
#######################################################
#                                                     #
#                        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   27 (  132),  selected   27 , name T0306TS239_3_2
# Molecule2: number of CA atoms   95 (  694),  selected   27 , name T0306.pdb
# PARAMETERS: T0306TS239_3_2.T0306.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        69 - 83          4.27    25.38
  LCS_AVERAGE:     13.80

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9        73 - 81          1.99    26.06
  LCS_AVERAGE:      7.17

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        75 - 80          0.66    23.51
  LCS_AVERAGE:      4.76

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:   95
LCS_GDT     S      69     S      69      3    3   15     0    3    3    3    3    4    5    6    6    7    8    8    8    8   10   14   15   15   15   15 
LCS_GDT     E      70     E      70      3    4   15     0    3    3    3    4    4    5    6    7    9   13   14   14   14   14   14   15   15   15   15 
LCS_GDT     T      71     T      71      4    6   15     3    4    5    5    7    9   12   12   13   13   13   14   14   14   14   14   15   15   15   15 
LCS_GDT     S      72     S      72      4    7   15     3    4    5    5   10   11   12   12   13   13   13   14   14   14   14   14   15   15   15   15 
LCS_GDT     P      73     P      73      4    9   15     3    4    6    9   10   11   12   12   13   13   13   14   14   14   14   14   15   15   15   15 
LCS_GDT     V      74     V      74      4    9   15     3    4    5    9   10   11   12   12   13   13   13   14   14   14   14   14   15   15   15   15 
LCS_GDT     D      75     D      75      6    9   15     4    6    6    9   10   11   12   12   13   13   13   14   14   14   14   14   15   15   15   15 
LCS_GDT     L      76     L      76      6    9   15     4    6    6    6    7   11   12   12   13   13   13   14   14   14   14   14   15   15   15   15 
LCS_GDT     C      77     C      77      6    9   15     4    6    6    9   10   11   12   12   13   13   13   14   14   14   14   14   15   16   16   16 
LCS_GDT     V      78     V      78      6    9   15     4    6    6    9   10   11   12   12   13   13   13   14   14   14   14   14   15   16   16   16 
LCS_GDT     I      79     I      79      6    9   15     4    6    6    6    6    9   11   12   13   13   13   14   14   14   14   14   15   16   16   16 
LCS_GDT     G      80     G      80      6    9   15     4    6    6    9   10   11   12   12   13   13   13   14   14   14   14   14   15   16   16   16 
LCS_GDT     I      81     I      81      5    9   15     4    5    6    9   10   11   12   12   13   13   13   14   14   14   14   14   15   15   15   16 
LCS_GDT     V      82     V      82      5    7   15     4    5    6    9   10   11   12   12   13   13   13   14   14   14   14   14   15   15   15   15 
LCS_GDT     D      83     D      83      5    7   15     4    5    5    9   10   11   12   12   13   13   13   14   14   14   14   14   15   15   15   15 
LCS_GDT     E      84     E      84      3    5    8     2    3    4    4    5    5    6    7    8    9    9   10   10   12   14   14   15   16   16   16 
LCS_GDT     V      85     V      85      3    5   11     3    3    4    4    5    5    6    7    8    9    9   10   11   12   14   14   15   16   16   16 
LCS_GDT     V      86     V      86      3    5   11     3    3    4    4    5    5    6    7    8    9    9   10   11   12   14   14   15   16   16   16 
LCS_GDT     S      87     S      87      3    6   11     3    3    4    4    5    6    6    7    8    9    9   10   11   12   14   14   15   16   16   16 
LCS_GDT     G      88     G      88      5    6   11     4    5    5    5    5    6    6    7    8    9    9   10   11   12   14   14   15   16   16   16 
LCS_GDT     G      89     G      89      5    6   11     4    5    5    5    6    7    7    7    8    9    9   10   11   12   14   14   15   16   16   16 
LCS_GDT     Q      90     Q      90      5    6   11     4    5    5    5    6    7    7    7    7    9    9   10   11   12   14   14   15   16   16   16 
LCS_GDT     V      91     V      91      5    6   11     4    5    5    5    6    7    7    7    7    8    8    9   11   12   14   14   15   16   16   16 
LCS_GDT     I      92     I      92      5    6   11     4    5    5    5    6    7    7    7    7    8    8    9   10   10   11   13   15   16   16   16 
LCS_GDT     F      93     F      93      4    6   11     4    4    4    5    6    7    7    7    7    8    8    9   11   11   14   14   15   16   16   16 
LCS_GDT     H      94     H      94      4    6   11     4    4    4    5    6    7    7    7    7    8    8    9   11   12   14   14   15   16   16   16 
LCS_GDT     K      95     K      95      4    6   11     3    4    4    5    6    7    7    7    7    7    8    9   11   12   14   14   15   16   16   16 
LCS_AVERAGE  LCS_A:   8.58  (   4.76    7.17   13.80 )

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      6      6      9     10     11     12     12     13     13     13     14     14     14     14     14     15     16     16     16 
GDT PERCENT_CA   4.21   6.32   6.32   9.47  10.53  11.58  12.63  12.63  13.68  13.68  13.68  14.74  14.74  14.74  14.74  14.74  15.79  16.84  16.84  16.84
GDT RMS_LOCAL    0.25   0.66   0.66   1.49   1.70   1.86   2.20   2.20   2.46   2.46   2.46   3.18   3.18   3.18   3.18   3.18   5.95   6.35   6.35   6.35
GDT RMS_ALL_CA  31.13  23.51  23.51  26.22  26.07  26.00  25.94  25.94  26.01  26.01  26.01  25.87  25.87  25.87  25.87  25.87  19.14  18.85  18.85  18.85

#      Molecule1      Molecule2       DISTANCE
LGA    S      69      S      69         14.289
LGA    E      70      E      70         10.368
LGA    T      71      T      71          5.535
LGA    S      72      S      72          3.057
LGA    P      73      P      73          1.252
LGA    V      74      V      74          1.963
LGA    D      75      D      75          1.062
LGA    L      76      L      76          3.064
LGA    C      77      C      77          1.293
LGA    V      78      V      78          1.765
LGA    I      79      I      79          3.975
LGA    G      80      G      80          1.051
LGA    I      81      I      81          1.371
LGA    V      82      V      82          2.088
LGA    D      83      D      83          2.567
LGA    E      84      E      84         21.269
LGA    V      85      V      85         25.345
LGA    V      86      V      86         31.838
LGA    S      87      S      87         37.189
LGA    G      88      G      88         43.432
LGA    G      89      G      89         46.432
LGA    Q      90      Q      90         47.721
LGA    V      91      V      91         46.098
LGA    I      92      I      92         45.377
LGA    F      93      F      93         39.860
LGA    H      94      H      94         37.804
LGA    K      95      K      95         30.873

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   27   95    4.0     12    2.19    10.789    10.385     0.523

LGA_LOCAL      RMSD =  2.195  Number of atoms =   12  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 26.083  Number of atoms =   27 
Std_ALL_ATOMS  RMSD = 16.187  (standard rmsd on all 27 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.209753 * X  +   0.378586 * Y  +  -0.901486 * Z  +  88.960236
  Y_new =  -0.775179 * X  +  -0.626311 * Y  +  -0.082659 * Z  +  33.565964
  Z_new =  -0.595903 * X  +   0.681475 * Y  +   0.424843 * Z  +  59.437984 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.013336   -2.128256  [ DEG:    58.0599   -121.9401 ]
  Theta =   0.638390    2.503202  [ DEG:    36.5771    143.4229 ]
  Phi   =  -1.835055    1.306537  [ DEG:  -105.1409     74.8591 ]
 
# 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: T0306TS239_3_2                                
REMARK     2: T0306.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0306TS239_3_2.T0306.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   27   95   4.0   12   2.19  10.385    16.19
REMARK  ---------------------------------------------------------- 
MOLECULE T0306TS239_3_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0306
PARENT 1fnf
ATOM      1  N   SER    69      11.048  31.746  63.587  1.00  9.99
ATOM      2  CA  SER    69      12.292  31.846  62.792  1.00  9.99
ATOM      3  C   SER    69      13.399  31.096  63.502  1.00  9.99
ATOM      4  O   SER    69      13.193  30.580  64.602  1.00  9.99
ATOM      5  CB  SER    69      12.637  33.324  62.631  1.00  9.99
ATOM      6  N   GLU    70      14.555  31.011  62.857  1.00  9.99
ATOM      7  CA  GLU    70      15.695  30.303  63.422  1.00  9.99
ATOM      8  C   GLU    70      16.800  31.299  63.743  1.00  9.99
ATOM      9  O   GLU    70      17.003  32.270  63.009  1.00  9.99
ATOM     10  CB  GLU    70      16.210  29.273  62.413  1.00  9.99
ATOM     11  N   THR    71      17.451  31.111  64.882  1.00  9.99
ATOM     12  CA  THR    71      18.552  31.974  65.276  1.00  9.99
ATOM     13  C   THR    71      19.777  31.317  64.652  1.00  9.99
ATOM     14  O   THR    71      19.915  30.090  64.673  1.00  9.99
ATOM     15  CB  THR    71      18.684  32.026  66.791  1.00  9.99
ATOM     16  N   SER    72      20.639  32.110  64.017  1.00  9.99
ATOM     17  CA  SER    72      21.844  31.585  63.373  1.00  9.99
ATOM     18  C   SER    72      22.923  31.143  64.362  1.00  9.99
ATOM     19  O   SER    72      22.780  31.318  65.579  1.00  9.99
ATOM     20  CB  SER    72      22.326  32.788  62.572  1.00  9.99
ATOM     21  N   PRO    73      23.980  30.477  63.858  1.00  9.99
ATOM     22  CA  PRO    73      25.036  30.062  64.782  1.00  9.99
ATOM     23  C   PRO    73      25.773  31.352  65.148  1.00  9.99
ATOM     24  O   PRO    73      25.571  32.402  64.511  1.00  9.99
ATOM     25  CB  PRO    73      25.922  29.173  63.907  1.00  9.99
ATOM     26  N   VAL    74      26.575  31.308  66.200  1.00  9.99
ATOM     27  CA  VAL    74      27.348  32.473  66.594  1.00  9.99
ATOM     28  C   VAL    74      28.742  31.950  66.858  1.00  9.99
ATOM     29  O   VAL    74      28.970  30.750  66.757  1.00  9.99
ATOM     30  CB  VAL    74      26.859  33.065  67.901  1.00  9.99
ATOM     31  N   ASP    75      29.668  32.848  67.176  1.00  9.99
ATOM     32  CA  ASP    75      31.036  32.461  67.506  1.00  9.99
ATOM     33  C   ASP    75      31.630  31.562  66.435  1.00  9.99
ATOM     34  O   ASP    75      31.987  30.412  66.700  1.00  9.99
ATOM     35  CB  ASP    75      31.042  31.740  68.856  1.00  9.99
ATOM     36  N   LEU    76      31.691  32.085  65.217  1.00  9.99
ATOM     37  CA  LEU    76      32.227  31.339  64.085  1.00  9.99
ATOM     38  C   LEU    76      33.753  31.392  64.131  1.00  9.99
ATOM     39  O   LEU    76      34.337  32.454  64.381  1.00  9.99
ATOM     40  CB  LEU    76      31.716  31.955  62.779  1.00  9.99
ATOM     41  N   CYS    77      34.387  30.238  63.953  1.00  9.99
ATOM     42  CA  CYS    77      35.847  30.149  63.953  1.00  9.99
ATOM     43  C   CYS    77      36.318  29.451  62.686  1.00  9.99
ATOM     44  O   CYS    77      35.774  28.419  62.297  1.00  9.99
ATOM     45  CB  CYS    77      36.372  29.418  65.197  1.00  9.99
ATOM     46  N   VAL    78      37.297  30.053  62.020  1.00  9.99
ATOM     47  CA  VAL    78      37.856  29.510  60.783  1.00  9.99
ATOM     48  C   VAL    78      39.331  29.183  60.996  1.00  9.99
ATOM     49  O   VAL    78      40.118  30.071  61.327  1.00  9.99
ATOM     50  CB  VAL    78      37.707  30.530  59.653  1.00  9.99
ATOM     51  N   ILE    79      39.695  27.913  60.823  1.00  9.99
ATOM     52  CA  ILE    79      41.079  27.473  61.013  1.00  9.99
ATOM     53  C   ILE    79      41.614  26.778  59.774  1.00  9.99
ATOM     54  O   ILE    79      41.235  25.646  59.480  1.00  9.99
ATOM     55  CB  ILE    79      41.177  26.525  62.209  1.00  9.99
ATOM     56  N   GLY    80      42.490  27.464  59.047  1.00  9.99
ATOM     57  CA  GLY    80      43.084  26.916  57.831  1.00  9.99
ATOM     58  C   GLY    80      44.481  26.379  58.109  1.00  9.99
ATOM     59  O   GLY    80      45.332  27.081  58.661  1.00  9.99
ATOM     60  N   ILE    81      44.701  25.122  57.743  1.00  9.99
ATOM     61  CA  ILE    81      45.993  24.485  57.933  1.00  9.99
ATOM     62  C   ILE    81      47.004  25.192  57.034  1.00  9.99
ATOM     63  O   ILE    81      46.721  25.431  55.859  1.00  9.99
ATOM     64  CB  ILE    81      45.899  23.012  57.541  1.00  9.99
ATOM     65  N   VAL    82      48.176  25.571  57.583  1.00  9.99
ATOM     66  CA  VAL    82      49.252  26.260  56.854  1.00  9.99
ATOM     67  C   VAL    82      49.472  25.667  55.468  1.00  9.99
ATOM     68  O   VAL    82      49.474  26.381  54.464  1.00  9.99
ATOM     69  CB  VAL    82      50.449  26.046  57.767  1.00  9.99
ATOM     70  N   ASP    83      49.694  24.360  55.425  1.00  9.99
ATOM     71  CA  ASP    83      49.857  23.647  54.166  1.00  9.99
ATOM     72  C   ASP    83      48.413  23.353  53.764  1.00  9.99
ATOM     73  O   ASP    83      47.884  22.263  54.002  1.00  9.99
ATOM     74  CB  ASP    83      50.670  22.359  54.365  1.00  9.99
ATOM     75  N   GLU    84      34.140  26.003  62.874  1.00  9.99
ATOM     76  CA  GLU    84      33.485  25.729  64.150  1.00  9.99
ATOM     77  C   GLU    84      32.565  26.883  64.555  1.00  9.99
ATOM     78  O   GLU    84      32.816  28.049  64.222  1.00  9.99
ATOM     79  CB  GLU    84      34.522  25.473  65.244  1.00  9.99
ATOM     80  N   VAL    85      31.505  26.568  65.285  1.00  9.99
ATOM     81  CA  VAL    85      30.567  27.599  65.697  1.00  9.99
ATOM     82  C   VAL    85      29.817  27.222  66.963  1.00  9.99
ATOM     83  O   VAL    85      29.803  26.062  67.391  1.00  9.99
ATOM     84  CB  VAL    85      29.545  27.850  64.578  1.00  9.99
ATOM     85  N   VAL    86      29.241  28.234  67.587  1.00  9.99
ATOM     86  CA  VAL    86      28.427  28.050  68.768  1.00  9.99
ATOM     87  C   VAL    86      27.079  27.669  68.153  1.00  9.99
ATOM     88  O   VAL    86      26.648  28.257  67.156  1.00  9.99
ATOM     89  CB  VAL    86      28.323  29.367  69.532  1.00  9.99
ATOM     90  N   SER    87      26.430  26.659  68.708  1.00  9.99
ATOM     91  CA  SER    87      25.159  26.208  68.161  1.00  9.99
ATOM     92  C   SER    87      24.041  27.245  68.289  1.00  9.99
ATOM     93  O   SER    87      24.094  28.106  69.175  1.00  9.99
ATOM     94  CB  SER    87      24.741  24.924  68.858  1.00  9.99
ATOM     95  N   GLY    88      23.039  27.153  67.408  1.00  9.99
ATOM     96  CA  GLY    88      21.869  28.040  67.426  1.00  9.99
ATOM     97  C   GLY    88      21.177  27.861  68.777  1.00  9.99
ATOM     98  O   GLY    88      21.352  26.836  69.442  1.00  9.99
ATOM     99  N   GLY    89      20.432  28.874  69.207  1.00  9.99
ATOM    100  CA  GLY    89      19.715  28.795  70.470  1.00  9.99
ATOM    101  C   GLY    89      18.242  28.459  70.230  1.00  9.99
ATOM    102  O   GLY    89      17.412  28.551  71.143  1.00  9.99
ATOM    103  N   GLN    90      17.926  28.094  68.990  1.00  9.99
ATOM    104  CA  GLN    90      16.570  27.707  68.602  1.00  9.99
ATOM    105  C   GLN    90      16.497  26.202  68.748  1.00  9.99
ATOM    106  O   GLN    90      17.360  25.487  68.222  1.00  9.99
ATOM    107  CB  GLN    90      16.298  28.032  67.117  1.00  9.99
ATOM    108  N   VAL    91      15.514  25.691  69.511  1.00  9.99
ATOM    109  CA  VAL    91      15.426  24.234  69.652  1.00  9.99
ATOM    110  C   VAL    91      14.659  23.604  68.476  1.00  9.99
ATOM    111  O   VAL    91      14.088  24.307  67.639  1.00  9.99
ATOM    112  CB  VAL    91      14.663  24.074  70.960  1.00  9.99
ATOM    113  N   ILE    92      14.727  22.283  68.369  1.00  9.99
ATOM    114  CA  ILE    92      14.009  21.543  67.339  1.00  9.99
ATOM    115  C   ILE    92      14.424  21.740  65.883  1.00  9.99
ATOM    116  O   ILE    92      13.606  21.574  64.963  1.00  9.99
ATOM    117  CB  ILE    92      12.503  21.776  67.507  1.00  9.99
ATOM    118  N   PHE    93      15.696  22.064  65.670  1.00  9.99
ATOM    119  CA  PHE    93      16.221  22.242  64.326  1.00  9.99
ATOM    120  C   PHE    93      16.799  20.897  63.829  1.00  9.99
ATOM    121  O   PHE    93      17.009  19.965  64.615  1.00  9.99
ATOM    122  CB  PHE    93      17.243  23.414  64.272  1.00  9.99
ATOM    123  N   HIS    94      17.049  20.782  62.531  1.00  9.99
ATOM    124  CA  HIS    94      17.543  19.528  61.958  1.00  9.99
ATOM    125  C   HIS    94      19.003  19.450  61.483  1.00  9.99
ATOM    126  O   HIS    94      19.457  18.389  61.054  1.00  9.99
ATOM    127  CB  HIS    94      16.653  19.123  60.804  1.00  9.99
ATOM    128  N   LYS    95      19.722  20.563  61.513  1.00  9.99
ATOM    129  CA  LYS    95      21.103  20.531  61.082  1.00  9.99
ATOM    130  C   LYS    95      21.710  21.889  60.833  1.00  9.99
ATOM    131  O   LYS    95      21.203  22.913  61.297  1.00  9.99
ATOM    132  CB  LYS    95      21.194  19.664  59.814  1.00  9.99
TER
END
