
#######################################################
#                                                     #
#                        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   25 (  100),  selected   25 , name T0289AL333_5-D2
# Molecule2: number of CA atoms   74 (  581),  selected   25 , name T0289_D2.pdb
# PARAMETERS: T0289AL333_5-D2.T0289_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:    15       261 - 275         4.89     9.70
  LCS_AVERAGE:     17.57

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       271 - 275         0.75    15.60
  LCS_AVERAGE:      5.51

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       271 - 275         0.75    15.60
  LCS_AVERAGE:      4.81

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:   74
LCS_GDT     F     261     F     261      3    3   15     0    5    6    6    6    7    9   10   12   13   14   15   17   18   19   21   21   21   21   22 
LCS_GDT     V     262     V     262      3    4   15     2    4    5    6    6    7    9   10   12   13   14   15   17   18   19   21   21   21   21   22 
LCS_GDT     S     263     S     263      3    4   15     2    4    5    6    6    7    9   10   12   13   14   15   17   18   19   21   21   21   21   22 
LCS_GDT     L     264     L     264      3    4   15     3    3    3    5    5    7    8    8   11   13   14   15   17   18   19   21   21   21   21   22 
LCS_GDT     D     265     D     265      3    4   15     3    3    3    3    6    7    8    8   10   11   14   15   17   18   19   21   21   21   21   22 
LCS_GDT     G     266     G     266      3    4   15     3    3    3    4    6    7    8    8    8   11   11   13   15   17   19   21   21   21   21   22 
LCS_GDT     K     267     K     267      3    4   15     3    3    3    4    6    7    8    8    8   11   14   15   17   18   19   21   21   21   21   22 
LCS_GDT     V     268     V     268      3    4   15     3    4    5    6    6    7    9   10   12   13   14   15   17   18   19   21   21   21   21   22 
LCS_GDT     I     269     I     269      3    4   15     1    3    3    3    4    7    9   10   12   13   14   15   17   18   19   21   21   21   21   22 
LCS_GDT     P     270     P     270      3    4   15     3    3    4    6    6    7    9   10   11   13   14   15   17   18   19   21   21   21   21   22 
LCS_GDT     L     271     L     271      5    5   15     3    5    6    6    6    6    9   10   12   13   14   15   17   18   19   21   21   21   21   22 
LCS_GDT     G     272     G     272      5    5   15     3    5    6    6    6    6    8   10   12   13   14   15   17   18   19   21   21   21   21   22 
LCS_GDT     G     273     G     273      5    5   15     3    5    6    6    6    6    8    9   12   13   14   15   17   18   19   21   21   21   21   22 
LCS_GDT     D     274     D     274      5    5   15     3    5    6    6    6    6    8   10   12   13   14   15   17   18   19   21   21   21   21   22 
LCS_GDT     C     275     C     275      5    5   15     3    5    6    6    6    6    8    9   10   11   14   15   17   17   19   20   20   21   21   22 
LCS_GDT     Y     288     Y     288      4    4   10     4    4    4    4    4    6    6    8    8   10   13   14   14   15   16   17   19   19   19   20 
LCS_GDT     E     289     E     289      4    4   10     4    4    4    4    4    5    6    7    7    8    9   10   14   15   16   17   18   18   18   18 
LCS_GDT     K     290     K     290      4    4   10     4    4    4    4    4    6    6    8    8   10   13   14   14   15   16   17   19   19   19   20 
LCS_GDT     K     291     K     291      4    4   10     4    4    4    4    4    5    6    7    7   10   13   14   15   17   18   21   21   21   21   22 
LCS_GDT     E     292     E     292      3    4   10     3    3    3    4    4    6    6    8    8   10   13   14   17   18   19   21   21   21   21   22 
LCS_GDT     A     293     A     293      3    4   10     3    3    3    4    4    5    6    7    7   10   12   14   15   17   18   21   21   21   21   22 
LCS_GDT     F     294     F     294      3    4   10     3    3    3    4    4    5    6    7    7   10   13   14   16   18   19   21   21   21   21   22 
LCS_GDT     A     295     A     295      3    4   10     1    3    3    5    5    7    8   10   12   13   14   15   17   18   19   21   21   21   21   22 
LCS_GDT     K     296     K     296      3    3   10     3    4    5    6    6    7    9   10   12   13   14   15   17   18   19   21   21   21   21   22 
LCS_GDT     T     297     T     297      3    3   10     3    4    5    6    6    7    9   10   12   13   14   15   17   18   19   21   21   21   21   22 
LCS_AVERAGE  LCS_A:   9.30  (   4.81    5.51   17.57 )

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      5      6      6      6      7      9     10     12     13     14     15     17     18     19     21     21     21     21     22 
GDT PERCENT_CA   5.41   6.76   8.11   8.11   8.11   9.46  12.16  13.51  16.22  17.57  18.92  20.27  22.97  24.32  25.68  28.38  28.38  28.38  28.38  29.73
GDT RMS_LOCAL    0.15   0.58   0.75   0.75   0.75   1.65   2.39   2.84   3.28   3.43   3.68   3.89   4.38   4.90   5.10   5.70   5.70   5.56   5.56   5.93
GDT RMS_ALL_CA  19.32  15.76  15.48  15.48  15.48  11.01  10.51   9.87   9.52   9.52   9.33   9.54   9.31   8.41   8.36   7.91   7.91   8.34   8.34   8.05

#      Molecule1      Molecule2       DISTANCE
LGA    F     261      F     261          2.766
LGA    V     262      V     262          2.208
LGA    S     263      S     263          3.631
LGA    L     264      L     264          5.189
LGA    D     265      D     265          6.624
LGA    G     266      G     266          9.038
LGA    K     267      K     267          6.423
LGA    V     268      V     268          1.991
LGA    I     269      I     269          2.798
LGA    P     270      P     270          3.641
LGA    L     271      L     271          3.168
LGA    G     272      G     272          5.518
LGA    G     273      G     273          5.693
LGA    D     274      D     274          4.509
LGA    C     275      C     275          6.259
LGA    Y     288      Y     288         18.347
LGA    E     289      E     289         21.334
LGA    K     290      K     290         20.220
LGA    K     291      K     291         14.699
LGA    E     292      E     292          9.800
LGA    A     293      A     293         11.901
LGA    F     294      F     294         10.262
LGA    A     295      A     295          3.749
LGA    K     296      K     296          3.340
LGA    T     297      T     297          2.364

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   25   74    4.0     10    2.84    14.189    11.768     0.340

LGA_LOCAL      RMSD =  2.840  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  9.311  Number of atoms =   25 
Std_ALL_ATOMS  RMSD =  7.667  (standard rmsd on all 25 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.002818 * X  +  -0.743634 * Y  +  -0.668581 * Z  +  84.537880
  Y_new =  -0.997636 * X  +   0.047998 * Y  +  -0.049181 * Z  +  60.560932
  Z_new =   0.068663 * X  +   0.666862 * Y  +  -0.742011 * Z  +  44.794743 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.409484   -0.732108  [ DEG:   138.0533    -41.9467 ]
  Theta =  -0.068718   -3.072875  [ DEG:    -3.9372   -176.0628 ]
  Phi   =  -1.573621    1.567972  [ DEG:   -90.1618     89.8382 ]
 
# 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: T0289AL333_5-D2                               
REMARK     2: T0289_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0289AL333_5-D2.T0289_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   25   74   4.0   10   2.84  11.768     7.67
REMARK  ---------------------------------------------------------- 
MOLECULE T0289AL333_5-D2
REMARK Aligment from pdb entry: 1jwq_A
ATOM    521  N   PHE   261      25.821  45.257  32.465  1.00  0.00              
ATOM    522  CA  PHE   261      26.384  46.449  33.103  1.00  0.00              
ATOM    523  C   PHE   261      27.187  46.160  34.358  1.00  0.00              
ATOM    524  O   PHE   261      26.682  45.568  35.308  1.00  0.00              
ATOM    525  N   VAL   262      28.444  46.595  34.353  1.00  0.00              
ATOM    526  CA  VAL   262      29.331  46.404  35.490  1.00  0.00              
ATOM    527  C   VAL   262      29.073  47.477  36.540  1.00  0.00              
ATOM    528  O   VAL   262      29.619  47.421  37.639  1.00  0.00              
ATOM    529  N   SER   263      28.246  48.453  36.181  1.00  0.00              
ATOM    530  CA  SER   263      27.903  49.557  37.073  1.00  0.00              
ATOM    531  C   SER   263      26.737  49.211  37.998  1.00  0.00              
ATOM    532  O   SER   263      26.386  49.987  38.889  1.00  0.00              
ATOM    533  N   LEU   264      26.134  48.049  37.770  1.00  0.00              
ATOM    534  CA  LEU   264      25.028  47.570  38.591  1.00  0.00              
ATOM    535  C   LEU   264      25.603  46.468  39.477  1.00  0.00              
ATOM    536  O   LEU   264      26.206  45.521  38.983  1.00  0.00              
ATOM    537  N   ASP   265      25.428  46.605  40.786  1.00  0.00              
ATOM    538  CA  ASP   265      25.964  45.637  41.738  1.00  0.00              
ATOM    539  C   ASP   265      25.613  44.182  41.445  1.00  0.00              
ATOM    540  O   ASP   265      26.498  43.328  41.371  1.00  0.00              
ATOM    541  N   GLY   266      24.325  43.895  41.290  1.00  0.00              
ATOM    542  CA  GLY   266      23.894  42.525  41.022  1.00  0.00              
ATOM    543  C   GLY   266      24.388  42.018  39.672  1.00  0.00              
ATOM    544  O   GLY   266      24.881  40.894  39.563  1.00  0.00              
ATOM    545  N   LYS   267      24.264  42.853  38.645  1.00  0.00              
ATOM    546  CA  LYS   267      24.686  42.459  37.311  1.00  0.00              
ATOM    547  C   LYS   267      26.194  42.239  37.214  1.00  0.00              
ATOM    548  O   LYS   267      26.646  41.320  36.529  1.00  0.00              
ATOM    549  N   VAL   268      26.975  43.073  37.892  1.00  0.00              
ATOM    550  CA  VAL   268      28.426  42.902  37.873  1.00  0.00              
ATOM    551  C   VAL   268      28.775  41.526  38.438  1.00  0.00              
ATOM    552  O   VAL   268      29.586  40.797  37.869  1.00  0.00              
ATOM    553  N   ILE   269      28.168  41.180  39.570  1.00  0.00              
ATOM    554  CA  ILE   269      28.419  39.885  40.198  1.00  0.00              
ATOM    555  C   ILE   269      28.066  38.766  39.223  1.00  0.00              
ATOM    556  O   ILE   269      28.804  37.789  39.080  1.00  0.00              
ATOM    557  N   PRO   270      26.934  38.920  38.550  1.00  0.00              
ATOM    558  CA  PRO   270      26.475  37.934  37.585  1.00  0.00              
ATOM    559  C   PRO   270      27.452  37.774  36.423  1.00  0.00              
ATOM    560  O   PRO   270      27.767  36.655  36.026  1.00  0.00              
ATOM    561  N   LEU   271      27.933  38.888  35.877  1.00  0.00              
ATOM    562  CA  LEU   271      28.864  38.810  34.757  1.00  0.00              
ATOM    563  C   LEU   271      30.156  38.093  35.132  1.00  0.00              
ATOM    564  O   LEU   271      30.803  37.490  34.276  1.00  0.00              
ATOM    565  N   GLY   272      30.534  38.151  36.405  1.00  0.00              
ATOM    566  CA  GLY   272      31.746  37.469  36.832  1.00  0.00              
ATOM    567  C   GLY   272      31.467  36.110  37.451  1.00  0.00              
ATOM    568  O   GLY   272      32.327  35.529  38.111  1.00  0.00              
ATOM    569  N   GLY   273      30.260  35.607  37.222  1.00  0.00              
ATOM    570  CA  GLY   273      29.873  34.292  37.714  1.00  0.00              
ATOM    571  C   GLY   273      30.257  33.290  36.627  1.00  0.00              
ATOM    572  O   GLY   273      29.891  33.454  35.462  1.00  0.00              
ATOM    573  N   ASP   274      31.000  32.257  37.010  1.00  0.00              
ATOM    574  CA  ASP   274      31.447  31.246  36.059  1.00  0.00              
ATOM    575  C   ASP   274      30.357  30.582  35.239  1.00  0.00              
ATOM    576  O   ASP   274      30.505  30.427  34.027  1.00  0.00              
ATOM    577  N   CYS   275      29.267  30.185  35.885  1.00  0.00              
ATOM    578  CA  CYS   275      28.185  29.526  35.168  1.00  0.00              
ATOM    579  C   CYS   275      27.557  30.467  34.149  1.00  0.00              
ATOM    580  O   CYS   275      27.236  30.061  33.034  1.00  0.00              
ATOM    581  N   TYR   288      27.388  31.726  34.538  1.00  0.00              
ATOM    582  CA  TYR   288      26.822  32.738  33.653  1.00  0.00              
ATOM    583  C   TYR   288      27.686  32.838  32.402  1.00  0.00              
ATOM    584  O   TYR   288      27.184  32.765  31.281  1.00  0.00              
ATOM    585  N   GLU   289      28.989  32.998  32.605  1.00  0.00              
ATOM    586  CA  GLU   289      29.926  33.120  31.492  1.00  0.00              
ATOM    587  C   GLU   289      29.866  31.924  30.552  1.00  0.00              
ATOM    588  O   GLU   289      29.836  32.086  29.335  1.00  0.00              
ATOM    589  N   LYS   290      29.847  30.722  31.113  1.00  0.00              
ATOM    590  CA  LYS   290      29.798  29.525  30.286  1.00  0.00              
ATOM    591  C   LYS   290      28.533  29.459  29.446  1.00  0.00              
ATOM    592  O   LYS   290      28.573  29.088  28.276  1.00  0.00              
ATOM    593  N   LYS   291      27.412  29.826  30.053  1.00  0.00              
ATOM    594  CA  LYS   291      26.125  29.812  29.375  1.00  0.00              
ATOM    595  C   LYS   291      26.106  30.842  28.244  1.00  0.00              
ATOM    596  O   LYS   291      25.662  30.560  27.129  1.00  0.00              
ATOM    597  N   GLU   292      26.598  32.037  28.547  1.00  0.00              
ATOM    598  CA  GLU   292      26.638  33.122  27.576  1.00  0.00              
ATOM    599  C   GLU   292      27.636  32.825  26.466  1.00  0.00              
ATOM    600  O   GLU   292      27.375  33.117  25.301  1.00  0.00              
ATOM    601  N   ALA   293      28.773  32.237  26.829  1.00  0.00              
ATOM    602  CA  ALA   293      29.790  31.891  25.846  1.00  0.00              
ATOM    603  C   ALA   293      29.196  30.913  24.842  1.00  0.00              
ATOM    604  O   ALA   293      29.485  30.978  23.646  1.00  0.00              
ATOM    605  N   PHE   294      28.367  29.996  25.329  1.00  0.00              
ATOM    606  CA  PHE   294      27.748  29.027  24.435  1.00  0.00              
ATOM    607  C   PHE   294      26.758  29.741  23.527  1.00  0.00              
ATOM    608  O   PHE   294      26.635  29.408  22.350  1.00  0.00              
ATOM    609  N   ALA   295      26.053  30.721  24.083  1.00  0.00              
ATOM    610  CA  ALA   295      25.091  31.473  23.299  1.00  0.00              
ATOM    611  C   ALA   295      25.788  32.237  22.187  1.00  0.00              
ATOM    612  O   ALA   295      25.318  32.268  21.049  1.00  0.00              
ATOM    613  N   LYS   296      26.914  32.858  22.517  1.00  0.00              
ATOM    614  CA  LYS   296      27.682  33.612  21.533  1.00  0.00              
ATOM    615  C   LYS   296      28.205  32.654  20.463  1.00  0.00              
ATOM    616  O   LYS   296      28.160  32.950  19.264  1.00  0.00              
ATOM    617  N   THR   297      28.684  31.495  20.902  1.00  0.00              
ATOM    618  CA  THR   297      29.189  30.493  19.976  1.00  0.00              
ATOM    619  C   THR   297      28.072  30.064  19.025  1.00  0.00              
ATOM    620  O   THR   297      28.292  29.938  17.826  1.00  0.00              
END
