
#######################################################
#                                                     #
#                        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   23 (  114),  selected   23 , name T0298TS102_1-D2
# Molecule2: number of CA atoms  186 ( 1394),  selected   23 , name T0298_D2.pdb
# PARAMETERS: T0298TS102_1-D2.T0298_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:    17       209 - 265         4.59    10.23
  LCS_AVERAGE:      7.69

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10       256 - 265         1.07    22.75
  LCS_AVERAGE:      4.02

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9       257 - 265         0.28    24.94
  LCS_AVERAGE:      3.65

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:  186
LCS_GDT     R     187     R     187      0    0    0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
LCS_GDT     V     204     V     204      6    6    6     4    6    6    6    6    6    6    6    6    6    6    6    6    6    7    7   10   12   13   16 
LCS_GDT     D     205     D     205      6    6    6     5    6    6    6    6    6    6    6    6    6    6    6    6    6    8    9   13   16   21   21 
LCS_GDT     A     206     A     206      6    6    6     5    6    6    6    6    6    6    6    6    6    6    7   11   14   15   17   19   20   21   21 
LCS_GDT     E     207     E     207      6    6    6     5    6    6    6    6    6    6    6    6    6   10   11   14   15   17   18   19   20   21   21 
LCS_GDT     G     208     G     208      6    6   16     5    6    6    6    6    6    6    6    6    6    8   11   12   15   16   18   19   20   21   21 
LCS_GDT     H     209     H     209      6    6   17     5    6    6    6    6    6    6    6    6    6    6    7   11   14   16   18   19   20   21   21 
LCS_GDT     V     248     V     248      6    6   17     4    4    6    6    6    6    7   10   12   14   15   15   16   16   17   17   19   20   21   21 
LCS_GDT     T     249     T     249      6    6   17     4    4    6    6    6    7    9   11   13   14   15   15   16   16   17   18   19   20   21   21 
LCS_GDT     L     250     L     250      6    6   17     4    4    6    6    6    7    9   11   13   14   15   15   16   16   17   18   19   20   21   21 
LCS_GDT     Q     251     Q     251      6    6   17     4    4    6    6    6    7    9   11   13   14   15   15   16   16   17   18   19   20   21   21 
LCS_GDT     C     252     C     252      6    6   17     3    4    6    6    6    7    9   11   13   14   15   15   16   16   17   18   19   20   21   21 
LCS_GDT     A     253     A     253      6    6   17     3    4    6    6    6    6    7    9   10   12   14   15   16   16   17   18   19   20   21   21 
LCS_GDT     V     256     V     256      3   10   17     2    3    5   10   10   10   10   11   13   14   15   15   16   16   17   18   19   20   21   21 
LCS_GDT     D     257     D     257      9   10   17     9    9    9   10   10   10   10   11   13   14   15   15   16   16   17   18   19   20   21   21 
LCS_GDT     L     258     L     258      9   10   17     9    9    9   10   10   10   10   11   13   14   15   15   16   16   17   18   19   20   21   21 
LCS_GDT     A     259     A     259      9   10   17     9    9    9   10   10   10   10   11   13   14   15   15   16   16   17   18   19   20   21   21 
LCS_GDT     A     260     A     260      9   10   17     9    9    9   10   10   10   10   11   13   14   15   15   16   16   17   18   19   20   21   21 
LCS_GDT     V     261     V     261      9   10   17     9    9    9   10   10   10   10   11   13   14   15   15   16   16   17   18   19   20   21   21 
LCS_GDT     T     262     T     262      9   10   17     9    9    9   10   10   10   10   11   13   14   15   15   16   16   17   18   19   20   21   21 
LCS_GDT     R     263     R     263      9   10   17     9    9    9   10   10   10   10   10   13   14   15   15   16   16   17   18   19   20   21   21 
LCS_GDT     V     264     V     264      9   10   17     9    9    9   10   10   10   10   10   11   13   15   15   16   16   17   18   19   20   21   21 
LCS_GDT     L     265     L     265      9   10   17     9    9    9   10   10   10   10   11   13   14   15   15   16   16   17   18   19   20   21   21 
LCS_AVERAGE  LCS_A:   5.12  (   3.65    4.02    7.69 )

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      9      9      9     10     10     10     10     11     13     14     15     15     16     16     17     18     19     20     21     21 
GDT PERCENT_CA   4.84   4.84   4.84   5.38   5.38   5.38   5.38   5.91   6.99   7.53   8.06   8.06   8.60   8.60   9.14   9.68  10.22  10.75  11.29  11.29
GDT RMS_LOCAL    0.28   0.28   0.28   1.07   1.07   1.07   1.07   2.92   3.25   3.44   3.60   3.60   3.88   3.88   4.42   5.05   5.22   5.59   6.12   6.12
GDT RMS_ALL_CA  24.94  24.94  24.94  22.75  22.75  22.75  22.75  10.90  10.52  10.44  10.49  10.49  10.34  10.34  10.43  10.26  10.20   9.99   9.78   9.78

#      Molecule1      Molecule2       DISTANCE
LGA    R     187      R     187         35.531
LGA    V     204      V     204         15.950
LGA    D     205      D     205         14.844
LGA    A     206      A     206         11.650
LGA    E     207      E     207          9.708
LGA    G     208      G     208          9.515
LGA    H     209      H     209         11.196
LGA    V     248      V     248          5.870
LGA    T     249      T     249          3.824
LGA    L     250      L     250          1.970
LGA    Q     251      Q     251          2.650
LGA    C     252      C     252          3.484
LGA    A     253      A     253          5.775
LGA    V     256      V     256          1.271
LGA    D     257      D     257          1.097
LGA    L     258      L     258          3.954
LGA    A     259      A     259          3.873
LGA    A     260      A     260          3.505
LGA    V     261      V     261          3.602
LGA    T     262      T     262          1.595
LGA    R     263      R     263          4.521
LGA    V     264      V     264          7.114
LGA    L     265      L     265          6.209

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   23  186    4.0     11    2.91     6.452     5.834     0.365

LGA_LOCAL      RMSD =  2.914  Number of atoms =   11  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 10.341  Number of atoms =   23 
Std_ALL_ATOMS  RMSD =  9.418  (standard rmsd on all 23 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.738263 * X  +  -0.268874 * Y  +  -0.618607 * Z  +   0.181105
  Y_new =   0.658286 * X  +   0.487161 * Y  +   0.573876 * Z  +  63.698524
  Z_new =   0.147061 * X  +  -0.830892 * Y  +   0.536649 * Z  +  17.157158 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.997329    2.144263  [ DEG:   -57.1428    122.8572 ]
  Theta =  -0.147597   -2.993996  [ DEG:    -8.4567   -171.5433 ]
  Phi   =   0.728194   -2.413399  [ DEG:    41.7224   -138.2776 ]
 
# 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: T0298TS102_1-D2                               
REMARK     2: T0298_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0298TS102_1-D2.T0298_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   23  186   4.0   11   2.91   5.834     9.42
REMARK  ---------------------------------------------------------- 
MOLECULE T0298TS102_1-D2
PFRMAT TS
TARGET T0298
MODEL 1
PARENT 1kaf_A
ATOM    389  N   ARG   187      -4.337  87.381   9.395  1.00  1.00
ATOM    390  CA  ARG   187      -3.073  87.604   8.711  1.00  1.00
ATOM    391  C   ARG   187      -2.435  86.242   8.508  1.00  1.00
ATOM    392  O   ARG   187      -2.267  85.484   9.461  1.00  1.00
ATOM    393  CB  ARG   187      -2.133  88.488   9.536  1.00  1.00
ATOM    394  N   VAL   204      -2.105  85.919   7.263  1.00  1.00
ATOM    395  CA  VAL   204      -1.463  84.646   6.966  1.00  1.00
ATOM    396  C   VAL   204      -0.005  84.951   6.664  1.00  1.00
ATOM    397  O   VAL   204       0.301  85.712   5.744  1.00  1.00
ATOM    398  CB  VAL   204      -2.108  83.950   5.752  1.00  1.00
ATOM    399  N   ASP   205       0.891  84.372   7.455  1.00  1.00
ATOM    400  CA  ASP   205       2.324  84.592   7.290  1.00  1.00
ATOM    401  C   ASP   205       2.918  83.745   6.172  1.00  1.00
ATOM    402  O   ASP   205       2.292  82.798   5.694  1.00  1.00
ATOM    403  CB  ASP   205       3.047  84.305   8.595  1.00  1.00
ATOM    404  N   ALA   206       4.133  84.096   5.762  1.00  1.00
ATOM    405  CA  ALA   206       4.819  83.371   4.703  1.00  1.00
ATOM    406  C   ALA   206       5.034  81.904   5.062  1.00  1.00
ATOM    407  O   ALA   206       4.984  81.031   4.193  1.00  1.00
ATOM    408  CB  ALA   206       6.166  84.035   4.401  1.00  1.00
ATOM    409  N   GLU   207       5.256  81.629   6.343  1.00  1.00
ATOM    410  CA  GLU   207       5.481  80.255   6.784  1.00  1.00
ATOM    411  C   GLU   207       4.196  79.445   6.938  1.00  1.00
ATOM    412  O   GLU   207       4.237  78.269   7.301  1.00  1.00
ATOM    413  CB  GLU   207       6.259  80.239   8.104  1.00  1.00
ATOM    414  N   GLY   208       3.055  80.071   6.670  1.00  1.00
ATOM    415  CA  GLY   208       1.794  79.359   6.782  1.00  1.00
ATOM    416  C   GLY   208       1.064  79.560   8.099  1.00  1.00
ATOM    417  O   GLY   208      -0.070  79.103   8.253  1.00  1.00
ATOM    418  N   HIS   209       1.707  80.220   9.054  1.00  1.00
ATOM    419  CA  HIS   209       1.072  80.482  10.344  1.00  1.00
ATOM    420  C   HIS   209      -0.076  81.445  10.118  1.00  1.00
ATOM    421  O   HIS   209       0.018  82.351   9.292  1.00  1.00
ATOM    422  CB  HIS   209       2.070  81.098  11.328  1.00  1.00
ATOM    423  N   VAL   248      -1.161  81.250  10.858  1.00  1.00
ATOM    424  CA  VAL   248      -2.327  82.109  10.708  1.00  1.00
ATOM    425  C   VAL   248      -2.614  82.805  12.026  1.00  1.00
ATOM    426  O   VAL   248      -2.583  82.179  13.079  1.00  1.00
ATOM    427  CB  VAL   248      -3.566  81.290  10.296  1.00  1.00
ATOM    428  N   THR   249      -2.870  84.107  11.962  1.00  1.00
ATOM    429  CA  THR   249      -3.184  84.873  13.158  1.00  1.00
ATOM    430  C   THR   249      -4.549  85.517  12.984  1.00  1.00
ATOM    431  O   THR   249      -4.744  86.352  12.103  1.00  1.00
ATOM    432  CB  THR   249      -2.124  85.951  13.405  1.00  1.00
ATOM    433  N   LEU   250      -5.496  85.101  13.817  1.00  1.00
ATOM    434  CA  LEU   250      -6.855  85.637  13.780  1.00  1.00
ATOM    435  C   LEU   250      -7.039  86.474  15.039  1.00  1.00
ATOM    436  O   LEU   250      -6.760  86.004  16.143  1.00  1.00
ATOM    437  CB  LEU   250      -7.864  84.488  13.752  1.00  1.00
ATOM    438  N   GLN   251      -7.487  87.715  14.868  1.00  1.00
ATOM    439  CA  GLN   251      -7.688  88.635  15.988  1.00  1.00
ATOM    440  C   GLN   251      -9.070  89.273  15.996  1.00  1.00
ATOM    441  O   GLN   251      -9.676  89.474  14.950  1.00  1.00
ATOM    442  CB  GLN   251      -6.672  89.780  15.927  1.00  1.00
ATOM    443  N   CYS   252      -9.552  89.602  17.190  1.00  1.00
ATOM    444  CA  CYS   252     -10.836  90.277  17.358  1.00  1.00
ATOM    445  C   CYS   252     -10.818  90.931  18.739  1.00  1.00
ATOM    446  O   CYS   252     -10.146  90.456  19.647  1.00  1.00
ATOM    447  CB  CYS   252     -12.025  89.298  17.238  1.00  1.00
ATOM    448  N   ALA   253     -11.530  92.039  18.908  1.00  1.00
ATOM    449  CA  ALA   253     -11.522  92.682  20.213  1.00  1.00
ATOM    450  C   ALA   253     -12.209  91.815  21.261  1.00  1.00
ATOM    451  O   ALA   253     -13.227  91.172  20.991  1.00  1.00
ATOM    452  CB  ALA   253     -12.195  94.058  20.139  1.00  1.00
ATOM    453  N   VAL   256     -11.637  91.790  22.458  1.00  1.00
ATOM    454  CA  VAL   256     -12.200  91.005  23.548  1.00  1.00
ATOM    455  C   VAL   256     -13.532  91.583  24.014  1.00  1.00
ATOM    456  O   VAL   256     -13.685  92.798  24.130  1.00  1.00
ATOM    457  CB  VAL   256     -11.226  90.975  24.732  1.00  1.00
ATOM    458  N   ASP   257     -14.487  90.692  24.261  1.00  1.00
ATOM    459  CA  ASP   257     -15.814  91.028  24.772  1.00  1.00
ATOM    460  C   ASP   257     -16.484  89.679  25.021  1.00  1.00
ATOM    461  O   ASP   257     -16.118  88.679  24.405  1.00  1.00
ATOM    462  CB  ASP   257     -16.629  91.850  23.763  1.00  1.00
ATOM    463  N   LEU   258     -17.440  89.635  25.942  1.00  1.00
ATOM    464  CA  LEU   258     -18.122  88.379  26.229  1.00  1.00
ATOM    465  C   LEU   258     -18.761  87.841  24.954  1.00  1.00
ATOM    466  O   LEU   258     -18.713  86.641  24.676  1.00  1.00
ATOM    467  CB  LEU   258     -19.186  88.592  27.296  1.00  1.00
ATOM    468  N   ALA   259     -19.351  88.743  24.178  1.00  1.00
ATOM    469  CA  ALA   259     -20.015  88.371  22.939  1.00  1.00
ATOM    470  C   ALA   259     -19.055  87.788  21.912  1.00  1.00
ATOM    471  O   ALA   259     -19.354  86.777  21.280  1.00  1.00
ATOM    472  CB  ALA   259     -20.717  89.582  22.319  1.00  1.00
ATOM    473  N   ALA   260     -17.902  88.423  21.741  1.00  1.00
ATOM    474  CA  ALA   260     -16.946  87.928  20.761  1.00  1.00
ATOM    475  C   ALA   260     -16.281  86.630  21.180  1.00  1.00
ATOM    476  O   ALA   260     -16.055  85.755  20.347  1.00  1.00
ATOM    477  CB  ALA   260     -15.885  88.987  20.454  1.00  1.00
ATOM    478  N   VAL   261     -15.974  86.494  22.466  1.00  1.00
ATOM    479  CA  VAL   261     -15.337  85.274  22.943  1.00  1.00
ATOM    480  C   VAL   261     -16.271  84.102  22.689  1.00  1.00
ATOM    481  O   VAL   261     -15.845  83.048  22.210  1.00  1.00
ATOM    482  CB  VAL   261     -14.992  85.379  24.438  1.00  1.00
ATOM    483  N   THR   262     -17.552  84.312  22.978  1.00  1.00
ATOM    484  CA  THR   262     -18.572  83.289  22.782  1.00  1.00
ATOM    485  C   THR   262     -18.695  82.920  21.306  1.00  1.00
ATOM    486  O   THR   262     -18.720  81.742  20.946  1.00  1.00
ATOM    487  CB  THR   262     -19.925  83.794  23.288  1.00  1.00
ATOM    488  N   ARG   263     -18.779  83.938  20.457  1.00  1.00
ATOM    489  CA  ARG   263     -18.913  83.735  19.019  1.00  1.00
ATOM    490  C   ARG   263     -17.712  83.000  18.427  1.00  1.00
ATOM    491  O   ARG   263     -17.869  82.092  17.608  1.00  1.00
ATOM    492  CB  ARG   263     -19.098  85.082  18.321  1.00  1.00
ATOM    493  N   VAL   264     -16.513  83.386  18.848  1.00  1.00
ATOM    494  CA  VAL   264     -15.294  82.768  18.337  1.00  1.00
ATOM    495  C   VAL   264     -15.189  81.283  18.655  1.00  1.00
ATOM    496  O   VAL   264     -14.880  80.474  17.782  1.00  1.00
ATOM    497  CB  VAL   264     -14.042  83.473  18.897  1.00  1.00
ATOM    498  N   LEU   265     -15.435  80.930  19.909  1.00  1.00
ATOM    499  CA  LEU   265     -15.351  79.539  20.332  1.00  1.00
ATOM    500  C   LEU   265     -16.447  78.710  19.671  1.00  1.00
ATOM    501  O   LEU   265     -16.236  77.552  19.314  1.00  1.00
ATOM    502  CB  LEU   265     -15.447  79.431  21.866  1.00  1.00
TER
END
