
#######################################################
#                                                     #
#                        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   16 (   64),  selected   16 , name T0316TS307_5u-D3
# Molecule2: number of CA atoms   90 (  711),  selected   16 , name T0316_D3.pdb
# PARAMETERS: T0316TS307_5u-D3.T0316_D3.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:    10       294 - 303         4.17    20.12
  LCS_AVERAGE:      9.44

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       296 - 302         0.69    22.64
  LCS_AVERAGE:      6.04

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       296 - 302         0.69    22.64
  LCS_AVERAGE:      5.42

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:   90
LCS_GDT     M     284     M     284      3    3    6     0    3    3    3    3    5    5    5    6    7    8    9    9    9    9   10   11   11   13   14 
LCS_GDT     S     285     S     285      3    4    6     3    3    3    4    4    5    5    6    7    7    8    9    9    9    9   10   12   12   13   14 
LCS_GDT     T     286     T     286      3    4    6     3    3    3    4    4    5    5    6    7    7    8    9    9    9    9   10   12   12   13   13 
LCS_GDT     S     287     S     287      3    4    6     3    3    3    4    4    5    5    6    7    7    8    9    9    9    9   10   12   12   13   14 
LCS_GDT     L     288     L     288      3    4    6     1    3    3    4    4    5    5    6    7    7    8    9    9    9    9   10   12   12   13   14 
LCS_GDT     E     289     E     289      3    3    6     0    3    3    3    3    4    5    6    7    7    8    9    9    9    9   10   12   12   13   14 
LCS_GDT     H     294     H     294      4    5   10     3    4    4    4    5    5    5    5    6    6    7    7    8    9    9   10   12   12   13   14 
LCS_GDT     F     295     F     295      4    5   10     3    4    4    4    5    5    7    8    8    8    8    9    9    9    9   10   12   12   13   14 
LCS_GDT     T     296     T     296      7    7   10     4    7    7    7    7    7    7    8    8    8    8    9    9    9    9   10   12   12   13   14 
LCS_GDT     R     297     R     297      7    7   10     5    7    7    7    7    7    7    8    8    8    8    9    9    9    9   10   12   12   13   14 
LCS_GDT     E     298     E     298      7    7   10     5    7    7    7    7    7    7    8    8    8    8    9    9    9    9   10   12   12   13   14 
LCS_GDT     M     299     M     299      7    7   10     5    7    7    7    7    7    7    8    8    8    8    9    9    9    9   10   12   12   13   14 
LCS_GDT     P     300     P     300      7    7   10     5    7    7    7    7    7    7    8    8    8    8    9    9    9    9   10   12   12   13   14 
LCS_GDT     E     301     E     301      7    7   10     5    7    7    7    7    7    7    8    8    8    8    9    9    9    9   10   11   12   13   14 
LCS_GDT     E     302     E     302      7    7   10     4    7    7    7    7    7    7    8    8    8    8    9    9    9    9   10   10   11   12   14 
LCS_GDT     F     303     F     303      3    6   10     3    3    4    4    4    5    6    7    7    7    8    9    9    9    9    9   10   10   11   11 
LCS_AVERAGE  LCS_A:   6.97  (   5.42    6.04    9.44 )

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      5      7      7      7      7      7      7      8      8      8      8      9      9      9      9     10     12     12     13     14 
GDT PERCENT_CA   5.56   7.78   7.78   7.78   7.78   7.78   7.78   8.89   8.89   8.89   8.89  10.00  10.00  10.00  10.00  11.11  13.33  13.33  14.44  15.56
GDT RMS_LOCAL    0.30   0.69   0.69   0.69   0.69   0.69   0.69   2.15   2.15   2.15   2.15   3.08   3.08   3.08   3.08   5.00   6.92   6.84   7.09   7.61
GDT RMS_ALL_CA  23.63  22.64  22.64  22.64  22.64  22.64  22.64  20.92  20.92  20.92  20.92  21.53  21.53  21.53  21.53  10.11   8.99   8.36   8.17   8.09

#      Molecule1      Molecule2       DISTANCE
LGA    M     284      M     284         38.022
LGA    S     285      S     285         37.413
LGA    T     286      T     286         34.405
LGA    S     287      S     287         28.161
LGA    L     288      L     288         24.331
LGA    E     289      E     289         22.801
LGA    H     294      H     294          7.584
LGA    F     295      F     295          3.748
LGA    T     296      T     296          2.948
LGA    R     297      R     297          1.789
LGA    E     298      E     298          2.059
LGA    M     299      M     299          1.358
LGA    P     300      P     300          1.785
LGA    E     301      E     301          2.001
LGA    E     302      E     302          3.814
LGA    F     303      F     303          9.098

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   16   90    4.0      8    2.15     8.889     8.011     0.356

LGA_LOCAL      RMSD =  2.145  Number of atoms =    8  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 19.571  Number of atoms =   16 
Std_ALL_ATOMS  RMSD =  7.995  (standard rmsd on all 16 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.137827 * X  +  -0.354846 * Y  +  -0.924710 * Z  +  21.847940
  Y_new =   0.884930 * X  +   0.375217 * Y  +  -0.275883 * Z  +  29.604170
  Z_new =   0.444862 * X  +  -0.856327 * Y  +   0.262299 * Z  +  14.313285 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.273563    1.868029  [ DEG:   -72.9698    107.0302 ]
  Theta =  -0.461020   -2.680572  [ DEG:   -26.4145   -153.5855 ]
  Phi   =   1.725304   -1.416289  [ DEG:    98.8526    -81.1474 ]
 
# 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: T0316TS307_5u-D3                              
REMARK     2: T0316_D3.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0316TS307_5u-D3.T0316_D3.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   16   90   4.0    8   2.15   8.011     8.00
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS307_5u-D3
PFRMAT   TS
TARGET   T0316
MODEL    5  UNREFINED
PARENT   1xng_A
ATOM   1868  N   MET   284      36.841  21.131  19.542  1.00 21.65           N  
ATOM   1869  CA  MET   284      37.009  19.698  19.769  1.00 22.93           C  
ATOM   1870  C   MET   284      35.912  19.103  20.643  1.00 23.71           C  
ATOM   1871  O   MET   284      35.514  17.953  20.453  1.00 25.42           O  
ATOM   1877  N   SER   285      35.426  19.883  21.598  1.00 23.27           N  
ATOM   1878  CA  SER   285      34.376  19.422  22.494  1.00 25.22           C  
ATOM   1879  C   SER   285      33.032  19.260  21.791  1.00 24.93           C  
ATOM   1880  O   SER   285      32.217  18.421  22.176  1.00 25.81           O  
ATOM   1886  N   THR   286      32.803  20.060  20.758  1.00 22.65           N  
ATOM   1887  CA  THR   286      31.531  20.013  20.053  1.00 22.35           C  
ATOM   1888  C   THR   286      31.571  19.454  18.634  1.00 22.20           C  
ATOM   1889  O   THR   286      30.597  19.579  17.895  1.00 21.75           O  
ATOM   1894  N   SER   287      32.678  18.822  18.254  1.00 22.27           N  
ATOM   1895  CA  SER   287      32.796  18.274  16.905  1.00 21.44           C  
ATOM   1896  C   SER   287      31.675  17.285  16.579  1.00 21.10           C  
ATOM   1897  O   SER   287      31.284  17.135  15.418  1.00 20.88           O  
ATOM   1899  N   LEU   288      31.151  16.630  17.610  1.00 21.94           N  
ATOM   1900  CA  LEU   288      30.084  15.643  17.450  1.00 21.80           C  
ATOM   1901  C   LEU   288      28.789  16.200  16.868  1.00 21.06           C  
ATOM   1902  O   LEU   288      28.002  15.455  16.285  1.00 21.74           O  
ATOM   1910  N   GLU   289      28.548  17.497  17.037  1.00 20.72           N  
ATOM   1911  CA  GLU   289      27.319  18.098  16.525  1.00 20.40           C  
ATOM   1912  C   GLU   289      27.283  18.189  15.005  1.00 22.27           C  
ATOM   1913  O   GLU   289      26.222  18.397  14.418  1.00 22.11           O  
ATOM   1919  N   HIS   294      28.442  18.018  14.375  1.00 24.15           N  
ATOM   1920  CA  HIS   294      28.567  18.094  12.919  1.00 26.32           C  
ATOM   1921  C   HIS   294      28.643  16.696  12.316  1.00 28.08           C  
ATOM   1922  O   HIS   294      28.874  16.531  11.112  1.00 28.88           O  
ATOM   1927  N   PHE   295      28.441  15.692  13.160  1.00 26.69           N  
ATOM   1928  CA  PHE   295      28.521  14.307  12.729  1.00 29.32           C  
ATOM   1929  C   PHE   295      27.229  13.552  12.996  1.00 27.54           C  
ATOM   1930  O   PHE   295      26.395  13.981  13.793  1.00 26.74           O  
ATOM   1936  N   THR   296      27.067  12.428  12.307  1.00 27.95           N  
ATOM   1937  CA  THR   296      25.902  11.574  12.485  1.00 27.22           C  
ATOM   1938  C   THR   296      26.149  10.717  13.726  1.00 25.81           C  
ATOM   1939  O   THR   296      27.296  10.519  14.132  1.00 28.08           O  
ATOM   1944  N   ARG   297      25.080  10.205  14.353  1.00 26.18           N  
ATOM   1945  CA  ARG   297      25.259   9.371  15.545  1.00 25.53           C  
ATOM   1946  C   ARG   297      26.010   8.091  15.196  1.00 25.64           C  
ATOM   1947  O   ARG   297      25.910   7.592  14.071  1.00 26.59           O  
ATOM   1951  N   GLU   298      26.775   7.582  16.156  1.00 24.57           N  
ATOM   1952  CA  GLU   298      27.551   6.361  15.972  1.00 24.88           C  
ATOM   1953  C   GLU   298      26.619   5.155  15.981  1.00 24.28           C  
ATOM   1954  O   GLU   298      25.898   4.937  16.954  1.00 23.34           O  
ATOM   1956  N   MET   299      26.642   4.379  14.903  1.00 24.24           N  
ATOM   1957  CA  MET   299      25.802   3.188  14.788  1.00 24.38           C  
ATOM   1958  C   MET   299      26.692   1.958  14.652  1.00 24.52           C  
ATOM   1959  O   MET   299      27.601   1.934  13.822  1.00 25.79           O  
ATOM   1964  N   PRO   300      26.434   0.940  15.462  1.00 25.46           N  
ATOM   1965  CA  PRO   300      27.223  -0.285  15.406  1.00 26.01           C  
ATOM   1966  C   PRO   300      27.098  -0.917  14.022  1.00 26.81           C  
ATOM   1967  O   PRO   300      25.990  -1.123  13.529  1.00 26.71           O  
ATOM   1969  N   GLU   301      28.232  -1.212  13.393  1.00 26.18           N  
ATOM   1970  CA  GLU   301      28.227  -1.820  12.066  1.00 27.84           C  
ATOM   1971  C   GLU   301      27.527  -3.175  12.099  1.00 28.66           C  
ATOM   1972  O   GLU   301      27.506  -3.852  13.128  1.00 26.57           O  
ATOM   1974  N   GLU   302      26.949  -3.568  10.968  1.00 29.84           N  
ATOM   1975  CA  GLU   302      26.248  -4.841  10.890  1.00 32.53           C  
ATOM   1976  C   GLU   302      27.201  -5.986  11.225  1.00 33.67           C  
ATOM   1977  O   GLU   302      28.240  -6.148  10.585  1.00 33.88           O  
ATOM   1985  N   PHE   303      26.838  -6.766  12.240  1.00 35.27           N  
ATOM   1986  CA  PHE   303      27.642  -7.901  12.688  1.00 37.06           C  
ATOM   1987  C   PHE   303      27.797  -8.937  11.583  1.00 37.32           C  
ATOM   1988  O   PHE   303      26.837  -9.624  11.235  1.00 38.58           O  
TER
END
