
#######################################################
#                                                     #
#                        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   32 (  128),  selected   32 , name T0363AL381_3-D1
# Molecule2: number of CA atoms   46 (  372),  selected   32 , name T0363_D1.pdb
# PARAMETERS: T0363AL381_3-D1.T0363_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:    32        16 - 56          3.74     3.74
  LCS_AVERAGE:     69.57

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15        31 - 45          1.47     6.35
  LCS_AVERAGE:     27.85

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11        34 - 44          1.00     6.36
  LONGEST_CONTINUOUS_SEGMENT:    11        35 - 45          0.68     7.49
  LCS_AVERAGE:     16.17

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:   46
LCS_GDT     E      16     E      16      7   13   32     3    6    9   11   12   17   23   27   29   30   31   31   31   31   32   32   32   32   32   32 
LCS_GDT     I      17     I      17      7   13   32     4    6    9   11   12   13   21   27   29   30   31   31   31   31   32   32   32   32   32   32 
LCS_GDT     A      18     A      18      7   13   32     4    6    9   15   16   18   23   27   29   30   31   31   31   31   32   32   32   32   32   32 
LCS_GDT     Y      19     Y      19      7   13   32     4    6    9   15   16   18   23   27   29   30   31   31   31   31   32   32   32   32   32   32 
LCS_GDT     A      20     A      20      7   13   32     4    6    9   15   16   18   23   27   29   30   31   31   31   31   32   32   32   32   32   32 
LCS_GDT     F      21     F      21      7   13   32     3    6    9   11   12   18   23   27   29   30   31   31   31   31   32   32   32   32   32   32 
LCS_GDT     P      22     P      22      7   13   32     3    4    9   10   12   17   23   27   29   30   31   31   31   31   32   32   32   32   32   32 
LCS_GDT     E      23     E      23      4   13   32     3    4    4   10   11   12   14   15   24   25   31   31   31   31   32   32   32   32   32   32 
LCS_GDT     R      24     R      24      5   13   32     3    4    5   11   12   18   23   27   29   30   31   31   31   31   32   32   32   32   32   32 
LCS_GDT     Y      25     Y      25      5   13   32     3    5    9   15   16   18   23   27   29   30   31   31   31   31   32   32   32   32   32   32 
LCS_GDT     Y      26     Y      26      5   13   32     4    5    9   15   16   18   23   27   29   30   31   31   31   31   32   32   32   32   32   32 
LCS_GDT     L      27     L      27      5   13   32     4    6    9   15   16   18   23   27   29   30   31   31   31   31   32   32   32   32   32   32 
LCS_GDT     K      28     K      28      5   13   32     4    6    9   15   16   18   23   27   29   30   31   31   31   31   32   32   32   32   32   32 
LCS_GDT     Q      31     Q      31      4   15   32     3    7    9   12   14   16   17   26   29   30   31   31   31   31   32   32   32   32   32   32 
LCS_GDT     V      32     V      32      4   15   32     3    8   10   12   14   16   23   27   29   30   31   31   31   31   32   32   32   32   32   32 
LCS_GDT     D      33     D      33      4   15   32     3    4    4   12   14   16   21   27   29   30   31   31   31   31   32   32   32   32   32   32 
LCS_GDT     E      34     E      34     11   15   32     3    4    6   12   13   16   23   27   29   30   31   31   31   31   32   32   32   32   32   32 
LCS_GDT     G      35     G      35     11   15   32     6   10   11   12   14   16   17   24   29   30   31   31   31   31   32   32   32   32   32   32 
LCS_GDT     I      36     I      36     11   15   32     4    9   11   12   14   18   23   27   29   30   31   31   31   31   32   32   32   32   32   32 
LCS_GDT     T      37     T      37     11   15   32     4   10   11   12   16   18   23   27   29   30   31   31   31   31   32   32   32   32   32   32 
LCS_GDT     V      38     V      38     11   15   32     7   10   11   15   16   18   23   27   29   30   31   31   31   31   32   32   32   32   32   32 
LCS_GDT     Q      39     Q      39     11   15   32     7   10   11   15   16   18   23   27   29   30   31   31   31   31   32   32   32   32   32   32 
LCS_GDT     T      40     T      40     11   15   32     7   10   11   15   16   18   23   27   29   30   31   31   31   31   32   32   32   32   32   32 
LCS_GDT     A      41     A      41     11   15   32     7   10   11   15   16   18   23   27   29   30   31   31   31   31   32   32   32   32   32   32 
LCS_GDT     I      42     I      42     11   15   32     7   10   11   15   16   18   23   27   29   30   31   31   31   31   32   32   32   32   32   32 
LCS_GDT     T      43     T      43     11   15   32     7   10   11   15   16   18   23   27   29   30   31   31   31   31   32   32   32   32   32   32 
LCS_GDT     Q      44     Q      44     11   15   32     7   10   11   15   16   18   23   27   29   30   31   31   31   31   32   32   32   32   32   32 
LCS_GDT     S      45     S      45     11   15   32     6   10   11   12   14   16   18   21   27   30   31   31   31   31   32   32   32   32   32   32 
LCS_GDT     E      53     E      53      4    4   32     3    4    4    4    5   11   13   15   15   16   17   26   28   31   32   32   32   32   32   32 
LCS_GDT     I      54     I      54      4    4   32     3    4    4   10   12   15   23   27   29   30   31   31   31   31   32   32   32   32   32   32 
LCS_GDT     D      55     D      55      4    4   32     3    4    5   10   13   18   23   27   29   30   31   31   31   31   32   32   32   32   32   32 
LCS_GDT     L      56     L      56      4    4   32     3    4    9   15   16   18   23   27   29   30   31   31   31   31   32   32   32   32   32   32 
LCS_AVERAGE  LCS_A:  37.86  (  16.17   27.85   69.57 )

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     10     11     15     16     18     23     27     29     30     31     31     31     31     32     32     32     32     32     32 
GDT PERCENT_CA  15.22  21.74  23.91  32.61  34.78  39.13  50.00  58.70  63.04  65.22  67.39  67.39  67.39  67.39  69.57  69.57  69.57  69.57  69.57  69.57
GDT RMS_LOCAL    0.32   0.55   0.68   1.54   1.66   1.90   2.54   2.98   3.18   3.28   3.41   3.41   3.41   3.41   3.74   3.74   3.74   3.74   3.74   3.74
GDT RMS_ALL_CA   6.84   7.76   7.49   4.68   4.56   4.46   3.99   3.81   3.80   3.81   3.77   3.77   3.77   3.77   3.74   3.74   3.74   3.74   3.74   3.74

#      Molecule1      Molecule2       DISTANCE
LGA    E      16      E      16          3.220
LGA    I      17      I      17          3.882
LGA    A      18      A      18          3.005
LGA    Y      19      Y      19          3.233
LGA    A      20      A      20          2.936
LGA    F      21      F      21          2.798
LGA    P      22      P      22          3.195
LGA    E      23      E      23          5.900
LGA    R      24      R      24          3.692
LGA    Y      25      Y      25          3.551
LGA    Y      26      Y      26          2.413
LGA    L      27      L      27          2.995
LGA    K      28      K      28          2.663
LGA    Q      31      Q      31          4.372
LGA    V      32      V      32          3.174
LGA    D      33      D      33          3.870
LGA    E      34      E      34          3.902
LGA    G      35      G      35          4.788
LGA    I      36      I      36          2.804
LGA    T      37      T      37          2.605
LGA    V      38      V      38          2.858
LGA    Q      39      Q      39          2.212
LGA    T      40      T      40          1.967
LGA    A      41      A      41          3.304
LGA    I      42      I      42          3.463
LGA    T      43      T      43          3.313
LGA    Q      44      Q      44          3.887
LGA    S      45      S      45          5.955
LGA    E      53      E      53          8.886
LGA    I      54      I      54          3.508
LGA    D      55      D      55          2.378
LGA    L      56      L      56          3.462

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   32   46    4.0     27    2.98    45.652    42.728     0.877

LGA_LOCAL      RMSD =  2.977  Number of atoms =   27  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.799  Number of atoms =   32 
Std_ALL_ATOMS  RMSD =  3.742  (standard rmsd on all 32 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.539792 * X  +  -0.327823 * Y  +  -0.775343 * Z  +  28.602579
  Y_new =  -0.473035 * X  +  -0.643756 * Y  +   0.601512 * Z  +  17.817554
  Z_new =  -0.696321 * X  +   0.691456 * Y  +   0.192422 * Z  +   7.701493 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.299378   -1.842215  [ DEG:    74.4489   -105.5511 ]
  Theta =   0.770259    2.371334  [ DEG:    44.1326    135.8674 ]
  Phi   =  -2.422011    0.719582  [ DEG:  -138.7710     41.2290 ]
 
# 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: T0363AL381_3-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0363AL381_3-D1.T0363_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   32   46   4.0   27   2.98  42.728     3.74
REMARK  ---------------------------------------------------------- 
MOLECULE T0363AL381_3-D1
REMARK Aligment from pdb entry: 1ryjA
ATOM      1  N   GLU    16      18.777  11.314   5.824  1.00  0.00              
ATOM      2  CA  GLU    16      19.203  12.011   4.625  1.00  0.00              
ATOM      3  C   GLU    16      19.501  13.464   4.952  1.00  0.00              
ATOM      4  O   GLU    16      18.673  14.166   5.533  1.00  0.00              
ATOM      5  N   ILE    17      20.691  13.905   4.589  1.00  0.00              
ATOM      6  CA  ILE    17      21.144  15.241   4.924  1.00  0.00              
ATOM      7  C   ILE    17      21.872  15.862   3.745  1.00  0.00              
ATOM      8  O   ILE    17      22.196  15.173   2.774  1.00  0.00              
ATOM      9  N   ALA    18      22.121  17.156   3.819  1.00  0.00              
ATOM     10  CA  ALA    18      22.830  17.833   2.756  1.00  0.00              
ATOM     11  C   ALA    18      24.043  18.573   3.298  1.00  0.00              
ATOM     12  O   ALA    18      23.967  19.267   4.315  1.00  0.00              
ATOM     13  N   TYR    19      25.167  18.379   2.636  1.00  0.00              
ATOM     14  CA  TYR    19      26.377  19.109   2.952  1.00  0.00              
ATOM     15  C   TYR    19      26.666  20.095   1.831  1.00  0.00              
ATOM     16  O   TYR    19      26.836  19.697   0.684  1.00  0.00              
ATOM     17  N   ALA    20      26.695  21.376   2.150  1.00  0.00              
ATOM     18  CA  ALA    20      26.920  22.391   1.134  1.00  0.00              
ATOM     19  C   ALA    20      28.374  22.851   1.171  1.00  0.00              
ATOM     20  O   ALA    20      28.923  23.152   2.231  1.00  0.00              
ATOM     21  N   PHE    21      29.006  22.837   0.007  1.00  0.00              
ATOM     22  CA  PHE    21      30.387  23.275  -0.141  1.00  0.00              
ATOM     23  C   PHE    21      30.529  24.037  -1.464  1.00  0.00              
ATOM     24  O   PHE    21      29.526  24.465  -2.034  1.00  0.00              
ATOM     25  N   PRO    22      31.758  24.214  -1.950  1.00  0.00              
ATOM     26  CA  PRO    22      31.995  24.865  -3.243  1.00  0.00              
ATOM     27  C   PRO    22      31.332  24.079  -4.368  1.00  0.00              
ATOM     28  O   PRO    22      30.958  24.632  -5.401  1.00  0.00              
ATOM     29  N   GLU    23      31.191  22.777  -4.141  1.00  0.00              
ATOM     30  CA  GLU    23      30.549  21.872  -5.093  1.00  0.00              
ATOM     31  C   GLU    23      29.031  22.072  -5.081  1.00  0.00              
ATOM     32  O   GLU    23      28.312  21.563  -5.941  1.00  0.00              
ATOM     33  N   ARG    24      28.557  22.847  -4.116  1.00  0.00              
ATOM     34  CA  ARG    24      27.137  23.078  -3.967  1.00  0.00              
ATOM     35  C   ARG    24      26.549  22.215  -2.874  1.00  0.00              
ATOM     36  O   ARG    24      27.284  21.679  -2.041  1.00  0.00              
ATOM     37  N   TYR    25      25.233  22.087  -2.863  1.00  0.00              
ATOM     38  CA  TYR    25      24.563  21.210  -1.919  1.00  0.00              
ATOM     39  C   TYR    25      24.701  19.762  -2.353  1.00  0.00              
ATOM     40  O   TYR    25      24.250  19.376  -3.435  1.00  0.00              
ATOM     41  N   TYR    26      25.333  18.970  -1.510  1.00  0.00              
ATOM     42  CA  TYR    26      25.548  17.561  -1.784  1.00  0.00              
ATOM     43  C   TYR    26      24.549  16.737  -0.981  1.00  0.00              
ATOM     44  O   TYR    26      24.491  16.844   0.244  1.00  0.00              
ATOM     45  N   LEU    27      23.749  15.941  -1.673  1.00  0.00              
ATOM     46  CA  LEU    27      22.725  15.138  -1.022  1.00  0.00              
ATOM     47  C   LEU    27      23.187  13.696  -0.859  1.00  0.00              
ATOM     48  O   LEU    27      23.519  13.021  -1.836  1.00  0.00              
ATOM     49  N   LYS    28      23.229  13.243   0.383  1.00  0.00              
ATOM     50  CA  LYS    28      23.585  11.866   0.680  1.00  0.00              
ATOM     51  C   LYS    28      22.777  11.364   1.870  1.00  0.00              
ATOM     52  O   LYS    28      22.518  12.111   2.819  1.00  0.00              
ATOM     53  N   GLN    31      22.354  10.112   1.809  1.00  0.00              
ATOM     54  CA  GLN    31      21.601   9.520   2.900  1.00  0.00              
ATOM     55  C   GLN    31      22.312   8.284   3.440  1.00  0.00              
ATOM     56  O   GLN    31      22.864   7.485   2.686  1.00  0.00              
ATOM     57  N   VAL    32      22.307   8.153   4.755  1.00  0.00              
ATOM     58  CA  VAL    32      22.995   7.068   5.432  1.00  0.00              
ATOM     59  C   VAL    32      21.987   6.246   6.229  1.00  0.00              
ATOM     60  O   VAL    32      21.172   6.801   6.970  1.00  0.00              
ATOM     61  N   ASP    33      22.036   4.930   6.064  1.00  0.00              
ATOM     62  CA  ASP    33      21.095   4.051   6.736  1.00  0.00              
ATOM     63  C   ASP    33      21.221   4.097   8.247  1.00  0.00              
ATOM     64  O   ASP    33      20.235   3.916   8.963  1.00  0.00              
ATOM     65  N   GLU    34      22.430   4.322   8.734  1.00  0.00              
ATOM     66  CA  GLU    34      22.666   4.415  10.165  1.00  0.00              
ATOM     67  C   GLU    34      22.924   5.861  10.574  1.00  0.00              
ATOM     68  O   GLU    34      23.809   6.517  10.025  1.00  0.00              
ATOM     69  N   GLY    35      22.132   6.384  11.522  1.00  0.00              
ATOM     70  CA  GLY    35      22.329   7.732  12.070  1.00  0.00              
ATOM     71  C   GLY    35      23.664   7.849  12.803  1.00  0.00              
ATOM     72  O   GLY    35      23.856   7.259  13.868  1.00  0.00              
ATOM     73  N   ILE    36      24.580   8.613  12.226  1.00  0.00              
ATOM     74  CA  ILE    36      25.952   8.669  12.710  1.00  0.00              
ATOM     75  C   ILE    36      26.334  10.071  13.167  1.00  0.00              
ATOM     76  O   ILE    36      25.548  11.015  13.061  1.00  0.00              
ATOM     77  N   THR    37      27.547  10.188  13.676  1.00  0.00              
ATOM     78  CA  THR    37      28.076  11.442  14.174  1.00  0.00              
ATOM     79  C   THR    37      28.783  12.195  13.046  1.00  0.00              
ATOM     80  O   THR    37      29.184  11.584  12.051  1.00  0.00              
ATOM     81  N   VAL    38      28.916  13.517  13.190  1.00  0.00              
ATOM     82  CA  VAL    38      29.618  14.341  12.204  1.00  0.00              
ATOM     83  C   VAL    38      30.984  13.740  11.886  1.00  0.00              
ATOM     84  O   VAL    38      31.344  13.573  10.720  1.00  0.00              
ATOM     85  N   GLN    39      31.713  13.381  12.936  1.00  0.00              
ATOM     86  CA  GLN    39      33.067  12.859  12.809  1.00  0.00              
ATOM     87  C   GLN    39      33.120  11.587  11.971  1.00  0.00              
ATOM     88  O   GLN    39      34.125  11.318  11.321  1.00  0.00              
ATOM     89  N   THR    40      32.047  10.807  11.982  1.00  0.00              
ATOM     90  CA  THR    40      32.015   9.556  11.227  1.00  0.00              
ATOM     91  C   THR    40      32.098   9.837   9.734  1.00  0.00              
ATOM     92  O   THR    40      33.046   9.435   9.065  1.00  0.00              
ATOM     93  N   ALA    41      31.104  10.552   9.223  1.00  0.00              
ATOM     94  CA  ALA    41      31.048  10.880   7.805  1.00  0.00              
ATOM     95  C   ALA    41      32.212  11.785   7.418  1.00  0.00              
ATOM     96  O   ALA    41      32.815  11.622   6.352  1.00  0.00              
ATOM     97  N   ILE    42      32.544  12.718   8.302  1.00  0.00              
ATOM     98  CA  ILE    42      33.651  13.634   8.073  1.00  0.00              
ATOM     99  C   ILE    42      34.967  12.867   7.988  1.00  0.00              
ATOM    100  O   ILE    42      35.813  13.169   7.155  1.00  0.00              
ATOM    101  N   THR    43      35.123  11.877   8.866  1.00  0.00              
ATOM    102  CA  THR    43      36.322  11.061   8.887  1.00  0.00              
ATOM    103  C   THR    43      36.427  10.114   7.701  1.00  0.00              
ATOM    104  O   THR    43      37.526   9.851   7.210  1.00  0.00              
ATOM    105  N   GLN    44      35.293   9.590   7.241  1.00  0.00              
ATOM    106  CA  GLN    44      35.283   8.665   6.105  1.00  0.00              
ATOM    107  C   GLN    44      35.742   9.356   4.825  1.00  0.00              
ATOM    108  O   GLN    44      36.505   8.793   4.042  1.00  0.00              
ATOM    109  N   SER    45      35.277  10.578   4.615  1.00  0.00              
ATOM    110  CA  SER    45      35.729  11.380   3.481  1.00  0.00              
ATOM    111  C   SER    45      37.002  12.129   3.856  1.00  0.00              
ATOM    112  O   SER    45      37.660  12.729   3.006  1.00  0.00              
ATOM    113  N   GLU    53      37.331  12.049   5.143  1.00  0.00              
ATOM    114  CA  GLU    53      38.428  12.793   5.759  1.00  0.00              
ATOM    115  C   GLU    53      38.505  14.219   5.233  1.00  0.00              
ATOM    116  O   GLU    53      39.408  14.575   4.470  1.00  0.00              
ATOM    117  N   ILE    54      37.528  15.024   5.610  1.00  0.00              
ATOM    118  CA  ILE    54      37.542  16.433   5.274  1.00  0.00              
ATOM    119  C   ILE    54      38.195  17.199   6.411  1.00  0.00              
ATOM    120  O   ILE    54      37.658  17.258   7.518  1.00  0.00              
ATOM    121  N   ASP    55      39.378  17.774   6.159  1.00  0.00              
ATOM    122  CA  ASP    55      40.176  18.423   7.195  1.00  0.00              
ATOM    123  C   ASP    55      39.450  19.586   7.857  1.00  0.00              
ATOM    124  O   ASP    55      39.349  20.678   7.290  1.00  0.00              
ATOM    125  N   LEU    56      38.955  19.342   9.067  1.00  0.00              
ATOM    126  CA  LEU    56      38.318  20.378   9.877  1.00  0.00              
ATOM    127  C   LEU    56      39.356  21.440  10.257  1.00  0.00              
ATOM    128  O   LEU    56      39.032  22.520  10.745  1.00  0.00              
END
