
#######################################################
#                                                     #
#                        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_2-D2
# Molecule2: number of CA atoms  148 ( 1130),  selected    6 , name T0321_D2.pdb
# PARAMETERS: T0321TS074_2-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         2.22     2.22
  LCS_AVERAGE:      4.05

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        97 - 101         1.25     2.93
  LONGEST_CONTINUOUS_SEGMENT:     5        98 - 102         1.90     3.11
  LCS_AVERAGE:      3.38

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          0.28     3.30
  LONGEST_CONTINUOUS_SEGMENT:     3        98 - 100         0.67     3.26
  LONGEST_CONTINUOUS_SEGMENT:     3        99 - 101         0.74     4.34
  LONGEST_CONTINUOUS_SEGMENT:     3       100 - 102         0.35     7.85
  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    4    4    4    5    5    6    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     I      98     I      98      3    5    6     3    4    4    4    5    5    6    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     F      99     F      99      3    5    6     3    3    3    4    5    5    6    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     S     100     S     100      3    5    6     3    4    4    4    5    5    6    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     D     101     D     101      3    5    6     3    4    4    4    5    5    6    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     A     102     A     102      3    5    6     3    3    3    4    5    5    6    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_AVERAGE  LCS_A:   3.15  (   2.03    3.38    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      4      4      4      5      5      6      6      6      6      6      6      6      6      6      6      6      6      6      6 
GDT PERCENT_CA   2.03   2.70   2.70   2.70   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   4.05   4.05
GDT RMS_LOCAL    0.28   0.60   0.60   0.60   1.25   1.25   2.22   2.22   2.22   2.22   2.22   2.22   2.22   2.22   2.22   2.22   2.22   2.22   2.22   2.22
GDT RMS_ALL_CA   3.30   3.14   3.14   3.14   2.93   2.93   2.22   2.22   2.22   2.22   2.22   2.22   2.22   2.22   2.22   2.22   2.22   2.22   2.22   2.22

#      Molecule1      Molecule2       DISTANCE
LGA    V      97      V      97          1.267
LGA    I      98      I      98          1.403
LGA    F      99      F      99          1.697
LGA    S     100      S     100          1.404
LGA    D     101      D     101          3.459
LGA    A     102      A     102          3.039

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   12  148    4.0      6    2.22     3.378     3.497     0.258

LGA_LOCAL      RMSD =  2.222  Number of atoms =    6  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  2.222  Number of atoms =    6 
Std_ALL_ATOMS  RMSD =  2.222  (standard rmsd on all 6 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.754243 * X  +   0.119295 * Y  +   0.645667 * Z  + -84.857895
  Y_new =  -0.648991 * X  +   0.284674 * Y  +   0.705529 * Z  +  34.614437
  Z_new =  -0.099638 * X  +  -0.951173 * Y  +   0.292135 * Z  + 169.447311 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.272810    1.868783  [ DEG:   -72.9266    107.0734 ]
  Theta =   0.099804    3.041789  [ DEG:     5.7183    174.2817 ]
  Phi   =  -0.710531    2.431062  [ DEG:   -40.7104    139.2896 ]
 
# 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_2-D2                               
REMARK     2: T0321_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0321TS074_2-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    6   2.22   3.497     2.22
REMARK  ---------------------------------------------------------- 
MOLECULE T0321TS074_2-D2
PFRMAT TS
TARGET T0321
MODEL  2
PARENT N/A
ATOM    817  N   VAL    97      -3.490  43.179  79.813  1.00  1.00
ATOM    818  CA  VAL    97      -2.487  43.849  80.632  1.00  1.00
ATOM    819  C   VAL    97      -3.153  44.572  81.798  1.00  1.00
ATOM    820  O   VAL    97      -4.336  44.925  81.729  1.00  1.00
ATOM    821  HN  VAL    97      -3.553  43.531  78.879  1.00  1.00
ATOM    822  CB  VAL    97      -1.660  44.821  79.804  1.00  1.00
ATOM    823  CG1 VAL    97      -0.647  45.677  80.588  1.00  1.00
ATOM    824  CG2 VAL    97      -2.458  45.885  79.025  1.00  1.00
ATOM    825  N   ILE    98      -2.440  44.611  82.931  1.00  1.00
ATOM    826  CA  ILE    98      -2.987  45.285  84.113  1.00  1.00
ATOM    827  C   ILE    98      -2.322  46.645  84.276  1.00  1.00
ATOM    828  O   ILE    98      -1.113  46.717  84.494  1.00  1.00
ATOM    829  HN  ILE    98      -1.532  44.214  83.072  1.00  1.00
ATOM    830  CB  ILE    98      -2.768  44.422  85.350  1.00  1.00
ATOM    831  CG1 ILE    98      -3.374  43.015  85.246  1.00  1.00
ATOM    832  CG2 ILE    98      -3.263  45.220  86.565  1.00  1.00
ATOM    833  CD1 ILE    98      -4.881  43.023  85.032  1.00  1.00
ATOM    834  N   PHE    99      -3.088  47.715  84.059  1.00  1.00
ATOM    835  CA  PHE    99      -2.517  49.058  84.116  1.00  1.00
ATOM    836  C   PHE    99      -2.304  49.499  85.561  1.00  1.00
ATOM    837  O   PHE    99      -3.244  49.579  86.348  1.00  1.00
ATOM    838  HN  PHE    99      -4.066  47.697  83.849  1.00  1.00
ATOM    839  CB  PHE    99      -3.401  50.060  83.373  1.00  1.00
ATOM    840  CG  PHE    99      -3.529  49.847  81.860  1.00  1.00
ATOM    841  CD1 PHE    99      -2.409  49.257  81.216  1.00  1.00
ATOM    842  CD2 PHE    99      -4.339  50.645  81.112  1.00  1.00
ATOM    843  CE1 PHE    99      -2.331  49.253  79.817  1.00  1.00
ATOM    844  CE2 PHE    99      -4.256  50.658  79.722  1.00  1.00
ATOM    845  CZ  PHE    99      -3.245  49.961  79.092  1.00  1.00
ATOM    846  N   SER   100      -1.043  49.639  85.939  1.00  1.00
ATOM    847  CA  SER   100      -0.647  50.028  87.287  1.00  1.00
ATOM    848  C   SER   100      -0.635  51.548  87.393  1.00  1.00
ATOM    849  O   SER   100      -0.861  52.108  88.466  1.00  1.00
ATOM    850  HN  SER   100      -0.274  49.486  85.317  1.00  1.00
ATOM    851  CB  SER   100       0.744  49.479  87.619  1.00  1.00
ATOM    852  OG  SER   100       1.853  50.004  86.723  1.00  1.00
ATOM    853  N   ASP   101      -0.376  52.209  86.268  1.00  1.00
ATOM    854  CA  ASP   101      -0.338  53.667  86.219  1.00  1.00
ATOM    855  C   ASP   101      -1.639  54.226  85.651  1.00  1.00
ATOM    856  O   ASP   101      -1.940  54.048  84.469  1.00  1.00
ATOM    857  HN  ASP   101      -0.191  51.768  85.390  1.00  1.00
ATOM    858  CB  ASP   101       0.852  54.134  85.377  1.00  1.00
ATOM    859  CG  ASP   101       2.183  53.873  86.054  1.00  1.00
ATOM    860  OD1 ASP   101       2.546  53.647  86.927  1.00  1.00
ATOM    861  OD2 ASP   101       3.016  54.266  84.787  1.00  1.00
ATOM    862  N   ALA   102      -2.423  54.924  86.490  1.00  1.00
ATOM    863  CA  ALA   102      -3.710  55.532  86.141  1.00  1.00
ATOM    864  C   ALA   102      -3.712  56.342  84.849  1.00  1.00
ATOM    865  O   ALA   102      -4.664  56.275  84.072  1.00  1.00
ATOM    866  HN  ALA   102      -2.150  55.068  87.443  1.00  1.00
ATOM    867  CB  ALA   102      -4.019  56.410  87.351  1.00  1.00
ATOM    868  N   LYS   103      -2.649  57.110  84.628  1.00  1.00
ATOM    869  CA  LYS   103      -2.549  57.950  83.439  1.00  1.00
ATOM    870  C   LYS   103      -2.466  57.158  82.138  1.00  1.00
ATOM    871  O   LYS   103      -2.601  57.727  81.055  1.00  1.00
ATOM    872  HN  LYS   103      -1.859  57.171  85.237  1.00  1.00
ATOM    873  CB  LYS   103      -1.329  58.873  83.546  1.00  1.00
ATOM    874  CG  LYS   103      -1.250  59.747  82.432  1.00  1.00
ATOM    875  CD  LYS   103      -2.445  60.807  82.446  1.00  1.00
ATOM    876  CE  LYS   103      -2.579  61.830  81.383  1.00  1.00
ATOM    877  NZ  LYS   103      -3.775  62.730  81.583  1.00  1.00
ATOM    878  N   ARG   104      -2.255  55.851  82.241  1.00  1.00
ATOM    879  CA  ARG   104      -2.135  55.008  81.056  1.00  1.00
ATOM    880  C   ARG   104      -3.411  54.263  80.674  1.00  1.00
ATOM    881  O   ARG   104      -3.453  53.590  79.642  1.00  1.00
ATOM    882  HN  ARG   104      -2.163  55.355  83.104  1.00  1.00
ATOM    883  CB  ARG   104      -1.004  53.999  81.252  1.00  1.00
ATOM    884  CG  ARG   104      -0.752  53.119  80.040  1.00  1.00
ATOM    885  CD  ARG   104       0.434  52.218  80.544  1.00  1.00
ATOM    886  NE  ARG   104      -0.115  51.424  81.637  1.00  1.00
ATOM    887  CZ  ARG   104       0.618  50.604  82.386  1.00  1.00
ATOM    888  NH1 ARG   104       1.906  50.419  82.094  1.00  1.00
ATOM    889  NH2 ARG   104       0.018  49.946  83.372  1.00  1.00
ATOM    890  N   VAL   105      -4.446  54.378  81.495  1.00  1.00
ATOM    891  CA  VAL   105      -5.705  53.698  81.214  1.00  1.00
ATOM    892  C   VAL   105      -6.523  54.409  80.141  1.00  1.00
ATOM    893  O   VAL   105      -6.882  55.581  80.276  1.00  1.00
ATOM    894  HN  VAL   105      -4.455  54.916  82.338  1.00  1.00
ATOM    895  CB  VAL   105      -6.570  53.548  82.483  1.00  1.00
ATOM    896  CG1 VAL   105      -5.816  52.739  83.526  1.00  1.00
ATOM    897  CG2 VAL   105      -7.885  52.849  82.142  1.00  1.00
ATOM    898  N   GLU   106      -6.808  53.678  79.068  1.00  1.00
ATOM    899  CA  GLU   106      -7.586  54.187  77.949  1.00  1.00
ATOM    900  C   GLU   106      -9.029  53.718  78.073  1.00  1.00
ATOM    901  O   GLU   106      -9.961  54.452  77.749  1.00  1.00
ATOM    902  HN  GLU   106      -6.507  52.731  78.957  1.00  1.00
ATOM    903  CB  GLU   106      -7.000  53.673  76.635  1.00  1.00
ATOM    904  CG  GLU   106      -5.608  54.177  76.332  1.00  1.00
ATOM    905  CD  GLU   106      -5.503  55.657  76.103  1.00  1.00
ATOM    906  OE1 GLU   106      -6.369  56.250  75.464  1.00  1.00
ATOM    907  OE2 GLU   106      -4.474  56.215  76.590  1.00  1.00
ATOM    908  N   ASP   107      -9.202  52.487  78.546  1.00  1.00
ATOM    909  CA  ASP   107     -10.531  51.912  78.704  1.00  1.00
ATOM    910  C   ASP   107     -10.535  50.866  79.810  1.00  1.00
ATOM    911  O   ASP   107      -9.489  50.332  80.181  1.00  1.00
ATOM    912  HN  ASP   107      -8.459  51.877  78.821  1.00  1.00
ATOM    913  CB  ASP   107     -10.981  51.278  77.396  1.00  1.00
ATOM    914  CG  ASP   107     -10.110  50.121  76.903  1.00  1.00
ATOM    915  OD1 ASP   107      -9.222  49.738  77.170  1.00  1.00
ATOM    916  OD2 ASP   107     -10.948  49.809  75.686  1.00  1.00
ATOM    917  N   ARG   108     -11.720  50.588  80.337  1.00  1.00
ATOM    918  CA  ARG   108     -11.883  49.595  81.392  1.00  1.00
ATOM    919  C   ARG   108     -11.991  48.215  80.762  1.00  1.00
ATOM    920  O   ARG   108     -12.324  48.088  79.585  1.00  1.00
ATOM    921  HN  ARG   108     -12.573  51.028  80.057  1.00  1.00
ATOM    922  CB  ARG   108     -13.159  49.873  82.186  1.00  1.00
ATOM    923  CG  ARG   108     -13.468  48.976  83.384  1.00  1.00
ATOM    924  CD  ARG   108     -12.410  49.218  84.365  1.00  1.00
ATOM    925  NE  ARG   108     -12.709  48.359  85.505  1.00  1.00
ATOM    926  CZ  ARG   108     -12.335  47.084  85.582  1.00  1.00
ATOM    927  NH1 ARG   108     -11.723  46.516  84.542  1.00  1.00
ATOM    928  NH2 ARG   108     -12.640  46.401  86.679  1.00  1.00
TER
END
