
#######################################################
#                                                     #
#                        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 (  120),  selected   24 , name T0301TS102_2-D1
# Molecule2: number of CA atoms  200 ( 1505),  selected   24 , name T0301_D1.pdb
# PARAMETERS: T0301TS102_2-D1.T0301_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:    11        13 - 129         4.64    13.55
  LONGEST_CONTINUOUS_SEGMENT:    11       120 - 173         4.33    13.09
  LCS_AVERAGE:      4.40

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10       120 - 129         1.34    14.45
  LCS_AVERAGE:      3.48

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9       120 - 128         0.79    14.75
  LCS_AVERAGE:      2.92

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:  200
LCS_GDT     Q       6     Q       6      6    7    8     3    4    5    6    6    7    7    8    8    8    8    8    8    8    8    8   11   17   17   17 
LCS_GDT     I       7     I       7      6    7    8     3    5    5    6    6    7    7    8    8    8    8    8    8    8    8    8   15   17   17   17 
LCS_GDT     R       8     R       8      6    7    8     4    5    5    6    6    7    7    8    8    8    8    8    8    8   14   14   15   17   17   17 
LCS_GDT     I       9     I       9      6    7    8     4    5    5    6    6    7    7    8    8    8    8    8    8    8   14   14   15   17   17   17 
LCS_GDT     P      10     P      10      6    7    8     4    5    5    6    6    7    7    8    8    8   10   11   12   12   14   14   15   17   17   17 
LCS_GDT     A      11     A      11      6    7    8     4    5    5    6    6    7    7    8    8    8   10   11   12   12   14   14   15   17   17   17 
LCS_GDT     T      12     T      12      3    7    8     0    3    3    4    6    7    7    8    8    8    8   11   12   12   14   14   15   17   17   17 
LCS_GDT     Y      13     Y      13      3    3   11     0    3    3    3    3    5    6    8    8    8    8    8    8    8    8    8   10   17   17   17 
LCS_GDT     L     120     L     120      9   10   11     3    7    9    9    9   10   10   10   10   10   10   11   12   12   14   14   15   17   17   17 
LCS_GDT     V     121     V     121      9   10   11     5    7    9    9    9   10   10   10   10   10   10   11   12   12   14   14   15   17   17   17 
LCS_GDT     D     122     D     122      9   10   11     5    7    9    9    9   10   10   10   10   10   10   11   12   12   14   14   15   17   17   17 
LCS_GDT     P     123     P     123      9   10   11     5    7    9    9    9   10   10   10   10   10   10   11   12   12   14   14   15   17   17   17 
LCS_GDT     A     124     A     124      9   10   11     5    7    9    9    9   10   10   10   10   10   10   11   12   12   14   14   15   17   17   17 
LCS_GDT     R     125     R     125      9   10   11     5    7    9    9    9   10   10   10   10   10   10   11   12   12   14   14   15   17   17   17 
LCS_GDT     I     126     I     126      9   10   11     5    7    9    9    9   10   10   10   10   10   10   11   12   12   14   14   15   17   17   17 
LCS_GDT     P     127     P     127      9   10   11     4    7    9    9    9   10   10   10   10   10   10   11   12   12   14   14   15   17   17   17 
LCS_GDT     E     128     E     128      9   10   11     5    7    9    9    9   10   10   10   10   10   10   11   12   12   14   14   15   17   17   17 
LCS_GDT     D     129     D     129      5   10   11     3    5    5    8    9   10   10   10   10   10   10   10   10   12   13   13   15   15   15   17 
LCS_GDT     E     173     E     173      0    3   11     0    0    0    0    0    3    3    3    3    4    4    5    5    5    5    6    6    9   11   12 
LCS_GDT     V     175     V     175      3    3    5     0    3    3    3    3    3    4    4    4    4    6    7    7    8    9   11   12   13   13   13 
LCS_GDT     L     176     L     176      3    3    5     0    3    3    3    3    3    4    4    4    4    8    8    8    8   10   11   12   13   13   13 
LCS_GDT     E     177     E     177      3    3    5     0    3    3    3    3    3    4    4    4    4    6    7    8    8   10   11   12   13   13   13 
LCS_GDT     F     178     F     178      3    3    5     0    3    3    3    3    3    4    4    4    4    4    5    5    8    9    9   10   13   13   13 
LCS_GDT     R     378     R     378      0    0    3     0    0    0    0    0    0    0    2    4    5    6    6    6    6    6    6    6    8    9    9 
LCS_AVERAGE  LCS_A:   3.60  (   2.92    3.48    4.40 )

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      5      7      9      9      9     10     10     10     10     10     10     11     12     12     14     14     15     17     17     17 
GDT PERCENT_CA   2.50   3.50   4.50   4.50   4.50   5.00   5.00   5.00   5.00   5.00   5.00   5.50   6.00   6.00   7.00   7.00   7.50   8.50   8.50   8.50
GDT RMS_LOCAL    0.17   0.50   0.79   0.79   0.79   1.34   1.34   1.34   1.34   1.34   1.34   3.72   4.29   3.92   5.83   5.83   5.96   7.18   7.18   6.97
GDT RMS_ALL_CA  14.08  14.35  14.75  14.75  14.75  14.45  14.45  14.45  14.45  14.45  14.45  14.71  14.63  14.55  13.94  13.94  13.79  13.60  13.60  13.50

#      Molecule1      Molecule2       DISTANCE
LGA    Q       6      Q       6         19.053
LGA    I       7      I       7         18.059
LGA    R       8      R       8         14.482
LGA    I       9      I       9         14.415
LGA    P      10      P      10         10.443
LGA    A      11      A      11         10.029
LGA    T      12      T      12         11.208
LGA    Y      13      Y      13         15.652
LGA    L     120      L     120          2.061
LGA    V     121      V     121          0.876
LGA    D     122      D     122          0.266
LGA    P     123      P     123          0.608
LGA    A     124      A     124          0.587
LGA    R     125      R     125          0.501
LGA    I     126      I     126          0.807
LGA    P     127      P     127          0.987
LGA    E     128      E     128          1.394
LGA    D     129      D     129          2.908
LGA    E     173      E     173         15.332
LGA    V     175      V     175         20.107
LGA    L     176      L     176         22.373
LGA    E     177      E     177         23.118
LGA    F     178      F     178         26.890
LGA    R     378      R     378         30.186

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   24  200    4.0     10    1.34     5.000     4.629     0.692

LGA_LOCAL      RMSD =  1.345  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 14.453  Number of atoms =   24 
Std_ALL_ATOMS  RMSD = 11.321  (standard rmsd on all 24 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.953987 * X  +  -0.009898 * Y  +  -0.299686 * Z  +  17.915123
  Y_new =  -0.281350 * X  +  -0.375172 * Y  +  -0.883226 * Z  +  48.969925
  Z_new =  -0.103691 * X  +   0.926902 * Y  +  -0.360694 * Z  +  26.033430 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.941905   -1.199688  [ DEG:   111.2630    -68.7370 ]
  Theta =   0.103878    3.037715  [ DEG:     5.9518    174.0482 ]
  Phi   =  -0.286790    2.854803  [ DEG:   -16.4318    163.5682 ]
 
# 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: T0301TS102_2-D1                               
REMARK     2: T0301_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0301TS102_2-D1.T0301_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   24  200   4.0   10   1.34   4.629    11.32
REMARK  ---------------------------------------------------------- 
MOLECULE T0301TS102_2-D1
PFRMAT TS
TARGET T0301
MODEL 2
PARENT 1ji7_A
ATOM      1  N   GLN     6      54.781  35.008   8.996  1.00  1.00
ATOM      2  CA  GLN     6      54.669  33.603   8.512  1.00  1.00
ATOM      3  C   GLN     6      55.033  32.628   9.625  1.00  1.00
ATOM      4  O   GLN     6      55.351  33.037  10.744  1.00  1.00
ATOM      5  CB  GLN     6      55.582  33.390   7.313  1.00  1.00
ATOM      6  N   ILE     7      54.988  31.337   9.312  1.00  1.00
ATOM      7  CA  ILE     7      55.307  30.303  10.288  1.00  1.00
ATOM      8  C   ILE     7      56.523  29.493   9.849  1.00  1.00
ATOM      9  O   ILE     7      56.474  28.752   8.867  1.00  1.00
ATOM     10  CB  ILE     7      54.105  29.361  10.497  1.00  1.00
ATOM     11  N   ARG     8      57.612  29.637  10.593  1.00  1.00
ATOM     12  CA  ARG     8      58.851  28.934  10.285  1.00  1.00
ATOM     13  C   ARG     8      59.330  28.126  11.482  1.00  1.00
ATOM     14  O   ARG     8      59.614  28.680  12.541  1.00  1.00
ATOM     15  CB  ARG     8      59.922  29.937   9.868  1.00  1.00
ATOM     16  N   ILE     9      59.423  26.813  11.308  1.00  1.00
ATOM     17  CA  ILE     9      59.882  25.944  12.381  1.00  1.00
ATOM     18  C   ILE     9      61.385  26.066  12.596  1.00  1.00
ATOM     19  O   ILE     9      62.133  26.382  11.670  1.00  1.00
ATOM     20  CB  ILE     9      59.563  24.481  12.058  1.00  1.00
ATOM     21  N   PRO    10      61.845  25.830  13.830  1.00  1.00
ATOM     22  CA  PRO    10      63.282  25.914  14.092  1.00  1.00
ATOM     23  C   PRO    10      63.940  24.762  13.340  1.00  1.00
ATOM     24  O   PRO    10      63.286  23.763  13.034  1.00  1.00
ATOM     25  CB  PRO    10      63.371  25.768  15.607  1.00  1.00
ATOM     26  N   ALA    11      65.228  24.897  13.049  1.00  1.00
ATOM     27  CA  ALA    11      65.947  23.882  12.290  1.00  1.00
ATOM     28  C   ALA    11      65.743  22.443  12.750  1.00  1.00
ATOM     29  O   ALA    11      65.603  21.547  11.919  1.00  1.00
ATOM     30  CB  ALA    11      67.437  24.212  12.269  1.00  1.00
ATOM     31  N   THR    12      65.718  22.223  14.062  1.00  1.00
ATOM     32  CA  THR    12      65.562  20.873  14.598  1.00  1.00
ATOM     33  C   THR    12      64.173  20.257  14.453  1.00  1.00
ATOM     34  O   THR    12      63.961  19.106  14.830  1.00  1.00
ATOM     35  CB  THR    12      65.990  20.821  16.075  1.00  1.00
ATOM     36  N   TYR    13      63.228  21.013  13.904  1.00  1.00
ATOM     37  CA  TYR    13      61.879  20.490  13.721  1.00  1.00
ATOM     38  C   TYR    13      61.411  20.505  12.273  1.00  1.00
ATOM     39  O   TYR    13      60.232  20.316  11.998  1.00  1.00
ATOM     40  CB  TYR    13      60.884  21.277  14.579  1.00  1.00
ATOM     41  N   LEU   120      62.331  20.718  11.340  1.00  1.00
ATOM     42  CA  LEU   120      61.941  20.759   9.940  1.00  1.00
ATOM     43  C   LEU   120      61.652  19.395   9.310  1.00  1.00
ATOM     44  O   LEU   120      61.049  19.315   8.240  1.00  1.00
ATOM     45  CB  LEU   120      62.988  21.547   9.149  1.00  1.00
ATOM     46  N   VAL   121      62.049  18.317   9.974  1.00  1.00
ATOM     47  CA  VAL   121      61.764  16.992   9.432  1.00  1.00
ATOM     48  C   VAL   121      60.246  16.800   9.475  1.00  1.00
ATOM     49  O   VAL   121      59.562  17.421  10.289  1.00  1.00
ATOM     50  CB  VAL   121      62.458  15.896  10.255  1.00  1.00
ATOM     51  N   ASP   122      59.715  15.957   8.598  1.00  1.00
ATOM     52  CA  ASP   122      58.274  15.722   8.571  1.00  1.00
ATOM     53  C   ASP   122      57.750  15.211   9.909  1.00  1.00
ATOM     54  O   ASP   122      58.396  14.398  10.567  1.00  1.00
ATOM     55  CB  ASP   122      57.919  14.719   7.481  1.00  1.00
ATOM     56  N   PRO   123      56.562  15.679  10.328  1.00  1.00
ATOM     57  CA  PRO   123      55.983  15.242  11.600  1.00  1.00
ATOM     58  C   PRO   123      55.903  13.721  11.772  1.00  1.00
ATOM     59  O   PRO   123      56.050  13.208  12.883  1.00  1.00
ATOM     60  CB  PRO   123      54.601  15.903  11.596  1.00  1.00
ATOM     61  N   ALA   124      55.690  12.991  10.680  1.00  1.00
ATOM     62  CA  ALA   124      55.582  11.539  10.795  1.00  1.00
ATOM     63  C   ALA   124      56.877  10.917  11.329  1.00  1.00
ATOM     64  O   ALA   124      56.860   9.794  11.833  1.00  1.00
ATOM     65  CB  ALA   124      55.173  10.894   9.438  1.00  1.00
ATOM     66  N   ARG   125      57.981  11.658  11.247  1.00  1.00
ATOM     67  CA  ARG   125      59.267  11.165  11.740  1.00  1.00
ATOM     68  C   ARG   125      59.634  11.716  13.110  1.00  1.00
ATOM     69  O   ARG   125      60.673  11.366  13.668  1.00  1.00
ATOM     70  CB  ARG   125      60.392  11.512  10.758  1.00  1.00
ATOM     71  N   ILE   126      58.788  12.579  13.667  1.00  1.00
ATOM     72  CA  ILE   126      59.078  13.149  14.974  1.00  1.00
ATOM     73  C   ILE   126      59.068  12.107  16.073  1.00  1.00
ATOM     74  O   ILE   126      58.191  11.245  16.128  1.00  1.00
ATOM     75  CB  ILE   126      58.048  14.213  15.378  1.00  1.00
ATOM     76  N   PRO   127      60.043  12.205  16.963  1.00  1.00
ATOM     77  CA  PRO   127      60.103  11.319  18.111  1.00  1.00
ATOM     78  C   PRO   127      59.188  11.936  19.169  1.00  1.00
ATOM     79  O   PRO   127      58.657  13.040  18.985  1.00  1.00
ATOM     80  CB  PRO   127      61.521  11.280  18.674  1.00  1.00
ATOM     81  N   GLU   128      59.001  11.242  20.282  1.00  1.00
ATOM     82  CA  GLU   128      58.192  11.799  21.349  1.00  1.00
ATOM     83  C   GLU   128      58.830  13.102  21.852  1.00  1.00
ATOM     84  O   GLU   128      58.126  14.062  22.185  1.00  1.00
ATOM     85  CB  GLU   128      58.057  10.781  22.481  1.00  1.00
ATOM     86  N   ASP   129      60.162  13.161  21.888  1.00  1.00
ATOM     87  CA  ASP   129      60.818  14.382  22.341  1.00  1.00
ATOM     88  C   ASP   129      60.617  15.506  21.329  1.00  1.00
ATOM     89  O   ASP   129      60.469  16.664  21.711  1.00  1.00
ATOM     90  CB  ASP   129      62.317  14.170  22.573  1.00  1.00
ATOM     91  N   GLU   173      60.619  15.174  20.042  1.00  1.00
ATOM     92  CA  GLU   173      60.398  16.194  19.020  1.00  1.00
ATOM     93  C   GLU   173      59.008  16.807  19.202  1.00  1.00
ATOM     94  O   GLU   173      58.839  18.020  19.060  1.00  1.00
ATOM     95  CB  GLU   173      60.494  15.613  17.609  1.00  1.00
ATOM     96  N   VAL   175      58.013  15.974  19.506  1.00  1.00
ATOM     97  CA  VAL   175      56.660  16.478  19.736  1.00  1.00
ATOM     98  C   VAL   175      56.696  17.481  20.894  1.00  1.00
ATOM     99  O   VAL   175      56.099  18.556  20.816  1.00  1.00
ATOM    100  CB  VAL   175      55.687  15.317  20.061  1.00  1.00
ATOM    101  N   LEU   176      57.421  17.147  21.963  1.00  1.00
ATOM    102  CA  LEU   176      57.530  18.046  23.110  1.00  1.00
ATOM    103  C   LEU   176      58.240  19.342  22.706  1.00  1.00
ATOM    104  O   LEU   176      57.866  20.422  23.168  1.00  1.00
ATOM    105  CB  LEU   176      58.289  17.361  24.253  1.00  1.00
ATOM    106  N   GLU   177      59.265  19.241  21.862  1.00  1.00
ATOM    107  CA  GLU   177      59.982  20.432  21.405  1.00  1.00
ATOM    108  C   GLU   177      59.052  21.311  20.572  1.00  1.00
ATOM    109  O   GLU   177      59.118  22.541  20.641  1.00  1.00
ATOM    110  CB  GLU   177      61.208  20.039  20.576  1.00  1.00
ATOM    111  N   PHE   178      58.189  20.679  19.783  1.00  1.00
ATOM    112  CA  PHE   178      57.234  21.423  18.963  1.00  1.00
ATOM    113  C   PHE   178      56.291  22.200  19.889  1.00  1.00
ATOM    114  O   PHE   178      56.005  23.370  19.638  1.00  1.00
ATOM    115  CB  PHE   178      56.446  20.448  18.082  1.00  1.00
ATOM    379  N   ARG   378      52.638  22.652   4.241  1.00  1.00
ATOM    380  CA  ARG   378      53.855  23.310   3.768  1.00  1.00
ATOM    381  C   ARG   378      54.747  22.354   2.990  1.00  1.00
ATOM    382  O   ARG   378      55.157  22.719   1.868  1.00  1.00
ATOM    383  CB  ARG   378      54.646  23.894   4.943  1.00  1.00
TER
END
