
#######################################################
#                                                     #
#                        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_3_4-D1
# Molecule2: number of CA atoms  119 (  920),  selected   21 , name T0382_D1.pdb
# PARAMETERS: T0382TS009_3_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         3.48     3.48
  LCS_AVERAGE:     17.65

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       116 - 120         1.93     9.38
  LCS_AVERAGE:      3.56

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       117 - 120         0.80    16.43
  LONGEST_CONTINUOUS_SEGMENT:     4       119 - 122         0.92    28.09
  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    6    8   13   15   17   18   19   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     P     103     P     103      3    4   21     3    5    5    7    9   13   15   17   18   19   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     Q     104     Q     104      3    4   21     3    3    4    6    7   10   12   15   18   19   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     A     105     A     105      3    4   21     3    5    5    7    9   13   15   17   18   19   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     G     106     G     106      3    4   21     3    3    4    4    5   10   15   17   18   19   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     D     107     D     107      3    4   21     3    5    5    7    9   11   15   17   18   19   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     A     108     A     108      3    4   21     3    3    4    7    9   13   15   17   18   19   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   17   18   19   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     M     110     M     110      3    4   21     3    5    5    7    9   13   15   17   18   19   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     C     111     C     111      3    4   21     3    3    4    5    6    9   12   13   18   19   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     L     112     L     112      3    4   21     3    5    5    7    9   13   15   17   18   19   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   17   18   19   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   17   18   19   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   17   18   19   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   18   19   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   17   18   19   21   21   21   21   21   21   21   21   21   21 
LCS_GDT     G     118     G     118      4    5   21     3    3    4    6    8   11   15   17   18   19   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   17   18   19   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   15   19   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   17   18   19   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   17   18   19   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      5      5      7      9     13     15     17     18     19     21     21     21     21     21     21     21     21     21     21 
GDT PERCENT_CA   2.52   4.20   4.20   5.88   7.56  10.92  12.61  14.29  15.13  15.97  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   0.76   0.76   1.39   1.89   2.49   2.63   2.81   2.95   3.11   3.48   3.48   3.48   3.48   3.48   3.48   3.48   3.48   3.48   3.48
GDT RMS_ALL_CA  27.40   5.25   5.25   4.87   4.09   3.55   3.59   3.54   3.53   3.50   3.48   3.48   3.48   3.48   3.48   3.48   3.48   3.48   3.48   3.48

#      Molecule1      Molecule2       DISTANCE
LGA    F     102      F     102          3.443
LGA    P     103      P     103          2.700
LGA    Q     104      Q     104          5.477
LGA    A     105      A     105          2.768
LGA    G     106      G     106          3.871
LGA    D     107      D     107          3.686
LGA    A     108      A     108          2.840
LGA    G     109      G     109          2.983
LGA    M     110      M     110          2.772
LGA    C     111      C     111          5.531
LGA    L     112      L     112          1.493
LGA    D     113      D     113          2.824
LGA    L     114      L     114          3.926
LGA    L     115      L     115          2.002
LGA    D     116      D     116          4.659
LGA    D     117      D     117          2.172
LGA    G     118      G     118          3.191
LGA    T     119      T     119          1.962
LGA    F     120      F     120          6.037
LGA    K     121      K     121          2.698
LGA    P     122      P     122          1.667

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   21  119    4.0     17    2.81    10.504     9.500     0.584

LGA_LOCAL      RMSD =  2.813  Number of atoms =   17  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.500  Number of atoms =   21 
Std_ALL_ATOMS  RMSD =  3.476  (standard rmsd on all 21 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.053239 * X  +   0.945517 * Y  +  -0.321190 * Z  + -35.431973
  Y_new =   0.044292 * X  +  -0.319093 * Y  +  -0.946688 * Z  +  28.764734
  Z_new =  -0.997599 * X  +  -0.064627 * Y  +  -0.024891 * Z  +  93.103249 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.938433    1.203160  [ DEG:  -111.0640     68.9360 ]
  Theta =   1.501486    1.640107  [ DEG:    86.0288     93.9712 ]
  Phi   =   2.447671   -0.693921  [ DEG:   140.2412    -39.7588 ]
 
# 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_3_4-D1                             
REMARK     2: T0382_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0382TS009_3_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   17   2.81   9.500     3.48
REMARK  ---------------------------------------------------------- 
MOLECULE T0382TS009_3_4-D1
REMARK PARENT number 4
PFRMAT TS                                                                       
TARGET T0382                                                                    
PARENT N/A       
ATOM    795  N   PHE   102     -18.665  42.057  20.366  1.00  0.00             
ATOM    796  CA  PHE   102     -17.530  41.934  19.458  1.00  0.00             
ATOM    797  C   PHE   102     -16.972  43.303  19.085  1.00  0.00             
ATOM    798  O   PHE   102     -17.266  43.840  18.017  1.00  0.00             
ATOM    799  CB  PHE   102     -16.433  41.071  20.085  1.00  0.00             
ATOM    800  CG  PHE   102     -16.103  39.839  19.291  1.00  0.00             
ATOM    801  CD1 PHE   102     -16.765  39.564  18.107  1.00  0.00             
ATOM    802  CD2 PHE   102     -15.131  38.957  19.727  1.00  0.00             
ATOM    803  CE1 PHE   102     -16.461  38.431  17.376  1.00  0.00             
ATOM    804  CE2 PHE   102     -14.827  37.824  18.996  1.00  0.00             
ATOM    805  CZ  PHE   102     -15.487  37.559  17.825  1.00  0.00             
ATOM    806  N   PRO   103     -16.151  43.885  19.971  1.00  0.00             
ATOM    807  CA  PRO   103     -15.543  45.200  19.739  1.00  0.00             
ATOM    808  C   PRO   103     -16.475  46.126  18.965  1.00  0.00             
ATOM    809  O   PRO   103     -16.024  47.037  18.271  1.00  0.00             
ATOM    810  CB  PRO   103     -15.329  45.735  21.157  1.00  0.00             
ATOM    811  CG  PRO   103     -16.556  45.323  21.901  1.00  0.00             
ATOM    812  CD  PRO   103     -15.755  43.304  21.265  1.00  0.00             
ATOM    813  N   GLN   104     -17.776  45.886  19.088  1.00  0.00             
ATOM    814  CA  GLN   104     -18.773  46.697  18.400  1.00  0.00             
ATOM    815  C   GLN   104     -18.257  47.177  17.048  1.00  0.00             
ATOM    816  O   GLN   104     -18.114  48.377  16.817  1.00  0.00             
ATOM    817  CB  GLN   104     -20.073  45.910  18.219  1.00  0.00             
ATOM    818  CG  GLN   104     -21.282  46.547  18.884  1.00  0.00             
ATOM    819  CD  GLN   104     -22.549  45.740  18.684  1.00  0.00             
ATOM    820  OE1 GLN   104     -23.620  46.118  19.160  1.00  0.00             
ATOM    821  NE2 GLN   104     -22.432  44.623  17.976  1.00  0.00             
ATOM    822  N   ALA   105     -17.978  46.230  16.158  1.00  0.00             
ATOM    823  CA  ALA   105     -17.477  46.553  14.827  1.00  0.00             
ATOM    824  C   ALA   105     -16.041  47.060  14.886  1.00  0.00             
ATOM    825  O   ALA   105     -15.656  47.954  14.134  1.00  0.00             
ATOM    826  CB  ALA   105     -17.567  45.337  13.917  1.00  0.00             
ATOM    827  N   GLY   106     -15.251  46.482  15.787  1.00  0.00             
ATOM    828  CA  GLY   106     -13.866  46.891  15.925  1.00  0.00             
ATOM    829  C   GLY   106     -13.684  48.387  15.767  1.00  0.00             
ATOM    830  O   GLY   106     -13.083  48.850  14.797  1.00  0.00             
ATOM    831  N   ASP   107     -14.205  49.151  16.722  1.00  0.00             
ATOM    832  CA  ASP   107     -14.099  50.604  16.685  1.00  0.00             
ATOM    833  C   ASP   107     -14.962  51.194  15.575  1.00  0.00             
ATOM    834  O   ASP   107     -14.831  52.367  15.230  1.00  0.00             
ATOM    835  CB  ASP   107     -14.495  51.205  18.035  1.00  0.00             
ATOM    836  CG  ASP   107     -13.372  52.001  18.671  1.00  0.00             
ATOM    837  OD1 ASP   107     -13.656  53.069  19.251  1.00  0.00             
ATOM    838  OD2 ASP   107     -12.208  51.555  18.589  1.00  0.00             
ATOM    839  N   ALA   108     -15.845  50.370  15.019  1.00  0.00             
ATOM    840  CA  ALA   108     -16.732  50.807  13.948  1.00  0.00             
ATOM    841  C   ALA   108     -16.216  52.082  13.291  1.00  0.00             
ATOM    842  O   ALA   108     -16.851  53.135  13.371  1.00  0.00             
ATOM    843  CB  ALA   108     -16.888  49.708  12.908  1.00  0.00             
ATOM    844  N   GLY   109     -15.060  51.983  12.643  1.00  0.00             
ATOM    845  CA  GLY   109     -14.481  53.138  11.983  1.00  0.00             
ATOM    846  C   GLY   109     -14.128  54.246  12.955  1.00  0.00             
ATOM    847  O   GLY   109     -13.815  55.365  12.549  1.00  0.00             
ATOM    848  N   MET   110     -14.178  53.936  14.247  1.00  0.00             
ATOM    849  CA  MET   110     -13.862  54.913  15.281  1.00  0.00             
ATOM    850  C   MET   110     -13.795  56.324  14.707  1.00  0.00             
ATOM    851  O   MET   110     -12.721  56.921  14.624  1.00  0.00             
ATOM    852  CB  MET   110     -14.895  54.853  16.409  1.00  0.00             
ATOM    853  CG  MET   110     -14.309  54.516  17.770  1.00  0.00             
ATOM    854  SD  MET   110     -15.558  54.456  19.069  1.00  0.00             
ATOM    855  CE  MET   110     -14.548  54.045  20.491  1.00  0.00             
ATOM    856  N   CYS   111     -14.949  56.851  14.311  1.00  0.00             
ATOM    857  CA  CYS   111     -15.023  58.193  13.742  1.00  0.00             
ATOM    858  C   CYS   111     -14.373  58.243  12.363  1.00  0.00             
ATOM    859  O   CYS   111     -13.877  59.287  11.939  1.00  0.00             
ATOM    860  CB  CYS   111     -16.478  58.658  13.656  1.00  0.00             
ATOM    861  SG  CYS   111     -16.840  60.172  14.604  1.00  0.00             
ATOM    862  N   LEU   112     -14.381  57.111  11.668  1.00  0.00             
ATOM    863  CA  LEU   112     -13.794  57.024  10.336  1.00  0.00             
ATOM    864  C   LEU   112     -12.669  58.040  10.163  1.00  0.00             
ATOM    865  O   LEU   112     -12.682  58.841   9.228  1.00  0.00             
ATOM    866  CB  LEU   112     -13.271  55.611  10.072  1.00  0.00             
ATOM    867  CG  LEU   112     -13.890  54.871   8.883  1.00  0.00             
ATOM    868  CD1 LEU   112     -12.889  53.902   8.275  1.00  0.00             
ATOM    869  CD2 LEU   112     -14.393  55.856   7.840  1.00  0.00             
ATOM    870  N   ASP   113     -11.698  58.001  11.070  1.00  0.00             
ATOM    871  CA  ASP   113     -10.566  58.917  11.018  1.00  0.00             
ATOM    872  C   ASP   113     -11.031  60.369  10.999  1.00  0.00             
ATOM    873  O   ASP   113     -10.465  61.202  10.291  1.00  0.00             
ATOM    874  CB  ASP   113      -9.631  58.680  12.206  1.00  0.00             
ATOM    875  CG  ASP   113      -8.230  58.291  11.777  1.00  0.00             
ATOM    876  OD1 ASP   113      -7.261  58.769  12.406  1.00  0.00             
ATOM    877  OD2 ASP   113      -8.100  57.509  10.812  1.00  0.00             
ATOM    878  N   LEU   114     -12.065  60.664  11.780  1.00  0.00             
ATOM    879  CA  LEU   114     -12.607  62.016  11.853  1.00  0.00             
ATOM    880  C   LEU   114     -12.618  62.681  10.481  1.00  0.00             
ATOM    881  O   LEU   114     -12.098  63.784  10.311  1.00  0.00             
ATOM    882  CB  LEU   114     -14.021  61.994  12.438  1.00  0.00             
ATOM    883  CG  LEU   114     -14.233  62.787  13.729  1.00  0.00             
ATOM    884  CD1 LEU   114     -15.660  63.307  13.812  1.00  0.00             
ATOM    885  CD2 LEU   114     -13.235  63.931  13.827  1.00  0.00             
ATOM    886  N   LEU   115     -13.214  62.004   9.505  1.00  0.00             
ATOM    887  CA  LEU   115     -13.293  62.527   8.146  1.00  0.00             
ATOM    888  C   LEU   115     -11.919  62.955   7.639  1.00  0.00             
ATOM    889  O   LEU   115     -11.787  63.973   6.961  1.00  0.00             
ATOM    890  CB  LEU   115     -13.902  61.487   7.205  1.00  0.00             
ATOM    891  CG  LEU   115     -15.194  61.890   6.492  1.00  0.00             
ATOM    892  CD1 LEU   115     -15.300  61.201   5.140  1.00  0.00             
ATOM    893  CD2 LEU   115     -15.272  63.401   6.336  1.00  0.00             
ATOM    894  N   ASP   116     -10.901  62.169   7.971  1.00  0.00             
ATOM    895  CA  ASP   116      -9.536  62.463   7.550  1.00  0.00             
ATOM    896  C   ASP   116      -9.240  63.955   7.648  1.00  0.00             
ATOM    897  O   ASP   116      -8.097  64.383   7.481  1.00  0.00             
ATOM    898  CB  ASP   116      -8.533  61.670   8.390  1.00  0.00             
ATOM    899  CG  ASP   116      -7.674  60.745   7.551  1.00  0.00             
ATOM    900  OD1 ASP   116      -6.462  60.640   7.836  1.00  0.00             
ATOM    901  OD2 ASP   116      -8.212  60.125   6.609  1.00  0.00             
ATOM    902  N   ASP   117     -10.275  64.744   7.920  1.00  0.00             
ATOM    903  CA  ASP   117     -10.127  66.189   8.041  1.00  0.00             
ATOM    904  C   ASP   117      -8.822  66.664   7.410  1.00  0.00             
ATOM    905  O   ASP   117      -7.742  66.455   7.964  1.00  0.00             
ATOM    906  CB  ASP   117     -11.314  66.905   7.396  1.00  0.00             
ATOM    907  CG  ASP   117     -12.079  67.768   8.379  1.00  0.00             
ATOM    908  OD1 ASP   117     -12.493  68.882   7.996  1.00  0.00             
ATOM    909  OD2 ASP   117     -12.264  67.331   9.534  1.00  0.00             
ATOM    910  N   GLY   118      -8.929  67.305   6.251  1.00  0.00             
ATOM    911  CA  GLY   118      -7.749  67.798   5.568  1.00  0.00             
ATOM    912  C   GLY   118      -6.663  66.745   5.450  1.00  0.00             
ATOM    913  O   GLY   118      -5.999  66.413   6.433  1.00  0.00             
ATOM    914  N   THR   119      -6.479  66.218   4.244  1.00  0.00             
ATOM    915  CA  THR   119      -5.445  65.174   3.995  1.00  0.00             
ATOM    916  C   THR   119      -5.691  64.458   2.672  1.00  0.00             
ATOM    917  O   THR   119      -5.690  63.229   2.611  1.00  0.00             
ATOM    918  CB  THR   119      -4.026  65.775   3.988  1.00  0.00             
ATOM    919  OG1 THR   119      -4.094  67.160   3.629  1.00  0.00             
ATOM    920  CG2 THR   119      -3.383  65.642   5.359  1.00  0.00             
ATOM    921  N   PHE   120      -5.902  65.235   1.615  1.00  0.00             
ATOM    922  CA  PHE   120      -6.151  64.677   0.291  1.00  0.00             
ATOM    923  C   PHE   120      -5.932  63.167   0.279  1.00  0.00             
ATOM    924  O   PHE   120      -4.796  62.695   0.265  1.00  0.00             
ATOM    925  CB  PHE   120      -7.570  65.007  -0.172  1.00  0.00             
ATOM    926  CG  PHE   120      -7.624  65.807  -1.442  1.00  0.00             
ATOM    927  CD1 PHE   120      -6.460  66.182  -2.089  1.00  0.00             
ATOM    928  CD2 PHE   120      -8.838  66.184  -1.989  1.00  0.00             
ATOM    929  CE1 PHE   120      -6.509  66.919  -3.258  1.00  0.00             
ATOM    930  CE2 PHE   120      -8.887  66.920  -3.157  1.00  0.00             
ATOM    931  CZ  PHE   120      -7.729  67.287  -3.792  1.00  0.00             
ATOM    932  N   LYS   121      -7.028  62.416   0.285  1.00  0.00             
ATOM    933  CA  LYS   121      -6.959  60.959   0.273  1.00  0.00             
ATOM    934  C   LYS   121      -8.267  60.342   0.756  1.00  0.00             
ATOM    935  O   LYS   121      -8.525  60.255   1.957  1.00  0.00             
ATOM    936  CB  LYS   121      -6.622  60.450  -1.128  1.00  0.00             
ATOM    937  CG  LYS   121      -5.335  59.643  -1.203  1.00  0.00             
ATOM    938  CD  LYS   121      -5.062  59.169  -2.621  1.00  0.00             
ATOM    939  CE  LYS   121      -3.776  58.363  -2.695  1.00  0.00             
ATOM    940  NZ  LYS   121      -3.495  57.891  -4.079  1.00  0.00             
ATOM    941  N   PRO   122      -9.114  59.902  -0.186  1.00  0.00             
ATOM    942  CA  PRO   122     -10.405  59.288   0.138  1.00  0.00             
ATOM    943  C   PRO   122     -11.573  60.199  -0.224  1.00  0.00             
ATOM    944  O   PRO   122     -12.532  60.325   0.537  1.00  0.00             
ATOM    945  CB  PRO   122     -10.421  58.037  -0.744  1.00  0.00             
ATOM    946  CG  PRO   122      -9.830  58.485  -2.039  1.00  0.00             
ATOM    947  CD  PRO   122      -8.874  59.972  -1.637  1.00  0.00             
TER
END
