
#######################################################
#                                                     #
#                        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 T0352AL381_2
# Molecule2: number of CA atoms  109 ( 1766),  selected   34 , name T0352.pdb
# PARAMETERS: T0352AL381_2.T0352.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:    32         6 - 38          4.42     5.99
  LCS_AVERAGE:     28.12

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    19         7 - 25          1.98     6.03
  LONGEST_CONTINUOUS_SEGMENT:    19         8 - 26          1.97     5.99
  LCS_AVERAGE:     13.17

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11        12 - 22          0.53     8.59
  LCS_AVERAGE:      6.26

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:  109
LCS_GDT     R       6     R       6      8   18   32     8    8    9   11   17   20   23   24   27   28   28   29   29   29   29   29   30   31   31   32 
LCS_GDT     V       7     V       7      8   19   32     8    8    9   13   17   20   23   24   27   28   28   29   29   29   29   29   30   31   31   32 
LCS_GDT     R       8     R       8      8   19   32     8    8   11   15   17   21   23   24   27   28   28   29   29   29   29   29   30   31   31   32 
LCS_GDT     L       9     L       9      8   19   32     8    8    9   15   17   21   23   24   27   28   28   29   29   29   29   29   30   31   31   32 
LCS_GDT     Q      10     Q      10      8   19   32     8    8   10   15   17   21   23   24   27   28   28   29   29   29   29   29   30   31   31   32 
LCS_GDT     L      11     L      11      8   19   32     8    8    9   15   17   21   23   24   27   28   28   29   29   29   29   29   30   31   31   32 
LCS_GDT     Q      12     Q      12     11   19   32     8   11   11   15   17   21   23   24   27   28   28   29   29   29   29   29   30   31   31   32 
LCS_GDT     A      13     A      13     11   19   32     9   11   11   15   17   21   23   24   27   28   28   29   29   29   29   29   30   31   31   32 
LCS_GDT     L      14     L      14     11   19   32     9   11   11   15   17   21   23   24   27   28   28   29   29   29   29   29   30   31   31   32 
LCS_GDT     E      15     E      15     11   19   32     9   11   11   15   17   21   23   24   27   28   28   29   29   29   29   29   30   31   31   32 
LCS_GDT     A      16     A      16     11   19   32     9   11   11   15   17   21   23   24   27   28   28   29   29   29   29   29   30   31   31   32 
LCS_GDT     L      17     L      17     11   19   32     9   11   11   15   17   21   23   24   27   28   28   29   29   29   29   29   30   31   31   32 
LCS_GDT     L      18     L      18     11   19   32     9   11   11   15   17   21   23   24   27   28   28   29   29   29   29   29   30   31   31   32 
LCS_GDT     R      19     R      19     11   19   32     9   11   11   15   17   21   23   24   27   28   28   29   29   29   29   29   30   31   31   32 
LCS_GDT     E      20     E      20     11   19   32     9   11   11   15   17   21   23   24   27   28   28   29   29   29   29   29   30   31   31   32 
LCS_GDT     H      21     H      21     11   19   32     9   11   11   15   17   21   23   24   27   28   28   29   29   29   29   29   30   31   31   32 
LCS_GDT     Q      22     Q      22     11   19   32     5   11   11   15   17   21   23   24   27   28   28   29   29   29   29   29   30   31   31   32 
LCS_GDT     H      23     H      23      4   19   32     4    6    9   13   17   21   23   24   27   28   28   29   29   29   29   29   30   31   31   32 
LCS_GDT     W      24     W      24      4   19   32     4    4    5    6   17   21   23   24   27   28   28   29   29   29   29   29   30   31   31   32 
LCS_GDT     R      25     R      25      5   19   32     4    6    8   13   17   21   23   24   27   28   28   29   29   29   29   29   30   31   31   32 
LCS_GDT     N      26     N      26      5   19   32     4    5    6   10   16   21   23   24   27   28   28   29   29   29   29   29   30   31   31   32 
LCS_GDT     D      27     D      27      5   16   32     3    5    6   10   17   21   23   24   27   28   28   29   29   29   29   29   30   31   31   32 
LCS_GDT     E      28     E      28      5   10   32     3    4    6    7   11   17   21   23   27   28   28   29   29   29   29   29   30   31   31   32 
LCS_GDT     P      29     P      29      5   10   32     3    5    9   11   16   20   23   24   27   28   28   29   29   29   29   29   30   31   31   32 
LCS_GDT     Q      30     Q      30      3    6   32     3    3    5    7    9   10   18   19   27   28   28   29   29   29   29   29   30   31   31   32 
LCS_GDT     H      32     H      32      3    6   32     3    3    3    3    3    6    7    8    9   12   18   20   26   27   29   29   30   30   31   32 
LCS_GDT     Q      33     Q      33      3    6   32     3    3    4    7    9   13   18   21   26   28   28   29   29   29   29   29   30   31   31   32 
LCS_GDT     F      34     F      34      3    6   32     3    4    4    7    9   13   18   23   27   28   28   29   29   29   29   29   30   31   31   32 
LCS_GDT     N      35     N      35      3    6   32     7    7    9   13   17   21   23   24   27   28   28   29   29   29   29   29   30   31   31   32 
LCS_GDT     S      36     S      36      3    5   32     3    3    3    4    4    6   20   22   24   25   27   29   29   29   29   29   30   31   31   32 
LCS_GDT     T      37     T      37      3    5   32     3    3    3    4    4    5    7    7    8    8   16   19   22   25   26   28   30   31   31   32 
LCS_GDT     Q      38     Q      38      3    5   32     3    3    3    4    4    5    7    7    8    9   10   19   22   22   26   26   29   31   31   32 
LCS_GDT     P      39     P      39      3    5    9     3    3    3    4    4    5    7    7    7    8   10   10   13   14   15   18   18   18   19   23 
LCS_GDT     F      40     F      40      3    4    9     3    3    3    4    4    5    6    6    6    7   10   10   13   14   15   19   25   25   26   27 
LCS_AVERAGE  LCS_A:  15.85  (   6.26   13.17   28.12 )

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     11     11     15     17     21     23     24     27     28     28     29     29     29     29     29     30     31     31     32 
GDT PERCENT_CA   8.26  10.09  10.09  13.76  15.60  19.27  21.10  22.02  24.77  25.69  25.69  26.61  26.61  26.61  26.61  26.61  27.52  28.44  28.44  29.36
GDT RMS_LOCAL    0.28   0.53   0.53   1.37   1.70   2.05   2.22   2.32   2.78   2.92   2.92   3.14   3.14   3.14   3.14   3.14   3.48   4.18   4.18   4.42
GDT RMS_ALL_CA   9.10   8.59   8.59   7.55   6.12   6.02   6.11   6.20   6.40   6.45   6.45   6.30   6.30   6.30   6.30   6.30   6.33   5.96   5.96   5.99

#      Molecule1      Molecule2       DISTANCE
LGA    R       6      R       6          3.220
LGA    V       7      V       7          2.730
LGA    R       8      R       8          1.500
LGA    L       9      L       9          1.271
LGA    Q      10      Q      10          0.855
LGA    L      11      L      11          1.799
LGA    Q      12      Q      12          1.540
LGA    A      13      A      13          2.976
LGA    L      14      L      14          3.633
LGA    E      15      E      15          2.250
LGA    A      16      A      16          1.320
LGA    L      17      L      17          2.060
LGA    L      18      L      18          2.429
LGA    R      19      R      19          2.750
LGA    E      20      E      20          1.674
LGA    H      21      H      21          1.396
LGA    Q      22      Q      22          2.929
LGA    H      23      H      23          1.331
LGA    W      24      W      24          2.349
LGA    R      25      R      25          1.954
LGA    N      26      N      26          3.403
LGA    D      27      D      27          2.662
LGA    E      28      E      28          4.394
LGA    P      29      P      29          3.271
LGA    Q      30      Q      30          6.048
LGA    H      32      H      32          9.819
LGA    Q      33      Q      33          6.668
LGA    F      34      F      34          5.812
LGA    N      35      N      35          1.406
LGA    S      36      S      36          6.218
LGA    T      37      T      37         11.095
LGA    Q      38      Q      38         12.429
LGA    P      39      P      39         19.108
LGA    F      40      F      40         17.256

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   34  109    4.0     24    2.32    18.119    17.951     0.992

LGA_LOCAL      RMSD =  2.319  Number of atoms =   24  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.278  Number of atoms =   34 
Std_ALL_ATOMS  RMSD =  5.781  (standard rmsd on all 34 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.210417 * X  +  -0.973994 * Y  +  -0.084030 * Z  +   8.463389
  Y_new =   0.737907 * X  +   0.101855 * Y  +   0.667172 * Z  + -87.116562
  Z_new =  -0.641262 * X  +  -0.202391 * Y  +   0.740149 * Z  +  81.128166 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.266921    2.874672  [ DEG:   -15.2934    164.7066 ]
  Theta =   0.696142    2.445450  [ DEG:    39.8860    140.1140 ]
  Phi   =   1.293015   -1.848578  [ DEG:    74.0843   -105.9157 ]
 
# 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: T0352AL381_2                                  
REMARK     2: T0352.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0352AL381_2.T0352.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   34  109   4.0   24   2.32  17.951     5.78
REMARK  ---------------------------------------------------------- 
MOLECULE T0352AL381_2
REMARK Aligment from pdb entry: 1x74A
ATOM      1  N   ARG     6      -5.907  -2.334 -12.140  1.00  0.00              
ATOM      2  CA  ARG     6      -7.119  -2.413 -11.321  1.00  0.00              
ATOM      3  C   ARG     6      -6.983  -1.521 -10.079  1.00  0.00              
ATOM      4  O   ARG     6      -7.884  -0.767  -9.748  1.00  0.00              
ATOM      5  N   VAL     7      -5.896  -1.705  -9.325  1.00  0.00              
ATOM      6  CA  VAL     7      -5.753  -0.978  -8.074  1.00  0.00              
ATOM      7  C   VAL     7      -5.761   0.534  -8.307  1.00  0.00              
ATOM      8  O   VAL     7      -6.385   1.269  -7.528  1.00  0.00              
ATOM      9  N   ARG     8      -5.063   1.019  -9.338  1.00  0.00              
ATOM     10  CA  ARG     8      -5.065   2.473  -9.584  1.00  0.00              
ATOM     11  C   ARG     8      -6.485   2.986  -9.922  1.00  0.00              
ATOM     12  O   ARG     8      -6.858   4.127  -9.550  1.00  0.00              
ATOM     13  N   LEU     9      -7.280   2.160 -10.599  1.00  0.00              
ATOM     14  CA  LEU     9      -8.686   2.497 -10.880  1.00  0.00              
ATOM     15  C   LEU     9      -9.498   2.658  -9.590  1.00  0.00              
ATOM     16  O   LEU     9     -10.274   3.616  -9.442  1.00  0.00              
ATOM     17  N   GLN    10      -9.342   1.729  -8.646  1.00  0.00              
ATOM     18  CA  GLN    10     -10.026   1.907  -7.359  1.00  0.00              
ATOM     19  C   GLN    10      -9.443   3.120  -6.618  1.00  0.00              
ATOM     20  O   GLN    10     -10.174   3.822  -5.936  1.00  0.00              
ATOM     21  N   LEU    11      -8.136   3.351  -6.738  1.00  0.00              
ATOM     22  CA  LEU    11      -7.508   4.500  -6.086  1.00  0.00              
ATOM     23  C   LEU    11      -8.158   5.822  -6.557  1.00  0.00              
ATOM     24  O   LEU    11      -8.288   6.777  -5.777  1.00  0.00              
ATOM     25  N   GLN    12      -8.576   5.862  -7.829  1.00  0.00              
ATOM     26  CA  GLN    12      -9.184   7.063  -8.383  1.00  0.00              
ATOM     27  C   GLN    12     -10.719   6.967  -8.424  1.00  0.00              
ATOM     28  O   GLN    12     -11.387   7.700  -9.159  1.00  0.00              
ATOM     29  N   ALA    13     -11.290   6.084  -7.616  1.00  0.00              
ATOM     30  CA  ALA    13     -12.751   5.899  -7.680  1.00  0.00              
ATOM     31  C   ALA    13     -13.519   7.218  -7.478  1.00  0.00              
ATOM     32  O   ALA    13     -14.630   7.387  -8.013  1.00  0.00              
ATOM     33  N   LEU    14     -12.942   8.134  -6.683  1.00  0.00              
ATOM     34  CA  LEU    14     -13.637   9.389  -6.424  1.00  0.00              
ATOM     35  C   LEU    14     -13.937  10.144  -7.728  1.00  0.00              
ATOM     36  O   LEU    14     -15.016  10.753  -7.865  1.00  0.00              
ATOM     37  N   GLU    15     -12.996  10.114  -8.676  1.00  0.00              
ATOM     38  CA  GLU    15     -13.243  10.766  -9.974  1.00  0.00              
ATOM     39  C   GLU    15     -14.284  10.040 -10.796  1.00  0.00              
ATOM     40  O   GLU    15     -15.102  10.691 -11.441  1.00  0.00              
ATOM     41  N   ALA    16     -14.263   8.701 -10.785  1.00  0.00              
ATOM     42  CA  ALA    16     -15.336   7.939 -11.456  1.00  0.00              
ATOM     43  C   ALA    16     -16.716   8.265 -10.875  1.00  0.00              
ATOM     44  O   ALA    16     -17.699   8.382 -11.616  1.00  0.00              
ATOM     45  N   LEU    17     -16.775   8.417  -9.551  1.00  0.00              
ATOM     46  CA  LEU    17     -18.026   8.772  -8.860  1.00  0.00              
ATOM     47  C   LEU    17     -18.467  10.174  -9.287  1.00  0.00              
ATOM     48  O   LEU    17     -19.616  10.387  -9.680  1.00  0.00              
ATOM     49  N   LEU    18     -17.541  11.118  -9.215  1.00  0.00              
ATOM     50  CA  LEU    18     -17.815  12.513  -9.616  1.00  0.00              
ATOM     51  C   LEU    18     -18.151  12.682 -11.095  1.00  0.00              
ATOM     52  O   LEU    18     -19.013  13.462 -11.436  1.00  0.00              
ATOM     53  N   ARG    19     -17.484  11.946 -11.982  1.00  0.00              
ATOM     54  CA  ARG    19     -17.879  11.988 -13.396  1.00  0.00              
ATOM     55  C   ARG    19     -19.357  11.675 -13.631  1.00  0.00              
ATOM     56  O   ARG    19     -20.013  12.302 -14.458  1.00  0.00              
ATOM     57  N   GLU    20     -19.883  10.710 -12.888  1.00  0.00              
ATOM     58  CA  GLU    20     -21.262  10.288 -13.024  1.00  0.00              
ATOM     59  C   GLU    20     -22.281  11.350 -12.623  1.00  0.00              
ATOM     60  O   GLU    20     -23.415  11.308 -13.082  1.00  0.00              
ATOM     61  N   HIS    21     -21.874  12.293 -11.766  1.00  0.00              
ATOM     62  CA  HIS    21     -22.803  13.329 -11.280  1.00  0.00              
ATOM     63  C   HIS    21     -22.470  14.728 -11.795  1.00  0.00              
ATOM     64  O   HIS    21     -23.000  15.728 -11.279  1.00  0.00              
ATOM     65  N   GLN    22     -21.633  14.822 -12.820  1.00  0.00              
ATOM     66  CA  GLN    22     -21.314  16.138 -13.369  1.00  0.00              
ATOM     67  C   GLN    22     -20.276  16.915 -12.576  1.00  0.00              
ATOM     68  O   GLN    22     -20.031  18.098 -12.867  1.00  0.00              
ATOM     69  N   HIS    23     -19.652  16.277 -11.586  1.00  0.00              
ATOM     70  CA  HIS    23     -18.693  16.957 -10.703  1.00  0.00              
ATOM     71  C   HIS    23     -17.234  16.860 -11.142  1.00  0.00              
ATOM     72  O   HIS    23     -16.326  17.390 -10.483  1.00  0.00              
ATOM     73  N   TRP    24     -16.995  16.188 -12.259  1.00  0.00              
ATOM     74  CA  TRP    24     -15.644  16.074 -12.801  1.00  0.00              
ATOM     75  C   TRP    24     -15.758  15.899 -14.308  1.00  0.00              
ATOM     76  O   TRP    24     -16.657  15.218 -14.789  1.00  0.00              
ATOM     77  N   ARG    25     -14.829  16.502 -15.049  1.00  0.00              
ATOM     78  CA  ARG    25     -14.887  16.426 -16.499  1.00  0.00              
ATOM     79  C   ARG    25     -13.590  15.805 -16.996  1.00  0.00              
ATOM     80  O   ARG    25     -12.559  15.838 -16.315  1.00  0.00              
ATOM     81  N   ASN    26     -13.651  15.282 -18.218  1.00  0.00              
ATOM     82  CA  ASN    26     -12.494  14.715 -18.906  1.00  0.00              
ATOM     83  C   ASN    26     -11.493  15.733 -19.442  1.00  0.00              
ATOM     84  O   ASN    26     -10.465  15.355 -19.995  1.00  0.00              
ATOM     85  N   ASP    27     -11.792  17.013 -19.283  1.00  0.00              
ATOM     86  CA  ASP    27     -10.872  18.066 -19.682  1.00  0.00              
ATOM     87  C   ASP    27      -9.701  18.183 -18.675  1.00  0.00              
ATOM     88  O   ASP    27      -9.898  18.507 -17.502  1.00  0.00              
ATOM     89  N   GLU    28      -8.486  17.922 -19.140  1.00  0.00              
ATOM     90  CA  GLU    28      -7.299  18.039 -18.282  1.00  0.00              
ATOM     91  C   GLU    28      -7.083  19.496 -17.863  1.00  0.00              
ATOM     92  O   GLU    28      -7.236  20.425 -18.673  1.00  0.00              
ATOM     93  N   PRO    29      -6.795  19.679 -16.583  1.00  0.00              
ATOM     94  CA  PRO    29      -6.396  20.956 -16.017  1.00  0.00              
ATOM     95  C   PRO    29      -7.573  21.904 -15.824  1.00  0.00              
ATOM     96  O   PRO    29      -7.374  23.099 -15.796  1.00  0.00              
ATOM     97  N   GLN    30      -8.799  21.387 -15.741  1.00  0.00              
ATOM     98  CA  GLN    30      -9.985  22.255 -15.726  1.00  0.00              
ATOM     99  C   GLN    30     -11.008  21.824 -14.678  1.00  0.00              
ATOM    100  O   GLN    30     -12.241  21.975 -14.881  1.00  0.00              
ATOM    101  N   HIS    32     -10.506  21.276 -13.574  1.00  0.00              
ATOM    102  CA  HIS    32     -11.394  20.763 -12.525  1.00  0.00              
ATOM    103  C   HIS    32     -10.935  21.234 -11.158  1.00  0.00              
ATOM    104  O   HIS    32      -9.925  21.963 -11.047  1.00  0.00              
ATOM    105  N   GLN    33     -11.679  20.847 -10.124  1.00  0.00              
ATOM    106  CA  GLN    33     -11.381  21.384  -8.793  1.00  0.00              
ATOM    107  C   GLN    33     -10.008  20.996  -8.234  1.00  0.00              
ATOM    108  O   GLN    33      -9.421  21.774  -7.497  1.00  0.00              
ATOM    109  N   PHE    34      -9.529  19.786  -8.532  1.00  0.00              
ATOM    110  CA  PHE    34      -8.400  19.199  -7.821  1.00  0.00              
ATOM    111  C   PHE    34      -7.208  18.919  -8.718  1.00  0.00              
ATOM    112  O   PHE    34      -6.265  18.255  -8.291  1.00  0.00              
ATOM    113  N   ASN    35      -7.237  19.429  -9.943  1.00  0.00              
ATOM    114  CA  ASN    35      -6.160  19.111 -10.899  1.00  0.00              
ATOM    115  C   ASN    35      -5.307  20.315 -11.263  1.00  0.00              
ATOM    116  O   ASN    35      -4.468  20.241 -12.154  1.00  0.00              
ATOM    117  N   SER    36      -5.538  21.437 -10.585  1.00  0.00              
ATOM    118  CA  SER    36      -4.859  22.659 -10.927  1.00  0.00              
ATOM    119  C   SER    36      -5.756  23.662 -11.605  1.00  0.00              
ATOM    120  O   SER    36      -5.380  24.839 -11.718  1.00  0.00              
ATOM    121  N   THR    37      -6.942  23.225 -12.038  1.00  0.00              
ATOM    122  CA  THR    37      -7.890  24.123 -12.686  1.00  0.00              
ATOM    123  C   THR    37      -8.429  25.250 -11.803  1.00  0.00              
ATOM    124  O   THR    37      -8.773  26.321 -12.310  1.00  0.00              
ATOM    125  N   GLN    38      -8.546  25.001 -10.498  1.00  0.00              
ATOM    126  CA  GLN    38      -9.145  25.967  -9.563  1.00  0.00              
ATOM    127  C   GLN    38      -8.043  26.854  -8.958  1.00  0.00              
ATOM    128  O   GLN    38      -7.047  26.313  -8.489  1.00  0.00              
ATOM    129  N   PRO    39      -8.218  28.187  -8.982  1.00  0.00              
ATOM    130  CA  PRO    39      -7.232  29.119  -8.390  1.00  0.00              
ATOM    131  C   PRO    39      -7.021  28.928  -6.894  1.00  0.00              
ATOM    132  O   PRO    39      -5.966  29.338  -6.372  1.00  0.00              
ATOM    133  N   PHE    40      -7.977  28.291  -6.211  1.00  0.00              
ATOM    134  CA  PHE    40      -7.818  28.006  -4.777  1.00  0.00              
ATOM    135  C   PHE    40      -7.291  26.614  -4.488  1.00  0.00              
ATOM    136  O   PHE    40      -7.216  26.189  -3.325  1.00  0.00              
END
