
#######################################################
#                                                     #
#                        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 T0309AL381_3
# Molecule2: number of CA atoms   62 (  501),  selected   34 , name T0309.pdb
# PARAMETERS: T0309AL381_3.T0309.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:    27        16 - 42          4.93     7.54
  LCS_AVERAGE:     40.09

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9        28 - 36          1.81     9.18
  LCS_AVERAGE:     12.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        20 - 25          0.82    11.62
  LCS_AVERAGE:      7.21

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:   62
LCS_GDT     D      16     D      16      3    4   27     3    3    3    4    9   12   14   14   14   18   21   23   26   27   29   29   29   31   31   31 
LCS_GDT     M      17     M      17      3    4   27     3    4    4    6    8   12   14   14   16   19   22   23   26   27   29   29   29   31   31   31 
LCS_GDT     D      18     D      18      4    5   27     3    3    4    5    7    8    9   14   16   19   22   23   26   27   29   29   29   31   31   31 
LCS_GDT     V      19     V      19      4    8   27     3    3    4    6    8   10   13   15   17   19   22   23   25   27   29   29   29   31   31   31 
LCS_GDT     M      20     M      20      6    8   27     3    5    6    7    8    8    9   14   16   19   22   23   26   27   29   29   29   31   31   31 
LCS_GDT     E      21     E      21      6    8   27     3    5    6    7    8   10   13   15   17   19   22   23   26   27   29   29   29   31   31   31 
LCS_GDT     V      22     V      22      6    8   27     4    5    6    7    8    8   13   15   17   19   22   23   26   27   29   29   29   31   31   31 
LCS_GDT     T      23     T      23      6    8   27     4    5    6    7    8    8   13   15   17   19   22   23   26   27   29   29   29   31   31   31 
LCS_GDT     E      24     E      24      6    8   27     4    5    6    7    8    8   13   15   17   19   22   23   26   27   29   29   29   31   31   31 
LCS_GDT     Q      25     Q      25      6    8   27     4    5    6    7    8    8   13   15   17   19   22   23   26   27   29   29   29   31   31   31 
LCS_GDT     T      26     T      26      3    8   27     3    3    4    6    8    8   13   15   17   19   22   23   26   27   29   29   29   31   31   31 
LCS_GDT     K      27     K      27      5    8   27     4    5    5    7    8   12   13   15   17   19   22   23   26   27   29   29   29   31   31   31 
LCS_GDT     E      28     E      28      5    9   27     4    4    6    7    9   12   14   14   17   18   20   23   26   27   29   29   29   31   31   31 
LCS_GDT     A      29     A      29      5    9   27     4    5    6    7    9   12   14   14   17   18   20   22   25   27   29   29   29   31   31   31 
LCS_GDT     E      30     E      30      5    9   27     4    5    6    7    9   12   14   15   17   19   22   23   26   27   29   29   29   31   31   31 
LCS_GDT     Y      31     Y      31      5    9   27     4    5    6    7    9   12   14   15   17   18   22   23   26   27   29   29   29   31   31   31 
LCS_GDT     T      32     T      32      5    9   27     4    5    6    7    9   12   14   15   17   19   22   23   26   27   29   29   29   31   31   31 
LCS_GDT     Y      33     Y      33      5    9   27     4    5    6    7    8   12   14   15   17   19   22   23   26   27   29   29   29   31   31   31 
LCS_GDT     D      34     D      34      4    9   27     4    5    6    7    9   12   14   15   17   19   22   23   26   27   29   29   29   31   31   31 
LCS_GDT     F      35     F      35      4    9   27     4    5    6    7    9   12   14   15   17   19   22   23   26   27   29   29   29   31   31   31 
LCS_GDT     K      36     K      36      4    9   27     4    5    6    7    9   12   14   15   17   19   22   23   26   27   29   29   29   31   31   31 
LCS_GDT     E      37     E      37      4    8   27     4    4    4    7    9   12   14   14   16   19   22   23   26   27   29   29   29   31   31   31 
LCS_GDT     I      38     I      38      4    6   27     4    4    4    5    9   12   14   14   15   19   22   23   26   27   29   29   29   31   31   31 
LCS_GDT     L      39     L      39      4    6   27     3    3    4    5    7   12   14   14   16   19   22   23   26   27   29   29   29   31   31   31 
LCS_GDT     S      40     S      40      4    6   27     3    4    4    5    6    7    8   11   14   19   21   23   26   27   29   29   29   31   31   31 
LCS_GDT     E      41     E      41      4    6   27     3    4    4    5    6    6    8   11   14   17   21   23   26   27   29   29   29   31   31   31 
LCS_GDT     F      42     F      42      4    6   27     3    4    4    5    6    7    7    9   10   14   17   23   26   27   29   29   29   31   31   31 
LCS_GDT     N      43     N      43      4    7   20     3    4    4    7    7    8    9   10   13   15   17   22   26   27   29   29   29   31   31   31 
LCS_GDT     G      44     G      44      4    7   16     3    3    4    5    5    7    7    8    9   10   12   14   15   17   19   19   20   21   27   30 
LCS_GDT     K      45     K      45      4    7   16     3    3    4    5    5    7    7    8   10   11   13   16   19   26   29   29   29   31   31   31 
LCS_GDT     N      46     N      46      4    7   16     1    4    4    5    5    7    7    8    9   10   11   14   15   16   18   28   29   31   31   31 
LCS_GDT     V      47     V      47      4    7   16     3    4    4    5    5    7    7    8   14   19   22   23   25   25   26   28   29   31   31   31 
LCS_GDT     S      48     S      48      4    7   16     3    4    4    5    5    6    7    8    9   10   12   20   23   25   25   26   26   26   27   29 
LCS_GDT     I      49     I      49      4    7   16     3    4    4    5    5    6    7    8    9   10   12   14   15   17   22   24   25   26   27   27 
LCS_AVERAGE  LCS_A:  19.77  (   7.21   12.00   40.09 )

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      5      6      7      9     12     14     15     17     19     22     23     26     27     29     29     29     31     31     31 
GDT PERCENT_CA   6.45   8.06   9.68  11.29  14.52  19.35  22.58  24.19  27.42  30.65  35.48  37.10  41.94  43.55  46.77  46.77  46.77  50.00  50.00  50.00
GDT RMS_LOCAL    0.31   0.59   0.82   1.09   1.81   2.14   2.35   2.90   3.20   3.79   4.06   4.22   4.85   4.94   5.21   5.21   5.21   5.69   5.69   5.69
GDT RMS_ALL_CA  24.43  12.62  11.62  11.26   9.04   8.39   8.30  10.38  11.40   7.25   7.41   7.44   7.77   7.72   7.58   7.58   7.58   7.17   7.17   7.17

#      Molecule1      Molecule2       DISTANCE
LGA    D      16      D      16         14.598
LGA    M      17      M      17         12.697
LGA    D      18      D      18          8.739
LGA    V      19      V      19          2.211
LGA    M      20      M      20          5.335
LGA    E      21      E      21          2.614
LGA    V      22      V      22          3.621
LGA    T      23      T      23          3.492
LGA    E      24      E      24          3.125
LGA    Q      25      Q      25          3.671
LGA    T      26      T      26          3.919
LGA    K      27      K      27          2.616
LGA    E      28      E      28          4.544
LGA    A      29      A      29          4.578
LGA    E      30      E      30          3.070
LGA    Y      31      Y      31          3.252
LGA    T      32      T      32          2.956
LGA    Y      33      Y      33          2.810
LGA    D      34      D      34          2.150
LGA    F      35      F      35          2.761
LGA    K      36      K      36          2.139
LGA    E      37      E      37          7.139
LGA    I      38      I      38         10.176
LGA    L      39      L      39         10.985
LGA    S      40      S      40         15.364
LGA    E      41      E      41         17.746
LGA    F      42      F      42         21.091
LGA    N      43      N      43         21.232
LGA    G      44      G      44         23.595
LGA    K      45      K      45         21.669
LGA    N      46      N      46         18.480
LGA    V      47      V      47         14.107
LGA    S      48      S      48         10.794
LGA    I      49      I      49         10.590

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   34   62    4.0     15    2.90    22.581    20.778     0.499

LGA_LOCAL      RMSD =  2.905  Number of atoms =   15  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 11.080  Number of atoms =   34 
Std_ALL_ATOMS  RMSD =  7.040  (standard rmsd on all 34 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.205735 * X  +  -0.884802 * Y  +   0.418090 * Z  + 108.231812
  Y_new =  -0.773672 * X  +   0.408675 * Y  +   0.484166 * Z  +  45.933823
  Z_new =  -0.599254 * X  +  -0.223855 * Y  +  -0.768625 * Z  +  88.708916 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.858191    0.283401  [ DEG:  -163.7623     16.2377 ]
  Theta =   0.642569    2.499024  [ DEG:    36.8165    143.1835 ]
  Phi   =  -1.830701    1.310892  [ DEG:  -104.8914     75.1086 ]
 
# 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: T0309AL381_3                                  
REMARK     2: T0309.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0309AL381_3.T0309.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   34   62   4.0   15   2.90  20.778     7.04
REMARK  ---------------------------------------------------------- 
MOLECULE T0309AL381_3
REMARK Aligment from pdb entry: 1tf7A
ATOM      1  N   ASP    16      -3.771   4.113 -16.175  1.00  0.00              
ATOM      2  CA  ASP    16      -4.100   3.525 -14.883  1.00  0.00              
ATOM      3  C   ASP    16      -2.981   3.783 -13.861  1.00  0.00              
ATOM      4  O   ASP    16      -1.805   3.722 -14.199  1.00  0.00              
ATOM      5  N   MET    17      -3.345   4.071 -12.617  1.00  0.00              
ATOM      6  CA  MET    17      -2.350   4.335 -11.577  1.00  0.00              
ATOM      7  C   MET    17      -2.070   3.091 -10.728  1.00  0.00              
ATOM      8  O   MET    17      -1.281   3.140  -9.783  1.00  0.00              
ATOM      9  N   ASP    18      -2.713   1.981 -11.059  1.00  0.00              
ATOM     10  CA  ASP    18      -2.543   0.763 -10.281  1.00  0.00              
ATOM     11  C   ASP    18      -1.285  -0.040 -10.577  1.00  0.00              
ATOM     12  O   ASP    18      -0.802  -0.083 -11.711  1.00  0.00              
ATOM     13  N   VAL    19      -0.761  -0.672  -9.532  1.00  0.00              
ATOM     14  CA  VAL    19       0.415  -1.518  -9.643  1.00  0.00              
ATOM     15  C   VAL    19      -0.167  -2.927  -9.675  1.00  0.00              
ATOM     16  O   VAL    19      -0.349  -3.568  -8.639  1.00  0.00              
ATOM     17  N   MET    20      -0.477  -3.385 -10.885  1.00  0.00              
ATOM     18  CA  MET    20      -1.084  -4.695 -11.117  1.00  0.00              
ATOM     19  C   MET    20      -0.095  -5.847 -11.163  1.00  0.00              
ATOM     20  O   MET    20       0.975  -5.734 -11.749  1.00  0.00              
ATOM     21  N   GLU    21      -0.450  -6.960 -10.537  1.00  0.00              
ATOM     22  CA  GLU    21       0.433  -8.112 -10.567  1.00  0.00              
ATOM     23  C   GLU    21       0.121  -8.829 -11.863  1.00  0.00              
ATOM     24  O   GLU    21      -0.997  -8.748 -12.367  1.00  0.00              
ATOM     25  N   VAL    22       1.109  -9.517 -12.413  1.00  0.00              
ATOM     26  CA  VAL    22       0.891 -10.235 -13.648  1.00  0.00              
ATOM     27  C   VAL    22       1.727 -11.500 -13.671  1.00  0.00              
ATOM     28  O   VAL    22       2.825 -11.544 -13.114  1.00  0.00              
ATOM     29  N   THR    23       1.181 -12.534 -14.299  1.00  0.00              
ATOM     30  CA  THR    23       1.849 -13.820 -14.420  1.00  0.00              
ATOM     31  C   THR    23       2.293 -13.981 -15.859  1.00  0.00              
ATOM     32  O   THR    23       1.868 -13.232 -16.738  1.00  0.00              
ATOM     33  N   GLU    24       3.152 -14.960 -16.099  1.00  0.00              
ATOM     34  CA  GLU    24       3.640 -15.225 -17.440  1.00  0.00              
ATOM     35  C   GLU    24       3.388 -16.694 -17.731  1.00  0.00              
ATOM     36  O   GLU    24       3.728 -17.558 -16.926  1.00  0.00              
ATOM     37  N   GLN    25       2.767 -16.968 -18.875  1.00  0.00              
ATOM     38  CA  GLN    25       2.447 -18.334 -19.272  1.00  0.00              
ATOM     39  C   GLN    25       2.796 -18.567 -20.734  1.00  0.00              
ATOM     40  O   GLN    25       3.462 -17.746 -21.363  1.00  0.00              
ATOM     41  N   THR    26       2.337 -19.689 -21.271  1.00  0.00              
ATOM     42  CA  THR    26       2.590 -20.020 -22.665  1.00  0.00              
ATOM     43  C   THR    26       1.838 -19.016 -23.526  1.00  0.00              
ATOM     44  O   THR    26       2.294 -18.634 -24.605  1.00  0.00              
ATOM     45  N   LYS    27       0.682 -18.586 -23.032  1.00  0.00              
ATOM     46  CA  LYS    27      -0.141 -17.621 -23.743  1.00  0.00              
ATOM     47  C   LYS    27       0.547 -16.255 -23.793  1.00  0.00              
ATOM     48  O   LYS    27       0.406 -15.509 -24.765  1.00  0.00              
ATOM     49  N   GLU    28       1.309 -15.941 -22.749  1.00  0.00              
ATOM     50  CA  GLU    28       2.003 -14.667 -22.685  1.00  0.00              
ATOM     51  C   GLU    28       1.791 -13.985 -21.345  1.00  0.00              
ATOM     52  O   GLU    28       1.832 -14.638 -20.306  1.00  0.00              
ATOM     53  N   ALA    29       1.559 -12.667 -21.335  1.00  0.00              
ATOM     54  CA  ALA    29       1.344 -11.899 -20.102  1.00  0.00              
ATOM     55  C   ALA    29      -0.115 -11.666 -19.706  1.00  0.00              
ATOM     56  O   ALA    29      -0.922 -11.207 -20.512  1.00  0.00              
ATOM     57  N   GLU    30      -0.441 -11.958 -18.454  1.00  0.00              
ATOM     58  CA  GLU    30      -1.797 -11.757 -17.971  1.00  0.00              
ATOM     59  C   GLU    30      -1.800 -10.782 -16.812  1.00  0.00              
ATOM     60  O   GLU    30      -1.411 -11.134 -15.704  1.00  0.00              
ATOM     61  N   TYR    31      -2.244  -9.556 -17.067  1.00  0.00              
ATOM     62  CA  TYR    31      -2.293  -8.533 -16.024  1.00  0.00              
ATOM     63  C   TYR    31      -3.536  -8.673 -15.158  1.00  0.00              
ATOM     64  O   TYR    31      -4.654  -8.428 -15.611  1.00  0.00              
ATOM     65  N   THR    32      -3.329  -9.047 -13.903  1.00  0.00              
ATOM     66  CA  THR    32      -4.425  -9.227 -12.966  1.00  0.00              
ATOM     67  C   THR    32      -4.748  -7.969 -12.153  1.00  0.00              
ATOM     68  O   THR    32      -4.853  -6.872 -12.710  1.00  0.00              
ATOM     69  N   TYR    33      -4.913  -8.130 -10.841  1.00  0.00              
ATOM     70  CA  TYR    33      -5.254  -7.005  -9.976  1.00  0.00              
ATOM     71  C   TYR    33      -4.089  -6.438  -9.189  1.00  0.00              
ATOM     72  O   TYR    33      -2.982  -6.982  -9.206  1.00  0.00              
ATOM     73  N   ASP    34      -4.359  -5.339  -8.494  1.00  0.00              
ATOM     74  CA  ASP    34      -3.362  -4.669  -7.671  1.00  0.00              
ATOM     75  C   ASP    34      -3.357  -5.301  -6.285  1.00  0.00              
ATOM     76  O   ASP    34      -4.246  -6.081  -5.949  1.00  0.00              
ATOM     77  N   PHE    35      -2.348  -4.974  -5.484  1.00  0.00              
ATOM     78  CA  PHE    35      -2.268  -5.501  -4.132  1.00  0.00              
ATOM     79  C   PHE    35      -2.807  -4.407  -3.225  1.00  0.00              
ATOM     80  O   PHE    35      -2.052  -3.731  -2.529  1.00  0.00              
ATOM     81  N   LYS    36      -4.122  -4.230  -3.244  1.00  0.00              
ATOM     82  CA  LYS    36      -4.755  -3.195  -2.441  1.00  0.00              
ATOM     83  C   LYS    36      -4.499  -3.344  -0.947  1.00  0.00              
ATOM     84  O   LYS    36      -4.478  -2.358  -0.213  1.00  0.00              
ATOM     85  N   GLU    37      -4.299  -4.575  -0.502  1.00  0.00              
ATOM     86  CA  GLU    37      -4.082  -4.851   0.911  1.00  0.00              
ATOM     87  C   GLU    37      -2.624  -4.921   1.369  1.00  0.00              
ATOM     88  O   GLU    37      -2.309  -5.584   2.357  1.00  0.00              
ATOM     89  N   ILE    38      -1.739  -4.228   0.663  1.00  0.00              
ATOM     90  CA  ILE    38      -0.326  -4.229   1.023  1.00  0.00              
ATOM     91  C   ILE    38       0.267  -2.835   1.164  1.00  0.00              
ATOM     92  O   ILE    38      -0.281  -1.849   0.663  1.00  0.00              
ATOM     93  N   LEU    39       1.404  -2.776   1.850  1.00  0.00              
ATOM     94  CA  LEU    39       2.136  -1.536   2.057  1.00  0.00              
ATOM     95  C   LEU    39       3.579  -1.745   1.610  1.00  0.00              
ATOM     96  O   LEU    39       4.088  -2.871   1.642  1.00  0.00              
ATOM     97  N   SER    40       4.236  -0.664   1.194  1.00  0.00              
ATOM     98  CA  SER    40       5.627  -0.736   0.745  1.00  0.00              
ATOM     99  C   SER    40       5.787  -1.817  -0.308  1.00  0.00              
ATOM    100  O   SER    40       6.520  -2.780  -0.104  1.00  0.00              
ATOM    101  N   GLU    41       5.092  -1.659  -1.427  1.00  0.00              
ATOM    102  CA  GLU    41       5.163  -2.630  -2.506  1.00  0.00              
ATOM    103  C   GLU    41       6.305  -2.250  -3.438  1.00  0.00              
ATOM    104  O   GLU    41       7.028  -3.115  -3.947  1.00  0.00              
ATOM    105  N   PHE    42       6.470  -0.948  -3.644  1.00  0.00              
ATOM    106  CA  PHE    42       7.531  -0.438  -4.507  1.00  0.00              
ATOM    107  C   PHE    42       8.875  -1.030  -4.105  1.00  0.00              
ATOM    108  O   PHE    42       9.744  -1.246  -4.951  1.00  0.00              
ATOM    109  N   ASN    43       9.019  -1.304  -2.812  1.00  0.00              
ATOM    110  CA  ASN    43      10.248  -1.849  -2.256  1.00  0.00              
ATOM    111  C   ASN    43      10.576  -3.289  -2.658  1.00  0.00              
ATOM    112  O   ASN    43      11.738  -3.690  -2.639  1.00  0.00              
ATOM    113  N   GLY    44       9.569  -4.070  -3.022  1.00  0.00              
ATOM    114  CA  GLY    44       9.841  -5.441  -3.411  1.00  0.00              
ATOM    115  C   GLY    44       9.512  -6.450  -2.324  1.00  0.00              
ATOM    116  O   GLY    44       9.349  -7.637  -2.607  1.00  0.00              
ATOM    117  N   LYS    45       9.435  -5.986  -1.078  1.00  0.00              
ATOM    118  CA  LYS    45       9.095  -6.852   0.048  1.00  0.00              
ATOM    119  C   LYS    45       7.994  -6.156   0.829  1.00  0.00              
ATOM    120  O   LYS    45       8.256  -5.468   1.819  1.00  0.00              
ATOM    121  N   ASN    46       6.735  -6.332   0.387  1.00  0.00              
ATOM    122  CA  ASN    46       5.541  -5.737   0.994  1.00  0.00              
ATOM    123  C   ASN    46       5.273  -6.155   2.423  1.00  0.00              
ATOM    124  O   ASN    46       5.967  -6.993   2.988  1.00  0.00              
ATOM    125  N   VAL    47       4.241  -5.550   2.989  1.00  0.00              
ATOM    126  CA  VAL    47       3.810  -5.834   4.341  1.00  0.00              
ATOM    127  C   VAL    47       2.299  -6.030   4.280  1.00  0.00              
ATOM    128  O   VAL    47       1.543  -5.058   4.236  1.00  0.00              
ATOM    129  N   SER    48       1.868  -7.287   4.246  1.00  0.00              
ATOM    130  CA  SER    48       0.446  -7.609   4.193  1.00  0.00              
ATOM    131  C   SER    48      -0.258  -6.941   5.361  1.00  0.00              
ATOM    132  O   SER    48       0.295  -6.840   6.455  1.00  0.00              
ATOM    133  N   ILE    49      -1.477  -6.477   5.126  1.00  0.00              
ATOM    134  CA  ILE    49      -2.241  -5.826   6.177  1.00  0.00              
ATOM    135  C   ILE    49      -3.742  -6.060   5.996  1.00  0.00              
ATOM    136  O   ILE    49      -4.432  -6.279   7.018  1.00  0.00              
END
