
#######################################################
#                                                     #
#                        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   30 (  120),  selected   30 , name T0335TS383_1-D1
# Molecule2: number of CA atoms   36 (  584),  selected   30 , name T0335_D1.pdb
# PARAMETERS: T0335TS383_1-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:    19        11 - 35          4.97     7.73
  LCS_AVERAGE:     51.30

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16         5 - 20          0.68    11.61
  LCS_AVERAGE:     38.24

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16         5 - 20          0.68    11.61
  LCS_AVERAGE:     36.02

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       5     A       5     16   16   18     8   15   16   16   16   16   16   16   16   16   17   19   22   24   25   27   29   29   29   30 
LCS_GDT     K       6     K       6     16   16   18     9   15   16   16   16   16   16   16   16   16   17   17   19   23   25   27   29   29   29   30 
LCS_GDT     I       7     I       7     16   16   18     9   15   16   16   16   16   16   16   16   16   17   19   22   24   25   27   29   29   29   30 
LCS_GDT     A       8     A       8     16   16   18     9   15   16   16   16   16   16   16   16   16   17   19   22   24   25   27   29   29   29   30 
LCS_GDT     R       9     R       9     16   16   18     9   15   16   16   16   16   16   16   16   16   17   19   22   24   25   27   29   29   29   30 
LCS_GDT     I      10     I      10     16   16   18     9   15   16   16   16   16   16   16   16   16   17   19   22   24   25   27   29   29   29   30 
LCS_GDT     N      11     N      11     16   16   19     9   15   16   16   16   16   16   16   16   16   17   19   22   24   25   27   29   29   29   30 
LCS_GDT     E      12     E      12     16   16   19     9   15   16   16   16   16   16   16   16   16   17   19   22   24   25   27   29   29   29   30 
LCS_GDT     L      13     L      13     16   16   19     9   15   16   16   16   16   16   16   16   16   17   19   22   24   25   27   29   29   29   30 
LCS_GDT     A      14     A      14     16   16   19     9   15   16   16   16   16   16   16   16   16   17   19   22   24   25   27   29   29   29   30 
LCS_GDT     A      15     A      15     16   16   19     9   15   16   16   16   16   16   16   16   16   17   19   22   24   25   27   29   29   29   30 
LCS_GDT     K      16     K      16     16   16   19     9   15   16   16   16   16   16   16   16   16   17   17   19   24   25   27   29   29   29   30 
LCS_GDT     A      17     A      17     16   16   19     7   15   16   16   16   16   16   16   16   16   17   17   19   20   24   27   29   29   29   30 
LCS_GDT     K      18     K      18     16   16   19     7   15   16   16   16   16   16   16   16   16   17   17   22   24   25   27   29   29   29   30 
LCS_GDT     A      19     A      19     16   16   19     7   15   16   16   16   16   16   16   16   16   17   17   19   20   24   27   29   29   29   30 
LCS_GDT     G      20     G      20     16   16   19     5   14   16   16   16   16   16   16   16   16   17   17   17   17   17   19   24   26   29   30 
LCS_GDT     K      27     K      27      4    5   19     4    4    5    6    7    8   10   13   15   16   17   19   22   24   25   27   29   29   29   30 
LCS_GDT     A      28     A      28      4    8   19     4    4    5    6    7   10   13   13   14   15   17   19   22   24   25   27   29   29   29   30 
LCS_GDT     E      29     E      29      4   12   19     4    4    5    6   10   12   13   13   14   14   15   17   19   22   24   26   29   29   29   30 
LCS_GDT     Q      30     Q      30     11   12   19     6   11   11   11   11   12   13   13   14   14   16   17   19   24   25   27   29   29   29   30 
LCS_GDT     Q      31     Q      31     11   12   19     6   11   11   11   11   12   13   13   14   15   17   19   22   24   25   27   29   29   29   30 
LCS_GDT     K      32     K      32     11   12   19     6   11   11   11   11   12   13   13   14   15   17   19   22   24   25   27   29   29   29   30 
LCS_GDT     L      33     L      33     11   12   19     8   11   11   11   11   12   13   13   14   15   17   19   22   24   25   27   29   29   29   30 
LCS_GDT     R      34     R      34     11   12   19     8   11   11   11   11   12   13   13   14   15   17   19   22   24   25   27   29   29   29   30 
LCS_GDT     Q      35     Q      35     11   12   19     8   11   11   11   11   12   13   13   14   15   17   19   22   24   25   27   29   29   29   30 
LCS_GDT     E      36     E      36     11   12   17     8   11   11   11   11   12   13   13   14   15   17   19   22   24   25   27   29   29   29   30 
LCS_GDT     Y      37     Y      37     11   12   17     8   11   11   11   11   12   13   13   14   14   17   19   22   24   25   27   29   29   29   30 
LCS_GDT     L      38     L      38     11   12   17     8   11   11   11   11   12   13   13   14   14   17   19   22   24   25   27   29   29   29   30 
LCS_GDT     K      39     K      39     11   12   17     8   11   11   11   11   12   13   13   14   14   14   19   22   24   25   27   29   29   29   30 
LCS_GDT     G      40     G      40     11   12   17     8   11   11   11   11   12   13   13   14   14   14   14   16   16   24   26   29   29   29   30 
LCS_AVERAGE  LCS_A:  41.85  (  36.02   38.24   51.30 )

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      9     15     16     16     16     16     16     16     16     16     17     19     22     24     25     27     29     29     29     30 
GDT PERCENT_CA  25.00  41.67  44.44  44.44  44.44  44.44  44.44  44.44  44.44  44.44  47.22  52.78  61.11  66.67  69.44  75.00  80.56  80.56  80.56  83.33
GDT RMS_LOCAL    0.26   0.63   0.68   0.68   0.68   0.68   0.68   0.68   0.68   0.68   2.30   4.37   4.73   5.07   5.19   5.54   5.79   5.79   5.79   6.08
GDT RMS_ALL_CA  11.17  11.48  11.61  11.61  11.61  11.61  11.61  11.61  11.61  11.61  10.69   6.52   6.35   6.20   6.20   6.11   6.11   6.11   6.11   6.08

#      Molecule1      Molecule2       DISTANCE
LGA    A       5      A       5          0.954
LGA    K       6      K       6          0.726
LGA    I       7      I       7          0.838
LGA    A       8      A       8          0.468
LGA    R       9      R       9          0.383
LGA    I      10      I      10          0.472
LGA    N      11      N      11          0.467
LGA    E      12      E      12          0.365
LGA    L      13      L      13          0.266
LGA    A      14      A      14          0.335
LGA    A      15      A      15          0.470
LGA    K      16      K      16          0.251
LGA    A      17      A      17          0.943
LGA    K      18      K      18          0.924
LGA    A      19      A      19          0.995
LGA    G      20      G      20          1.053
LGA    K      27      K      27          9.956
LGA    A      28      A      28         16.684
LGA    E      29      E      29         19.421
LGA    Q      30      Q      30         16.830
LGA    Q      31      Q      31         15.811
LGA    K      32      K      32         17.968
LGA    L      33      L      33         17.558
LGA    R      34      R      34         15.921
LGA    Q      35      Q      35         16.214
LGA    E      36      E      36         18.253
LGA    Y      37      Y      37         17.479
LGA    L      38      L      38         16.187
LGA    K      39      K      39         17.924
LGA    G      40      G      40         19.494

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   30   36    4.0     16    0.68    51.389    46.207     2.052

LGA_LOCAL      RMSD =  0.680  Number of atoms =   16  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 11.612  Number of atoms =   30 
Std_ALL_ATOMS  RMSD =  6.077  (standard rmsd on all 30 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.927630 * X  +   0.319561 * Y  +  -0.193346 * Z  + -23.434038
  Y_new =   0.256857 * X  +  -0.169991 * Y  +   0.951382 * Z  +   3.908372
  Z_new =   0.271158 * X  +  -0.932193 * Y  +  -0.239770 * Z  +  17.979145 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.822550    1.319043  [ DEG:  -104.4244     75.5756 ]
  Theta =  -0.274595   -2.866997  [ DEG:   -15.7332   -164.2668 ]
  Phi   =   0.270128   -2.871465  [ DEG:    15.4772   -164.5228 ]
 
# 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: T0335TS383_1-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0335TS383_1-D1.T0335_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   30   36   4.0   16   0.68  46.207     6.08
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS383_1-D1
PFRMAT TS
TARGET T0335
MODEL 1
PARENT 1x0tA
ATOM      9  N   ALA     5      -0.531 -10.292  -7.684  1.00  0.00
ATOM     10  CA  ALA     5      -0.987 -10.645  -6.343  1.00  0.00
ATOM     11  C   ALA     5      -0.575  -9.555  -5.365  1.00  0.00
ATOM     12  O   ALA     5      -1.357  -9.139  -4.510  1.00  0.00
ATOM     13  N   LYS     6       0.666  -9.100  -5.497  1.00  0.00
ATOM     14  CA  LYS     6       1.192  -8.060  -4.626  1.00  0.00
ATOM     15  C   LYS     6       0.341  -6.803  -4.734  1.00  0.00
ATOM     16  O   LYS     6      -0.010  -6.194  -3.724  1.00  0.00
ATOM     17  N   ILE     7       0.011  -6.418  -5.961  1.00  0.00
ATOM     18  CA  ILE     7      -0.803  -5.230  -6.172  1.00  0.00
ATOM     19  C   ILE     7      -2.193  -5.438  -5.576  1.00  0.00
ATOM     20  O   ILE     7      -2.764  -4.517  -4.986  1.00  0.00
ATOM     21  N   ALA     8      -2.724  -6.651  -5.721  1.00  0.00
ATOM     22  CA  ALA     8      -4.041  -6.985  -5.178  1.00  0.00
ATOM     23  C   ALA     8      -4.032  -6.823  -3.660  1.00  0.00
ATOM     24  O   ALA     8      -4.966  -6.268  -3.074  1.00  0.00
ATOM     25  N   ARG     9      -2.971  -7.320  -3.027  1.00  0.00
ATOM     26  CA  ARG     9      -2.830  -7.240  -1.578  1.00  0.00
ATOM     27  C   ARG     9      -2.708  -5.792  -1.119  1.00  0.00
ATOM     28  O   ARG     9      -3.311  -5.399  -0.118  1.00  0.00
ATOM     29  N   ILE    10      -1.925  -5.004  -1.849  1.00  0.00
ATOM     30  CA  ILE    10      -1.736  -3.596  -1.512  1.00  0.00
ATOM     31  C   ILE    10      -3.075  -2.863  -1.561  1.00  0.00
ATOM     32  O   ILE    10      -3.393  -2.069  -0.672  1.00  0.00
ATOM     33  N   ASN    11      -3.858  -3.128  -2.602  1.00  0.00
ATOM     34  CA  ASN    11      -5.164  -2.492  -2.746  1.00  0.00
ATOM     35  C   ASN    11      -6.077  -2.849  -1.573  1.00  0.00
ATOM     36  O   ASN    11      -6.792  -1.997  -1.045  1.00  0.00
ATOM     37  N   GLU    12      -6.042  -4.111  -1.163  1.00  0.00
ATOM     38  CA  GLU    12      -6.868  -4.576  -0.055  1.00  0.00
ATOM     39  C   GLU    12      -6.443  -3.944   1.272  1.00  0.00
ATOM     40  O   GLU    12      -7.285  -3.540   2.077  1.00  0.00
ATOM     41  N   LEU    13      -5.137  -3.857   1.501  1.00  0.00
ATOM     42  CA  LEU    13      -4.627  -3.270   2.733  1.00  0.00
ATOM     43  C   LEU    13      -5.003  -1.795   2.855  1.00  0.00
ATOM     44  O   LEU    13      -5.326  -1.320   3.943  1.00  0.00
ATOM     45  N   ALA    14      -4.967  -1.069   1.742  1.00  0.00
ATOM     46  CA  ALA    14      -5.335   0.344   1.764  1.00  0.00
ATOM     47  C   ALA    14      -6.839   0.483   1.938  1.00  0.00
ATOM     48  O   ALA    14      -7.312   1.431   2.557  1.00  0.00
ATOM     49  N   ALA    15      -7.593  -0.459   1.384  1.00  0.00
ATOM     50  CA  ALA    15      -9.042  -0.418   1.530  1.00  0.00
ATOM     51  C   ALA    15      -9.366  -0.571   3.013  1.00  0.00
ATOM     52  O   ALA    15     -10.214   0.143   3.551  1.00  0.00
ATOM     53  N   LYS    16      -8.685  -1.500   3.676  1.00  0.00
ATOM     54  CA  LYS    16      -8.898  -1.718   5.098  1.00  0.00
ATOM     55  C   LYS    16      -8.426  -0.497   5.883  1.00  0.00
ATOM     56  O   LYS    16      -9.082  -0.072   6.829  1.00  0.00
ATOM     57  N   ALA    17      -7.293   0.072   5.485  1.00  0.00
ATOM     58  CA  ALA    17      -6.770   1.253   6.164  1.00  0.00
ATOM     59  C   ALA    17      -7.805   2.376   6.149  1.00  0.00
ATOM     60  O   ALA    17      -8.059   3.011   7.169  1.00  0.00
ATOM     61  N   LYS    18      -8.406   2.612   4.988  1.00  0.00
ATOM     62  CA  LYS    18      -9.399   3.674   4.865  1.00  0.00
ATOM     63  C   LYS    18     -10.610   3.428   5.756  1.00  0.00
ATOM     64  O   LYS    18     -11.134   4.354   6.373  1.00  0.00
ATOM     65  N   ALA    19     -11.048   2.175   5.830  1.00  0.00
ATOM     66  CA  ALA    19     -12.204   1.826   6.645  1.00  0.00
ATOM     67  C   ALA    19     -11.974   1.992   8.143  1.00  0.00
ATOM     68  O   ALA    19     -12.890   2.368   8.874  1.00  0.00
ATOM     69  N   GLY    20     -10.752   1.738   8.603  1.00  0.00
ATOM     70  CA  GLY    20     -10.467   1.841  10.033  1.00  0.00
ATOM     71  C   GLY    20      -9.760   3.120  10.468  1.00  0.00
ATOM     72  O   GLY    20      -9.662   3.385  11.658  1.00  0.00
ATOM     73  N   LYS    27      -9.292   3.912   9.510  1.00  0.00
ATOM     74  CA  LYS    27      -8.541   5.132   9.807  1.00  0.00
ATOM     75  C   LYS    27      -9.138   6.146  10.779  1.00  0.00
ATOM     76  O   LYS    27      -8.448   6.619  11.679  1.00  0.00
ATOM     77  N   ALA    28     -10.404   6.494  10.602  1.00  0.00
ATOM     78  CA  ALA    28     -11.017   7.492  11.469  1.00  0.00
ATOM     79  C   ALA    28     -11.132   7.069  12.928  1.00  0.00
ATOM     80  O   ALA    28     -10.940   7.885  13.833  1.00  0.00
ATOM     81  N   GLU    29     -11.418   5.793  13.151  1.00  0.00
ATOM     82  CA  GLU    29     -11.587   5.256  14.498  1.00  0.00
ATOM     83  C   GLU    29     -10.296   4.687  15.086  1.00  0.00
ATOM     84  O   GLU    29     -10.033   4.827  16.285  1.00  0.00
ATOM     85  N   GLN    30      -9.495   4.044  14.241  1.00  0.00
ATOM     86  CA  GLN    30      -8.253   3.419  14.685  1.00  0.00
ATOM     87  C   GLN    30      -7.085   3.799  13.779  1.00  0.00
ATOM     88  O   GLN    30      -6.595   2.972  13.004  1.00  0.00
ATOM     89  N   GLN    31      -6.610   5.051  13.880  1.00  0.00
ATOM     90  CA  GLN    31      -5.491   5.519  13.052  1.00  0.00
ATOM     91  C   GLN    31      -4.208   4.707  13.185  1.00  0.00
ATOM     92  O   GLN    31      -3.464   4.569  12.217  1.00  0.00
ATOM     93  N   LYS    32      -3.936   4.172  14.371  1.00  0.00
ATOM     94  CA  LYS    32      -2.729   3.374  14.539  1.00  0.00
ATOM     95  C   LYS    32      -2.830   2.097  13.712  1.00  0.00
ATOM     96  O   LYS    32      -1.843   1.649  13.127  1.00  0.00
ATOM     97  N   LEU    33      -4.024   1.512  13.664  1.00  0.00
ATOM     98  CA  LEU    33      -4.228   0.299  12.884  1.00  0.00
ATOM     99  C   LEU    33      -4.103   0.627  11.396  1.00  0.00
ATOM    100  O   LEU    33      -3.530  -0.147  10.631  1.00  0.00
ATOM    101  N   ARG    34      -4.634   1.776  10.984  1.00  0.00
ATOM    102  CA  ARG    34      -4.545   2.167   9.579  1.00  0.00
ATOM    103  C   ARG    34      -3.081   2.338   9.190  1.00  0.00
ATOM    104  O   ARG    34      -2.672   1.945   8.100  1.00  0.00
ATOM    105  N   GLN    35      -2.293   2.915  10.092  1.00  0.00
ATOM    106  CA  GLN    35      -0.870   3.112   9.830  1.00  0.00
ATOM    107  C   GLN    35      -0.199   1.744   9.661  1.00  0.00
ATOM    108  O   GLN    35       0.671   1.568   8.806  1.00  0.00
ATOM    109  N   GLU    36      -0.607   0.774  10.473  1.00  0.00
ATOM    110  CA  GLU    36      -0.050  -0.568  10.368  1.00  0.00
ATOM    111  C   GLU    36      -0.364  -1.159   8.993  1.00  0.00
ATOM    112  O   GLU    36       0.506  -1.750   8.353  1.00  0.00
ATOM    113  N   TYR    37      -1.602  -1.000   8.530  1.00  0.00
ATOM    114  CA  TYR    37      -1.969  -1.536   7.224  1.00  0.00
ATOM    115  C   TYR    37      -1.187  -0.862   6.107  1.00  0.00
ATOM    116  O   TYR    37      -0.791  -1.509   5.143  1.00  0.00
ATOM    117  N   LEU    38      -0.962   0.441   6.239  1.00  0.00
ATOM    118  CA  LEU    38      -0.202   1.169   5.233  1.00  0.00
ATOM    119  C   LEU    38       1.216   0.604   5.179  1.00  0.00
ATOM    120  O   LEU    38       1.766   0.365   4.102  1.00  0.00
ATOM    121  N   LYS    39       1.806   0.371   6.346  1.00  0.00
ATOM    122  CA  LYS    39       3.162  -0.159   6.377  1.00  0.00
ATOM    123  C   LYS    39       3.246  -1.573   5.811  1.00  0.00
ATOM    124  O   LYS    39       4.238  -1.924   5.171  1.00  0.00
ATOM    125  N   GLY    40       2.221  -2.390   6.036  1.00  0.00
ATOM    126  CA  GLY    40       2.238  -3.742   5.483  1.00  0.00
ATOM    127  C   GLY    40       2.194  -3.638   3.960  1.00  0.00
ATOM    128  O   GLY    40       2.844  -4.411   3.253  1.00  0.00
TER
END
