
#######################################################
#                                                     #
#                        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   11 (   54),  selected   11 , name T0320TS102_5-D2
# Molecule2: number of CA atoms   73 (  604),  selected   11 , name T0320_D2.pdb
# PARAMETERS: T0320TS102_5-D2.T0320_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:    11       246 - 256         1.56     1.56
  LCS_AVERAGE:     15.07

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11       246 - 256         1.56     1.56
  LCS_AVERAGE:     15.07

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9       247 - 255         0.67     1.94
  LCS_AVERAGE:     10.83

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:   73
LCS_GDT     H     246     H     246      3   11   11     3    3    3    4   10   11   11   11   11   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     F     247     F     247      9   11   11     8    8    9    9   10   11   11   11   11   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     E     248     E     248      9   11   11     8    8    9    9   10   11   11   11   11   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     W     249     W     249      9   11   11     8    8    9    9   10   11   11   11   11   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     E     250     E     250      9   11   11     8    8    9    9   10   11   11   11   11   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     I     251     I     251      9   11   11     8    8    9    9   10   11   11   11   11   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     I     252     I     252      9   11   11     8    8    9    9   10   11   11   11   11   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     H     253     H     253      9   11   11     8    8    9    9   10   11   11   11   11   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     A     254     A     254      9   11   11     8    8    9    9   10   11   11   11   11   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     F     255     F     255      9   11   11     3    7    9    9   10   11   11   11   11   11   11   11   11   11   11   11   11   11   11   11 
LCS_GDT     G     256     G     256      3   11   11     3    3    3    6   10   11   11   11   11   11   11   11   11   11   11   11   11   11   11   11 
LCS_AVERAGE  LCS_A:  13.66  (  10.83   15.07   15.07 )

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      8      8      9      9     10     11     11     11     11     11     11     11     11     11     11     11     11     11     11     11 
GDT PERCENT_CA  10.96  10.96  12.33  12.33  13.70  15.07  15.07  15.07  15.07  15.07  15.07  15.07  15.07  15.07  15.07  15.07  15.07  15.07  15.07  15.07
GDT RMS_LOCAL    0.30   0.30   0.67   0.67   1.23   1.56   1.56   1.56   1.56   1.56   1.56   1.56   1.56   1.56   1.56   1.56   1.56   1.56   1.56   1.56
GDT RMS_ALL_CA   2.08   2.08   1.94   1.94   1.68   1.56   1.56   1.56   1.56   1.56   1.56   1.56   1.56   1.56   1.56   1.56   1.56   1.56   1.56   1.56

#      Molecule1      Molecule2       DISTANCE
LGA    H     246      H     246          2.934
LGA    F     247      F     247          1.364
LGA    E     248      E     248          1.127
LGA    W     249      W     249          1.282
LGA    E     250      E     250          0.786
LGA    I     251      I     251          0.544
LGA    I     252      I     252          0.962
LGA    H     253      H     253          1.061
LGA    A     254      A     254          0.812
LGA    F     255      F     255          1.854
LGA    G     256      G     256          2.485

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   11   73    4.0     11    1.56    13.356    14.257     0.664

LGA_LOCAL      RMSD =  1.556  Number of atoms =   11  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  1.556  Number of atoms =   11 
Std_ALL_ATOMS  RMSD =  1.556  (standard rmsd on all 11 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.806844 * X  +   0.304263 * Y  +  -0.506386 * Z  + -41.339321
  Y_new =   0.536525 * X  +  -0.736180 * Y  +   0.412529 * Z  + -18.860950
  Z_new =  -0.247274 * X  +  -0.604535 * Y  +  -0.757227 * Z  + -27.831129 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.467856    0.673736  [ DEG:  -141.3978     38.6022 ]
  Theta =   0.249866    2.891727  [ DEG:    14.3163    165.6837 ]
  Phi   =   0.586825   -2.554767  [ DEG:    33.6226   -146.3774 ]
 
# 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: T0320TS102_5-D2                               
REMARK     2: T0320_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0320TS102_5-D2.T0320_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   11   73   4.0   11   1.56  14.257     1.56
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS102_5-D2
PFRMAT TS
TARGET T0320
MODEL 5
PARENT 1ihg_A
ATOM    680  N   HIS   246      -0.140  13.369  10.598  1.00  1.00
ATOM    681  CA  HIS   246      -0.003  14.225  11.776  1.00  1.00
ATOM    682  C   HIS   246       0.339  15.664  11.436  1.00  1.00
ATOM    683  O   HIS   246      -0.256  16.655  11.907  1.00  1.00
ATOM    684  CB  HIS   246       1.080  13.619  12.691  1.00  1.00
ATOM    685  N   PHE   247       1.344  15.855  10.582  1.00  1.00
ATOM    686  CA  PHE   247       1.749  17.216  10.210  1.00  1.00
ATOM    687  C   PHE   247       0.646  17.973   9.469  1.00  1.00
ATOM    688  O   PHE   247       0.449  19.190   9.640  1.00  1.00
ATOM    689  CB  PHE   247       3.015  17.141   9.376  1.00  1.00
ATOM    690  N   GLU   248      -0.090  17.260   8.620  1.00  1.00
ATOM    691  CA  GLU   248      -1.169  17.858   7.822  1.00  1.00
ATOM    692  C   GLU   248      -2.338  18.273   8.710  1.00  1.00
ATOM    693  O   GLU   248      -2.832  19.400   8.571  1.00  1.00
ATOM    694  CB  GLU   248      -1.614  16.874   6.742  1.00  1.00
ATOM    695  N   TRP   249      -2.751  17.360   9.590  1.00  1.00
ATOM    696  CA  TRP   249      -3.790  17.641  10.569  1.00  1.00
ATOM    697  C   TRP   249      -3.377  18.768  11.517  1.00  1.00
ATOM    698  O   TRP   249      -4.225  19.549  11.947  1.00  1.00
ATOM    699  CB  TRP   249      -4.124  16.426  11.431  1.00  1.00
ATOM    700  N   GLU   250      -2.084  18.839  11.848  1.00  1.00
ATOM    701  CA  GLU   250      -1.646  19.899  12.760  1.00  1.00
ATOM    702  C   GLU   250      -1.754  21.264  12.086  1.00  1.00
ATOM    703  O   GLU   250      -2.207  22.201  12.740  1.00  1.00
ATOM    704  CB  GLU   250      -0.224  19.681  13.276  1.00  1.00
ATOM    705  N   ILE   251      -1.348  21.347  10.830  1.00  1.00
ATOM    706  CA  ILE   251      -1.411  22.566  10.046  1.00  1.00
ATOM    707  C   ILE   251      -2.857  23.021   9.866  1.00  1.00
ATOM    708  O   ILE   251      -3.156  24.217   9.861  1.00  1.00
ATOM    709  CB  ILE   251      -0.804  22.398   8.657  1.00  1.00
ATOM    710  N   ILE   252      -3.731  22.028   9.691  1.00  1.00
ATOM    711  CA  ILE   252      -5.139  22.393   9.460  1.00  1.00
ATOM    712  C   ILE   252      -5.766  22.922  10.730  1.00  1.00
ATOM    713  O   ILE   252      -6.601  23.835  10.674  1.00  1.00
ATOM    714  CB  ILE   252      -5.898  21.182   8.875  1.00  1.00
ATOM    715  N   HIS   253      -5.383  22.429  11.914  1.00  1.00
ATOM    716  CA  HIS   253      -6.029  22.973  13.107  1.00  1.00
ATOM    717  C   HIS   253      -5.253  24.071  13.829  1.00  1.00
ATOM    718  O   HIS   253      -5.832  24.692  14.729  1.00  1.00
ATOM    719  CB  HIS   253      -6.307  21.840  14.105  1.00  1.00
ATOM    720  N   ALA   254      -3.997  24.336  13.498  1.00  1.00
ATOM    721  CA  ALA   254      -3.175  25.293  14.244  1.00  1.00
ATOM    722  C   ALA   254      -3.747  26.693  14.171  1.00  1.00
ATOM    723  O   ALA   254      -4.254  27.123  13.137  1.00  1.00
ATOM    724  CB  ALA   254      -1.735  25.281  13.724  1.00  1.00
ATOM    725  N   PHE   255      -3.648  27.417  15.290  1.00  1.00
ATOM    726  CA  PHE   255      -4.142  28.784  15.323  1.00  1.00
ATOM    727  C   PHE   255      -3.193  29.616  16.184  1.00  1.00
ATOM    728  O   PHE   255      -2.706  29.086  17.174  1.00  1.00
ATOM    729  CB  PHE   255      -5.573  28.845  15.847  1.00  1.00
ATOM    730  N   GLY   256      -2.933  30.860  15.804  1.00  1.00
ATOM    731  CA  GLY   256      -2.023  31.712  16.550  1.00  1.00
ATOM    732  C   GLY   256      -2.462  31.909  18.001  1.00  1.00
ATOM    733  O   GLY   256      -3.684  31.940  18.220  1.00  1.00
TER
END
