
#######################################################
#                                                     #
#                        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   26 (  104),  selected   26 , name T0363AL242_1-D1
# Molecule2: number of CA atoms   46 (  372),  selected   26 , name T0363_D1.pdb
# PARAMETERS: T0363AL242_1-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:    26        31 - 56          4.54     4.54
  LCS_AVERAGE:     56.52

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    18        31 - 48          1.62     6.82
  LCS_AVERAGE:     30.43

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12        35 - 46          0.93     7.44
  LCS_AVERAGE:     19.48

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     Q      31     Q      31     11   18   26     5    9   13   15   18   18   18   19   21   21   23   24   24   24   26   26   26   26   26   26 
LCS_GDT     V      32     V      32     11   18   26     4    8   12   15   18   18   18   19   21   21   23   24   24   25   26   26   26   26   26   26 
LCS_GDT     D      33     D      33     11   18   26     4    6    9   13   18   18   18   19   21   21   23   24   24   25   26   26   26   26   26   26 
LCS_GDT     E      34     E      34     11   18   26     4    8   12   15   18   18   18   19   21   21   23   24   24   25   26   26   26   26   26   26 
LCS_GDT     G      35     G      35     12   18   26     5   10   13   15   18   18   18   19   21   21   23   24   24   25   26   26   26   26   26   26 
LCS_GDT     I      36     I      36     12   18   26     3   10   13   15   18   18   18   19   21   21   23   24   24   25   26   26   26   26   26   26 
LCS_GDT     T      37     T      37     12   18   26     7   10   13   15   18   18   18   19   21   21   23   24   24   25   26   26   26   26   26   26 
LCS_GDT     V      38     V      38     12   18   26     5   10   13   15   18   18   18   19   21   21   23   24   24   25   26   26   26   26   26   26 
LCS_GDT     Q      39     Q      39     12   18   26     7   10   13   15   18   18   18   19   21   21   23   24   24   25   26   26   26   26   26   26 
LCS_GDT     T      40     T      40     12   18   26     7   10   13   15   18   18   18   19   21   21   23   24   24   25   26   26   26   26   26   26 
LCS_GDT     A      41     A      41     12   18   26     7   10   13   15   18   18   18   19   21   21   23   24   24   25   26   26   26   26   26   26 
LCS_GDT     I      42     I      42     12   18   26     7   10   13   15   18   18   18   19   21   21   23   24   24   25   26   26   26   26   26   26 
LCS_GDT     T      43     T      43     12   18   26     7   10   13   15   18   18   18   19   21   21   23   24   24   25   26   26   26   26   26   26 
LCS_GDT     Q      44     Q      44     12   18   26     7    9   13   15   18   18   18   19   21   21   23   24   24   25   26   26   26   26   26   26 
LCS_GDT     S      45     S      45     12   18   26     7   10   13   15   18   18   18   19   21   21   23   24   24   25   26   26   26   26   26   26 
LCS_GDT     G      46     G      46     12   18   26     3    5   13   15   18   18   18   19   21   21   23   24   24   25   26   26   26   26   26   26 
LCS_GDT     I      47     I      47      8   18   26     3    5    9   14   18   18   18   19   21   21   23   24   24   25   26   26   26   26   26   26 
LCS_GDT     L      48     L      48      5   18   26     0    5    6   12   18   18   18   19   21   21   23   24   24   25   26   26   26   26   26   26 
LCS_GDT     S      49     S      49      4    5   26     3    4    4    5    6    9   11   19   21   21   23   24   24   25   26   26   26   26   26   26 
LCS_GDT     Q      50     Q      50      4    5   26     3    4    4    5    6    9   11   14   17   20   22   24   24   25   26   26   26   26   26   26 
LCS_GDT     F      51     F      51      4    5   26     3    4    4    5    5    9   14   19   21   21   23   24   24   25   26   26   26   26   26   26 
LCS_GDT     P      52     P      52      4    5   26     3    4    4    5    6    9   11   18   21   21   23   24   24   25   26   26   26   26   26   26 
LCS_GDT     E      53     E      53      4    5   26     0    4    4    5    6    9   11   14   16   20   23   24   24   25   26   26   26   26   26   26 
LCS_GDT     I      54     I      54      4    5   26     3    4    4    4    6    9   11   14   16   20   23   24   24   25   26   26   26   26   26   26 
LCS_GDT     D      55     D      55      4    5   26     3    4    4    4    5    9   11   14   15   17   18   21   24   25   26   26   26   26   26   26 
LCS_GDT     L      56     L      56      4    5   26     3    4    4    4    5    9   11   14   15   17   18   21   24   25   26   26   26   26   26   26 
LCS_AVERAGE  LCS_A:  35.48  (  19.48   30.43   56.52 )

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     13     15     18     18     18     19     21     21     23     24     24     25     26     26     26     26     26     26 
GDT PERCENT_CA  15.22  21.74  28.26  32.61  39.13  39.13  39.13  41.30  45.65  45.65  50.00  52.17  52.17  54.35  56.52  56.52  56.52  56.52  56.52  56.52
GDT RMS_LOCAL    0.26   0.69   0.99   1.21   1.62   1.62   1.62   2.36   3.07   3.07   3.65   3.82   3.82   4.49   4.54   4.54   4.54   4.54   4.54   4.54
GDT RMS_ALL_CA   8.10   7.48   7.34   7.20   6.82   6.82   6.82   6.23   5.43   5.43   4.88   4.86   4.86   4.58   4.54   4.54   4.54   4.54   4.54   4.54

#      Molecule1      Molecule2       DISTANCE
LGA    Q      31      Q      31          1.676
LGA    V      32      V      32          1.252
LGA    D      33      D      33          2.765
LGA    E      34      E      34          2.408
LGA    G      35      G      35          2.721
LGA    I      36      I      36          2.093
LGA    T      37      T      37          2.435
LGA    V      38      V      38          2.960
LGA    Q      39      Q      39          2.834
LGA    T      40      T      40          0.718
LGA    A      41      A      41          0.662
LGA    I      42      I      42          2.742
LGA    T      43      T      43          2.680
LGA    Q      44      Q      44          2.596
LGA    S      45      S      45          3.172
LGA    G      46      G      46          3.735
LGA    I      47      I      47          3.494
LGA    L      48      L      48          2.035
LGA    S      49      S      49          5.522
LGA    Q      50      Q      50          5.450
LGA    F      51      F      51          3.991
LGA    P      52      P      52          7.809
LGA    E      53      E      53         10.022
LGA    I      54      I      54         10.558
LGA    D      55      D      55         15.712
LGA    L      56      L      56         15.231

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   26   46    4.0     19    2.36    38.043    37.862     0.772

LGA_LOCAL      RMSD =  2.360  Number of atoms =   19  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.022  Number of atoms =   26 
Std_ALL_ATOMS  RMSD =  4.540  (standard rmsd on all 26 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.461108 * X  +  -0.810538 * Y  +  -0.361119 * Z  +  26.532534
  Y_new =   0.814756 * X  +   0.225531 * Y  +   0.534143 * Z  +  14.762741
  Z_new =  -0.351500 * X  +  -0.540522 * Y  +   0.764385 * Z  +   6.891953 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.615497    2.526096  [ DEG:   -35.2654    144.7346 ]
  Theta =   0.359173    2.782420  [ DEG:    20.5791    159.4209 ]
  Phi   =   1.055793   -2.085800  [ DEG:    60.4925   -119.5075 ]
 
# 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: T0363AL242_1-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0363AL242_1-D1.T0363_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   26   46   4.0   19   2.36  37.862     4.54
REMARK  ---------------------------------------------------------- 
MOLECULE T0363AL242_1-D1
REMARK Aligment from pdb entry: 1f0z_A
ATOM     41  N   GLN    31      20.323   4.857   3.407  1.00  0.00              
ATOM     42  CA  GLN    31      20.190   4.027   4.631  1.00  0.00              
ATOM     43  C   GLN    31      21.591   3.729   5.146  1.00  0.00              
ATOM     44  O   GLN    31      22.407   3.116   4.486  1.00  0.00              
ATOM     45  N   VAL    32      21.861   4.195   6.308  1.00  0.00              
ATOM     46  CA  VAL    32      23.214   4.006   6.923  1.00  0.00              
ATOM     47  C   VAL    32      23.118   3.565   8.385  1.00  0.00              
ATOM     48  O   VAL    32      22.126   3.016   8.823  1.00  0.00              
ATOM     49  N   ASP    33      24.173   3.781   9.126  1.00  0.00              
ATOM     50  CA  ASP    33      24.212   3.368  10.554  1.00  0.00              
ATOM     51  C   ASP    33      23.646   4.445  11.482  1.00  0.00              
ATOM     52  O   ASP    33      24.318   5.402  11.813  1.00  0.00              
ATOM     53  N   GLU    34      22.431   4.286  11.926  1.00  0.00              
ATOM     54  CA  GLU    34      21.850   5.295  12.858  1.00  0.00              
ATOM     55  C   GLU    34      22.744   5.447  14.087  1.00  0.00              
ATOM     56  O   GLU    34      23.252   4.483  14.628  1.00  0.00              
ATOM     57  N   GLY    35      22.930   6.650  14.526  1.00  0.00              
ATOM     58  CA  GLY    35      23.777   6.903  15.716  1.00  0.00              
ATOM     59  C   GLY    35      25.202   7.207  15.261  1.00  0.00              
ATOM     60  O   GLY    35      26.026   7.676  16.019  1.00  0.00              
ATOM     61  N   ILE    36      25.490   6.951  14.018  1.00  0.00              
ATOM     62  CA  ILE    36      26.852   7.225  13.486  1.00  0.00              
ATOM     63  C   ILE    36      26.989   8.716  13.137  1.00  0.00              
ATOM     64  O   ILE    36      26.220   9.235  12.368  1.00  0.00              
ATOM     65  N   THR    37      27.941   9.421  13.690  1.00  0.00              
ATOM     66  CA  THR    37      28.055  10.871  13.347  1.00  0.00              
ATOM     67  C   THR    37      28.090  11.074  11.846  1.00  0.00              
ATOM     68  O   THR    37      27.895  10.177  11.059  1.00  0.00              
ATOM     69  N   VAL    38      28.410  12.272  11.479  1.00  0.00              
ATOM     70  CA  VAL    38      28.559  12.653  10.056  1.00  0.00              
ATOM     71  C   VAL    38      29.854  12.090   9.552  1.00  0.00              
ATOM     72  O   VAL    38      29.902  11.328   8.616  1.00  0.00              
ATOM     73  N   GLN    39      30.923  12.408  10.240  1.00  0.00              
ATOM     74  CA  GLN    39      32.216  11.822   9.859  1.00  0.00              
ATOM     75  C   GLN    39      31.956  10.336   9.753  1.00  0.00              
ATOM     76  O   GLN    39      32.570   9.614   8.989  1.00  0.00              
ATOM     77  N   THR    40      30.973   9.902  10.504  1.00  0.00              
ATOM     78  CA  THR    40      30.581   8.471  10.450  1.00  0.00              
ATOM     79  C   THR    40      29.618   8.281   9.277  1.00  0.00              
ATOM     80  O   THR    40      29.668   7.297   8.565  1.00  0.00              
ATOM     81  N   ALA    41      28.748   9.236   9.065  1.00  0.00              
ATOM     82  CA  ALA    41      27.783   9.141   7.932  1.00  0.00              
ATOM     83  C   ALA    41      28.543   9.272   6.618  1.00  0.00              
ATOM     84  O   ALA    41      28.532   8.392   5.789  1.00  0.00              
ATOM     85  N   ILE    42      29.216  10.370   6.441  1.00  0.00              
ATOM     86  CA  ILE    42      29.995  10.591   5.197  1.00  0.00              
ATOM     87  C   ILE    42      30.915   9.412   4.946  1.00  0.00              
ATOM     88  O   ILE    42      30.887   8.792   3.903  1.00  0.00              
ATOM     89  N   THR    43      31.727   9.098   5.904  1.00  0.00              
ATOM     90  CA  THR    43      32.652   7.945   5.725  1.00  0.00              
ATOM     91  C   THR    43      31.857   6.677   5.426  1.00  0.00              
ATOM     92  O   THR    43      32.238   5.880   4.593  1.00  0.00              
ATOM     93  N   GLN    44      30.746   6.478   6.087  1.00  0.00              
ATOM     94  CA  GLN    44      29.948   5.257   5.802  1.00  0.00              
ATOM     95  C   GLN    44      29.490   5.308   4.354  1.00  0.00              
ATOM     96  O   GLN    44      29.624   4.358   3.607  1.00  0.00              
ATOM     97  N   SER    45      28.975   6.432   3.953  1.00  0.00              
ATOM     98  CA  SER    45      28.525   6.599   2.558  1.00  0.00              
ATOM     99  C   SER    45      29.729   6.473   1.636  1.00  0.00              
ATOM    100  O   SER    45      29.578   6.234   0.460  1.00  0.00              
ATOM    101  N   GLY    46      30.913   6.668   2.194  1.00  0.00              
ATOM    102  CA  GLY    46      32.206   6.610   1.431  1.00  0.00              
ATOM    103  C   GLY    46      32.575   8.023   1.006  1.00  0.00              
ATOM    104  O   GLY    46      33.146   8.250  -0.041  1.00  0.00              
ATOM    105  N   ILE    47      32.241   8.979   1.823  1.00  0.00              
ATOM    106  CA  ILE    47      32.556  10.389   1.486  1.00  0.00              
ATOM    107  C   ILE    47      33.414  10.986   2.601  1.00  0.00              
ATOM    108  O   ILE    47      33.260  10.649   3.757  1.00  0.00              
ATOM    109  N   LEU    48      34.316  11.864   2.269  1.00  0.00              
ATOM    110  CA  LEU    48      35.176  12.472   3.323  1.00  0.00              
ATOM    111  C   LEU    48      34.867  13.968   3.441  1.00  0.00              
ATOM    112  O   LEU    48      33.796  14.350   3.873  1.00  0.00              
ATOM    113  N   SER    49      35.779  14.821   3.055  1.00  0.00              
ATOM    114  CA  SER    49      35.513  16.285   3.142  1.00  0.00              
ATOM    115  C   SER    49      36.365  17.037   2.117  1.00  0.00              
ATOM    116  O   SER    49      35.872  17.497   1.106  1.00  0.00              
ATOM    117  N   GLN    50      37.640  17.169   2.368  1.00  0.00              
ATOM    118  CA  GLN    50      38.515  17.897   1.404  1.00  0.00              
ATOM    119  C   GLN    50      38.055  19.332   1.277  1.00  0.00              
ATOM    120  O   GLN    50      38.389  20.025   0.335  1.00  0.00              
ATOM    121  N   PHE    51      37.271  19.781   2.198  1.00  0.00              
ATOM    122  CA  PHE    51      36.771  21.163   2.103  1.00  0.00              
ATOM    123  C   PHE    51      35.263  21.116   1.873  1.00  0.00              
ATOM    124  O   PHE    51      34.763  21.626   0.894  1.00  0.00              
ATOM    125  N   PRO    52      34.531  20.482   2.748  1.00  0.00              
ATOM    126  CA  PRO    52      33.060  20.392   2.537  1.00  0.00              
ATOM    127  C   PRO    52      32.284  20.731   3.804  1.00  0.00              
ATOM    128  O   PRO    52      32.680  20.396   4.902  1.00  0.00              
ATOM    129  N   GLU    53      31.148  21.338   3.639  1.00  0.00              
ATOM    130  CA  GLU    53      30.279  21.649   4.800  1.00  0.00              
ATOM    131  C   GLU    53      28.914  21.025   4.503  1.00  0.00              
ATOM    132  O   GLU    53      28.641  20.671   3.378  1.00  0.00              
ATOM    133  N   ILE    54      28.078  20.829   5.484  1.00  0.00              
ATOM    134  CA  ILE    54      26.764  20.172   5.202  1.00  0.00              
ATOM    135  C   ILE    54      25.684  20.672   6.170  1.00  0.00              
ATOM    136  O   ILE    54      25.977  21.089   7.274  1.00  0.00              
ATOM    137  N   ASP    55      24.436  20.613   5.776  1.00  0.00              
ATOM    138  CA  ASP    55      23.352  21.061   6.700  1.00  0.00              
ATOM    139  C   ASP    55      22.426  19.887   6.998  1.00  0.00              
ATOM    140  O   ASP    55      21.793  19.348   6.113  1.00  0.00              
ATOM    141  N   LEU    56      22.330  19.477   8.231  1.00  0.00              
ATOM    142  CA  LEU    56      21.425  18.332   8.533  1.00  0.00              
ATOM    143  C   LEU    56      20.152  18.851   9.203  1.00  0.00              
ATOM    144  O   LEU    56      20.200  19.696  10.069  1.00  0.00              
END
