
#######################################################
#                                                     #
#                        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   12 (  112),  selected    6 , name T0321TS074_5-D2
# Molecule2: number of CA atoms  148 ( 1130),  selected    6 , name T0321_D2.pdb
# PARAMETERS: T0321TS074_5-D2.T0321_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:     6        97 - 102         2.74     2.74
  LCS_AVERAGE:      4.05

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        97 - 101         1.55     3.46
  LCS_AVERAGE:      3.27

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
# WARNING! The change of the parameter DIST cutoff may give you better result.

  LONGEST_CONTINUOUS_SEGMENT:     3        97 - 99          0.35     5.75
  LONGEST_CONTINUOUS_SEGMENT:     3        98 - 100         0.85     4.47
  LONGEST_CONTINUOUS_SEGMENT:     3        99 - 101         0.36     4.73
  LONGEST_CONTINUOUS_SEGMENT:     3       100 - 102         0.02     8.51
  LCS_AVERAGE:      2.03

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:  148
LCS_GDT     V      97     V      97      3    5    6     3    3    4    4    5    5    5    5    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     I      98     I      98      3    5    6     3    3    4    4    5    5    5    5    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     F      99     F      99      3    5    6     3    3    4    4    5    5    5    5    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     S     100     S     100      3    5    6     3    3    4    4    5    5    5    5    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     D     101     D     101      3    5    6     3    3    4    4    5    5    5    5    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     A     102     A     102      3    4    6     3    3    3    3    4    5    5    5    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_AVERAGE  LCS_A:   3.12  (   2.03    3.27    4.05 )

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      3      4      4      5      5      5      5      6      6      6      6      6      6      6      6      6      6      6      6 
GDT PERCENT_CA   2.03   2.03   2.70   2.70   3.38   3.38   3.38   3.38   4.05   4.05   4.05   4.05   4.05   4.05   4.05   4.05   4.05   4.05   4.05   4.05
GDT RMS_LOCAL    0.02   0.02   0.94   0.94   1.55   1.55   1.55   1.55   2.74   2.74   2.74   2.74   2.74   2.74   2.74   2.74   2.74   2.74   2.74   2.74
GDT RMS_ALL_CA   8.51   8.51   3.49   3.49   3.46   3.46   3.46   3.46   2.74   2.74   2.74   2.74   2.74   2.74   2.74   2.74   2.74   2.74   2.74   2.74

#      Molecule1      Molecule2       DISTANCE
LGA    V      97      V      97          0.721
LGA    I      98      I      98          2.016
LGA    F      99      F      99          2.459
LGA    S     100      S     100          0.843
LGA    D     101      D     101          0.839
LGA    A     102      A     102          7.745

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   12  148    4.0      5    1.55     3.041     3.341     0.303

LGA_LOCAL      RMSD =  1.552  Number of atoms =    5  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.465  Number of atoms =    6 
Std_ALL_ATOMS  RMSD =  2.738  (standard rmsd on all 6 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.602528 * X  +   0.750558 * Y  +   0.271334 * Z  +  -5.272251
  Y_new =   0.239330 * X  +   0.494251 * Y  +  -0.835726 * Z  +  34.175133
  Z_new =  -0.761368 * X  +  -0.438610 * Y  +  -0.477431 * Z  +  81.681534 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.398549    0.743044  [ DEG:  -137.4267     42.5733 ]
  Theta =   0.865421    2.276172  [ DEG:    49.5849    130.4151 ]
  Phi   =   2.763494   -0.378099  [ DEG:   158.3365    -21.6635 ]
 
# 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: T0321TS074_5-D2                               
REMARK     2: T0321_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0321TS074_5-D2.T0321_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   12  148   4.0    5   1.55   3.341     2.74
REMARK  ---------------------------------------------------------- 
MOLECULE T0321TS074_5-D2
PFRMAT TS
TARGET T0321
MODEL  5
PARENT N/A
ATOM    817  N   VAL    97      -4.067  44.335  80.300  1.00  1.00
ATOM    818  CA  VAL    97      -3.314  43.330  81.040  1.00  1.00
ATOM    819  C   VAL    97      -2.463  44.043  82.106  1.00  1.00
ATOM    820  O   VAL    97      -2.332  43.588  83.242  1.00  1.00
ATOM    821  HN  VAL    97      -3.764  44.458  79.356  1.00  1.00
ATOM    822  CB  VAL    97      -2.403  42.495  80.067  1.00  1.00
ATOM    823  CG1 VAL    97      -3.238  41.775  79.006  1.00  1.00
ATOM    824  CG2 VAL    97      -1.596  41.458  80.828  1.00  1.00
ATOM    825  N   ILE    98      -1.867  45.152  81.705  1.00  1.00
ATOM    826  CA  ILE    98      -1.057  45.931  82.643  1.00  1.00
ATOM    827  C   ILE    98      -1.965  46.833  83.470  1.00  1.00
ATOM    828  O   ILE    98      -2.641  47.702  82.924  1.00  1.00
ATOM    829  HN  ILE    98      -1.909  45.540  80.784  1.00  1.00
ATOM    830  CB  ILE    98       0.016  46.716  81.898  1.00  1.00
ATOM    831  CG1 ILE    98       0.901  45.750  81.067  1.00  1.00
ATOM    832  CG2 ILE    98       0.754  47.586  82.926  1.00  1.00
ATOM    833  CD1 ILE    98       1.586  44.710  82.095  1.00  1.00
ATOM    834  N   PHE    99      -1.939  46.649  84.775  1.00  1.00
ATOM    835  CA  PHE    99      -2.873  47.296  85.689  1.00  1.00
ATOM    836  C   PHE    99      -2.620  48.772  85.963  1.00  1.00
ATOM    837  O   PHE    99      -3.554  49.508  86.279  1.00  1.00
ATOM    838  HN  PHE    99      -1.276  46.051  85.226  1.00  1.00
ATOM    839  CB  PHE    99      -2.912  46.544  87.013  1.00  1.00
ATOM    840  CG  PHE    99      -3.466  45.122  86.932  1.00  1.00
ATOM    841  CD1 PHE    99      -4.425  44.824  85.954  1.00  1.00
ATOM    842  CD2 PHE    99      -3.189  44.182  87.893  1.00  1.00
ATOM    843  CE1 PHE    99      -5.034  43.586  85.963  1.00  1.00
ATOM    844  CE2 PHE    99      -3.760  42.937  87.915  1.00  1.00
ATOM    845  CZ  PHE    99      -4.703  42.624  86.900  1.00  1.00
ATOM    846  N   SER   100      -1.370  49.199  85.846  1.00  1.00
ATOM    847  CA  SER   100      -0.993  50.582  86.127  1.00  1.00
ATOM    848  C   SER   100      -1.930  51.636  85.524  1.00  1.00
ATOM    849  O   SER   100      -2.143  51.684  84.318  1.00  1.00
ATOM    850  HN  SER   100      -0.606  48.619  85.563  1.00  1.00
ATOM    851  CB  SER   100       0.467  50.827  85.684  1.00  1.00
ATOM    852  OG  SER   100       0.746  50.650  84.195  1.00  1.00
ATOM    853  N   ASP   101      -2.515  52.440  86.408  1.00  1.00
ATOM    854  CA  ASP   101      -3.403  53.535  86.049  1.00  1.00
ATOM    855  C   ASP   101      -4.796  53.210  85.507  1.00  1.00
ATOM    856  O   ASP   101      -5.531  54.104  85.087  1.00  1.00
ATOM    857  HN  ASP   101      -2.375  52.338  87.392  1.00  1.00
ATOM    858  CB  ASP   101      -2.678  54.473  85.087  1.00  1.00
ATOM    859  CG  ASP   101      -1.567  55.245  85.767  1.00  1.00
ATOM    860  OD1 ASP   101      -1.448  55.336  86.921  1.00  1.00
ATOM    861  OD2 ASP   101      -0.813  55.846  84.884  1.00  1.00
ATOM    862  N   ALA   102      -5.166  51.940  85.523  1.00  1.00
ATOM    863  CA  ALA   102      -6.479  51.561  85.064  1.00  1.00
ATOM    864  C   ALA   102      -7.479  51.789  86.197  1.00  1.00
ATOM    865  O   ALA   102      -7.102  51.840  87.374  1.00  1.00
ATOM    866  HN  ALA   102      -4.607  51.173  85.835  1.00  1.00
ATOM    867  CB  ALA   102      -6.485  50.090  84.651  1.00  1.00
ATOM    868  N   LYS   103      -8.748  51.937  85.836  1.00  1.00
ATOM    869  CA  LYS   103      -9.826  52.134  86.813  1.00  1.00
ATOM    870  C   LYS   103     -10.321  50.821  87.407  1.00  1.00
ATOM    871  O   LYS   103     -10.789  50.781  88.543  1.00  1.00
ATOM    872  HN  LYS   103      -9.058  51.926  84.885  1.00  1.00
ATOM    873  CB  LYS   103     -10.987  52.920  86.183  1.00  1.00
ATOM    874  CG  LYS   103     -12.086  53.202  87.192  1.00  1.00
ATOM    875  CD  LYS   103     -13.211  53.993  86.482  1.00  1.00
ATOM    876  CE  LYS   103     -14.004  53.294  85.445  1.00  1.00
ATOM    877  NZ  LYS   103     -15.067  54.172  84.830  1.00  1.00
ATOM    878  N   ARG   104     -10.206  49.747  86.638  1.00  1.00
ATOM    879  CA  ARG   104     -10.611  48.427  87.100  1.00  1.00
ATOM    880  C   ARG   104      -9.567  47.918  88.086  1.00  1.00
ATOM    881  O   ARG   104      -9.892  47.202  89.035  1.00  1.00
ATOM    882  HN  ARG   104      -9.844  49.758  85.706  1.00  1.00
ATOM    883  CB  ARG   104     -10.725  47.459  85.913  1.00  1.00
ATOM    884  CG  ARG   104     -11.761  47.855  84.898  1.00  1.00
ATOM    885  CD  ARG   104     -13.095  47.656  85.687  1.00  1.00
ATOM    886  NE  ARG   104     -14.165  48.023  84.767  1.00  1.00
ATOM    887  CZ  ARG   104     -15.456  47.979  85.091  1.00  1.00
ATOM    888  NH1 ARG   104     -15.819  47.505  86.283  1.00  1.00
ATOM    889  NH2 ARG   104     -16.347  48.358  84.182  1.00  1.00
ATOM    890  N   VAL   105      -8.316  48.302  87.844  1.00  1.00
ATOM    891  CA  VAL   105      -7.179  47.895  88.667  1.00  1.00
ATOM    892  C   VAL   105      -7.131  48.570  90.039  1.00  1.00
ATOM    893  O   VAL   105      -7.210  49.794  90.152  1.00  1.00
ATOM    894  HN  VAL   105      -8.071  48.896  87.078  1.00  1.00
ATOM    895  CB  VAL   105      -5.850  48.181  87.931  1.00  1.00
ATOM    896  CG1 VAL   105      -5.824  47.427  86.606  1.00  1.00
ATOM    897  CG2 VAL   105      -4.665  47.751  88.789  1.00  1.00
ATOM    898  N   GLU   106      -6.977  47.753  91.076  1.00  1.00
ATOM    899  CA  GLU   106      -6.923  48.241  92.443  1.00  1.00
ATOM    900  C   GLU   106      -5.502  48.592  92.871  1.00  1.00
ATOM    901  O   GLU   106      -5.225  49.740  93.213  1.00  1.00
ATOM    902  HN  GLU   106      -6.889  46.760  90.995  1.00  1.00
ATOM    903  CB  GLU   106      -7.496  47.194  93.395  1.00  1.00
ATOM    904  CG  GLU   106      -7.511  47.687  94.723  1.00  1.00
ATOM    905  CD  GLU   106      -8.115  46.610  95.792  1.00  1.00
ATOM    906  OE1 GLU   106      -8.489  45.516  95.377  1.00  1.00
ATOM    907  OE2 GLU   106      -8.187  46.971  97.004  1.00  1.00
ATOM    908  N   ASP   107      -4.611  47.601  92.860  1.00  1.00
ATOM    909  CA  ASP   107      -3.214  47.831  93.250  1.00  1.00
ATOM    910  C   ASP   107      -2.287  47.930  92.048  1.00  1.00
ATOM    911  O   ASP   107      -2.288  47.034  91.176  1.00  1.00
ATOM    912  HN  ASP   107      -4.810  46.657  92.596  1.00  1.00
ATOM    913  CB  ASP   107      -2.729  46.743  94.200  1.00  1.00
ATOM    914  CG  ASP   107      -0.979  46.951  94.720  1.00  1.00
ATOM    915  OD1 ASP   107      -0.559  47.575  94.538  1.00  1.00
ATOM    916  OD2 ASP   107      -1.161  45.488  95.221  1.00  1.00
ATOM    917  N   ARG   108      -1.466  48.987  91.988  1.00  1.00
ATOM    918  CA  ARG   108      -0.543  49.156  90.837  1.00  1.00
ATOM    919  C   ARG   108       0.474  48.026  90.758  1.00  1.00
ATOM    920  O   ARG   108       1.030  47.759  89.688  1.00  1.00
ATOM    921  HN  ARG   108      -1.403  49.717  92.670  1.00  1.00
ATOM    922  CB  ARG   108       0.195  50.518  90.920  1.00  1.00
ATOM    923  CG  ARG   108      -0.829  51.751  90.722  1.00  1.00
ATOM    924  CD  ARG   108       0.292  52.891  90.873  1.00  1.00
ATOM    925  NE  ARG   108       1.122  52.638  89.701  1.00  1.00
ATOM    926  CZ  ARG   108       0.857  53.131  88.494  1.00  1.00
ATOM    927  NH1 ARG   108      -0.263  53.829  88.300  1.00  1.00
ATOM    928  NH2 ARG   108       1.696  52.857  87.502  1.00  1.00
TER
END
