
#######################################################
#                                                     #
#                        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   33 , name T0335AL381_3-D1
# Molecule2: number of CA atoms   36 (  584),  selected   33 , name T0335_D1.pdb
# PARAMETERS: T0335AL381_3-D1.T0335_D1.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:    18         8 - 25          4.60    12.78
  LONGEST_CONTINUOUS_SEGMENT:    18         9 - 26          4.93    13.24
  LCS_AVERAGE:     45.29

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13        28 - 40          1.78    27.19
  LCS_AVERAGE:     28.62

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12        29 - 40          0.47    27.03
  LCS_AVERAGE:     25.67

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:   36
LCS_GDT     A       8     A       8     11   11   18    10   11   11   12   12   12   13   13   13   14   15   16   17   18   20   20   22   23   24   26 
LCS_GDT     R       9     R       9     11   11   18    10   11   11   12   12   12   13   13   13   14   15   16   17   18   20   20   22   23   24   26 
LCS_GDT     I      10     I      10     11   11   18    10   11   11   12   12   12   13   13   13   14   15   16   17   18   20   20   22   23   24   26 
LCS_GDT     N      11     N      11     11   11   18    10   11   11   12   12   12   13   13   13   14   15   16   17   18   20   20   22   23   24   26 
LCS_GDT     E      12     E      12     11   11   18    10   11   11   12   12   12   13   13   13   14   15   16   17   18   20   20   22   23   24   26 
LCS_GDT     L      13     L      13     11   11   18    10   11   11   12   12   12   13   13   13   14   15   16   17   18   20   20   22   23   24   26 
LCS_GDT     A      14     A      14     11   11   18    10   11   11   12   12   12   13   13   13   14   15   16   17   18   20   20   22   23   24   26 
LCS_GDT     A      15     A      15     11   11   18    10   11   11   12   12   12   13   13   13   14   15   16   17   18   20   20   22   23   24   26 
LCS_GDT     K      16     K      16     11   11   18    10   11   11   12   12   12   13   13   13   14   15   16   17   18   20   20   22   23   24   26 
LCS_GDT     A      17     A      17     11   11   18    10   11   11   12   12   12   13   13   13   14   15   16   17   18   20   20   22   23   24   25 
LCS_GDT     K      18     K      18     11   11   18    10   11   11   12   12   12   13   13   13   14   15   16   17   18   20   20   22   23   24   25 
LCS_GDT     A      19     A      19      3    6   18     3    3    3    6    6    7    9   12   13   14   15   16   17   18   20   20   22   23   24   26 
LCS_GDT     G      20     G      20      5    6   18     3    5    5    6    6    7    9   11   13   13   15   16   17   18   20   20   22   23   24   26 
LCS_GDT     V      21     V      21      5    6   18     4    5    5    6    6    7    9   11   13   13   15   16   17   18   20   20   22   23   24   26 
LCS_GDT     I      22     I      22      5    6   18     4    5    5    6    6    7    9   11   13   13   15   16   17   18   20   20   22   23   24   26 
LCS_GDT     T      23     T      23      5    6   18     4    5    5    6    6    7    9   11   13   13   15   16   16   17   18   20   22   23   24   26 
LCS_GDT     E      24     E      24      5    6   18     4    5    5    6    6    7    9   11   13   13   15   16   16   17   18   20   22   23   24   26 
LCS_GDT     E      25     E      25      3    6   18     0    3    3    5    5    6    7   10   13   13   14   16   16   17   18   18   20   22   24   26 
LCS_GDT     E      26     E      26      3    4   18     0    3    3    3    4    4    5    6    6    7    9   11   14   14   16   17   20   22   23   26 
LCS_GDT     K      27     K      27      3    4   14     0    3    3    3    4    4    5    6    6    7    7   11   13   14   15   17   20   21   23   26 
LCS_GDT     A      28     A      28      3   13   14     0    3    3    3    4    5    5   12   13   13   13   13   13   13   13   13   14   15   16   16 
LCS_GDT     E      29     E      29     12   13   14     6   12   12   12   12   12   12   12   13   13   13   13   13   13   13   13   14   15   16   16 
LCS_GDT     Q      30     Q      30     12   13   14     7   12   12   12   12   12   12   12   13   13   13   13   13   13   13   13   14   15   16   16 
LCS_GDT     Q      31     Q      31     12   13   14     6   12   12   12   12   12   12   12   13   13   13   13   13   13   13   14   14   15   17   17 
LCS_GDT     K      32     K      32     12   13   14     6   12   12   12   12   12   12   12   13   13   13   13   13   14   15   17   20   21   22   26 
LCS_GDT     L      33     L      33     12   13   14     8   12   12   12   12   12   12   12   13   13   13   13   13   14   15   16   20   21   22   26 
LCS_GDT     R      34     R      34     12   13   14     8   12   12   12   12   12   12   12   13   13   13   13   13   14   15   16   17   20   22   26 
LCS_GDT     Q      35     Q      35     12   13   14     8   12   12   12   12   12   12   12   13   13   13   13   14   14   18   20   22   23   24   26 
LCS_GDT     E      36     E      36     12   13   14     8   12   12   12   12   12   12   12   13   13   14   16   17   18   20   20   22   23   24   26 
LCS_GDT     Y      37     Y      37     12   13   14     8   12   12   12   12   12   12   12   13   13   13   13   17   18   20   20   22   23   24   26 
LCS_GDT     L      38     L      38     12   13   14     8   12   12   12   12   12   12   12   13   13   15   16   17   18   20   20   22   23   24   26 
LCS_GDT     K      39     K      39     12   13   14     8   12   12   12   12   12   13   13   13   14   15   16   17   18   20   20   22   23   24   26 
LCS_GDT     G      40     G      40     12   13   14     8   12   12   12   12   12   13   13   13   14   15   16   17   18   20   20   21   23   24   25 
LCS_AVERAGE  LCS_A:  33.19  (  25.67   28.62   45.29 )

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     10     12     12     12     12     12     13     13     13     14     15     16     17     18     20     20     22     23     24     26 
GDT PERCENT_CA  27.78  33.33  33.33  33.33  33.33  33.33  36.11  36.11  36.11  38.89  41.67  44.44  47.22  50.00  55.56  55.56  61.11  63.89  66.67  72.22
GDT RMS_LOCAL    0.29   0.47   0.47   0.47   0.47   0.47   1.86   1.86   1.86   2.56   3.01   3.55   4.03   4.24   4.93   4.93   5.82   5.91   6.23   7.28
GDT RMS_ALL_CA  16.44  27.03  27.03  27.03  27.03  27.03  13.92  13.92  13.92  13.26  13.06  12.51  12.13  12.13  11.42  11.42  10.38  10.52  10.27   9.31

#      Molecule1      Molecule2       DISTANCE
LGA    A       8      A       8          2.619
LGA    R       9      R       9          0.712
LGA    I      10      I      10          2.057
LGA    N      11      N      11          1.445
LGA    E      12      E      12          0.795
LGA    L      13      L      13          1.845
LGA    A      14      A      14          1.447
LGA    A      15      A      15          0.937
LGA    K      16      K      16          2.474
LGA    A      17      A      17          3.106
LGA    K      18      K      18          1.700
LGA    A      19      A      19          5.809
LGA    G      20      G      20          9.608
LGA    V      21      V      21         11.042
LGA    I      22      I      22         10.757
LGA    T      23      T      23         13.500
LGA    E      24      E      24         13.760
LGA    E      25      E      25         16.171
LGA    E      26      E      26         17.606
LGA    K      27      K      27         18.295
LGA    A      28      A      28         26.738
LGA    E      29      E      29         26.325
LGA    Q      30      Q      30         25.028
LGA    Q      31      Q      31         23.090
LGA    K      32      K      32         18.882
LGA    L      33      L      33         16.490
LGA    R      34      R      34         16.436
LGA    Q      35      Q      35         13.180
LGA    E      36      E      36          8.342
LGA    Y      37      Y      37          8.350
LGA    L      38      L      38          7.072
LGA    K      39      K      39          3.011
LGA    G      40      G      40          3.499

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   33   36    4.0     13    1.86    39.583    36.078     0.664

LGA_LOCAL      RMSD =  1.858  Number of atoms =   13  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 12.947  Number of atoms =   33 
Std_ALL_ATOMS  RMSD =  9.213  (standard rmsd on all 33 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.931815 * X  +  -0.002983 * Y  +  -0.362922 * Z  + -20.176411
  Y_new =  -0.052316 * X  +   0.988419 * Y  +  -0.142449 * Z  +   9.401739
  Z_new =   0.359144 * X  +   0.151723 * Y  +   0.920867 * Z  + -33.850742 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.163293   -2.978299  [ DEG:     9.3560   -170.6440 ]
  Theta =  -0.367350   -2.774242  [ DEG:   -21.0476   -158.9524 ]
  Phi   =  -0.056086    3.085507  [ DEG:    -3.2135    176.7865 ]
 
# 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: T0335AL381_3-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0335AL381_3-D1.T0335_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   33   36   4.0   13   1.86  36.078     9.21
REMARK  ---------------------------------------------------------- 
MOLECULE T0335AL381_3-D1
REMARK Aligment from pdb entry: 1dpmA
ATOM      1  N   ALA     8      -0.857  -5.184  -4.481  1.00  0.00              
ATOM      2  CA  ALA     8      -2.258  -5.558  -4.534  1.00  0.00              
ATOM      3  C   ALA     8      -2.728  -5.885  -3.110  1.00  0.00              
ATOM      4  O   ALA     8      -3.852  -5.690  -2.764  1.00  0.00              
ATOM      5  N   ARG     9      -1.831  -6.399  -2.276  1.00  0.00              
ATOM      6  CA  ARG     9      -2.184  -6.713  -0.927  1.00  0.00              
ATOM      7  C   ARG     9      -2.409  -5.442  -0.144  1.00  0.00              
ATOM      8  O   ARG     9      -3.389  -5.313   0.616  1.00  0.00              
ATOM      9  N   ILE    10      -1.502  -4.500  -0.354  1.00  0.00              
ATOM     10  CA  ILE    10      -1.569  -3.198   0.302  1.00  0.00              
ATOM     11  C   ILE    10      -2.863  -2.514  -0.097  1.00  0.00              
ATOM     12  O   ILE    10      -3.584  -1.933   0.709  1.00  0.00              
ATOM     13  N   ASN    11      -3.154  -2.576  -1.400  1.00  0.00              
ATOM     14  CA  ASN    11      -4.352  -1.962  -1.893  1.00  0.00              
ATOM     15  C   ASN    11      -5.607  -2.517  -1.251  1.00  0.00              
ATOM     16  O   ASN    11      -6.480  -1.784  -0.858  1.00  0.00              
ATOM     17  N   GLU    12      -5.691  -3.833  -1.131  1.00  0.00              
ATOM     18  CA  GLU    12      -6.852  -4.521  -0.528  1.00  0.00              
ATOM     19  C   GLU    12      -7.085  -4.206   0.963  1.00  0.00              
ATOM     20  O   GLU    12      -8.179  -3.896   1.410  1.00  0.00              
ATOM     21  N   LEU    13      -6.061  -4.279   1.776  1.00  0.00              
ATOM     22  CA  LEU    13      -6.286  -3.944   3.162  1.00  0.00              
ATOM     23  C   LEU    13      -6.491  -2.436   3.305  1.00  0.00              
ATOM     24  O   LEU    13      -7.161  -1.997   4.212  1.00  0.00              
ATOM     25  N   ALA    14      -5.898  -1.621   2.410  1.00  0.00              
ATOM     26  CA  ALA    14      -6.101  -0.200   2.567  1.00  0.00              
ATOM     27  C   ALA    14      -7.563   0.194   2.440  1.00  0.00              
ATOM     28  O   ALA    14      -8.069   1.044   3.177  1.00  0.00              
ATOM     29  N   ALA    15      -8.206  -0.429   1.467  1.00  0.00              
ATOM     30  CA  ALA    15      -9.610  -0.229   1.101  1.00  0.00              
ATOM     31  C   ALA    15     -10.558  -0.690   2.233  1.00  0.00              
ATOM     32  O   ALA    15     -11.491   0.005   2.642  1.00  0.00              
ATOM     33  N   LYS    16     -10.245  -1.856   2.730  1.00  0.00              
ATOM     34  CA  LYS    16     -10.957  -2.557   3.761  1.00  0.00              
ATOM     35  C   LYS    16     -10.851  -1.908   5.126  1.00  0.00              
ATOM     36  O   LYS    16     -11.829  -1.841   5.825  1.00  0.00              
ATOM     37  N   ALA    17      -9.687  -1.419   5.507  1.00  0.00              
ATOM     38  CA  ALA    17      -9.493  -0.757   6.835  1.00  0.00              
ATOM     39  C   ALA    17      -9.738   0.716   6.816  1.00  0.00              
ATOM     40  O   ALA    17      -9.750   1.345   7.867  1.00  0.00              
ATOM     41  N   LYS    18      -9.872   1.267   5.602  1.00  0.00              
ATOM     42  CA  LYS    18     -10.066   2.674   5.393  1.00  0.00              
ATOM     43  C   LYS    18      -8.907   3.501   5.936  1.00  0.00              
ATOM     44  O   LYS    18      -9.058   4.492   6.637  1.00  0.00              
ATOM     45  N   ALA    19      -7.704   3.063   5.627  1.00  0.00              
ATOM     46  CA  ALA    19      -6.528   3.794   6.041  1.00  0.00              
ATOM     47  C   ALA    19      -5.659   4.064   4.798  1.00  0.00              
ATOM     48  O   ALA    19      -5.496   3.167   3.940  1.00  0.00              
ATOM     49  N   GLY    20      -5.098   5.274   4.690  1.00  0.00              
ATOM     50  CA  GLY    20      -4.275   5.551   3.564  1.00  0.00              
ATOM     51  C   GLY    20      -2.934   4.793   3.710  1.00  0.00              
ATOM     52  O   GLY    20      -2.331   4.659   4.789  1.00  0.00              
ATOM     53  N   VAL    21      -2.450   4.285   2.613  1.00  0.00              
ATOM     54  CA  VAL    21      -1.175   3.593   2.621  1.00  0.00              
ATOM     55  C   VAL    21      -0.292   4.149   1.519  1.00  0.00              
ATOM     56  O   VAL    21      -0.691   4.198   0.361  1.00  0.00              
ATOM     57  N   ILE    22       0.889   4.586   1.910  1.00  0.00              
ATOM     58  CA  ILE    22       1.918   5.062   1.009  1.00  0.00              
ATOM     59  C   ILE    22       2.915   3.925   0.757  1.00  0.00              
ATOM     60  O   ILE    22       3.426   3.333   1.701  1.00  0.00              
ATOM     61  N   THR    23       3.099   3.580  -0.538  1.00  0.00              
ATOM     62  CA  THR    23       4.000   2.506  -1.032  1.00  0.00              
ATOM     63  C   THR    23       5.419   3.051  -1.280  1.00  0.00              
ATOM     64  O   THR    23       5.639   4.274  -1.422  1.00  0.00              
ATOM     65  N   GLU    24       6.387   2.130  -1.282  1.00  0.00              
ATOM     66  CA  GLU    24       7.758   2.539  -1.451  1.00  0.00              
ATOM     67  C   GLU    24       8.470   1.846  -2.591  1.00  0.00              
ATOM     68  O   GLU    24       8.097   0.776  -3.076  1.00  0.00              
ATOM     69  N   GLU    25       9.537   2.488  -2.988  1.00  0.00              
ATOM     70  CA  GLU    25      10.398   1.940  -3.966  1.00  0.00              
ATOM     71  C   GLU    25      11.738   1.935  -3.241  1.00  0.00              
ATOM     72  O   GLU    25      11.788   2.325  -2.049  1.00  0.00              
ATOM     73  N   GLU    26      12.795   1.470  -3.924  1.00  0.00              
ATOM     74  CA  GLU    26      14.116   1.423  -3.346  1.00  0.00              
ATOM     75  C   GLU    26      14.533  -0.002  -3.154  1.00  0.00              
ATOM     76  O   GLU    26      13.968  -0.916  -3.762  1.00  0.00              
ATOM     77  N   LYS    27      15.536  -0.199  -2.312  1.00  0.00              
ATOM     78  CA  LYS    27      15.985  -1.558  -2.065  1.00  0.00              
ATOM     79  C   LYS    27      16.456  -1.628  -0.650  1.00  0.00              
ATOM     80  O   LYS    27      16.961  -0.629  -0.113  1.00  0.00              
ATOM     81  N   ALA    28      23.143  -4.634 -11.322  1.00  0.00              
ATOM     82  CA  ALA    28      22.850  -3.414 -12.042  1.00  0.00              
ATOM     83  C   ALA    28      23.749  -2.258 -11.706  1.00  0.00              
ATOM     84  O   ALA    28      24.367  -2.185 -10.639  1.00  0.00              
ATOM     85  N   GLU    29      23.772  -1.304 -12.634  1.00  0.00              
ATOM     86  CA  GLU    29      24.573  -0.086 -12.465  1.00  0.00              
ATOM     87  C   GLU    29      23.743   0.985 -11.802  1.00  0.00              
ATOM     88  O   GLU    29      22.509   0.855 -11.687  1.00  0.00              
ATOM     89  N   GLN    30      24.416   2.040 -11.353  1.00  0.00              
ATOM     90  CA  GLN    30      23.710   3.127 -10.705  1.00  0.00              
ATOM     91  C   GLN    30      22.651   3.655 -11.686  1.00  0.00              
ATOM     92  O   GLN    30      21.526   3.907 -11.338  1.00  0.00              
ATOM     93  N   GLN    31      23.007   3.764 -12.954  1.00  0.00              
ATOM     94  CA  GLN    31      22.088   4.237 -13.936  1.00  0.00              
ATOM     95  C   GLN    31      20.881   3.306 -14.119  1.00  0.00              
ATOM     96  O   GLN    31      19.774   3.773 -14.256  1.00  0.00              
ATOM     97  N   LYS    32      21.084   1.986 -14.111  1.00  0.00              
ATOM     98  CA  LYS    32      19.958   1.109 -14.269  1.00  0.00              
ATOM     99  C   LYS    32      19.081   1.141 -13.035  1.00  0.00              
ATOM    100  O   LYS    32      17.869   1.129 -13.140  1.00  0.00              
ATOM    101  N   LEU    33      19.716   1.184 -11.871  1.00  0.00              
ATOM    102  CA  LEU    33      18.966   1.243 -10.638  1.00  0.00              
ATOM    103  C   LEU    33      18.086   2.505 -10.625  1.00  0.00              
ATOM    104  O   LEU    33      16.896   2.426 -10.333  1.00  0.00              
ATOM    105  N   ARG    34      18.661   3.668 -10.988  1.00  0.00              
ATOM    106  CA  ARG    34      17.912   4.934 -11.035  1.00  0.00              
ATOM    107  C   ARG    34      16.658   4.777 -11.881  1.00  0.00              
ATOM    108  O   ARG    34      15.566   5.240 -11.535  1.00  0.00              
ATOM    109  N   GLN    35      16.822   4.097 -13.012  1.00  0.00              
ATOM    110  CA  GLN    35      15.688   3.881 -13.896  1.00  0.00              
ATOM    111  C   GLN    35      14.588   3.043 -13.216  1.00  0.00              
ATOM    112  O   GLN    35      13.409   3.295 -13.343  1.00  0.00              
ATOM    113  N   GLU    36      14.983   2.017 -12.508  1.00  0.00              
ATOM    114  CA  GLU    36      13.991   1.186 -11.872  1.00  0.00              
ATOM    115  C   GLU    36      13.180   2.013 -10.874  1.00  0.00              
ATOM    116  O   GLU    36      11.954   2.016 -10.871  1.00  0.00              
ATOM    117  N   TYR    37      13.903   2.754 -10.043  1.00  0.00              
ATOM    118  CA  TYR    37      13.302   3.606  -9.045  1.00  0.00              
ATOM    119  C   TYR    37      12.336   4.567  -9.634  1.00  0.00              
ATOM    120  O   TYR    37      11.227   4.751  -9.101  1.00  0.00              
ATOM    121  N   LEU    38      12.746   5.198 -10.731  1.00  0.00              
ATOM    122  CA  LEU    38      11.869   6.171 -11.377  1.00  0.00              
ATOM    123  C   LEU    38      10.630   5.503 -11.927  1.00  0.00              
ATOM    124  O   LEU    38       9.531   6.063 -11.945  1.00  0.00              
ATOM    125  N   LYS    39      10.845   4.305 -12.422  1.00  0.00              
ATOM    126  CA  LYS    39       9.754   3.534 -12.989  1.00  0.00              
ATOM    127  C   LYS    39       8.604   3.366 -11.994  1.00  0.00              
ATOM    128  O   LYS    39       7.423   3.576 -12.322  1.00  0.00              
ATOM    129  N   GLY    40       8.984   2.906 -10.772  1.00  0.00              
ATOM    130  CA  GLY    40       8.061   2.642  -9.675  1.00  0.00              
ATOM    131  C   GLY    40       7.353   3.878  -9.200  1.00  0.00              
ATOM    132  O   GLY    40       6.186   3.845  -8.844  1.00  0.00              
END
