
#######################################################
#                                                     #
#                        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   26 (  104),  selected   26 , name T0348AL381_3
# Molecule2: number of CA atoms   61 (  465),  selected   26 , name T0348.pdb
# PARAMETERS: T0348AL381_3.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:    26        10 - 35          1.83     1.83
  LCS_AVERAGE:     42.62

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    26        10 - 35          1.83     1.83
  LCS_AVERAGE:     42.62

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11        25 - 35          0.97     2.70
  LCS_AVERAGE:     12.36

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   26     5   12   18   21   23   25   25   26   26   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     C      11     C      11      6   26   26     5   12   18   21   23   25   25   26   26   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     P      12     P      12      6   26   26     5   10   18   21   23   25   25   26   26   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     L      13     L      13      6   26   26     5   12   18   21   23   25   25   26   26   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     C      14     C      14      6   26   26     3    6   18   21   23   25   25   26   26   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     K      15     K      15      6   26   26     3   10   18   21   23   25   25   26   26   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     G      16     G      16      3   26   26     3    3    4   10   21   25   25   26   26   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     P      17     P      17      3   26   26     0    3    3   11   15   25   25   26   26   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     L      18     L      18      5   26   26     5   11   18   21   23   25   25   26   26   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     V      19     V      19      5   26   26     6   12   18   21   23   25   25   26   26   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     F      20     F      20      5   26   26     6   12   18   21   23   25   25   26   26   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     D      21     D      21      5   26   26     4   12   17   21   23   25   25   26   26   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     K      22     K      22      5   26   26     3    6   16   21   23   25   25   26   26   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     S      23     S      23      4   26   26     3    4   12   19   23   25   25   26   26   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     K      24     K      24      4   26   26     3    4   10   20   23   25   25   26   26   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     D      25     D      25     11   26   26     3    3    7   15   17   22   23   26   26   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     E      26     E      26     11   26   26     6   12   17   21   23   25   25   26   26   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     L      27     L      27     11   26   26     6   12   18   21   23   25   25   26   26   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     I      28     I      28     11   26   26     3   12   18   21   23   25   25   26   26   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     C      29     C      29     11   26   26     6   12   18   21   23   25   25   26   26   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     K      30     K      30     11   26   26     3   12   18   21   23   25   25   26   26   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     G      31     G      31     11   26   26     6   12   18   21   23   25   25   26   26   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     D      32     D      32     11   26   26     5   12   18   21   23   25   25   26   26   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     R      33     R      33     11   26   26     4   12   18   21   23   25   25   26   26   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     L      34     L      34     11   26   26     5   12   18   21   23   25   25   26   26   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     A      35     A      35     11   26   26     4   12   18   21   23   25   25   26   26   26   26   26   26   26   26   26   26   26   26   26 
LCS_AVERAGE  LCS_A:  32.53  (  12.36   42.62   42.62 )

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      6     12     18     21     23     25     25     26     26     26     26     26     26     26     26     26     26     26     26     26 
GDT PERCENT_CA   9.84  19.67  29.51  34.43  37.70  40.98  40.98  42.62  42.62  42.62  42.62  42.62  42.62  42.62  42.62  42.62  42.62  42.62  42.62  42.62
GDT RMS_LOCAL    0.33   0.65   0.98   1.21   1.37   1.61   1.61   1.83   1.83   1.83   1.83   1.83   1.83   1.83   1.83   1.83   1.83   1.83   1.83   1.83
GDT RMS_ALL_CA   2.71   2.11   2.11   1.87   1.88   1.86   1.86   1.83   1.83   1.83   1.83   1.83   1.83   1.83   1.83   1.83   1.83   1.83   1.83   1.83

#      Molecule1      Molecule2       DISTANCE
LGA    V      10      V      10          0.606
LGA    C      11      C      11          0.903
LGA    P      12      P      12          1.863
LGA    L      13      L      13          1.600
LGA    C      14      C      14          1.511
LGA    K      15      K      15          1.928
LGA    G      16      G      16          3.328
LGA    P      17      P      17          3.322
LGA    L      18      L      18          1.854
LGA    V      19      V      19          1.475
LGA    F      20      F      20          1.168
LGA    D      21      D      21          1.487
LGA    K      22      K      22          1.826
LGA    S      23      S      23          3.564
LGA    K      24      K      24          2.394
LGA    D      25      D      25          3.928
LGA    E      26      E      26          1.242
LGA    L      27      L      27          1.271
LGA    I      28      I      28          0.946
LGA    C      29      C      29          0.334
LGA    K      30      K      30          1.434
LGA    G      31      G      31          0.947
LGA    D      32      D      32          0.546
LGA    R      33      R      33          1.083
LGA    L      34      L      34          0.567
LGA    A      35      A      35          0.899

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   26   61    4.0     26    1.83    34.836    38.740     1.344

LGA_LOCAL      RMSD =  1.835  Number of atoms =   26  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  1.875  Number of atoms =   26 
Std_ALL_ATOMS  RMSD =  1.835  (standard rmsd on all 26 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.244348 * X  +  -0.229131 * Y  +   0.942228 * Z  +   8.541237
  Y_new =  -0.941094 * X  +   0.290258 * Y  +  -0.173469 * Z  +  31.891054
  Z_new =  -0.233742 * X  +  -0.929112 * Y  +  -0.286558 * Z  +  47.282867 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.869961    1.271631  [ DEG:  -107.1409     72.8591 ]
  Theta =   0.235925    2.905668  [ DEG:    13.5175    166.4825 ]
  Phi   =  -1.824829    1.316763  [ DEG:  -104.5550     75.4450 ]
 
# 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_3                                  
REMARK     2: T0348.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0348AL381_3.T0348.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   26   61   4.0   26   1.83  38.740     1.83
REMARK  ---------------------------------------------------------- 
MOLECULE T0348AL381_3
REMARK Aligment from pdb entry: 1dl6A
ATOM      1  N   VAL    10       7.776  34.166  58.824  1.00  0.00              
ATOM      2  CA  VAL    10       8.133  33.193  59.852  1.00  0.00              
ATOM      3  C   VAL    10       7.129  32.046  59.901  1.00  0.00              
ATOM      4  O   VAL    10       6.144  32.034  59.163  1.00  0.00              
ATOM      5  N   CYS    11       7.391  31.083  60.779  1.00  0.00              
ATOM      6  CA  CYS    11       6.520  29.925  60.937  1.00  0.00              
ATOM      7  C   CYS    11       5.359  30.247  61.880  1.00  0.00              
ATOM      8  O   CYS    11       5.565  30.803  62.958  1.00  0.00              
ATOM      9  N   PRO    12       4.119  29.902  61.487  1.00  0.00              
ATOM     10  CA  PRO    12       2.930  30.165  62.308  1.00  0.00              
ATOM     11  C   PRO    12       3.038  29.561  63.702  1.00  0.00              
ATOM     12  O   PRO    12       2.583  30.150  64.682  1.00  0.00              
ATOM     13  N   LEU    13       3.638  28.380  63.783  1.00  0.00              
ATOM     14  CA  LEU    13       3.799  27.689  65.059  1.00  0.00              
ATOM     15  C   LEU    13       5.222  27.831  65.602  1.00  0.00              
ATOM     16  O   LEU    13       5.598  27.149  66.554  1.00  0.00              
ATOM     17  N   CYS    14       6.010  28.717  64.997  1.00  0.00              
ATOM     18  CA  CYS    14       7.384  28.936  65.436  1.00  0.00              
ATOM     19  C   CYS    14       7.847  30.351  65.098  1.00  0.00              
ATOM     20  O   CYS    14       8.408  30.590  64.029  1.00  0.00              
ATOM     21  N   LYS    15       7.620  31.311  66.011  1.00  0.00              
ATOM     22  CA  LYS    15       8.019  32.706  65.804  1.00  0.00              
ATOM     23  C   LYS    15       9.533  32.886  65.848  1.00  0.00              
ATOM     24  O   LYS    15      10.114  33.553  64.993  1.00  0.00              
ATOM     25  N   GLY    16      10.166  32.285  66.851  1.00  0.00              
ATOM     26  CA  GLY    16      11.613  32.377  67.006  1.00  0.00              
ATOM     27  C   GLY    16      12.326  31.711  65.835  1.00  0.00              
ATOM     28  O   GLY    16      13.353  32.198  65.362  1.00  0.00              
ATOM     29  N   PRO    17      11.774  30.595  65.371  1.00  0.00              
ATOM     30  CA  PRO    17      12.355  29.861  64.254  1.00  0.00              
ATOM     31  C   PRO    17      11.726  30.291  62.933  1.00  0.00              
ATOM     32  O   PRO    17      10.511  30.215  62.759  1.00  0.00              
ATOM     33  N   LEU    18      11.403  29.889  58.778  1.00  0.00              
ATOM     34  CA  LEU    18      11.569  28.926  57.693  1.00  0.00              
ATOM     35  C   LEU    18      12.704  29.353  56.767  1.00  0.00              
ATOM     36  O   LEU    18      12.601  30.364  56.071  1.00  0.00              
ATOM     37  N   VAL    19      13.785  28.580  56.759  1.00  0.00              
ATOM     38  CA  VAL    19      14.934  28.885  55.916  1.00  0.00              
ATOM     39  C   VAL    19      14.647  28.528  54.464  1.00  0.00              
ATOM     40  O   VAL    19      13.778  27.705  54.181  1.00  0.00              
ATOM     41  N   PHE    20      15.380  29.148  53.546  1.00  0.00              
ATOM     42  CA  PHE    20      15.198  28.891  52.122  1.00  0.00              
ATOM     43  C   PHE    20      16.501  28.432  51.477  1.00  0.00              
ATOM     44  O   PHE    20      17.584  28.879  51.855  1.00  0.00              
ATOM     45  N   ASP    21      16.388  27.537  50.501  1.00  0.00              
ATOM     46  CA  ASP    21      17.557  27.016  49.802  1.00  0.00              
ATOM     47  C   ASP    21      18.021  27.989  48.720  1.00  0.00              
ATOM     48  O   ASP    21      17.630  29.156  48.714  1.00  0.00              
ATOM     49  N   LYS    22      18.858  27.503  47.809  1.00  0.00              
ATOM     50  CA  LYS    22      19.375  28.331  46.726  1.00  0.00              
ATOM     51  C   LYS    22      18.511  28.201  45.475  1.00  0.00              
ATOM     52  O   LYS    22      18.412  29.135  44.680  1.00  0.00              
ATOM     53  N   SER    23      17.885  27.037  45.309  1.00  0.00              
ATOM     54  CA  SER    23      17.025  26.777  44.163  1.00  0.00              
ATOM     55  C   SER    23      16.607  25.314  44.136  1.00  0.00              
ATOM     56  O   SER    23      17.443  24.412  44.096  1.00  0.00              
ATOM     57  N   LYS    24      15.303  25.095  44.157  1.00  0.00              
ATOM     58  CA  LYS    24      14.738  23.748  44.136  1.00  0.00              
ATOM     59  C   LYS    24      14.880  23.069  45.494  1.00  0.00              
ATOM     60  O   LYS    24      14.951  21.843  45.581  1.00  0.00              
ATOM     61  N   ASP    25      14.920  23.873  46.552  1.00  0.00              
ATOM     62  CA  ASP    25      15.052  23.329  47.892  1.00  0.00              
ATOM     63  C   ASP    25      13.868  23.666  48.781  1.00  0.00              
ATOM     64  O   ASP    25      13.679  23.050  49.830  1.00  0.00              
ATOM     65  N   GLU    26      13.067  24.644  48.364  1.00  0.00              
ATOM     66  CA  GLU    26      11.898  25.058  49.132  1.00  0.00              
ATOM     67  C   GLU    26      12.312  25.715  50.444  1.00  0.00              
ATOM     68  O   GLU    26      13.496  25.955  50.684  1.00  0.00              
ATOM     69  N   LEU    27      11.329  26.003  51.291  1.00  0.00              
ATOM     70  CA  LEU    27      11.589  26.630  52.582  1.00  0.00              
ATOM     71  C   LEU    27      11.166  25.710  53.723  1.00  0.00              
ATOM     72  O   LEU    27       9.994  25.355  53.842  1.00  0.00              
ATOM     73  N   ILE    28      12.127  25.316  54.554  1.00  0.00              
ATOM     74  CA  ILE    28      11.857  24.431  55.666  1.00  0.00              
ATOM     75  C   ILE    28      12.007  25.145  57.006  1.00  0.00              
ATOM     76  O   ILE    28      12.720  26.140  57.113  1.00  0.00              
ATOM     77  N   CYS    29      11.332  24.625  58.029  1.00  0.00              
ATOM     78  CA  CYS    29      11.397  25.213  59.364  1.00  0.00              
ATOM     79  C   CYS    29      12.360  24.425  60.252  1.00  0.00              
ATOM     80  O   CYS    29      12.355  23.195  60.240  1.00  0.00              
ATOM     81  N   LYS    30      13.210  25.121  61.030  1.00  0.00              
ATOM     82  CA  LYS    30      14.183  24.469  61.913  1.00  0.00              
ATOM     83  C   LYS    30      13.550  23.885  63.176  1.00  0.00              
ATOM     84  O   LYS    30      14.248  23.335  64.029  1.00  0.00              
ATOM     85  N   GLY    31      12.230  24.003  63.295  1.00  0.00              
ATOM     86  CA  GLY    31      11.520  23.485  64.458  1.00  0.00              
ATOM     87  C   GLY    31      10.573  22.352  64.062  1.00  0.00              
ATOM     88  O   GLY    31      10.884  21.179  64.267  1.00  0.00              
ATOM     89  N   ASP    32       9.419  22.699  63.490  1.00  0.00              
ATOM     90  CA  ASP    32       8.454  21.684  63.070  1.00  0.00              
ATOM     91  C   ASP    32       8.991  20.875  61.894  1.00  0.00              
ATOM     92  O   ASP    32       8.444  19.826  61.552  1.00  0.00              
ATOM     93  N   ARG    33      10.063  21.365  61.275  1.00  0.00              
ATOM     94  CA  ARG    33      10.642  20.667  60.144  1.00  0.00              
ATOM     95  C   ARG    33       9.667  20.535  58.995  1.00  0.00              
ATOM     96  O   ARG    33       9.417  19.433  58.507  1.00  0.00              
ATOM     97  N   LEU    34       9.111  21.662  58.560  1.00  0.00              
ATOM     98  CA  LEU    34       8.157  21.659  57.459  1.00  0.00              
ATOM     99  C   LEU    34       8.851  22.015  56.150  1.00  0.00              
ATOM    100  O   LEU    34      10.053  22.275  56.131  1.00  0.00              
ATOM    101  N   ALA    35       8.086  22.020  55.064  1.00  0.00              
ATOM    102  CA  ALA    35       8.625  22.340  53.748  1.00  0.00              
ATOM    103  C   ALA    35       7.591  23.069  52.895  1.00  0.00              
ATOM    104  O   ALA    35       6.784  22.441  52.210  1.00  0.00              
END
