
#######################################################
#                                                     #
#                        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 (  103),  selected    7 , name T0342TS239_1_1
# Molecule2: number of CA atoms  169 ( 1343),  selected    7 , name T0342.pdb
# PARAMETERS: T0342TS239_1_1.T0342.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:     7       176 - 182         2.64     2.64
  LCS_AVERAGE:      4.14

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       176 - 180         1.25     4.29
  LCS_AVERAGE:      2.62

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       176 - 179         0.17     4.23
  LCS_AVERAGE:      2.11

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:  169
LCS_GDT     I     176     I     176      4    5    7     4    4    4    5    5    6    6    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     E     177     E     177      4    5    7     4    4    4    5    5    6    6    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     D     178     D     178      4    5    7     4    4    4    5    5    6    6    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     I     179     I     179      4    5    7     4    4    4    5    5    6    6    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     I     180     I     180      3    5    7     3    3    3    5    5    5    6    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     K     181     K     181      3    3    7     3    3    3    4    5    6    6    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     K     182     K     182      3    3    7     3    3    3    3    3    6    6    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_AVERAGE  LCS_A:   2.96  (   2.11    2.62    4.14 )

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      4      4      4      5      5      6      6      7      7      7      7      7      7      7      7      7      7      7      7      7 
GDT PERCENT_CA   2.37   2.37   2.37   2.96   2.96   3.55   3.55   4.14   4.14   4.14   4.14   4.14   4.14   4.14   4.14   4.14   4.14   4.14   4.14   4.14
GDT RMS_LOCAL    0.17   0.17   0.17   1.25   1.25   2.08   2.08   2.64   2.64   2.64   2.64   2.64   2.64   2.64   2.64   2.64   2.64   2.64   2.64   2.64
GDT RMS_ALL_CA   4.23   4.23   4.23   4.29   4.29   2.78   2.78   2.64   2.64   2.64   2.64   2.64   2.64   2.64   2.64   2.64   2.64   2.64   2.64   2.64

#      Molecule1      Molecule2       DISTANCE
LGA    I     176      I     176          3.474
LGA    E     177      E     177          1.788
LGA    D     178      D     178          2.952
LGA    I     179      I     179          1.658
LGA    I     180      I     180          3.983
LGA    K     181      K     181          1.600
LGA    K     182      K     182          3.154

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   21  169    4.0      7    2.64     3.402     3.258     0.256

LGA_LOCAL      RMSD =  2.637  Number of atoms =    7  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  2.806  Number of atoms =    7 
Std_ALL_ATOMS  RMSD =  2.637  (standard rmsd on all 7 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.568770 * X  +  -0.673219 * Y  +   0.472521 * Z  +   7.764780
  Y_new =  -0.158462 * X  +   0.474042 * Y  +   0.866126 * Z  +  59.748219
  Z_new =  -0.807087 * X  +  -0.567503 * Y  +   0.162942 * Z  +  54.430378 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.291197    1.850395  [ DEG:   -73.9801    106.0199 ]
  Theta =   0.939202    2.202390  [ DEG:    53.8123    126.1877 ]
  Phi   =  -0.271714    2.869879  [ DEG:   -15.5681    164.4319 ]
 
# 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: T0342TS239_1_1                                
REMARK     2: T0342.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0342TS239_1_1.T0342.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   21  169   4.0    7   2.64   3.258     2.64
REMARK  ---------------------------------------------------------- 
MOLECULE T0342TS239_1_1
REMARK PARENT number 1
PFRMAT TS
TARGET T0342
PARENT 1kdg_A
ATOM      1  N   SER     1      17.615  59.518  51.515  1.00  9.99
ATOM      2  CA  SER     1      18.664  60.518  51.145  1.00  9.99
ATOM      3  C   SER     1      18.193  61.440  50.003  1.00  9.99
ATOM      4  O   SER     1      18.941  62.331  49.560  1.00  9.99
ATOM      5  CB  SER     1      19.976  59.871  50.760  1.00  9.99
ATOM      6  N   ALA     2      17.010  61.189  49.463  1.00  9.99
ATOM      7  CA  ALA     2      16.533  62.026  48.358  1.00  9.99
ATOM      8  C   ALA     2      16.367  63.454  48.813  1.00  9.99
ATOM      9  O   ALA     2      15.902  63.660  49.947  1.00  9.99
ATOM     10  CB  ALA     2      15.242  61.521  47.760  1.00  9.99
ATOM     11  N   ASN     3      16.679  64.444  47.970  1.00  9.99
ATOM     12  CA  ASN     3      16.520  65.871  48.310  1.00  9.99
ATOM     13  C   ASN     3      15.347  66.431  47.505  1.00  9.99
ATOM     14  O   ASN     3      15.361  66.445  46.289  1.00  9.99
ATOM     15  CB  ASN     3      17.776  66.635  47.965  1.00  9.99
ATOM     16  N   SER     4      14.321  66.865  48.201  1.00  9.99
ATOM     17  CA  SER     4      13.127  67.392  47.610  1.00  9.99
ATOM     18  C   SER     4      13.288  68.851  47.283  1.00  9.99
ATOM     19  O   SER     4      13.284  69.692  48.169  1.00  9.99
ATOM     20  CB  SER     4      11.932  67.218  48.584  1.00  9.99
ATOM     21  N   GLY     5      13.470  69.109  45.997  1.00  9.99
ATOM     22  CA  GLY     5      13.630  70.448  45.468  1.00  9.99
ATOM     23  C   GLY     5      12.783  70.589  44.214  1.00  9.99
ATOM     24  O   GLY     5      12.523  69.600  43.511  1.00  9.99
ATOM     25  N   CYS     6      12.385  71.798  43.907  1.00  9.99
ATOM     26  CA  CYS     6      11.511  72.043  42.728  1.00  9.99
ATOM     27  C   CYS     6      12.158  71.995  41.352  1.00  9.99
ATOM     28  O   CYS     6      12.018  72.910  40.524  1.00  9.99
ATOM     29  CB  CYS     6      10.939  73.427  43.042  1.00  9.99
ATOM     30  N   LYS     7      12.940  70.953  41.150  1.00  9.99
ATOM     31  CA  LYS     7      13.630  70.738  39.872  1.00  9.99
ATOM     32  C   LYS     7      12.643  70.494  38.729  1.00  9.99
ATOM     33  O   LYS     7      11.841  69.578  38.803  1.00  9.99
ATOM     34  CB  LYS     7      14.596  69.530  39.995  1.00  9.99
ATOM     35  N   ASP     8      12.687  71.313  37.700  1.00  9.99
ATOM     36  CA  ASP     8      11.791  71.208  36.578  1.00  9.99
ATOM     37  C   ASP     8      10.546  72.110  36.798  1.00  9.99
ATOM     38  O   ASP     8       9.838  72.410  35.836  1.00  9.99
ATOM     39  CB  ASP     8      11.408  69.731  36.387  1.00  9.99
ATOM    851  N   ILE   176      -4.800  82.876  17.732  1.00  9.99
ATOM    852  CA  ILE   176      -4.174  82.475  18.981  1.00  9.99
ATOM    853  C   ILE   176      -4.888  81.271  19.590  1.00  9.99
ATOM    854  O   ILE   176      -4.256  80.353  20.109  1.00  9.99
ATOM    855  CB  ILE   176      -4.045  83.658  19.979  1.00  9.99
ATOM    856  N   GLU   177      -6.228  81.256  19.488  1.00  9.99
ATOM    857  CA  GLU   177      -6.982  80.151  20.108  1.00  9.99
ATOM    858  C   GLU   177      -6.805  78.812  19.380  1.00  9.99
ATOM    859  O   GLU   177      -6.912  77.730  19.960  1.00  9.99
ATOM    860  CB  GLU   177      -8.468  80.508  20.260  1.00  9.99
ATOM    861  N   ASP   178      -6.561  78.899  18.085  1.00  9.99
ATOM    862  CA  ASP   178      -6.367  77.719  17.260  1.00  9.99
ATOM    863  C   ASP   178      -4.884  77.289  17.214  1.00  9.99
ATOM    864  O   ASP   178      -4.556  76.236  16.676  1.00  9.99
ATOM    865  CB  ASP   178      -6.863  78.009  15.907  1.00  9.99
ATOM    866  N   ILE   179      -4.010  78.124  17.798  1.00  9.99
ATOM    867  CA  ILE   179      -2.561  77.885  17.714  1.00  9.99
ATOM    868  C   ILE   179      -2.153  76.649  18.542  1.00  9.99
ATOM    869  O   ILE   179      -2.606  76.409  19.649  1.00  9.99
ATOM    870  CB  ILE   179      -1.828  79.128  18.188  1.00  9.99
ATOM    871  N   ILE   180      -1.284  75.838  17.989  1.00  9.99
ATOM    872  CA  ILE   180      -0.819  74.657  18.699  1.00  9.99
ATOM    873  C   ILE   180       0.111  75.144  19.787  1.00  9.99
ATOM    874  O   ILE   180       1.123  75.752  19.475  1.00  9.99
ATOM    875  CB  ILE   180      -0.098  73.738  17.719  1.00  9.99
ATOM    876  N   LYS   181      -0.215  74.927  21.045  1.00  9.99
ATOM    877  CA  LYS   181       0.637  75.452  22.123  1.00  9.99
ATOM    878  C   LYS   181       2.091  75.095  21.984  1.00  9.99
ATOM    879  O   LYS   181       2.954  75.943  22.210  1.00  9.99
ATOM    880  CB  LYS   181       0.035  74.830  23.364  1.00  9.99
ATOM    881  N   LYS   182       2.361  73.879  21.575  1.00  9.99
ATOM    882  CA  LYS   182       3.712  73.394  21.467  1.00  9.99
ATOM    883  C   LYS   182       4.521  74.212  20.477  1.00  9.99
ATOM    884  O   LYS   182       5.764  74.371  20.601  1.00  9.99
ATOM    885  CB  LYS   182       3.733  71.913  21.122  1.00  9.99
ATOM    886  N   GLY   183       3.850  74.806  19.499  1.00  9.99
ATOM    887  CA  GLY   183       4.553  75.597  18.505  1.00  9.99
ATOM    888  C   GLY   183       4.878  77.005  19.000  1.00  9.99
ATOM    889  O   GLY   183       5.575  77.748  18.300  1.00  9.99
ATOM    890  N   GLU   184       4.405  77.342  20.209  1.00  9.99
ATOM    891  CA  GLU   184       4.725  78.636  20.839  1.00  9.99
ATOM    892  C   GLU   184       6.136  78.615  21.453  1.00  9.99
ATOM    893  O   GLU   184       6.624  79.631  21.920  1.00  9.99
ATOM    894  CB  GLU   184       3.714  79.005  21.898  1.00  9.99
ATOM    895  N   THR   185       6.713  77.429  21.568  1.00  9.99
ATOM    896  CA  THR   185       8.039  77.242  22.146  1.00  9.99
ATOM    897  C   THR   185       9.035  78.141  21.438  1.00  9.99
ATOM    898  O   THR   185       9.195  78.103  20.214  1.00  9.99
ATOM    899  CB  THR   185       8.426  75.766  21.954  1.00  9.99
ATOM    900  N   GLN   186       9.719  78.934  22.226  1.00  9.99
ATOM    901  CA  GLN   186      10.723  79.860  21.760  1.00  9.99
ATOM    902  C   GLN   186      12.144  79.338  21.973  1.00  9.99
ATOM    903  O   GLN   186      13.117  80.001  21.607  1.00  9.99
ATOM    904  CB  GLN   186      10.568  81.138  22.535  1.00  9.99
ATOM    905  N   THR   187      12.263  78.160  22.555  1.00  9.99
ATOM    906  CA  THR   187      13.563  77.532  22.848  1.00  9.99
ATOM    907  C   THR   187      14.393  78.359  23.812  1.00  9.99
ATOM    908  O   THR   187      15.632  78.305  23.763  1.00  9.99
ATOM    909  CB  THR   187      14.363  77.287  21.588  1.00  9.99
ATOM    910  N   LEU   188      13.709  79.068  24.708  1.00  9.99
ATOM    911  CA  LEU   188      14.385  79.937  25.681  1.00  9.99
ATOM    912  C   LEU   188      14.207  79.502  27.131  1.00  9.99
ATOM    913  O   LEU   188      14.143  80.339  28.034  1.00  9.99
ATOM    914  CB  LEU   188      13.819  81.355  25.533  1.00  9.99
TER
END
