
#######################################################
#                                                     #
#                        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   14 (   56),  selected   14 , name T0318AL333_2-D2
# Molecule2: number of CA atoms  335 ( 2465),  selected   14 , name T0318_D2.pdb
# PARAMETERS: T0318AL333_2-D2.T0318_D2.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:    14       156 - 170         2.44     2.44
  LCS_AVERAGE:      4.18

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10       160 - 170         1.99     2.68
  LCS_AVERAGE:      2.90

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8       162 - 170         0.99     4.03
  LCS_AVERAGE:      2.26

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:  335
LCS_GDT     T     156     T     156      7    9   14     3    4    7    8   10   12   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     N     157     N     157      7    9   14     6    6    7    8   10   12   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     E     158     E     158      7    9   14     6    6    8    8   10   12   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     D     159     D     159      7    9   14     6    6    7    8   10   12   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     A     160     A     160      7   10   14     6    6    7    8   10   12   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     V     161     V     161      7   10   14     6    6    7    8   10   12   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     F     162     F     162      8   10   14     6    6    7    8   10   12   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     T     164     T     164      8   10   14     7    7    8    8   10   12   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     D     165     D     165      8   10   14     7    7    8    8   10   12   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     L     166     L     166      8   10   14     7    7    8    8   10   12   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     S     167     S     167      8   10   14     7    7    8    8   10   12   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     E     168     E     168      8   10   14     7    7    8    8   10   12   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     S     169     S     169      8   10   14     7    7    8    8    9   12   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     V     170     V     170      8   10   14     7    7    8    8    9   12   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_AVERAGE  LCS_A:   3.11  (   2.26    2.90    4.18 )

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      7      8      8     10     12     14     14     14     14     14     14     14     14     14     14     14     14     14     14 
GDT PERCENT_CA   2.09   2.09   2.39   2.39   2.99   3.58   4.18   4.18   4.18   4.18   4.18   4.18   4.18   4.18   4.18   4.18   4.18   4.18   4.18   4.18
GDT RMS_LOCAL    0.29   0.29   0.65   0.65   1.87   2.10   2.44   2.44   2.44   2.44   2.44   2.44   2.44   2.44   2.44   2.44   2.44   2.44   2.44   2.44
GDT RMS_ALL_CA   3.10   3.10   3.51   3.51   3.06   2.75   2.44   2.44   2.44   2.44   2.44   2.44   2.44   2.44   2.44   2.44   2.44   2.44   2.44   2.44

#      Molecule1      Molecule2       DISTANCE
LGA    T     156      T     156          3.323
LGA    N     157      N     157          2.703
LGA    E     158      E     158          2.788
LGA    D     159      D     159          2.895
LGA    A     160      A     160          2.031
LGA    V     161      V     161          2.345
LGA    F     162      F     162          3.150
LGA    T     164      T     164          2.180
LGA    D     165      D     165          1.546
LGA    L     166      L     166          1.421
LGA    S     167      S     167          1.800
LGA    E     168      E     168          1.674
LGA    S     169      S     169          2.529
LGA    V     170      V     170          2.827

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   14  335    4.0     14    2.44     3.209     3.320     0.550

LGA_LOCAL      RMSD =  2.444  Number of atoms =   14  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  2.444  Number of atoms =   14 
Std_ALL_ATOMS  RMSD =  2.444  (standard rmsd on all 14 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.168535 * X  +  -0.704067 * Y  +   0.689845 * Z  +  60.019268
  Y_new =  -0.783088 * X  +   0.329404 * Y  +   0.527510 * Z  +  63.121910
  Z_new =  -0.598640 * X  +  -0.629113 * Y  +  -0.495830 * Z  +  26.386086 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.238265    0.903328  [ DEG:  -128.2431     51.7569 ]
  Theta =   0.641802    2.499791  [ DEG:    36.7725    143.2275 ]
  Phi   =  -1.358811    1.782781  [ DEG:   -77.8542    102.1458 ]
 
# 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: T0318AL333_2-D2                               
REMARK     2: T0318_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0318AL333_2-D2.T0318_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   14  335   4.0   14   2.44   3.320     2.44
REMARK  ---------------------------------------------------------- 
MOLECULE T0318AL333_2-D2
REMARK Aligment from pdb entry: 1gyt_A
ATOM    585  N   THR   156      26.396  25.949  11.464  1.00  0.00              
ATOM    586  CA  THR   156      27.629  26.714  11.341  1.00  0.00              
ATOM    587  C   THR   156      27.327  28.179  11.129  1.00  0.00              
ATOM    588  O   THR   156      27.789  29.020  11.908  1.00  0.00              
ATOM    589  N   ASN   157      26.543  28.487  10.093  1.00  0.00              
ATOM    590  CA  ASN   157      26.192  29.872   9.811  1.00  0.00              
ATOM    591  C   ASN   157      24.993  30.392  10.599  1.00  0.00              
ATOM    592  O   ASN   157      24.302  31.307  10.161  1.00  0.00              
ATOM    593  N   GLU   158      24.750  29.809  11.765  1.00  0.00              
ATOM    594  CA  GLU   158      23.684  30.291  12.616  1.00  0.00              
ATOM    595  C   GLU   158      24.177  31.561  13.322  1.00  0.00              
ATOM    596  O   GLU   158      23.386  32.455  13.635  1.00  0.00              
ATOM    597  N   ASP   159      25.486  31.637  13.564  1.00  0.00              
ATOM    598  CA  ASP   159      26.092  32.789  14.235  1.00  0.00              
ATOM    599  C   ASP   159      26.218  33.998  13.294  1.00  0.00              
ATOM    600  O   ASP   159      25.888  35.134  13.668  1.00  0.00              
ATOM    601  N   ALA   160      26.703  33.748  12.082  1.00  0.00              
ATOM    602  CA  ALA   160      26.876  34.822  11.129  1.00  0.00              
ATOM    603  C   ALA   160      25.509  35.377  10.753  1.00  0.00              
ATOM    604  O   ALA   160      25.372  36.540  10.390  1.00  0.00              
ATOM    605  N   VAL   161      24.494  34.535  10.867  1.00  0.00              
ATOM    606  CA  VAL   161      23.158  34.963  10.526  1.00  0.00              
ATOM    607  C   VAL   161      22.531  35.836  11.591  1.00  0.00              
ATOM    608  O   VAL   161      21.768  36.757  11.279  1.00  0.00              
ATOM    609  N   PHE   162      22.841  35.563  12.853  1.00  0.00              
ATOM    610  CA  PHE   162      22.249  36.347  13.913  1.00  0.00              
ATOM    611  C   PHE   162      22.839  37.744  13.880  1.00  0.00              
ATOM    612  O   PHE   162      22.167  38.720  14.219  1.00  0.00              
ATOM    613  N   THR   164      24.096  37.816  13.453  1.00  0.00              
ATOM    614  CA  THR   164      24.809  39.073  13.324  1.00  0.00              
ATOM    615  C   THR   164      24.215  39.857  12.162  1.00  0.00              
ATOM    616  O   THR   164      24.100  41.076  12.222  1.00  0.00              
ATOM    617  N   ASP   165      23.853  39.143  11.100  1.00  0.00              
ATOM    618  CA  ASP   165      23.271  39.767   9.923  1.00  0.00              
ATOM    619  C   ASP   165      21.913  40.409  10.270  1.00  0.00              
ATOM    620  O   ASP   165      21.616  41.524   9.848  1.00  0.00              
ATOM    621  N   LEU   166      21.102  39.713  11.054  1.00  0.00              
ATOM    622  CA  LEU   166      19.821  40.259  11.446  1.00  0.00              
ATOM    623  C   LEU   166      20.083  41.472  12.322  1.00  0.00              
ATOM    624  O   LEU   166      19.416  42.498  12.181  1.00  0.00              
ATOM    625  N   SER   167      21.052  41.362  13.229  1.00  0.00              
ATOM    626  CA  SER   167      21.358  42.476  14.120  1.00  0.00              
ATOM    627  C   SER   167      21.736  43.743  13.313  1.00  0.00              
ATOM    628  O   SER   167      21.169  44.820  13.519  1.00  0.00              
ATOM    629  N   GLU   168      22.686  43.599  12.392  1.00  0.00              
ATOM    630  CA  GLU   168      23.122  44.712  11.569  1.00  0.00              
ATOM    631  C   GLU   168      22.007  45.200  10.679  1.00  0.00              
ATOM    632  O   GLU   168      21.717  46.385  10.633  1.00  0.00              
ATOM    633  N   SER   169      21.396  44.271   9.963  1.00  0.00              
ATOM    634  CA  SER   169      20.315  44.602   9.055  1.00  0.00              
ATOM    635  C   SER   169      19.211  45.408   9.716  1.00  0.00              
ATOM    636  O   SER   169      18.696  46.337   9.115  1.00  0.00              
ATOM    637  N   VAL   170      18.847  45.076  10.952  1.00  0.00              
ATOM    638  CA  VAL   170      17.796  45.825  11.595  1.00  0.00              
ATOM    639  C   VAL   170      18.250  47.225  11.999  1.00  0.00              
ATOM    640  O   VAL   170      17.473  48.168  11.922  1.00  0.00              
END
