
#######################################################
#                                                     #
#                        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   33 (  132),  selected   28 , name T0326AL044_2
# Molecule2: number of CA atoms  289 ( 2373),  selected   28 , name T0326.pdb
# PARAMETERS: T0326AL044_2.T0326.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:    11         9 - 19          4.58    21.10
  LCS_AVERAGE:      2.92

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5         9 - 13          1.91    29.57
  LONGEST_CONTINUOUS_SEGMENT:     5        17 - 21          1.65    25.97
  LCS_AVERAGE:      0.99

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4        18 - 21          0.24    27.59
  LONGEST_CONTINUOUS_SEGMENT:     4        38 - 41          0.18    25.41
  LCS_AVERAGE:      0.69

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:  289
LCS_GDT     I       3     I       3      0    0    5     0    0    0    0    0    3    3    3    3    4    5    5    5    5    5    6    6    7    8    8 
LCS_GDT     V       5     V       5      0    0    5     0    1    2    2    3    4    4    4    4    4    5    5    5    5    5    6    6    7    8    8 
LCS_GDT     P       6     P       6      0    0    5     0    0    0    0    2    4    4    4    4    4    5    5    5    5    5    6    8   10   14   14 
LCS_GDT     S       7     S       7      0    0    5     0    0    1    2    3    4    4    4    4    8    9    9   11   12   12   12   13   14   14   15 
LCS_GDT     G       8     G       8      0    0    5     0    0    2    2    3    4    4    4    4    4    5    5    5    8   10   12   13   14   15   15 
LCS_GDT     L       9     L       9      0    5   11     3    4    5    5    5    5    6    7    8    8    9    9   11   12   12   13   13   14   15   15 
LCS_GDT     P      10     P      10      0    5   11     3    4    5    5    5    5    6    7    8    8    9   10   11   12   12   13   13   14   15   15 
LCS_GDT     A      11     A      11      3    5   11     0    3    3    4    5    5    6    6    7    7    8   10   11   12   12   12   13   14   15   15 
LCS_GDT     V      12     V      12      3    5   11     3    3    3    4    5    5    6    6    8    8    8   10   11   12   12   12   13   14   15   15 
LCS_GDT     K      13     K      13      3    5   11     3    3    3    4    5    5    6    6    8    8    9   10   11   12   12   12   13   14   15   15 
LCS_GDT     V      14     V      14      3    4   11     3    4    5    5    5    5    6    7    8    8    9   10   11   12   12   13   13   14   15   15 
LCS_GDT     L      15     L      15      3    4   11     3    4    5    5    5    5    6    7    8    8    9   10   11   12   12   13   13   14   15   15 
LCS_GDT     A      16     A      16      3    3   11     3    4    5    5    5    5    6    7    8    8    9   10   11   12   12   13   13   14   15   15 
LCS_GDT     K      17     K      17      3    5   11     3    3    4    5    5    5    6    7    8    8    9   10   11   12   12   13   13   14   15   15 
LCS_GDT     E      18     E      18      4    5   11     4    4    4    5    5    5    6    7    8    8    9   10   11   12   12   13   13   14   15   15 
LCS_GDT     G      19     G      19      4    5   11     4    4    4    5    5    5    6    7    8    8    9   10   11   12   12   13   13   14   15   15 
LCS_GDT     I      20     I      20      4    5    9     4    4    4    4    4    5    6    6    7    7    9    9   11   12   12   13   13   14   15   15 
LCS_GDT     F      21     F      21      4    5    8     4    4    4    4    4    5    6    6    7    7    7    8   11   12   12   13   13   14   15   15 
LCS_GDT     V      22     V      22      3    3    8     3    3    4    4    4    5    6    6    7    7    7    8   11   12   12   13   13   14   15   15 
LCS_GDT     T      24     T      24      0    0    8     1    1    1    1    2    3    3    4    5    6    7    7    9   11   12   13   13   14   14   14 
LCS_GDT     K      26     K      26      0    0    8     0    0    0    1    2    2    3    4    4    4    4    4    5    5    9   11   12   12   13   14 
LCS_GDT     I      33     I      33      0    0    7     0    1    1    1    2    3    5    6    7    7    9    9   11   12   12   13   13   14   14   15 
LCS_GDT     R      34     R      34      0    0    7     0    0    0    0    2    3    4    6    7    7    7    7    8    9   10   10   12   13   14   14 
LCS_GDT     P      35     P      35      0    0    7     0    0    0    1    2    3    4    6    7    7    7    7    7    7    8   10   12   13   13   14 
LCS_GDT     I      38     I      38      4    4    7     4    4    4    4    4    4    5    6    7    7    7    7    7    7    8   10   12   13   13   14 
LCS_GDT     L      39     L      39      4    4    7     4    4    4    4    4    4    5    6    7    7    7    7    7    7    8   10   12   13   13   14 
LCS_GDT     I      40     I      40      4    4    7     4    4    4    4    4    4    5    6    7    7    7    7    7    7    8   10   12   13   13   14 
LCS_GDT     L      41     L      41      4    4    7     4    4    4    4    4    4    5    6    7    7    7    7    7    7    8   10   11   13   13   14 
LCS_AVERAGE  LCS_A:   1.53  (   0.69    0.99    2.92 )

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      4      4      5      5      5      5      6      7      8      8      9     10     11     12     12     13     13     14     15     15 
GDT PERCENT_CA   1.38   1.38   1.73   1.73   1.73   1.73   2.08   2.42   2.77   2.77   3.11   3.46   3.81   4.15   4.15   4.50   4.50   4.84   5.19   5.19
GDT RMS_LOCAL    0.18   0.18   1.02   0.92   0.92   0.92   2.32   2.70   3.11   3.11   3.79   4.43   4.58   4.86   4.86   5.89   5.33   5.84   6.58   6.39
GDT RMS_ALL_CA  25.41  25.41  19.49  19.09  19.09  19.09  20.16  18.88  19.94  19.94  18.93  22.64  21.10  20.66  20.66  15.20  19.65  19.32  18.39  19.30

#      Molecule1      Molecule2       DISTANCE
LGA    I       3      I       3         24.395
LGA    V       5      V       5         19.026
LGA    P       6      P       6         13.158
LGA    S       7      S       7          7.853
LGA    G       8      G       8          8.847
LGA    L       9      L       9          2.456
LGA    P      10      P      10          2.226
LGA    A      11      A      11          7.859
LGA    V      12      V      12          9.120
LGA    K      13      K      13          7.425
LGA    V      14      V      14          3.132
LGA    L      15      L      15          4.822
LGA    A      16      A      16          3.039
LGA    K      17      K      17          3.635
LGA    E      18      E      18          3.697
LGA    G      19      G      19          3.567
LGA    I      20      I      20          8.157
LGA    F      21      F      21         10.977
LGA    V      22      V      22         11.535
LGA    T      24      T      24         17.601
LGA    K      26      K      26         23.322
LGA    I      33      I      33         20.516
LGA    R      34      R      34         25.250
LGA    P      35      P      35         26.117
LGA    I      38      I      38         32.629
LGA    L      39      L      39         36.411
LGA    I      40      I      40         36.503
LGA    L      41      L      41         41.246

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   33  289    4.0      7    2.70     2.509     2.093     0.250

LGA_LOCAL      RMSD =  2.699  Number of atoms =    7  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 18.805  Number of atoms =   28 
Std_ALL_ATOMS  RMSD = 14.529  (standard rmsd on all 28 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.099908 * X  +  -0.935605 * Y  +  -0.338617 * Z  +  54.991856
  Y_new =  -0.857604 * X  +  -0.091587 * Y  +   0.506090 * Z  + -22.947296
  Z_new =  -0.504514 * X  +   0.340962 * Y  +  -0.793228 * Z  +  59.690468 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.735629   -0.405963  [ DEG:   156.7400    -23.2600 ]
  Theta =   0.528818    2.612774  [ DEG:    30.2991    149.7009 ]
  Phi   =  -1.686770    1.454823  [ DEG:   -96.6448     83.3552 ]
 
# 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: T0326AL044_2                                  
REMARK     2: T0326.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0326AL044_2.T0326.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   33  289   4.0    7   2.70   2.093    14.53
REMARK  ---------------------------------------------------------- 
MOLECULE T0326AL044_2
REMARK Aligment from pdb entry: 1vcn_A
ATOM      1  N   ILE     3      14.053   3.525  -7.012  1.00  0.00              
ATOM      2  CA  ILE     3      14.628   4.362  -8.061  1.00  0.00              
ATOM      3  C   ILE     3      15.768   5.252  -7.557  1.00  0.00              
ATOM      4  O   ILE     3      16.753   5.452  -8.265  1.00  0.00              
ATOM      5  N   VAL     5      15.646   5.778  -6.338  1.00  0.00              
ATOM      6  CA  VAL     5      16.687   6.655  -5.799  1.00  0.00              
ATOM      7  C   VAL     5      17.714   6.043  -4.853  1.00  0.00              
ATOM      8  O   VAL     5      18.450   6.780  -4.191  1.00  0.00              
ATOM      9  N   PRO     6      17.792   4.716  -4.792  1.00  0.00              
ATOM     10  CA  PRO     6      18.761   4.070  -3.904  1.00  0.00              
ATOM     11  C   PRO     6      19.545   2.976  -4.604  1.00  0.00              
ATOM     12  O   PRO     6      20.355   2.301  -3.976  1.00  0.00              
ATOM     13  N   SER     7      16.793  -2.775  -6.390  1.00  0.00              
ATOM     14  CA  SER     7      15.712  -3.337  -7.214  1.00  0.00              
ATOM     15  C   SER     7      14.381  -3.159  -6.502  1.00  0.00              
ATOM     16  O   SER     7      14.293  -3.372  -5.295  1.00  0.00              
ATOM     17  N   GLY     8      13.319  -2.799  -7.243  1.00  0.00              
ATOM     18  CA  GLY     8      11.993  -2.604  -6.653  1.00  0.00              
ATOM     19  C   GLY     8      11.512  -3.828  -5.863  1.00  0.00              
ATOM     20  O   GLY     8      10.888  -3.693  -4.814  1.00  0.00              
ATOM     21  N   LEU     9      15.626 -12.932  -0.090  1.00  0.00              
ATOM     22  CA  LEU     9      16.888 -13.275   0.557  1.00  0.00              
ATOM     23  C   LEU     9      17.442 -14.577  -0.005  1.00  0.00              
ATOM     24  O   LEU     9      18.644 -14.716  -0.274  1.00  0.00              
ATOM     25  N   PRO    10      16.543 -15.530  -0.185  1.00  0.00              
ATOM     26  CA  PRO    10      16.883 -16.846  -0.701  1.00  0.00              
ATOM     27  C   PRO    10      17.620 -16.780  -2.042  1.00  0.00              
ATOM     28  O   PRO    10      18.717 -17.322  -2.184  1.00  0.00              
ATOM     29  N   ALA    11      21.742 -17.133  -3.615  1.00  0.00              
ATOM     30  CA  ALA    11      22.011 -18.229  -4.530  1.00  0.00              
ATOM     31  C   ALA    11      21.531 -19.576  -4.021  1.00  0.00              
ATOM     32  O   ALA    11      22.187 -20.598  -4.230  1.00  0.00              
ATOM     33  N   VAL    12      20.388 -19.574  -3.346  1.00  0.00              
ATOM     34  CA  VAL    12      19.813 -20.794  -2.802  1.00  0.00              
ATOM     35  C   VAL    12      18.560 -21.144  -3.585  1.00  0.00              
ATOM     36  O   VAL    12      17.725 -20.276  -3.832  1.00  0.00              
ATOM     37  N   LYS    13      18.442 -22.410  -3.982  1.00  0.00              
ATOM     38  CA  LYS    13      17.265 -22.880  -4.705  1.00  0.00              
ATOM     39  C   LYS    13      16.104 -22.633  -3.757  1.00  0.00              
ATOM     40  O   LYS    13      16.218 -22.893  -2.558  1.00  0.00              
ATOM     41  N   VAL    14      14.993 -22.137  -4.292  1.00  0.00              
ATOM     42  CA  VAL    14      13.826 -21.848  -3.471  1.00  0.00              
ATOM     43  C   VAL    14      13.325 -23.074  -2.707  1.00  0.00              
ATOM     44  O   VAL    14      13.390 -24.205  -3.199  1.00  0.00              
ATOM     45  N   LEU    15      12.827 -22.838  -1.499  1.00  0.00              
ATOM     46  CA  LEU    15      12.298 -23.903  -0.649  1.00  0.00              
ATOM     47  C   LEU    15      11.073 -23.341   0.059  1.00  0.00              
ATOM     48  O   LEU    15      11.199 -22.421   0.875  1.00  0.00              
ATOM     49  N   ALA    16       9.892 -23.867  -0.264  1.00  0.00              
ATOM     50  CA  ALA    16       8.672 -23.388   0.373  1.00  0.00              
ATOM     51  C   ALA    16       8.912 -23.505   1.868  1.00  0.00              
ATOM     52  O   ALA    16       9.342 -24.549   2.353  1.00  0.00              
ATOM     53  N   LYS    17       8.670 -22.421   2.616  1.00  0.00              
ATOM     54  CA  LYS    17       8.880 -22.447   4.065  1.00  0.00              
ATOM     55  C   LYS    17       7.718 -23.091   4.803  1.00  0.00              
ATOM     56  O   LYS    17       6.570 -22.984   4.384  1.00  0.00              
ATOM     57  N   GLU    18       8.023 -23.772   5.898  1.00  0.00              
ATOM     58  CA  GLU    18       6.986 -24.397   6.711  1.00  0.00              
ATOM     59  C   GLU    18       6.757 -23.411   7.854  1.00  0.00              
ATOM     60  O   GLU    18       7.558 -23.335   8.783  1.00  0.00              
ATOM     61  N   GLY    19       5.678 -22.642   7.775  1.00  0.00              
ATOM     62  CA  GLY    19       5.381 -21.657   8.805  1.00  0.00              
ATOM     63  C   GLY    19       4.167 -22.072   9.636  1.00  0.00              
ATOM     64  O   GLY    19       3.469 -21.220  10.194  1.00  0.00              
ATOM     65  N   ILE    20       3.926 -23.378   9.717  1.00  0.00              
ATOM     66  CA  ILE    20       2.788 -23.903  10.463  1.00  0.00              
ATOM     67  C   ILE    20       2.781 -23.442  11.917  1.00  0.00              
ATOM     68  O   ILE    20       1.757 -22.982  12.420  1.00  0.00              
ATOM     69  N   PHE    21       3.918 -23.555  12.595  1.00  0.00              
ATOM     70  CA  PHE    21       3.971 -23.133  13.988  1.00  0.00              
ATOM     71  C   PHE    21       3.473 -21.702  14.173  1.00  0.00              
ATOM     72  O   PHE    21       2.492 -21.466  14.880  1.00  0.00              
ATOM     73  N   VAL    22       4.160 -20.754  13.536  1.00  0.00              
ATOM     74  CA  VAL    22       3.812 -19.336  13.637  1.00  0.00              
ATOM     75  C   VAL    22       2.364 -19.059  13.276  1.00  0.00              
ATOM     76  O   VAL    22       1.713 -18.209  13.887  1.00  0.00              
ATOM     77  N   THR    24       1.859 -19.772  12.277  1.00  0.00              
ATOM     78  CA  THR    24       0.478 -19.595  11.864  1.00  0.00              
ATOM     79  C   THR    24      -0.435 -20.066  13.000  1.00  0.00              
ATOM     80  O   THR    24      -1.343 -19.351  13.422  1.00  0.00              
ATOM     81  N   LYS    26      -0.178 -21.268  13.503  1.00  0.00              
ATOM     82  CA  LYS    26      -0.989 -21.816  14.585  1.00  0.00              
ATOM     83  C   LYS    26      -0.840 -20.967  15.836  1.00  0.00              
ATOM     84  O   LYS    26      -1.794 -20.806  16.593  1.00  0.00              
ATOM     85  N   ARG    27       0.356 -20.423  16.049  1.00  0.00              
ATOM     86  CA  ARG    27       0.615 -19.581  17.216  1.00  0.00              
ATOM     87  C   ARG    27      -0.264 -18.336  17.181  1.00  0.00              
ATOM     88  O   ARG    27      -0.928 -18.012  18.159  1.00  0.00              
ATOM     89  N   ALA    28      -0.263 -17.636  16.050  1.00  0.00              
ATOM     90  CA  ALA    28      -1.086 -16.439  15.898  1.00  0.00              
ATOM     91  C   ALA    28      -2.556 -16.858  15.934  1.00  0.00              
ATOM     92  O   ALA    28      -3.423 -16.091  16.342  1.00  0.00              
ATOM     93  N   HIS    30      -2.823 -18.089  15.508  1.00  0.00              
ATOM     94  CA  HIS    30      -4.180 -18.626  15.502  1.00  0.00              
ATOM     95  C   HIS    30      -4.733 -18.557  16.920  1.00  0.00              
ATOM     96  O   HIS    30      -5.832 -18.049  17.147  1.00  0.00              
ATOM     97  N   GLN    31      -3.952 -19.066  17.870  1.00  0.00              
ATOM     98  CA  GLN    31      -4.337 -19.071  19.276  1.00  0.00              
ATOM     99  C   GLN    31      -4.385 -17.650  19.821  1.00  0.00              
ATOM    100  O   GLN    31      -5.245 -17.315  20.634  1.00  0.00              
ATOM    101  N   ASP    32      -3.457 -16.815  19.369  1.00  0.00              
ATOM    102  CA  ASP    32      -3.400 -15.428  19.811  1.00  0.00              
ATOM    103  C   ASP    32      -4.605 -14.630  19.322  1.00  0.00              
ATOM    104  O   ASP    32      -5.126 -13.823  20.123  1.00  0.00              
ATOM    105  N   ILE    33      -8.407 -16.041  21.640  1.00  0.00              
ATOM    106  CA  ILE    33      -8.117 -17.181  22.512  1.00  0.00              
ATOM    107  C   ILE    33      -9.320 -18.084  22.737  1.00  0.00              
ATOM    108  O   ILE    33     -10.121 -18.321  21.830  1.00  0.00              
ATOM    109  N   ARG    34      -7.627 -14.634  31.520  1.00  0.00              
ATOM    110  CA  ARG    34      -7.358 -14.389  32.930  1.00  0.00              
ATOM    111  C   ARG    34      -6.415 -13.211  33.121  1.00  0.00              
ATOM    112  O   ARG    34      -5.506 -12.993  32.326  1.00  0.00              
ATOM    113  N   PRO    35      -6.635 -12.455  34.187  1.00  0.00              
ATOM    114  CA  PRO    35      -5.807 -11.297  34.483  1.00  0.00              
ATOM    115  C   PRO    35      -4.923 -11.619  35.683  1.00  0.00              
ATOM    116  O   PRO    35      -5.421 -12.046  36.726  1.00  0.00              
ATOM    117  N   ILE    38      -3.614 -11.430  35.531  1.00  0.00              
ATOM    118  CA  ILE    38      -2.678 -11.685  36.621  1.00  0.00              
ATOM    119  C   ILE    38      -2.015 -10.374  37.007  1.00  0.00              
ATOM    120  O   ILE    38      -1.930  -9.455  36.192  1.00  0.00              
ATOM    121  N   LEU    39      -1.543 -10.287  38.245  1.00  0.00              
ATOM    122  CA  LEU    39      -0.888  -9.075  38.711  1.00  0.00              
ATOM    123  C   LEU    39       0.614  -9.279  38.820  1.00  0.00              
ATOM    124  O   LEU    39       1.079 -10.332  39.258  1.00  0.00              
ATOM    125  N   ILE    40       1.371  -8.269  38.403  1.00  0.00              
ATOM    126  CA  ILE    40       2.826  -8.322  38.481  1.00  0.00              
ATOM    127  C   ILE    40       3.259  -7.241  39.460  1.00  0.00              
ATOM    128  O   ILE    40       2.988  -6.058  39.251  1.00  0.00              
ATOM    129  N   LEU    41       3.911  -7.661  40.540  1.00  0.00              
ATOM    130  CA  LEU    41       4.382  -6.743  41.565  1.00  0.00              
ATOM    131  C   LEU    41       5.569  -5.931  41.067  1.00  0.00              
ATOM    132  O   LEU    41       6.702  -6.412  41.050  1.00  0.00              
END
