.859   0.263  1.00  0.00              
ATOM     29  N   LYS    16      -1.817  -9.339  -0.792  1.00  0.00              
ATOM     30  CA  LYS    16      -0.597  -9.716  -0.081  1.00  0.00              
ATOM     31  C   LYS    16      -0.539  -9.182   1.352  1.00  0.00              
ATOM     32  O   LYS    16       0.263  -9.654   2.156  1.00  0.00              
ATOM     33  N   ALA    17      -1.369  -8.184   1.651  1.00  0.00              
ATOM     34  CA  ALA    17      -1.424  -7.562   2.976  1.00  0.00              
ATOM     35  C   ALA    17      -0.065  -7.011   3.405  1.00  0.00              
ATOM     36  O   ALA    17       0.197  -6.848   4.600  1.00  0.00              
ATOM     37  N   LYS    18       0.795  -6.723   2.430  1.00  0.00              
ATOM     38  CA  LYS    18       2.129  -6.201   2.711  1.00  0.00              
ATOM     39  C   LYS    18       2.198  -4.670   2.733  1.00  0.00              
ATOM     40  O   LYS    18       3.241  -4.093   3.033  1.00  0.00              
ATOM     41  N   ALA    19       1.093  -4.017   2.390  1.00  0.00              
ATOM     42  CA  ALA    19       1.042  -2.558   2.373  1.00  0.00              
ATOM     43  C   ALA    19       0.132  -2.087   3.502  1.00  0.00              
ATOM     44  O   ALA    19      -1.072  -2.345   3.486  1.00  0.00              
ATOM     45  N   GLY    20       0.697  -1.376   4.492  1.00  0.00              
ATOM     46  CA  GLY    20      -0.079  -0.872   5.633  1.00  0.00              
ATOM     47  C   GLY    20      -1.222   0.035   5.171  1.00  0.00              
ATOM     48  O   GLY    20      -0.991   1.034   4.492  1.00  0.00              
ATOM     49  N   VAL    21      -2.454  -0.341   5.502  1.00  0.00              
ATOM     50  CA  VAL    21      -3.607   0.448   5.110  1.00  0.00              
ATOM     51  C   VAL    21      -4.310  -0.016   3.842  1.00  0.00              
ATOM     52  O   VAL    21      -5.489   0.286   3.651  1.00  0.00              
ATOM     53  N   ILE    22      -3.594  -0.730   2.971  1.00  0.00              
ATOM     54  CA  ILE    22      -4.160  -1.228   1.718  1.00  0.00              
ATOM     55  C   ILE    22      -4.922  -2.529   1.953  1.00  0.00              
ATOM     56  O   ILE    22      -4.324  -3.603   2.065  1.00  0.00              
ATOM     57  N   THR    23      -6.245  -2.430   1.967  1.00  0.00              
ATOM     58  CA  THR    23      -7.105  -3.582   2.219  1.00  0.00              
ATOM     59  C   THR    23      -8.451  -3.446   1.515  1.00  0.00              
ATOM     60  O   THR    23      -8.835  -2.354   1.104  1.00  0.00              
ATOM     61  N   GLU    24       3.488  12.790  11.319  1.00  0.00              
ATOM     62  CA  GLU    24       3.098  11.400  11.464  1.00  0.00              
ATOM     63  C   GLU    24       3.362  10.648  10.178  1.00  0.00              
ATOM     64  O   GLU    24       3.360   9.419  10.158  1.00  0.00              
ATOM     65  N   GLU    25       3.570  11.390   9.093  1.00  0.00              
ATOM     66  CA  GLU    25       3.850  10.783   7.801  1.00  0.00              
ATOM     67  C   GLU    25       5.254  10.203   7.844  1.00  0.00              
ATOM     68  O   GLU    25       6.176  10.804   8.400  1.00  0.00              
ATOM     69  N   GLU    26       5.407   9.048   7.213  1.00  0.00              
ATOM     70  CA  GLU    26       6.672   8.337   7.167  1.00  0.00              
ATOM     71  C   GLU    26       6.720   7.643   5.808  1.00  0.00              
ATOM     72  O   GLU    26       5.717   7.094   5.355  1.00  0.00              
ATOM     73  N   LYS    27       7.871   7.695   5.146  1.00  0.00              
ATOM     74  CA  LYS    27       8.013   7.078   3.832  1.00  0.00              
ATOM     75  C   LYS    27       7.714   5.574   3.847  1.00  0.00              
ATOM     76  O   LYS    27       7.006   5.073   2.971  1.00  0.00              
ATOM     77  N   ALA    28       8.185   4.884   4.888  1.00  0.00              
ATOM     78  CA  ALA    28       7.986   3.437   5.033  1.00  0.00              
ATOM     79  C   ALA    28       6.553   3.030   5.342  1.00  0.00              
ATOM     80  O   ALA    28       6.109   1.954   4.942  1.00  0.00              
ATOM     81  N   GLU    29       5.834   3.886   6.059  1.00  0.00              
ATOM     82  CA  GLU    29       4.456   3.605   6.429  1.00  0.00              
ATOM     83  C   GLU    29       3.422   4.092   5.425  1.00  0.00              
ATOM     84  O   GLU    29       2.433   3.406   5.166  1.00  0.00              
ATOM     85  N   GLN    30       3.673   5.250   4.821  1.00  0.00              
ATOM     86  CA  GLN    30       2.711   5.840   3.895  1.00  0.00              
ATOM     87  C   GLN    30       2.988   5.768   2.394  1.00  0.00              
ATOM     88  O   GLN    30       2.061   5.875   1.591  1.00  0.00              
ATOM     89  N   GLN    31       4.243   5.572   2.007  1.00  0.00              
ATOM     90  CA  GLN    31       4.570   5.496   0.586  1.00  0.00              
ATOM     91  C   GLN    31       5.001   4.142  -0.001  1.00  0.00              
ATOM     92  O   GLN    31       5.316   4.082  -1.189  1.00  0.00              
ATOM     93  N   LYS    32       4.978   3.037   0.785  1.00  0.00              
ATOM     94  CA  LYS    32       5.404   1.755   0.199  1.00  0.00              
ATOM     95  C   LYS    32       4.688   1.339  -1.090  1.00  0.00              
ATOM     96  O   LYS    32       5.312   0.807  -1.994  1.00  0.00              
ATOM     97  N   LEU    33       3.389   1.604  -1.182  1.00  0.00              
ATOM     98  CA  LEU    33       2.628   1.252  -2.378  1.00  0.00              
ATOM     99  C   LEU    33       3.066   2.074  -3.589  1.00  0.00              
ATOM    100  O   LEU    33       3.140   1.560  -4.707  1.00  0.00              
ATOM    101  N   ARG    34       3.336   3.356  -3.360  1.00  0.00              
ATOM    102  CA  ARG    34       3.760   4.261  -4.423  1.00  0.00              
ATOM    103  C   ARG    34       5.167   3.901  -4.868  1.00  0.00              
ATOM    104  O   ARG    34       5.470   3.931  -6.057  1.00  0.00              
ATOM    105  N   GLN    35       6.010   3.533  -3.909  1.00  0.00              
ATOM    106  CA  GLN    35       7.383   3.136  -4.189  1.00  0.00              
ATOM    107  C   GLN    35       7.382   1.836  -5.010  1.00  0.00              
ATOM    108  O   GLN    35       8.112   1.717  -5.995  1.00  0.00              
ATOM    109  N   GLU    36       6.539   0.884  -4.607  1.00  0.00              
ATOM    110  CA  GLU    36       6.414  -0.407  -5.282  1.00  0.00              
ATOM    111  C   GLU    36       6.030  -0.260  -6.740  1.00  0.00              
ATOM    112  O   GLU    36       6.515  -1.004  -7.586  1.00  0.00              
ATOM    113  N   TYR    37       5.125   0.673  -7.028  1.00  0.00              
ATOM    114  CA  TYR    37       4.699   0.907  -8.404  1.00  0.00              
ATOM    115  C   TYR    37       5.859   1.501  -9.202  1.00  0.00              
ATOM    116  O   TYR    37       6.075   1.147 -10.357  1.00  0.00              
ATOM    117  N   LEU    38       6.622   2.374  -8.555  1.00  0.00              
ATOM    118  CA  LEU    38       7.768   3.016  -9.183  1.00  0.00              
ATOM    119  C   LEU    38       8.862   2.000  -9.485  1.00  0.00              
ATOM    120  O   LEU    38       9.526   2.077 -10.517  1.00  0.00              
ATOM    121  N   LYS    39       6.973  12.163  -3.555  1.00  0.00              
ATOM    122  CA  LYS    39       6.046  13.083  -4.207  1.00  0.00              
ATOM    123  C   LYS    39       5.713  12.644  -5.623  1.00  0.00              
ATOM    124  O   LYS    39       4.547  12.647  -6.015  1.00  0.00              
ATOM    125  N   GLY    40       6.735  12.250  -6.378  1.00  0.00              
ATOM    126  CA  GLY    40       6.543  11.787  -7.752  1.00  0.00              
ATOM    127  C   GLY    40       5.905  10.404  -7.765  1.00  0.00              
ATOM    128  O   GLY    40       5.014  10.142  -8.571  1.00  0.00              
END
