
#######################################################
#                                                     #
#                        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   21 (  153),  selected   21 , name T0382TS009_2_4-D1
# Molecule2: number of CA atoms  119 (  920),  selected   21 , name T0382_D1.pdb
# PARAMETERS: T0382TS009_2_4-D1.T0382_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:    21       102 - 122         3.46     3.46
  LCS_AVERAGE:     17.65

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       116 - 120         1.93     9.41
  LCS_AVERAGE:      3.56

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       117 - 120         0.80    16.13
  LONGEST_CONTINUOUS_SEGMENT:     4       119 - 122         0.92    27.97
  LCS_AVERAGE:      2.76

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:  119
LCS_GDT     F     102     F     102      3    4   21     3    3    3    7    8   13   15   18   19   20   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     P     103     P     103      3    4   21     3    3    5    7    8   12   15   18   19   20   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     Q     104     Q     104      3    4   21     3    3    4    6    7   12   13   18   19   20   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     A     105     A     105      3    4   21     3    3    5    7    9   13   15   18   19   20   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     G     106     G     106      3    4   21     3    3    4    4    9   13   15   18   19   20   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     D     107     D     107      3    4   21     3    3    5    7    8   12   14   18   19   20   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     A     108     A     108      3    4   21     3    3    4    6    8   13   15   18   19   20   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     G     109     G     109      3    4   21     3    3    5    7    9   13   15   18   19   20   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     M     110     M     110      3    4   21     3    3    5    7    8   13   15   18   19   20   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     C     111     C     111      3    4   21     3    3    4    5    7   10   12   14   19   20   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     L     112     L     112      3    4   21     3    3    5    7    9   13   15   18   19   20   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     D     113     D     113      3    4   21     3    3    4    6    9   13   15   18   19   20   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     L     114     L     114      3    4   21     3    3    5    7    8   10   15   18   19   20   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     L     115     L     115      3    4   21     3    3    4    5    9   13   15   18   19   20   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     D     116     D     116      3    5   21     3    3    4    6    8   10   12   13   19   20   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     D     117     D     117      4    5   21     3    3    4    6    9   13   15   18   19   20   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     G     118     G     118      4    5   21     3    3    4    6    9   12   15   18   19   20   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     T     119     T     119      4    5   21     3    3    4    6    9   13   15   18   19   20   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     F     120     F     120      4    5   21     3    3    4    4    5    7   10   12   16   20   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     K     121     K     121      4    4   21     3    3    4    5    9   13   15   18   19   20   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     P     122     P     122      4    4   21     3    3    4    6    9   13   15   18   19   20   21   21   21   21   21   21   21   21   21   21 
LCS_AVERAGE  LCS_A:   7.99  (   2.76    3.56   17.65 )

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      5      7      9     13     15     18     19     20     21     21     21     21     21     21     21     21     21     21 
GDT PERCENT_CA   2.52   2.52   4.20   5.88   7.56  10.92  12.61  15.13  15.97  16.81  17.65  17.65  17.65  17.65  17.65  17.65  17.65  17.65  17.65  17.65
GDT RMS_LOCAL    0.02   0.02   0.91   1.31   1.85   2.40   2.66   2.99   3.10   3.24   3.46   3.46   3.46   3.46   3.46   3.46   3.46   3.46   3.46   3.46
GDT RMS_ALL_CA  27.18  27.18   5.64   5.88   4.24   3.73   3.56   3.49   3.48   3.48   3.46   3.46   3.46   3.46   3.46   3.46   3.46   3.46   3.46   3.46

#      Molecule1      Molecule2       DISTANCE
LGA    F     102      F     102          2.878
LGA    P     103      P     103          2.229
LGA    Q     104      Q     104          3.946
LGA    A     105      A     105          3.496
LGA    G     106      G     106          3.820
LGA    D     107      D     107          3.222
LGA    A     108      A     108          1.994
LGA    G     109      G     109          3.637
LGA    M     110      M     110          1.823
LGA    C     111      C     111          5.071
LGA    L     112      L     112          1.718
LGA    D     113      D     113          3.292
LGA    L     114      L     114          3.760
LGA    L     115      L     115          2.196
LGA    D     116      D     116          4.693
LGA    D     117      D     117          2.768
LGA    G     118      G     118          3.644
LGA    T     119      T     119          2.894
LGA    F     120      F     120          7.055
LGA    K     121      K     121          3.053
LGA    P     122      P     122          2.407

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   21  119    4.0     18    2.99    10.294     9.489     0.583

LGA_LOCAL      RMSD =  2.989  Number of atoms =   18  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.527  Number of atoms =   21 
Std_ALL_ATOMS  RMSD =  3.457  (standard rmsd on all 21 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.308649 * X  +   0.862547 * Y  +  -0.400934 * Z  + -42.170078
  Y_new =   0.851446 * X  +  -0.062648 * Y  +   0.520687 * Z  +  -1.368563
  Z_new =   0.424000 * X  +  -0.502083 * Y  +  -0.753748 * Z  + -46.440659 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.553972    0.587621  [ DEG:  -146.3318     33.6682 ]
  Theta =  -0.437857   -2.703736  [ DEG:   -25.0874   -154.9126 ]
  Phi   =   1.223030   -1.918563  [ DEG:    70.0744   -109.9256 ]
 
# 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: T0382TS009_2_4-D1                             
REMARK     2: T0382_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0382TS009_2_4-D1.T0382_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   21  119   4.0   18   2.99   9.489     3.46
REMARK  ---------------------------------------------------------- 
MOLECULE T0382TS009_2_4-D1
REMARK PARENT number 4
PFRMAT TS                                                                       
TARGET T0382                                                                    
PARENT N/A                                                                     
ATOM    795  N   PHE   102     -17.908  42.243  18.814  1.00  0.00             
ATOM    796  CA  PHE   102     -16.507  42.385  18.435  1.00  0.00             
ATOM    797  C   PHE   102     -16.161  43.840  18.140  1.00  0.00             
ATOM    798  O   PHE   102     -16.158  44.273  16.987  1.00  0.00             
ATOM    799  CB  PHE   102     -15.595  41.840  19.537  1.00  0.00             
ATOM    800  CG  PHE   102     -14.712  40.711  19.088  1.00  0.00             
ATOM    801  CD1 PHE   102     -14.761  40.250  17.785  1.00  0.00             
ATOM    802  CD2 PHE   102     -13.830  40.112  19.971  1.00  0.00             
ATOM    803  CE1 PHE   102     -13.947  39.211  17.372  1.00  0.00             
ATOM    804  CE2 PHE   102     -13.016  39.073  19.558  1.00  0.00             
ATOM    805  CZ  PHE   102     -13.072  38.623  18.266  1.00  0.00             
ATOM    806  N   PRO   103     -15.861  44.618  19.191  1.00  0.00             
ATOM    807  CA  PRO   103     -15.511  46.034  19.051  1.00  0.00             
ATOM    808  C   PRO   103     -16.326  46.714  17.956  1.00  0.00             
ATOM    809  O   PRO   103     -15.865  47.668  17.329  1.00  0.00             
ATOM    810  CB  PRO   103     -15.878  46.617  20.418  1.00  0.00             
ATOM    811  CG  PRO   103     -17.157  45.940  20.781  1.00  0.00             
ATOM    812  CD  PRO   103     -15.844  44.171  20.595  1.00  0.00             
ATOM    813  N   GLN   104     -17.538  46.217  17.733  1.00  0.00             
ATOM    814  CA  GLN   104     -18.418  46.776  16.713  1.00  0.00             
ATOM    815  C   GLN   104     -17.628  47.229  15.490  1.00  0.00             
ATOM    816  O   GLN   104     -17.572  48.420  15.182  1.00  0.00             
ATOM    817  CB  GLN   104     -19.480  45.754  16.304  1.00  0.00             
ATOM    818  CG  GLN   104     -20.909  46.211  16.548  1.00  0.00             
ATOM    819  CD  GLN   104     -21.932  45.173  16.132  1.00  0.00             
ATOM    820  OE1 GLN   104     -23.137  45.389  16.263  1.00  0.00             
ATOM    821  NE2 GLN   104     -21.454  44.042  15.626  1.00  0.00             
ATOM    822  N   ALA   105     -17.019  46.273  14.798  1.00  0.00             
ATOM    823  CA  ALA   105     -16.231  46.572  13.607  1.00  0.00             
ATOM    824  C   ALA   105     -14.898  47.215  13.975  1.00  0.00             
ATOM    825  O   ALA   105     -14.436  48.135  13.302  1.00  0.00             
ATOM    826  CB  ALA   105     -15.997  45.307  12.796  1.00  0.00             
ATOM    827  N   GLY   106     -14.286  46.723  15.048  1.00  0.00             
ATOM    828  CA  GLY   106     -13.012  47.265  15.484  1.00  0.00             
ATOM    829  C   GLY   106     -12.961  48.776  15.387  1.00  0.00             
ATOM    830  O   GLY   106     -12.259  49.331  14.542  1.00  0.00             
ATOM    831  N   ASP   107     -13.706  49.449  16.258  1.00  0.00             
ATOM    832  CA  ASP   107     -13.744  50.907  16.268  1.00  0.00             
ATOM    833  C   ASP   107     -14.529  51.447  15.077  1.00  0.00             
ATOM    834  O   ASP   107     -14.439  52.630  14.748  1.00  0.00             
ATOM    835  CB  ASP   107     -14.354  51.418  17.575  1.00  0.00             
ATOM    836  CG  ASP   107     -13.400  52.297  18.359  1.00  0.00             
ATOM    837  OD1 ASP   107     -13.856  53.311  18.927  1.00  0.00             
ATOM    838  OD2 ASP   107     -12.195  51.970  18.407  1.00  0.00             
ATOM    839  N   ALA   108     -15.297  50.572  14.436  1.00  0.00             
ATOM    840  CA  ALA   108     -16.098  50.960  13.281  1.00  0.00             
ATOM    841  C   ALA   108     -15.561  52.235  12.639  1.00  0.00             
ATOM    842  O   ALA   108     -16.206  53.282  12.680  1.00  0.00             
ATOM    843  CB  ALA   108     -16.135  49.834  12.260  1.00  0.00             
ATOM    844  N   GLY   109     -14.375  52.138  12.046  1.00  0.00             
ATOM    845  CA  GLY   109     -13.774  53.292  11.404  1.00  0.00             
ATOM    846  C   GLY   109     -13.412  54.383  12.393  1.00  0.00             
ATOM    847  O   GLY   109     -13.128  55.516  12.006  1.00  0.00             
ATOM    848  N   MET   110     -13.423  54.043  13.678  1.00  0.00             
ATOM    849  CA  MET   110     -13.095  55.001  14.726  1.00  0.00             
ATOM    850  C   MET   110     -13.132  56.431  14.198  1.00  0.00             
ATOM    851  O   MET   110     -12.096  57.084  14.075  1.00  0.00             
ATOM    852  CB  MET   110     -14.055  54.851  15.909  1.00  0.00             
ATOM    853  CG  MET   110     -13.373  54.501  17.221  1.00  0.00             
ATOM    854  SD  MET   110     -14.539  54.334  18.587  1.00  0.00             
ATOM    855  CE  MET   110     -13.428  53.931  19.932  1.00  0.00             
ATOM    856  N   CYS   111     -14.332  56.912  13.888  1.00  0.00             
ATOM    857  CA  CYS   111     -14.506  58.264  13.372  1.00  0.00             
ATOM    858  C   CYS   111     -13.943  58.392  11.961  1.00  0.00             
ATOM    859  O   CYS   111     -13.524  59.473  11.545  1.00  0.00             
ATOM    860  CB  CYS   111     -15.983  58.657  13.388  1.00  0.00             
ATOM    861  SG  CYS   111     -16.364  60.118  14.407  1.00  0.00             
ATOM    862  N   LEU   112     -13.935  57.284  11.229  1.00  0.00             
ATOM    863  CA  LEU   112     -13.424  57.271   9.863  1.00  0.00             
ATOM    864  C   LEU   112     -12.364  58.348   9.660  1.00  0.00             
ATOM    865  O   LEU   112     -12.471  59.177   8.757  1.00  0.00             
ATOM    866  CB  LEU   112     -12.849  55.895   9.519  1.00  0.00             
ATOM    867  CG  LEU   112     -13.499  55.164   8.344  1.00  0.00             
ATOM    868  CD1 LEU   112     -12.489  54.267   7.643  1.00  0.00             
ATOM    869  CD2 LEU   112     -14.112  56.155   7.365  1.00  0.00             
ATOM    870  N   ASP   113     -11.339  58.330  10.508  1.00  0.00             
ATOM    871  CA  ASP   113     -10.258  59.304  10.424  1.00  0.00             
ATOM    872  C   ASP   113     -10.795  60.730  10.482  1.00  0.00             
ATOM    873  O   ASP   113     -10.315  61.614   9.773  1.00  0.00             
ATOM    874  CB  ASP   113      -9.245  59.078  11.548  1.00  0.00             
ATOM    875  CG  ASP   113      -7.854  58.775  11.025  1.00  0.00             
ATOM    876  OD1 ASP   113      -6.875  59.282  11.613  1.00  0.00             
ATOM    877  OD2 ASP   113      -7.743  58.033  10.027  1.00  0.00             
ATOM    878  N   LEU   114     -11.795  60.947  11.331  1.00  0.00             
ATOM    879  CA  LEU   114     -12.399  62.265  11.483  1.00  0.00             
ATOM    880  C   LEU   114     -12.523  62.974  10.138  1.00  0.00             
ATOM    881  O   LEU   114     -12.069  64.106   9.978  1.00  0.00             
ATOM    882  CB  LEU   114     -13.772  62.152  12.148  1.00  0.00             
ATOM    883  CG  LEU   114     -13.946  62.892  13.475  1.00  0.00             
ATOM    884  CD1 LEU   114     -15.390  63.334  13.659  1.00  0.00             
ATOM    885  CD2 LEU   114     -13.001  64.081  13.556  1.00  0.00             
ATOM    886  N   LEU   115     -13.141  62.297   9.175  1.00  0.00             
ATOM    887  CA  LEU   115     -13.326  62.860   7.842  1.00  0.00             
ATOM    888  C   LEU   115     -12.008  63.373   7.272  1.00  0.00             
ATOM    889  O   LEU   115     -11.966  64.419   6.625  1.00  0.00             
ATOM    890  CB  LEU   115     -13.937  61.820   6.902  1.00  0.00             
ATOM    891  CG  LEU   115     -15.288  62.180   6.278  1.00  0.00             
ATOM    892  CD1 LEU   115     -15.439  61.530   4.912  1.00  0.00             
ATOM    893  CD2 LEU   115     -15.450  63.689   6.181  1.00  0.00             
ATOM    894  N   ASP   116     -10.934  62.631   7.517  1.00  0.00             
ATOM    895  CA  ASP   116      -9.614  63.008   7.029  1.00  0.00             
ATOM    896  C   ASP   116      -9.385  64.510   7.163  1.00  0.00             
ATOM    897  O   ASP   116      -8.277  65.001   6.946  1.00  0.00             
ATOM    898  CB  ASP   116      -8.524  62.242   7.782  1.00  0.00             
ATOM    899  CG  ASP   116      -7.672  61.390   6.863  1.00  0.00             
ATOM    900  OD1 ASP   116      -6.441  61.337   7.073  1.00  0.00             
ATOM    901  OD2 ASP   116      -8.232  60.774   5.933  1.00  0.00             
ATOM    902  N   ASP   117     -10.440  65.234   7.521  1.00  0.00             
ATOM    903  CA  ASP   117     -10.357  66.681   7.684  1.00  0.00             
ATOM    904  C   ASP   117      -9.116  67.243   6.997  1.00  0.00             
ATOM    905  O   ASP   117      -7.997  67.072   7.479  1.00  0.00             
ATOM    906  CB  ASP   117     -11.614  67.356   7.133  1.00  0.00             
ATOM    907  CG  ASP   117     -12.361  68.147   8.189  1.00  0.00             
ATOM    908  OD1 ASP   117     -12.852  69.249   7.870  1.00  0.00             
ATOM    909  OD2 ASP   117     -12.456  67.663   9.337  1.00  0.00             
ATOM    910  N   GLY   118      -9.324  67.913   5.869  1.00  0.00             
ATOM    911  CA  GLY   118      -8.211  68.489   5.136  1.00  0.00             
ATOM    912  C   GLY   118      -7.085  67.499   4.920  1.00  0.00             
ATOM    913  O   GLY   118      -6.348  67.168   5.850  1.00  0.00             
ATOM    914  N   THR   119      -6.946  67.020   3.688  1.00  0.00             
ATOM    915  CA  THR   119      -5.878  66.039   3.343  1.00  0.00             
ATOM    916  C   THR   119      -6.166  65.354   2.011  1.00  0.00             
ATOM    917  O   THR   119      -6.107  64.129   1.907  1.00  0.00             
ATOM    918  CB  THR   119      -4.494  66.713   3.274  1.00  0.00             
ATOM    919  OG1 THR   119      -4.652  68.104   2.970  1.00  0.00             
ATOM    920  CG2 THR   119      -3.766  66.568   4.602  1.00  0.00             
ATOM    921  N   PHE   120      -6.479  66.153   0.997  1.00  0.00             
ATOM    922  CA  PHE   120      -6.777  65.627  -0.330  1.00  0.00             
ATOM    923  C   PHE   120      -6.485  64.131  -0.407  1.00  0.00             
ATOM    924  O   PHE   120      -5.329  63.719  -0.503  1.00  0.00             
ATOM    925  CB  PHE   120      -8.236  65.898  -0.698  1.00  0.00             
ATOM    926  CG  PHE   120      -8.404  66.734  -1.935  1.00  0.00             
ATOM    927  CD1 PHE   120      -7.301  67.190  -2.634  1.00  0.00             
ATOM    928  CD2 PHE   120      -9.666  67.066  -2.397  1.00  0.00             
ATOM    929  CE1 PHE   120      -7.455  67.960  -3.772  1.00  0.00             
ATOM    930  CE2 PHE   120      -9.819  67.836  -3.535  1.00  0.00             
ATOM    931  CZ  PHE   120      -8.721  68.283  -4.220  1.00  0.00             
ATOM    932  N   LYS   121      -7.540  63.325  -0.366  1.00  0.00             
ATOM    933  CA  LYS   121      -7.399  61.875  -0.432  1.00  0.00             
ATOM    934  C   LYS   121      -8.645  61.175   0.103  1.00  0.00             
ATOM    935  O   LYS   121      -8.826  61.037   1.313  1.00  0.00             
ATOM    936  CB  LYS   121      -7.121  61.428  -1.867  1.00  0.00             
ATOM    937  CG  LYS   121      -5.802  60.692  -2.044  1.00  0.00             
ATOM    938  CD  LYS   121      -5.591  60.278  -3.492  1.00  0.00             
ATOM    939  CE  LYS   121      -4.272  59.542  -3.668  1.00  0.00             
ATOM    940  NZ  LYS   121      -4.051  59.130  -5.081  1.00  0.00             
ATOM    941  N   PRO   122      -9.523  60.723  -0.804  1.00  0.00             
ATOM    942  CA  PRO   122     -10.760  60.033  -0.428  1.00  0.00             
ATOM    943  C   PRO   122     -11.991  60.895  -0.689  1.00  0.00             
ATOM    944  O   PRO   122     -12.909  60.947   0.129  1.00  0.00             
ATOM    945  CB  PRO   122     -10.767  58.812  -1.351  1.00  0.00             
ATOM    946  CG  PRO   122     -10.276  59.332  -2.660  1.00  0.00             
ATOM    947  CD  PRO   122      -9.372  60.852  -2.263  1.00  0.00             
TER
END
