
#######################################################
#                                                     #
#                        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   17 (  145),  selected   17 , name T0386TS009_3_2-D1
# Molecule2: number of CA atoms  206 ( 1668),  selected   17 , name T0386_D1.pdb
# PARAMETERS: T0386TS009_3_2-D1.T0386_D1.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:    17        80 - 96          4.31     4.31
  LCS_AVERAGE:      8.25

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        86 - 91          1.76     8.22
  LCS_AVERAGE:      2.31

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4        88 - 91          0.99     7.17
  LCS_AVERAGE:      1.57

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:  206
LCS_GDT     F      80     F      80      3    3   17     3    3    3    6    7    9   10   11   12   13   15   16   16   16   17   17   17   17   17   17 
LCS_GDT     E      81     E      81      3    3   17     3    3    3    3    4    5    9   11   12   12   13   14   16   16   17   17   17   17   17   17 
LCS_GDT     W      82     W      82      3    4   17     3    3    4    6    7    9   10   11   13   14   15   16   16   16   17   17   17   17   17   17 
LCS_GDT     A      83     A      83      3    4   17     3    3    5    5    5    8   10   11   13   14   15   16   16   16   17   17   17   17   17   17 
LCS_GDT     G      84     G      84      3    4   17     3    3    3    6    7    8   10   11   13   14   15   16   16   16   17   17   17   17   17   17 
LCS_GDT     Y      85     Y      85      3    4   17     3    3    5    6    7    9   10   11   13   14   15   16   16   16   17   17   17   17   17   17 
LCS_GDT     L      86     L      86      3    6   17     3    4    5    6    7    9   10   11   13   14   15   16   16   16   17   17   17   17   17   17 
LCS_GDT     R      87     R      87      3    6   17     3    4    5    6    7    9   10   11   13   14   15   16   16   16   17   17   17   17   17   17 
LCS_GDT     H      88     H      88      4    6   17     3    3    5    5    7    9   10   11   13   14   15   16   16   16   17   17   17   17   17   17 
LCS_GDT     I      89     I      89      4    6   17     3    3    5    6    7    9   10   11   13   14   15   16   16   16   17   17   17   17   17   17 
LCS_GDT     P      90     P      90      4    6   17     3    3    5    6    7    9   10   11   12   14   15   16   16   16   17   17   17   17   17   17 
LCS_GDT     F      91     F      91      4    6   17     3    3    5    6    7    9   10   11   13   14   15   16   16   16   17   17   17   17   17   17 
LCS_GDT     T      92     T      92      3    5   17     3    3    3    6    7    8   10   11   13   14   15   16   16   16   17   17   17   17   17   17 
LCS_GDT     F      93     F      93      3    5   17     3    4    5    6    7    8   10   11   13   14   15   16   16   16   17   17   17   17   17   17 
LCS_GDT     A      94     A      94      3    5   17     3    3    4    5    5    5   10   10   12   14   15   16   16   16   17   17   17   17   17   17 
LCS_GDT     D      95     D      95      3    5   17     3    4    5    6    7    8   10   11   13   14   15   16   16   16   17   17   17   17   17   17 
LCS_GDT     G      96     G      96      3    3   17     3    3    3    3    5    8   10   11   13   14   15   16   16   16   17   17   17   17   17   17 
LCS_AVERAGE  LCS_A:   4.05  (   1.57    2.31    8.25 )

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      5      6      7      9     10     11     13     14     15     16     16     16     17     17     17     17     17     17 
GDT PERCENT_CA   1.46   1.94   2.43   2.91   3.40   4.37   4.85   5.34   6.31   6.80   7.28   7.77   7.77   7.77   8.25   8.25   8.25   8.25   8.25   8.25
GDT RMS_LOCAL    0.02   0.77   0.99   1.34   1.57   2.06   2.28   2.55   3.33   3.49   3.71   3.94   3.94   3.94   4.31   4.31   4.31   4.31   4.31   4.31
GDT RMS_ALL_CA  15.58   5.27   7.72   5.47   5.30   6.99   6.87   6.70   4.51   4.52   4.54   4.37   4.37   4.37   4.31   4.31   4.31   4.31   4.31   4.31

#      Molecule1      Molecule2       DISTANCE
LGA    F      80      F      80          1.840
LGA    E      81      E      81          5.748
LGA    W      82      W      82          1.252
LGA    A      83      A      83          3.714
LGA    G      84      G      84          3.997
LGA    Y      85      Y      85          2.679
LGA    L      86      L      86          1.047
LGA    R      87      R      87          3.275
LGA    H      88      H      88          2.443
LGA    I      89      I      89          2.294
LGA    P      90      P      90          2.220
LGA    F      91      F      91          1.713
LGA    T      92      T      92          6.901
LGA    F      93      F      93          8.850
LGA    A      94      A      94         12.682
LGA    D      95      D      95         14.435
LGA    G      96      G      96         13.075

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   17  206    4.0     11    2.55     4.612     4.315     0.416

LGA_LOCAL      RMSD =  2.546  Number of atoms =   11  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.739  Number of atoms =   17 
Std_ALL_ATOMS  RMSD =  4.311  (standard rmsd on all 17 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.093859 * X  +   0.273753 * Y  +  -0.957209 * Z  +  85.652473
  Y_new =  -0.632774 * X  +   0.725873 * Y  +   0.269639 * Z  +  74.143883
  Z_new =   0.768627 * X  +   0.631006 * Y  +   0.105094 * Z  +  -0.218345 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.405761   -1.735832  [ DEG:    80.5442    -99.4558 ]
  Theta =  -0.876692   -2.264901  [ DEG:   -50.2307   -129.7693 ]
  Phi   =  -1.718052    1.423541  [ DEG:   -98.4371     81.5629 ]
 
# 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: T0386TS009_3_2-D1                             
REMARK     2: T0386_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0386TS009_3_2-D1.T0386_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   17  206   4.0   11   2.55   4.315     4.31
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS009_3_2-D1
REMARK PARENT number 2
PFRMAT TS                                                                       
TARGET T0386                                                                    
PARENT N/A                                                                      
ATOM    647  N   PHE    80      16.116  69.358  44.500  1.00  0.00             
ATOM    648  CA  PHE    80      16.284  69.052  43.085  1.00  0.00             
ATOM    649  C   PHE    80      15.471  67.827  42.685  1.00  0.00             
ATOM    650  O   PHE    80      14.988  67.732  41.556  1.00  0.00             
ATOM    651  CB  PHE    80      15.884  70.254  42.226  1.00  0.00             
ATOM    652  CG  PHE    80      16.840  71.408  42.315  1.00  0.00             
ATOM    653  CD1 PHE    80      17.791  71.464  43.320  1.00  0.00             
ATOM    654  CD2 PHE    80      16.790  72.439  41.394  1.00  0.00             
ATOM    655  CE1 PHE    80      18.671  72.525  43.401  1.00  0.00             
ATOM    656  CE2 PHE    80      17.671  73.502  41.474  1.00  0.00             
ATOM    657  CZ  PHE    80      18.608  73.547  42.473  1.00  0.00             
ATOM    658  N   GLU    81      15.321  66.891  43.616  1.00  0.00             
ATOM    659  CA  GLU    81      14.566  65.670  43.363  1.00  0.00             
ATOM    660  C   GLU    81      13.375  65.939  42.449  1.00  0.00             
ATOM    661  O   GLU    81      12.321  65.318  42.587  1.00  0.00             
ATOM    662  CB  GLU    81      15.469  64.599  42.750  1.00  0.00             
ATOM    663  CG  GLU    81      16.939  64.984  42.694  1.00  0.00             
ATOM    664  CD  GLU    81      17.753  64.341  43.799  1.00  0.00             
ATOM    665  OE1 GLU    81      17.310  64.386  44.966  1.00  0.00             
ATOM    666  OE2 GLU    81      18.833  63.792  43.499  1.00  0.00             
ATOM    667  N   TRP    82      13.552  66.867  41.513  1.00  0.00             
ATOM    668  CA  TRP    82      12.493  67.219  40.574  1.00  0.00             
ATOM    669  C   TRP    82      11.644  66.002  40.218  1.00  0.00             
ATOM    670  O   TRP    82      12.023  65.197  39.369  1.00  0.00             
ATOM    671  CB  TRP    82      11.609  68.326  41.153  1.00  0.00             
ATOM    672  CG  TRP    82      12.360  69.577  41.491  1.00  0.00             
ATOM    673  CD1 TRP    82      12.144  70.825  40.984  1.00  0.00             
ATOM    674  CD2 TRP    82      13.450  69.701  42.413  1.00  0.00             
ATOM    675  NE1 TRP    82      13.030  71.721  41.532  1.00  0.00             
ATOM    676  CE2 TRP    82      13.844  71.054  42.413  1.00  0.00             
ATOM    677  CE3 TRP    82      14.130  68.799  43.238  1.00  0.00             
ATOM    678  CZ2 TRP    82      14.888  71.527  43.206  1.00  0.00             
ATOM    679  CZ3 TRP    82      15.165  69.272  44.023  1.00  0.00             
ATOM    680  CH2 TRP    82      15.536  70.625  44.003  1.00  0.00             
ATOM    681  N   ALA    83      10.496  65.877  40.875  1.00  0.00             
ATOM    682  CA  ALA    83       9.591  64.759  40.631  1.00  0.00             
ATOM    683  C   ALA    83      10.048  63.507  41.372  1.00  0.00             
ATOM    684  O   ALA    83       9.706  62.388  40.990  1.00  0.00             
ATOM    685  CB  ALA    83       8.173  65.124  41.042  1.00  0.00             
ATOM    686  N   GLY    84      10.822  63.704  42.434  1.00  0.00             
ATOM    687  CA  GLY    84      11.311  62.580  43.210  1.00  0.00             
ATOM    688  C   GLY    84      11.373  61.299  42.401  1.00  0.00             
ATOM    689  O   GLY    84      11.199  60.205  42.939  1.00  0.00             
ATOM    690  N   TYR    85      11.621  61.431  41.103  1.00  0.00             
ATOM    691  CA  TYR    85      11.706  60.277  40.217  1.00  0.00             
ATOM    692  C   TYR    85      11.058  59.049  40.848  1.00  0.00             
ATOM    693  O   TYR    85      11.169  57.939  40.327  1.00  0.00             
ATOM    694  CB  TYR    85      11.046  60.585  38.871  1.00  0.00             
ATOM    695  CG  TYR    85       9.832  61.481  38.973  1.00  0.00             
ATOM    696  CD1 TYR    85       9.497  62.346  37.940  1.00  0.00             
ATOM    697  CD2 TYR    85       9.025  61.458  40.104  1.00  0.00             
ATOM    698  CE1 TYR    85       8.389  63.168  38.025  1.00  0.00             
ATOM    699  CE2 TYR    85       7.914  62.272  40.206  1.00  0.00             
ATOM    700  CZ  TYR    85       7.600  63.132  39.154  1.00  0.00             
ATOM    701  OH  TYR    85       6.496  63.947  39.246  1.00  0.00             
ATOM    702  N   LEU    86      10.382  59.255  41.974  1.00  0.00             
ATOM    703  CA  LEU    86       9.716  58.167  42.679  1.00  0.00             
ATOM    704  C   LEU    86      10.285  56.813  42.266  1.00  0.00             
ATOM    705  O   LEU    86       9.698  56.106  41.446  1.00  0.00             
ATOM    706  CB  LEU    86       9.844  58.351  44.193  1.00  0.00             
ATOM    707  CG  LEU    86       9.489  57.138  45.055  1.00  0.00             
ATOM    708  CD1 LEU    86       8.927  57.580  46.398  1.00  0.00             
ATOM    709  CD2 LEU    86      10.701  56.240  45.244  1.00  0.00             
ATOM    710  N   ARG    87      11.431  56.459  42.838  1.00  0.00             
ATOM    711  CA  ARG    87      12.082  55.191  42.530  1.00  0.00             
ATOM    712  C   ARG    87      12.924  55.295  41.264  1.00  0.00             
ATOM    713  O   ARG    87      12.963  54.369  40.455  1.00  0.00             
ATOM    714  CB  ARG    87      12.950  54.735  43.705  1.00  0.00             
ATOM    715  CG  ARG    87      14.382  54.396  43.323  1.00  0.00             
ATOM    716  CD  ARG    87      14.516  54.175  41.825  1.00  0.00             
ATOM    717  NE  ARG    87      13.248  53.789  41.213  1.00  0.00             
ATOM    718  CZ  ARG    87      13.118  53.390  39.953  1.00  0.00             
ATOM    719  NH1 ARG    87      14.182  53.324  39.164  1.00  0.00             
ATOM    720  NH2 ARG    87      11.924  53.058  39.482  1.00  0.00             
ATOM    721  N   HIS    88      13.597  56.430  41.099  1.00  0.00             
ATOM    722  CA  HIS    88      14.440  56.658  39.932  1.00  0.00             
ATOM    723  C   HIS    88      13.661  57.342  38.814  1.00  0.00             
ATOM    724  O   HIS    88      14.186  57.564  37.723  1.00  0.00             
ATOM    725  CB  HIS    88      15.664  57.495  40.310  1.00  0.00             
ATOM    726  CG  HIS    88      16.931  57.046  39.651  1.00  0.00             
ATOM    727  ND1 HIS    88      17.023  55.867  38.943  1.00  0.00             
ATOM    728  CD2 HIS    88      18.157  57.616  39.593  1.00  0.00             
ATOM    729  CE1 HIS    88      18.253  55.733  38.478  1.00  0.00             
ATOM    730  NE2 HIS    88      18.960  56.779  38.857  1.00  0.00             
ATOM    731  N   ILE    89      12.405  57.676  39.093  1.00  0.00             
ATOM    732  CA  ILE    89      11.532  58.352  38.090  1.00  0.00             
ATOM    733  C   ILE    89      12.355  59.194  37.121  1.00  0.00             
ATOM    734  O   ILE    89      11.875  60.189  36.578  1.00  0.00             
ATOM    735  CB  ILE    89      10.698  57.332  37.291  1.00  0.00             
ATOM    736  CG2 ILE    89      10.414  56.099  38.134  1.00  0.00             
ATOM    737  CG1 ILE    89      11.421  56.950  35.998  1.00  0.00             
ATOM    738  CD1 ILE    89      10.748  55.833  35.231  1.00  0.00             
ATOM    739  N   PRO    90      13.615  58.797  36.893  1.00  0.00             
ATOM    740  CA  PRO    90      14.516  59.514  35.985  1.00  0.00             
ATOM    741  C   PRO    90      13.750  60.246  34.889  1.00  0.00             
ATOM    742  O   PRO    90      13.711  59.802  33.741  1.00  0.00             
ATOM    743  CB  PRO    90      15.206  60.520  36.908  1.00  0.00             
ATOM    744  CG  PRO    90      14.590  60.284  38.246  1.00  0.00             
ATOM    745  CD  PRO    90      14.256  57.620  37.506  1.00  0.00             
ATOM    746  N   PHE    91      13.141  61.371  35.250  1.00  0.00             
ATOM    747  CA  PHE    91      12.376  62.168  34.298  1.00  0.00             
ATOM    748  C   PHE    91      11.772  61.292  33.206  1.00  0.00             
ATOM    749  O   PHE    91      11.616  61.724  32.064  1.00  0.00             
ATOM    750  CB  PHE    91      11.273  62.947  35.017  1.00  0.00             
ATOM    751  CG  PHE    91      11.785  64.056  35.890  1.00  0.00             
ATOM    752  CD1 PHE    91      11.877  63.893  37.262  1.00  0.00             
ATOM    753  CD2 PHE    91      12.175  65.266  35.339  1.00  0.00             
ATOM    754  CE1 PHE    91      12.348  64.915  38.064  1.00  0.00             
ATOM    755  CE2 PHE    91      12.647  66.287  36.142  1.00  0.00             
ATOM    756  CZ  PHE    91      12.734  66.115  37.499  1.00  0.00             
ATOM    757  N   THR    92      11.434  60.057  33.564  1.00  0.00             
ATOM    758  CA  THR    92      10.833  59.097  32.595  1.00  0.00             
ATOM    759  C   THR    92      11.182  59.473  31.158  1.00  0.00             
ATOM    760  O   THR    92      10.695  58.857  30.209  1.00  0.00             
ATOM    761  CB  THR    92      11.300  57.655  32.866  1.00  0.00             
ATOM    762  OG1 THR    92      12.289  57.657  33.902  1.00  0.00             
ATOM    763  CG2 THR    92      10.125  56.787  33.295  1.00  0.00             
ATOM    764  N   PHE    93      12.030  60.485  31.006  1.00  0.00             
ATOM    765  CA  PHE    93      12.446  60.944  29.686  1.00  0.00             
ATOM    766  C   PHE    93      13.459  59.988  29.064  1.00  0.00             
ATOM    767  O   PHE    93      13.814  58.971  29.660  1.00  0.00             
ATOM    768  CB  PHE    93      11.233  61.098  28.766  1.00  0.00             
ATOM    769  CG  PHE    93      11.591  61.268  27.317  1.00  0.00             
ATOM    770  CD1 PHE    93      11.753  60.167  26.494  1.00  0.00             
ATOM    771  CD2 PHE    93      11.765  62.531  26.776  1.00  0.00             
ATOM    772  CE1 PHE    93      12.081  60.325  25.161  1.00  0.00             
ATOM    773  CE2 PHE    93      12.094  62.688  25.443  1.00  0.00             
ATOM    774  CZ  PHE    93      12.252  61.592  24.637  1.00  0.00             
ATOM    775  N   ALA    94      13.921  60.323  27.864  1.00  0.00             
ATOM    776  CA  ALA    94      14.893  59.495  27.160  1.00  0.00             
ATOM    777  C   ALA    94      14.695  59.577  25.649  1.00  0.00             
ATOM    778  O   ALA    94      15.583  59.218  24.877  1.00  0.00             
ATOM    779  CB  ALA    94      16.309  59.913  27.526  1.00  0.00             
ATOM    780  N   ASP    95      13.524  60.051  25.235  1.00  0.00             
ATOM    781  CA  ASP    95      13.207  60.180  23.818  1.00  0.00             
ATOM    782  C   ASP    95      13.584  58.917  23.052  1.00  0.00             
ATOM    783  O   ASP    95      13.007  58.618  22.006  1.00  0.00             
ATOM    784  CB  ASP    95      11.720  60.486  23.628  1.00  0.00             
ATOM    785  CG  ASP    95      11.041  60.900  24.918  1.00  0.00             
ATOM    786  OD1 ASP    95      11.754  61.271  25.874  1.00  0.00             
ATOM    787  OD2 ASP    95       9.793  60.854  24.974  1.00  0.00             
ATOM    788  N   GLY    96      14.556  58.179  23.579  1.00  0.00             
ATOM    789  CA  GLY    96      14.991  56.958  22.928  1.00  0.00             
ATOM    790  C   GLY    96      14.788  56.995  21.426  1.00  0.00             
ATOM    791  O   GLY    96      14.134  57.897  20.901  1.00  0.00             
TER
END
