
#######################################################
#                                                     #
#                        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   15 (   60),  selected   15 , name T0386AL509_1-D2
# Molecule2: number of CA atoms   81 (  636),  selected   15 , name T0386_D2.pdb
# PARAMETERS: T0386AL509_1-D2.T0386_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       222 - 262         4.99     6.26
  LCS_AVERAGE:     16.95

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12       222 - 233         0.56     8.15
  LCS_AVERAGE:     12.59

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12       222 - 233         0.56     8.15
  LCS_AVERAGE:     12.59

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:   81
LCS_GDT     K     222     K     222     12   12   14     7   11   12   12   12   12   12   12   12   12   12   12   12   13   13   14   15   15   15   15 
LCS_GDT     I     223     I     223     12   12   14     9   11   12   12   12   12   12   12   12   12   12   12   12   13   13   14   15   15   15   15 
LCS_GDT     R     224     R     224     12   12   14     9   11   12   12   12   12   12   12   12   12   12   12   12   13   13   14   15   15   15   15 
LCS_GDT     L     225     L     225     12   12   14     9   11   12   12   12   12   12   12   12   12   12   12   12   13   13   14   15   15   15   15 
LCS_GDT     L     226     L     226     12   12   14     9   11   12   12   12   12   12   12   12   12   12   12   12   13   13   14   15   15   15   15 
LCS_GDT     K     227     K     227     12   12   14     9   11   12   12   12   12   12   12   12   12   12   12   12   13   13   14   15   15   15   15 
LCS_GDT     E     228     E     228     12   12   14     9   11   12   12   12   12   12   12   12   12   12   12   12   13   13   14   15   15   15   15 
LCS_GDT     F     229     F     229     12   12   14     9   11   12   12   12   12   12   12   12   12   12   12   12   13   13   14   15   15   15   15 
LCS_GDT     M     230     M     230     12   12   14     9   11   12   12   12   12   12   12   12   12   12   12   12   13   13   14   15   15   15   15 
LCS_GDT     H     231     H     231     12   12   14     9   11   12   12   12   12   12   12   12   12   12   12   12   13   13   14   15   15   15   15 
LCS_GDT     T     232     T     232     12   12   14     6   11   12   12   12   12   12   12   12   12   12   12   12   13   13   14   15   15   15   15 
LCS_GDT     M     233     M     233     12   12   14     4   11   12   12   12   12   12   12   12   12   12   12   12   13   13   14   15   15   15   15 
LCS_GDT     A     261     A     261      3    3   14     0    3    3    3    3    3    4    6    6    7   10   10   11   13   13   14   15   15   15   15 
LCS_GDT     G     262     G     262      3    3   14     0    3    3    3    3    3    4    6    6    7    8   10   11   11   12   14   15   15   15   15 
LCS_GDT     L     263     L     263      3    3   10     0    3    3    3    3    3    4    6    6    7    8   10   11   11   12   14   15   15   15   15 
LCS_AVERAGE  LCS_A:  14.05  (  12.59   12.59   16.95 )

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     11     12     12     12     12     12     12     12     12     12     12     12     13     13     14     15     15     15     15 
GDT PERCENT_CA  11.11  13.58  14.81  14.81  14.81  14.81  14.81  14.81  14.81  14.81  14.81  14.81  14.81  16.05  16.05  17.28  18.52  18.52  18.52  18.52
GDT RMS_LOCAL    0.16   0.45   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   0.56   3.72   3.72   5.71   5.97   5.97   5.97   5.97
GDT RMS_ALL_CA   7.93   8.05   8.15   8.15   8.15   8.15   8.15   8.15   8.15   8.15   8.15   8.15   8.15   6.89   6.89   6.11   5.97   5.97   5.97   5.97

#      Molecule1      Molecule2       DISTANCE
LGA    K     222      K     222          0.958
LGA    I     223      I     223          0.187
LGA    R     224      R     224          0.134
LGA    L     225      L     225          0.399
LGA    L     226      L     226          0.322
LGA    K     227      K     227          0.284
LGA    E     228      E     228          0.297
LGA    F     229      F     229          0.443
LGA    M     230      M     230          0.473
LGA    H     231      H     231          0.185
LGA    T     232      T     232          0.820
LGA    M     233      M     233          1.122
LGA    A     261      A     261         15.553
LGA    G     262      G     262         18.050
LGA    L     263      L     263         20.595

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   15   81    4.0     12    0.56    15.123    14.362     1.813

LGA_LOCAL      RMSD =  0.562  Number of atoms =   12  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  8.147  Number of atoms =   15 
Std_ALL_ATOMS  RMSD =  5.975  (standard rmsd on all 15 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.726093 * X  +   0.214540 * Y  +   0.653270 * Z  +  11.949961
  Y_new =  -0.686178 * X  +   0.287086 * Y  +   0.668387 * Z  +  39.996834
  Z_new =  -0.044149 * X  +  -0.933571 * Y  +   0.355664 * Z  + 128.904465 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.206801    1.934792  [ DEG:   -69.1446    110.8554 ]
  Theta =   0.044164    3.097429  [ DEG:     2.5304    177.4696 ]
  Phi   =  -0.757143    2.384450  [ DEG:   -43.3811    136.6189 ]
 
# 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: T0386AL509_1-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0386AL509_1-D2.T0386_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   15   81   4.0   12   0.56  14.362     5.97
REMARK  ---------------------------------------------------------- 
MOLECULE T0386AL509_1-D2
REMARK Aligment from pdb entry: 2f6sA_
ATOM    337  N   LYS   222       5.946  58.522  78.538  1.00  0.00              
ATOM    338  CA  LYS   222       7.213  58.958  77.924  1.00  0.00              
ATOM    339  C   LYS   222       7.018  60.056  76.854  1.00  0.00              
ATOM    340  O   LYS   222       7.957  60.827  76.618  1.00  0.00              
ATOM    341  N   ILE   223       5.824  60.162  76.256  1.00  0.00              
ATOM    342  CA  ILE   223       5.538  61.296  75.353  1.00  0.00              
ATOM    343  C   ILE   223       5.664  62.635  76.110  1.00  0.00              
ATOM    344  O   ILE   223       6.377  63.551  75.672  1.00  0.00              
ATOM    345  N   ARG   224       4.983  62.721  77.253  1.00  0.00              
ATOM    346  CA  ARG   224       5.047  63.878  78.142  1.00  0.00              
ATOM    347  C   ARG   224       6.494  64.198  78.543  1.00  0.00              
ATOM    348  O   ARG   224       6.903  65.356  78.548  1.00  0.00              
ATOM    349  N   LEU   225       7.256  63.157  78.857  1.00  0.00              
ATOM    350  CA  LEU   225       8.625  63.307  79.303  1.00  0.00              
ATOM    351  C   LEU   225       9.528  63.816  78.179  1.00  0.00              
ATOM    352  O   LEU   225      10.360  64.695  78.398  1.00  0.00              
ATOM    353  N   LEU   226       9.342  63.284  76.977  1.00  0.00              
ATOM    354  CA  LEU   226      10.116  63.710  75.815  1.00  0.00              
ATOM    355  C   LEU   226       9.799  65.165  75.439  1.00  0.00              
ATOM    356  O   LEU   226      10.715  65.947  75.193  1.00  0.00              
ATOM    357  N   LYS   227       8.516  65.522  75.415  1.00  0.00              
ATOM    358  CA  LYS   227       8.113  66.916  75.230  1.00  0.00              
ATOM    359  C   LYS   227       8.778  67.836  76.249  1.00  0.00              
ATOM    360  O   LYS   227       9.245  68.925  75.903  1.00  0.00              
ATOM    361  N   GLU   228       8.836  67.379  77.495  1.00  0.00              
ATOM    362  CA  GLU   228       9.493  68.094  78.558  1.00  0.00              
ATOM    363  C   GLU   228      10.971  68.314  78.298  1.00  0.00              
ATOM    364  O   GLU   228      11.477  69.443  78.429  1.00  0.00              
ATOM    365  N   PHE   229      11.674  67.249  77.924  1.00  0.00              
ATOM    366  CA  PHE   229      13.115  67.344  77.736  1.00  0.00              
ATOM    367  C   PHE   229      13.456  68.146  76.492  1.00  0.00              
ATOM    368  O   PHE   229      14.438  68.865  76.484  1.00  0.00              
ATOM    369  N   MET   230      12.632  68.041  75.450  1.00  0.00              
ATOM    370  CA  MET   230      12.807  68.844  74.251  1.00  0.00              
ATOM    371  C   MET   230      12.739  70.331  74.624  1.00  0.00              
ATOM    372  O   MET   230      13.510  71.135  74.118  1.00  0.00              
ATOM    373  N   HIS   231      11.831  70.696  75.519  1.00  0.00              
ATOM    374  CA  HIS   231      11.690  72.084  75.917  1.00  0.00              
ATOM    375  C   HIS   231      12.892  72.514  76.751  1.00  0.00              
ATOM    376  O   HIS   231      13.407  73.627  76.582  1.00  0.00              
ATOM    377  N   THR   232      13.350  71.621  77.633  1.00  0.00              
ATOM    378  CA  THR   232      14.527  71.882  78.432  1.00  0.00              
ATOM    379  C   THR   232      15.708  72.255  77.524  1.00  0.00              
ATOM    380  O   THR   232      16.422  73.222  77.792  1.00  0.00              
ATOM    381  N   MET   233      15.905  71.489  76.449  1.00  0.00              
ATOM    382  CA  MET   233      16.978  71.763  75.485  1.00  0.00              
ATOM    383  C   MET   233      16.716  73.033  74.683  1.00  0.00              
ATOM    384  O   MET   233      17.651  73.745  74.298  1.00  0.00              
ATOM    385  N   ALA   261      18.038  76.230  76.199  1.00  0.00              
ATOM    386  CA  ALA   261      19.445  76.458  75.946  1.00  0.00              
ATOM    387  C   ALA   261      19.712  76.902  74.502  1.00  0.00              
ATOM    388  O   ALA   261      20.872  77.039  74.106  1.00  0.00              
ATOM    389  N   GLY   262      18.649  77.117  73.715  1.00  0.00              
ATOM    390  CA  GLY   262      18.778  77.589  72.332  1.00  0.00              
ATOM    391  C   GLY   262      18.745  76.537  71.227  1.00  0.00              
ATOM    392  O   GLY   262      19.069  76.834  70.073  1.00  0.00              
ATOM    393  N   LEU   263      18.363  75.305  71.558  1.00  0.00              
ATOM    394  CA  LEU   263      18.210  74.262  70.541  1.00  0.00              
ATOM    395  C   LEU   263      16.810  74.319  69.929  1.00  0.00              
ATOM    396  O   LEU   263      15.816  74.119  70.630  1.00  0.00              
END
