
#######################################################
#                                                     #
#                        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   10 (   81),  selected   10 , name T0320TS105_2_1-D2
# Molecule2: number of CA atoms   73 (  604),  selected   10 , name T0320_D2.pdb
# PARAMETERS: T0320TS105_2_1-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:    10       228 - 237         3.62     3.62
  LCS_AVERAGE:     13.70

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       229 - 235         1.76     5.46
  LCS_AVERAGE:      8.36

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       229 - 232         0.57     5.91
  LONGEST_CONTINUOUS_SEGMENT:     4       232 - 235         0.72    10.55
  LCS_AVERAGE:      5.07

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     N     228     N     228      3    6   10     3    4    5    5    6    6    7    8    9    9   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     N     229     N     229      4    7   10     3    5    5    5    6    7    7    8    9    9   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     S     230     S     230      4    7   10     3    5    5    5    6    7    7    8    9    9   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     L     231     L     231      4    7   10     3    5    5    5    6    7    7    8    9    9   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     P     232     P     232      4    7   10     3    5    5    5    6    7    7    8    8    8   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     N     233     N     233      4    7   10     3    4    4    5    6    7    7    8    9    9   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     P     234     P     234      4    7   10     3    5    5    5    5    7    7    8    9    9   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     H     235     H     235      4    7   10     0    4    5    5    6    7    7    8    9    9   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     L     236     L     236      3    3   10     0    3    5    5    5    6    7    7    9    9   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     R     237     R     237      3    3   10     0    3    3    4    5    6    7    8    9    9   10   10   10   10   10   10   10   10   10   10 
LCS_AVERAGE  LCS_A:   9.04  (   5.07    8.36   13.70 )

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      3      5      5      5      6      7      7      8      9      9     10     10     10     10     10     10     10     10     10     10 
GDT PERCENT_CA   4.11   6.85   6.85   6.85   8.22   9.59   9.59  10.96  12.33  12.33  13.70  13.70  13.70  13.70  13.70  13.70  13.70  13.70  13.70  13.70
GDT RMS_LOCAL    0.07   0.63   0.63   0.63   1.30   1.76   1.76   2.41   3.06   3.06   3.62   3.62   3.62   3.62   3.62   3.62   3.62   3.62   3.62   3.62
GDT RMS_ALL_CA  10.48   6.01   6.01   6.01   5.48   5.46   5.46   5.21   3.77   3.77   3.62   3.62   3.62   3.62   3.62   3.62   3.62   3.62   3.62   3.62

#      Molecule1      Molecule2       DISTANCE
LGA    N     228      N     228          3.591
LGA    N     229      N     229          2.748
LGA    S     230      S     230          1.622
LGA    L     231      L     231          0.883
LGA    P     232      P     232          1.961
LGA    N     233      N     233          2.088
LGA    P     234      P     234          2.749
LGA    H     235      H     235          2.647
LGA    L     236      L     236          9.450
LGA    R     237      R     237         11.654

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   10   73    4.0      8    2.41     9.589     9.713     0.318

LGA_LOCAL      RMSD =  2.414  Number of atoms =    8  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  5.213  Number of atoms =   10 
Std_ALL_ATOMS  RMSD =  3.622  (standard rmsd on all 10 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.630085 * X  +   0.568627 * Y  +  -0.528825 * Z  +  50.023712
  Y_new =   0.663277 * X  +  -0.748238 * Y  +  -0.014273 * Z  +  -2.016618
  Z_new =  -0.403803 * X  +  -0.341764 * Y  +  -0.848611 * Z  +  93.195107 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.758732    0.382861  [ DEG:  -158.0637     21.9363 ]
  Theta =   0.415670    2.725923  [ DEG:    23.8161    156.1839 ]
  Phi   =   0.811055   -2.330537  [ DEG:    46.4700   -133.5300 ]
 
# 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: T0320TS105_2_1-D2                             
REMARK     2: T0320_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0320TS105_2_1-D2.T0320_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   10   73   4.0    8   2.41   9.713     3.62
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS105_2_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0320
PARENT 1sur
ATOM   1865  N   ASN   228      31.976  19.719   9.960  1.00222.96       1SG1866
ATOM   1866  CA  ASN   228      30.827  19.192   9.295  1.00222.96       1SG1867
ATOM   1867  CB  ASN   228      29.716  18.735  10.258  1.00222.96       1SG1868
ATOM   1868  CG  ASN   228      30.149  17.438  10.928  1.00222.96       1SG1869
ATOM   1869  OD1 ASN   228      31.114  16.795  10.517  1.00222.96       1SG1870
ATOM   1870  ND2 ASN   228      29.397  17.028  11.984  1.00222.96       1SG1871
ATOM   1871  C   ASN   228      30.196  20.149   8.341  1.00222.96       1SG1872
ATOM   1872  O   ASN   228      30.336  21.369   8.435  1.00222.96       1SG1873
ATOM   1873  N   ASN   229      29.498  19.539   7.361  1.00269.50       1SG1874
ATOM   1874  CA  ASN   229      28.688  20.165   6.358  1.00269.50       1SG1875
ATOM   1875  CB  ASN   229      29.202  19.923   4.927  1.00269.50       1SG1876
ATOM   1876  CG  ASN   229      28.465  20.854   3.979  1.00269.50       1SG1877
ATOM   1877  OD1 ASN   229      28.415  22.062   4.201  1.00269.50       1SG1878
ATOM   1878  ND2 ASN   229      27.884  20.282   2.890  1.00269.50       1SG1879
ATOM   1879  C   ASN   229      27.376  19.456   6.502  1.00269.50       1SG1880
ATOM   1880  O   ASN   229      27.342  18.334   7.006  1.00269.50       1SG1881
ATOM   1881  N   SER   230      26.244  20.068   6.104  1.00236.37       1SG1882
ATOM   1882  CA  SER   230      25.045  19.333   6.388  1.00236.37       1SG1883
ATOM   1883  CB  SER   230      24.307  19.851   7.632  1.00236.37       1SG1884
ATOM   1884  OG  SER   230      25.151  19.786   8.773  1.00236.37       1SG1885
ATOM   1885  C   SER   230      24.061  19.443   5.268  1.00236.37       1SG1886
ATOM   1886  O   SER   230      23.973  20.459   4.583  1.00236.37       1SG1887
ATOM   1887  N   LEU   231      23.305  18.345   5.054  1.00284.74       1SG1888
ATOM   1888  CA  LEU   231      22.198  18.319   4.141  1.00284.74       1SG1889
ATOM   1889  CB  LEU   231      22.424  17.499   2.859  1.00284.74       1SG1890
ATOM   1890  CG  LEU   231      21.202  17.505   1.918  1.00284.74       1SG1891
ATOM   1891  CD1 LEU   231      20.872  18.925   1.435  1.00284.74       1SG1892
ATOM   1892  CD2 LEU   231      21.378  16.509   0.762  1.00284.74       1SG1893
ATOM   1893  C   LEU   231      21.097  17.657   4.898  1.00284.74       1SG1894
ATOM   1894  O   LEU   231      21.242  16.525   5.363  1.00284.74       1SG1895
ATOM   1895  N   PRO   232      20.008  18.344   5.052  1.00176.77       1SG1896
ATOM   1896  CA  PRO   232      18.916  17.828   5.828  1.00176.77       1SG1897
ATOM   1897  CD  PRO   232      20.037  19.796   5.057  1.00176.77       1SG1898
ATOM   1898  CB  PRO   232      18.042  19.032   6.189  1.00176.77       1SG1899
ATOM   1899  CG  PRO   232      18.577  20.185   5.320  1.00176.77       1SG1900
ATOM   1900  C   PRO   232      18.151  16.685   5.239  1.00176.77       1SG1901
ATOM   1901  O   PRO   232      17.455  16.011   5.996  1.00176.77       1SG1902
ATOM   1902  N   ASN   233      18.232  16.439   3.918  1.00167.70       1SG1903
ATOM   1903  CA  ASN   233      17.402  15.405   3.364  1.00167.70       1SG1904
ATOM   1904  CB  ASN   233      17.267  15.486   1.836  1.00167.70       1SG1905
ATOM   1905  CG  ASN   233      16.525  16.779   1.524  1.00167.70       1SG1906
ATOM   1906  OD1 ASN   233      16.035  17.455   2.427  1.00167.70       1SG1907
ATOM   1907  ND2 ASN   233      16.438  17.138   0.216  1.00167.70       1SG1908
ATOM   1908  C   ASN   233      17.947  14.058   3.725  1.00167.70       1SG1909
ATOM   1909  O   ASN   233      19.131  13.764   3.565  1.00167.70       1SG1910
ATOM   1910  N   PRO   234      17.065  13.247   4.249  1.00113.15       1SG1911
ATOM   1911  CA  PRO   234      17.412  11.900   4.626  1.00113.15       1SG1912
ATOM   1912  CD  PRO   234      15.993  13.777   5.074  1.00113.15       1SG1913
ATOM   1913  CB  PRO   234      16.458  11.510   5.758  1.00113.15       1SG1914
ATOM   1914  CG  PRO   234      15.317  12.537   5.674  1.00113.15       1SG1915
ATOM   1915  C   PRO   234      17.322  10.973   3.453  1.00113.15       1SG1916
ATOM   1916  O   PRO   234      16.663  11.317   2.472  1.00113.15       1SG1917
ATOM   1917  N   HIS   235      17.989   9.801   3.534  1.00309.10       1SG1918
ATOM   1918  CA  HIS   235      17.909   8.805   2.506  1.00309.10       1SG1919
ATOM   1919  ND1 HIS   235      17.036   7.864  -0.436  1.00309.10       1SG1920
ATOM   1920  CG  HIS   235      18.266   8.254   0.055  1.00309.10       1SG1921
ATOM   1921  CB  HIS   235      18.452   9.269   1.142  1.00309.10       1SG1922
ATOM   1922  NE2 HIS   235      18.567   6.715  -1.569  1.00309.10       1SG1923
ATOM   1923  CD2 HIS   235      19.187   7.543  -0.649  1.00309.10       1SG1924
ATOM   1924  CE1 HIS   235      17.275   6.944  -1.403  1.00309.10       1SG1925
ATOM   1925  C   HIS   235      18.714   7.633   2.977  1.00309.10       1SG1926
ATOM   1926  O   HIS   235      19.536   7.759   3.883  1.00309.10       1SG1927
ATOM   1927  N   LEU   236      18.470   6.446   2.386  1.00337.57       1SG1928
ATOM   1928  CA  LEU   236      19.197   5.272   2.769  1.00337.57       1SG1929
ATOM   1929  CB  LEU   236      18.315   4.163   3.366  1.00337.57       1SG1930
ATOM   1930  CG  LEU   236      19.117   2.909   3.757  1.00337.57       1SG1931
ATOM   1931  CD1 LEU   236      20.204   3.232   4.796  1.00337.57       1SG1932
ATOM   1932  CD2 LEU   236      18.185   1.769   4.192  1.00337.57       1SG1933
ATOM   1933  C   LEU   236      19.838   4.712   1.545  1.00337.57       1SG1934
ATOM   1934  O   LEU   236      19.367   4.940   0.431  1.00337.57       1SG1935
ATOM   1935  N   ARG   237      20.956   3.976   1.719  1.00349.53       1SG1936
ATOM   1936  CA  ARG   237      21.599   3.385   0.585  1.00349.53       1SG1937
ATOM   1937  CB  ARG   237      23.040   3.853   0.348  1.00349.53       1SG1938
ATOM   1938  CG  ARG   237      23.666   3.181  -0.875  1.00349.53       1SG1939
ATOM   1939  CD  ARG   237      25.192   3.267  -0.917  1.00349.53       1SG1940
ATOM   1940  NE  ARG   237      25.717   2.193  -0.026  1.00349.53       1SG1941
ATOM   1941  CZ  ARG   237      26.951   1.659  -0.265  1.00349.53       1SG1942
ATOM   1942  NH1 ARG   237      27.695   2.111  -1.315  1.00349.53       1SG1943
ATOM   1943  NH2 ARG   237      27.439   0.672   0.541  1.00349.53       1SG1944
ATOM   1944  C   ARG   237      21.716   1.917   0.830  1.00349.53       1SG1945
ATOM   1945  O   ARG   237      21.996   1.476   1.943  1.00349.53       1SG1946
TER
END
