
#######################################################
#                                                     #
#                        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   19 (   76),  selected   19 , name T0335AL381_4
# Molecule2: number of CA atoms   42 (  691),  selected   19 , name T0335.pdb
# PARAMETERS: T0335AL381_4.T0335.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         6 - 27          4.81     5.27
  LCS_AVERAGE:     42.36

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14         6 - 19          0.61     7.78
  LCS_AVERAGE:     27.69

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14         6 - 19          0.61     7.78
  LCS_AVERAGE:     27.69

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:   42
LCS_GDT     K       6     K       6     14   14   18     7   14   14   14   14   14   14   14   14   14   14   15   16   16   17   19   19   19   19   19 
LCS_GDT     I       7     I       7     14   14   18     9   14   14   14   14   14   14   14   14   14   14   15   16   16   17   19   19   19   19   19 
LCS_GDT     A       8     A       8     14   14   18     9   14   14   14   14   14   14   14   14   14   14   15   16   16   17   19   19   19   19   19 
LCS_GDT     R       9     R       9     14   14   18     7   14   14   14   14   14   14   14   14   14   14   15   16   16   17   19   19   19   19   19 
LCS_GDT     I      10     I      10     14   14   18     7   14   14   14   14   14   14   14   14   14   14   15   16   16   17   19   19   19   19   19 
LCS_GDT     N      11     N      11     14   14   18     9   14   14   14   14   14   14   14   14   14   14   15   16   16   17   19   19   19   19   19 
LCS_GDT     E      12     E      12     14   14   18     9   14   14   14   14   14   14   14   14   14   14   15   16   16   17   19   19   19   19   19 
LCS_GDT     L      13     L      13     14   14   18     9   14   14   14   14   14   14   14   14   14   14   15   16   16   17   19   19   19   19   19 
LCS_GDT     A      14     A      14     14   14   18     9   14   14   14   14   14   14   14   14   14   14   15   16   16   17   19   19   19   19   19 
LCS_GDT     A      15     A      15     14   14   18     9   14   14   14   14   14   14   14   14   14   14   15   16   16   17   19   19   19   19   19 
LCS_GDT     K      16     K      16     14   14   18     9   14   14   14   14   14   14   14   14   14   14   15   16   16   17   19   19   19   19   19 
LCS_GDT     A      17     A      17     14   14   18     9   14   14   14   14   14   14   14   14   14   14   15   16   16   17   19   19   19   19   19 
LCS_GDT     K      18     K      18     14   14   18     8   14   14   14   14   14   14   14   14   14   14   15   16   16   17   19   19   19   19   19 
LCS_GDT     A      19     A      19     14   14   18     8   14   14   14   14   14   14   14   14   14   14   15   16   16   17   19   19   19   19   19 
LCS_GDT     E      24     E      24      5    5   18     5    5    5    5    5    5    5    5    6    8   14   14   16   16   17   19   19   19   19   19 
LCS_GDT     E      25     E      25      5    5   18     5    5    5    5    5    5    5    7    8   11   14   15   16   16   17   19   19   19   19   19 
LCS_GDT     E      26     E      26      5    5   18     5    5    5    5    5    5    5    5    6    8   10   11   13   15   17   19   19   19   19   19 
LCS_GDT     K      27     K      27      5    5   18     5    5    5    5    5    5    5    5    6    8   10   12   14   15   17   19   19   19   19   19 
LCS_GDT     A      28     A      28      5    5   14     5    5    5    5    5    5    5    5    6    8   10   12   14   15   17   19   19   19   19   19 
LCS_AVERAGE  LCS_A:  32.58  (  27.69   27.69   42.36 )

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     14     14     14     14     14     14     14     14     14     14     15     16     16     17     19     19     19     19     19 
GDT PERCENT_CA  21.43  33.33  33.33  33.33  33.33  33.33  33.33  33.33  33.33  33.33  33.33  35.71  38.10  38.10  40.48  45.24  45.24  45.24  45.24  45.24
GDT RMS_LOCAL    0.36   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   0.61   2.90   3.63   3.63   4.28   5.17   5.17   5.17   5.17   5.17
GDT RMS_ALL_CA   7.72   7.78   7.78   7.78   7.78   7.78   7.78   7.78   7.78   7.78   7.78   6.50   5.85   5.85   5.52   5.17   5.17   5.17   5.17   5.17

#      Molecule1      Molecule2       DISTANCE
LGA    K       6      K       6          0.490
LGA    I       7      I       7          0.604
LGA    A       8      A       8          0.457
LGA    R       9      R       9          0.736
LGA    I      10      I      10          0.782
LGA    N      11      N      11          0.461
LGA    E      12      E      12          0.479
LGA    L      13      L      13          0.691
LGA    A      14      A      14          0.675
LGA    A      15      A      15          0.318
LGA    K      16      K      16          0.393
LGA    A      17      A      17          0.441
LGA    K      18      K      18          0.520
LGA    A      19      A      19          1.080
LGA    E      24      E      24         13.090
LGA    E      25      E      25         12.755
LGA    E      26      E      26         14.457
LGA    K      27      K      27         16.289
LGA    A      28      A      28         18.346

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   19   42    4.0     14    0.61    36.310    32.957     1.969

LGA_LOCAL      RMSD =  0.611  Number of atoms =   14  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  7.780  Number of atoms =   19 
Std_ALL_ATOMS  RMSD =  5.170  (standard rmsd on all 19 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.396296 * X  +  -0.144629 * Y  +   0.906660 * Z  +   2.072787
  Y_new =   0.630442 * X  +  -0.760765 * Y  +   0.154207 * Z  + -14.502785
  Z_new =   0.667452 * X  +   0.632708 * Y  +   0.392669 * Z  + -13.644053 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.015356   -2.126237  [ DEG:    58.1756   -121.8244 ]
  Theta =  -0.730782   -2.410811  [ DEG:   -41.8707   -138.1293 ]
  Phi   =   2.131981   -1.009612  [ DEG:   122.1535    -57.8465 ]
 
# 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: T0335AL381_4                                  
REMARK     2: T0335.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0335AL381_4.T0335.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   19   42   4.0   14   0.61  32.957     5.17
REMARK  ---------------------------------------------------------- 
MOLECULE T0335AL381_4
REMARK Aligment from pdb entry: 1hj0A
ATOM      1  N   LYS     6       0.449  -9.027  -5.845  1.00  0.00              
ATOM      2  CA  LYS     6       0.898  -7.897  -4.969  1.00  0.00              
ATOM      3  C   LYS     6      -0.051  -6.706  -5.059  1.00  0.00              
ATOM      4  O   LYS     6      -0.732  -6.383  -4.110  1.00  0.00              
ATOM      5  N   ILE     7      -0.116  -6.062  -6.183  1.00  0.00              
ATOM      6  CA  ILE     7      -1.038  -4.904  -6.333  1.00  0.00              
ATOM      7  C   ILE     7      -2.377  -5.270  -5.709  1.00  0.00              
ATOM      8  O   ILE     7      -3.147  -4.420  -5.305  1.00  0.00              
ATOM      9  N   ALA     8      -2.657  -6.536  -5.635  1.00  0.00              
ATOM     10  CA  ALA     8      -3.951  -6.974  -5.042  1.00  0.00              
ATOM     11  C   ALA     8      -3.921  -6.835  -3.520  1.00  0.00              
ATOM     12  O   ALA     8      -4.633  -6.034  -2.944  1.00  0.00              
ATOM     13  N   ARG     9      -3.115  -7.618  -2.862  1.00  0.00              
ATOM     14  CA  ARG     9      -3.055  -7.539  -1.373  1.00  0.00              
ATOM     15  C   ARG     9      -2.902  -6.084  -0.943  1.00  0.00              
ATOM     16  O   ARG     9      -3.418  -5.665   0.077  1.00  0.00              
ATOM     17  N   ILE    10      -2.192  -5.307  -1.706  1.00  0.00              
ATOM     18  CA  ILE    10      -2.011  -3.883  -1.313  1.00  0.00              
ATOM     19  C   ILE    10      -3.318  -3.125  -1.514  1.00  0.00              
ATOM     20  O   ILE    10      -3.774  -2.454  -0.623  1.00  0.00              
ATOM     21  N   ASN    11      -3.946  -3.223  -2.657  1.00  0.00              
ATOM     22  CA  ASN    11      -5.229  -2.488  -2.829  1.00  0.00              
ATOM     23  C   ASN    11      -6.127  -2.820  -1.632  1.00  0.00              
ATOM     24  O   ASN    11      -6.794  -1.960  -1.082  1.00  0.00              
ATOM     25  N   GLU    12      -6.120  -4.053  -1.193  1.00  0.00              
ATOM     26  CA  GLU    12      -6.943  -4.414  -0.008  1.00  0.00              
ATOM     27  C   GLU    12      -6.392  -3.669   1.214  1.00  0.00              
ATOM     28  O   GLU    12      -7.134  -3.195   2.047  1.00  0.00              
ATOM     29  N   LEU    13      -5.090  -3.568   1.323  1.00  0.00              
ATOM     30  CA  LEU    13      -4.475  -2.859   2.479  1.00  0.00              
ATOM     31  C   LEU    13      -4.914  -1.383   2.487  1.00  0.00              
ATOM     32  O   LEU    13      -5.225  -0.835   3.523  1.00  0.00              
ATOM     33  N   ALA    14      -4.939  -0.732   1.354  1.00  0.00              
ATOM     34  CA  ALA    14      -5.357   0.696   1.339  1.00  0.00              
ATOM     35  C   ALA    14      -6.827   0.793   1.752  1.00  0.00              
ATOM     36  O   ALA    14      -7.183   1.551   2.633  1.00  0.00              
ATOM     37  N   ALA    15      -7.687   0.027   1.133  1.00  0.00              
ATOM     38  CA  ALA    15      -9.126   0.089   1.515  1.00  0.00              
ATOM     39  C   ALA    15      -9.306  -0.390   2.970  1.00  0.00              
ATOM     40  O   ALA    15     -10.263  -0.033   3.632  1.00  0.00              
ATOM     41  N   LYS    16      -8.392  -1.183   3.487  1.00  0.00              
ATOM     42  CA  LYS    16      -8.530  -1.658   4.891  1.00  0.00              
ATOM     43  C   LYS    16      -8.155  -0.528   5.838  1.00  0.00              
ATOM     44  O   LYS    16      -8.983  -0.009   6.549  1.00  0.00              
ATOM     45  N   ALA    17      -6.914  -0.132   5.852  1.00  0.00              
ATOM     46  CA  ALA    17      -6.517   0.979   6.755  1.00  0.00              
ATOM     47  C   ALA    17      -7.543   2.106   6.602  1.00  0.00              
ATOM     48  O   ALA    17      -7.940   2.733   7.565  1.00  0.00              
ATOM     49  N   LYS    18      -7.986   2.357   5.395  1.00  0.00              
ATOM     50  CA  LYS    18      -8.993   3.435   5.178  1.00  0.00              
ATOM     51  C   LYS    18     -10.299   3.078   5.876  1.00  0.00              
ATOM     52  O   LYS    18     -10.937   3.928   6.445  1.00  0.00              
ATOM     53  N   ALA    19     -10.723   1.846   5.845  1.00  0.00              
ATOM     54  CA  ALA    19     -12.001   1.525   6.537  1.00  0.00              
ATOM     55  C   ALA    19     -11.787   1.600   8.042  1.00  0.00              
ATOM     56  O   ALA    19     -12.441   2.347   8.733  1.00  0.00              
ATOM     57  N   GLU    24     -10.878   0.849   8.564  1.00  0.00              
ATOM     58  CA  GLU    24     -10.640   0.916  10.022  1.00  0.00              
ATOM     59  C   GLU    24     -10.414   2.375  10.427  1.00  0.00              
ATOM     60  O   GLU    24     -10.661   2.753  11.551  1.00  0.00              
ATOM     61  N   GLU    25      -9.934   3.201   9.529  1.00  0.00              
ATOM     62  CA  GLU    25      -9.686   4.625   9.914  1.00  0.00              
ATOM     63  C   GLU    25     -10.986   5.426   9.912  1.00  0.00              
ATOM     64  O   GLU    25     -11.328   6.044  10.895  1.00  0.00              
ATOM     65  N   GLU    26     -11.725   5.435   8.840  1.00  0.00              
ATOM     66  CA  GLU    26     -12.989   6.219   8.861  1.00  0.00              
ATOM     67  C   GLU    26     -13.839   5.724  10.033  1.00  0.00              
ATOM     68  O   GLU    26     -14.332   6.503  10.834  1.00  0.00              
ATOM     69  N   LYS    27     -14.004   4.433  10.157  1.00  0.00              
ATOM     70  CA  LYS    27     -14.815   3.910  11.284  1.00  0.00              
ATOM     71  C   LYS    27     -14.097   4.177  12.615  1.00  0.00              
ATOM     72  O   LYS    27     -14.731   4.379  13.630  1.00  0.00              
ATOM     73  N   ALA    28     -12.783   4.188  12.630  1.00  0.00              
ATOM     74  CA  ALA    28     -12.070   4.459  13.916  1.00  0.00              
ATOM     75  C   ALA    28     -12.425   5.868  14.371  1.00  0.00              
ATOM     76  O   ALA    28     -13.041   6.055  15.395  1.00  0.00              
END
