
#######################################################
#                                                     #
#                        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   24 (  118),  selected   24 , name T0381TS239_5_2-D1
# Molecule2: number of CA atoms   61 (  477),  selected   24 , name T0381_D1.pdb
# PARAMETERS: T0381TS239_5_2-D1.T0381_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:    15        60 - 74          4.89    12.06
  LONGEST_CONTINUOUS_SEGMENT:    15        63 - 77          4.95    14.02
  LCS_AVERAGE:     24.18

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8        63 - 70          1.85    12.17
  LCS_AVERAGE:      9.36

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        59 - 63          0.83    16.57
  LCS_AVERAGE:      6.01

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:   61
LCS_GDT     R      54     R      54      3    3   14     0    3    3    3    3    4    4    6    7   10   11   13   14   14   14   14   15   17   17   17 
LCS_GDT     R      55     R      55      3    3   14     3    3    3    3    3    6    7    8    9   11   13   13   14   15   15   15   16   17   18   20 
LCS_GDT     F      56     F      56      3    4   14     3    3    3    4    5    6    6    8    9   10   13   13   14   15   15   15   17   17   18   20 
LCS_GDT     L      57     L      57      3    4   14     3    3    3    4    5    6    7    8    9   11   13   13   14   15   15   15   16   17   18   20 
LCS_GDT     L      58     L      58      3    7   14     3    3    4    4    5    6    7    8    9   11   13   13   14   15   15   15   17   17   18   20 
LCS_GDT     T      59     T      59      5    7   14     4    4    5    6    6    6    7    8    9   11   13   13   14   15   15   18   19   19   19   20 
LCS_GDT     L      60     L      60      5    7   15     4    4    5    6    6    6    7    8    9   11   13   13   14   15   17   18   19   19   19   20 
LCS_GDT     V      61     V      61      5    7   15     4    4    5    6    6    6    7    8    9   10   13   13   14   15   17   18   19   19   19   20 
LCS_GDT     E      62     E      62      5    7   15     4    4    5    6    6    7    8    8    9   11   13   14   16   16   17   18   19   19   19   20 
LCS_GDT     L      63     L      63      5    8   15     4    4    5    6    7    8    8    9   10   11   13   14   16   16   17   18   19   19   19   20 
LCS_GDT     G      64     G      64      4    8   15     4    4    5    6    7    8    8    9   11   11   13   14   16   16   17   18   19   19   19   20 
LCS_GDT     Y      65     Y      65      4    8   15     4    4    5    6    7    8    8   10   11   11   13   14   16   16   16   18   19   19   19   20 
LCS_GDT     V      66     V      66      4    8   15     4    4    5    6    7    8    8   10   11   11   13   14   16   16   17   18   19   19   19   20 
LCS_GDT     A      67     A      67      4    8   15     3    3    4    6    7    8    8   10   11   11   13   14   16   16   17   18   19   19   19   20 
LCS_GDT     T      68     T      68      4    8   15     3    3    5    5    7    8    8   10   11   11   12   14   16   16   17   18   19   19   19   20 
LCS_GDT     D      69     D      69      0    8   15     2    3    4    6    7    8    8   10   11   11   12   14   16   16   17   18   19   19   19   20 
LCS_GDT     G      70     G      70      4    8   15     3    3    5    5    7    8    8   10   11   11   12   14   16   16   17   18   19   19   19   20 
LCS_GDT     S      71     S      71      4    4   15     3    3    4    4    5    6    7   10   11   11   12   14   16   16   17   18   19   19   19   20 
LCS_GDT     A      72     A      72      4    4   15     3    3    4    4    4    5    7   10   11   11   12   14   16   16   17   18   19   19   19   20 
LCS_GDT     F      73     F      73      4    4   15     0    3    4    4    4    4    7   10   11   11   12   14   16   16   17   18   19   19   19   20 
LCS_GDT     W      74     W      74      3    3   15     1    3    3    4    6    7    8   10   11   11   12   14   16   16   17   18   19   19   19   20 
LCS_GDT     L      75     L      75      3    3   15     1    3    4    5    6    7    8    8    9   10   12   14   16   16   17   18   19   19   19   19 
LCS_GDT     T      76     T      76      3    3   15     0    3    4    5    6    7    8    8    9   10   11   13   16   16   17   18   19   19   19   19 
LCS_GDT     P      77     P      77      3    3   15     0    3    3    3    4    6    8    8    9   10   11   14   16   16   17   18   19   19   19   19 
LCS_AVERAGE  LCS_A:  13.18  (   6.01    9.36   24.18 )

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      4      4      5      6      7      8      8     10     11     11     13     14     16     16     17     18     19     19     19     20 
GDT PERCENT_CA   6.56   6.56   8.20   9.84  11.48  13.11  13.11  16.39  18.03  18.03  21.31  22.95  26.23  26.23  27.87  29.51  31.15  31.15  31.15  32.79
GDT RMS_LOCAL    0.26   0.26   0.83   1.18   1.60   1.85   1.85   3.11   3.46   3.46   4.16   4.76   5.08   5.08   5.58   5.70   6.06   6.06   6.06   7.00
GDT RMS_ALL_CA  16.01  16.01  16.57  16.25  12.13  12.17  12.17  14.37  14.19  14.19  11.10  14.15  13.38  13.38  12.43  12.53  11.79  11.79  11.79   9.57

#      Molecule1      Molecule2       DISTANCE
LGA    R      54      R      54         35.708
LGA    R      55      R      55         32.092
LGA    F      56      F      56         26.097
LGA    L      57      L      57         23.173
LGA    L      58      L      58         21.117
LGA    T      59      T      59         18.007
LGA    L      60      L      60         12.835
LGA    V      61      V      61         11.799
LGA    E      62      E      62         12.450
LGA    L      63      L      63         10.493
LGA    G      64      G      64          5.921
LGA    Y      65      Y      65          1.882
LGA    V      66      V      66          3.501
LGA    A      67      A      67          2.907
LGA    T      68      T      68          3.646
LGA    D      69      D      69          3.229
LGA    G      70      G      70          3.340
LGA    S      71      S      71          2.667
LGA    A      72      A      72          3.005
LGA    F      73      F      73          3.910
LGA    W      74      W      74          3.846
LGA    L      75      L      75          9.314
LGA    T      76      T      76         12.928
LGA    P      77      P      77         12.141

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   24   61    4.0     10    3.11    15.574    14.081     0.312

LGA_LOCAL      RMSD =  3.107  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 15.005  Number of atoms =   24 
Std_ALL_ATOMS  RMSD =  8.851  (standard rmsd on all 24 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.998133 * X  +  -0.044477 * Y  +  -0.041849 * Z  +  56.307152
  Y_new =   0.023151 * X  +  -0.909690 * Y  +   0.414642 * Z  +  59.619755
  Z_new =  -0.056512 * X  +   0.412899 * Y  +   0.909022 * Z  +  29.379766 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.426360   -2.715232  [ DEG:    24.4287   -155.5714 ]
  Theta =   0.056542    3.085051  [ DEG:     3.2396    176.7604 ]
  Phi   =   3.118403   -0.023190  [ DEG:   178.6713     -1.3287 ]
 
# 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: T0381TS239_5_2-D1                             
REMARK     2: T0381_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0381TS239_5_2-D1.T0381_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   24   61   4.0   10   3.11  14.081     8.85
REMARK  ---------------------------------------------------------- 
MOLECULE T0381TS239_5_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0381
PARENT 1f5m_B
ATOM      1  N   ARG    54      26.691  33.681  15.068  1.00  9.99
ATOM      2  CA  ARG    54      25.939  34.466  14.038  1.00  9.99
ATOM      3  C   ARG    54      25.244  35.733  14.589  1.00  9.99
ATOM      4  O   ARG    54      24.015  35.789  14.626  1.00  9.99
ATOM      5  CB  ARG    54      24.897  33.559  13.374  1.00  9.99
ATOM      6  N   ARG    55      26.012  36.757  14.960  1.00  9.99
ATOM      7  CA  ARG    55      25.447  37.984  15.529  1.00  9.99
ATOM      8  C   ARG    55      24.849  38.953  14.506  1.00  9.99
ATOM      9  O   ARG    55      25.472  39.262  13.498  1.00  9.99
ATOM     10  CB  ARG    55      26.517  38.708  16.363  1.00  9.99
ATOM     11  N   PHE    56      23.654  39.481  14.774  1.00  9.99
ATOM     12  CA  PHE    56      23.069  40.380  13.788  1.00  9.99
ATOM     13  C   PHE    56      23.845  41.654  13.708  1.00  9.99
ATOM     14  O   PHE    56      23.710  42.370  12.735  1.00  9.99
ATOM     15  CB  PHE    56      21.656  40.790  14.091  1.00  9.99
ATOM     16  N   LEU    57      24.670  41.935  14.709  1.00  9.99
ATOM     17  CA  LEU    57      25.397  43.199  14.706  1.00  9.99
ATOM     18  C   LEU    57      24.478  44.326  15.224  1.00  9.99
ATOM     19  O   LEU    57      24.857  45.505  15.240  1.00  9.99
ATOM     20  CB  LEU    57      25.912  43.487  13.286  1.00  9.99
ATOM     21  N   LEU    58      23.256  43.994  15.632  1.00  9.99
ATOM     22  CA  LEU    58      22.384  45.037  16.164  1.00  9.99
ATOM     23  C   LEU    58      22.224  44.790  17.664  1.00  9.99
ATOM     24  O   LEU    58      22.586  43.720  18.162  1.00  9.99
ATOM     25  CB  LEU    58      21.011  45.019  15.513  1.00  9.99
ATOM     26  N   THR    59      21.729  45.787  18.392  1.00  9.99
ATOM     27  CA  THR    59      21.466  45.657  19.835  1.00  9.99
ATOM     28  C   THR    59      20.133  46.333  20.027  1.00  9.99
ATOM     29  O   THR    59      19.698  47.119  19.139  1.00  9.99
ATOM     30  CB  THR    59      22.516  46.382  20.685  1.00  9.99
ATOM     31  N   LEU    60      19.482  46.034  21.153  1.00  9.99
ATOM     32  CA  LEU    60      18.177  46.623  21.455  1.00  9.99
ATOM     33  C   LEU    60      18.198  48.137  21.355  1.00  9.99
ATOM     34  O   LEU    60      17.270  48.755  20.819  1.00  9.99
ATOM     35  CB  LEU    60      17.697  46.213  22.867  1.00  9.99
ATOM     36  N   VAL    61      19.274  48.736  21.844  1.00  9.99
ATOM     37  CA  VAL    61      19.404  50.187  21.837  1.00  9.99
ATOM     38  C   VAL    61      19.303  50.840  20.441  1.00  9.99
ATOM     39  O   VAL    61      18.947  52.021  20.320  1.00  9.99
ATOM     40  CB  VAL    61      20.716  50.568  22.511  1.00  9.99
ATOM     41  N   GLU    62      19.565  50.058  19.392  1.00  9.99
ATOM     42  CA  GLU    62      19.543  50.565  18.030  1.00  9.99
ATOM     43  C   GLU    62      18.196  51.023  17.515  1.00  9.99
ATOM     44  O   GLU    62      18.108  51.701  16.508  1.00  9.99
ATOM     45  CB  GLU    62      20.166  49.546  17.070  1.00  9.99
ATOM     46  N   LEU    63      17.129  50.661  18.199  1.00  9.99
ATOM     47  CA  LEU    63      15.830  51.133  17.774  1.00  9.99
ATOM     48  C   LEU    63      15.740  52.630  17.947  1.00  9.99
ATOM     49  O   LEU    63      14.854  53.302  17.397  1.00  9.99
ATOM     50  CB  LEU    63      14.749  50.489  18.625  1.00  9.99
ATOM     51  N   GLY    64      16.668  53.164  18.722  1.00  9.99
ATOM     52  CA  GLY    64      16.662  54.575  19.034  1.00  9.99
ATOM     53  C   GLY    64      17.900  55.257  18.433  1.00  9.99
ATOM     54  O   GLY    64      18.193  56.422  18.709  1.00  9.99
ATOM     55  N   TYR    65      18.621  54.520  17.586  1.00  9.99
ATOM     56  CA  TYR    65      19.814  55.061  16.945  1.00  9.99
ATOM     57  C   TYR    65      19.527  55.216  15.463  1.00  9.99
ATOM     58  O   TYR    65      19.574  54.238  14.709  1.00  9.99
ATOM     59  CB  TYR    65      21.026  54.122  17.121  1.00  9.99
ATOM     60  N   VAL    66      19.185  56.426  15.053  1.00  9.99
ATOM     61  CA  VAL    66      18.932  56.708  13.647  1.00  9.99
ATOM     62  C   VAL    66      19.214  58.177  13.419  1.00  9.99
ATOM     63  O   VAL    66      19.278  58.954  14.368  1.00  9.99
ATOM     64  CB  VAL    66      17.504  56.370  13.275  1.00  9.99
ATOM     65  N   ALA    67      19.381  58.557  12.162  1.00  9.99
ATOM     66  CA  ALA    67      19.716  59.934  11.854  1.00  9.99
ATOM     67  C   ALA    67      18.557  60.863  12.083  1.00  9.99
ATOM     68  O   ALA    67      17.401  60.480  11.932  1.00  9.99
ATOM     69  CB  ALA    67      20.187  60.078  10.403  1.00  9.99
ATOM     70  N   THR    68      18.887  62.089  12.464  1.00  9.99
ATOM     71  CA  THR    68      17.883  63.122  12.695  1.00  9.99
ATOM     72  C   THR    68      17.512  63.760  11.363  1.00  9.99
ATOM     73  O   THR    68      16.712  64.707  11.334  1.00  9.99
ATOM     74  CB  THR    68      18.431  64.181  13.655  1.00  9.99
ATOM     75  N   ASP    69      18.081  63.244  10.262  1.00  9.99
ATOM     76  CA  ASP    69      17.787  63.761   8.916  1.00  9.99
ATOM     77  C   ASP    69      16.609  63.046   8.305  1.00  9.99
ATOM     78  O   ASP    69      16.226  63.336   7.183  1.00  9.99
ATOM     79  CB  ASP    69      18.968  63.625   7.942  1.00  9.99
ATOM     80  N   GLY    70      12.710  62.420   7.964  1.00  9.99
ATOM     81  CA  GLY    70      11.600  63.350   8.173  1.00  9.99
ATOM     82  C   GLY    70      10.636  62.755   9.200  1.00  9.99
ATOM     83  O   GLY    70      10.622  61.548   9.413  1.00  9.99
ATOM     84  N   SER    71       9.819  63.600   9.816  1.00  9.99
ATOM     85  CA  SER    71       8.898  63.161  10.846  1.00  9.99
ATOM     86  C   SER    71       8.032  61.917  10.529  1.00  9.99
ATOM     87  O   SER    71       7.886  61.032  11.379  1.00  9.99
ATOM     88  CB  SER    71       8.017  64.348  11.277  1.00  9.99
ATOM     89  N   ALA    72       7.463  61.825   9.325  1.00  9.99
ATOM     90  CA  ALA    72       6.657  60.647   9.016  1.00  9.99
ATOM     91  C   ALA    72       7.493  59.378   9.103  1.00  9.99
ATOM     92  O   ALA    72       7.030  58.366   9.620  1.00  9.99
ATOM     93  CB  ALA    72       6.008  60.765   7.626  1.00  9.99
ATOM     94  N   PHE    73       8.722  59.426   8.600  1.00  9.99
ATOM     95  CA  PHE    73       9.611  58.246   8.639  1.00  9.99
ATOM     96  C   PHE    73       9.912  57.824  10.075  1.00  9.99
ATOM     97  O   PHE    73       9.869  56.637  10.418  1.00  9.99
ATOM     98  CB  PHE    73      10.969  58.535   7.982  1.00  9.99
ATOM     99  N   TRP    74      10.270  58.813  10.897  1.00  9.99
ATOM    100  CA  TRP    74      10.612  58.583  12.289  1.00  9.99
ATOM    101  C   TRP    74       9.451  57.961  13.071  1.00  9.99
ATOM    102  O   TRP    74       9.622  57.010  13.823  1.00  9.99
ATOM    103  CB  TRP    74      11.054  59.914  12.945  1.00  9.99
ATOM    104  N   LEU    75       8.256  58.474  12.882  1.00  9.99
ATOM    105  CA  LEU    75       7.127  57.944  13.624  1.00  9.99
ATOM    106  C   LEU    75       6.692  56.591  13.091  1.00  9.99
ATOM    107  O   LEU    75       6.206  55.717  13.851  1.00  9.99
ATOM    108  CB  LEU    75       5.964  58.951  13.574  1.00  9.99
ATOM    109  N   THR    76       6.844  56.395  11.788  1.00  9.99
ATOM    110  CA  THR    76       6.444  55.118  11.247  1.00  9.99
ATOM    111  C   THR    76       7.431  54.066  11.746  1.00  9.99
ATOM    112  O   THR    76       7.048  52.944  12.052  1.00  9.99
ATOM    113  CB  THR    76       6.406  55.158   9.708  1.00  9.99
ATOM    114  N   PRO    77       8.698  54.443  11.841  1.00  9.99
ATOM    115  CA  PRO    77       9.726  53.525  12.338  1.00  9.99
ATOM    116  C   PRO    77       9.500  53.198  13.796  1.00  9.99
ATOM    117  O   PRO    77       9.892  52.131  14.268  1.00  9.99
ATOM    118  CB  PRO    77      11.119  54.142  12.220  1.00  9.99
TER
END
