
#######################################################
#                                                     #
#                        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   33 (  132),  selected   33 , name T0363AL242_3-D1
# Molecule2: number of CA atoms   46 (  372),  selected   33 , name T0363_D1.pdb
# PARAMETERS: T0363AL242_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:    18        38 - 55          4.77    12.98
  LONGEST_CONTINUOUS_SEGMENT:    18        39 - 56          4.83    13.48
  LCS_AVERAGE:     31.95

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9        11 - 19          0.57    13.18
  LCS_AVERAGE:     14.56

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9        11 - 19          0.57    13.18
  LCS_AVERAGE:     13.18

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     N      11     N      11      9    9    9     7    9    9   10   10   10   10   11   11   11   12   12   13   14   15   15   16   22   24   25 
LCS_GDT     Q      12     Q      12      9    9    9     7    9    9   10   10   10   10   11   11   11   12   12   13   16   18   20   22   23   24   25 
LCS_GDT     I      13     I      13      9    9    9     4    9    9   10   10   10   10   11   11   11   12   12   13   16   18   20   22   23   24   25 
LCS_GDT     N      14     N      14      9    9    9     7    9    9   10   10   10   10   11   11   14   14   15   17   17   18   20   22   23   24   25 
LCS_GDT     I      15     I      15      9    9    9     7    9    9   10   10   10   10   11   11   14   14   15   17   17   18   20   22   23   24   25 
LCS_GDT     E      16     E      16      9    9    9     7    9    9   10   10   10   10   11   12   13   14   16   17   17   18   20   22   23   24   25 
LCS_GDT     I      17     I      17      9    9    9     7    9    9   10   10   10   12   12   13   13   14   16   17   17   18   20   22   23   24   25 
LCS_GDT     A      18     A      18      9    9    9     7    9    9   10   10   10   12   12   13   13   14   16   17   17   18   20   22   23   24   25 
LCS_GDT     Y      19     Y      19      9    9    9     4    9    9   10   10   10   10   11   11   12   14   16   17   17   18   20   22   23   24   25 
LCS_GDT     D      33     D      33      3    4   10     3    3    3    4    5    5    7    8    8   10   11   12   14   15   16   17   18   19   20   21 
LCS_GDT     E      34     E      34      3    5   13     3    3    3    5    5    6    7    8    8   10   11   12   14   15   16   17   18   19   20   21 
LCS_GDT     G      35     G      35      5    5   13     4    4    5    5    5    6    7    8    8   11   13   15   16   17   18   19   19   20   22   23 
LCS_GDT     I      36     I      36      5    5   13     4    4    5    5    5    6    8    9   11   14   14   15   17   17   18   19   21   22   23   25 
LCS_GDT     T      37     T      37      5    5   13     4    4    5    5    5    7    9   10   11   14   14   15   17   18   18   20   21   22   23   25 
LCS_GDT     V      38     V      38      5    5   18     4    4    5    5    5    7    9   10   12   14   14   15   17   18   18   20   21   22   23   25 
LCS_GDT     Q      39     Q      39      5    5   18     0    3    5    6    7    8    9   10   12   13   14   15   16   18   18   20   21   22   23   25 
LCS_GDT     T      40     T      40      3    3   18     0    3    3    6    7    8    9   10   12   13   14   15   16   18   18   20   21   22   23   25 
LCS_GDT     A      41     A      41      4    4   18     3    4    5    6    7    8    9   10   12   13   14   15   16   18   18   20   22   23   24   25 
LCS_GDT     I      42     I      42      4    4   18     3    4    4    4    4    4    5    6   11   13   13   15   16   17   18   18   19   20   21   25 
LCS_GDT     T      43     T      43      4    4   18     3    4    4    4    4    4    8    8    9   11   12   15   16   17   18   20   22   23   24   25 
LCS_GDT     Q      44     Q      44      4    4   18     3    4    5    5    7    8    9   10   12   13   14   16   17   18   18   20   22   23   24   25 
LCS_GDT     S      45     S      45      4    8   18     3    4    5    6    7    8    9   10   12   13   14   16   17   18   18   20   22   23   24   25 
LCS_GDT     G      46     G      46      7    8   18     6    7    7    7    7   10   12   12   13   14   14   16   17   18   18   20   22   23   24   25 
LCS_GDT     I      47     I      47      7    8   18     6    7    7    7    7   10   12   12   13   14   14   16   17   18   18   20   22   23   24   25 
LCS_GDT     L      48     L      48      7    8   18     6    7    7    7    7   10   12   12   13   14   14   16   17   18   18   20   22   23   24   25 
LCS_GDT     S      49     S      49      7    8   18     6    7    7    7    7   10   12   12   13   14   14   16   17   18   18   20   22   23   24   25 
LCS_GDT     Q      50     Q      50      7    8   18     6    7    7    7    7    9   12   12   13   13   14   16   17   18   18   20   22   23   24   25 
LCS_GDT     F      51     F      51      7    8   18     6    7    7    7    7    7    9   11   13   13   14   16   17   18   18   20   22   23   24   25 
LCS_GDT     P      52     P      52      7    8   18     4    7    7    7    7   10   12   12   13   14   14   16   17   18   18   20   22   23   24   25 
LCS_GDT     E      53     E      53      4    8   18     4    4    4    6    6   10   12   12   13   14   14   16   17   18   18   20   22   23   24   25 
LCS_GDT     I      54     I      54      4    5   18     4    4    4    6    6   10   12   12   13   14   14   16   17   18   18   20   22   23   24   25 
LCS_GDT     D      55     D      55      4    5   18     3    4    4    6    6   10   12   12   13   14   14   16   17   18   18   20   22   23   24   25 
LCS_GDT     L      56     L      56      4    5   18     3    4    4   10   10   10   12   12   13   14   14   15   17   18   18   20   21   23   24   25 
LCS_AVERAGE  LCS_A:  19.89  (  13.18   14.56   31.95 )

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      9      9     10     10     10     12     12     13     14     14     16     17     18     18     20     22     23     24     25 
GDT PERCENT_CA  15.22  19.57  19.57  21.74  21.74  21.74  26.09  26.09  28.26  30.43  30.43  34.78  36.96  39.13  39.13  43.48  47.83  50.00  52.17  54.35
GDT RMS_LOCAL    0.25   0.57   0.57   1.03   1.03   1.03   2.64   2.64   2.87   3.85   3.17   4.51   4.44   4.70   4.70   5.32   6.13   6.34   6.55   6.90
GDT RMS_ALL_CA  13.11  13.18  13.18  13.55  13.55  13.55  15.47  15.47  15.63  10.35  14.47  13.52  10.28  11.22  11.22  10.73  11.91  11.74  11.87  11.85

#      Molecule1      Molecule2       DISTANCE
LGA    N      11      N      11         33.166
LGA    Q      12      Q      12         28.084
LGA    I      13      I      13         23.005
LGA    N      14      N      14         18.069
LGA    I      15      I      15         12.715
LGA    E      16      E      16          7.072
LGA    I      17      I      17          3.149
LGA    A      18      A      18          3.416
LGA    Y      19      Y      19          7.613
LGA    D      33      D      33         21.929
LGA    E      34      E      34         23.290
LGA    G      35      G      35         21.851
LGA    I      36      I      36         19.516
LGA    T      37      T      37         19.453
LGA    V      38      V      38         18.541
LGA    Q      39      Q      39         19.927
LGA    T      40      T      40         22.090
LGA    A      41      A      41         19.412
LGA    I      42      I      42         20.145
LGA    T      43      T      43         18.584
LGA    Q      44      Q      44         14.977
LGA    S      45      S      45          9.928
LGA    G      46      G      46          3.439
LGA    I      47      I      47          2.580
LGA    L      48      L      48          2.543
LGA    S      49      S      49          1.446
LGA    Q      50      Q      50          3.157
LGA    F      51      F      51          4.678
LGA    P      52      P      52          2.630
LGA    E      53      E      53          1.868
LGA    I      54      I      54          2.089
LGA    D      55      D      55          2.066
LGA    L      56      L      56          2.795

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   33   46    4.0     12    2.64    27.717    23.996     0.438

LGA_LOCAL      RMSD =  2.639  Number of atoms =   12  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 15.629  Number of atoms =   33 
Std_ALL_ATOMS  RMSD =  9.915  (standard rmsd on all 33 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.255784 * X  +   0.414130 * Y  +  -0.873539 * Z  +  29.456730
  Y_new =   0.689147 * X  +  -0.555587 * Y  +  -0.465187 * Z  +  14.724278
  Z_new =  -0.677975 * X  +  -0.720984 * Y  +  -0.143286 * Z  +   3.154771 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.766977    1.374616  [ DEG:  -101.2403     78.7597 ]
  Theta =   0.745005    2.396588  [ DEG:    42.6856    137.3144 ]
  Phi   =   1.926197   -1.215396  [ DEG:   110.3630    -69.6370 ]
 
# 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_3-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0363AL242_3-D1.T0363_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   33   46   4.0   12   2.64  23.996     9.92
REMARK  ---------------------------------------------------------- 
MOLECULE T0363AL242_3-D1
REMARK Aligment from pdb entry: 1ryj_A
ATOM      9  N   ASN    11      31.045  13.217 -16.493  1.00  0.00              
ATOM     10  CA  ASN    11      31.413  13.272 -15.087  1.00  0.00              
ATOM     11  C   ASN    11      31.053  14.621 -14.485  1.00  0.00              
ATOM     12  O   ASN    11      31.334  15.673 -15.066  1.00  0.00              
ATOM     13  N   GLN    12      30.418  14.575 -13.324  1.00  0.00              
ATOM     14  CA  GLN    12      29.968  15.777 -12.656  1.00  0.00              
ATOM     15  C   GLN    12      28.889  15.461 -11.644  1.00  0.00              
ATOM     16  O   GLN    12      27.751  15.167 -12.014  1.00  0.00              
ATOM     17  N   ILE    13      29.246  15.506 -10.372  1.00  0.00              
ATOM     18  CA  ILE    13      28.327  15.113  -9.314  1.00  0.00              
ATOM     19  C   ILE    13      27.885  16.319  -8.496  1.00  0.00              
ATOM     20  O   ILE    13      28.708  17.121  -8.061  1.00  0.00              
ATOM     21  N   ASN    14      26.587  16.450  -8.298  1.00  0.00              
ATOM     22  CA  ASN    14      26.054  17.493  -7.442  1.00  0.00              
ATOM     23  C   ASN    14      25.378  16.872  -6.232  1.00  0.00              
ATOM     24  O   ASN    14      24.517  16.002  -6.363  1.00  0.00              
ATOM     25  N   ILE    15      25.783  17.312  -5.055  1.00  0.00              
ATOM     26  CA  ILE    15      25.293  16.738  -3.816  1.00  0.00              
ATOM     27  C   ILE    15      25.022  17.832  -2.800  1.00  0.00              
ATOM     28  O   ILE    15      25.418  18.984  -2.997  1.00  0.00              
ATOM     29  N   GLU    16      24.345  17.484  -1.722  1.00  0.00              
ATOM     30  CA  GLU    16      24.057  18.450  -0.686  1.00  0.00              
ATOM     31  C   GLU    16      24.546  17.957   0.667  1.00  0.00              
ATOM     32  O   GLU    16      24.330  16.802   1.043  1.00  0.00              
ATOM     33  N   ILE    17      25.244  18.828   1.370  1.00  0.00              
ATOM     34  CA  ILE    17      25.670  18.553   2.726  1.00  0.00              
ATOM     35  C   ILE    17      24.872  19.426   3.681  1.00  0.00              
ATOM     36  O   ILE    17      24.915  20.648   3.586  1.00  0.00              
ATOM     37  N   ALA    18      24.127  18.809   4.580  1.00  0.00              
ATOM     38  CA  ALA    18      23.298  19.564   5.504  1.00  0.00              
ATOM     39  C   ALA    18      23.988  19.664   6.861  1.00  0.00              
ATOM     40  O   ALA    18      24.473  18.672   7.406  1.00  0.00              
ATOM     41  N   TYR    19      24.082  20.885   7.365  1.00  0.00              
ATOM     42  CA  TYR    19      24.683  21.153   8.664  1.00  0.00              
ATOM     43  C   TYR    19      23.876  22.250   9.370  1.00  0.00              
ATOM     44  O   TYR    19      22.738  22.516   8.984  1.00  0.00              
ATOM     45  N   ASP    33      24.448  22.880  10.396  1.00  0.00              
ATOM     46  CA  ASP    33      23.789  23.991  11.090  1.00  0.00              
ATOM     47  C   ASP    33      23.533  25.146  10.129  1.00  0.00              
ATOM     48  O   ASP    33      22.602  25.930  10.304  1.00  0.00              
ATOM     49  N   GLU    34      24.378  25.228   9.106  1.00  0.00              
ATOM     50  CA  GLU    34      24.267  26.250   8.067  1.00  0.00              
ATOM     51  C   GLU    34      23.105  25.931   7.123  1.00  0.00              
ATOM     52  O   GLU    34      22.703  26.754   6.301  1.00  0.00              
ATOM     53  N   GLY    35      22.548  24.737   7.274  1.00  0.00              
ATOM     54  CA  GLY    35      21.473  24.295   6.414  1.00  0.00              
ATOM     55  C   GLY    35      21.976  23.366   5.333  1.00  0.00              
ATOM     56  O   GLY    35      23.082  22.831   5.438  1.00  0.00              
ATOM     57  N   ILE    36      21.170  23.163   4.304  1.00  0.00              
ATOM     58  CA  ILE    36      21.583  22.366   3.163  1.00  0.00              
ATOM     59  C   ILE    36      22.520  23.163   2.273  1.00  0.00              
ATOM     60  O   ILE    36      22.152  24.214   1.740  1.00  0.00              
ATOM     61  N   THR    37      23.731  22.663   2.125  1.00  0.00              
ATOM     62  CA  THR    37      24.742  23.311   1.309  1.00  0.00              
ATOM     63  C   THR    37      24.854  22.579  -0.023  1.00  0.00              
ATOM     64  O   THR    37      25.106  21.375  -0.056  1.00  0.00              
ATOM     65  N   VAL    38      24.639  23.300  -1.112  1.00  0.00              
ATOM     66  CA  VAL    38      24.675  22.704  -2.440  1.00  0.00              
ATOM     67  C   VAL    38      26.004  22.985  -3.126  1.00  0.00              
ATOM     68  O   VAL    38      26.394  24.141  -3.307  1.00  0.00              
ATOM     69  N   GLN    39      26.706  21.921  -3.480  1.00  0.00              
ATOM     70  CA  GLN    39      27.959  22.039  -4.204  1.00  0.00              
ATOM     71  C   GLN    39      28.100  20.891  -5.195  1.00  0.00              
ATOM     72  O   GLN    39      27.703  19.757  -4.909  1.00  0.00              
ATOM     73  N   THR    40      28.635  21.187  -6.369  1.00  0.00              
ATOM     74  CA  THR    40      28.843  20.166  -7.378  1.00  0.00              
ATOM     75  C   THR    40      30.316  20.079  -7.764  1.00  0.00              
ATOM     76  O   THR    40      31.004  21.091  -7.888  1.00  0.00              
ATOM     77  N   ALA    41      30.790  18.856  -7.929  1.00  0.00              
ATOM     78  CA  ALA    41      32.187  18.598  -8.233  1.00  0.00              
ATOM     79  C   ALA    41      32.289  17.869  -9.570  1.00  0.00              
ATOM     80  O   ALA    41      31.583  16.886  -9.803  1.00  0.00              
ATOM     81  N   ILE    42      33.157  18.362 -10.445  1.00  0.00              
ATOM     82  CA  ILE    42      33.307  17.779 -11.767  1.00  0.00              
ATOM     83  C   ILE    42      33.809  16.348 -11.727  1.00  0.00              
ATOM     84  O   ILE    42      33.473  15.541 -12.595  1.00  0.00              
ATOM     85  N   THR    43      34.624  16.034 -10.734  1.00  0.00              
ATOM     86  CA  THR    43      35.146  14.687 -10.578  1.00  0.00              
ATOM     87  C   THR    43      34.473  13.982  -9.405  1.00  0.00              
ATOM     88  O   THR    43      34.471  14.494  -8.286  1.00  0.00              
ATOM     89  N   GLN    44      33.864  12.813  -9.656  1.00  0.00              
ATOM     90  CA  GLN    44      33.256  11.990  -8.604  1.00  0.00              
ATOM     91  C   GLN    44      34.301  11.489  -7.609  1.00  0.00              
ATOM     92  O   GLN    44      35.144  10.653  -7.941  1.00  0.00              
ATOM     93  N   SER    45      34.241  12.007  -6.391  1.00  0.00              
ATOM     94  CA  SER    45      35.279  11.766  -5.399  1.00  0.00              
ATOM     95  C   SER    45      34.733  11.047  -4.171  1.00  0.00              
ATOM     96  O   SER    45      33.534  10.780  -4.067  1.00  0.00              
ATOM     97  N   GLY    46      35.630  10.740  -3.252  1.00  0.00              
ATOM     98  CA  GLY    46      35.295  10.045  -2.024  1.00  0.00              
ATOM     99  C   GLY    46      34.937  11.054  -0.934  1.00  0.00              
ATOM    100  O   GLY    46      35.324  12.223  -1.021  1.00  0.00              
ATOM    101  N   ILE    47      34.183  10.611   0.077  1.00  0.00              
ATOM    102  CA  ILE    47      33.814  11.467   1.208  1.00  0.00              
ATOM    103  C   ILE    47      35.052  12.153   1.778  1.00  0.00              
ATOM    104  O   ILE    47      35.063  13.367   1.982  1.00  0.00              
ATOM    105  N   LEU    48      36.099  11.365   1.991  1.00  0.00              
ATOM    106  CA  LEU    48      37.332  11.847   2.600  1.00  0.00              
ATOM    107  C   LEU    48      37.973  12.971   1.794  1.00  0.00              
ATOM    108  O   LEU    48      38.644  13.829   2.359  1.00  0.00              
ATOM    109  N   SER    49      37.771  12.970   0.483  1.00  0.00              
ATOM    110  CA  SER    49      38.365  13.996  -0.373  1.00  0.00              
ATOM    111  C   SER    49      37.790  15.363  -0.037  1.00  0.00              
ATOM    112  O   SER    49      38.506  16.263   0.395  1.00  0.00              
ATOM    113  N   GLN    50      36.483  15.504  -0.219  1.00  0.00              
ATOM    114  CA  GLN    50      35.805  16.765   0.047  1.00  0.00              
ATOM    115  C   GLN    50      35.874  17.109   1.530  1.00  0.00              
ATOM    116  O   GLN    50      36.076  18.268   1.904  1.00  0.00              
ATOM    117  N   PHE    51      35.735  16.091   2.371  1.00  0.00              
ATOM    118  CA  PHE    51      35.805  16.270   3.814  1.00  0.00              
ATOM    119  C   PHE    51      37.189  16.766   4.221  1.00  0.00              
ATOM    120  O   PHE    51      37.315  17.630   5.081  1.00  0.00              
ATOM    121  N   PRO    52      38.220  16.201   3.594  1.00  0.00              
ATOM    122  CA  PRO    52      39.588  16.589   3.877  1.00  0.00              
ATOM    123  C   PRO    52      39.944  17.973   3.355  1.00  0.00              
ATOM    124  O   PRO    52      40.721  18.694   3.981  1.00  0.00              
ATOM    125  N   GLU    53      39.388  18.348   2.204  1.00  0.00              
ATOM    126  CA  GLU    53      39.665  19.659   1.613  1.00  0.00              
ATOM    127  C   GLU    53      39.135  20.786   2.492  1.00  0.00              
ATOM    128  O   GLU    53      39.799  21.803   2.685  1.00  0.00              
ATOM    129  N   ILE    54      37.936  20.604   3.025  1.00  0.00              
ATOM    130  CA  ILE    54      37.369  21.563   3.969  1.00  0.00              
ATOM    131  C   ILE    54      37.843  21.237   5.380  1.00  0.00              
ATOM    132  O   ILE    54      37.635  22.012   6.315  1.00  0.00              
ATOM    133  N   ASP    55      38.501  20.087   5.490  1.00  0.00              
ATOM    134  CA  ASP    55      38.930  19.502   6.758  1.00  0.00              
ATOM    135  C   ASP    55      37.869  19.663   7.839  1.00  0.00              
ATOM    136  O   ASP    55      38.018  20.456   8.773  1.00  0.00              
ATOM    137  N   LEU    56      36.777  18.936   7.683  1.00  0.00              
ATOM    138  CA  LEU    56      35.741  18.910   8.696  1.00  0.00              
ATOM    139  C   LEU    56      36.008  17.747   9.636  1.00  0.00              
ATOM    140  O   LEU    56      35.932  16.585   9.234  1.00  0.00              
END
