
#######################################################
#                                                     #
#                        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   18 (   90),  selected   18 , name T0378TS102_4-D1
# Molecule2: number of CA atoms   89 (  716),  selected   18 , name T0378_D1.pdb
# PARAMETERS: T0378TS102_4-D1.T0378_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:     9        72 - 88          4.94    17.31
  LCS_AVERAGE:      7.62

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        72 - 77          1.39    17.55
  LCS_AVERAGE:      4.99

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        72 - 76          0.61    17.66
  LCS_AVERAGE:      4.49

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:   89
LCS_GDT     L      20     L      20      4    4    4     4    4    4    4    4    4    5    5    7    8    8    8    8    8    8    9   10   10   11   11 
LCS_GDT     R      21     R      21      4    4    4     4    4    4    4    4    4    6    6    7    8    8    8    8    8    8    9   10   10   11   11 
LCS_GDT     E      22     E      22      4    4    4     4    4    4    4    4    4    6    6    7    8    8    8    8    8    8    9   10   10   11   11 
LCS_GDT     Q      23     Q      23      4    4    4     4    4    4    4    4    4    4    4    5    8    8    8    8    8    8    9   10   10   11   11 
LCS_GDT     A      49     A      49      4    4    5     3    4    4    4    4    4    4    4    4    5    5    6    7    8    9   10   11   12   12   13 
LCS_GDT     A      50     A      50      4    4    5     3    4    4    4    4    4    4    4    4    5    5    6    7    8    9   10   11   12   12   13 
LCS_GDT     M      51     M      51      4    4    5     3    4    4    4    4    4    4    4    4    5    5    6    7    8    9   10   11   12   12   13 
LCS_GDT     L      52     L      52      4    4    7     0    4    4    4    4    4    4    4    4    4    4    6    7    7    8    9   11   12   12   13 
LCS_GDT     F      72     F      72      5    6    9     4    5    5    5    6    6    6    6    7    7    7    7    8    9    9   10   11   12   12   13 
LCS_GDT     K      73     K      73      5    6    9     4    5    5    5    6    6    6    6    7    7    7    7    8    9    9   10   11   12   12   13 
LCS_GDT     R      74     R      74      5    6    9     3    5    5    5    6    6    6    6    7    7    7    7    8    9    9   10   11   12   12   13 
LCS_GDT     I      75     I      75      5    6    9     4    5    5    5    6    6    6    6    7    8    8    8    8    9    9   10   11   12   12   13 
LCS_GDT     S      76     S      76      5    6    9     4    5    5    5    6    6    6    6    7    8    8    8    8    9    9   10   11   12   12   13 
LCS_GDT     T      77     T      77      3    6    9     3    3    5    5    6    6    6    6    7    8    8    8    8    9    9   10   11   12   12   13 
LCS_GDT     Q      78     Q      78      3    3    9     3    3    3    4    4    4    6    6    7    8    8    8    8    8    9   10   11   12   12   13 
LCS_GDT     V      87     V      87      3    3    9     0    3    3    3    3    3    3    4    6    7    7    7    8    9    9   10   11   12   12   13 
LCS_GDT     F      88     F      88      3    3    9     0    3    3    3    3    3    3    4    5    5    5    7    8    9    9   10   11   11   11   13 
LCS_GDT     D      89     D      89      3    3    3     0    3    3    3    3    3    3    3    5    5    5    6    7    9    9    9    9   10   10   11 
LCS_AVERAGE  LCS_A:   5.70  (   4.49    4.99    7.62 )

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      5      5      6      6      6      6      7      8      8      8      8      9      9     10     11     12     12     13 
GDT PERCENT_CA   4.49   5.62   5.62   5.62   6.74   6.74   6.74   6.74   7.87   8.99   8.99   8.99   8.99  10.11  10.11  11.24  12.36  13.48  13.48  14.61
GDT RMS_LOCAL    0.33   0.61   0.61   0.61   1.39   1.39   1.39   1.39   2.77   3.80   3.80   3.80   3.80   4.51   4.51   5.61   6.31   6.74   6.74   7.22
GDT RMS_ALL_CA  17.65  17.66  17.66  17.66  17.55  17.55  17.55  17.55  17.19  14.71  14.71  14.71  14.71  16.94  16.94  15.91  15.69  15.76  15.76  15.85

#      Molecule1      Molecule2       DISTANCE
LGA    L      20      L      20         34.419
LGA    R      21      R      21         32.411
LGA    E      22      E      22         28.423
LGA    Q      23      Q      23         28.547
LGA    A      49      A      49         13.851
LGA    A      50      A      50         18.082
LGA    M      51      M      51         18.068
LGA    L      52      L      52         16.695
LGA    F      72      F      72          0.732
LGA    K      73      K      73          0.576
LGA    R      74      R      74          2.126
LGA    I      75      I      75          0.664
LGA    S      76      S      76          0.727
LGA    T      77      T      77          2.270
LGA    Q      78      Q      78          8.359
LGA    V      87      V      87          8.471
LGA    F      88      F      88         13.504
LGA    D      89      D      89         15.125

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   18   89    4.0      6    1.39     7.303     6.847     0.404

LGA_LOCAL      RMSD =  1.385  Number of atoms =    6  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 17.554  Number of atoms =   18 
Std_ALL_ATOMS  RMSD = 13.025  (standard rmsd on all 18 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.671273 * X  +   0.628527 * Y  +  -0.392870 * Z  +  27.061548
  Y_new =   0.275891 * X  +  -0.280079 * Y  +  -0.919478 * Z  +  33.483089
  Z_new =  -0.687951 * X  +  -0.725610 * Y  +   0.014605 * Z  +  60.927975 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.550672    1.590921  [ DEG:   -88.8469     91.1531 ]
  Theta =   0.758662    2.382930  [ DEG:    43.4682    136.5318 ]
  Phi   =   2.751642   -0.389950  [ DEG:   157.6575    -22.3425 ]
 
# 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: T0378TS102_4-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0378TS102_4-D1.T0378_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   18   89   4.0    6   1.39   6.847    13.02
REMARK  ---------------------------------------------------------- 
MOLECULE T0378TS102_4-D1
PFRMAT TS
TARGET T0378
MODEL 4
PARENT 1v2x_A
ATOM      1  N   LEU    20      -4.333  38.356  37.298  1.00  1.00
ATOM      2  CA  LEU    20      -4.049  36.967  36.826  1.00  1.00
ATOM      3  C   LEU    20      -2.558  36.653  36.768  1.00  1.00
ATOM      4  O   LEU    20      -2.126  35.591  37.220  1.00  1.00
ATOM      5  CB  LEU    20      -4.653  36.739  35.438  1.00  1.00
ATOM      6  N   ARG    21      -1.771  37.563  36.199  1.00  1.00
ATOM      7  CA  ARG    21      -0.338  37.326  36.108  1.00  1.00
ATOM      8  C   ARG    21       0.321  37.729  37.426  1.00  1.00
ATOM      9  O   ARG    21       1.437  37.318  37.731  1.00  1.00
ATOM     10  CB  ARG    21       0.277  38.104  34.933  1.00  1.00
ATOM     11  N   GLU    22      -0.375  38.533  38.216  1.00  1.00
ATOM     12  CA  GLU    22       0.163  38.945  39.504  1.00  1.00
ATOM     13  C   GLU    22       0.094  37.697  40.395  1.00  1.00
ATOM     14  O   GLU    22       0.968  37.431  41.226  1.00  1.00
ATOM     15  CB  GLU    22      -0.697  40.073  40.087  1.00  1.00
ATOM     16  N   GLN    23      -0.964  36.928  40.175  1.00  1.00
ATOM     17  CA  GLN    23      -1.238  35.695  40.894  1.00  1.00
ATOM     18  C   GLN    23      -0.322  34.561  40.432  1.00  1.00
ATOM     19  O   GLN    23       0.109  33.720  41.224  1.00  1.00
ATOM     20  CB  GLN    23      -2.714  35.318  40.667  1.00  1.00
ATOM     21  N   ALA    49      -0.006  34.554  39.145  1.00  1.00
ATOM     22  CA  ALA    49       0.812  33.493  38.593  1.00  1.00
ATOM     23  C   ALA    49       2.227  33.969  38.225  1.00  1.00
ATOM     24  O   ALA    49       3.218  33.431  38.717  1.00  1.00
ATOM     25  CB  ALA    49       0.051  32.860  37.378  1.00  1.00
ATOM     26  N   ALA    50       2.320  35.001  37.398  1.00  1.00
ATOM     27  CA  ALA    50       3.615  35.517  36.968  1.00  1.00
ATOM     28  C   ALA    50       4.496  35.909  38.143  1.00  1.00
ATOM     29  O   ALA    50       5.715  35.878  38.036  1.00  1.00
ATOM     30  CB  ALA    50       3.412  36.722  36.042  1.00  1.00
ATOM     31  N   MET    51       3.891  36.258  39.268  1.00  1.00
ATOM     32  CA  MET    51       4.688  36.670  40.414  1.00  1.00
ATOM     33  C   MET    51       4.832  35.612  41.500  1.00  1.00
ATOM     34  O   MET    51       5.794  34.847  41.512  1.00  1.00
ATOM     35  CB  MET    51       4.113  37.953  41.008  1.00  1.00
ATOM     36  N   LEU    52       3.872  35.593  42.418  1.00  1.00
ATOM     37  CA  LEU    52       3.874  34.664  43.529  1.00  1.00
ATOM     38  C   LEU    52       4.244  33.262  43.058  1.00  1.00
ATOM     39  O   LEU    52       5.223  32.681  43.521  1.00  1.00
ATOM     40  CB  LEU    52       2.493  34.650  44.185  1.00  1.00
ATOM     41  N   PHE    72       3.457  32.743  42.122  1.00  1.00
ATOM     42  CA  PHE    72       3.646  31.414  41.565  1.00  1.00
ATOM     43  C   PHE    72       5.074  31.140  41.074  1.00  1.00
ATOM     44  O   PHE    72       5.695  30.165  41.490  1.00  1.00
ATOM     45  CB  PHE    72       2.639  31.199  40.428  1.00  1.00
ATOM     46  N   LYS    73       5.580  32.005  40.201  1.00  1.00
ATOM     47  CA  LYS    73       6.922  31.873  39.620  1.00  1.00
ATOM     48  C   LYS    73       8.066  32.035  40.625  1.00  1.00
ATOM     49  O   LYS    73       9.015  31.247  40.600  1.00  1.00
ATOM     50  CB  LYS    73       7.081  32.879  38.456  1.00  1.00
ATOM     51  N   ARG    74       7.999  33.035  41.505  1.00  1.00
ATOM     52  CA  ARG    74       9.079  33.207  42.474  1.00  1.00
ATOM     53  C   ARG    74       9.142  32.051  43.481  1.00  1.00
ATOM     54  O   ARG    74      10.223  31.618  43.864  1.00  1.00
ATOM     55  CB  ARG    74       8.952  34.533  43.243  1.00  1.00
ATOM     56  N   ILE    75       7.989  31.548  43.910  1.00  1.00
ATOM     57  CA  ILE    75       7.970  30.446  44.860  1.00  1.00
ATOM     58  C   ILE    75       8.576  29.161  44.266  1.00  1.00
ATOM     59  O   ILE    75       9.274  28.398  44.950  1.00  1.00
ATOM     60  CB  ILE    75       6.519  30.139  45.319  1.00  1.00
ATOM     61  N   SER    76       8.297  28.905  42.995  1.00  1.00
ATOM     62  CA  SER    76       8.811  27.689  42.394  1.00  1.00
ATOM     63  C   SER    76      10.285  27.883  42.186  1.00  1.00
ATOM     64  O   SER    76      11.054  26.944  42.346  1.00  1.00
ATOM     65  CB  SER    76       8.162  27.421  41.042  1.00  1.00
ATOM     66  N   THR    77      10.678  29.091  41.819  1.00  1.00
ATOM     67  CA  THR    77      12.096  29.363  41.603  1.00  1.00
ATOM     68  C   THR    77      12.883  28.968  42.842  1.00  1.00
ATOM     69  O   THR    77      13.930  28.326  42.751  1.00  1.00
ATOM     70  CB  THR    77      12.349  30.832  41.275  1.00  1.00
ATOM     71  N   GLN    78      12.375  29.352  44.003  1.00  1.00
ATOM     72  CA  GLN    78      13.009  29.022  45.262  1.00  1.00
ATOM     73  C   GLN    78      12.891  27.539  45.619  1.00  1.00
ATOM     74  O   GLN    78      13.829  26.930  46.153  1.00  1.00
ATOM     75  CB  GLN    78      12.383  29.865  46.386  1.00  1.00
ATOM     76  N   VAL    87      11.740  26.936  45.305  1.00  1.00
ATOM     77  CA  VAL    87      11.542  25.535  45.600  1.00  1.00
ATOM     78  C   VAL    87      12.555  24.709  44.811  1.00  1.00
ATOM     79  O   VAL    87      12.994  23.640  45.250  1.00  1.00
ATOM     80  CB  VAL    87      10.139  25.118  45.173  1.00  1.00
ATOM     81  N   PHE    88      12.914  25.226  43.647  1.00  1.00
ATOM     82  CA  PHE    88      13.865  24.542  42.764  1.00  1.00
ATOM     83  C   PHE    88      15.296  24.547  43.287  1.00  1.00
ATOM     84  O   PHE    88      16.156  23.825  42.775  1.00  1.00
ATOM     85  CB  PHE    88      13.798  25.151  41.353  1.00  1.00
ATOM     86  N   ASP    89      15.566  25.360  44.306  1.00  1.00
ATOM     87  CA  ASP    89      16.890  25.394  44.902  1.00  1.00
ATOM     88  C   ASP    89      16.881  24.657  46.259  1.00  1.00
ATOM     89  O   ASP    89      17.894  24.603  46.922  1.00  1.00
ATOM     90  CB  ASP    89      17.384  26.851  45.120  1.00  1.00
TER
END
