
#######################################################
#                                                     #
#                        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   21 (   84),  selected   21 , name T0306AL381_2
# Molecule2: number of CA atoms   95 (  694),  selected   21 , name T0306.pdb
# PARAMETERS: T0306AL381_2.T0306.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:    21        44 - 64          3.78     3.78
  LCS_AVERAGE:     22.11

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12        53 - 64          1.92     5.54
  LCS_AVERAGE:     11.08

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8        57 - 64          0.48     6.33
  LCS_AVERAGE:      5.96

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:   95
LCS_GDT     I      44     I      44      3    5   21     3    3    4    7   10   12   14   15   17   18   20   20   21   21   21   21   21   21   21   21 
LCS_GDT     D      45     D      45      3    5   21     3    3    4    4   10   12   14   15   17   18   20   20   21   21   21   21   21   21   21   21 
LCS_GDT     N      46     N      46      3    6   21     3    3    4    4   10   10   13   15   15   17   20   20   21   21   21   21   21   21   21   21 
LCS_GDT     I      47     I      47      3    6   21     3    3    6    7   10   12   14   15   17   18   20   20   21   21   21   21   21   21   21   21 
LCS_GDT     G      48     G      48      4   11   21     3    3    4    6   10   13   14   16   17   18   20   20   21   21   21   21   21   21   21   21 
LCS_GDT     A      49     A      49      4   11   21     3    3    8   10   12   14   15   16   17   18   20   20   21   21   21   21   21   21   21   21 
LCS_GDT     G      50     G      50      4   11   21     3    5    8   10   12   14   15   16   17   18   20   20   21   21   21   21   21   21   21   21 
LCS_GDT     T      51     T      51      4   11   21     3    4    6    9   12   14   15   16   16   18   20   20   21   21   21   21   21   21   21   21 
LCS_GDT     G      52     G      52      3   11   21     3    3    4    6    9    9   14   15   16   18   20   20   21   21   21   21   21   21   21   21 
LCS_GDT     E      53     E      53      6   12   21     4    5    6    9   12   14   15   16   17   18   20   20   21   21   21   21   21   21   21   21 
LCS_GDT     W      54     W      54      6   12   21     4    5    6    9   12   13   15   16   17   18   20   20   21   21   21   21   21   21   21   21 
LCS_GDT     V      55     V      55      6   12   21     4    5    8   10   12   14   15   16   17   18   20   20   21   21   21   21   21   21   21   21 
LCS_GDT     L      56     L      56      6   12   21     4    5    8   10   12   14   15   16   17   18   20   20   21   21   21   21   21   21   21   21 
LCS_GDT     L      57     L      57      8   12   21     5    8    8   10   12   14   15   16   17   18   20   20   21   21   21   21   21   21   21   21 
LCS_GDT     V      58     V      58      8   12   21     4    8    8   10   12   14   15   16   17   18   20   20   21   21   21   21   21   21   21   21 
LCS_GDT     S      59     S      59      8   12   21     4    8    8   10   12   14   15   16   17   18   20   20   21   21   21   21   21   21   21   21 
LCS_GDT     G      60     G      60      8   12   21     5    8    8   10   12   14   15   16   17   18   20   20   21   21   21   21   21   21   21   21 
LCS_GDT     S      61     S      61      8   12   21     5    8    8   10   12   14   15   16   17   18   20   20   21   21   21   21   21   21   21   21 
LCS_GDT     S      62     S      62      8   12   21     5    8    8   10   12   14   15   16   17   18   20   20   21   21   21   21   21   21   21   21 
LCS_GDT     A      63     A      63      8   12   21     5    8    8   10   12   14   15   16   17   18   20   20   21   21   21   21   21   21   21   21 
LCS_GDT     R      64     R      64      8   12   21     4    8    8   10   12   14   15   16   16   18   18   20   21   21   21   21   21   21   21   21 
LCS_AVERAGE  LCS_A:  13.05  (   5.96   11.08   22.11 )

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      5      8      8     10     12     14     15     16     17     18     20     20     21     21     21     21     21     21     21     21 
GDT PERCENT_CA   5.26   8.42   8.42  10.53  12.63  14.74  15.79  16.84  17.89  18.95  21.05  21.05  22.11  22.11  22.11  22.11  22.11  22.11  22.11  22.11
GDT RMS_LOCAL    0.22   0.48   0.48   1.37   1.58   2.04   2.16   2.39   3.07   3.25   3.58   3.58   3.78   3.78   3.78   3.78   3.78   3.78   3.78   3.78
GDT RMS_ALL_CA   6.06   6.33   6.33   5.09   5.02   5.04   4.91   4.60   3.86   3.80   3.83   3.83   3.78   3.78   3.78   3.78   3.78   3.78   3.78   3.78

#      Molecule1      Molecule2       DISTANCE
LGA    I      44      I      44          8.695
LGA    D      45      D      45          8.397
LGA    N      46      N      46          9.408
LGA    I      47      I      47          7.044
LGA    G      48      G      48          3.838
LGA    A      49      A      49          1.664
LGA    G      50      G      50          1.934
LGA    T      51      T      51          3.982
LGA    G      52      G      52          6.244
LGA    E      53      E      53          2.866
LGA    W      54      W      54          3.274
LGA    V      55      V      55          0.649
LGA    L      56      L      56          1.566
LGA    L      57      L      57          2.774
LGA    V      58      V      58          2.409
LGA    S      59      S      59          1.295
LGA    G      60      G      60          1.074
LGA    S      61      S      61          2.125
LGA    S      62      S      62          1.770
LGA    A      63      A      63          1.540
LGA    R      64      R      64          3.057

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   21   95    4.0     16    2.39    14.474    14.302     0.643

LGA_LOCAL      RMSD =  2.387  Number of atoms =   16  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.460  Number of atoms =   21 
Std_ALL_ATOMS  RMSD =  3.781  (standard rmsd on all 21 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.718129 * X  +  -0.136182 * Y  +   0.682455 * Z  +  18.889544
  Y_new =   0.685413 * X  +   0.308096 * Y  +  -0.659762 * Z  + 113.928345
  Z_new =  -0.120414 * X  +   0.941558 * Y  +   0.314593 * Z  + 118.116875 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.248338   -1.893255  [ DEG:    71.5245   -108.4755 ]
  Theta =   0.120707    3.020886  [ DEG:     6.9160    173.0840 ]
  Phi   =   0.762093   -2.379500  [ DEG:    43.6647   -136.3353 ]
 
# 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: T0306AL381_2                                  
REMARK     2: T0306.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0306AL381_2.T0306.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   21   95   4.0   16   2.39  14.302     3.78
REMARK  ---------------------------------------------------------- 
MOLECULE T0306AL381_2
REMARK Aligment from pdb entry: 1kekA
ATOM      1  N   ILE    44      34.457  28.773  73.829  1.00  0.00              
ATOM      2  CA  ILE    44      35.217  28.774  72.597  1.00  0.00              
ATOM      3  C   ILE    44      34.788  27.469  71.883  1.00  0.00              
ATOM      4  O   ILE    44      34.810  26.436  72.548  1.00  0.00              
ATOM      5  N   ASP    45      34.447  27.523  70.620  1.00  0.00              
ATOM      6  CA  ASP    45      34.059  26.250  69.952  1.00  0.00              
ATOM      7  C   ASP    45      35.071  26.015  68.848  1.00  0.00              
ATOM      8  O   ASP    45      35.618  27.016  68.375  1.00  0.00              
ATOM      9  N   ASN    46      35.391  24.772  68.516  1.00  0.00              
ATOM     10  CA  ASN    46      36.319  24.458  67.437  1.00  0.00              
ATOM     11  C   ASN    46      35.560  23.791  66.287  1.00  0.00              
ATOM     12  O   ASN    46      34.693  22.937  66.549  1.00  0.00              
ATOM     13  N   ILE    47      35.985  24.053  65.085  1.00  0.00              
ATOM     14  CA  ILE    47      35.438  23.475  63.848  1.00  0.00              
ATOM     15  C   ILE    47      36.592  23.159  62.893  1.00  0.00              
ATOM     16  O   ILE    47      37.603  23.875  62.821  1.00  0.00              
ATOM     17  N   GLY    48      36.468  22.074  62.122  1.00  0.00              
ATOM     18  CA  GLY    48      37.568  21.746  61.201  1.00  0.00              
ATOM     19  C   GLY    48      38.228  20.412  61.528  1.00  0.00              
ATOM     20  O   GLY    48      37.836  19.624  62.411  1.00  0.00              
ATOM     21  N   ALA    49      39.274  20.101  60.783  1.00  0.00              
ATOM     22  CA  ALA    49      40.032  18.858  61.013  1.00  0.00              
ATOM     23  C   ALA    49      40.574  18.684  62.414  1.00  0.00              
ATOM     24  O   ALA    49      41.259  19.524  63.006  1.00  0.00              
ATOM     25  N   GLY    50      40.269  17.546  63.052  1.00  0.00              
ATOM     26  CA  GLY    50      40.693  17.231  64.400  1.00  0.00              
ATOM     27  C   GLY    50      42.198  17.212  64.576  1.00  0.00              
ATOM     28  O   GLY    50      42.757  17.394  65.668  1.00  0.00              
ATOM     29  N   THR    51      42.901  16.978  63.458  1.00  0.00              
ATOM     30  CA  THR    51      44.361  16.944  63.474  1.00  0.00              
ATOM     31  C   THR    51      44.913  18.187  62.763  1.00  0.00              
ATOM     32  O   THR    51      45.990  18.171  62.159  1.00  0.00              
ATOM     33  N   GLY    52      44.186  19.329  62.824  1.00  0.00              
ATOM     34  CA  GLY    52      44.573  20.502  62.083  1.00  0.00              
ATOM     35  C   GLY    52      45.975  20.990  62.482  1.00  0.00              
ATOM     36  O   GLY    52      46.213  20.966  63.682  1.00  0.00              
ATOM     37  N   GLU    53      46.735  21.378  61.484  1.00  0.00              
ATOM     38  CA  GLU    53      48.034  21.991  61.744  1.00  0.00              
ATOM     39  C   GLU    53      48.036  23.541  61.699  1.00  0.00              
ATOM     40  O   GLU    53      48.916  24.208  62.267  1.00  0.00              
ATOM     41  N   TRP    54      47.080  24.079  60.980  1.00  0.00              
ATOM     42  CA  TRP    54      46.924  25.552  60.858  1.00  0.00              
ATOM     43  C   TRP    54      45.526  25.961  61.331  1.00  0.00              
ATOM     44  O   TRP    54      44.540  25.530  60.714  1.00  0.00              
ATOM     45  N   VAL    55      45.407  26.796  62.337  1.00  0.00              
ATOM     46  CA  VAL    55      44.143  27.172  62.948  1.00  0.00              
ATOM     47  C   VAL    55      43.972  28.715  62.999  1.00  0.00              
ATOM     48  O   VAL    55      44.903  29.425  63.358  1.00  0.00              
ATOM     49  N   LEU    56      42.797  29.181  62.688  1.00  0.00              
ATOM     50  CA  LEU    56      42.445  30.615  62.806  1.00  0.00              
ATOM     51  C   LEU    56      41.703  30.749  64.134  1.00  0.00              
ATOM     52  O   LEU    56      40.982  29.844  64.537  1.00  0.00              
ATOM     53  N   LEU    57      41.874  31.864  64.833  1.00  0.00              
ATOM     54  CA  LEU    57      41.017  32.247  65.976  1.00  0.00              
ATOM     55  C   LEU    57      40.269  33.517  65.529  1.00  0.00              
ATOM     56  O   LEU    57      40.939  34.412  65.008  1.00  0.00              
ATOM     57  N   VAL    58      38.934  33.535  65.644  1.00  0.00              
ATOM     58  CA  VAL    58      38.195  34.696  65.088  1.00  0.00              
ATOM     59  C   VAL    58      36.900  34.880  65.841  1.00  0.00              
ATOM     60  O   VAL    58      36.502  34.008  66.657  1.00  0.00              
ATOM     61  N   SER    59      36.229  36.034  65.658  1.00  0.00              
ATOM     62  CA  SER    59      35.041  36.325  66.420  1.00  0.00              
ATOM     63  C   SER    59      34.043  37.090  65.551  1.00  0.00              
ATOM     64  O   SER    59      34.427  37.979  64.790  1.00  0.00              
ATOM     65  N   GLY    60      32.767  36.827  65.663  1.00  0.00              
ATOM     66  CA  GLY    60      31.744  37.526  64.912  1.00  0.00              
ATOM     67  C   GLY    60      31.510  36.850  63.561  1.00  0.00              
ATOM     68  O   GLY    60      31.947  35.698  63.302  1.00  0.00              
ATOM     69  N   SER    61      30.833  37.554  62.649  1.00  0.00              
ATOM     70  CA  SER    61      30.384  36.969  61.390  1.00  0.00              
ATOM     71  C   SER    61      31.436  36.311  60.510  1.00  0.00              
ATOM     72  O   SER    61      31.154  35.387  59.729  1.00  0.00              
ATOM     73  N   SER    62      32.704  36.724  60.639  1.00  0.00              
ATOM     74  CA  SER    62      33.823  36.146  59.919  1.00  0.00              
ATOM     75  C   SER    62      33.888  34.642  60.179  1.00  0.00              
ATOM     76  O   SER    62      34.188  33.840  59.337  1.00  0.00              
ATOM     77  N   ALA    63      33.479  34.183  61.383  1.00  0.00              
ATOM     78  CA  ALA    63      33.504  32.766  61.716  1.00  0.00              
ATOM     79  C   ALA    63      32.628  31.914  60.770  1.00  0.00              
ATOM     80  O   ALA    63      32.942  30.736  60.579  1.00  0.00              
ATOM     81  N   ARG    64      31.509  32.432  60.285  1.00  0.00              
ATOM     82  CA  ARG    64      30.643  31.648  59.424  1.00  0.00              
ATOM     83  C   ARG    64      31.392  31.340  58.122  1.00  0.00              
ATOM     84  O   ARG    64      31.362  30.233  57.578  1.00  0.00              
END
