
#######################################################
#                                                     #
#                        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   19 (  149),  selected   17 , name T0382TS009_2_1
# Molecule2: number of CA atoms  121 (  929),  selected   17 , name T0382.pdb
# PARAMETERS: T0382TS009_2_1.T0382.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:    16         4 - 19          4.92     5.77
  LCS_AVERAGE:     13.13

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6         5 - 10          1.29     8.01
  LONGEST_CONTINUOUS_SEGMENT:     6        14 - 19          1.58    12.63
  LCS_AVERAGE:      4.62

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5         6 - 10          0.95     8.21
  LCS_AVERAGE:      3.40

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:  121
LCS_GDT     K       3     K       3      3    4   14     3    3    3    4    4    4    4    4    7    9   10   10   11   11   13   14   14   14   16   17 
LCS_GDT     L       4     L       4      3    4   16     3    3    3    4    4    6    7    8   10   11   12   13   13   13   13   16   16   16   16   17 
LCS_GDT     D       5     D       5      4    6   16     3    4    5    7    7    7    8   10   11   12   13   14   15   15   15   16   16   16   16   17 
LCS_GDT     L       6     L       6      5    6   16     3    4    5    7    7    7    8   10   11   13   14   14   15   15   15   16   16   16   16   17 
LCS_GDT     H       7     H       7      5    6   16     3    4    5    7    7    7    8   10   12   13   14   14   15   15   15   16   16   16   16   17 
LCS_GDT     Q       8     Q       8      5    6   16     3    4    5    7    7    7    8   10   12   13   14   14   15   15   15   16   16   16   16   17 
LCS_GDT     M       9     M       9      5    6   16     3    4    5    7    7    7    8   10   12   13   14   14   15   15   15   16   16   16   16   17 
LCS_GDT     T      10     T      10      5    6   16     4    4    5    7    7    7    8   10   12   13   14   14   15   15   15   16   16   16   16   17 
LCS_GDT     T      11     T      11      4    5   16     4    4    4    5    5    6    8   10   12   13   14   14   15   15   15   16   16   16   16   17 
LCS_GDT     Q      12     Q      12      4    5   16     4    4    4    5    5    7    8   10   12   13   14   14   15   15   15   16   16   16   16   17 
LCS_GDT     D      13     D      13      4    5   16     4    4    5    7    7    7    8   10   12   13   14   14   15   15   15   16   16   16   16   17 
LCS_GDT     L      14     L      14      3    6   16     3    3    4    5    6    7    8   10   12   13   14   14   15   15   15   16   16   16   16   17 
LCS_GDT     V      15     V      15      4    6   16     4    4    4    5    6    7    8   10   12   13   14   14   15   15   15   16   16   16   16   17 
LCS_GDT     A      16     A      16      4    6   16     4    4    4    5    6    7    8   10   12   13   14   14   15   15   15   16   16   16   16   17 
LCS_GDT     L      17     L      17      4    6   16     4    4    4    5    6    7    8   10   11   12   14   14   15   15   15   16   16   16   16   17 
LCS_GDT     F      18     F      18      4    6   16     4    4    4    5    6    7    8   10   12   13   14   14   15   15   15   16   16   16   16   17 
LCS_GDT     A      19     A      19      4    6   16     0    3    4    5    6    7    8   10   12   13   14   14   15   15   15   16   16   16   16   17 
LCS_AVERAGE  LCS_A:   7.05  (   3.40    4.62   13.13 )

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      7      7      7      8     10     12     13     14     14     15     15     15     16     16     16     16     17 
GDT PERCENT_CA   3.31   3.31   4.13   5.79   5.79   5.79   6.61   8.26   9.92  10.74  11.57  11.57  12.40  12.40  12.40  13.22  13.22  13.22  13.22  14.05
GDT RMS_LOCAL    0.22   0.22   0.95   1.44   1.44   1.44   2.36   2.80   3.44   3.61   3.81   3.81   4.16   4.16   4.16   4.92   4.92   4.92   4.92   5.54
GDT RMS_ALL_CA  13.46  13.46   8.21   7.20   7.20   7.20   6.42   6.47   7.29   6.72   6.89   6.89   6.29   6.29   6.29   5.77   5.77   5.77   5.77   5.54

#      Molecule1      Molecule2       DISTANCE
LGA    K       3      K       3         14.598
LGA    L       4      L       4          8.961
LGA    D       5      D       5          2.086
LGA    L       6      L       6          3.047
LGA    H       7      H       7          2.603
LGA    Q       8      Q       8          0.283
LGA    M       9      M       9          2.728
LGA    T      10      T      10          3.051
LGA    T      11      T      11          6.079
LGA    Q      12      Q      12          6.607
LGA    D      13      D      13          2.351
LGA    L      14      L      14          3.788
LGA    V      15      V      15          3.005
LGA    A      16      A      16          3.541
LGA    L      17      L      17          8.382
LGA    F      18      F      18          8.857
LGA    A      19      A      19         10.467

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   19  121    4.0     10    2.80     7.645     7.048     0.344

LGA_LOCAL      RMSD =  2.805  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.467  Number of atoms =   17 
Std_ALL_ATOMS  RMSD =  5.540  (standard rmsd on all 17 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.083799 * X  +  -0.523358 * Y  +   0.847983 * Z  +   3.711727
  Y_new =  -0.287536 * X  +   0.827479 * Y  +   0.482288 * Z  +  40.580627
  Z_new =  -0.954097 * X  +  -0.203410 * Y  +  -0.219826 * Z  + -22.354544 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.394962    0.746631  [ DEG:  -137.2212     42.7788 ]
  Theta =   1.266630    1.874963  [ DEG:    72.5725    107.4275 ]
  Phi   =  -1.854380    1.287212  [ DEG:  -106.2482     73.7518 ]
 
# 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: T0382TS009_2_1                                
REMARK     2: T0382.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0382TS009_2_1.T0382.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   19  121   4.0   10   2.80   7.048     5.54
REMARK  ---------------------------------------------------------- 
MOLECULE T0382TS009_2_1
REMARK PARENT number 1
PFRMAT TS                                                                       
TARGET T0382                                                                    
PARENT N/A                                                                      
ATOM      1  N   MET     1       3.712  40.581 -22.355  1.00  0.00              
ATOM      2  CA  MET     1       3.712  39.153 -21.924  1.00  0.00              
ATOM      3  C   MET     1       2.303  38.681 -21.582  1.00  0.00              
ATOM      4  O   MET     1       2.040  38.237 -20.464  1.00  0.00              
ATOM      5  CB  MET     1       4.314  38.265 -23.015  1.00  0.00              
ATOM      6  CG  MET     1       5.053  37.046 -22.485  1.00  0.00              
ATOM      7  SD  MET     1       5.840  36.086 -23.793  1.00  0.00              
ATOM      8  CE  MET     1       6.873  34.985 -22.829  1.00  0.00              
ATOM      9  N   SER     2       1.399  38.778 -22.552  1.00  0.00              
ATOM     10  CA  SER     2       0.016  38.361 -22.356  1.00  0.00              
ATOM     11  C   SER     2      -0.454  38.662 -20.937  1.00  0.00              
ATOM     12  O   SER     2      -0.085  39.681 -20.352  1.00  0.00              
ATOM     13  CB  SER     2      -0.900  39.050 -23.370  1.00  0.00              
ATOM     14  OG  SER     2      -1.103  38.233 -24.510  1.00  0.00              
ATOM     15  N   LYS     3      -1.270  37.767 -20.387  1.00  0.00              
ATOM     16  CA  LYS     3      -1.792  37.935 -19.036  1.00  0.00              
ATOM     17  C   LYS     3      -1.405  36.759 -18.146  1.00  0.00              
ATOM     18  O   LYS     3      -0.733  35.828 -18.589  1.00  0.00              
ATOM     19  CB  LYS     3      -1.289  39.244 -18.426  1.00  0.00              
ATOM     20  CG  LYS     3      -2.395  40.200 -18.011  1.00  0.00              
ATOM     21  CD  LYS     3      -1.841  41.381 -17.229  1.00  0.00              
ATOM     22  CE  LYS     3      -2.951  42.322 -16.790  1.00  0.00              
ATOM     23  NZ  LYS     3      -2.416  43.519 -16.084  1.00  0.00              
ATOM     24  N   LEU     4      -1.833  36.808 -16.888  1.00  0.00              
ATOM     25  CA  LEU     4      -1.532  35.747 -15.935  1.00  0.00              
ATOM     26  C   LEU     4      -2.636  35.613 -14.892  1.00  0.00              
ATOM     27  O   LEU     4      -3.682  35.018 -15.154  1.00  0.00              
ATOM     28  CB  LEU     4      -1.328  34.416 -16.660  1.00  0.00              
ATOM     29  CG  LEU     4       0.071  33.803 -16.572  1.00  0.00              
ATOM     30  CD1 LEU     4       0.001  32.287 -16.675  1.00  0.00              
ATOM     31  CD2 LEU     4       0.764  34.226 -15.286  1.00  0.00              
ATOM     32  N   ASP     5      -2.399  36.171 -13.710  1.00  0.00              
ATOM     33  CA  ASP     5      -3.373  36.115 -12.626  1.00  0.00              
ATOM     34  C   ASP     5      -4.525  37.084 -12.870  1.00  0.00              
ATOM     35  O   ASP     5      -5.484  36.759 -13.570  1.00  0.00              
ATOM     36  CB  ASP     5      -3.908  34.691 -12.460  1.00  0.00              
ATOM     37  CG  ASP     5      -3.314  33.981 -11.261  1.00  0.00              
ATOM     38  OD1 ASP     5      -4.067  33.693 -10.306  1.00  0.00              
ATOM     39  OD2 ASP     5      -2.094  33.712 -11.275  1.00  0.00              
ATOM     40  N   LEU     6      -4.423  38.274 -12.286  1.00  0.00              
ATOM     41  CA  LEU     6      -5.457  39.292 -12.439  1.00  0.00              
ATOM     42  C   LEU     6      -6.185  39.143 -13.771  1.00  0.00              
ATOM     43  O   LEU     6      -7.314  39.609 -13.926  1.00  0.00              
ATOM     44  CB  LEU     6      -6.455  39.219 -11.282  1.00  0.00              
ATOM     45  CG  LEU     6      -6.745  40.534 -10.554  1.00  0.00              
ATOM     46  CD1 LEU     6      -8.180  40.562 -10.048  1.00  0.00              
ATOM     47  CD2 LEU     6      -6.469  41.723 -11.462  1.00  0.00              
ATOM     48  N   HIS     7      -5.532  38.492 -14.727  1.00  0.00              
ATOM     49  CA  HIS     7      -6.117  38.280 -16.046  1.00  0.00              
ATOM     50  C   HIS     7      -7.578  37.855 -15.940  1.00  0.00              
ATOM     51  O   HIS     7      -8.484  38.665 -16.131  1.00  0.00              
ATOM     52  CB  HIS     7      -5.998  39.548 -16.894  1.00  0.00              
ATOM     53  CG  HIS     7      -5.435  39.309 -18.261  1.00  0.00              
ATOM     54  ND1 HIS     7      -4.631  38.229 -18.557  1.00  0.00              
ATOM     55  CD2 HIS     7      -5.558  40.012 -19.411  1.00  0.00              
ATOM     56  CE1 HIS     7      -4.285  38.278 -19.832  1.00  0.00              
ATOM     57  NE2 HIS     7      -4.834  39.349 -20.372  1.00  0.00              
ATOM     58  N   GLN     8      -7.798  36.581 -15.636  1.00  0.00              
ATOM     59  CA  GLN     8      -9.147  36.046 -15.505  1.00  0.00              
ATOM     60  C   GLN     8      -9.697  36.273 -14.100  1.00  0.00              
ATOM     61  O   GLN     8     -10.837  36.703 -13.931  1.00  0.00              
ATOM     62  CB  GLN     8     -10.078  36.679 -16.541  1.00  0.00              
ATOM     63  CG  GLN     8     -10.969  35.683 -17.266  1.00  0.00              
ATOM     64  CD  GLN     8     -12.035  36.359 -18.106  1.00  0.00              
ATOM     65  OE1 GLN     8     -12.935  35.703 -18.628  1.00  0.00              
ATOM     66  NE2 GLN     8     -11.936  37.677 -18.238  1.00  0.00              
ATOM     67  N   MET     9      -8.876  35.982 -13.095  1.00  0.00              
ATOM     68  CA  MET     9      -9.278  36.153 -11.704  1.00  0.00              
ATOM     69  C   MET     9     -10.697  36.703 -11.604  1.00  0.00              
ATOM     70  O   MET     9     -11.455  36.331 -10.708  1.00  0.00              
ATOM     71  CB  MET     9      -9.173  34.827 -10.949  1.00  0.00              
ATOM     72  CG  MET     9      -7.839  34.613 -10.253  1.00  0.00              
ATOM     73  SD  MET     9      -7.514  32.877  -9.890  1.00  0.00              
ATOM     74  CE  MET     9      -5.885  32.984  -9.155  1.00  0.00              
ATOM     75  N   THR    10     -11.049  37.591 -12.528  1.00  0.00              
ATOM     76  CA  THR    10     -12.406  38.207 -12.545  1.00  0.00              
ATOM     77  C   THR    10     -13.465  37.224 -12.055  1.00  0.00              
ATOM     78  O   THR    10     -14.431  37.614 -11.400  1.00  0.00              
ATOM     79  CB  THR    10     -12.461  39.479 -11.679  1.00  0.00              
ATOM     80  OG1 THR    10     -11.255  39.589 -10.912  1.00  0.00              
ATOM     81  CG2 THR    10     -12.615  40.714 -12.554  1.00  0.00              
ATOM     82  N   THR    11     -13.275  35.949 -12.376  1.00  0.00              
ATOM     83  CA  THR    11     -14.233  34.884 -11.961  1.00  0.00             
ATOM     84  C   THR    11     -14.543  34.974 -10.470  1.00  0.00             
ATOM     85  O   THR    11     -15.701  34.890 -10.061  1.00  0.00             
ATOM     86  CB  THR    11     -15.549  34.969 -12.755  1.00  0.00             
ATOM     87  OG1 THR    11     -15.601  36.209 -13.471  1.00  0.00             
ATOM     88  CG2 THR    11     -15.651  33.815 -13.740  1.00  0.00             
ATOM     89  N   GLN    12     -13.501  35.146  -9.663  1.00  0.00             
ATOM     90  CA  GLN    12     -13.660  35.247  -8.217  1.00  0.00             
ATOM     91  C   GLN    12     -14.814  36.176  -7.853  1.00  0.00             
ATOM     92  O   GLN    12     -15.407  36.054  -6.782  1.00  0.00             
ATOM     93  CB  GLN    12     -13.885  33.863  -7.605  1.00  0.00             
ATOM     94  CG  GLN    12     -13.149  33.637  -6.295  1.00  0.00             
ATOM     95  CD  GLN    12     -13.277  32.213  -5.794  1.00  0.00             
ATOM     96  OE1 GLN    12     -12.511  31.776  -4.934  1.00  0.00             
ATOM     97  NE2 GLN    12     -14.246  31.482  -6.331  1.00  0.00             
ATOM     98  N   ASP    13     -15.127  37.103  -8.753  1.00  0.00             
ATOM     99  CA  ASP    13     -16.210  38.054  -8.528  1.00  0.00             
ATOM    100  C   ASP    13     -16.864  37.834  -7.167  1.00  0.00             
ATOM    101  O   ASP    13     -17.849  38.487  -6.829  1.00  0.00             
ATOM    102  CB  ASP    13     -15.694  39.490  -8.636  1.00  0.00             
ATOM    103  CG  ASP    13     -16.328  40.252  -9.783  1.00  0.00             
ATOM    104  OD1 ASP    13     -16.708  41.424  -9.579  1.00  0.00             
ATOM    105  OD2 ASP    13     -16.446  39.677 -10.885  1.00  0.00             
ATOM    106  N   LEU    14     -16.308  36.909  -6.392  1.00  0.00             
ATOM    107  CA  LEU    14     -16.835  36.600  -5.069  1.00  0.00             
ATOM    108  C   LEU    14     -17.988  37.530  -4.704  1.00  0.00             
ATOM    109  O   LEU    14     -18.008  38.114  -3.620  1.00  0.00             
ATOM    110  CB  LEU    14     -17.295  35.142  -5.001  1.00  0.00             
ATOM    111  CG  LEU    14     -16.304  34.147  -4.392  1.00  0.00             
ATOM    112  CD1 LEU    14     -16.966  33.339  -3.286  1.00  0.00             
ATOM    113  CD2 LEU    14     -15.070  34.867  -3.871  1.00  0.00             
ATOM    114  N   VAL    15     -18.945  37.664  -5.616  1.00  0.00             
ATOM    115  CA  VAL    15     -20.128  38.542  -5.387  1.00  0.00             
ATOM    116  C   VAL    15     -20.768  38.263  -4.031  1.00  0.00             
ATOM    117  O   VAL    15     -21.239  39.178  -3.355  1.00  0.00             
ATOM    118  CB  VAL    15     -19.748  40.032  -5.467  1.00  0.00             
ATOM    119  CG1 VAL    15     -20.146  40.611  -6.816  1.00  0.00             
ATOM    120  CG2 VAL    15     -18.259  40.217  -5.218  1.00  0.00             
ATOM    121  N   ALA    16     -20.781  36.993  -3.639  1.00  0.00             
ATOM    122  CA  ALA    16     -21.364  36.591  -2.365  1.00  0.00             
ATOM    123  C   ALA    16     -21.847  37.801  -1.572  1.00  0.00             
ATOM    124  O   ALA    16     -23.047  38.056  -1.479  1.00  0.00             
ATOM    125  CB  ALA    16     -22.512  35.619  -2.588  1.00  0.00             
ATOM    126  N   LEU    17     -20.902  38.545  -1.002  1.00  0.00             
ATOM    127  CA  LEU    17     -21.230  39.729  -0.218  1.00  0.00             
ATOM    128  C   LEU    17     -22.154  40.664  -0.990  1.00  0.00             
ATOM    129  O   LEU    17     -23.358  40.710  -0.738  1.00  0.00             
ATOM    130  CB  LEU    17     -21.875  39.330   1.110  1.00  0.00             
ATOM    131  CG  LEU    17     -21.203  39.862   2.378  1.00  0.00             
ATOM    132  CD1 LEU    17     -22.223  40.039   3.493  1.00  0.00             
ATOM    133  CD2 LEU    17     -20.480  41.170   2.093  1.00  0.00             
ATOM    134  N   PHE    18     -21.583  41.408  -1.931  1.00  0.00             
ATOM    135  CA  PHE    18     -22.354  42.344  -2.742  1.00  0.00             
ATOM    136  C   PHE    18     -23.069  41.625  -3.882  1.00  0.00             
ATOM    137  O   PHE    18     -23.429  40.454  -3.761  1.00  0.00             
ATOM    138  CB  PHE    18     -23.366  43.095  -1.875  1.00  0.00             
ATOM    139  CG  PHE    18     -23.123  44.576  -1.805  1.00  0.00             
ATOM    140  CD1 PHE    18     -22.292  45.200  -2.719  1.00  0.00             
ATOM    141  CD2 PHE    18     -23.725  45.345  -0.825  1.00  0.00             
ATOM    142  CE1 PHE    18     -22.068  46.561  -2.655  1.00  0.00             
ATOM    143  CE2 PHE    18     -23.500  46.707  -0.759  1.00  0.00             
ATOM    144  CZ  PHE    18     -22.676  47.316  -1.669  1.00  0.00             
ATOM    145  N   ALA    19     -23.274  42.336  -4.986  1.00  0.00             
ATOM    146  CA  ALA    19     -23.947  41.769  -6.148  1.00  0.00             
ATOM    147  C   ALA    19     -23.120  41.965  -7.414  1.00  0.00             
ATOM    148  O   ALA    19     -22.182  42.761  -7.438  1.00  0.00             
ATOM    149  CB  ALA    19     -24.227  40.290  -5.929  1.00  0.00             
TER
END
