
#######################################################
#                                                     #
#                        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   25 (  100),  selected   21 , name T0320TS550_2_2-D2
# Molecule2: number of CA atoms   73 (  604),  selected   21 , name T0320_D2.pdb
# PARAMETERS: T0320TS550_2_2-D2.T0320_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:    14       248 - 265         4.52    11.16
  LCS_AVERAGE:     16.76

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       252 - 256         1.58    15.32
  LONGEST_CONTINUOUS_SEGMENT:     5       254 - 258         1.89    12.04
  LONGEST_CONTINUOUS_SEGMENT:     5       263 - 267         1.79    14.49
  LCS_AVERAGE:      6.20

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       252 - 255         0.80    18.14
  LONGEST_CONTINUOUS_SEGMENT:     4       269 - 272         0.69    20.65
  LCS_AVERAGE:      4.63

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:   73
LCS_GDT     E     248     E     248      3    3   14     3    3    3    3    4    4    4    5    7   11   12   14   14   14   16   19   19   19   20   20 
LCS_GDT     W     249     W     249      3    4   14     3    3    3    4    4    4    4    7    9   11   12   14   14   14   16   19   19   19   20   20 
LCS_GDT     E     250     E     250      3    4   14     3    3    3    4    4    5    5    5    6   11   12   14   14   14   16   19   19   19   20   20 
LCS_GDT     I     251     I     251      3    4   14     3    4    5    5    6    7    8    8   10   11   12   14   14   14   16   19   19   19   20   20 
LCS_GDT     I     252     I     252      4    5   14     3    4    5    5    6    7    8    8   10   11   12   14   14   14   16   19   19   19   20   20 
LCS_GDT     H     253     H     253      4    5   14     3    4    5    5    6    7    8    8   10   11   12   14   14   14   16   19   19   19   20   20 
LCS_GDT     A     254     A     254      4    5   14     3    4    4    5    5    7    8    8   10   11   12   14   14   14   16   19   19   19   20   20 
LCS_GDT     F     255     F     255      4    5   14     3    4    4    5    5    7    8    8   10   11   12   14   14   14   16   19   19   19   20   20 
LCS_GDT     G     256     G     256      3    5   14     3    3    4    5    5    7    8    8   10   11   12   14   14   14   16   19   19   19   20   20 
LCS_GDT     K     257     K     257      3    5   14     0    3    3    4    5    7    8    8   10   11   11   14   14   14   16   19   19   19   20   20 
LCS_GDT     D     258     D     258      3    5   14     0    3    5    5    6    7    8    8   10   11   12   14   14   14   16   19   19   19   20   20 
LCS_GDT     R     263     R     263      3    5   14     0    3    4    4    5    6    8    8    9   10   11   14   14   14   16   19   19   19   20   20 
LCS_GDT     S     264     S     264      3    5   14     0    3    4    4    4    5    5    5    7   10   12   14   14   14   16   19   19   19   20   20 
LCS_GDT     S     265     S     265      3    5   14     3    3    4    4    4    5    5    5    8   10   12   14   14   14   16   19   19   19   20   20 
LCS_GDT     A     266     A     266      3    5   13     3    3    3    4    4    5    6    6    7    7    8   10   12   13   16   19   19   19   20   20 
LCS_GDT     I     267     I     267      3    5    8     3    3    4    4    5    5    6    6    7    7    9   10   12   14   16   19   19   19   20   20 
LCS_GDT     N     268     N     268      3    4    8     3    4    5    5    6    6    7    7    7   10   11   11   12   14   16   19   19   19   20   20 
LCS_GDT     T     269     T     269      4    4    8     3    4    5    5    6    6    7    7   10   10   11   11   12   14   16   19   19   19   20   20 
LCS_GDT     S     270     S     270      4    4    8     3    4    4    4    5    6    7    7   10   10   11   11   12   14   16   19   19   19   20   20 
LCS_GDT     P     271     P     271      4    4    8     3    4    4    4    5    5    6    6    7    7    7    7    8   12   12   13   17   18   20   20 
LCS_GDT     I     272     I     272      4    4    8     3    4    4    4    4    5    5    6    7    7    7    7    8    8    9    9   10   10   11   11 
LCS_AVERAGE  LCS_A:   9.20  (   4.63    6.20   16.76 )

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      5      6      7      8      8     10     11     12     14     14     14     16     19     19     19     20     20 
GDT PERCENT_CA   4.11   5.48   6.85   6.85   8.22   9.59  10.96  10.96  13.70  15.07  16.44  19.18  19.18  19.18  21.92  26.03  26.03  26.03  27.40  27.40
GDT RMS_LOCAL    0.22   0.69   0.85   0.85   1.44   2.10   2.35   2.35   3.59   3.84   4.25   4.52   4.52   4.52   5.71   6.30   6.30   6.30   6.56   6.56
GDT RMS_ALL_CA  15.65  20.65   8.93   8.93   8.48  13.32  11.82  11.82   8.06  11.54  11.44  11.16  11.16  11.16   7.31   7.39   7.39   7.39   7.29   7.29

#      Molecule1      Molecule2       DISTANCE
LGA    E     248      E     248         10.062
LGA    W     249      W     249         10.616
LGA    E     250      E     250         10.519
LGA    I     251      I     251          3.445
LGA    I     252      I     252          0.658
LGA    H     253      H     253          3.498
LGA    A     254      A     254          2.371
LGA    F     255      F     255          0.814
LGA    G     256      G     256          1.714
LGA    K     257      K     257          5.356
LGA    D     258      D     258          1.328
LGA    R     263      R     263          2.938
LGA    S     264      S     264          5.908
LGA    S     265      S     265          6.630
LGA    A     266      A     266         12.186
LGA    I     267      I     267         17.170
LGA    N     268      N     268         17.136
LGA    T     269      T     269         16.849
LGA    S     270      S     270         20.695
LGA    P     271      P     271         19.802
LGA    I     272      I     272         24.798

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   25   73    4.0      8    2.35    12.329    10.670     0.327

LGA_LOCAL      RMSD =  2.349  Number of atoms =    8  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 11.817  Number of atoms =   21 
Std_ALL_ATOMS  RMSD =  7.214  (standard rmsd on all 21 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.087217 * X  +   0.273447 * Y  +  -0.957925 * Z  +   9.978123
  Y_new =  -0.869001 * X  +   0.491030 * Y  +   0.061048 * Z  +  43.166023
  Z_new =   0.487064 * X  +   0.827113 * Y  +   0.280452 * Z  +  11.871365 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.243889   -1.897704  [ DEG:    71.2696   -108.7304 ]
  Theta =  -0.508724   -2.632868  [ DEG:   -29.1478   -150.8522 ]
  Phi   =  -1.470767    1.670825  [ DEG:   -84.2687     95.7313 ]
 
# 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: T0320TS550_2_2-D2                             
REMARK     2: T0320_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0320TS550_2_2-D2.T0320_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   25   73   4.0    8   2.35  10.670     7.21
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS550_2_2-D2
REMARK PARENT number 2
PFRMAT TS
TARGET T0320
PARENT 1mkn_A
ATOM      1  N   GLU   248      -5.462  19.026  -1.866  1.00  0.00
ATOM      2  CA  GLU   248      -4.168  19.029  -1.123  1.00  0.00
ATOM      3  C   GLU   248      -4.069  20.385  -0.424  1.00  0.00
ATOM      4  O   GLU   248      -3.594  21.338  -0.992  1.00  0.00
ATOM      5  N   TRP   249      -4.577  20.507   0.773  1.00  0.00
ATOM      6  CA  TRP   249      -4.571  21.844   1.446  1.00  0.00
ATOM      7  C   TRP   249      -3.444  21.944   2.477  1.00  0.00
ATOM      8  O   TRP   249      -3.555  21.457   3.584  1.00  0.00
ATOM      9  N   GLU   250      -2.368  22.607   2.129  1.00  0.00
ATOM     10  CA  GLU   250      -1.252  22.773   3.105  1.00  0.00
ATOM     11  C   GLU   250      -1.817  23.496   4.325  1.00  0.00
ATOM     12  O   GLU   250      -2.905  24.020   4.258  1.00  0.00
ATOM     13  N   ILE   251      -1.637  23.226   5.521  1.00  0.00
ATOM     14  CA  ILE   251      -1.558  22.634   6.845  1.00  0.00
ATOM     15  C   ILE   251      -2.466  23.450   7.738  1.00  0.00
ATOM     16  O   ILE   251      -2.470  24.671   7.651  1.00  0.00
ATOM     17  N   ILE   252      -3.230  22.779   8.596  1.00  0.00
ATOM     18  CA  ILE   252      -4.166  23.461   9.484  1.00  0.00
ATOM     19  C   ILE   252      -3.537  24.008  10.780  1.00  0.00
ATOM     20  O   ILE   252      -3.047  23.245  11.617  1.00  0.00
ATOM     21  N   HIS   253      -3.571  25.333  10.935  1.00  0.00
ATOM     22  CA  HIS   253      -3.014  26.007  12.109  1.00  0.00
ATOM     23  C   HIS   253      -3.894  25.750  13.333  1.00  0.00
ATOM     24  O   HIS   253      -5.103  25.977  13.307  1.00  0.00
ATOM     25  N   ALA   254      -3.269  25.296  14.412  1.00  0.00
ATOM     26  CA  ALA   254      -3.987  24.970  15.630  1.00  0.00
ATOM     27  C   ALA   254      -3.910  26.028  16.727  1.00  0.00
ATOM     28  O   ALA   254      -4.446  25.834  17.818  1.00  0.00
ATOM     29  N   PHE   255      -3.232  27.136  16.450  1.00  0.00
ATOM     30  CA  PHE   255      -3.127  28.212  17.431  1.00  0.00
ATOM     31  C   PHE   255      -3.607  29.513  16.800  1.00  0.00
ATOM     32  O   PHE   255      -3.580  29.670  15.578  1.00  0.00
ATOM     33  N   GLY   256      -4.044  30.442  17.639  1.00  0.00
ATOM     34  CA  GLY   256      -4.527  31.714  17.139  1.00  0.00
ATOM     35  C   GLY   256      -5.966  31.668  16.654  1.00  0.00
ATOM     36  O   GLY   256      -6.702  30.719  16.935  1.00  0.00
ATOM     37  N   LYS   257      -6.366  32.705  15.923  1.00  0.00
ATOM     38  CA  LYS   257      -7.713  32.790  15.396  1.00  0.00
ATOM     39  C   LYS   257      -7.745  32.144  14.017  1.00  0.00
ATOM     40  O   LYS   257      -7.012  32.544  13.109  1.00  0.00
ATOM     41  N   ASP   258      -8.602  31.127  13.845  1.00  0.00
ATOM     42  CA  ASP   258      -8.765  30.385  12.592  1.00  0.00
ATOM     43  C   ASP   258      -9.117  31.295  11.429  1.00  0.00
ATOM     44  O   ASP   258      -8.832  30.982  10.277  1.00  0.00
ATOM     45  N   ALA   259      -9.757  32.416  11.739  1.00  0.00
ATOM     46  CA  ALA   259     -10.159  33.362  10.710  1.00  0.00
ATOM     47  C   ALA   259      -8.941  34.034  10.098  1.00  0.00
ATOM     48  O   ALA   259      -8.916  34.337   8.901  1.00  0.00
ATOM     49  N   GLU   260      -7.927  34.252  10.928  1.00  0.00
ATOM     50  CA  GLU   260      -6.699  34.889  10.481  1.00  0.00
ATOM     51  C   GLU   260      -5.724  33.891   9.830  1.00  0.00
ATOM     52  O   GLU   260      -4.646  34.264   9.363  1.00  0.00
ATOM     53  N   GLY   261      -6.122  32.624   9.791  1.00  0.00
ATOM     54  CA  GLY   261      -5.309  31.579   9.187  1.00  0.00
ATOM     55  C   GLY   261      -5.626  31.526   7.688  1.00  0.00
ATOM     56  O   GLY   261      -6.751  31.811   7.279  1.00  0.00
ATOM     57  N   GLU   262      -4.631  31.178   6.875  1.00  0.00
ATOM     58  CA  GLU   262      -4.790  31.094   5.419  1.00  0.00
ATOM     59  C   GLU   262      -3.937  29.949   4.862  1.00  0.00
ATOM     60  O   GLU   262      -2.765  30.139   4.536  1.00  0.00
ATOM     61  N   ARG   263      -4.466  28.484   4.751  1.00  0.00
ATOM     62  CA  ARG   263      -3.698  27.305   4.280  1.00  0.00
ATOM     63  C   ARG   263      -3.485  27.502   2.787  1.00  0.00
ATOM     64  O   ARG   263      -3.889  28.507   2.236  1.00  0.00
ATOM     65  N   SER   264      -2.849  26.595   2.110  1.00  0.00
ATOM     66  CA  SER   264      -2.642  26.836   0.657  1.00  0.00
ATOM     67  C   SER   264      -2.306  25.541  -0.071  1.00  0.00
ATOM     68  O   SER   264      -1.474  24.777   0.377  1.00  0.00
ATOM     69  N   SER   265      -2.923  25.272  -1.199  1.00  0.00
ATOM     70  CA  SER   265      -2.558  24.011  -1.891  1.00  0.00
ATOM     71  C   SER   265      -3.202  23.872  -3.266  1.00  0.00
ATOM     72  O   SER   265      -3.281  24.807  -4.033  1.00  0.00
ATOM     73  N   ALA   266      -3.610  22.674  -3.597  1.00  0.00
ATOM     74  CA  ALA   266      -4.191  22.417  -4.939  1.00  0.00
ATOM     75  C   ALA   266      -5.351  21.422  -4.848  1.00  0.00
ATOM     76  O   ALA   266      -5.442  20.640  -3.929  1.00  0.00
ATOM     77  N   ILE   267      -6.228  22.143  -5.590  1.00  0.00
ATOM     78  CA  ILE   267      -7.306  23.099  -5.306  1.00  0.00
ATOM     79  C   ILE   267      -7.114  24.211  -4.263  1.00  0.00
ATOM     80  O   ILE   267      -7.068  25.390  -4.621  1.00  0.00
ATOM     81  N   ASN   268      -7.023  23.840  -2.983  1.00  0.00
ATOM     82  CA  ASN   268      -6.879  24.811  -1.891  1.00  0.00
ATOM     83  C   ASN   268      -5.743  25.818  -2.045  1.00  0.00
ATOM     84  O   ASN   268      -5.805  26.908  -1.475  1.00  0.00
ATOM     85  N   THR   269      -4.726  25.443  -2.821  1.00  0.00
ATOM     86  CA  THR   269      -3.538  26.269  -3.091  1.00  0.00
ATOM     87  C   THR   269      -3.772  27.779  -3.050  1.00  0.00
ATOM     88  O   THR   269      -3.175  28.486  -2.239  1.00  0.00
ATOM     89  N   SER   270      -4.646  27.708  -4.484  1.00  0.00
ATOM     90  CA  SER   270      -4.784  29.069  -3.882  1.00  0.00
ATOM     91  C   SER   270      -4.741  28.982  -2.363  1.00  0.00
ATOM     92  O   SER   270      -4.365  27.976  -1.795  1.00  0.00
ATOM     93  N   PRO   271      -5.105  30.042  -1.696  1.00  0.00
ATOM     94  CA  PRO   271      -5.063  30.030  -0.216  1.00  0.00
ATOM     95  C   PRO   271      -6.424  30.413   0.355  1.00  0.00
ATOM     96  O   PRO   271      -7.267  30.985  -0.307  1.00  0.00
ATOM     97  N   ILE   272      -6.613  30.098   1.598  1.00  0.00
ATOM     98  CA  ILE   272      -7.883  30.411   2.315  1.00  0.00
ATOM     99  C   ILE   272      -7.527  30.582   3.758  1.00  0.00
ATOM    100  O   ILE   272      -6.729  29.858   4.280  1.00  0.00
TER
END
