
#######################################################
#                                                     #
#                        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   27 (  135),  selected   25 , name T0361TS239_5_1
# Molecule2: number of CA atoms  166 ( 1335),  selected   25 , name T0361.pdb
# PARAMETERS: T0361TS239_5_1.T0361.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:    19         3 - 21          4.24    11.26
  LCS_AVERAGE:     10.29

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14         4 - 17          1.93    13.36
  LCS_AVERAGE:      5.98

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12         6 - 17          0.85    14.16
  LCS_AVERAGE:      4.55

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:  166
LCS_GDT     T       3     T       3      3    5   19     2    3    5    5    5    5    7   15   15   16   17   18   18   18   18   18   18   19   19   19 
LCS_GDT     L       4     L       4      4   14   19     3    3    5    6   11   13   14   15   16   16   17   18   18   18   18   18   18   19   19   19 
LCS_GDT     T       5     T       5      4   14   19     3    3    5    5   10   13   14   15   16   16   17   18   18   18   18   18   18   19   19   19 
LCS_GDT     E       6     E       6     12   14   19     7   11   11   12   12   13   14   15   16   16   17   18   18   18   18   18   18   19   19   19 
LCS_GDT     D       7     D       7     12   14   19     7   11   11   12   12   13   14   15   16   16   17   18   18   18   18   18   18   19   19   19 
LCS_GDT     D       8     D       8     12   14   19     7   11   11   12   12   13   14   15   16   16   17   18   18   18   18   18   18   19   19   19 
LCS_GDT     V       9     V       9     12   14   19     7   11   11   12   12   13   14   15   16   16   17   18   18   18   18   18   18   19   19   19 
LCS_GDT     L      10     L      10     12   14   19     7   11   11   12   12   13   14   15   16   16   17   18   18   18   18   18   18   19   19   19 
LCS_GDT     E      11     E      11     12   14   19     7   11   11   12   12   13   14   15   16   16   17   18   18   18   18   18   18   19   19   19 
LCS_GDT     Q      12     Q      12     12   14   19     7   11   11   12   12   13   14   15   16   16   17   18   18   18   18   18   18   19   19   19 
LCS_GDT     L      13     L      13     12   14   19     6   11   11   12   12   13   14   15   16   16   17   18   18   18   18   18   18   19   19   19 
LCS_GDT     D      14     D      14     12   14   19     6   11   11   12   12   13   14   15   16   16   17   18   18   18   18   18   18   19   19   19 
LCS_GDT     A      15     A      15     12   14   19     6   11   11   12   12   13   14   15   16   16   17   18   18   18   18   18   18   19   19   19 
LCS_GDT     Q      16     Q      16     12   14   19     7   11   11   12   12   13   14   15   16   16   17   18   18   18   18   18   18   19   19   19 
LCS_GDT     D      17     D      17     12   14   19     3    3    4   12   12   13   14   15   16   16   17   18   18   18   18   18   18   19   19   19 
LCS_GDT     N      18     N      18      3   13   19     3    3    3    4    4    7   14   15   16   16   17   18   18   18   18   18   18   19   19   19 
LCS_GDT     L      19     L      19      3    4   19     3    3    3    4    4    7    8   12   12   15   17   18   18   18   18   18   18   19   19   19 
LCS_GDT     F      20     F      20      3    3   19     3    3    3    4    9   11   14   15   16   16   17   18   18   18   18   18   18   19   19   19 
LCS_GDT     S      21     S      21      3    4   19     3    3    3    3    4    5    5    6    6    8    9   10   14   15   16   17   18   19   19   19 
LCS_GDT     F      22     F      22      3    4   11     3    3    3    3    4    5    5    6    6    8    9   10   11   12   13   13   14   14   17   18 
LCS_GDT     M      23     M      23      4    4   11     3    3    4    4    4    5    5    6    6    8    9   10   11   12   13   13   14   14   17   17 
LCS_GDT     K      24     K      24      4    4   11     3    3    4    4    4    5    5    6    6    8    9   10   11   12   13   13   13   14   15   16 
LCS_GDT     T      25     T      25      4    4   11     3    3    4    4    4    5    5    6    6    8    9   10   11   11   11   11   12   13   14   14 
LCS_GDT     A      26     A      26      4    4   11     3    3    4    4    4    5    5    6    6    7    9   10   11   12   13   13   13   14   15   16 
LCS_GDT     H      27     H      27      3    3   11     3    3    3    3    3    5    5    6    6    7    7    9   11   12   13   13   13   14   16   16 
LCS_AVERAGE  LCS_A:   6.94  (   4.55    5.98   10.29 )

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      7     11     11     12     12     13     14     15     16     16     17     18     18     18     18     18     18     19     19     19 
GDT PERCENT_CA   4.22   6.63   6.63   7.23   7.23   7.83   8.43   9.04   9.64   9.64  10.24  10.84  10.84  10.84  10.84  10.84  10.84  11.45  11.45  11.45
GDT RMS_LOCAL    0.21   0.53   0.53   0.85   0.85   1.69   1.93   2.43   2.61   2.61   3.02   3.33   3.33   3.33   3.33   3.33   3.33   4.24   4.24   4.24
GDT RMS_ALL_CA  14.76  14.19  14.19  14.16  14.16  13.68  13.36  12.00  12.31  12.31  12.03  11.84  11.84  11.84  11.84  11.84  11.84  11.26  11.26  11.26

#      Molecule1      Molecule2       DISTANCE
LGA    T       3      T       3          9.017
LGA    L       4      L       4          3.126
LGA    T       5      T       5          2.524
LGA    E       6      E       6          3.130
LGA    D       7      D       7          1.476
LGA    D       8      D       8          2.411
LGA    V       9      V       9          2.365
LGA    L      10      L      10          1.602
LGA    E      11      E      11          1.789
LGA    Q      12      Q      12          0.642
LGA    L      13      L      13          1.610
LGA    D      14      D      14          2.375
LGA    A      15      A      15          2.239
LGA    Q      16      Q      16          2.797
LGA    D      17      D      17          5.061
LGA    N      18      N      18          3.626
LGA    L      19      L      19          5.865
LGA    F      20      F      20          3.446
LGA    S      21      S      21         12.657
LGA    F      22      F      22         15.654
LGA    M      23      M      23         18.224
LGA    K      24      K      24         22.966
LGA    T      25      T      25         27.379
LGA    A      26      A      26         24.843
LGA    H      27      H      27         28.728

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   27  166    4.0     15    2.43     8.434     7.943     0.593

LGA_LOCAL      RMSD =  2.431  Number of atoms =   15  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 12.149  Number of atoms =   25 
Std_ALL_ATOMS  RMSD =  9.363  (standard rmsd on all 25 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.145546 * X  +  -0.787728 * Y  +   0.598582 * Z  +  52.190723
  Y_new =   0.830952 * X  +   0.425707 * Y  +   0.358180 * Z  + -76.395218
  Z_new =  -0.536969 * X  +   0.445261 * Y  +   0.716524 * Z  +  21.626421 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.556020   -2.585573  [ DEG:    31.8576   -148.1424 ]
  Theta =   0.566840    2.574753  [ DEG:    32.4775    147.5225 ]
  Phi   =   1.397400   -1.744193  [ DEG:    80.0651    -99.9349 ]
 
# 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: T0361TS239_5_1                                
REMARK     2: T0361.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0361TS239_5_1.T0361.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   27  166   4.0   15   2.43   7.943     9.36
REMARK  ---------------------------------------------------------- 
MOLECULE T0361TS239_5_1
REMARK PARENT number 1
PFRMAT TS
TARGET T0361
PARENT 1f5q_B
ATOM      1  N   MET     1      20.451   1.202  21.544  1.00  9.99
ATOM      2  CA  MET     1      19.771   2.415  21.135  1.00  9.99
ATOM      3  C   MET     1      19.009   3.126  22.235  1.00  9.99
ATOM      4  O   MET     1      17.856   3.492  22.045  1.00  9.99
ATOM      5  CB  MET     1      18.812   2.042  20.017  1.00  9.99
ATOM      6  N   ALA     2      19.657   3.354  23.369  1.00  9.99
ATOM      7  CA  ALA     2      18.992   3.989  24.510  1.00  9.99
ATOM      8  C   ALA     2      19.664   5.241  25.086  1.00  9.99
ATOM      9  O   ALA     2      19.181   5.807  26.063  1.00  9.99
ATOM     10  CB  ALA     2      18.851   2.952  25.625  1.00  9.99
ATOM     11  N   THR     3      20.767   5.668  24.487  1.00  9.99
ATOM     12  CA  THR     3      21.502   6.828  24.973  1.00  9.99
ATOM     13  C   THR     3      20.759   8.152  25.021  1.00  9.99
ATOM     14  O   THR     3      21.002   8.953  25.915  1.00  9.99
ATOM     15  CB  THR     3      22.768   7.023  24.144  1.00  9.99
ATOM     16  N   LEU     4      19.855   8.380  24.076  1.00  9.99
ATOM     17  CA  LEU     4      19.119   9.645  23.995  1.00  9.99
ATOM     18  C   LEU     4      17.868   9.756  24.851  1.00  9.99
ATOM     19  O   LEU     4      17.148  10.761  24.778  1.00  9.99
ATOM     20  CB  LEU     4      18.755   9.935  22.535  1.00  9.99
ATOM     21  N   THR     5      17.610   8.736  25.656  1.00  9.99
ATOM     22  CA  THR     5      16.446   8.727  26.526  1.00  9.99
ATOM     23  C   THR     5      16.588   9.668  27.712  1.00  9.99
ATOM     24  O   THR     5      17.662   9.811  28.275  1.00  9.99
ATOM     25  CB  THR     5      16.198   7.309  27.055  1.00  9.99
ATOM     26  N   GLU     6      15.484  10.307  28.082  1.00  9.99
ATOM     27  CA  GLU     6      15.449  11.201  29.235  1.00  9.99
ATOM     28  C   GLU     6      14.384  10.639  30.163  1.00  9.99
ATOM     29  O   GLU     6      13.424  10.033  29.703  1.00  9.99
ATOM     30  CB  GLU     6      15.080  12.617  28.817  1.00  9.99
ATOM     31  N   ASP     7      14.547  10.837  31.464  1.00  9.99
ATOM     32  CA  ASP     7      13.593  10.307  32.435  1.00  9.99
ATOM     33  C   ASP     7      12.159  10.141  31.932  1.00  9.99
ATOM     34  O   ASP     7      11.571   9.081  32.078  1.00  9.99
ATOM     35  CB  ASP     7      13.579  11.165  33.712  1.00  9.99
ATOM     36  N   ASP     8      11.604  11.174  31.319  1.00  9.99
ATOM     37  CA  ASP     8      10.231  11.101  30.866  1.00  9.99
ATOM     38  C   ASP     8       9.928   9.960  29.901  1.00  9.99
ATOM     39  O   ASP     8       8.832   9.389  29.949  1.00  9.99
ATOM     40  CB  ASP     8       9.806  12.425  30.246  1.00  9.99
ATOM     41  N   VAL     9      10.880   9.636  29.025  1.00  9.99
ATOM     42  CA  VAL     9      10.695   8.557  28.062  1.00  9.99
ATOM     43  C   VAL     9      10.575   7.232  28.810  1.00  9.99
ATOM     44  O   VAL     9       9.720   6.397  28.493  1.00  9.99
ATOM     45  CB  VAL     9      11.879   8.476  27.100  1.00  9.99
ATOM     46  N   LEU    10      11.451   7.048  29.795  1.00  9.99
ATOM     47  CA  LEU    10      11.476   5.847  30.609  1.00  9.99
ATOM     48  C   LEU    10      10.172   5.748  31.395  1.00  9.99
ATOM     49  O   LEU    10       9.673   4.652  31.679  1.00  9.99
ATOM     50  CB  LEU    10      12.663   5.894  31.580  1.00  9.99
ATOM     51  N   GLU    11       9.621   6.901  31.759  1.00  9.99
ATOM     52  CA  GLU    11       8.373   6.911  32.498  1.00  9.99
ATOM     53  C   GLU    11       7.231   6.505  31.590  1.00  9.99
ATOM     54  O   GLU    11       6.322   5.806  32.022  1.00  9.99
ATOM     55  CB  GLU    11       8.121   8.284  33.108  1.00  9.99
ATOM     56  N   GLN    12       7.278   6.940  30.332  1.00  9.99
ATOM     57  CA  GLN    12       6.252   6.584  29.360  1.00  9.99
ATOM     58  C   GLN    12       6.164   5.076  29.211  1.00  9.99
ATOM     59  O   GLN    12       5.080   4.517  29.101  1.00  9.99
ATOM     60  CB  GLN    12       6.573   7.180  27.994  1.00  9.99
ATOM     61  N   LEU    13       7.329   4.441  29.197  1.00  9.99
ATOM     62  CA  LEU    13       7.465   2.995  29.055  1.00  9.99
ATOM     63  C   LEU    13       6.884   2.307  30.281  1.00  9.99
ATOM     64  O   LEU    13       6.205   1.290  30.182  1.00  9.99
ATOM     65  CB  LEU    13       8.952   2.639  28.896  1.00  9.99
ATOM     66  N   ASP    14       7.152   2.866  31.448  1.00  9.99
ATOM     67  CA  ASP    14       6.632   2.278  32.672  1.00  9.99
ATOM     68  C   ASP    14       5.115   2.381  32.655  1.00  9.99
ATOM     69  O   ASP    14       4.427   1.437  33.010  1.00  9.99
ATOM     70  CB  ASP    14       7.198   2.998  33.915  1.00  9.99
ATOM     71  N   ALA    15       4.609   3.534  32.228  1.00  9.99
ATOM     72  CA  ALA    15       3.180   3.767  32.157  1.00  9.99
ATOM     73  C   ALA    15       2.560   2.764  31.192  1.00  9.99
ATOM     74  O   ALA    15       1.403   2.373  31.336  1.00  9.99
ATOM     75  CB  ALA    15       2.894   5.198  31.664  1.00  9.99
ATOM     76  N   GLN    16       3.336   2.343  30.204  1.00  9.99
ATOM     77  CA  GLN    16       2.830   1.397  29.231  1.00  9.99
ATOM     78  C   GLN    16       2.737  -0.010  29.797  1.00  9.99
ATOM     79  O   GLN    16       1.886  -0.785  29.374  1.00  9.99
ATOM     80  CB  GLN    16       3.701   1.382  27.982  1.00  9.99
ATOM     81  N   ASP    17       3.608  -0.356  30.737  1.00  9.99
ATOM     82  CA  ASP    17       3.536  -1.688  31.318  1.00  9.99
ATOM     83  C   ASP    17       2.454  -1.673  32.389  1.00  9.99
ATOM     84  O   ASP    17       1.892  -2.706  32.727  1.00  9.99
ATOM     85  CB  ASP    17       4.890  -2.117  31.910  1.00  9.99
ATOM     86  N   ASN    18       2.159  -0.490  32.911  1.00  9.99
ATOM     87  CA  ASN    18       1.124  -0.338  33.921  1.00  9.99
ATOM     88  C   ASN    18      -0.213  -0.643  33.262  1.00  9.99
ATOM     89  O   ASN    18      -1.046  -1.370  33.802  1.00  9.99
ATOM     90  CB  ASN    18       1.112   1.092  34.466  1.00  9.99
ATOM     91  N   LEU    19      -0.398  -0.078  32.076  1.00  9.99
ATOM     92  CA  LEU    19      -1.615  -0.268  31.310  1.00  9.99
ATOM     93  C   LEU    19      -1.767  -1.703  30.826  1.00  9.99
ATOM     94  O   LEU    19      -2.867  -2.253  30.847  1.00  9.99
ATOM     95  CB  LEU    19      -1.651   0.714  30.128  1.00  9.99
ATOM     96  N   PHE    20      -0.667  -2.312  30.401  1.00  9.99
ATOM     97  CA  PHE    20      -0.703  -3.686  29.929  1.00  9.99
ATOM     98  C   PHE    20      -1.051  -4.598  31.098  1.00  9.99
ATOM     99  O   PHE    20      -1.775  -5.575  30.940  1.00  9.99
ATOM    100  CB  PHE    20       0.647  -4.082  29.322  1.00  9.99
ATOM    101  N   SER    21      -5.131  -7.613  33.695  1.00  9.99
ATOM    102  CA  SER    21      -5.676  -7.875  35.033  1.00  9.99
ATOM    103  C   SER    21      -7.199  -7.758  35.184  1.00  9.99
ATOM    104  O   SER    21      -7.792  -8.427  36.036  1.00  9.99
ATOM    105  CB  SER    21      -5.000  -6.959  36.061  1.00  9.99
ATOM    106  N   PHE    22      -7.837  -6.903  34.390  1.00  9.99
ATOM    107  CA  PHE    22      -9.286  -6.777  34.487  1.00  9.99
ATOM    108  C   PHE    22      -9.892  -8.032  33.832  1.00  9.99
ATOM    109  O   PHE    22     -10.941  -7.994  33.163  1.00  9.99
ATOM    110  CB  PHE    22      -9.791  -5.451  33.810  1.00  9.99
ATOM    111  N   MET    23      -9.211  -9.155  34.051  1.00  9.99
ATOM    112  CA  MET    23      -9.653 -10.414  33.497  1.00  9.99
ATOM    113  C   MET    23     -10.797 -11.056  34.258  1.00  9.99
ATOM    114  O   MET    23     -11.570 -10.406  34.973  1.00  9.99
ATOM    115  CB  MET    23      -8.445 -11.364  33.433  1.00  9.99
ATOM    116  N   LYS    24     -10.886 -12.368  34.091  1.00  9.99
ATOM    117  CA  LYS    24     -11.919 -13.190  34.703  1.00  9.99
ATOM    118  C   LYS    24     -11.229 -14.189  35.649  1.00  9.99
ATOM    119  O   LYS    24     -10.297 -14.870  35.247  1.00  9.99
ATOM    120  CB  LYS    24     -12.711 -13.922  33.571  1.00  9.99
ATOM    121  N   THR    25     -11.670 -14.255  36.905  1.00  9.99
ATOM    122  CA  THR    25     -11.068 -15.168  37.877  1.00  9.99
ATOM    123  C   THR    25      -9.547 -14.979  37.916  1.00  9.99
ATOM    124  O   THR    25      -8.795 -15.958  37.783  1.00  9.99
ATOM    125  CB  THR    25     -11.352 -16.636  37.508  1.00  9.99
ATOM    126  N   ALA    26      -9.089 -13.743  38.098  1.00  9.99
ATOM    127  CA  ALA    26      -7.653 -13.475  38.126  1.00  9.99
ATOM    128  C   ALA    26      -6.877 -14.350  39.114  1.00  9.99
ATOM    129  O   ALA    26      -6.020 -15.133  38.722  1.00  9.99
ATOM    130  CB  ALA    26      -7.375 -11.978  38.433  1.00  9.99
ATOM    131  N   HIS    27      -7.182 -14.228  40.396  1.00  9.99
ATOM    132  CA  HIS    27      -6.487 -14.987  41.426  1.00  9.99
ATOM    133  C   HIS    27      -6.519 -16.494  41.206  1.00  9.99
ATOM    134  O   HIS    27      -5.542 -17.190  41.466  1.00  9.99
ATOM    135  CB  HIS    27      -7.079 -14.656  42.805  1.00  9.99
TER
END
