
#######################################################
#                                                     #
#                        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 T0318AL242_4-D2
# Molecule2: number of CA atoms  335 ( 2465),  selected   14 , name T0318_D2.pdb
# PARAMETERS: T0318AL242_4-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 - 169         0.51     0.51
  LCS_AVERAGE:      4.18

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14       156 - 169         0.51     0.51
  LCS_AVERAGE:      4.18

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14       156 - 169         0.51     0.51
  LCS_AVERAGE:      4.18

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:  335
LCS_GDT     T     156     T     156     14   14   14     8   13   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     N     157     N     157     14   14   14    11   13   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     E     158     E     158     14   14   14    11   13   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     D     159     D     159     14   14   14    11   13   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     A     160     A     160     14   14   14    11   13   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     V     161     V     161     14   14   14    11   13   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     F     162     F     162     14   14   14    11   13   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     L     163     L     163     14   14   14    11   13   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     T     164     T     164     14   14   14    11   13   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     D     165     D     165     14   14   14    11   13   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     L     166     L     166     14   14   14    11   13   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     S     167     S     167     14   14   14    11   13   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     E     168     E     168     14   14   14    11   13   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     S     169     S     169     14   14   14     5   13   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_AVERAGE  LCS_A:   4.18  (   4.18    4.18    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     11     13     14     14     14     14     14     14     14     14     14     14     14     14     14     14     14     14     14     14 
GDT PERCENT_CA   3.28   3.88   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   4.18   4.18   4.18   4.18
GDT RMS_LOCAL    0.27   0.42   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51
GDT RMS_ALL_CA   0.57   0.55   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51

#      Molecule1      Molecule2       DISTANCE
LGA    T     156      T     156          1.001
LGA    N     157      N     157          0.522
LGA    E     158      E     158          0.354
LGA    D     159      D     159          0.308
LGA    A     160      A     160          0.314
LGA    V     161      V     161          0.199
LGA    F     162      F     162          0.185
LGA    L     163      L     163          0.094
LGA    T     164      T     164          0.217
LGA    D     165      D     165          0.328
LGA    L     166      L     166          0.500
LGA    S     167      S     167          0.526
LGA    E     168      E     168          0.670
LGA    S     169      S     169          0.926

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   14  335    4.0     14    0.51     4.104     4.156     2.290

LGA_LOCAL      RMSD =  0.511  Number of atoms =   14  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  0.511  Number of atoms =   14 
Std_ALL_ATOMS  RMSD =  0.511  (standard rmsd on all 14 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.558147 * X  +   0.463220 * Y  +  -0.688403 * Z  + -22.517218
  Y_new =  -0.588563 * X  +   0.805831 * Y  +   0.065037 * Z  +  29.223013
  Z_new =   0.584863 * X  +   0.368868 * Y  +   0.722406 * Z  +  11.720747 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.472100   -2.669492  [ DEG:    27.0494   -152.9507 ]
  Theta =  -0.624712   -2.516881  [ DEG:   -35.7933   -144.2067 ]
  Phi   =  -0.811917    2.329676  [ DEG:   -46.5194    133.4806 ]
 
# 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: T0318AL242_4-D2                               
REMARK     2: T0318_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0318AL242_4-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   0.51   4.156     0.51
REMARK  ---------------------------------------------------------- 
MOLECULE T0318AL242_4-D2
REMARK Aligment from pdb entry: 1gyt_A
ATOM    557  N   THR   156      28.211  26.735  14.210  1.00  0.00              
ATOM    558  CA  THR   156      27.642  28.059  14.418  1.00  0.00              
ATOM    559  C   THR   156      27.928  29.052  13.296  1.00  0.00              
ATOM    560  O   THR   156      27.949  30.260  13.516  1.00  0.00              
ATOM    561  N   ASN   157      28.147  28.543  12.091  1.00  0.00              
ATOM    562  CA  ASN   157      28.347  29.413  10.953  1.00  0.00              
ATOM    563  C   ASN   157      26.975  29.940  10.512  1.00  0.00              
ATOM    564  O   ASN   157      26.866  31.053   9.991  1.00  0.00              
ATOM    565  N   GLU   158      25.931  29.139  10.730  1.00  0.00              
ATOM    566  CA  GLU   158      24.567  29.513  10.354  1.00  0.00              
ATOM    567  C   GLU   158      23.961  30.530  11.336  1.00  0.00              
ATOM    568  O   GLU   158      23.352  31.529  10.923  1.00  0.00              
ATOM    569  N   ASP   159      24.125  30.265  12.627  1.00  0.00              
ATOM    570  CA  ASP   159      23.578  31.153  13.631  1.00  0.00              
ATOM    571  C   ASP   159      24.292  32.495  13.548  1.00  0.00              
ATOM    572  O   ASP   159      23.739  33.532  13.895  1.00  0.00              
ATOM    573  N   ALA   160      25.522  32.464  13.060  1.00  0.00              
ATOM    574  CA  ALA   160      26.287  33.684  12.950  1.00  0.00              
ATOM    575  C   ALA   160      25.862  34.539  11.776  1.00  0.00              
ATOM    576  O   ALA   160      25.893  35.772  11.853  1.00  0.00              
ATOM    577  N   VAL   161      25.461  33.902  10.681  1.00  0.00              
ATOM    578  CA  VAL   161      25.070  34.669   9.520  1.00  0.00              
ATOM    579  C   VAL   161      23.758  35.371   9.812  1.00  0.00              
ATOM    580  O   VAL   161      23.504  36.468   9.311  1.00  0.00              
ATOM    581  N   PHE   162      22.944  34.724  10.641  1.00  0.00              
ATOM    582  CA  PHE   162      21.662  35.261  11.059  1.00  0.00              
ATOM    583  C   PHE   162      21.905  36.444  11.986  1.00  0.00              
ATOM    584  O   PHE   162      21.179  37.431  11.945  1.00  0.00              
ATOM    585  N   LEU   163      22.925  36.324  12.830  1.00  0.00              
ATOM    586  CA  LEU   163      23.267  37.380  13.769  1.00  0.00              
ATOM    587  C   LEU   163      23.713  38.648  13.013  1.00  0.00              
ATOM    588  O   LEU   163      23.320  39.760  13.360  1.00  0.00              
ATOM    589  N   THR   164      24.514  38.476  11.972  1.00  0.00              
ATOM    590  CA  THR   164      24.954  39.615  11.196  1.00  0.00              
ATOM    591  C   THR   164      23.734  40.211  10.514  1.00  0.00              
ATOM    592  O   THR   164      23.582  41.433  10.468  1.00  0.00              
ATOM    593  N   ASP   165      22.864  39.355   9.983  1.00  0.00              
ATOM    594  CA  ASP   165      21.672  39.846   9.298  1.00  0.00              
ATOM    595  C   ASP   165      20.813  40.726  10.241  1.00  0.00              
ATOM    596  O   ASP   165      20.458  41.859   9.904  1.00  0.00              
ATOM    597  N   LEU   166      20.497  40.197  11.421  1.00  0.00              
ATOM    598  CA  LEU   166      19.701  40.927  12.391  1.00  0.00              
ATOM    599  C   LEU   166      20.427  42.157  12.874  1.00  0.00              
ATOM    600  O   LEU   166      19.878  43.248  12.873  1.00  0.00              
ATOM    601  N   SER   167      21.664  41.965  13.300  1.00  0.00              
ATOM    602  CA  SER   167      22.472  43.058  13.804  1.00  0.00              
ATOM    603  C   SER   167      22.542  44.234  12.846  1.00  0.00              
ATOM    604  O   SER   167      22.476  45.373  13.279  1.00  0.00              
ATOM    605  N   GLU   168      22.664  43.977  11.547  1.00  0.00              
ATOM    606  CA  GLU   168      22.739  45.080  10.620  1.00  0.00              
ATOM    607  C   GLU   168      21.397  45.787  10.456  1.00  0.00              
ATOM    608  O   GLU   168      21.357  47.002  10.308  1.00  0.00              
ATOM    609  N   SER   169      20.300  45.035  10.463  1.00  0.00              
ATOM    610  CA  SER   169      18.987  45.653  10.287  1.00  0.00              
ATOM    611  C   SER   169      18.681  46.496  11.525  1.00  0.00              
ATOM    612  O   SER   169      18.215  47.622  11.419  1.00  0.00              
END
