
#######################################################
#                                                     #
#                        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   29 (  145),  selected   29 , name T0320TS239_5_1-D1
# Molecule2: number of CA atoms  214 ( 1760),  selected   29 , name T0320_D1.pdb
# PARAMETERS: T0320TS239_5_1-D1.T0320_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:    29         1 - 43          4.81     4.81
  LCS_AVERAGE:     13.55

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14        30 - 43          0.65     8.96
  LCS_AVERAGE:      5.08

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14        30 - 43          0.65     8.96
  LCS_AVERAGE:      4.62

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:  214
LCS_GDT     M       1     M       1      0   10   29     0    0    2    9   10   11   11   12   12   14   20   25   25   27   27   27   29   29   29   29 
LCS_GDT     Q       2     Q       2      8   10   29     0    2    5    8   10   11   11   12   12   13   13   14   16   17   20   27   29   29   29   29 
LCS_GDT     S       4     S       4      8   10   29     8    8    8    9   10   11   11   12   12   13   16   18   22   22   24   27   29   29   29   29 
LCS_GDT     K       5     K       5      8   10   29     8    8    8    9   10   13   16   17   18   19   22   25   26   27   27   27   29   29   29   29 
LCS_GDT     A       6     A       6      8   10   29     8    8    8    9   10   11   11   12   16   19   22   25   26   27   27   27   29   29   29   29 
LCS_GDT     A       7     A       7      8   10   29     8    8    8    9   10   11   11   15   18   19   22   25   26   27   27   27   29   29   29   29 
LCS_GDT     E       8     E       8      8   10   29     8    8    8    9   14   15   16   18   19   19   22   25   26   27   27   27   29   29   29   29 
LCS_GDT     M       9     M       9      8   10   29     8    8    8    9   10   18   18   18   19   19   21   25   26   27   27   27   29   29   29   29 
LCS_GDT     C      10     C      10      8   10   29     8    8    8    9   10   11   15   16   19   19   21   25   26   27   27   27   29   29   29   29 
LCS_GDT     Y      11     Y      11      8   10   29     8    8    8   14   16   18   18   18   19   19   22   25   26   27   27   27   29   29   29   29 
LCS_GDT     E      12     E      12      3    3   29     3    5   11   14   16   18   18   18   19   19   22   25   26   27   27   27   29   29   29   29 
LCS_GDT     I      13     I      13      4    4   29     3    7   11   14   16   18   18   18   19   19   22   25   26   27   27   27   29   29   29   29 
LCS_GDT     T      14     T      14      4    4   29     3    3    4    4    5    7    8   10   13   19   22   25   26   27   27   27   29   29   29   29 
LCS_GDT     N      15     N      15      4    4   29     3    3    4    4    5    7    8   13   18   19   22   25   26   27   27   27   29   29   29   29 
LCS_GDT     S      16     S      16      4    4   29     0    3    4    4    5    7    8   10   16   19   22   25   26   27   27   27   29   29   29   29 
LCS_GDT     T      30     T      30     14   14   29    12   13   13   14   16   18   18   18   19   19   22   25   26   27   27   27   29   29   29   29 
LCS_GDT     Q      31     Q      31     14   14   29    12   13   13   14   16   18   18   18   19   19   22   25   26   27   27   27   29   29   29   29 
LCS_GDT     E      32     E      32     14   14   29    12   13   13   14   16   18   18   18   19   19   22   25   26   27   27   27   29   29   29   29 
LCS_GDT     A      33     A      33     14   14   29    12   13   13   14   16   18   18   18   19   19   22   25   26   27   27   27   29   29   29   29 
LCS_GDT     I      34     I      34     14   14   29    12   13   13   14   16   18   18   18   19   19   22   25   26   27   27   27   29   29   29   29 
LCS_GDT     R      35     R      35     14   14   29    12   13   13   14   16   18   18   18   19   19   22   25   26   27   27   27   29   29   29   29 
LCS_GDT     L      36     L      36     14   14   29    12   13   13   14   16   18   18   18   19   19   22   25   26   27   27   27   29   29   29   29 
LCS_GDT     T      37     T      37     14   14   29    12   13   13   14   16   18   18   18   19   19   22   25   26   27   27   27   29   29   29   29 
LCS_GDT     R      38     R      38     14   14   29    12   13   13   14   16   18   18   18   19   19   22   25   26   27   27   27   29   29   29   29 
LCS_GDT     K      39     K      39     14   14   29    12   13   13   14   16   18   18   18   19   19   22   25   26   27   27   27   29   29   29   29 
LCS_GDT     Y      40     Y      40     14   14   29    12   13   13   14   16   18   18   18   19   19   22   25   26   27   27   27   29   29   29   29 
LCS_GDT     L      41     L      41     14   14   29    12   13   13   14   16   18   18   18   19   19   22   25   26   27   27   27   29   29   29   29 
LCS_GDT     L      42     L      42     14   14   29     3   13   13   14   16   18   18   18   19   19   21   25   26   27   27   27   29   29   29   29 
LCS_GDT     S      43     S      43     14   14   29     3    4    7   14   14   18   18   18   19   19   21   25   26   27   27   27   29   29   29   29 
LCS_AVERAGE  LCS_A:   7.75  (   4.62    5.08   13.55 )

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     12     13     13     14     16     18     18     18     19     19     22     25     26     27     27     27     29     29     29     29 
GDT PERCENT_CA   5.61   6.07   6.07   6.54   7.48   8.41   8.41   8.41   8.88   8.88  10.28  11.68  12.15  12.62  12.62  12.62  13.55  13.55  13.55  13.55
GDT RMS_LOCAL    0.28   0.39   0.39   0.65   1.54   1.80   1.80   1.80   2.16   2.16   3.52   3.89   3.96   4.21   4.21   4.21   4.81   4.81   4.81   4.81
GDT RMS_ALL_CA   8.44   8.61   8.61   8.96   6.45   6.63   6.63   6.63   6.39   6.39   5.04   5.15   5.15   4.96   4.96   4.96   4.81   4.81   4.81   4.81

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1         13.477
LGA    Q       2      Q       2         16.448
LGA    S       4      S       4         14.172
LGA    K       5      K       5          7.375
LGA    A       6      A       6          9.604
LGA    A       7      A       7          9.412
LGA    E       8      E       8          4.953
LGA    M       9      M       9          3.598
LGA    C      10      C      10          6.303
LGA    Y      11      Y      11          1.872
LGA    E      12      E      12          1.569
LGA    I      13      I      13          1.817
LGA    T      14      T      14          7.073
LGA    N      15      N      15          8.344
LGA    S      16      S      16          7.011
LGA    T      30      T      30          2.084
LGA    Q      31      Q      31          0.743
LGA    E      32      E      32          1.267
LGA    A      33      A      33          1.430
LGA    I      34      I      34          1.480
LGA    R      35      R      35          1.264
LGA    L      36      L      36          1.040
LGA    T      37      T      37          1.478
LGA    R      38      R      38          1.904
LGA    K      39      K      39          1.277
LGA    Y      40      Y      40          0.327
LGA    L      41      L      41          1.554
LGA    L      42      L      42          2.865
LGA    S      43      S      43          3.230

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   29  214    4.0     18    1.80     8.411     7.784     0.946

LGA_LOCAL      RMSD =  1.803  Number of atoms =   18  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.394  Number of atoms =   29 
Std_ALL_ATOMS  RMSD =  4.814  (standard rmsd on all 29 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.490255 * X  +   0.807281 * Y  +  -0.328554 * Z  + -38.266396
  Y_new =   0.215725 * X  +  -0.252843 * Y  +  -0.943151 * Z  +  84.022049
  Z_new =  -0.844460 * X  +  -0.533261 * Y  +  -0.050193 * Z  +  87.623650 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.664645    1.476948  [ DEG:   -95.3771     84.6229 ]
  Theta =   1.005557    2.136036  [ DEG:    57.6141    122.3859 ]
  Phi   =   2.727064   -0.414529  [ DEG:   156.2492    -23.7508 ]
 
# 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: T0320TS239_5_1-D1                             
REMARK     2: T0320_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0320TS239_5_1-D1.T0320_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   29  214   4.0   18   1.80   7.784     4.81
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS239_5_1-D1
REMARK PARENT number 1
PFRMAT TS
TARGET T0320
PARENT 2nsy_A
ATOM      1  N   MET     1      -5.734  40.905  17.258  1.00  9.99
ATOM      2  CA  MET     1      -5.722  40.898  18.738  1.00  9.99
ATOM      3  C   MET     1      -5.812  39.441  19.200  1.00  9.99
ATOM      4  O   MET     1      -5.191  39.177  20.253  1.00  9.99
ATOM      5  CB  MET     1      -6.840  41.730  19.324  1.00  9.99
ATOM      6  N   GLN     2      -6.409  38.560  18.437  1.00  9.99
ATOM      7  CA  GLN     2      -6.428  37.148  18.812  1.00  9.99
ATOM      8  C   GLN     2      -5.034  36.597  18.952  1.00  9.99
ATOM      9  O   GLN     2      -4.660  35.887  19.928  1.00  9.99
ATOM     10  CB  GLN     2      -7.338  36.356  17.862  1.00  9.99
ATOM     11  N   SER     4      -4.201  36.821  17.948  1.00  9.99
ATOM     12  CA  SER     4      -2.822  36.377  17.941  1.00  9.99
ATOM     13  C   SER     4      -2.034  36.994  19.059  1.00  9.99
ATOM     14  O   SER     4      -1.210  36.344  19.738  1.00  9.99
ATOM     15  CB  SER     4      -2.139  36.744  16.604  1.00  9.99
ATOM     16  N   LYS     5      -2.253  38.244  19.392  1.00  9.99
ATOM     17  CA  LYS     5      -1.597  38.951  20.444  1.00  9.99
ATOM     18  C   LYS     5      -1.970  38.271  21.775  1.00  9.99
ATOM     19  O   LYS     5      -1.118  38.014  22.631  1.00  9.99
ATOM     20  CB  LYS     5      -1.911  40.415  20.503  1.00  9.99
ATOM     21  N   ALA     6      -3.253  38.059  22.048  1.00  9.99
ATOM     22  CA  ALA     6      -3.691  37.475  23.315  1.00  9.99
ATOM     23  C   ALA     6      -3.173  36.053  23.439  1.00  9.99
ATOM     24  O   ALA     6      -2.661  35.689  24.522  1.00  9.99
ATOM     25  CB  ALA     6      -5.219  37.464  23.371  1.00  9.99
ATOM     26  N   ALA     7      -3.131  35.291  22.355  1.00  9.99
ATOM     27  CA  ALA     7      -2.543  33.959  22.378  1.00  9.99
ATOM     28  C   ALA     7      -1.133  34.031  22.820  1.00  9.99
ATOM     29  O   ALA     7      -0.620  33.209  23.619  1.00  9.99
ATOM     30  CB  ALA     7      -2.553  33.372  20.976  1.00  9.99
ATOM     31  N   GLU     8      -0.314  34.956  22.286  1.00  9.99
ATOM     32  CA  GLU     8       1.092  35.083  22.640  1.00  9.99
ATOM     33  C   GLU     8       1.246  35.485  24.069  1.00  9.99
ATOM     34  O   GLU     8       2.071  34.986  24.880  1.00  9.99
ATOM     35  CB  GLU     8       1.834  36.068  21.697  1.00  9.99
ATOM     36  N   MET     9       0.450  36.451  24.530  1.00  9.99
ATOM     37  CA  MET     9       0.543  36.986  25.869  1.00  9.99
ATOM     38  C   MET     9       0.192  35.901  26.904  1.00  9.99
ATOM     39  O   MET     9       0.763  35.957  28.007  1.00  9.99
ATOM     40  CB  MET     9      -0.323  38.245  26.041  1.00  9.99
ATOM     41  N   CYS    10      -0.749  35.059  26.593  1.00  9.99
ATOM     42  CA  CYS    10      -1.193  34.020  27.551  1.00  9.99
ATOM     43  C   CYS    10      -0.419  32.735  27.355  1.00  9.99
ATOM     44  O   CYS    10      -0.745  31.725  28.033  1.00  9.99
ATOM     45  CB  CYS    10      -2.700  33.845  27.428  1.00  9.99
ATOM     46  N   TYR    11       0.526  32.698  26.412  1.00  9.99
ATOM     47  CA  TYR    11       1.411  31.521  26.223  1.00  9.99
ATOM     48  C   TYR    11       0.684  30.371  25.654  1.00  9.99
ATOM     49  O   TYR    11       1.014  29.155  25.964  1.00  9.99
ATOM     50  CB  TYR    11       2.262  31.289  27.473  1.00  9.99
ATOM     51  N   GLU    12      -0.340  30.397  24.825  1.00  9.99
ATOM     52  CA  GLU    12      -1.145  29.356  24.344  1.00  9.99
ATOM     53  C   GLU    12      -0.719  28.672  23.015  1.00  9.99
ATOM     54  O   GLU    12      -0.456  29.401  22.027  1.00  9.99
ATOM     55  CB  GLU    12      -2.608  29.759  24.093  1.00  9.99
ATOM     56  N   ILE    13      -0.710  27.364  22.888  1.00  9.99
ATOM     57  CA  ILE    13      -0.516  26.631  21.619  1.00  9.99
ATOM     58  C   ILE    13      -1.771  26.163  20.990  1.00  9.99
ATOM     59  O   ILE    13      -2.684  25.719  21.622  1.00  9.99
ATOM     60  CB  ILE    13       0.195  25.271  21.905  1.00  9.99
ATOM     61  N   THR    14      -1.849  26.155  19.635  1.00  9.99
ATOM     62  CA  THR    14      -2.984  25.704  18.884  1.00  9.99
ATOM     63  C   THR    14      -3.064  24.173  19.018  1.00  9.99
ATOM     64  O   THR    14      -4.083  23.600  19.028  1.00  9.99
ATOM     65  CB  THR    14      -2.726  25.969  17.378  1.00  9.99
ATOM     66  N   ASN    15      -1.766  23.746  19.161  1.00  9.99
ATOM     67  CA  ASN    15      -1.213  22.435  19.187  1.00  9.99
ATOM     68  C   ASN    15      -0.109  22.109  20.275  1.00  9.99
ATOM     69  O   ASN    15       0.953  22.714  20.284  1.00  9.99
ATOM     70  CB  ASN    15      -0.515  22.134  17.817  1.00  9.99
ATOM     71  N   SER    16      -0.556  21.085  20.990  1.00  9.99
ATOM     72  CA  SER    16       0.290  20.488  22.045  1.00  9.99
ATOM     73  C   SER    16       0.295  18.927  21.886  1.00  9.99
ATOM     74  O   SER    16      -0.468  18.122  21.377  1.00  9.99
ATOM     75  CB  SER    16      -0.183  20.860  23.473  1.00  9.99
ATOM     76  N   THR    30       1.376  18.527  22.598  1.00  9.99
ATOM     77  CA  THR    30       1.711  17.085  22.821  1.00  9.99
ATOM     78  C   THR    30       1.457  16.899  24.321  1.00  9.99
ATOM     79  O   THR    30       2.234  17.420  25.161  1.00  9.99
ATOM     80  CB  THR    30       3.174  16.932  22.476  1.00  9.99
ATOM     81  N   GLN    31       0.517  16.102  24.716  1.00  9.99
ATOM     82  CA  GLN    31       0.105  15.992  26.122  1.00  9.99
ATOM     83  C   GLN    31       1.205  15.448  26.994  1.00  9.99
ATOM     84  O   GLN    31       1.414  15.984  28.094  1.00  9.99
ATOM     85  CB  GLN    31      -1.116  15.066  26.164  1.00  9.99
ATOM     86  N   GLU    32       1.982  14.449  26.579  1.00  9.99
ATOM     87  CA  GLU    32       3.023  13.903  27.406  1.00  9.99
ATOM     88  C   GLU    32       4.096  14.938  27.607  1.00  9.99
ATOM     89  O   GLU    32       4.671  15.050  28.679  1.00  9.99
ATOM     90  CB  GLU    32       3.582  12.597  26.790  1.00  9.99
ATOM     91  N   ALA    33       4.476  15.697  26.567  1.00  9.99
ATOM     92  CA  ALA    33       5.478  16.711  26.712  1.00  9.99
ATOM     93  C   ALA    33       4.990  17.823  27.671  1.00  9.99
ATOM     94  O   ALA    33       5.782  18.351  28.410  1.00  9.99
ATOM     95  CB  ALA    33       5.942  17.316  25.368  1.00  9.99
ATOM     96  N   ILE    34       3.714  18.193  27.540  1.00  9.99
ATOM     97  CA  ILE    34       3.171  19.244  28.443  1.00  9.99
ATOM     98  C   ILE    34       3.321  18.827  29.916  1.00  9.99
ATOM     99  O   ILE    34       3.702  19.630  30.740  1.00  9.99
ATOM    100  CB  ILE    34       1.704  19.536  28.129  1.00  9.99
ATOM    101  N   ARG    35       2.984  17.559  30.169  1.00  9.99
ATOM    102  CA  ARG    35       3.131  17.045  31.555  1.00  9.99
ATOM    103  C   ARG    35       4.544  17.069  32.033  1.00  9.99
ATOM    104  O   ARG    35       4.882  17.566  33.085  1.00  9.99
ATOM    105  CB  ARG    35       2.526  15.632  31.638  1.00  9.99
ATOM    106  N   LEU    36       5.482  16.616  31.152  1.00  9.99
ATOM    107  CA  LEU    36       6.884  16.661  31.488  1.00  9.99
ATOM    108  C   LEU    36       7.380  18.054  31.786  1.00  9.99
ATOM    109  O   LEU    36       8.070  18.385  32.715  1.00  9.99
ATOM    110  CB  LEU    36       7.690  16.020  30.351  1.00  9.99
ATOM    111  N   THR    37       6.989  19.016  30.908  1.00  9.99
ATOM    112  CA  THR    37       7.441  20.370  31.046  1.00  9.99
ATOM    113  C   THR    37       6.949  21.013  32.386  1.00  9.99
ATOM    114  O   THR    37       7.606  21.759  33.015  1.00  9.99
ATOM    115  CB  THR    37       6.951  21.244  29.891  1.00  9.99
ATOM    116  N   ARG    38       5.690  20.682  32.722  1.00  9.99
ATOM    117  CA  ARG    38       5.046  21.342  33.877  1.00  9.99
ATOM    118  C   ARG    38       5.539  20.730  35.183  1.00  9.99
ATOM    119  O   ARG    38       5.824  21.449  36.132  1.00  9.99
ATOM    120  CB  ARG    38       3.533  21.365  33.649  1.00  9.99
ATOM    121  N   LYS    39       5.731  19.401  35.172  1.00  9.99
ATOM    122  CA  LYS    39       6.395  18.774  36.327  1.00  9.99
ATOM    123  C   LYS    39       7.830  19.308  36.448  1.00  9.99
ATOM    124  O   LYS    39       8.277  19.646  37.535  1.00  9.99
ATOM    125  CB  LYS    39       6.394  17.245  36.169  1.00  9.99
ATOM    126  N   TYR    40       8.531  19.426  35.308  1.00  9.99
ATOM    127  CA  TYR    40       9.917  19.897  35.362  1.00  9.99
ATOM    128  C   TYR    40      10.018  21.324  35.859  1.00  9.99
ATOM    129  O   TYR    40      10.923  21.662  36.595  1.00  9.99
ATOM    130  CB  TYR    40      10.587  19.753  34.005  1.00  9.99
ATOM    131  N   LEU    41       9.027  22.168  35.520  1.00  9.99
ATOM    132  CA  LEU    41       8.977  23.509  36.054  1.00  9.99
ATOM    133  C   LEU    41       8.830  23.534  37.554  1.00  9.99
ATOM    134  O   LEU    41       9.547  24.234  38.268  1.00  9.99
ATOM    135  CB  LEU    41       7.789  24.245  35.405  1.00  9.99
ATOM    136  N   LEU    42       7.895  22.713  38.082  1.00  9.99
ATOM    137  CA  LEU    42       7.712  22.643  39.525  1.00  9.99
ATOM    138  C   LEU    42       9.005  22.222  40.183  1.00  9.99
ATOM    139  O   LEU    42       9.418  22.749  41.210  1.00  9.99
ATOM    140  CB  LEU    42       6.560  21.741  39.914  1.00  9.99
ATOM    141  N   SER    43       9.695  21.198  39.642  1.00  9.99
ATOM    142  CA  SER    43      10.970  20.757  40.215  1.00  9.99
ATOM    143  C   SER    43      12.054  21.842  40.090  1.00  9.99
ATOM    144  O   SER    43      12.764  22.011  41.093  1.00  9.99
ATOM    145  CB  SER    43      11.425  19.485  39.485  1.00  9.99
TER
END
