
#######################################################
#                                                     #
#                        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 T0348AL381_1
# Molecule2: number of CA atoms   61 (  465),  selected   34 , name T0348.pdb
# PARAMETERS: T0348AL381_1.T0348.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:    33        10 - 44          4.05     5.28
  LCS_AVERAGE:     52.89

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    26        10 - 37          1.71     5.52
  LCS_AVERAGE:     34.72

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    19        16 - 34          0.94     5.50
  LCS_AVERAGE:     20.64

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      10     V      10      6   26   33     3   16   21   23   25   25   25   27   28   29   30   31   31   31   31   32   32   32   32   33 
LCS_GDT     C      11     C      11      6   26   33     5   16   21   23   25   25   25   27   28   29   30   31   31   31   31   32   32   32   32   33 
LCS_GDT     P      12     P      12      6   26   33     5   16   21   23   25   25   25   27   28   29   30   31   31   31   31   32   32   32   32   33 
LCS_GDT     L      13     L      13      6   26   33     5   14   20   23   25   25   25   27   28   29   30   31   31   31   31   32   32   32   32   33 
LCS_GDT     C      14     C      14      6   26   33     5    6   19   22   25   25   25   27   28   29   30   31   31   31   31   32   32   32   32   33 
LCS_GDT     K      15     K      15      6   26   33     5    6   10   21   25   25   25   27   28   29   30   31   31   31   31   32   32   32   32   33 
LCS_GDT     G      16     G      16     19   26   33     6   16   21   23   25   25   25   27   28   29   30   31   31   31   31   32   32   32   32   33 
LCS_GDT     P      17     P      17     19   26   33     3    6   19   23   25   25   25   27   28   29   30   31   31   31   31   32   32   32   32   33 
LCS_GDT     L      18     L      18     19   26   33     3   16   21   23   25   25   25   27   28   29   30   31   31   31   31   32   32   32   32   33 
LCS_GDT     V      19     V      19     19   26   33     9   16   21   23   25   25   25   27   28   29   30   31   31   31   31   32   32   32   32   33 
LCS_GDT     F      20     F      20     19   26   33     9   16   21   23   25   25   25   27   28   29   30   31   31   31   31   32   32   32   32   33 
LCS_GDT     D      21     D      21     19   26   33     9   16   21   23   25   25   25   27   28   29   30   31   31   31   31   32   32   32   32   33 
LCS_GDT     K      22     K      22     19   26   33     9   16   21   23   25   25   25   27   28   29   30   31   31   31   31   32   32   32   32   33 
LCS_GDT     S      23     S      23     19   26   33     9   16   21   23   25   25   25   27   28   29   30   31   31   31   31   32   32   32   32   33 
LCS_GDT     K      24     K      24     19   26   33     9   16   21   23   25   25   25   27   28   29   30   31   31   31   31   32   32   32   32   33 
LCS_GDT     D      25     D      25     19   26   33     9   16   21   23   25   25   25   27   28   29   30   31   31   31   31   32   32   32   32   33 
LCS_GDT     E      26     E      26     19   26   33     9   16   21   23   25   25   25   27   28   29   30   31   31   31   31   32   32   32   32   33 
LCS_GDT     L      27     L      27     19   26   33     9   16   21   23   25   25   25   27   28   29   30   31   31   31   31   32   32   32   32   33 
LCS_GDT     I      28     I      28     19   26   33     8   16   21   23   25   25   25   27   28   29   30   31   31   31   31   32   32   32   32   33 
LCS_GDT     C      29     C      29     19   26   33     9   16   21   23   25   25   25   27   28   29   30   31   31   31   31   32   32   32   32   33 
LCS_GDT     K      30     K      30     19   26   33     3    6   21   23   25   25   25   27   28   29   30   31   31   31   31   32   32   32   32   33 
LCS_GDT     G      31     G      31     19   26   33     6   16   21   23   25   25   25   27   28   29   30   31   31   31   31   32   32   32   32   33 
LCS_GDT     D      32     D      32     19   26   33     5   16   21   23   25   25   25   27   28   29   30   31   31   31   31   32   32   32   32   33 
LCS_GDT     R      33     R      33     19   26   33     4   16   21   23   25   25   25   27   28   29   30   31   31   31   31   32   32   32   32   33 
LCS_GDT     L      34     L      34     19   26   33     4   16   21   23   25   25   25   27   28   29   30   31   31   31   31   32   32   32   32   33 
LCS_GDT     P      37     P      37      3   26   33     3    3    3    3    7    8   24   27   28   29   30   31   31   31   31   32   32   32   32   33 
LCS_GDT     I      38     I      38      3    4   33     3    3    3    3    4    4    6   15   28   29   30   31   31   31   31   32   32   32   32   33 
LCS_GDT     K      39     K      39      3    4   33     3    3    3    4    4    8   16   26   28   29   30   31   31   31   31   32   32   32   32   33 
LCS_GDT     D      40     D      40      3    6   33     3    3    4    5    5    5    7    8   16   23   27   31   31   31   31   32   32   32   32   33 
LCS_GDT     G      41     G      41      3    6   33     3    3    4    7   12   17   24   27   27   29   30   31   31   31   31   32   32   32   32   33 
LCS_GDT     I      42     I      42      4    6   33     3    3    6   11   18   24   25   26   27   29   30   31   31   31   31   32   32   32   32   33 
LCS_GDT     P      43     P      43      4    6   33     3    3    4    5    5    5    7    8    9    9   17   17   26   28   30   32   32   32   32   33 
LCS_GDT     M      44     M      44      4    6   33     3    3    4    5    5    5    7    8    9    9   11   11   12   12   14   16   18   29   30   33 
LCS_GDT     M      45     M      45      4    6    8     3    3    4    5    5    5    6    8    9    9   11   11   12   12   13   13   13   16   17   17 
LCS_AVERAGE  LCS_A:  36.08  (  20.64   34.72   52.89 )

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     16     21     23     25     25     25     27     28     29     30     31     31     31     31     32     32     32     32     33 
GDT PERCENT_CA  14.75  26.23  34.43  37.70  40.98  40.98  40.98  44.26  45.90  47.54  49.18  50.82  50.82  50.82  50.82  52.46  52.46  52.46  52.46  54.10
GDT RMS_LOCAL    0.38   0.65   0.90   1.05   1.30   1.30   1.30   1.97   2.30   2.46   2.62   2.91   2.91   2.91   2.91   3.36   3.36   3.36   3.36   4.05
GDT RMS_ALL_CA   5.48   5.44   5.47   5.48   5.53   5.53   5.53   5.48   5.65   5.60   5.49   5.52   5.52   5.52   5.52   5.40   5.40   5.40   5.40   5.28

#      Molecule1      Molecule2       DISTANCE
LGA    V      10      V      10          0.867
LGA    C      11      C      11          1.445
LGA    P      12      P      12          1.930
LGA    L      13      L      13          3.113
LGA    C      14      C      14          3.549
LGA    K      15      K      15          2.692
LGA    G      16      G      16          1.788
LGA    P      17      P      17          1.750
LGA    L      18      L      18          0.418
LGA    V      19      V      19          0.474
LGA    F      20      F      20          0.415
LGA    D      21      D      21          0.838
LGA    K      22      K      22          0.822
LGA    S      23      S      23          0.679
LGA    K      24      K      24          2.521
LGA    D      25      D      25          2.527
LGA    E      26      E      26          2.359
LGA    L      27      L      27          1.911
LGA    I      28      I      28          2.337
LGA    C      29      C      29          1.998
LGA    K      30      K      30          2.273
LGA    G      31      G      31          2.553
LGA    D      32      D      32          2.416
LGA    R      33      R      33          3.467
LGA    L      34      L      34          3.511
LGA    P      37      P      37          3.984
LGA    I      38      I      38          5.465
LGA    K      39      K      39          5.100
LGA    D      40      D      40          6.962
LGA    G      41      G      41          3.605
LGA    I      42      I      42          6.125
LGA    P      43      P      43         11.082
LGA    M      44      M      44         15.636
LGA    M      45      M      45         22.517

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   34   61    4.0     27    1.97    40.164    40.179     1.305

LGA_LOCAL      RMSD =  1.968  Number of atoms =   27  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  5.849  Number of atoms =   34 
Std_ALL_ATOMS  RMSD =  5.215  (standard rmsd on all 34 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.180450 * X  +  -0.336391 * Y  +   0.924272 * Z  +  10.857242
  Y_new =  -0.917497 * X  +  -0.281070 * Y  +  -0.281423 * Z  +  31.108158
  Z_new =   0.354454 * X  +  -0.898800 * Y  +  -0.257919 * Z  +  50.108097 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.850247    1.291346  [ DEG:  -106.0113     73.9887 ]
  Theta =  -0.362330   -2.779263  [ DEG:   -20.7600   -159.2400 ]
  Phi   =  -1.764994    1.376599  [ DEG:  -101.1267     78.8733 ]
 
# 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: T0348AL381_1                                  
REMARK     2: T0348.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0348AL381_1.T0348.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   34   61   4.0   27   1.97  40.179     5.22
REMARK  ---------------------------------------------------------- 
MOLECULE T0348AL381_1
REMARK Aligment from pdb entry: 1pft
ATOM      1  N   VAL    10       8.748  34.864  59.020  1.00  0.00              
ATOM      2  CA  VAL    10       8.641  33.840  60.042  1.00  0.00              
ATOM      3  C   VAL    10       7.864  32.632  59.530  1.00  0.00              
ATOM      4  O   VAL    10       7.592  32.502  58.339  1.00  0.00              
ATOM      5  N   CYS    11       7.421  31.808  60.476  1.00  0.00              
ATOM      6  CA  CYS    11       6.464  30.754  60.200  1.00  0.00              
ATOM      7  C   CYS    11       5.069  31.173  60.737  1.00  0.00              
ATOM      8  O   CYS    11       4.738  30.909  61.906  1.00  0.00              
ATOM      9  N   PRO    12       4.157  31.396  59.759  1.00  0.00              
ATOM     10  CA  PRO    12       2.710  31.553  60.034  1.00  0.00              
ATOM     11  C   PRO    12       2.034  30.279  60.540  1.00  0.00              
ATOM     12  O   PRO    12       0.831  30.275  60.804  1.00  0.00              
ATOM     13  N   LEU    13       2.746  29.166  60.368  1.00  0.00              
ATOM     14  CA  LEU    13       2.201  27.853  60.684  1.00  0.00              
ATOM     15  C   LEU    13       2.336  27.564  62.174  1.00  0.00              
ATOM     16  O   LEU    13       1.368  27.662  62.927  1.00  0.00              
ATOM     17  N   CYS    14       3.565  27.265  62.601  1.00  0.00              
ATOM     18  CA  CYS    14       3.768  26.640  63.905  1.00  0.00              
ATOM     19  C   CYS    14       4.121  27.659  64.973  1.00  0.00              
ATOM     20  O   CYS    14       4.367  27.295  66.130  1.00  0.00              
ATOM     21  N   LYS    15       4.323  28.905  64.558  1.00  0.00              
ATOM     22  CA  LYS    15       5.046  29.888  65.366  1.00  0.00              
ATOM     23  C   LYS    15       6.466  29.404  65.637  1.00  0.00              
ATOM     24  O   LYS    15       6.809  29.000  66.744  1.00  0.00              
ATOM     25  N   GLY    16      10.053  31.135  64.302  1.00  0.00              
ATOM     26  CA  GLY    16      10.574  32.241  63.507  1.00  0.00              
ATOM     27  C   GLY    16      11.804  31.829  62.702  1.00  0.00              
ATOM     28  O   GLY    16      12.337  32.622  61.924  1.00  0.00              
ATOM     29  N   PRO    17      12.376  30.693  63.089  1.00  0.00              
ATOM     30  CA  PRO    17      13.523  30.140  62.378  1.00  0.00              
ATOM     31  C   PRO    17      13.063  29.467  61.084  1.00  0.00              
ATOM     32  O   PRO    17      12.682  28.297  61.090  1.00  0.00              
ATOM     33  N   LEU    18      13.316  30.148  59.972  1.00  0.00              
ATOM     34  CA  LEU    18      13.197  29.543  58.651  1.00  0.00              
ATOM     35  C   LEU    18      14.577  29.341  58.034  1.00  0.00              
ATOM     36  O   LEU    18      15.585  29.789  58.575  1.00  0.00              
ATOM     37  N   VAL    19      14.580  28.799  56.819  1.00  0.00              
ATOM     38  CA  VAL    19      15.822  28.448  56.143  1.00  0.00              
ATOM     39  C   VAL    19      15.599  28.350  54.637  1.00  0.00              
ATOM     40  O   VAL    19      14.470  28.195  54.176  1.00  0.00              
ATOM     41  N   PHE    20      16.670  28.589  53.887  1.00  0.00              
ATOM     42  CA  PHE    20      16.579  28.754  52.443  1.00  0.00              
ATOM     43  C   PHE    20      16.985  27.465  51.734  1.00  0.00              
ATOM     44  O   PHE    20      17.507  26.543  52.358  1.00  0.00              
ATOM     45  N   ASP    21      16.553  27.346  50.482  1.00  0.00              
ATOM     46  CA  ASP    21      16.703  26.117  49.724  1.00  0.00              
ATOM     47  C   ASP    21      17.066  26.447  48.262  1.00  0.00              
ATOM     48  O   ASP    21      16.197  26.527  47.381  1.00  0.00              
ATOM     49  N   LYS    22      18.364  26.744  48.046  1.00  0.00              
ATOM     50  CA  LYS    22      18.859  27.258  46.745  1.00  0.00              
ATOM     51  C   LYS    22      18.616  26.301  45.578  1.00  0.00              
ATOM     52  O   LYS    22      18.874  26.641  44.424  1.00  0.00              
ATOM     53  N   SER    23      18.377  25.042  45.930  1.00  0.00              
ATOM     54  CA  SER    23      18.236  23.979  44.943  1.00  0.00              
ATOM     55  C   SER    23      16.876  24.083  44.250  1.00  0.00              
ATOM     56  O   SER    23      16.801  24.085  43.023  1.00  0.00              
ATOM     57  N   LYS    24      15.874  24.459  45.041  1.00  0.00              
ATOM     58  CA  LYS    24      14.525  24.639  44.530  1.00  0.00              
ATOM     59  C   LYS    24      14.215  26.124  44.355  1.00  0.00              
ATOM     60  O   LYS    24      13.266  26.491  43.666  1.00  0.00              
ATOM     61  N   ASP    25      14.926  26.947  45.118  1.00  0.00              
ATOM     62  CA  ASP    25      14.590  28.358  45.255  1.00  0.00              
ATOM     63  C   ASP    25      13.540  28.549  46.346  1.00  0.00              
ATOM     64  O   ASP    25      12.597  29.321  46.184  1.00  0.00              
ATOM     65  N   GLU    26      13.652  27.738  47.392  1.00  0.00              
ATOM     66  CA  GLU    26      12.598  27.626  48.396  1.00  0.00              
ATOM     67  C   GLU    26      13.048  28.279  49.701  1.00  0.00              
ATOM     68  O   GLU    26      14.244  28.418  49.953  1.00  0.00              
ATOM     69  N   LEU    27      12.084  28.499  50.587  1.00  0.00              
ATOM     70  CA  LEU    27      12.372  28.874  51.965  1.00  0.00              
ATOM     71  C   LEU    27      11.405  28.175  52.917  1.00  0.00              
ATOM     72  O   LEU    27      10.194  28.371  52.843  1.00  0.00              
ATOM     73  N   ILE    28      11.959  27.317  53.764  1.00  0.00              
ATOM     74  CA  ILE    28      11.158  26.410  54.573  1.00  0.00              
ATOM     75  C   ILE    28      11.205  26.843  56.042  1.00  0.00              
ATOM     76  O   ILE    28      12.125  27.549  56.451  1.00  0.00              
ATOM     77  N   CYS    29      10.360  26.206  56.844  1.00  0.00              
ATOM     78  CA  CYS    29      10.493  26.246  58.297  1.00  0.00              
ATOM     79  C   CYS    29      11.688  25.404  58.737  1.00  0.00              
ATOM     80  O   CYS    29      11.957  24.348  58.167  1.00  0.00              
ATOM     81  N   LYS    30      12.278  25.801  59.859  1.00  0.00              
ATOM     82  CA  LYS    30      13.317  25.014  60.505  1.00  0.00              
ATOM     83  C   LYS    30      12.731  24.217  61.671  1.00  0.00              
ATOM     84  O   LYS    30      13.438  23.888  62.622  1.00  0.00              
ATOM     85  N   GLY    31      11.403  24.149  61.691  1.00  0.00              
ATOM     86  CA  GLY    31      10.681  23.541  62.796  1.00  0.00              
ATOM     87  C   GLY    31       9.695  22.497  62.292  1.00  0.00              
ATOM     88  O   GLY    31       9.997  21.301  62.286  1.00  0.00              
ATOM     89  N   ASP    32       8.647  22.975  61.613  1.00  0.00              
ATOM     90  CA  ASP    32       7.542  22.099  61.240  1.00  0.00              
ATOM     91  C   ASP    32       7.782  21.437  59.890  1.00  0.00              
ATOM     92  O   ASP    32       6.959  20.641  59.430  1.00  0.00              
ATOM     93  N   ARG    33       8.740  21.998  59.146  1.00  0.00              
ATOM     94  CA  ARG    33       9.086  21.464  57.836  1.00  0.00              
ATOM     95  C   ARG    33       8.452  22.286  56.713  1.00  0.00              
ATOM     96  O   ARG    33       8.523  21.892  55.544  1.00  0.00              
ATOM     97  N   LEU    34       7.537  23.165  57.124  1.00  0.00              
ATOM     98  CA  LEU    34       6.655  23.854  56.193  1.00  0.00              
ATOM     99  C   LEU    34       7.462  24.806  55.310  1.00  0.00              
ATOM    100  O   LEU    34       8.015  25.790  55.803  1.00  0.00              
ATOM    101  N   PRO    37       7.281  24.651  54.001  1.00  0.00              
ATOM    102  CA  PRO    37       7.757  25.630  53.036  1.00  0.00              
ATOM    103  C   PRO    37       7.087  26.985  53.283  1.00  0.00              
ATOM    104  O   PRO    37       5.968  27.043  53.790  1.00  0.00              
ATOM    105  N   ILE    38       7.633  27.995  52.616  1.00  0.00              
ATOM    106  CA  ILE    38       7.043  29.328  52.609  1.00  0.00              
ATOM    107  C   ILE    38       6.656  29.713  51.180  1.00  0.00              
ATOM    108  O   ILE    38       5.523  29.484  50.758  1.00  0.00              
ATOM    109  N   LYS    39       7.670  30.064  50.396  1.00  0.00              
ATOM    110  CA  LYS    39       7.539  30.128  48.943  1.00  0.00              
ATOM    111  C   LYS    39       8.609  29.259  48.285  1.00  0.00              
ATOM    112  O   LYS    39       9.486  28.727  48.964  1.00  0.00              
ATOM    113  N   ASP    40       8.343  28.901  47.032  1.00  0.00              
ATOM    114  CA  ASP    40       9.229  28.021  46.281  1.00  0.00              
ATOM    115  C   ASP    40       9.122  28.323  44.785  1.00  0.00              
ATOM    116  O   ASP    40       9.228  27.414  43.958  1.00  0.00              
ATOM    117  N   GLY    41       9.216  29.611  44.466  1.00  0.00              
ATOM    118  CA  GLY    41       9.359  30.056  43.086  1.00  0.00              
ATOM    119  C   GLY    41       9.953  31.460  43.040  1.00  0.00              
ATOM    120  O   GLY    41       9.309  32.403  42.582  1.00  0.00              
ATOM    121  N   ILE    42      11.127  31.601  43.647  1.00  0.00              
ATOM    122  CA  ILE    42      11.724  32.909  43.876  1.00  0.00              
ATOM    123  C   ILE    42      12.313  33.459  42.581  1.00  0.00              
ATOM    124  O   ILE    42      13.527  33.463  42.390  1.00  0.00              
ATOM    125  N   PRO    43      11.425  33.726  41.625  1.00  0.00              
ATOM    126  CA  PRO    43      11.824  34.325  40.359  1.00  0.00              
ATOM    127  C   PRO    43      10.596  34.702  39.538  1.00  0.00              
ATOM    128  O   PRO    43       9.573  34.022  39.586  1.00  0.00              
ATOM    129  N   MET    44      10.766  35.708  38.687  1.00  0.00              
ATOM    130  CA  MET    44       9.761  36.055  37.693  1.00  0.00              
ATOM    131  C   MET    44      10.376  36.920  36.595  1.00  0.00              
ATOM    132  O   MET    44      10.040  38.094  36.456  1.00  0.00              
ATOM    133  N   MET    45      11.155  36.275  35.734  1.00  0.00              
ATOM    134  CA  MET    45      11.642  36.902  34.513  1.00  0.00              
ATOM    135  C   MET    45      11.384  35.996  33.312  1.00  0.00              
ATOM    136  O   MET    45      10.608  36.341  32.421  1.00  0.00              
END
