
#######################################################
#                                                     #
#                        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   28 (  112),  selected   26 , name T0348TS550_3
# Molecule2: number of CA atoms   61 (  465),  selected   26 , name T0348.pdb
# PARAMETERS: T0348TS550_3.T0348.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:    16        27 - 62          4.94     6.05
  LCS_AVERAGE:     25.16

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        22 - 27          1.39    12.47
  LONGEST_CONTINUOUS_SEGMENT:     6        26 - 31          1.48     8.87
  LONGEST_CONTINUOUS_SEGMENT:     6        31 - 36          1.93    12.88
  LONGEST_CONTINUOUS_SEGMENT:     6        33 - 38          1.60     7.42
  LCS_AVERAGE:      8.83

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        22 - 26          0.83    12.48
  LONGEST_CONTINUOUS_SEGMENT:     5        27 - 31          0.97     8.35
  LCS_AVERAGE:      7.00

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     P      17     P      17      3    3   14     0    3    3    6    6    7    8   11   12   15   17   21   23   24   24   25   26   26   26   26 
LCS_GDT     L      18     L      18      3    4   14     3    4    4    5    6    7    9   11   12   15   17   21   23   24   24   25   26   26   26   26 
LCS_GDT     V      19     V      19      3    5   14     3    3    3    4    6    7    9   11   12   15   17   21   23   24   24   25   26   26   26   26 
LCS_GDT     F      20     F      20      4    5   14     3    4    4    4    4    6    9   11   12   15   17   21   23   24   24   25   26   26   26   26 
LCS_GDT     D      21     D      21      4    5   14     3    4    4    4    4    7    9   11   12   15   17   21   23   24   24   25   26   26   26   26 
LCS_GDT     K      22     K      22      5    6   14     3    4    5    6    6    7    9    9   10   14   16   20   23   24   24   25   26   26   26   26 
LCS_GDT     S      23     S      23      5    6   14     4    4    5    6    6    7    9    9   10   14   15   17   20   22   24   25   26   26   26   26 
LCS_GDT     K      24     K      24      5    6   15     4    4    5    6    6    8    9   10   12   14   17   21   23   24   24   25   26   26   26   26 
LCS_GDT     D      25     D      25      5    6   15     4    4    5    6    6    8    9   10   12   14   17   21   23   24   24   25   26   26   26   26 
LCS_GDT     E      26     E      26      5    6   15     4    4    5    6    6    7    9   11   13   14   17   21   23   24   24   25   26   26   26   26 
LCS_GDT     L      27     L      27      5    6   16     3    4    5    6    6    9   11   11   13   14   17   21   23   24   24   25   26   26   26   26 
LCS_GDT     I      28     I      28      5    6   16     3    4    5    6    6    9   11   11   13   14   17   21   23   24   24   25   26   26   26   26 
LCS_GDT     C      29     C      29      5    6   16     3    4    5    6    6    9   11   11   13   15   17   21   23   24   24   25   26   26   26   26 
LCS_GDT     K      30     K      30      5    6   16     4    4    5    6    6    7   10   10   13   15   17   21   23   24   24   25   26   26   26   26 
LCS_GDT     G      31     G      31      5    6   16     4    4    5    6    6    9   11   11   13   15   17   20   21   23   24   25   26   26   26   26 
LCS_GDT     D      32     D      32      4    6   16     4    4    4    4    5    9   11   11   13   15   17   21   23   24   24   25   26   26   26   26 
LCS_GDT     R      33     R      33      4    6   16     4    4    4    5    6    9   11   11   13   14   17   21   23   24   24   25   26   26   26   26 
LCS_GDT     L      34     L      34      4    6   16     3    4    5    5    6    9   11   11   13   14   17   21   23   24   24   25   26   26   26   26 
LCS_GDT     A      35     A      35      4    6   16     3    4    5    6    6    9   11   11   13   14   17   21   23   24   24   25   26   26   26   26 
LCS_GDT     F      36     F      36      4    6   16     3    4    5    5    6    9   11   11   13   15   17   21   23   24   24   25   26   26   26   26 
LCS_GDT     P      37     P      37      4    6   16     3    4    5    5    6    8   11   11   13   15   17   20   22   24   24   25   26   26   26   26 
LCS_GDT     I      38     I      38      4    6   16     3    3    5    5    6    8   11   11   13   15   17   21   23   24   24   25   26   26   26   26 
LCS_GDT     V      59     V      59      4    4   16     4    4    4    6    6    7    8   10   12   15   17   21   23   24   24   25   26   26   26   26 
LCS_GDT     K      60     K      60      4    4   16     4    4    4    6    6    7    8   10   12   15   17   21   23   24   24   25   26   26   26   26 
LCS_GDT     L      61     L      61      4    4   16     4    4    4    6    6    6    8   10   12   15   17   21   23   24   24   25   26   26   26   26 
LCS_GDT     E      62     E      62      4    4   16     4    4    4    6    6    6    8   10   12   15   17   21   23   24   24   25   26   26   26   26 
LCS_AVERAGE  LCS_A:  13.66  (   7.00    8.83   25.16 )

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      6      9     11     11     13     15     17     21     23     24     24     25     26     26     26     26 
GDT PERCENT_CA   6.56   6.56   8.20   9.84   9.84  14.75  18.03  18.03  21.31  24.59  27.87  34.43  37.70  39.34  39.34  40.98  42.62  42.62  42.62  42.62
GDT RMS_LOCAL    0.20   0.20   0.83   1.30   1.30   2.41   2.80   2.80   3.26   3.87   4.23   4.73   4.91   5.02   5.02   5.18   5.38   5.38   5.38   5.38
GDT RMS_ALL_CA  13.16  13.16  12.48  11.29  11.29  12.58  12.45  12.45  12.33   6.68   6.01   5.44   5.40   5.40   5.40   5.42   5.38   5.38   5.38   5.38

#      Molecule1      Molecule2       DISTANCE
LGA    P      17      P      17         17.190
LGA    L      18      L      18         13.209
LGA    V      19      V      19         15.402
LGA    F      20      F      20         15.371
LGA    D      21      D      21         13.892
LGA    K      22      K      22         14.232
LGA    S      23      S      23         16.267
LGA    K      24      K      24         13.647
LGA    D      25      D      25          8.807
LGA    E      26      E      26          5.820
LGA    L      27      L      27          2.415
LGA    I      28      I      28          2.618
LGA    C      29      C      29          3.408
LGA    K      30      K      30          4.857
LGA    G      31      G      31          2.390
LGA    D      32      D      32          0.808
LGA    R      33      R      33          2.784
LGA    L      34      L      34          2.913
LGA    A      35      A      35          2.213
LGA    F      36      F      36          3.585
LGA    P      37      P      37          3.644
LGA    I      38      I      38          3.387
LGA    V      59      V      59         23.280
LGA    K      60      K      60         22.525
LGA    L      61      L      61         18.400
LGA    E      62      E      62         22.879

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   28   61    4.0     11    2.80    18.852    16.867     0.380

LGA_LOCAL      RMSD =  2.797  Number of atoms =   11  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 12.288  Number of atoms =   26 
Std_ALL_ATOMS  RMSD =  5.381  (standard rmsd on all 26 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.164543 * X  +   0.580954 * Y  +  -0.797131 * Z  +   8.213875
  Y_new =   0.644634 * X  +  -0.548342 * Y  +  -0.532699 * Z  +  27.482920
  Z_new =  -0.746574 * X  +  -0.601509 * Y  +  -0.284277 * Z  +  61.259144 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.012290    1.129303  [ DEG:  -115.2957     64.7043 ]
  Theta =   0.842898    2.298695  [ DEG:    48.2945    131.7055 ]
  Phi   =   1.820710   -1.320883  [ DEG:   104.3190    -75.6810 ]
 
# 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: T0348TS550_3                                  
REMARK     2: T0348.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0348TS550_3.T0348.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   28   61   4.0   11   2.80  16.867     5.38
REMARK  ---------------------------------------------------------- 
MOLECULE T0348TS550_3
PFRMAT TS
TARGET T0348
MODEL 3
PARENT 1wee_A
ATOM      1  N   PRO    17      10.617  17.518  52.299  1.00  0.00
ATOM      2  CA  PRO    17       9.194  17.727  52.097  1.00  0.00
ATOM      3  C   PRO    17       8.922  19.173  51.664  1.00  0.00
ATOM      4  O   PRO    17       9.017  20.101  52.472  1.00  0.00
ATOM      5  N   LEU    18       8.588  19.355  50.394  1.00  0.00
ATOM      6  CA  LEU    18       8.298  20.676  49.858  1.00  0.00
ATOM      7  C   LEU    18       6.825  20.818  49.502  1.00  0.00
ATOM      8  O   LEU    18       6.398  20.437  48.423  1.00  0.00
ATOM      9  N   VAL    19       5.842  19.963  50.318  1.00  0.00
ATOM     10  CA  VAL    19       4.411  20.277  50.320  1.00  0.00
ATOM     11  C   VAL    19       3.700  20.172  51.669  1.00  0.00
ATOM     12  O   VAL    19       2.461  20.153  51.702  1.00  0.00
ATOM     13  N   PHE    20       4.449  20.113  52.771  1.00  0.00
ATOM     14  CA  PHE    20       3.825  19.985  54.090  1.00  0.00
ATOM     15  C   PHE    20       3.547  21.324  54.754  1.00  0.00
ATOM     16  O   PHE    20       2.419  21.818  54.745  1.00  0.00
ATOM     17  N   ASP    21       4.584  21.899  55.348  1.00  0.00
ATOM     18  CA  ASP    21       4.461  23.185  56.015  1.00  0.00
ATOM     19  C   ASP    21       5.657  24.046  55.645  1.00  0.00
ATOM     20  O   ASP    21       6.770  23.538  55.463  1.00  0.00
ATOM     21  N   LYS    22       5.418  25.350  55.537  1.00  0.00
ATOM     22  CA  LYS    22       6.462  26.300  55.176  1.00  0.00
ATOM     23  C   LYS    22       6.856  27.190  56.340  1.00  0.00
ATOM     24  O   LYS    22       6.121  28.105  56.708  1.00  0.00
ATOM     25  N   SER    23       8.013  26.897  56.927  1.00  0.00
ATOM     26  CA  SER    23       8.524  27.700  58.020  1.00  0.00
ATOM     27  C   SER    23       9.420  28.717  57.347  1.00  0.00
ATOM     28  O   SER    23       9.194  29.064  56.184  1.00  0.00
ATOM     29  N   LYS    24      10.438  29.193  58.054  1.00  0.00
ATOM     30  CA  LYS    24      11.375  30.170  57.492  1.00  0.00
ATOM     31  C   LYS    24      11.531  30.074  55.960  1.00  0.00
ATOM     32  O   LYS    24      12.120  29.121  55.443  1.00  0.00
ATOM     33  N   ASP    25      10.966  31.043  55.215  1.00  0.00
ATOM     34  CA  ASP    25      11.093  31.006  53.754  1.00  0.00
ATOM     35  C   ASP    25      12.504  31.230  53.156  1.00  0.00
ATOM     36  O   ASP    25      12.825  32.296  52.605  1.00  0.00
ATOM     37  N   GLU    26      13.330  30.188  53.299  1.00  0.00
ATOM     38  CA  GLU    26      14.689  30.103  52.756  1.00  0.00
ATOM     39  C   GLU    26      14.397  29.321  51.466  1.00  0.00
ATOM     40  O   GLU    26      15.284  28.769  50.812  1.00  0.00
ATOM     41  N   LEU    27      13.130  29.130  50.159  1.00  0.00
ATOM     42  CA  LEU    27      12.262  28.387  51.062  1.00  0.00
ATOM     43  C   LEU    27      12.969  28.109  52.380  1.00  0.00
ATOM     44  O   LEU    27      14.171  28.323  52.514  1.00  0.00
ATOM     45  N   ILE    28      12.210  27.612  53.364  1.00  0.00
ATOM     46  CA  ILE    28      12.769  27.299  54.671  1.00  0.00
ATOM     47  C   ILE    28      12.051  26.105  55.299  1.00  0.00
ATOM     48  O   ILE    28      10.838  25.998  55.206  1.00  0.00
ATOM     49  N   CYS    29      12.812  25.225  55.939  1.00  0.00
ATOM     50  CA  CYS    29      12.250  24.054  56.579  1.00  0.00
ATOM     51  C   CYS    29      11.701  24.399  57.962  1.00  0.00
ATOM     52  O   CYS    29      12.318  25.161  58.711  1.00  0.00
ATOM     53  N   LYS    30      10.614  24.187  58.116  1.00  0.00
ATOM     54  CA  LYS    30       9.868  24.341  59.369  1.00  0.00
ATOM     55  C   LYS    30      10.666  23.709  60.484  1.00  0.00
ATOM     56  O   LYS    30      11.136  22.584  60.345  1.00  0.00
ATOM     57  N   GLY    31      10.842  24.436  61.584  1.00  0.00
ATOM     58  CA  GLY    31      11.621  23.937  62.706  1.00  0.00
ATOM     59  C   GLY    31      10.997  22.720  63.365  1.00  0.00
ATOM     60  O   GLY    31      11.692  21.887  63.949  1.00  0.00
ATOM     61  N   ASP    32       9.684  22.615  63.287  1.00  0.00
ATOM     62  CA  ASP    32       9.001  21.483  63.906  1.00  0.00
ATOM     63  C   ASP    32       8.795  20.245  63.012  1.00  0.00
ATOM     64  O   ASP    32       9.134  19.133  63.410  1.00  0.00
ATOM     65  N   ARG    33       8.248  20.438  61.813  1.00  0.00
ATOM     66  CA  ARG    33       7.970  19.286  60.965  1.00  0.00
ATOM     67  C   ARG    33       8.890  19.143  59.720  1.00  0.00
ATOM     68  O   ARG    33       8.672  18.281  58.855  1.00  0.00
ATOM     69  N   LEU    34       9.905  20.018  59.638  1.00  0.00
ATOM     70  CA  LEU    34      10.914  19.979  58.566  1.00  0.00
ATOM     71  C   LEU    34      10.387  20.116  57.118  1.00  0.00
ATOM     72  O   LEU    34      11.090  19.789  56.175  1.00  0.00
ATOM     73  N   ALA    35       9.418  20.870  57.012  1.00  0.00
ATOM     74  CA  ALA    35       8.828  21.063  55.701  1.00  0.00
ATOM     75  C   ALA    35       9.217  22.409  55.116  1.00  0.00
ATOM     76  O   ALA    35       9.082  23.443  55.772  1.00  0.00
ATOM     77  N   PHE    36       9.708  22.389  53.880  1.00  0.00
ATOM     78  CA  PHE    36      10.118  23.620  53.204  1.00  0.00
ATOM     79  C   PHE    36       8.910  24.418  52.739  1.00  0.00
ATOM     80  O   PHE    36       8.008  23.876  52.096  1.00  0.00
ATOM     81  N   PRO    37       8.898  25.707  53.065  1.00  0.00
ATOM     82  CA  PRO    37       7.801  26.583  52.670  1.00  0.00
ATOM     83  C   PRO    37       8.324  27.840  51.979  1.00  0.00
ATOM     84  O   PRO    37       9.506  28.173  52.087  1.00  0.00
ATOM     85  N   ILE    38       7.436  28.532  51.273  1.00  0.00
ATOM     86  CA  ILE    38       7.809  29.743  50.562  1.00  0.00
ATOM     87  C   ILE    38       8.003  30.905  51.535  1.00  0.00
ATOM     88  O   ILE    38       7.051  31.389  52.136  1.00  0.00
ATOM     89  N   VAL    59       1.525  25.604  60.951  1.00  0.00
ATOM     90  CA  VAL    59       0.223  25.498  61.601  1.00  0.00
ATOM     91  C   VAL    59       0.015  24.086  62.156  1.00  0.00
ATOM     92  O   VAL    59      -0.578  23.903  63.213  1.00  0.00
ATOM     93  N   LYS    60       0.500  23.100  61.412  1.00  0.00
ATOM     94  CA  LYS    60       0.362  21.698  61.825  1.00  0.00
ATOM     95  C   LYS    60       1.134  21.432  63.113  1.00  0.00
ATOM     96  O   LYS    60       0.731  20.608  63.924  1.00  0.00
ATOM     97  N   LEU    61       2.247  22.138  63.277  1.00  0.00
ATOM     98  CA  LEU    61       3.085  21.977  64.467  1.00  0.00
ATOM     99  C   LEU    61       2.381  22.542  65.699  1.00  0.00
ATOM    100  O   LEU    61       2.394  21.917  66.764  1.00  0.00
ATOM    101  N   GLU    62       1.786  23.719  65.547  1.00  0.00
ATOM    102  CA  GLU    62       1.088  24.364  66.646  1.00  0.00
ATOM    103  C   GLU    62       0.422  23.337  67.554  1.00  0.00
ATOM    104  O   GLU    62       0.488  23.427  68.783  1.00  0.00
ATOM    105  N   HIS    63      -0.224  22.340  66.942  1.00  0.00
ATOM    106  CA  HIS    63      -0.896  21.291  67.698  1.00  0.00
ATOM    107  C   HIS    63       0.009  20.084  67.877  1.00  0.00
ATOM    108  O   HIS    63      -0.089  19.364  68.870  1.00  0.00
ATOM    109  N   HIS    64       0.887  19.852  66.907  1.00  0.00
ATOM    110  CA  HIS    64       1.815  18.737  66.958  1.00  0.00
ATOM    111  C   HIS    64       2.657  18.772  68.223  1.00  0.00
ATOM    112  O   HIS    64       2.845  17.756  68.898  1.00  0.00
TER
END
